91 results on '"Kennedy NA"'
Search Results
2. Implications for sequencing of biologic therapy and choice of second anti-TNF in patients with inflammatory bowel disease: Results from the IMmunogenicity to Second Anti-TNF therapy (IMSAT) therapeutic drug monitoring study
- Author
-
Chanchlani, N, Lin, S, Auth, MK, Lee, CL, Robbins, H, Looi, S, Murugesan, SV, Riley, T, Preston, C, Stephenson, S, Cardozo, W, Sonwalkar, SA, Allah-Ditta, M, Mansfield, L, Durai, D, Baker, M, London, I, London, E, Gupta, S, Di Mambro, A, Murphy, A, Gaynor, E, Jones, KDJ, Claridge, A, Sebastian, S, Ramachandran, S, Selinger, CP, Borg-Bartolo, SP, Knight, P, Sprakes, MB, Burton, J, Kane, P, Lupton, S, Fletcher, A, Gaya, DR, Colbert, R, Seenan, JP, MacDonald, J, Lynch, L, McLachlan, I, Shields, S, Hansen, R, Gervais, L, Jere, M, Akhtar, M, Black, K, Henderson, P, Russell, RK, Lees, CW, Derikx, LAAP, Lockett, M, Betteridge, F, De Silva, A, Hussenbux, A, Beckly, J, Bendall, O, Hart, JW, Thomas, A, Hamilton, B, Gordon, C, Chee, D, McDonald, TJ, Nice, R, Parkinson, M, Gardner-Thorpe, H, Butterworth, JR, Javed, A, Al-Shakhshir, S, Yadagiri, R, Maher, S, Pollok, RCG, Ng, T, Appiahene, P, Donovan, F, Lok, J, Chandy, R, Jagdish, R, Baig, D, Mahmood, Z, Marsh, L, Moss, A, Abdulgader, A, Kitchin, A, Walker, GJ, George, B, Lim, Y-H, Gulliver, J, Bloom, S, Theaker, H, Carlson, S, Cummings, JRF, Livingstone, R, Beale, A, Carter, JO, Bell, A, Coulter, A, Snook, J, Stone, H, Kennedy, NA, Goodhand, JR, Ahmad, T, and IMSAT study investigators
- Abstract
BACKGROUND: Anti-drug antibodies are associated with treatment failure to anti-TNF agents in patients with inflammatory bowel disease (IBD). AIM: To assess whether immunogenicity to a patient's first anti-TNF agent would be associated with immunogenicity to their second, irrespective of drug sequence METHODS: We conducted a UK-wide, multicentre, retrospective cohort study to report rates of immunogenicity and treatment failure of second anti-TNF therapies in 1058 patients with IBD who underwent therapeutic drug monitoring for both infliximab and adalimumab. The primary outcome was immunogenicity to the second anti-TNF drug, defined at any timepoint as an anti-TNF antibody concentration ≥9 AU/ml for infliximab and ≥6 AU/ml for adalimumab. RESULTS: In patients treated with infliximab and then adalimumab, those who developed antibodies to infliximab were more likely to develop antibodies to adalimumab, than patients who did not develop antibodies to infliximab (OR 1.99, 95%CI 1.27-3.20, p = 0.002). Similarly, in patients treated with adalimumab and then infliximab, immunogenicity to adalimumab was associated with subsequent immunogenicity to infliximab (OR 2.63, 95%CI 1.46-4.80, p
- Published
- 2022
3. COVID-19 vaccine-induced antibody and T cell responses in immunosuppressed patients with inflammatory bowel disease after the third vaccine dose
- Author
-
Alexander, JL, Liu, Z, Mūnoz Sandoval, D, Reynolds, C, Ibraheim, H, Anandabaskaran, S, Saifuddin, A, Castro Seoane, R, Anand, N, Nice, R, Bewshea, C, D&apos, Mello, A, Constable, L, Jones, G, Balarajah, S, Fiorentino, F, Sebastian, S, Irving, P, Hicks, L, Williams, HRT, Kent, A, Linger, R, Parkes, M, Kok, K, Patel, K, Teare, JP, Altmann, D, Goodhand, J, Hart, A, Lees, C, Boyton, RJ, Kennedy, NA, Ahmad, T, Powell, N, and Investigators, VIPS
- Abstract
Background: COVID-19 vaccine-induced antibody responses are reduced in patients with inflammatory bowel disease (IBD) taking infliximab or tofacitinib after two vaccine doses. We sought to determine whether immunosuppressive treatments were associated with reduced antibody and T cell responses after a third vaccine dose. Methods: 352 adults (72 healthy controls and 280 IBD) from the prospectively recruited study cohort were sampled 28-49 days after a third dose of SARS-CoV-2 vaccine. IBD medications studied included thiopurines (n=65), infliximab (n=46), thiopurine/infliximab combination therapy (n=49), ustekinumab (n=44), vedolizumab (n=50) or tofacitinib (n=26). SARS-CoV-2 spike antibody binding and T cell responses were measured. Findings: Geometric mean [geometric SD] anti-S1 RBD antibody concentrations increased in all study groups following a third dose of vaccine, but were significantly lower in patients treated with infliximab (2736.8 U/mL [4.3]; P
- Published
- 2022
4. Ambulatory care management of 69 patients with acute severe ulcerative colitis in comparison to 695 inpatients: insights from a multicentre UK cohort study
- Author
-
Sebastian, S, Patel, K, Segal, JP, Subramanian, S, Conley, TE, Gonzalez, HA, Kent, AJ, Saifuddin, A, Hicks, L, Mehta, S, Bhala, N, Brookes, MJ, Lamb, CA, Kennedy, NA, Walker, GJ, Sebastian, S, Patel, K, Segal, JP, Subramanian, S, Conley, TE, Gonzalez, HA, Kent, AJ, Saifuddin, A, Hicks, L, Mehta, S, Bhala, N, Brookes, MJ, Lamb, CA, Kennedy, NA, and Walker, GJ
- Abstract
INTRODUCTION: Acute severe ulcerative colitis (ASUC) traditionally requires inpatient hospital management for intravenous therapies and/or colectomy. Ambulatory ASUC care has not yet been evaluated in large cohorts. AIMS: We used data from PROTECT, a UK multicentre observational COVID-19 inflammatory bowel disease study, to report the extent, safety and effectiveness of ASUC ambulatory pathways. METHODS: Adults (≥18 years old) meeting Truelove and Witts criteria between 1 January 2019-1 June 2019 and 1 March 2020-30 June 2020 were recruited to PROTECT. We used demographic, disease phenotype, treatment outcomes and 3-month follow-up data. Primary outcome was rate of colectomy during the index ASUC episode. Secondary outcomes included corticosteroid response, time to and rate of rescue or primary induction therapy, response to rescue or primary induction therapy, time to colectomy, mortality, duration of inpatient treatment and hospital readmission and colectomy within 3 months of index flare. We compared outcomes in three cohorts: (1) patients treated entirely in inpatient setting; ambulatory patients subdivided into; (2) patients managed as ambulatory from diagnosis and (3) patients hospitalised and subsequently discharged to ambulatory care for continued intravenous steroids. RESULTS: 37% (22/60) participating hospitals used ambulatory pathways. Of 764 eligible patients, 695 (91%) patients received entirely inpatient care, 15 (2%) patients were managed as ambulatory from diagnosis and 54 (7%) patients were discharged to ambulatory pathways. Aside from younger age in patients treated as ambulatory from diagnosis, no significant differences in disease or patient phenotype were observed. The rate of colectomy (15.0% (104/695) vs 13.3% (2/15) vs 13.0% (7/54), respectively, p=0.96) and secondary outcomes were similar among all three cohorts. Stool culture and flexible sigmoidoscopy were less frequently performed in ambulatory cohorts. Forty per cent of patients treated
- Published
- 2022
5. Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in inflammatory bowel disease patients treated with infliximab and vedolizumab
- Author
-
Lin, S, Kennedy, NA, Saifuddin, A, Sandoval, DM, Reynolds, CJ, Seoane, RC, Kottoor, SH, Pieper, FP, Lin, K-M, Butler, DK, Chanchlani, N, Nice, R, Chee, D, Bewshea, C, Janjua, M, McDonald, TJ, Sebastian, S, Alexander, JL, Constable, L, Lee, JC, Murray, CD, Hart, AL, Irving, PM, Jones, G-R, Kok, KB, Lamb, CA, Lees, CW, Altmann, DM, Boyton, RJ, Goodhand, JR, Powell, N, Ahmad, T, Lin, S, Kennedy, NA, Saifuddin, A, Sandoval, DM, Reynolds, CJ, Seoane, RC, Kottoor, SH, Pieper, FP, Lin, K-M, Butler, DK, Chanchlani, N, Nice, R, Chee, D, Bewshea, C, Janjua, M, McDonald, TJ, Sebastian, S, Alexander, JL, Constable, L, Lee, JC, Murray, CD, Hart, AL, Irving, PM, Jones, G-R, Kok, KB, Lamb, CA, Lees, CW, Altmann, DM, Boyton, RJ, Goodhand, JR, Powell, N, and Ahmad, T
- Abstract
Anti tumour necrosis factor (anti-TNF) drugs increase the risk of serious respiratory infection and impair protective immunity following pneumococcal and influenza vaccination. Here we report SARS-CoV-2 vaccine-induced immune responses and breakthrough infections in patients with inflammatory bowel disease, who are treated either with the anti-TNF antibody, infliximab, or with vedolizumab targeting a gut-specific anti-integrin that does not impair systemic immunity. Geometric mean [SD] anti-S RBD antibody concentrations are lower and half-lives shorter in patients treated with infliximab than vedolizumab, following two doses of BNT162b2 (566.7 U/mL [6.2] vs 4555.3 U/mL [5.4], p <0.0001; 26.8 days [95% CI 26.2 - 27.5] vs 47.6 days [45.5 - 49.8], p <0.0001); similar results are also observed with ChAdOx1 nCoV-19 vaccination (184.7 U/mL [5.0] vs 784.0 U/mL [3.5], p <0.0001; 35.9 days [34.9 - 36.8] vs 58.0 days [55.0 - 61.3], p value < 0.0001). One fifth of patients fail to mount a T cell response in both treatment groups. Breakthrough SARS-CoV-2 infections are more frequent (5.8% (201/3441) vs 3.9% (66/1682), p = 0.0039) in patients treated with infliximab than vedolizumab, and the risk of breakthrough SARS-CoV-2 infection is predicted by peak anti-S RBD antibody concentration after two vaccine doses. Irrespective of the treatments, higher, more sustained antibody levels are observed in patients with a history of SARS-CoV-2 infection prior to vaccination. Our results thus suggest that adapted vaccination schedules may be required to induce immunity in at-risk, anti-TNF-treated patients.
- Published
- 2022
6. Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.
- Author
-
Eijsbouts, C, Zheng, T, Kennedy, NA, Bonfiglio, F, Anderson, CA, Moutsianas, L, Holliday, J, Shi, J, Shringarpure, S, 23andMe Research Team, Voda, A-I, Bellygenes Initiative, Farrugia, G, Franke, A, Hübenthal, M, Abecasis, G, Zawistowski, M, Skogholt, AH, Ness-Jensen, E, Hveem, K, Esko, T, Teder-Laving, M, Zhernakova, A, Camilleri, M, Boeckxstaens, G, Whorwell, PJ, Spiller, R, McVean, G, D'Amato, M, Jostins, L, Parkes, M, Eijsbouts, C, Zheng, T, Kennedy, NA, Bonfiglio, F, Anderson, CA, Moutsianas, L, Holliday, J, Shi, J, Shringarpure, S, 23andMe Research Team, Voda, A-I, Bellygenes Initiative, Farrugia, G, Franke, A, Hübenthal, M, Abecasis, G, Zawistowski, M, Skogholt, AH, Ness-Jensen, E, Hveem, K, Esko, T, Teder-Laving, M, Zhernakova, A, Camilleri, M, Boeckxstaens, G, Whorwell, PJ, Spiller, R, McVean, G, D'Amato, M, Jostins, L, and Parkes, M
- Abstract
Irritable bowel syndrome (IBS) results from disordered brain-gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain-gut interactions underlying IBS.
- Published
- 2021
7. Assessment, endoscopy, and treatment in patients with acute severe ulcerative colitis during the COVID-19 pandemic (PROTECT-ASUC): a multicentre, observational, case-control study
- Author
-
Sebastian, S, Walker, GJ, Kennedy, NA, Conley, TE, Patel, K, Subramanian, S, Kent, AJ, Segal, JP, Brookes, MJ, Bhala, N, Gonzalez, HA, Hicks, LC, Mehta, SJ, Lamb, CA, Sebastian, S, Walker, GJ, Kennedy, NA, Conley, TE, Patel, K, Subramanian, S, Kent, AJ, Segal, JP, Brookes, MJ, Bhala, N, Gonzalez, HA, Hicks, LC, Mehta, SJ, and Lamb, CA
- Abstract
BACKGROUND: There is a paucity of evidence to support safe and effective management of patients with acute severe ulcerative colitis during the COVID-19 pandemic. We sought to identify alterations to established conventional evidence-based management of acute severe ulcerative colitis during the early COVID-19 pandemic, the effect on outcomes, and any associations with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severe COVID-19 outcomes. METHODS: The PROTECT-ASUC study was a multicentre, observational, case-control study in 60 acute secondary care hospitals throughout the UK. We included adults (≥18 years) with either ulcerative colitis or inflammatory bowel disease unclassified, who presented with acute severe ulcerative colitis and fulfilled the Truelove and Witts criteria. Cases and controls were identified as either admitted or managed in emergency ambulatory care settings between March 1, 2020, and June 30, 2020 (COVID-19 pandemic period cohort), or between Jan 1, 2019, and June 30, 2019 (historical control cohort), respectively. The primary outcome was the proportion of patients with acute severe ulcerative colitis receiving rescue therapy (including primary induction) or colectomy. The study is registered with ClinicalTrials.gov, NCT04411784. FINDINGS: We included 782 patients (398 in the pandemic period cohort and 384 in the historical control cohort) who met the Truelove and Witts criteria for acute severe ulcerative colitis. The proportion of patients receiving rescue therapy (including primary induction) or surgery was higher during the pandemic period than in the historical period (217 [55%] of 393 patients vs 159 [42%] of 380 patients; p=0·00024) and the time to rescue therapy was shorter in the pandemic cohort than in the historical cohort (p=0·0026). This difference was driven by a greater use of rescue and primary induction therapies with biologicals, ciclosporin, or tofacitinib in the COVID-19 pandemic period cohort th
- Published
- 2021
8. Letter: risk of severe COVID-19 outcomes associated with inflammatory bowel disease medications-reassuring insights from the United Kingdom PREPARE-IBD multicentre cohort study
- Author
-
Lamb, CA, Sebastian, S, Kent, AJ, Segal, JP, Gonzalez, HA, Brookes, MJ, Mehta, SJ, Subramanian, S, Bhala, N, Hicks, LC, Conley, TE, Patel, KV, Walker, GJ, Kennedy, NA, Lamb, CA, Sebastian, S, Kent, AJ, Segal, JP, Gonzalez, HA, Brookes, MJ, Mehta, SJ, Subramanian, S, Bhala, N, Hicks, LC, Conley, TE, Patel, KV, Walker, GJ, and Kennedy, NA
- Abstract
LINKED CONTENT This article is linked to Taxonera et al paper. To view this article, visit https://doi.org/10.1111/apt.15804
- Published
- 2021
9. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility
- Author
-
Patsopoulos, NA, Baranzini, SE, Santaniello, A, Shoostari, P, Cotsapas, C, Wong, G, Beecham, AH, James, T, Replogle, J, Vlachos, IS, McCabe, C, Pers, TH, Brandes, A, White, C, Keenan, B, Cimpean, M, Winn, P, Panteliadis, IP, Robbins, A, Andlauer, TFM, Zarzycki, O, Dubois, B, Goris, A, Sondergaard, HB, Sellebjerg, F, Sorensen, PS, Ullum, H, Thorner, LW, Saarela, J, Cournu-Rebeix, I, Damotte, V, Fontaine, B, Guillot-Noel, L, Lathrop, M, Vukusic, S, Berthele, A, Pongratz, V, Gasperi, C, Graetz, C, Grummel, V, Hemmer, B, Hoshi, M, Knier, B, Korn, T, Lill, CM, Luessi, F, Muhlau, M, Zipp, F, Dardiotis, E, Agliardi, C, Amoroso, A, Barizzone, N, Benedetti, MD, Bernardinelli, L, Cavalla, P, Clarelli, F, Comi, G, Cusi, D, Esposito, F, Ferre, L, Galimberti, D, Guaschino, C, Leone, MA, Martinelli, V, Moiola, L, Salvetti, M, Sorosina, M, Vecchio, D, Zauli, A, Santoro, S, Mancini, N, Zuccala, M, Mescheriakova, J, van Duijn, C, Bos, SD, Celius, EG, Spurkland, A, Comabella, M, Montalban, X, Alfredsson, L, Bomfim, IL, Gomez-Cabrero, D, Hillert, J, Jagodic, M, Linden, M, Piehl, F, Jelcic, I, Martin, R, Sospedra, M, Baker, A, Ban, M, Hawkins, C, Hysi, P, Kalra, S, Karpe, F, Khadake, J, Lachance, G, Molyneux, P, Neville, M, Thorpe, J, Bradshaw, E, Caillier, SJ, Calabresi, P, Cree, BAC, Cross, A, Davis, M, de Bakker, PWI, Delgado, S, Dembele, M, Edwards, K, Fitzgerald, K, Frohlich, IY, Gourraud, PA, Haines, JL, Hakonarson, H, Kimbrough, D, Isobe, N, Konidari, I, Lathi, E, Lee, MH, Li, T, An, D, Zimmer, A, Madireddy, L, Manrique, CP, Mitrovic, M, Olah, M, Patrick, E, Pericak-Vance, MA, Piccio, L, Schaefer, C, Weiner, H, Lage, K, Scott, RJ, Lechner-Scott, J, Leal, R, Moscato, P, Booth, DR, Stewart, GJ, Vucic, S, Pame, G, BamettO, M, Mason, D, GriffithS, L, Broadley, S, Tajouri, L, Baxter, A, Slee, M, Taylor, BV, Charlesworth, J, Kilpatrick, TJ, Rubio, J, Jokubaitis, V, Wiley, J, Butzkueven, H, Leslie, S, Motyer, A, Stankovich, J, Carroll, WM, Kermode, AG, Edrin, M, Barclay, M, Peyrin-Biroulet, L, Chamaillard, M, Colombe, JF, Cottone, M, Croft, A, D'Inca, R, Halfvarson, J, Hanigan, K, Henderson, P, Hugot, JP, Karban, A, Kennedy, NA, Khan, MA, Lemann, M, Levine, A, Massey, D, Milla, M, Motoey, GW, Ng, SME, Oikonomnou, J, Peeters, H, Proctor, DD, Rahier, JF, Roberts, R, Rutgeerts, P, Seibold, F, Stronati, L, Taylor, KM, Torkvist, L, Ublick, K, Van Limbergen, J, Van Gossum, A, Vatn, MH, Zhang, H, Zhang, W, Donnelly, P, Barroso, I, Blackwe, JM, Bramon, E, Brown, MA, Casas, JP, Corvin, A, Deloukas, P, Duncanson, A, Jankowski, J, Markus, HS, Mathew, CG, Palmer, CNA, Plomin, R, Rautanen, A, Sawcer, SJ, Trembath, RC, Viswanathan, AC, Wood, NW, Spencer, CCA, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Giannoulatou, E, Pirinen, M, Pearson, R, Strange, A, Sul, Z, Vukcevic, DA, Langford, C, Hunt, SE, Edkins, S, Gwilliam, R, Blackburn, H, Bumpstead, SJ, Dronov, S, Gillman, M, Gray, E, Hammond, N, Jayakumar, A, McCann, OT, Liddle, J, Potter, SC, Ravindrarajah, R, Ricketts, M, Waller, M, Weston, P, Widaa, S, Whittaker, P, Compston, A, Hafler, D, Harbo, HF, Hauser, SL, Stewart, G, D'Alfonso, S, Hadjigeorgiou, G, Taylor, B, Barcellos, LF, Booth, D, Hintzen, R, Kockum, I, Martinelli-Boneschi, F, McCauley, JL, Oksenberg, JR, Oturai, A, Sawcer, S, Ivinson, AJ, Olsson, T, De Jager, PL, Patsopoulos, Na, Baranzini, Se, Santaniello, A, Shoostari, P, Cotsapas, C, Wong, G, Beecham, Ah, James, T, Replogle, J, Vlachos, I, Mccabe, C, Pers, Th, Brandes, A, White, C, Keenan, B, Cimpean, M, Winn, P, Panteliadis, Ip, Robbins, A, Andlauer, Tfm, Zarzycki, O, Dubois, B, Goris, A, Sondergaard, Hb, Sellebjerg, F, Sorensen, P, Ullum, H, Thorner, Lw, Saarela, J, Cournu-Rebeix, I, Damotte, V, Fontaine, B, Guillot-Noel, L, Lathrop, M, Vukusic, S, Berthele, A, Pongratz, V, Gasperi, C, Graetz, C, Grummel, V, Hemmer, B, Hoshi, M, Knier, B, Korn, T, Lill, Cm, Luessi, F, Muhlau, M, Zipp, F, Dardiotis, E, Agliardi, C, Amoroso, A, Barizzone, N, Benedetti, Md, Bernardinelli, L, Cavalla, P, Clarelli, F, Comi, G, Cusi, D, Esposito, F, Ferre, L, Galimberti, D, Guaschino, C, Leone, Ma, Martinelli, V, Moiola, L, Salvetti, M, Sorosina, M, Vecchio, D, Zauli, A, Santoro, S, Mancini, N, Zuccala, M, Mescheriakova, J, van Duijn, C, Bos, Sd, Celius, Eg, Spurkland, A, Comabella, M, Montalban, X, Alfredsson, L, Bomfim, Il, Gomez-Cabrero, D, Hillert, J, Jagodic, M, Linden, M, Piehl, F, Jelcic, I, Martin, R, Sospedra, M, Baker, A, Ban, M, Hawkins, C, Hysi, P, Kalra, S, Karpe, F, Khadake, J, Lachance, G, Molyneux, P, Neville, M, Thorpe, J, Bradshaw, E, Caillier, Sj, Calabresi, P, Cree, Bac, Cross, A, Davis, M, de Bakker, Pwi, Delgado, S, Dembele, M, Edwards, K, Fitzgerald, K, Frohlich, Iy, Gourraud, Pa, Haines, Jl, Hakonarson, H, Kimbrough, D, Isobe, N, Konidari, I, Lathi, E, Lee, Mh, Li, T, An, D, Zimmer, A, Madireddy, L, Manrique, Cp, Mitrovic, M, Olah, M, Patrick, E, Pericak-Vance, Ma, Piccio, L, Schaefer, C, Weiner, H, Lage, K, Scott, Rj, Lechner-Scott, J, Leal, R, Moscato, P, Booth, Dr, Stewart, Gj, Vucic, S, Pame, G, Bametto, M, Mason, D, Griffiths, L, Broadley, S, Tajouri, L, Baxter, A, Slee, M, Taylor, Bv, Charlesworth, J, Kilpatrick, Tj, Rubio, J, Jokubaitis, V, Wiley, J, Butzkueven, H, Leslie, S, Motyer, A, Stankovich, J, Carroll, Wm, Kermode, Ag, Edrin, M, Barclay, M, Peyrin-Biroulet, L, Chamaillard, M, Colombe, Jf, Cottone, M, Croft, A, D'Inca, R, Halfvarson, J, Hanigan, K, Henderson, P, Hugot, Jp, Karban, A, Kennedy, Na, Khan, Ma, Lemann, M, Levine, A, Massey, D, Milla, M, Motoey, Gw, Ng, Sme, Oikonomnou, J, Peeters, H, Proctor, Dd, Rahier, Jf, Roberts, R, Rutgeerts, P, Seibold, F, Stronati, L, Taylor, Km, Torkvist, L, Ublick, K, Van Limbergen, J, Van Gossum, A, Vatn, Mh, Zhang, H, Zhang, W, Donnelly, P, Barroso, I, Blackwe, Jm, Bramon, E, Brown, Ma, Casas, Jp, Corvin, A, Deloukas, P, Duncanson, A, Jankowski, J, Markus, H, Mathew, Cg, Palmer, Cna, Plomin, R, Rautanen, A, Sawcer, Sj, Trembath, Rc, Viswanathan, Ac, Wood, Nw, Spencer, Cca, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Giannoulatou, E, Pirinen, M, Pearson, R, Strange, A, Sul, Z, Vukcevic, Da, Langford, C, Hunt, Se, Edkins, S, Gwilliam, R, Blackburn, H, Bumpstead, Sj, Dronov, S, Gillman, M, Gray, E, Hammond, N, Jayakumar, A, Mccann, Ot, Liddle, J, Potter, Sc, Ravindrarajah, R, Ricketts, M, Waller, M, Weston, P, Widaa, S, Whittaker, P, Compston, A, Hafler, D, Harbo, Hf, Hauser, Sl, Stewart, G, D'Alfonso, S, Hadjigeorgiou, G, Taylor, B, Barcellos, Lf, Booth, D, Hintzen, R, Kockum, I, Martinelli-Boneschi, F, Mccauley, Jl, Oksenberg, Jr, Oturai, A, Sawcer, S, Ivinson, Aj, Olsson, T, De Jager, Pl, Neurology, and Immunology
- Subjects
0301 basic medicine ,Multiple Sclerosis ,Quantitative Trait Loci ,Inheritance Patterns ,Cell Cycle Proteins ,Genome-wide association study ,Biology ,Major histocompatibility complex ,Polymorphism, Single Nucleotide ,Major Histocompatibility Complex ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Gene Frequency ,Autoimmune Process ,medicine ,Humans ,RNA-Seq ,X chromosome ,Genetics ,Chromosomes, Human, X ,Multidisciplinary ,Microglia ,Multiple sclerosis ,GTPase-Activating Proteins ,Chromosome Mapping ,Genomics ,medicine.disease ,3. Good health ,030104 developmental biology ,medicine.anatomical_structure ,Genetic Loci ,Case-Control Studies ,biology.protein ,Genome-Wide Association Study ,030217 neurology & neurosurgery - Abstract
Genetic roots of multiple sclerosis The genetics underlying who develops multiple sclerosis (MS) have been difficult to work out. Examining more than 47,000 cases and 68,000 controls with multiple genome-wide association studies, the International Multiple Sclerosis Genetics Consortium identified more than 200 risk loci in MS (see the Perspective by Briggs). Focusing on the best candidate genes, including a model of the major histocompatibility complex region, the authors identified statistically independent effects at the genome level. Gene expression studies detected that every major immune cell type is enriched for MS susceptibility genes and that MS risk variants are enriched in brain-resident immune cells, especially microglia. Up to 48% of the genetic contribution of MS can be explained through this analysis. Science , this issue p. eaav7188 ; see also p. 1383
- Published
- 2019
10. Developing a core outcome set for fistulising perianal Crohn’s disease
- Author
-
Sahnan, K, Tozer, PJ, Adegbola, SO, Lee, MJ, Heywood, N, McNair, AGK, Hind, D, Yassin, N, Lobo, AJ, Brown, SR, Sebastian, S, Phillips, RKS, Lung, PFC, Faiz, OD, Crook, K, Blackwell, S, Verjee, A, Hart, AL, Fearnhead, NS, John, A, Austin, A, Simon, A, Aidan, A, James, A, Katherine, A, Sathish, B, Ian, B, Gauraang, B, Stuart, B, Dominic, B, Matthew, B, David, B, Jeffrey, B, Christopher, C, Rachel, C, Peter, C, Thomas, C, Tamzin, C, Robert, D, Walter, D, Irene, D, Jayne, E, Jonathan, E, Martyn, E, Simon, F, Beverley, F, Catherine, F, James, G, Catherine, G, Ben, G, Arun, G, Sanjay, G, Richard, G, Alex, H, Diane, H, Nigel, H, Steve, H, Laura, H, Marcus, H, Rachel, H, Barney, H, Bu, H, Emma, H, Paul, H, Tim, H, Stephen, H, Rajapandian, I, Matthew, J, Cheryl, K, Kennedy, NA, Fevronia, K, Charles, K, Bee, L, Wendy, L, Jimmy, L, Richard, L, Peter, M, Janis, M, Steven, M, John, M, Michele, M, Charles, M-A, Alistair, M, Jasbir, N, Arvind, P, Gareth, P, Rajan, P, Uday, P, Leon, P, Kathryn, P, Thomas, P, Katie, P, Richard, P, Niall, P, Mark, P, Abdul, R, Kerry, R, Dan, R, Russell, RK, Mathew, R, Suzanne, R, Judith, S, John, S, Christian, S, Irshad, S, Ian, S, Baljit, S, Ederis, S, Christopher, S, Neil, S, Adam, S, Ben, S, Taylor, SA, Julian, T, Tham, TC, Pradeep, T, John, T, Jared, T, Simon, T, Mark, T, Tracey, T, Christos, T, Carolynne, V, Oliver, W, Janindra, W, Emma, W, Debbie, W, Graham, W, Mark, W, Graeme, W, Eleanor, W, Hannah, Y, Lisa, Y, and Royal College of Surgeons of England
- Subjects
PROTOCOL ,0301 basic medicine ,Research design ,Delphi Technique ,Consensus Development Conferences as Topic ,Delphi method ,ENiGMA collaborators ,0302 clinical medicine ,Crohn Disease ,Quality of life ,Risk Factors ,Outcome Assessment, Health Care ,Medicine ,ANTI-TNF ,Response rate (survey) ,FISTULAS ,Gastroenterology ,TRIALS ,crohn’s disease ,Systematic review ,Centre for Surgical Research ,Research Design ,Disease Progression ,030211 gastroenterology & hepatology ,Life Sciences & Biomedicine ,STEM-CELLS ,medicine.medical_specialty ,Likert scale ,Interviews as Topic ,Outcome Assessment (Health Care) ,03 medical and health sciences ,Crohn Disease/pathology ,MANAGEMENT ,Rectal Fistula ,Humans ,Patient Reported Outcome Measures ,clinical trials ,Science & Technology ,Gastroenterology & Hepatology ,business.industry ,Inflammatory Bowel Disease ,Perianal Abscess ,ibd ,1103 Clinical Sciences ,CARE ,Clinical trial ,030104 developmental biology ,Family medicine ,Quality of Life ,1114 Paediatrics and Reproductive Medicine ,Rectal Fistula/pathology ,anal sepsis ,business ,COSTS ,Fecal Incontinence ,Fecal Incontinence/etiology ,Systematic Reviews as Topic - Abstract
ObjectiveLack of standardised outcomes hampers effective analysis and comparison of data when comparing treatments in fistulising perianal Crohn’s disease (pCD). Development of a standardised set of outcomes would resolve these issues. This study provides the definitive core outcome set (COS) for fistulising pCD.DesignCandidate outcomes were generated through a systematic review and patient interviews. Consensus was established via a three-round Delphi process using a 9-point Likert scale based on how important they felt it was in determining treatment success culminating in a final consensus meeting. Stakeholders were recruited nationally and grouped into three panels (surgeons and radiologists, gastroenterologists and IBD specialist nurses, and patients). Participants received feedback from their panel (in the second round) and all participants (in the third round) to allow refinement of their scores.ResultsA total of 295 outcomes were identified from systematic reviews and interviews that were categorised into 92 domains. 187 stakeholders (response rate 78.5%) prioritised 49 outcomes through a three-round Delphi study. The final consensus meeting of 41 experts and patients generated agreement on an eight domain COS. The COS comprised three patient-reported outcome domains (quality of life, incontinence and a combined score of patient priorities) and five clinician-reported outcome domains (perianal disease activity, development of new perianal abscess/sepsis, new/recurrent fistula, unplanned surgery and faecal diversion).ConclusionA fistulising pCD COS has been produced by all key stakeholders. Application of the COS will reduce heterogeneity in outcome reporting, thereby facilitating more meaningful comparisons between treatments, data synthesis and ultimately benefit patient care.
- Published
- 2018
11. IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes
- Author
-
Momozawa, Y, Dmitrieva, J, Theatre, E, Deffontaine, V, Rahmouni, S, Charloteaux, B, Crins, F, Docampo, E, Elansary, M, Gori, AS, Lecut, C, Mariman, R, Mni, M, Oury, C, Altukhov, I, Alexeev, D, Aulchenko, Y, Amininejad, L, Bouma, G, Hoentjen, F, Lowenberg, M, Oldenburg, B, Pierik, MJ, de Jong, AE, van der Woude, C.J., Visschedijk, MC, Lathrop, M, Hugot, JP, Weersma, RK, Vos, M, Franchimont, D, Vermeire, S, Kubo, M, Louis, E, Georges, M, Abraham, C, Achkar, JP, Ahmad, T, Ananthakrishnan, AN, Andersen, V, Anderson, CA, Andrews, JM, Annese, V, Aumais, G, Baidoo, L, Baldassano, RN, Bampton, PA, Barclay, M, Barrett, JC, Bayless, TM, Bethge, J, Bitton, A, Boucher, G, Brand, S, Brandt, B, Brant, SR, Buning, C, Chew, A, Cho, JH, Cleynen, I, Cohain, A, Croft, A, Daly, MJ, D'Amato, M, Danese, S, Jong, D, Denapiene, G, Denson, LA, Devaney, KL, Dewit, O, D'Inca, R, Dubinsky, M, Duerr, RH, Edwards, C, Ellinghaus, D, Essers, J, Ferguson, LR, Festen, EA, Fleshner, P, Florin, T, Franke, A, Fransen, K, Gearry, R, Gieger, C, Glas, J, Goyette, P, Green, T, Griffiths, AM, Guthery, SL, Hakonarson, H, Halfvarson, J, Hanigan, K, Haritunians, T, de Hart, A, Hawkey, C, Hayward, NK, Hedl, M, Henderson, P, Hu, XH, Huang, HL, Hui, KY, Imielinski, M, Ippoliti, A, Jonaitis, L, Jostins, L, Karlsen, TH, Kennedy, NA, Khan, MA, Kiudelis, G, Krishnaprasad, K, Kugathasan, S, Kupcinskas, L, Latiano, A, Laukens, D, Lawrance, IC, Lee, JC, Lees, CW, Leja, M, van Limbergen, J, Lionetti, P, Liu, JZ, Mahy, G, Mansfield, J, Massey, D, Mathew, CG, McGovern, DPB, Milgrom, R, Mitrovic, M, Montgomery, GW, Mowat, C, Newman, W, Ng, A, Ng, SC, Ng, SME, Nikolaus, S, Ning, K, Nothen, M, Oikonomou, I, Palmieri, O, Parkes, M, Phillips, A, Ponsioen, CY, Potocnik, U, Prescott, NJ, Proctor, DD, Radford-Smith, G, Rahier, JF, Raychaudhuri, S, Regueiro, M, Rieder, F, Rioux, JD, Ripke, S, Roberts, R, Russell, RK, Sanderson, JD, Sans, M, Satsangi, J, Schadt, EE, Schreiber, S, Schulte, D, Schumm, LP, Scott, R, Seielstad, M, Sharma, Y, Silverberg, MS, Simms, LA, Skieceviciene, J, Spain, SL, Steinhart, AH, Stempak, JM, Stronati, L, Sventoraityte, J, Targan, SR, Taylor, KM, Velde, A, Torkvist, L, Tremelling, M, van Sommeren, S, Vasiliauskas, E, Verspaget, HW, Walters, T, Wang, K, Wang, MH, Wei, Z, Whiteman, D, Wijmenga, C, Wilson, DC, Winkelmann, J, Xavier, RJ, Zhang, B, Zhang, CK, Zhang, H, Zhang, W, Zhao, HY, Zhao, ZZ, Momozawa, Y, Dmitrieva, J, Theatre, E, Deffontaine, V, Rahmouni, S, Charloteaux, B, Crins, F, Docampo, E, Elansary, M, Gori, A, Lecut, C, Mariman, R, Mni, M, Oury, C, Altukhov, I, Alexeev, D, Aulchenko, Y, Amininejad, L, Bouma, G, Hoentjen, F, Lowenberg, M, Oldenburg, B, Pierik, Mj, vander Meulen-de Jong, Ae, van der Woude, Cj, Visschedijk, Mc, Lathrop, M, Hugot, Jp, Weersma, Rk, De Vos, M, Franchimont, D, Vermeire, S, Kubo, M, Louis, E, Georges, M, Abraham, C, Achkar, Jp, Ahmad, T, Ananthakrishnan, An, Andersen, V, Anderson, Ca, Andrews, Jm, Annese, V, Aumais, G, Baidoo, L, Baldassano, Rn, Bampton, Pa, Barclay, M, Barrett, Jc, Bayless, Tm, Bethge, J, Bitton, A, Boucher, G, Brand, S, Brandt, B, Brant, Sr, Buning, C, Chew, A, Cho, Jh, Cleynen, I, Cohain, A, Croft, A, Daly, Mj, D'Amato, M, Danese, S, De Jong, D, Denapiene, G, Denson, La, Devaney, Kl, Dewit, O, D'Inca, R, Dubinsky, M, Duerr, Rh, Edwards, C, Ellinghaus, D, Essers, J, Ferguson, Lr, Festen, Ea, Fleshner, P, Florin, T, Franke, A, Fransen, K, Gearry, R, Gieger, C, Glas, J, Goyette, P, Green, T, Griffiths, Am, Guthery, Sl, Hakonarson, H, Halfvarson, J, Hanigan, K, Haritunians, T, Hart, A, Hawkey, C, Hayward, Nk, Hedl, M, Henderson, P, Hu, Xh, Huang, Hl, Hui, Ky, Imielinski, M, Ippoliti, A, Jonaitis, L, Jostins, L, Karlsen, Th, Kennedy, Na, Khan, Ma, Kiudelis, G, Krishnaprasad, K, Kugathasan, S, Kupcinskas, L, Latiano, A, Laukens, D, Lawrance, Ic, Lee, Jc, Lees, Cw, Leja, M, Van Limbergen, J, Lionetti, P, Liu, Jz, Mahy, G, Mansfield, J, Massey, D, Mathew, Cg, Mcgovern, Dpb, Milgrom, R, Mitrovic, M, Montgomery, Gw, Mowat, C, Newman, W, Ng, A, Ng, Sc, Ng, Sme, Nikolaus, S, Ning, K, Nothen, M, Oikonomou, I, Palmieri, O, Parkes, M, Phillips, A, Ponsioen, Cy, Potocnik, U, Prescott, Nj, Proctor, Dd, Radford-Smith, G, Rahier, Jf, Raychaudhuri, S, Regueiro, M, Rieder, F, Rioux, Jd, Ripke, S, Roberts, R, Russell, Rk, Sanderson, Jd, Sans, M, Satsangi, J, Schadt, Ee, Schreiber, S, Schulte, D, Schumm, Lp, Scott, R, Seielstad, M, Sharma, Y, Silverberg, M, Simms, La, Skieceviciene, J, Spain, Sl, Steinhart, Ah, Stempak, Jm, Stronati, L, Sventoraityte, J, Targan, Sr, Taylor, Km, ter Velde, A, Torkvist, L, Tremelling, M, van Sommeren, S, Vasiliauskas, E, Verspaget, Hw, Walters, T, Wang, K, Wang, Mh, Wei, Z, Whiteman, D, Wijmenga, C, Wilson, Dc, Winkelmann, J, Xavier, Rj, Zhang, B, Zhang, Ck, Zhang, H, Zhang, W, Zhao, Hy, Zhao, Zz, Gastroenterology & Hepatology, UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, and UCL - (MGD) Service de gastro-entérologie
- Subjects
Adult ,Male ,Multifactorial Inheritance ,QUANTITATIVE TRAIT LOCUS ,Genotype ,SEQUENCING DATA ,Quantitative Trait Loci ,SUSCEPTIBILITY ,Polymorphism, Single Nucleotide ,Article ,Cohort Studies ,CODING VARIANTS ,Crohn Disease ,80 and over ,Journal Article ,Medicine and Health Sciences ,LOCUS ,Humans ,Genetic Predisposition to Disease ,Polymorphism ,GENOME-WIDE ASSOCIATION ,Genetic Association Studies ,Aged ,Aged, 80 and over ,Science & Technology ,Female ,Gene Expression Profiling ,Inflammatory Bowel Diseases ,Middle Aged ,Sequence Analysis, DNA ,COMPLEX TRAITS ,Biology and Life Sciences ,Single Nucleotide ,DNA ,CROHNS-DISEASE ,Multidisciplinary Sciences ,QUANTITATIVE TRAIT ,RARE VARIANTS ,Science & Technology - Other Topics ,LOW-FREQUENCY ,Sequence Analysis ,INFLAMMATORY-BOWEL-DISEASE - Abstract
GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach., Most of the more than 200 known genetic risk loci for inflammatory bowel disease (IBD) reside in regulatory regions. Here, the authors provide eQTL datasets for six circulating immune cell types and ileal, colonic and rectal biopsies to map regulatory modules and identify potential causative genes for IBD.
- Published
- 2018
12. Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease
- Author
-
Walker, GJ, Harrison, JW, Heap, GA, Voskuil, MD, Andersen, V, Anderson, CA, Ananthakrishnan, AN, Barrett, JC, Beaugerie, L, Bewshea, CM, Cole, AT, Cummings, FR, Daly, MJ, Ellul, P, Fedorak, RN, Festen, EAM, Florin, TH, Gaya, DR, Halfvarson, J, Hart, AL, Heerasing, NM, Hendy, P, Irving, PM, Jones, SE, Koskela, J, Lindsay, JO, Mansfield, JC, McGovern, D, Parkes, M, Pollok, RCG, Ramakrishnan, S, Rampton, DS, Rivas, MA, Russell, RK, Schultz, M, Sebastian, S, Seksik, P, Singh, A, So, K, Sokol, H, Subramaniam, K, Todd, A, Annese, V, Weersma, RK, Xavier, R, Ward, R, Weedon, MN, Goodhand, JR, Kennedy, NA, Ahmad, T, Holden, AL, Andrews, J, Auth, M, Babu, S, Bampton, P, Banim, P, Barnes, T, Basude, D, Beckly, J, Bell, A, Bell, S, Bhandari, P, Bloom, S, Border, D, Bredin, F, Brookes, MJ, Brown, M, Calvert, C, Campbell, D, Chanchlani, N, Chaudhary, B, Chaudhary, R, Chung-Faye, G, Colleypriest, B, Connor, S, Cooney, R, Cooper, S, Creed, TJ, Croft, N, Cullen, S, D'Amato, M, Dalal, H, Daneshmend, TK, Das, D, Delaney, M, Desilva, S, Dhar, A, Dharmasiri, S, Direkze, N, Dunckley, P, Elphick, D, Everett, SM, Feeney, M, Fell, J, Foley, S, Franke, A, Gavin, D, Gee, I, Ghosh, D, Goldsmith, C, Gorard, D, Gordon, JN, Gore, S, Green, J, Grimes, D, Hamill, G, Harbord, M, Hart, J, Hawkey, C, Iqbal, T, Ireland, A, Johnson, M, Jones, C, Kanegasundaram, S, Karban, A, Katsanos, KH, Kiparissi, F, Kirkham, S, Lal, S, Langlands, S, Lawrance, IC, Lees, CW, Lev-Tzion, R, Levison, S, Lewis, SJ, Li, A, Limdi, J, Lin, S, Lobo, A, Lockett, M, Loehry, J, MacDonald, C, MacFaul, G, Mahmood, T, Mann, S, Mawdsley, J, Mazhar, Z, McGovern, JF, McNair, A, Modi, A, Monahan, K, Moran, A, Morris, M-A, Mortimore, M, Mowat, C, Muhammed, R, Murray, CDR, Olivier, H, Orchard, TR, Panter, S, Patel, V, Phillips, R, Prasad, N, Preston, C, Radford-Smith, G, Rajasekhar, P, Roy, D, Saich, R, Satsangi, J, Schreiber, S, Sen, S, Shah, N, Shenderay, R, Shenoy, A, Shutt, J, Silverberg, M, Simmons, A, Simmons, J, Singh, S, Smith, M, Snook, JA, Sonwalker, S, Stevens, CR, Sturniolo, G, Subramanian, S, Thomas, A, Tighe, M, Torrente, F, Tremelling, M, Tsianos, E, Vani, D, Walsh, A, Watermeyer, G, Watts, D, Watts, G, Weaver, S, Wesley, E, Willmott, A, Yearsley, K, Zambar, V, Zeissig, S, University of Helsinki, Broad Institute, University of Helsinki, Complex Disease Genetics, Institute for Molecular Medicine Finland, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Simmons, A
- Subjects
Male ,PREDICTOR ,AZATHIOPRINE ,Azathioprine ,Genome-wide association study ,CHILDREN ,S-METHYLTRANSFERASE ,SUSCEPTIBILITY ,Gastroenterology ,THERAPY ,Leukocyte Count ,0302 clinical medicine ,Crohn Disease ,Interquartile range ,Medicine ,Exome ,Pyrophosphatases ,11 Medical and Health Sciences ,0303 health sciences ,Thiopurine methyltransferase ,biology ,IBD Pharmacogenetics Study Group ,General Medicine ,3. Good health ,Editorial Commentary ,Cohort ,030211 gastroenterology & hepatology ,Female ,Life Sciences & Biomedicine ,medicine.drug ,Adult ,medicine.medical_specialty ,Adolescent ,MERCAPTOPURINE INTOLERANCE ,European Continental Ancestry Group ,3121 Internal medicine ,Polymorphism, Single Nucleotide ,White People ,03 medical and health sciences ,Young Adult ,Medicine, General & Internal ,Internal medicine ,General & Internal Medicine ,MANAGEMENT ,Humans ,POLYMORPHISMS ,030304 developmental biology ,ACUTE LYMPHOBLASTIC-LEUKEMIA ,Science & Technology ,business.industry ,Case-control study ,Odds ratio ,Methyltransferases ,Sequence Analysis, DNA ,Haplotypes ,3121 General medicine, internal medicine and other clinical medicine ,Case-Control Studies ,biology.protein ,Colitis, Ulcerative ,business ,Pharmacogenetics ,Genome-Wide Association Study - Abstract
Funding Information: reported serving as a consultant for AbbVie UK; receiving honoraria from Falk and AbbVie UK; receiving grants from Crohn’s & Colitis UK and Tillott’s Pharmaceuticals; having a fellowship from the UK National Institute for Health Research; and receiving travel reimbursement from Merck Sharp & Dohme and Norgine. Dr Heap reported receiving travel reimbursement from AbbVie; and being a current employee of AbbVie and owning stock in the company. Dr Andersen reported receiving personal fees from Merck Sharp & Dohme and Janssen. Dr Ananthakrishnan reported receiving a grant from Pfizer; and receiving personal fees from Takeda. Dr Beaugerie reported receiving advisory board fees from Allergan, Janssen, and Pfizer; receiving a grant from Hospira; and receiving grants and honoraria from AbbVie, Merck Sharp & Dohme, Ferring, Takeda, and Tillott’s Pharmaceuticals. Dr Cummings reported receiving personal fees from AbbVie, Takeda, Biogen, Janssen, Merck Sharp & Dohme, Amgen, Hakim Pharmaceuticals, and Pfizer/Hospira; and receiving grants from Takeda, Biogen, AstraZeneca, and Pfizer/Hospira. Dr Halfvarson reported receiving personal fees from AbbVie, Hospira, Janssen, Medivir, Merck Sharp & Dohme, Pfizer, RenapharmaVifor, Takeda, Tillott’s Pharmaceuticals, Celgene, Sandoz, and Shire; and receiving grants from Janssen, Merck Sharp & Dohme, and Takeda. Dr Hart reported receiving advisory board fees from AbbVie, Atlantic, Bristol-Myers Squibb, Celltrion, Janssen, Merck Sharp & Dohme, Pfizer, Shire, and Takeda; receiving honoraria from Falk and Ferring; and receiving a grant from Takeda. Dr Irving reported receiving personal fees from Janssen, AbbVie, Takeda, Ferring, Pfizer, Lilly, Merck Sharp & Dohme, Samsung, and Sandoz; and receiving grants from Takeda and Merck Sharp & Dohme. Dr Lindsay reported receiving advisory board fees from Atlantic Health, AbbVie UK/global, Merck Sharp & Dohme, Shire UK, Vifor Pharma, Ferring International, Celltrion, Takeda, Napp, Pfizer, and Janssen; serving as a consultant for AbbVie UK/global, Takeda, and Pfizer; receiving grants from Shire UK, AbbVie UK/global, Warner Chilcott, Funding Information: Takeda, Hospira, Ferring International, and Merck Sharp & Dohme; receiving honoraria from Takeda, Cornerstones US, Tillott’s Pharmaceuticals, Napp, Shire International, Janssen, AbbVie, and Pfizer; and receiving travel reimbursement from AbbVie UK, Merck Sharp & Dohme, Warner Chilcott, Takeda, and Shire International. Dr McGovern reported receiving grants from the National Institutes of Health, Helmsley Charitable Trust, and Janssen; and serving as a consultant for Pfizer, Q Biologics, Cidara, Gilead, and Janssen. Dr Seksik reported receiving advisory board fees from Astellas; receiving honoraria from Takeda, AbbVie, and Ferring; and receiving grants from Merck Sharp & Dohme and Biocodex. Dr Sokol reported receiving grants from Biocodex, Danone, and BiomX; serving as a consultant for Enterome, Takeda, AbbVie, Roche, Amgen, Danone, BiomX, Ferring, Bristol-Myers Squibb, Astellas, Merck Sharp & Dohme, Novartis, Tillott’s Pharmaceuticals, and Biose; and being the co-founder of Nextbiotix. Dr Annese reported receiving advisory board fees from Takeda, AbbVie, and Medtronic; and receiving honoraria from Janssen, Takeda, AbbVie, and Medtronic. Dr Weersma reported receiving grants from Takeda, Ferring, and Tramedico; and receiving personal fees from AbbVie. Dr Goodhand reported receiving honoraria from Falk, AbbVie, and Shield Therapeutics. Dr Kennedy reported serving as a consultant for Falk; receiving honoraria from Falk, Allergan, Pharmacosmos, and Takeda; and being a deputy editor of Alimentary Pharmacology & Therapeutics. Dr Ahmad reported receiving unrestricted grants, advisory board fees, speaker honoraria, and support to attend international meetings from AbbVie, Merck Sharp & Dohme, Janssen, Takeda, Ferring, Tillott’s Pharmaceuticals, Ferring, Pfizer, Napp, Celltrion, and Hospira. No other disclosures were reported. Funding Information: Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California), Alistair McNair, PhD (Queen Elizabeth Hospital, London, UK), Anita Modi, MD (Luton and Dunstable University Hospital, Luton, UK), Kevin Monahan, PhD (West Middlesex University Hospital, Middlesex, UK), Alex Moran, MD (Northern Devon Healthcare Trust, Barnstaple, UK), Mary-Anne Morris, MD (Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK), Marianne Mortimore, MBBS (Mater Research Institute, University of Queensland, South Brisbane, Australia), Craig Mowat, MD (Ninewells Hospital, NHS Tayside, Dundee, UK), Rafeeq Muhammed, MD (Birmingham Children's Hospital, Birmingham, UK), Charles D. R. Murray, PhD (Royal Free Hospital, Royal Free London NHS Foundation Trust, London, UK), Hanlie Olivier (IBD Pharmacogenetics Group, University of Exeter, Exeter, UK), Timothy R. Orchard, DM (Imperial College Healthcare NHS Trust, London, UK), Simon Panter, MD (South Tyneside District Hospital, South Tyneside, UK), Vinod Patel, MBBS (Tameside and Glossop Integrated Care NHS Foundation Trust, Ashton-under-Lyne, UK), Rosemary Phillips, MD (Princess Alexandra Hospital, Essex, UK), Neeraj Prasad, MSc (Wrightington Hospital, Wrightington, UK), Cathryn Preston, MBChB (Bradford Royal Infirmary, Bradford, UK), Graham Radford-Smith, PhD (Royal Brisbane and Women’s Hospital, Brisbane, Australia), Praveen Rajasekhar, MD (Northumbria NHS Trust, Tyne and Wear, UK), Dipak Roy, PhD (Tameside and Glossop Integrated Care NHS Foundation Trust, Ashton-under-Lyne, UK), Rebecca Saich, PhD (Basingstoke and North Hampshire Hospital, Basingstoke, UK), Jack Satsangi, PhD (Western General Hospital, NHS Lothian, Edinburgh, UK), Stefan Schreiber, PhD (Kiel University, Kiel, Germany), Sandip Sen, MD (Royal Stoke University Hospital, Stoke-on-Trent, UK), Neil Shah, MD (Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK), Richard Shenderay, MBBS (Airedale NHS Foundation Trust, Keighley, UK), Acuth Shenoy, MD (Colchester Hospital University NHS Foundation Trust, Colchester, UK), James Shutt, DM (Dorset County Hospital NHS Foundation Trust, Dorchester, UK), Mark Silverberg, PhD (Mount Sinai Hospital, Toronto, Ontario, Canada), Alison Simmons, PhD (Oxford University Hospitals, Oxford, UK), Jonathan Simmons, DM (Royal Berkshire Hospital, Royal Berkshire NHS Foundation Trust, Reading, UK), Salil Singh, PhD (Bolton NHS Foundation Trust, Bolton, UK), Malcolm Smith, MBChB (Aberdeen Royal Infirmary, Aberdeen, UK), Mark Smith, MD (Shrewsbury and Telford Hospital NHS Trust, Shrewsbury, UK), Melissa Smith, MB (Royal Sussex County Hospital, Brighton, UK), Jonathon A. Snook, DPhil (Poole Hospital NHS Foundation Trust, Poole, UK), Sunil Sonwalker, MD (Calderdale Royal Hospital, Halifax, UK), Christine R. Stevens, PhD (Broad Institute, Harvard University, Cambridge, Massachusetts), Giacomo Sturniolo, PhD (Univerita di Padova, Padova, Italy), Sreedhar Subramanian, MD (Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK), Amanda Thomas, MBBS (Department of Gastroenterology, Royal Devon and Exeter Hospital NHS Foundation Trust, Exeter, UK), Mark Tighe, BM (Poole Hospital NHS Foundation Trust, Poole, UK), Franco Torrente, MD (Department of Gastroenterology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK), Mark Tremelling, MD (Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK), Epameinondas Tsianos, PhD (University Hospital of Ioannina, Ioannina, Greece), Deven Vani, MD (Mid Yorkshire Hospitals NHS Trust, Wakefield, UK), Alissa Walsh, MBBS (St Vincent’s Hospital, Sydney, Australia), Gillian Watermeyer, MBChB (Groote Schuur Hospital, Cape Town, South Africa), David Watts, MBChB (Forth Valley Royal Hospital, Larbert, UK), Gill Watts, MD (Wythenshawe Hospital, South Manchester, UK), Sean Weaver, PhD (Royal Bournemouth General Hospital, Bournemouth, UK), Emma Wesley, MBBS (Musgrove Park Hospital, Taunton and Somerset NHS Hospitals, Taunton, UK), Anne Willmott, MBChB (Leicester Royal Infirmary-Paediatric, Leicester, UK), Karen Yearsley, BM (Nevill Hall Hospital, Abergavenny, UK), Veena Zambar, MBBS (Leeds General Infirmary, Leeds, UK), and Sebastian Zeissig, MD (University Medical Center Schleswig-Hostein, Kiel, Germany). These individuals identified and recruited patient s to the study and provided comments on a draft of the manuscript. Funding Information: Adverse Events Consortium funded the sample collection and genotyping at the Broad Institute. The UK National Institute for Health Research provided research nurse support to facilitate recruitment at all UK research sites. Crohn’s & Colitis UK and forCrohns provided funding support and publicized this study to their members. The Exeter National Institute for Health Research Clinical Research Facility provided DNA storage and management. Institutional strategic support award WT097835MF from Wellcome Trust supported the management of the study. Samples from Cedars-Sinai were collected and processed through the MIRIAD biobank that was funded by grant P01DK046763 from the National Institutes of Health. Publisher Copyright: © 2019 American Medical Association. All rights reserved. IMPORTANCE Use of thiopurines may be limited by myelosuppression. TPMT pharmacogenetic testing identifies only 25% of at-risk patients of European ancestry. Among patients of East Asian ancestry, NUDT15 variants are associated with thiopurine-induced myelosuppression (TIM). OBJECTIVE To identify genetic variants associated with TIM among patients of European ancestry with inflammatory bowel disease (IBD). DESIGN, SETTING, AND PARTICIPANTS Case-control study of 491 patients affected by TIM and 679 thiopurine-tolerant unaffected patients who were recruited from 89 international sites between March 2012 and November 2015. Genome-wide association studies (GWAS) and exome-wide association studies (EWAS) were conducted in patients of European ancestry. The replication cohort comprised 73 patients affected by TIM and 840 thiopurine-tolerant unaffected patients. EXPOSURES Genetic variants associated with TIM. MAIN OUTCOMES AND MEASURES Thiopurine-induced myelosuppression, defined as a decline in absolute white blood cell count to 2.5 x 10(9)/L or less or a decline in absolute neutrophil cell count to 1.0 x 10(9)/L or less leading to a dose reduction or drug withdrawal. RESULTS Among 1077 patients (398 affected and 679 unaffected; median age at IBD diagnosis, 31.0 years [interquartile range, 21.2 to 44.1 years]; 540 [50%] women; 602 [56%] diagnosed as having Crohn disease), 919 (311 affected and 608 unaffected) were included in the GWAS analysis and 961 (328 affected and 633 unaffected) in the EWAS analysis. The GWAS analysis confirmed association of TPMT (chromosome 6, rs11969064) with TIM (30.5% [95/311] affected vs 16.4% [100/608] unaffected patients; odds ratio [OR], 2.3 [95% CI, 1.7 to 3.1], P = 5.2 x 10(-9)). The EWAS analysis demonstrated an association with an in-frame deletion in NUDT15 (chromosome 13, rs746071566) and TIM (5.8% [19/328] affected vs 0.2% [1/633] unaffected patients; OR, 38.2 [95% CI, 5.1 to 286.1], P = 1.3 x 10(-8)), which was replicated in a different cohort (2.7% [2/73] affected vs 0.2% [2/840] unaffected patients; OR, 11.8 [95% CI, 1.6 to 85.0], P = .03). Carriage of any of 3 coding NUDT15 variants was associated with an increased risk (OR, 27.3 [95% CI, 9.3 to 116.7], P = 1.1 x 10(-7)) of TIM, independent of TPMT genotype and thiopurine dose. CONCLUSIONS AND RELEVANCE Among patients of European ancestry with IBD, variants in NUDT15 were associated with increased risk of TIM. These findings suggest that NUDT15 genotyping may be considered prior to initiation of thiopurine therapy; however, further study including additional validation in independent cohorts is required.
- Published
- 2019
13. The spatial heterogeneity of urban green space distribution and configuration in Lilongwe City, Malawi.
- Author
-
Odala Nambazo and Kennedy Nazombe
- Subjects
Medicine ,Science - Abstract
Urban green spaces provide several benefits related to the quality of urban life. The existence and spatial arrangement of these spaces within neighbourhoods and functional land uses have significant implications for the well-being of urban dwellers. Previous studies on green spaces in urban areas of Malawi have focused on a broader and macro-level perspective, offering insightful information on general trends in different cities. However, there is a significant research shortage in localised understanding, which requires carrying out micro-level assessments concentrating on land use zones and neighbourhoods within these cities. In this study, we used remote sensing data and landscape metrics to understand the distribution and configuration of urban green spaces in the city's neighbourhoods and functional land uses and their relationship with urban form. The study revealed that 20% of neighbourhoods fail to meet the WHO-recommended standard of 9 m2 of green space per person, with a predominant concentration of these undersupplied areas in high-density and quasi-residential zones. In addition, 56.2% of Lilongwe City's total green area was contained under functional land uses. Particularly, high-rise residential, medium-density residential, low-density residential, quasi-residential, high-rise flat area, commercial class, high-rise commercial, heavy industry, light industry, and government land use zones contained 17.3%, 12.0%, 22.2%, 12.0%, 4.1%, 6.4%, 6.1%, 5.0%, 1.6%, and 13.3% of the total green spaces in functional land uses, respectively. Importantly, this research found significant correlations between urban form metrics, namely building coverage, building density, building perimeter area ratio, road density, and the distribution and configuration of urban green spaces. This necessitates an integrated approach to urban planning and design, emphasising the importance of balancing development with green space preservation.
- Published
- 2024
- Full Text
- View/download PDF
14. Assessment of Psychosocial Hazards among Workers at the University of Port Harcourt
- Author
-
Kennedy Na
- Subjects
medicine.medical_specialty ,business.industry ,Family medicine ,Medicine ,General Medicine ,Port harcourt ,business ,Psychosocial - Published
- 2018
15. The impact of NOD2 variants on fecal microbiota in Crohn's disease and controls without gastrointestinal disease
- Author
-
Kennedy, NA, Lamb, CA, Berry, SH, Walker, AW, Mansfield, J, Parkes, M, Simpkins, R, Tremelling, M, Nutland, S, Parkhill, J, Probert, C, Hold, GL, Lees, CW, Kennedy, NA, Lamb, CA, Berry, SH, Walker, AW, Mansfield, J, Parkes, M, Simpkins, R, Tremelling, M, Nutland, S, Parkhill, J, Probert, C, Hold, GL, and Lees, CW
- Abstract
Background/Aims Current models of Crohn's disease (CD) describe an inappropriate immune response to gut microbiota in genetically susceptible individuals. NOD2 variants are strongly associated with development of CD, and NOD2 is part of the innate immune response to bacteria. This study aimed to identify differences in fecal microbiota in CD patients and non-IBD controls stratified by NOD2 genotype. Methods Patients with CD and non-IBD controls of known NOD2 genotype were identified from patients in previous UK IBD genetics studies and the Cambridge bioresource (genotyped/phenotyped volunteers). Individuals with known CD-associated NOD2 mutations were matched to those with wild-type genotype. We obtained fecal samples from patients in clinical remission with low fecal calprotectin (<250 μg/g) and controls without gastrointestinal disease. After extracting DNA, the V1-2 region of 16S rRNA genes were polymerase chain reaction (PCR)-amplified and sequenced. Analysis was undertaken using the mothur package. Volatile organic compounds (VOC) were also measured. Results Ninety-one individuals were in the primary analysis (37 CD, 30 bioresource controls, and 24 household controls). Comparing CD with nonIBD controls, there were reductions in bacterial diversity, Ruminococcaceae, Rikenellaceae, and Christensenellaceae and an increase in Enterobacteriaceae. No significant differences could be identified in microbiota by NOD2 genotype, but fecal butanoic acid was higher in Crohn's patients carrying NOD2 mutations. Conclusions In this well-controlled study of NOD2 genotype and fecal microbiota, we identified no significant genotype-microbiota associations. This suggests that the changes associated with NOD2 genotype might only be seen at the mucosal level, or that environmental factors and prior inflammation are the predominant determinant of the observed dysbiosis in gut microbiota.
- Published
- 2018
16. Mercaptopurine versus placebo to prevent recurrence of Crohn's disease after surgical resection (TOPPIC): a multicentre, double-blind, randomised controlled trial
- Author
-
Mowat, C, Arnott, I, Cahill, A, Smith, M, Ahmad, T, Subramanian, S, Travis, S, Morris, J, Hamlin, J, Dhar, A, Nwokolo, C, Edwards, C, Creed, T, Bloom, S, Yousif, M, Thomas, L, Campbell, S, Lewis, SJ, Sebastian, S, Sen, S, Lal, S, Hawkey, C, Murray, C, Cummings, F, Goh, J, Lindsay, JO, Arebi, N, Potts, L, McKinley, AJ, Thomson, JM, Todd, JA, Collie, M, Dunlop, MG, Mowat, A, Gaya, DR, Winter, J, Naismith, GD, Ennis, H, Keerie, C, Lewis, S, Prescott, RJ, Kennedy, NA, Satsangi, J, and TOPPIC Study Group
- Abstract
BACKGROUND: Up to 60% of patients with Crohn's disease need intestinal resection within the first 10 years of diagnosis, and postoperative recurrence is common. We investigated whether mercaptopurine can prevent or delay postoperative clinical recurrence of Crohn's disease. METHODS: We did a randomised, placebo-controlled, double-blind trial at 29 UK secondary and tertiary hospitals of patients (aged >16 years in Scotland or >18 years in England and Wales) who had a confirmed diagnosis of Crohn's disease and had undergone intestinal resection. Patients were randomly assigned (1:1) by a computer-generated web-based randomisation system to oral daily mercaptopurine at a dose of 1 mg/kg bodyweight rounded to the nearest 25 mg or placebo; patients with low thiopurine methyltransferase activity received half the normal dose. Patients and their carers and physicians were masked to the treatment allocation. Patients were followed up for 3 years. The primary endpoint was clinical recurrence of Crohn's disease (Crohn's Disease Activity Index >150 plus 100-point increase in score) and the need for anti-inflammatory rescue treatment or primary surgical intervention. Primary and safety analyses were by intention to treat. Subgroup analyses by smoking status, previous thiopurines, previous infliximab or methotrexate, previous surgery, duration of disease, or age at diagnosis were also done. This trial is registered with the International Standard Randomised Controlled Trial Register (ISRCTN89489788) and the European Clinical Trials Database (EudraCT number 2006-005800-15). FINDINGS: Between June 6, 2008, and April 23, 2012, 240 patients with Crohn's disease were randomly assigned: 128 to mercaptopurine and 112 to placebo. All patients received at least one dose of study drug, and no randomly assigned patients were excluded from the analysis. 16 (13%) of patients in the mercaptopurine group versus 26 (23%) patients in the placebo group had a clinical recurrence of Crohn's disease and needed anti-inflammatory rescue treatment or primary surgical intervention (adjusted hazard ratio [HR] 0·54, 95% CI 0·27-1·06; p=0·07; unadjusted HR 0·53, 95% CI 0·28-0·99; p=0·046). In a subgroup analysis, three (10%) of 29 smokers in the mercaptopurine group and 12 (46%) of 26 in the placebo group had a clinical recurrence that needed treatment (HR 0·13, 95% CI 0·04-0·46), compared with 13 (13%) of 99 non-smokers in the mercaptopurine group and 14 (16%) of 86 in the placebo group (0·90, 0·42-1·94; pinteraction=0·018). The effect of mercaptopurine did not significantly differ from placebo for any of the other planned subgroup analyses (previous thiopurines, previous infliximab or methotrexate, previous surgery, duration of disease, or age at diagnosis). The incidence and types of adverse events were similar in the mercaptopurine and placebo groups. One patient on placebo died of ischaemic heart disease. Adverse events caused discontinuation of treatment in 39 (30%) of 128 patients in the mercaptopurine group versus 41 (37%) of 112 in the placebo group. INTERPRETATION: Mercaptopurine is effective in preventing postoperative clinical recurrence of Crohn's disease, but only in patients who are smokers. Thus, in smokers, thiopurine treatment seems to be justified in the postoperative period, although smoking cessation should be strongly encouraged given that smoking increases the risk of recurrence.
- Published
- 2017
17. From the Global North to the Global South: preparing students for away rotations
- Author
-
Riccardo Serraino, Darius Owachi, Susan Nassaka Byekwaso, Catherine Misango Namara, Kennedy Naigambi, Francesco Castelli, and Carlo Torti
- Subjects
International medicine ,Medical education ,Global health ,Global world ,Training ,Special aspects of education ,LC8-6691 ,Medicine - Abstract
Abstract Makerere University College of Health Sciences, Kampala, Uganda, has established partnerships with several other institutions worldwide, including the University of Brescia and “Magna Græcia” University, which have agreed to collaborate for the primary purpose of student exchange. Our aim is to comment on students’ preparation for away rotations based on the authors’ own experiences and opinions alongside a review of selected papers on the preparation of students for global health and ethical collaboration. Medical electives represent a unique opportunity for all medical students, not merely for those who will work in resource-limited settings due to increasing globalization. The emergence of ethical international collaborations is of paramount importance to stimulate these projects and ensure that they are implemented safely and with adequate preparation even and especially during the COVID-19 pandemic.
- Published
- 2023
- Full Text
- View/download PDF
18. Monitoring and assessment of urban green space loss and fragmentation using remote sensing data in the four cities of Malawi from 1986 to 2021
- Author
-
Kennedy Nazombe and Odala Nambazo
- Subjects
Urban green spaces ,Per capita green space ,Fragmentation ,Remote sensing ,Landscape metrics ,Malawi ,Science - Abstract
Urban green spaces enhance cities' natural beauty, boost biodiversity, and promote the health and happiness of city residents, among other benefits. Despite the benefits of urban green spaces, their spatial configuration and composition are impacted by urban expansion. This study aims to investigate the spatial-temporal fragmentation trends of urban green spaces in four cities in Malawi (Blantyre, Zomba, Lilongwe, and Mzuzu). We, therefore, applied multi-temporal Landsat images to understand trends in urban green spaces from 1986 to 2021. Five landscape metrics, namely: percentage of land area (PLAND), number of patches (NP), patch density, largest patch index (LPI), landscape shape index (LSI), and mean patch size (MPS), were used to quantify the degree of urban green space fragmentation in Fragstats software. The results showed an increase in the NP, PD, and LSI and a decline in the LPI and MPA in the four cities. This is an indication of fragmentation and a reduction in green space. Rapid urbanisation has resulted in the loss and fragmentation of urban green space areas, which has been attributed to the rapid expansion of built-up areas at the expense of green spaces. The present study is the first to incorporate landscape metrics to understand the spatial heterogeneity of the composition and configuration of green spaces in all the cities of Malawi. The findings of this study contribute to an understanding of how urban growth impacts fragmentation and the loss of urban green spaces and offer valuable insights for better spatial planning and management of cities.
- Published
- 2023
- Full Text
- View/download PDF
19. Relapse after withdrawal from anti‐TNF therapy for inflammatory bowel disease: an observational study, plus systematic review and meta‐analysis
- Author
-
Kennedy, NA, Warner, B, Johnston, EL, Flanders, L, Hendy, P, Ding, NS, Harris, R, Fadra, AS, Basquill, C, Lamb, CA, Cameron, FL, Murray, CD, Parkes, M, Gooding, I, Ahmad, T, Gaya, DR, Mann, S, Lindsay, JO, Gordon, J, Satsangi, J, Hart, A, McCartney, S, Irving, P, and Lees, CW
- Abstract
Background Infliximab and adalimumab have established roles in inflammatory bowel disease (IBD) therapy. UK regulators mandate reassessment after 12 months' anti‐TNF therapy for IBD, with consideration of treatment withdrawal. There is a need for more data to establish the relapse rates following treatment cessation. Aim To establish outcomes following anti‐TNF withdrawal for sustained remission using new data from a large UK cohort, and assimilation of all available literature for systematic review and meta‐analysis. Methods A retrospective observational study was performed on 166 patients with IBD (146 with Crohn's disease (CD) and 20 with ulcerative colitis [UC) and IBD unclassified (IBDU)] withdrawn from anti‐TNF for sustained remission. Meta‐analysis was undertaken of all published studies incorporating 11 further cohorts totalling 746 patients (624 CD, 122 UC). Results Relapse rates in the UK cohort were 36% by 1 year and 56% by 2 years for CD, and 42% by 1 year and 47% by 2 years for UC/IBDU. Increased relapse risk in CD was associated with age at diagnosis [hazard ratio (HR) 2.78 for age 5.25 × 109/L) and faecal calprotectin (HR 2.95 for >50 μg/g) at drug withdrawal. Neither continued immunomodulators nor endoscopic remission were predictors. In the meta‐analysis, estimated 1‐year relapse rates were 39% and 35% for CD and UC/IBDU respectively. Retreatment with anti‐TNF was successful in 88% for CD and 76% UC/IBDU. Conclusions Assimilation of all available data reveals remarkable homogeneity. Approximately one‐third of patients with IBD flare within 12 months of withdrawal of anti‐TNF therapy for sustained remission.
- Published
- 2016
20. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes:a genetic association study
- Author
-
Cleynen, Isabelle, Boucher, Gabrielle, Jostins, Luke, Schumm, L. Philip, Zeissig, Sebastian, Ahmad, Tariq, Andersen, Vibeke, Andrews, Jane M., Annese, Vito, Brand, Stephan, Brant, Steven R., Cho, Judy H., Daly, Mark J., Dubinsky, Marla, Duerr, Richard H., Ferguson, Lynnette R., Franke, Andre, Gearry, Richard B., Goyette, Philippe, Hakonarson, Hakon, Halfvarson, Jonas, Hov, Johannes R., Huang, Hailang, Kennedy, Nicholas A., Kupcinskas, Limas, Lawrance, Ian C., Lee, James C., Satsangi, Jack, Schreiber, Stephan, Théâtre, Emilie, Van Der Meulen De Jong, Andrea E, Weersma, Rinse K., Wilson, David C., Parkes, Miles, Vermeire, Severine, Rioux, John D., Mansfield, John, Silverberg, Mark S., Radford Smith, Graham, Mcgovern, Dermot P. B., Barrett, Jeffrey C., Lees, Charlie W, Abraham, C, Achkar, Jp, Ahmad, T, Amininejad, L, Ananthakrishnan, An, Andersen, V, Anderson, Ca, Andrews, Jm, Annese, V, Aumais, G, Baidoo, L, Baldassano, Rn, Bampton, Pa, Barclay, M, Barrett, Jc, Bayless, Tm, Bethge, J, Bis, Jc, Bitton, A, Boucher, G, Brand, S, Brandt, B, Brant, Sr, Büning, C, Chew, A, Cho, Jh, Cleynen, I, Cohain, A, Croft, A, Daly, Mj, D'Amato, M, Danese, S, De Jong, D, De Vos, M, Denapiene, G, Denson, La, Devaney, K, Dewit, O, D'Inca, R, Dubinsky, M, Duerr, Rh, Edwards, C, Ellinghaus, D, Essers, J, Ferguson, Lr, Festen, Ea, Fleshner, P, Florin, T, Franchimont, D, Franke, A, Fransen, K, Gearry, R, Georges, M, Gieger, C, Glas, J, Goyette, P, Green, T, Griffiths, Am, Guthery, Sl, Hakonarson, H, Halfvarson, J, Hanigan, K, Haritunians, T, Hart, A, Hawkey, C, Hayward, Nk, Hedl, M, Henderson, P, Hu, X, Huang, H, Hui, Ky, Imielinski, M, Ippoliti, A, Jonaitis, L, Jostins, L, Karlsen, Th, Kennedy, Na, Khan, Ma, Kiudelis, G, Krishnaprasad, K, Kugathasan, S, Kupcinskas, L, Latiano, A, Laukens, D, Lawrance, Ic, Lee, Jc, Lees, Cw, Leja, M, Van Limbergen, J, Lionetti, P, Liu, Jz, Louis, E, Mahy, G, Mansfield, J, Massey, D, Mathew, Cg, Mcgovern, Dp, Milgrom, R, Mitrovic, M, Montgomery, Gw, Mowat, C, Newman, W, Ng, A, Ng, Sc, Ng, Sm, Nikolaus, S, Ning, K, Nöthen, M, Oikonomou, I, Palmieri, O, Parkes, M, Phillips, A, Ponsioen, Cy, Potocnik, U, Prescott, Nj, Proctor, Dd, Radford Smith, G, Rahier, Jf, Raychaudhuri, S, Regueiro, M, Rieder, F, Rioux, Jd, Ripke, S, Roberts, R, Russell, Rk, Sanderson, Jd, Sans, M, Satsangi, J, Schadt, Ee, Schreiber, S, Schumm, Lp, Scott, R, Seielstad, M, Sharma, Y, Silverberg, Ms, Simms, La, Skieceviciene, J, Spain, Sl, Steinhart, A, Stempak, Jm, Stronati, Laura, Sventoraityte, J, Targan, Sr, Taylor, Km, ter Velde, A, Theatre, E, Torkvist, L, Tremelling, M, van der Meulen, A, van Sommeren, S, Vasiliauskas, E, Vermeire, S, Verspaget, Hw, Walters, T, Wang, K, Wang, Mh, Weersma, Rk, Wei, Z, Whiteman, D, Wijmenga, C, Wilson, Dc, Winkelmann, J, Xavier, Rj, Zeissig, S, Zhang, B, Zhang, Ck, Zhang, H, Zhang, W, Zhao, H, Zhao, Zz, UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, UCL - (MGD) Service de gastro-entérologie, and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
- Subjects
Male ,0301 basic medicine ,CLINICAL-COURSE ,Nod2 Signaling Adaptor Protein ,Disease ,SUSCEPTIBILITY ,Inflammatory bowel disease ,Major Histocompatibility Complex ,0302 clinical medicine ,Crohn Disease ,Maintenance therapy ,NOD2 ,Medicine and Health Sciences ,POPULATION ,Immunoassay ,RISK ,Medicine(all) ,education.field_of_study ,Crohn's disease ,Hepatocyte Growth Factor ,Medicine (all) ,INDUCTION ,Articles ,General Medicine ,PRIMARY SCLEROSING CHOLANGITIS ,Ulcerative colitis ,3. Good health ,Phenotype ,Female ,030211 gastroenterology & hepatology ,Adult ,medicine.medical_specialty ,MAINTENANCE THERAPY ,Genotype ,Population ,Polymorphism, Single Nucleotide ,Risk Assessment ,CLASSIFICATION ,Primary sclerosing cholangitis ,Young Adult ,03 medical and health sciences ,inflammatory bowel disease ,Proto-Oncogene Proteins ,Internal medicine ,medicine ,Humans ,Genetic Predisposition to Disease ,education ,Alleles ,Genetic Association Studies ,business.industry ,medicine.disease ,digestive system diseases ,030104 developmental biology ,Immunology ,Colitis, Ulcerative ,business ,FOLLOW-UP ,HLA-DRB1 Chains ,INFLAMMATORY-BOWEL-DISEASE - Abstract
Background: Crohn's disease and ulcerative colitis are the two major forms of inflammatory bowel disease; treatment strategies have historically been determined by this binary categorisation. Genetic studies have identified 163 susceptibility loci for inflammatory bowel disease, mostly shared between Crohn's disease and ulcerative colitis. We undertook the largest genotype association study, to date, in widely used clinical subphenotypes of inflammatory bowel disease with the goal of further understanding the biological relations between diseases.Methods: This study included patients from 49 centres in 16 countries in Europe, North America, and Australasia. We applied the Montreal classification system of inflammatory bowel disease subphenotypes to 34 819 patients (19 713 with Crohn's disease, 14 683 with ulcerative colitis) genotyped on the Immunochip array. We tested for genotype–phenotype associations across 156 154 genetic variants. We generated genetic risk scores by combining information from all known inflammatory bowel disease associations to summarise the total load of genetic risk for a particular phenotype. We used these risk scores to test the hypothesis that colonic Crohn's disease, ileal Crohn's disease, and ulcerative colitis are all genetically distinct from each other, and to attempt to identify patients with a mismatch between clinical diagnosis and genetic risk profile.Findings: After quality control, the primary analysis included 29 838 patients (16 902 with Crohn's disease, 12 597 with ulcerative colitis). Three loci (NOD2, MHC, and MST1 3p21) were associated with subphenotypes of inflammatory bowel disease, mainly disease location (essentially fixed over time; median follow-up of 10·5 years). Little or no genetic association with disease behaviour (which changed dramatically over time) remained after conditioning on disease location and age at onset. The genetic risk score representing all known risk alleles for inflammatory bowel disease showed strong association with disease subphenotype (p=1·65 × 10−78), even after exclusion of NOD2, MHC, and 3p21 (p=9·23 × 10−18). Predictive models based on the genetic risk score strongly distinguished colonic from ileal Crohn's disease. Our genetic risk score could also identify a small number of patients with discrepant genetic risk profiles who were significantly more likely to have a revised diagnosis after follow-up (p=6·8 × 10−4).Interpretation: Our data support a continuum of disorders within inflammatory bowel disease, much better explained by three groups (ileal Crohn's disease, colonic Crohn's disease, and ulcerative colitis) than by Crohn's disease and ulcerative colitis as currently defined. Disease location is an intrinsic aspect of a patient's disease, in part genetically determined, and the major driver to changes in disease behaviour over time.Funding: International Inflammatory Bowel Disease Genetics Consortium members funding sources (see Acknowledgments for full list).
- Published
- 2016
21. Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease
- Author
-
Ventham, Nt, Kennedy, Na, Adams, At, Kalla, R, Heath, S, O'Leary, Kr, Drummond, H, Consortium, Ibd Biom, CHARACTER consortium, Ibd, Lionetti, Paolo, Wilson, Dc, Gut, Ig, Nimmo, Er, and Satsangi, J.
- Subjects
inflammatory bowel disease, DNA methylation - Published
- 2016
22. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease
- Author
-
Jostins, Luke, Ripke, Stephan, Weersma, Rinse K., Duerr, Richard H., Mcgovern, Dermot P., Hui, Ken Y., Lee, James C., Philip Schumm, L., Sharma, Yashoda, Anderson, Carl A., Essers, Jonah, Mitrovic, Mitja, Ning, Kaida, Cleynen, Isabelle, Theatre, Emilie, Spain, Sarah L., Raychaudhuri, Soumya, Goyette, Philippe, Wei, Zhi, Abraham, Clara, Achkar, Jean Paul, Ahmad, Tariq, Amininejad, Leila, Ananthakrishnan, Ashwin N., Andersen, Vibeke, Andrews, Jane M., Baidoo, Leonard, Balschun, Tobias, Bampton, Peter A., Bitton, Alain, Boucher, Gabrielle, Brand, Stephan, Büning, Carsten, Cohain, Ariella, Cichon, Sven, D'Amato, Mauro, De Jong, Dirk, Devaney, Kathy L., Dubinsky, Marla, Edwards, Cathryn, Ellinghaus, David, Ferguson, Lynnette R., Franchimont, Denis, Fransen, Karin, Gearry, Richard, Georges, Michel, Gieger, Christian, Glas, Jürgen, Haritunians, Talin, Hart, Ailsa, Hawkey, Chris, Hedl, Matija, Xinli, Hu, Karlsen, Tom H., Kupcinskas, Limas, Kugathasan, Subra, Latiano, Anna, Laukens, Debby, Lawrance, Ian C., Lees, Charlie W., Louis, Edouard, Mahy, Gillian, Mansfield, John, Morgan, Angharad R., Mowat, Craig, Newman, William, Palmieri, Orazio, Ponsioen, Cyriel Y., Potocnik, Uros, Prescott, Natalie J., Regueiro, Miguel, Rotter, Jerome I., Russell, Richard K., Sanderson, Jeremy D., Sans, Miquel, Satsangi, Jack, Schreiber, Stefan, Simms, Lisa A., Sventoraityte, Jurgita, Targan, Stephan R., Taylor, Kent D., Tremelling, Mark, Verspaget, Hein W., De Vos, Martine, Wijmenga, Cisca, Wilson, David C., Winkelmann, Juliane, Xavier, Ramnik J., Zeissig, Sebastian, Zhang, Bin, Zhang, Clarence K., Zhao, Hongyu, Silverberg, Mark S., Annese, Vito, Hakonarson, Hakon, Brant, Steven R., Radford Smith, Graham, Mathew, Christopher G., Rioux, John D., Schadt, Eric E., Daly, Mark J., Franke, Andre, Parkes, Miles, Vermeire, Severine, Barrett, Jeffrey C., Cho, Judy H., Barclay, M, Peyrin Biroulet, L, Chamaillard, M, Colombel, Jf, Cottone, M, Croft, A, D'Incà, R, Halfvarson J, Hanigan K, Henderson, P, Hugot, Jp, Karban, A, Kennedy, Na, Khan, Ma, Lémann, M, Levine, A, Massey, D, Milla, M, Montgomery, Gw, Ng, Sm, Oikonomou, I, Peeters, H, Proctor, Dd, Rahier, Jf, Roberts, R, Rutgeerts, P, Seibold, F, Stronati, Laura, Taylor, Km, Törkvist, L, Ublick, K, Van Limbergen, J, Van Gossum, A, Vatn, Mh, Zhang, H, Zhang, W, Andrews, Jm, Bampton, Pa, Florin, Th, Gearry, R, Krishnaprasad, K, Lawrance, Ic, Mahy, G, Radford Smith, G, Roberts, Rl, Simms, La, Amininijad, L, Cleynen, I, Dewit, O, Franchimont, D, Georges, M, Laukens, D, Theatre, E, Vermeire, S, Aumais, G, Baidoo, L, Barrie AM 3rd, Beck, K, Bernard, Ej, Binion, Dg, Bitton, A, Brant, Sr, Cho, Jh, Cohen, A, Croitoru, K, Daly, Mj, Datta, Lw, Deslandres, C, Duerr, Rh, Dutridge, D, Ferguson, J, Fultz, J, Goyette, P, Greenberg, Gr, Haritunians, T, Jobin, G, Katz, S, Lahaie, Rg, Mcgovern, Dp, Nelson, L, Ning, K, Paré, P, Regueiro, Md, Rioux, Jd, Ruggiero, E, Schumm, L, Schwartz, M, Scott, R, Sharma, Y, Silverberg, Ms, Spears, D, Steinhart, A, Stempak, Jm, Swoger, Jm, Tsagarelis, C, Zhang, C, Zhao, H, Aerts, J, Ahmad, T, Arbury, H, Attwood, A, Auton, A, Ball, Sg, Balmforth, Aj, Barnes, C, Barrett, Jc, Barroso, I, Barton, A, Bennett, Aj, Bhaskar, S, Blaszczyk, K, Bowes, J, Brand, Oj, Braund, Ps, Bredin, F, Breen, G, Brown, Mj, Bruce, In, Bull, J, Burren, Os, Burton, J, Byrnes, J, Caesar, S, Cardin, N, Clee, Cm, Coffey, Aj, Connell, Jm, Conrad, Df, Cooper, Jd, Dominiczak, Af, Downes, K, Drummond, He, Dudakia, D, Dunham, A, Ebbs, B, Eccles, D, Edkins, S, Edwards, C, Elliot, A, Emery, P, Evans, Dm, Evans, G, Eyre, S, Farmer, A, Ferrier, In, Flynn, E, Forbes, A, Forty, L, Franklyn, Ja, Frayling, Tm, Freathy, Rm, Giannoulatou, E, Gibbs, P, Gilbert, P, Gordon Smith, K, Gray, E, Green, E, Groves, Cj, Grozeva, D, Gwilliam, R, Hall, A, Hammond, N, Hardy, M, Harrison, P, Hassanali, N, Hebaishi, H, Hines, S, Hinks, A, Hitman, Ga, Hocking, L, Holmes, C, Howard, E, Howard, P, Howson, Jm, Hughes, D, Hunt, S, Isaacs, Jd, Jain, M, Jewell, Dp, Johnson, T, Jolley, Jd, Jones, Ir, Jones, La, Kirov, G, Langford, Cf, Lango Allen, H, Lathrop, Gm, Lee, J, Lee, Kl, Lees, C, Lewis, K, Lindgren, Cm, Maisuria Armer, M, Maller, J, Mansfield, J, Marchini, Jl, Martin, P, Massey, Dc, Mcardle, Wl, Mcguffin, P, Mclay, Ke, Mcvean, G, Mentzer, A, Mimmack, Ml, Morgan, Ae, Morris, Ap, Mowat, C, Munroe, Pb, Myers, S, Newman, W, Nimmo, Er, O'Donovan, Mc, Onipinla, A, Ovington, Nr, Owen, Mj, Palin, K, Palotie, A, Parnell, K, Pearson, R, Pernet, D, Perry, Jr, Phillips, A, Plagnol, V, Prescott, Nj, Prokopenko, I, Quail, Ma, Rafelt, S, Rayner, Nw, Reid, Dm, Renwick, A, Ring, Sm, Robertson, N, Robson, S, Russell, E, St Clair, D, Sambrook, Jg, Sanderson, Jd, Sawcer, Sj, Schuilenburg, H, Scott, Ce, Seal, S, Shaw Hawkins, S, Shields, Bm, Simmonds, Mj, Smyth, Dj, Somaskantharajah, E, Spanova, K, Steer, S, Stephens, J, Stevens, He, Stirrups, K, Stone, Ma, Strachan, Dp, Su, Z, Symmons, Dp, Thompson, Jr, Thomson, W, Tobin, Md, Travers, Me, Turnbull, C, Vukcevic, D, Wain, Lv, Walker, M, Walker, Nm, Wallace, C, Warren Perry, M, Watkins, Na, Webster, J, Weedon, Mn, Wilson, Ag, Woodburn, M, Wordsworth, Bp, Yau, C, Young, Ah, Zeggini, E, Brown, Ma, Burton, Pr, Caulfield, Mj, Compston, A, Farrall, M, Gough, Sc, Hall, As, Hattersley, At, Hill, Av, Mathew, Cg, Pembrey, M, Satsangi, J, Stratton, Mr, Worthington, J, Hurles, Me, Duncanson, A, Ouwehand, Wh, Parkes, M, Rahman, N, Todd, Ja, Samani, Nj, Kwiatkowski, Dp, Mccarthy, Mi, Craddock, N, Deloukas, P, Donnelly, P, Blackwell, Jm, Bramon, E, Casas, Jp, Corvin, A, Jankowski, J, Markus, Hs, Palmer, Cn, Plomin, R, Rautanen, A, Trembath, Rc, Viswanathan, Ac, Wood, Nw, Spencer, Cc, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Pirinen, M, Strange, A, Blackburn, H, Bumpstead, Sj, Dronov, S, Gillman, M, Jayakumar, A, Mccann, Ot, Liddle, J, Potter, Sc, Ravindrarajah, R, Ricketts, M, Waller, M, Weston, P, Widaa, S, Whittaker, P., AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Gastroenterology and Hepatology, and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
- Subjects
Genome-wide association study ,Disease ,SUSCEPTIBILITY ,Inflammatory bowel disease ,NUMBER ,0302 clinical medicine ,Crohn Disease ,NETWORK ,Genetics ,0303 health sciences ,Multidisciplinary ,Genomics ,Ulcerative colitis ,3. Good health ,Colitis, Ulcerative ,Genetic Predisposition to Disease ,Genome, Human ,Haplotypes ,Humans ,Inflammatory Bowel Diseases ,Mycobacterium ,Mycobacterium Infections ,Mycobacterium tuberculosis ,Phenotype ,Polymorphism, Single Nucleotide ,Reproducibility of Results ,Genome-Wide Association Study ,Host-Pathogen Interactions ,IRGM ,Medical genetics ,030211 gastroenterology & hepatology ,EXPRESSION ,medicine.medical_specialty ,Immunology ,Biology ,Molecular gastro-enterology and hepatology Pathogenesis and modulation of inflammation [IGMD 2] ,TUBERCULOSIS ,03 medical and health sciences ,Medical research ,medicine ,Allele ,METAANALYSIS ,030304 developmental biology ,HYPER-IGE SYNDROME ,MUTATIONS ,medicine.disease ,RISK LOCI ,Genetic architecture ,digestive system diseases - Abstract
Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations(1). Genome-wide association studies and subsequent meta-analyses of these two diseases(2,3) as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy(4), in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases(5). Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
- Published
- 2012
23. Two-stage genome-wide methylation profiling in childhood-onset Crohn's disease implicates epigenetic alterations at the VMP1/MIR21 and HLA loci
- Author
-
Adams, AT, Kennedy, NA, Hansen, R, Ventham, NT, O'Leary, KR, Drummond, HE, Noble, CL, El-Omar, E, Russell, RK, Wilson, DC, Nimmo, ER, Hold, GL, Satsangi, J, Adams, AT, Kennedy, NA, Hansen, R, Ventham, NT, O'Leary, KR, Drummond, HE, Noble, CL, El-Omar, E, Russell, RK, Wilson, DC, Nimmo, ER, Hold, GL, and Satsangi, J
- Abstract
Background: As a result of technological and analytical advances, genome-wide characterization of key epigenetic alterations is now feasible in complex diseases. We hypothesized that this may provide important insights into gene-environmental interactions in Crohn's disease (CD) and is especially pertinent to early onset disease. Methods: The Illumina 450K platform was applied to assess epigenome-wide methylation profiles in circulating leukocyte DNA in discovery and replication pediatric CD cohorts and controls. Data were corrected for differential leukocyte proportions. Targeted replication was performed in adults using pyrosequencing. Methylation changes were correlated with gene expression in blood and intestinal mucosa. Results: We identified 65 individual CpG sites with methylation alterations achieving epigenome-wide significance after Bonferroni correction (P < 1.1 × 10-7), and 19 differently methylated regions displaying unidirectional methylation change. There was a highly significant enrichment of methylation changes around GWAS single nucleotide polymorphisms (P = 3.7 × 10-7), notably the HLA region and MIR21. Two-locus discriminant analysis in the discovery cohort predicted disease in the pediatric replication cohort with high accuracy (area under the curve, 0.98). The findings strongly implicate the transcriptional start site of MIR21 as a region of extended epigenetic alteration, containing the most significant individual probes (P = 1.97 × 10-15) within a GWAS risk locus. In extension studies, we confirmed hypomethylation of MIR21 in adults (P = 6.6 × 10-5, n = 172) and show increased mRNA expression in leukocytes (P < 0.005, n = 66) and in the inflamed intestine (P = 1.4 × 10-6, n = 99). Conclusions: We demonstrate highly significant and replicable differences in DNA methylation in CD, defining the disease-associated epigenome. The data strongly implicate known GWAS loci, with compelling evidence implicating MIR21 and the HLA region.
- Published
- 2014
24. Ex-PTPN-II Cultivation Rights Issues and The Current Development
- Author
-
Kennedy Nasib P. Sibarani and Jamaluddin Mahasari
- Subjects
hak guna usaha, aset negara, administrasi pertanahan. ,Land use ,HD101-1395.5 - Abstract
Abstract: Plantation Limited Company (PTPN)-II has been underway since 2002 and has been 18 years unfinished until now. The problems faced in its settlement are not only issues of land administration but are related to various aspects. This research uses empirical methods with the description approach. The type of data used is primary and secondary data. Data collection is done by interview and a literature study with primary, secondary, and tertiary legal materials. The results of this study are to explain and give an overview of the very long process of land settlement in the ex-PTPN-II cultivation rights in North Sumatra Province. In conclusion, it is necessary to revise Decree of the Head of the National Land Agency Number 42/HGU/BPN/2002 concerning the granting of an extension of the term of the land use rights located in the Deli Serdang Regency, North Sumatra Province, Decree of the Head of the National Land Agency Number 43/HGU/BPN/2002 concerning the granting of an extension of the term of the land use rights located in the Langkat Regency, North Sumatra Province, and Decree of the Head of the National Land Agency Number 44/HGU/BPN/2002 concerning the rejection of the application for the extension of the period of the land use rights located in the city of Binjai, North Sumatra Province, respectively dated November 29, 2002. It needs to be formulated legal consensus to accelerate the completion of ex-PTPN-II cultivation rights, and the President makes a Presidential Decree, which can be the legal basis for its resolution. Intisari: Penyelesaian masalah Hak Guna Usaha (HGU) Ex. PTPN-II telah berlangsung sejak tahun 2002 dan telah 18 tahun belum selesai hingga sekarang. Masalah yang dihadapi bukan hanya masalah administrasi pertanahan tetapi terkait dengan berbagai aspek. Penelitian ini menggunakan metode empiris dengan pendekatan deskriptif. Jenis data yang digunakan adalah data primer dan sekunder. Pengumpulan data dilakukan dengan wawancara dan studi literatur dengan materi hukum primer, sekunder, dan tersier. Hasil penelitian ini adalah menjelaskan dan memberikan gambaran umum dari proses penyelesaian lahan yang sangat lama terhadap HGU ex PTPN-II di Provinsi Sumatera Utara. Kesimpulannya adalah perlu untuk merevisi Keputusan Kepala Badan Pertanahan Nasional Nomor 42 / HGU / BPN / 2002, Keputusan Kepala Badan Pertanahan Nasional Nomor 43 / HGU / BPN / 2002, dan Keputusan Kepala Tanah Nasional Badan Nomor 44 / HGU / BPN / 2002. Perlu dirumuskan secara legal konsensus untuk mempercepat penyelesaian HGU ex-PTPN-II, dan diperlukan Keputusan Presiden, yang dapat menjadi dasar hukum untuk penyelesaiannya
- Published
- 2020
- Full Text
- View/download PDF
25. Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- Author
-
Romagnoni, A., Jegou, S., Van Steen, K., Wainrib, G., Hugot, J. -P., Peyrin-Biroulet, L., Chamaillard, M., Colombel, J. -F., Cottone, M., D'Amato, M., D'Inca, R., Halfvarson, J., Henderson, P., Karban, A., Kennedy, N. A., Khan, M. A., Lemann, M., Levine, A., Massey, D., Milla, M., S. M. E., Ng, Oikonomou, I., Peeters, H., Proctor, D. D., Rahier, J. -F., Rutgeerts, P., Seibold, F., Stronati, L., Taylor, K. M., Torkvist, L., Ublick, K., Van Limbergen, J., Van Gossum, A., Vatn, M. H., Zhang, H., Zhang, W., Andrews, J. M., Bampton, P. A., Barclay, M., Florin, T. H., Gearry, R., Krishnaprasad, K., Lawrance, I. C., Mahy, G., Montgomery, G. W., Radford-Smith, G., Roberts, R. L., Simms, L. A., Hanigan, K., Croft, A., Amininijad, L., Cleynen, I., Dewit, O., Franchimont, D., Georges, M., Laukens, D., Theatre, E., Vermeire, S., Aumais, G., Baidoo, L., Barrie, A. M., Beck, K., Bernard, E. -J., Binion, D. G., Bitton, A., Brant, S. R., Cho, J. H., Cohen, A., Croitoru, K., Daly, M. J., Datta, L. W., Deslandres, C., Duerr, R. H., Dutridge, D., Ferguson, J., Fultz, J., Goyette, P., Greenberg, G. R., Haritunians, T., Jobin, G., Katz, S., Lahaie, R. G., Mcgovern, D. P., Nelson, L., S. M., Ng, Ning, K., Pare, P., Regueiro, M. D., Rioux, J. D., Ruggiero, E., Schumm, L. P., Schwartz, M., Scott, R., Sharma, Y., Silverberg, M. S., Spears, D., Steinhart, A. H., Stempak, J. M., Swoger, J. M., Tsagarelis, C., Zhang, C., Zhao, H., Aerts, J., Ahmad, T., Arbury, H., Attwood, A., Auton, A., Ball, S. G., Balmforth, A. J., Barnes, C., Barrett, J. C., Barroso, I., Barton, A., Bennett, A. J., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O. J., Braund, P. S., Bredin, F., Breen, G., Brown, M. J., Bruce, I. N., Bull, J., Burren, O. S., Burton, J., Byrnes, J., Caesar, S., Cardin, N., Clee, C. M., Coffey, A. J., MC Connell, J., Conrad, D. F., Cooper, J. D., Dominiczak, A. F., Downes, K., Drummond, H. E., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D. M., Evans, G., Eyre, S., Farmer, A., Ferrier, I. N., Flynn, E., Forbes, A., Forty, L., Franklyn, J. A., Frayling, T. M., Freathy, R. M., Giannoulatou, E., Gibbs, P., Gilbert, P., Gordon-Smith, K., Gray, E., Green, E., Groves, C. J., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G. A., Hocking, L., Holmes, C., Howard, E., Howard, P., Howson, J. M. M., Hughes, D., Hunt, S., Isaacs, J. D., Jain, M., Jewell, D. P., Johnson, T., Jolley, J. D., Jones, I. R., Jones, L. A., Kirov, G., Langford, C. F., Lango-Allen, H., Lathrop, G. M., Lee, J., Lee, K. L., Lees, C., Lewis, K., Lindgren, C. M., Maisuria-Armer, M., Maller, J., Mansfield, J., Marchini, J. L., Martin, P., Massey, D. C., Mcardle, W. L., Mcguffin, P., Mclay, K. E., Mcvean, G., Mentzer, A., Mimmack, M. L., Morgan, A. E., Morris, A. P., Mowat, C., Munroe, P. B., Myers, S., Newman, W., Nimmo, E. R., O'Donovan, M. C., Onipinla, A., Ovington, N. R., Owen, M. J., Palin, K., Palotie, A., Parnell, K., Pearson, R., Pernet, D., Perry, J. R., Phillips, A., Plagnol, V., Prescott, N. J., Prokopenko, I., Quail, M. A., Rafelt, S., Rayner, N. W., Reid, D. M., Renwick, A., Ring, S. M., Robertson, N., Robson, S., Russell, E., Clair, D. S., Sambrook, J. G., Sanderson, J. D., Sawcer, S. J., Schuilenburg, H., Scott, C. E., Seal, S., Shaw-Hawkins, S., Shields, B. M., Simmonds, M. J., Smyth, D. J., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H. E., Stirrups, K., Stone, M. A., Strachan, D. P., Su, Z., Symmons, D. P. M., Thompson, J. R., Thomson, W., Tobin, M. D., Travers, M. E., Turnbull, C., Vukcevic, D., Wain, L. V., Walker, M., Walker, N. M., Wallace, C., Warren-Perry, M., Watkins, N. A., Webster, J., Weedon, M. N., Wilson, A. G., Woodburn, M., Wordsworth, B. P., Yau, C., Young, A. H., Zeggini, E., Brown, M. A., Burton, P. R., Caulfield, M. J., Compston, A., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Mathew, C. G., Pembrey, M., Satsangi, J., Stratton, M. R., Worthington, J., Hurles, M. E., Duncanson, A., Ouwehand, W. H., Parkes, M., Rahman, N., Todd, J. A., Samani, N. J., Kwiatkowski, D. P., Mccarthy, M. I., Craddock, N., Deloukas, P., Donnelly, P., Blackwell, J. M., Bramon, E., Casas, J. P., Corvin, A., Jankowski, J., Markus, H. S., Palmer, C. N., Plomin, R., Rautanen, A., Trembath, R. C., Viswanathan, A. C., Wood, N. W., Spencer, C. C. A., Band, G., Bellenguez, C., Freeman, C., Hellenthal, G., Pirinen, M., Strange, A., Blackburn, H., Bumpstead, S. J., Dronov, S., Gillman, M., Jayakumar, A., Mccann, O. T., Liddle, J., Potter, S. C., Ravindrarajah, R., Ricketts, M., Waller, M., Weston, P., Widaa, S., Whittaker, P., Romagnoni, A., Jegou, S., Van Steen, K., Wainrib, G., Hugot, J. -P., Peyrin-Biroulet, L., Chamaillard, M., Colombel, J. -F., Cottone, M., D'Amato, M., D'Inca, R., Halfvarson, J., Henderson, P., Karban, A., Kennedy, N. A., Khan, M. A., Lemann, M., Levine, A., Massey, D., Milla, M., Ng, S. M. E., Oikonomou, I., Peeters, H., Proctor, D. D., Rahier, J. -F., Rutgeerts, P., Seibold, F., Stronati, L., Taylor, K. M., Torkvist, L., Ublick, K., Van Limbergen, J., Van Gossum, A., Vatn, M. H., Zhang, H., Zhang, W., Andrews, J. M., Bampton, P. A., Barclay, M., Florin, T. H., Gearry, R., Krishnaprasad, K., Lawrance, I. C., Mahy, G., Montgomery, G. W., Radford-Smith, G., Roberts, R. L., Simms, L. A., Hanigan, K., Croft, A., Amininijad, L., Cleynen, I., Dewit, O., Franchimont, D., Georges, M., Laukens, D., Theatre, E., Vermeire, S., Aumais, G., Baidoo, L., Barrie, A. M., Beck, K., Bernard, E. -J., Binion, D. G., Bitton, A., Brant, S. R., Cho, J. H., Cohen, A., Croitoru, K., Daly, M. J., Datta, L. W., Deslandres, C., Duerr, R. H., Dutridge, D., Ferguson, J., Fultz, J., Goyette, P., Greenberg, G. R., Haritunians, T., Jobin, G., Katz, S., Lahaie, R. G., Mcgovern, D. P., Nelson, L., Ng, S. M., Ning, K., Pare, P., Regueiro, M. D., Rioux, J. D., Ruggiero, E., Schumm, L. P., Schwartz, M., Scott, R., Sharma, Y., Silverberg, M. S., Spears, D., Steinhart, A. H., Stempak, J. M., Swoger, J. M., Tsagarelis, C., Zhang, C., Zhao, H., Aerts, J., Ahmad, T., Arbury, H., Attwood, A., Auton, A., Ball, S. G., Balmforth, A. J., Barnes, C., Barrett, J. C., Barroso, I., Barton, A., Bennett, A. J., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O. J., Braund, P. S., Bredin, F., Breen, G., Brown, M. J., Bruce, I. N., Bull, J., Burren, O. S., Burton, J., Byrnes, J., Caesar, S., Cardin, N., Clee, C. M., Coffey, A. J., MC Connell, J., Conrad, D. F., Cooper, J. D., Dominiczak, A. F., Downes, K., Drummond, H. E., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D. M., Evans, G., Eyre, S., Farmer, A., Ferrier, I. N., Flynn, E., Forbes, A., Forty, L., Franklyn, J. A., Frayling, T. M., Freathy, R. M., Giannoulatou, E., Gibbs, P., Gilbert, P., Gordon-Smith, K., Gray, E., Green, E., Groves, C. J., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G. A., Hocking, L., Holmes, C., Howard, E., Howard, P., Howson, J. M. M., Hughes, D., Hunt, S., Isaacs, J. D., Jain, M., Jewell, D. P., Johnson, T., Jolley, J. D., Jones, I. R., Jones, L. A., Kirov, G., Langford, C. F., Lango-Allen, H., Lathrop, G. M., Lee, J., Lee, K. L., Lees, C., Lewis, K., Lindgren, C. M., Maisuria-Armer, M., Maller, J., Mansfield, J., Marchini, J. L., Martin, P., Massey, D. C., Mcardle, W. L., Mcguffin, P., Mclay, K. E., Mcvean, G., Mentzer, A., Mimmack, M. L., Morgan, A. E., Morris, A. P., Mowat, C., Munroe, P. B., Myers, S., Newman, W., Nimmo, E. R., O'Donovan, M. C., Onipinla, A., Ovington, N. R., Owen, M. J., Palin, K., Palotie, A., Parnell, K., Pearson, R., Pernet, D., Perry, J. R., Phillips, A., Plagnol, V., Prescott, N. J., Prokopenko, I., Quail, M. A., Rafelt, S., Rayner, N. W., Reid, D. M., Renwick, A., Ring, S. M., Robertson, N., Robson, S., Russell, E., Clair, D. S., Sambrook, J. G., Sanderson, J. D., Sawcer, S. J., Schuilenburg, H., Scott, C. E., Seal, S., Shaw-Hawkins, S., Shields, B. M., Simmonds, M. J., Smyth, D. J., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H. E., Stirrups, K., Stone, M. A., Strachan, D. P., Su, Z., Symmons, D. P. M., Thompson, J. R., Thomson, W., Tobin, M. D., Travers, M. E., Turnbull, C., Vukcevic, D., Wain, L. V., Walker, M., Walker, N. M., Wallace, C., Warren-Perry, M., Watkins, N. A., Webster, J., Weedon, M. N., Wilson, A. G., Woodburn, M., Wordsworth, B. P., Yau, C., Young, A. H., Zeggini, E., Brown, M. A., Burton, P. R., Caulfield, M. J., Compston, A., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Mathew, C. G., Pembrey, M., Satsangi, J., Stratton, M. R., Worthington, J., Hurles, M. E., Duncanson, A., Ouwehand, W. H., Parkes, M., Rahman, N., Todd, J. A., Samani, N. J., Kwiatkowski, D. P., Mccarthy, M. I., Craddock, N., Deloukas, P., Donnelly, P., Blackwell, J. M., Bramon, E., Casas, J. P., Corvin, A., Jankowski, J., Markus, H. S., Palmer, C. N., Plomin, R., Rautanen, A., Trembath, R. C., Viswanathan, A. C., Wood, N. W., Spencer, C. C. A., Band, G., Bellenguez, C., Freeman, C., Hellenthal, G., Pirinen, M., Strange, A., Blackburn, H., Bumpstead, S. J., Dronov, S., Gillman, M., Jayakumar, A., Mccann, O. T., Liddle, J., Potter, S. C., Ravindrarajah, R., Ricketts, M., Waller, M., Weston, P., Widaa, S., Whittaker, P., Daly, Mark J. [0000-0002-0949-8752], Apollo - University of Cambridge Repository, Hugot, Jean-Pierre [0000-0002-8446-6056], UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, UCL - (MGD) Service de gastro-entérologie, Romagnoni, A, Jegou, S, VAN STEEN, Kristel, Wainrib, G, Hugot, JP, Peyrin-Biroulet, L, Chamaillard, M, Colombel, JF, Cottone, M, D'Amato, M, D'Inca, R, Halfvarson, J, Henderson, P, Karban, A, Kennedy, NA, Khan, MA, Lemann, M, Levine, A, Massey, D, Milla, M, Ng, SME, Oikonomou, I, Peeters, H, Proctor, DD, Rahier, JF, Rutgeerts, P, Seibold, F, Stronati, L, Taylor, KM, Torkvist, L, Ublick, K, Van Limbergen, J, Van Gossum, A, Vatn, MH, Zhang, H, Zhang, W, Andrews, JM, Bampton, PA, Barclay, M, Florin, TH, Gearry, R, Krishnaprasad, K, Lawrance, IC, Mahy, G, Montgomery, GW, Radford-Smith, G, Roberts, RL, Simms, LA, Hanigan, K, Croft, A, Amininijad, L, Cleynen, I, Dewit, O, Franchimont, D, Georges, M, Laukens, D, Theatre, E, Vermeire, S, Aumais, G, Baidoo, L, Barrie, AM, Beck, K, Bernard, EJ, Binion, DG, Bitton, A, Brant, SR, Cho, JH, Cohen, A, Croitoru, K, Daly, MJ, Datta, LW, Deslandres, C, Duerr, RH, Dutridge, D, Ferguson, J, Fultz, J, Goyette, P, Greenberg, GR, Haritunians, T, Jobin, G, Katz, S, Lahaie, RG, McGovern, DP, Nelson, L, Ng, SM, Ning, K, Pare, P, Regueiro, MD, Rioux, JD, Ruggiero, E, Schumm, LP, Schwartz, M, Scott, R, Sharma, Y, Silverberg, MS, Spears, D, Steinhart, AH, Stempak, JM, Swoger, JM, Tsagarelis, C, Zhang, C, Zhao, HY, AERTS, Jan, Ahmad, T, Arbury, H, Attwood, A, Auton, A, Ball, SG, Balmforth, AJ, Barnes, C, Barrett, JC, Barroso, I, Barton, A, Bennett, AJ, Bhaskar, S, Blaszczyk, K, Bowes, J, Brand, OJ, Braund, PS, Bredin, F, Breen, G, Brown, MJ, Bruce, IN, Bull, J, Burren, OS, Burton, J, Byrnes, J, Caesar, S, Cardin, N, Clee, CM, Coffey, AJ, Mc Connell, J, Conrad, DF, Cooper, JD, Dominiczak, AF, Downes, K, Drummond, HE, Dudakia, D, Dunham, A, Ebbs, B, Eccles, D, Edkins, S, Edwards, C, Elliot, A, Emery, P, Evans, DM, Evans, G, Eyre, S, Farmer, A, Ferrier, IN, Flynn, E, Forbes, A, Forty, L, Franklyn, JA, Frayling, TM, Freathy, RM, Giannoulatou, E, Gibbs, P, Gilbert, P, Gordon-Smith, K, Gray, E, Green, E, Groves, CJ, Grozeva, D, Gwilliam, R, Hall, A, Hammond, N, Hardy, M, Harrison, P, Hassanali, N, Hebaishi, H, Hines, S, Hinks, A, Hitman, GA, Hocking, L, Holmes, C, Howard, E, Howard, P, Howson, JMM, Hughes, D, Hunt, S, Isaacs, JD, Jain, M, Jewell, DP, Johnson, T, Jolley, JD, Jones, IR, Jones, LA, Kirov, G, Langford, CF, Lango-Allen, H, Lathrop, GM, Lee, J, Lee, KL, Lees, C, Lewis, K, Lindgren, CM, Maisuria-Armer, M, Maller, J, Mansfield, J, Marchini, JL, Martin, P, Massey, DCO, McArdle, WL, McGuffin, P, McLay, KE, McVean, G, Mentzer, A, Mimmack, ML, Morgan, AE, Morris, AP, Mowat, C, Munroe, PB, Myers, S, Newman, W, Nimmo, ER, O'Donovan, MC, Onipinla, A, Ovington, NR, Owen, MJ, Palin, K, Palotie, A, Parnell, K, Pearson, R, Pernet, D, Perry, JRB, Phillips, A, Plagnol, V, Prescott, NJ, Prokopenko, I, Quail, MA, Rafelt, S, Rayner, NW, Reid, DM, Renwick, A, Ring, SM, Robertson, N, Robson, S, Russell, E, St Clair, D, Sambrook, JG, Sanderson, JD, Sawcer, SJ, Schuilenburg, H, Scott, CE, Seal, S, Shaw-Hawkins, S, Shields, BM, Simmonds, MJ, Smyth, DJ, Somaskantharajah, E, Spanova, K, Steer, S, Stephens, J, Stevens, HE, Stirrups, K, Stone, MA, Strachan, DP, Su, Z, Symmons, DPM, Thompson, JR, Thomson, W, Tobin, MD, Travers, ME, Turnbull, C, Vukcevic, D, Wain, LV, Walker, M, Walker, NM, Wallace, C, Warren-Perry, M, Watkins, NA, Webster, J, Weedon, MN, Wilson, AG, Woodburn, M, Wordsworth, BP, Yau, C, Young, AH, Zeggini, E, Brown, MA, Burton, PR, Caulfield, MJ, Compston, A, Farrall, M, Gough, SCL, Hall, AS, Hattersley, AT, Hill, AVS, Mathew, CG, Pembrey, M, Satsangi, J, Stratton, MR, Worthington, J, Hurles, ME, Duncanson, A, Ouwehand, WH, Parkes, M, Rahman, N, Todd, JA, Samani, NJ, Kwiatkowski, DP, McCarthy, MI, Craddock, N, Deloukas, P, Donnelly, P, Blackwell, JM, Bramon, E, Casas, JP, Corvin, A, Jankowski, J, Markus, HS, Palmer, CNA, Plomin, R, Rautanen, A, Trembath, RC, Viswanathan, AC, Wood, NW, Spencer, CCA, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Pirinen, M, Strange, A, Blackburn, H, Bumpstead, SJ, Dronov, S, Gillman, M, Jayakumar, A, McCann, OT, Liddle, J, Potter, SC, Ravindrarajah, R, Ricketts, M, Waller, M, Weston, P, Widaa, S, Whittaker, P, and Kwiatkowski, D
- Subjects
Male ,692/4020/1503/257/1402 ,Genotype ,Genotyping Techniques ,LOCI ,45/43 ,lcsh:Medicine ,Polymorphism, Single Nucleotide ,Crohn's disease, genetics, genome wide association ,Article ,Deep Learning ,Crohn Disease ,INDEL Mutation ,Genetics research ,Humans ,genetics ,Genetic Predisposition to Disease ,129 ,lcsh:Science ,Alleles ,Science & Technology ,genome wide association ,RISK PREDICTION ,45 ,Models, Genetic ,lcsh:R ,Decision Trees ,692/308/2056 ,ASSOCIATION ,Multidisciplinary Sciences ,Crohn's disease ,Logistic Models ,Nonlinear Dynamics ,ROC Curve ,Area Under Curve ,Science & Technology - Other Topics ,lcsh:Q ,Female ,Neural Networks, Computer ,INFLAMMATORY-BOWEL-DISEASE ,Genome-Wide Association Study - Abstract
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers. Tis work was supported by Fondation pour la Recherche Médical (ref DEI20151234405) and Investissements d’Avenir programme ANR-11-IDEX-0005-02, Sorbonne Paris Cite, Laboratoire d’excellence INFLAMEX. Te authors thank the students that participated to the wisdom of the crowd exercise.
- Published
- 2019
26. Glycosylation of Immunoglobulin G Associates With Clinical Features of Inflammatory Bowel Diseases
- Author
-
Anna Latiano, Gordan Lauc, Paula Dobrinić, Mislav Novokmet, Carol J. Landers, Dermot P.B. McGovern, Igor Rudan, Ivana Samaržija, Alan G. Shand, Yurii S. Aulchenko, Marieke Pierik, Charlie W. Lees, Harry Campbell, Ray Boyapati, Lee Murphy, Malcolm G. Dunlop, Silvio Danese, Tim van den Heuve, Gionata Fiorino, Evropi Theorodorou, Richard A. Gardner, G.C. Sturniolo, Noortje de Haan, Natalia Manetti, Jude Gibson, Nicholas A. Kennedy, Ray Doran, Frano Vučković, Angie Fawkes, Manfred Wuhrer, Colin L. Noble, Daisy Jonkers, Olga Gornik, Genadij Razdorov, David Falck, Paolo Lionetti, Daryl L. Fernandes, Tamara Gilchrist, Anna Khon, Renata D'Incà, Stephan R. Targan, Jerko Štambuk, Louise Evenden, Florent Clerc, Gwo-Tzer Ho, Mirna Šimurina, Aleksandar Vojta, Laura Cantoro, Ian D. Arnott, Maja Pučić-Baković, Daniel I. R. Spencer, Marla Dubinsky, Marija Klasić, Nicola Wrobel, Daniel Kolarich, Vlatka Zoldoš, Vito Annese, Irena Trbojević-Akmačić, Victoria Merrick, Jasminka Krištić, Guinevere S. M. Kammeijer, Angelo Andriulli, Dora Markulin, Archana Shubhakar, Iain K. Permberton, Simurina, M, de Haan, N, Vuckovic, F, Kennedy, Na, Stambuk, J, Falck, D, Trbojevic-Akmacic, I, Clerc, F, Razdorov, G, Khon, A, Latiano, A, D'Inca, R, Danese, S, Targan, S, Landers, C, Dubinsky, M, Mcgovern, Dpb, Annese, V, Wuhrer, M, and Lauc, G
- Subjects
0301 basic medicine ,Male ,Glycosylation ,IBD ,glycans ,glycopeptides ,biomarker ,Azathioprine ,Gastroenterology ,Inflammatory bowel disease ,Severity of Illness Index ,Immunoglobulin G ,Crohn Disease ,Risk Factors ,Odds Ratio ,Medicine ,Crohn's disease ,biology ,Area under the curve ,Glycopeptides ,Middle Aged ,Prognosis ,Ulcerative colitis ,3. Good health ,Italy ,Area Under Curve ,Biomarker (medicine) ,Female ,medicine.drug ,Adult ,medicine.medical_specialty ,Glycans ,Article ,03 medical and health sciences ,Predictive Value of Tests ,Internal medicine ,Humans ,Hepatology ,business.industry ,Odds ratio ,Biomarker ,medicine.disease ,United States ,Immunoglobulin Fc Fragments ,030104 developmental biology ,Logistic Models ,ROC Curve ,Case-Control Studies ,biology.protein ,Colitis, Ulcerative ,business ,Protein Processing, Post-Translational - Abstract
BACKGROUND AND AIMS: Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn's disease (CD) and ulcerative colitis (UC), are sometimes hard to distinguish. Glycosylation of IgG has been associated with CD and UC. IgG Fc-glycosylation affects IgG effector functions. We evaluated changes in IgG Fc- glycosylation associated with UC and CD, as well as with disease characteristics in different patient groups. METHODS: We analyzed 3441 plasma samples obtained from 2 independent cohorts of patients with CD (874 patients from Italy and 391 from the United States) or UC (1056 from Italy and 253 from the US and healthy individuals [controls] ; 427 in Italy and 440 from the United States). IgG Fc-glycosylation (tryptic glycopeptides) was analyzed by liquid chromatography coupled to mass spectrometry. We analyzed associations between disease status (UC vs controls, CD vs controls, and UC vs CD) and glycopeptide traits, and associations between clinical characteristics and glycopeptide traits, using a logistic regression model with age and sex included as covariates. RESULTS: Patients with CD or UC had lower levels of IgG galactosylation than controls. For example, the odds ratio (OR) for IgG1 galactosylation in patients with CD was 0.59 (95% confidence interval [CI], 0.51-0.69) and for patients with UC was 0.81 (95% CI, 0.71-0.92). Fucosylation of IgG was increased in patients with CD vs controls (for IgG1: OR, 1.27 ; 95% CI, 1.12-1.44), but decreased in patients with UC vs controls (for IgG23: OR, 0.72 ; 95% CI, 0.63-0.82). Decreased galactosylation associated with more severe CD or UC, including the need for surgery in patients with UC vs controls (for IgG1: OR, 0.69 ; 95% CI, 0.54-0.89) and in patients with CD vs controls (for IgG23: OR, 0.78 ; 95% CI, 0.66-0.91). CONCLUSIONS: In a retrospective analysis of plasma samples from patients with CD or UC, we associated levels of IgG Fc-glycosylation with disease (compared to controls) and its clinical features. These findings could increase our understanding of mechanisms of CD and UC pathogenesis and be used to develop diagnostics or guide treatment.
- Full Text
- View/download PDF
27. Real-world effectiveness of upadacitinib in Crohn's disease: a UK multicentre retrospective cohort study.
- Author
-
Elford AT, Bishara M, Plevris N, Gros B, Constantine-Cooke N, Goodhand J, Kennedy NA, Ahmad T, and Lees CW
- Abstract
Background: Upadacitinib is a Janus kinase inhibitor, which has recently been approved for treating Crohn's disease. There are limited real-world studies on the outcomes of upadacitinib in Crohn's disease., Objective: Our aim was to evaluate the outcomes of upadacitinib in a real-world Crohn's disease cohort., Methods: We conducted a retrospective, multicentre, cohort study over a 2-year period across National Health Service (NHS) Lothian and Royal Devon University Healthcare NHS Foundation Trust. The primary outcome was treatment persistence at week 24. Secondary endpoints were corticosteroid-free clinical remission (Harvey-Bradshaw Index (HBI)<5) and biomarker remission (C-reactive protein (CRP)≤5 mg/L and faecal calprotectin (FCAL)<250 µg/g) at 12, 24 and 52 weeks. We recorded adverse events., Results: 135 patients commenced upadacitinib as of the 1 January 2024, of which 93 patients with active Crohn's disease were included with a minimum of 12 weeks follow-up. The median follow-up time was 25 weeks (IQR 15-42 weeks). 82% of the cohort had exposure to at least two classes of advanced therapies, and 52% had exposure to at least three classes of advanced therapies. Treatment persistence was 87.1% at week 12, 81.7% at week 24 and 62.8% at week 52. Rates of clinical remission were 64% (42/66), 48% (22/46) and 38% (8/21) at weeks 12, 24 and 52, respectively. Significant reductions in HBI, CRP and FCAL were observed during follow-up. 14% (13/91) had a hospitalisation due to Crohn's disease. Adverse events occurred in 40% (37/93) of the cohort, of which 12% (11/93) were serious., Conclusion: Upadacitinib was effective in a real-world, highly refractory, Crohn's disease cohort with good persistence., Competing Interests: Competing interests: BG has served as consultant to Galapagos and Abbvie and as speaker for Abbvie, Janssen, Takeda, Pfizer and Galapagos. NP has served as a speaker for Janssen, Takeda and Pfizer. JG has received grants from F. Hoffmann-La Roche AG, grants from Biogen, grants from Celltrion Healthcare, grants from Galapagos NV, nonfinancial support from Immundiagnostik, outside the submitted work. NAK has acted as a consultant to Amgen, Bristol Myers Squibb, Celltrion, Falk, Janssen, Pfizer, Pharmacosmos, Galapagos, Takeda and Tillotts, received speaking fees from Amgen, Celltrion, Falk, Janssen, Pharmacosmos, Galapagos, Takeda and Tillotts and travel support from AbbVie, Falk, Janssen and Pharmacosmos. His institution has received grants from AbbVie, Biogen, Celgene, Celltrion, Galapagos, MSD, Napp, Pfizer, Pharmacosmos, Roche and Takeda. TA reports grants and non-financial support from F. Hoffmann-La Roche AG, grants from Biogen, grants from Celltrion Healthcare, grants from Galapagos NV, non-financial support from Immundiagnostik, personal fees from Biogen, grants and personal fees from Celltrion Healthcare, personal fees and nonfinancial support from Immundiagnostik, personal fees from Takeda, personal fees from ARENA, personal fees from Gilead, personal fees from Adcock Ingram Healthcare, personal fees from Pfizer, personal fees from Genentech, nonfinancial support from Tillotts, outside the submitted work. CWL has acted as a consultant to Abbvie, Janssen, Takeda, Pfizer, Galapagos, Bristol Myers Squibb, B.I., Sandoz, Novartis, GSK, Gilead, ViforPharma, Dr Falk and Iterative Health; he has received speaking fees and travel support from Pfizer, Janssen, Abbvie, Galapagos, MSD, Takeda, Shire, Ferring, Hospira and Dr Falk., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2024
- Full Text
- View/download PDF
28. Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine.
- Author
-
Wyatt NJ, Watson H, Anderson CA, Kennedy NA, Raine T, Ahmad T, Allerton D, Bardgett M, Clark E, Clewes D, Cotobal Martin C, Doona M, Doyle JA, Frith K, Hancock HC, Hart AL, Hildreth V, Irving PM, Iqbal S, Kennedy C, King A, Lawrence S, Lees CW, Lees R, Letchford L, Liddle T, Lindsay JO, Maier RH, Mansfield JC, Marchesi JR, McGregor N, McIntyre RE, Ostermayer J, Osunnuyi T, Powell N, Prescott NJ, Satsangi J, Sharma S, Shrestha T, Speight A, Strickland M, Wason JM, Whelan K, Wood R, Young GR, Zhang X, Parkes M, Stewart CJ, Jostins-Dean L, and Lamb CA
- Subjects
- Humans, Multicenter Studies as Topic, Observational Studies as Topic, Precision Medicine, Prospective Studies, Quality of Life, Colitis, Ulcerative therapy, Crohn Disease drug therapy, Inflammatory Bowel Diseases drug therapy
- Abstract
Introduction: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments., Methods and Analysis: This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures., Ethics and Dissemination: Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk., Trial Registration Number: ISRCTN96296121., Competing Interests: Competing interests: TA reports personal grants from F. Hoffmann-La Roche, Biogen, AbbVie, Janssen, Celltrion, Galapagos, Immunodiagnostik and Takeda, outside the submitted work; personal fees for educational development/delivery from Pfizer, payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Pfizer, Takeda and F. Hoffman-La Roche; support for attending meetings from Celltrion, Tillotts and Pfizer. CAA reports grants from the Wellcome Sanger Institute Quinquennial Review 2021–2026, Crohn’s and Colitis Foundation (USA), the Medical Research Council, Open Targets UK and the Helmsley Charitable Trust; consulting fees from BridgeBio, Genomics and Brigham & Women’s Hospital Boston; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from GlaxoSmithKline; support for attending meetings and/or travel membership from the Wellcome Sanger Institute Quinquennial Review 2021–2026; (Chair) of the Board of Trustees for the Sanger Prize; other interests as Director of Anderson Genomics Consultancy. MB reports partial personal salary funding from the Medical Research Council. ALH reports personal consulting fees from AbbVie, BMS, Celltrion, Falk, Galapagos, Janssen, Pfizer, Takeda and Roche; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from BMS, Celltrion, Falk, Galapagos, Janssen, Pfizer, Takeda, Roche and AbbVie; support for attending meetings and/or travel from BMS, Celltrion, Falk, Galapagos, Janssen, Pfizer, Takeda, Roche and AbbVie. PI reports personal grants from Celltrion, Galapagos and Pfizer, outside the submitted work; personal consulting fees from AbbVie, Takeda, BMS, Janssen, Arena, Pfizer, Galapagos, Lilly, Boehringer-Ingelheim and Celgene; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from AbbVie, Takeda, Janssen, Lilly, BMS, Pfizer and Galapagos; support for attending meetings and/or travel from AbbVie and Tillotts. LJ-D reports grants from the Wellcome Trust, the Royal Society, the Kennedy Trust for Rheumatology Research, the Helmsley Charitable Trust and the Medical Research Council; grants from Novartis Pharmaceutical, outside the submitted work; consulting fees from Nightingale Health and Genomics. CK reports partial salary funding from the Medical Research Council. NAK reports grants from AbbVie, Biogen, Celltrion, Galapagos and Immunodiagnostik; consulting fees from AbbVie, Bristol-Meyers Squibb and Dr Falk; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from AbbVie, Dr Falk, Tillotts, Galapagos and Takeda; support for attending meetings and/or travel from Tillotts; participation (Chair) on the Board of the British Society of Gastroenterology IBD Clinical Research Group. CAL reports grants from and/or consultancy for Janssen, Takeda, AbbVie, AstraZeneca, Eli Lilly, Orion, Pfizer, Roche, Sanofi Aventis, UCB, Biogen, GSK, Bristol-Myers Squibb and Genentech; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Ferring, Takeda, Janssen, Nordic Pharma and Dr Falk; participation (Secretary) on the British Society of Gastroenterology IBD Section; participation on the Steering Committee of IBD UK. CWL reports grants from UKRI Future Leaders Fellowship; personal consulting fees from AbbVie, Pfizer, Janssen, Takeda, Galapagos, Fresnius Kabi, Novartis/Sandoz, BMS and Celltrion; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from AbbVie, Pfizer, Janssen, Takeda, Galapagos, Fresnius Kabi, Novartis/Sandoz, BMS, Ferring, Dr Falk and Celltrion. JOL reports grants from AbbVie, and Gilead; personal consulting fees from Allergan, AbbVie, Bristol-Myers Squibb, Celgene, Cornerstones US, Galapagos, Gilead, GSK, Lilly, MSD UK, Shire UK, Shire International, Ferring UK, Ferring International, Celltrion, Takeda, Pfizer and Janssen; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from AbbVie, Bristol-Myers Squibb, Cornerstones US, Galapagos, Ferring UK, Ferring International, Celltrion, Takeda, Pfizer and Janssen; support to attend meetings and/or travel from AbbVie and Janssen. RHM reports that she is an independent membership on the Trial Steering Committee for the National Institute for Health and Care Research funded ALLEGRO trial. JRM reports personal consulting fees from EnteroBiotix and Cultech; patent held (without financial gain) on Clostridium difficile therapy (WO2019197836A1), participation (Chair) on the IDMC Board. NMcG reports partial (10%) salary funding from the Medical Research Council. REM reports personal salary funding from the Wellcome Sanger Institute. JO reports stock held in Novartis. MP reports grants from Pfizer and Gilead; personal consulting fees from Galapagos; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Janssen. NP reports grants from Bristol-Myers Squibb, Takeda and Pfizer; consulting fees from AbbVie, Allergan, AstraZeneca, Bristol-Myers Squibb, Celgene, Celltrion, Galapagos, GSK, Takeda and Vifor; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from AbbVie, Bristol-Myers Squibb, Ferring, Galapagos, Janssen, Roche, Pfizer, Takeda and Tillotts; support for attending meetings and/or travel from AbbVie, Allergan, Celltrion, Janssen and Takeda; participation on a data safety monitoring board or advisory board for AbbVie, Allergan, AstraZeneca, Bristol-Myers Squibb, Celgene, Celltrion, Galapagos, GSK, Takeda and Vifor. TR reports personal grants from AbbVie; personal consulting fees from AbbVie, Arena, Aslan, AstraZeneca, Boehringer-Ingelheim, BMS, Celgene, Ferring, Galapagos, Gilead, GSK, Heptares, LabGenius, Janssen, Mylan, MSD, Novartis, Pfizer, Roche, Sandoz, Takeda, UCB and XAP therapeutics; participation on the board of UCB, membership (Chair) of the ECCO Guidelines Committee, membership of the UEG Scientific Committee. JS reports grants from Crohn’s and Colitis UK, the Helmsley Charitable Trust, ECCO, the European Commission, CCFA and Action Medical Research; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Roche; participation on a Data Safety Monitoring Board or Advisory Board for the MODULATE trial and the TRIBUTE trial; leadership or fiduciary role as the Director of the Royal College of Physicians IBD Registry, and Governing Body Fellow at Green Templeton College. AS reports personal consulting fees from GSK; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Falk, and AbbVie; payment of conference fees to attend the British Society of Gastroenterology Annual Conference 2022 from Celltrion; participation on a Data Safety Monitoring Board or Advisory Board for the IBD-RESPONSE study (unpaid), and AbbVie; participation on the British Society of Gastroenterology IBD Section Committee. CJS reports personal consultancy fees from Astarte Medical; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Nestle Nutrition Institute. JW reports grants from Intercept; consulting fees from Worg and UCB; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Janssen; participation on a Data Safety Monitoring Board or Advisory Board for Roche. KW reports grants from the Helsmsley Charitable Trust, Crohn’s and Colitis UK, Almond Board of California, Danone, International Dried Fruit and Nut Council, Medical Research Council, National Institute for Health and care Research; royalty or license payments for Volatile organic compounds in the diagnosis and management of irritable bowel syndrome, and Wiley BDA Advances in Nutrition & Dietetics book series; personal consulting fees from Danone; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Janssen; support for attending meetings and/or travel from Yakult; participation on a Data Safety Monitoring Board or Advisory Board for the MODULATE trial (unpaid)., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.)
- Published
- 2024
- Full Text
- View/download PDF
29. Neutralising antibody responses against SARS-CoV-2 Omicron BA.4/5 and wild-type virus in patients with inflammatory bowel disease following three doses of COVID-19 vaccine (VIP): a prospective, multicentre, cohort study.
- Author
-
Liu Z, Alexander JL, Le K, Zhou X, Ibraheim H, Anandabaskaran S, Saifuddin A, Lin KW, McFarlane LR, Constable L, Seoane RC, Anand N, Bewshea C, Nice R, D'Mello A, Jones GR, Balarajah S, Fiorentino F, Sebastian S, Irving PM, Hicks LC, Williams HR, Kent AJ, Linger R, Parkes M, Kok K, Patel KV, Teare JP, Altmann DM, Boyton RJ, Hart AL, Lees CW, Goodhand JR, Kennedy NA, Pollock KM, Ahmad T, and Powell N
- Abstract
Background: Patients with inflammatory bowel disease (IBD) receiving anti-TNF and JAK-inhibitor therapy have attenuated responses to COVID-19 vaccination. We aimed to determine how IBD treatments affect neutralising antibody responses against the Omicron BA.4/5 variant., Methods: In this multicentre cohort study, we prospectively recruited 340 adults (69 healthy controls and 271 IBD) at nine UK hospitals between May 28, 2021 and March 29, 2022. The IBD study population was established (>12 weeks therapy) on either thiopurine (n = 63), infliximab (n = 45), thiopurine and infliximab combination therapy (n = 48), ustekinumab (n = 45), vedolizumab (n = 46) or tofacitinib (n = 24). Patients were excluded if they were being treated with any other immunosuppressive therapies. Participants had two doses of either ChAdOx1 nCoV-19 or BNT162b2 vaccines, followed by a third dose of either BNT162b2 or mRNA1273. Pseudo-neutralisation assays against SARS-CoV-2 wild-type and BA.4/5 were performed. The half maximal inhibitory concentration (NT50) of participant sera was calculated. The primary outcome was anti-SARS-CoV-2 neutralising response against wild-type virus and Omicron BA.4/5 variant after the second and third doses of anti-SARS-CoV-2 vaccine, stratified by immunosuppressive therapy, adjusting for prior infection, vaccine type, age, and interval between vaccination and blood collection. This study is registered with ISRCTN (No. 13495664)., Findings: Both heterologous (first two doses adenovirus vaccine, third dose mRNA vaccine) and homologous (three doses mRNA vaccine) vaccination strategies significantly increased neutralising titres against both wild-type SARS-CoV-2 virus and the Omicron BA.4/5 variant in healthy participants and patients with IBD. Antibody titres against BA.4/5 were significantly lower than antibodies against wild-type virus in both healthy participants and patients with IBD (p < 0.0001). Multivariable models demonstrated that neutralising antibodies against BA.4/5 after three doses of vaccine were significantly lower in patients with IBD on infliximab (Geometric Mean Ratio (GMR) 0.19 [0.10, 0.36], p < 0.0001), infliximab and thiopurine combination (GMR 0.25 [0.13, 0.49], p < 0.0001) or tofacitinib (GMR 0.43 [0.20, 0.91], p = 0.028), but not in patients on thiopurine monotherapy, ustekinumab, or vedolizumab. Breakthrough infection was associated with lower neutralising antibodies against wild-type (p = 0.037) and BA.4/5 (p = 0.045)., Interpretation: A third dose of a COVID-19 mRNA vaccine based on the wild-type spike glycoprotein significantly boosts neutralising antibody titres in patients with IBD. However, responses are lower against the Omicron variant BA.4/5, particularly in patients taking anti-TNF and JAK-inhibitor therapy. Breakthrough infections are associated with lower neutralising antibodies and immunosuppressed patients with IBD may receive additional benefit from bivalent vaccine boosters which target Omicron variants., Funding: Pfizer., Competing Interests: ALH reports payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from AbbVie, Arena, Atlantic, Bristol Myers Squibb, Celltrion, Ferring, Dr Falk, Galapagos, Janssen, MSD, Napp, Pfizer, Pharmacosmos, Shire, and Takeda; participation on the Global Steering Committee for Genentech. AJK reports consulting fees from Janssen; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from Pfizer and Takeda; support for attending meetings or travel from Janssen, Tillotts, and Norgine; and participation in a data safety monitoring board or advisory board for AbbVie. CWL received personal consulting fees from Galapagos, AbbVie, Takeda, Pfizer, Janssen and Iterative Scopes; institutional consulting fees from Trellus Health; and support for attending meetings from Galapagos, AbbVie, Takeda, Pfizer, Janssen, GSK, Gilead, Fresenius Kabi, Ferring, and Dr Falk. GRJ received speaker fees from Takeda, Ferring, Janssen, AbbVie and Fresenius Kabi. JLA received support for attending meetings from Takeda. JRG reports grants from Roche, Biogen, Celltrion Healthcare, Takeda and Galapagos. KVP received consulting fees from AbbVie, Janssen, Galapagos and Pfizer; reports payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from AbbVie, Dr Falk, Janssen, Galapagos, Pfizer, Takeda, Tillotts and Ferring; support for attending meetings or travel from AbbVie, Dr Falk, Janssen, Galapagos, Pfizer, Takeda, Tillotts and Ferring; and participation on a data safety monitoring board or advisory board for AbbVie, Galapagos, Pfizer and Janssen. SB received research grant from Bowel Research UK and support for attending conferences from Ferring and Dr Falk, outside the submitted work. KMP is a member of the data safety monitoring board for NCT05249829 and NCT05575492; has received a fee for speaking from Seqirus and Sanofi Pasteur, and has research funding from the Chan Zuckerberg Initiative, the MRC/UKRI, the Vaccine Task Force, and NIHR Imperial BRC outside the submitted work. KK reports payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from Janssen and Ferring; support for attending meetings or travel from Janssen and Takeda; and participation on a data safety monitoring board or advisory board for Janssen and PredictImmune. MP received research grant from Pfizer and speaker fees from Janssen. NAK reports grants from AbbVie, Biogen, Celgene, Celltrion, Galapagos, MSD, Napp, Pfizer, Pharmacosmos, Roche, and Takeda; consulting fees from Amgen, Bristol Myers Squibb, Dr Falk, Janssen, Mylan, Pharmacosmos, Galapagos, Takeda, and Tillotts; personal fees from Allergan, Celltrion, Dr Falk, Ferring, Janssen, Pharmacosmos, Takeda, Tillotts, and Galapagos; and support for attending meetings from AbbVie, Dr Falk, Tillotts and Janssen, outside the submitted work. PMI reports grants from Celltrion, Takeda, MSD, Pfizer, and Galapagos; personal fees from Gilead, Pfizer, Galapagos, Takeda, AbbVie, Celltrion, Janssen, Bristol Myers Squibb, Lilly, and Arena; speaker fees from Pfizer, Galapagos, Takeda, AbbVie, Celltrion, Janssen, Bristol Myers Squibb, Lilly, and Arena, outside the submitted work. SS reports grants from Tillotts, Takeda, Janssen, Pfizer and AbbVie; received personal fees from AbbVie, Tillotts, Janssen, Takeda, Dr Falk, Lilly and Bristol Myers Squibb; received support for attending meetings from Janssen, AbbVie and Celltrion; and serves as a member of the data safety monitoring board for AbbVie, Janssen, Takeda, Celltrion, Lilly and Bristol Myers Squibb. TA reports grant funding from Pfizer to deliver this study; grants from Celltrion, Roche, Takeda, Biogen, and Galapagos; and honoraria for lectures from Takeda and Roche, outside the submitted work. NP is the principal investigator on the research grant from Pfizer that funded the VIP study; has received research grants from Bristol Myers Squibb, Roche, Biogen, Celltrion Healthcare, Takeda, Galapagos, CCUK, AstraZeneca, Helmsley Charitable Trust, outside the submitted work; reports personal fees from Takeda, Janssen, Pfizer, Galapagos, Bristol Myers Squibb, AbbVie, Roche, Lilly, Allergan, Celgene and AstraZeneca outside the submitted work; and has served as a speaker or advisory board member for AbbVie, Allergan, Bristol Myers Squibb, Celgene, Dr Falk, AstraZeneca, Galapagos and Vifor; and serves as a member of the data safety monitoring board for Bristol Myers Squibb and AstraZeneca. All other authors declare no competing interests., (© 2023 The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
30. Opioid use and associated factors in 1676 patients with inflammatory bowel disease: a multicentre quality improvement project.
- Author
-
Baillie S, Limdi JK, Bassi A, Fraser A, Parkes G, Scott G, Raine T, Lamb CA, Kennedy NA, Fumis N, Smith MA, Nicolaou A, Emms H, Wye J, Lehmann A, Carbery I, Goodhand J, Lees R, Beshyah W, Luthra P, Pollok R, and Selinger C
- Abstract
Objective: Despite its association with poorer outcomes, opioid use in inflammatory bowel disease (IBD) is not well characterised in the UK. We aimed to examine the extent of opioid use, the associated factors and the use of mitigation techniques such as pain-service review and opioid weaning plans among individuals with IBD., Methods: Data were collected from consecutive patients attending IBD outpatient appointments at 12 UK hospitals. A predefined questionnaire was used to collect data including patient demographics, IBD history, opioid use in the past year (>2 weeks) and opioid-use mitigation techniques. Additionally, consecutive IBD-related hospital stays leading up to July 2019 were reviewed with data collected regarding opioid use at admission, discharge and follow-up as well as details of the admission indication., Results: In 1352 outpatients, 12% had used opioids within the past 12 months. Over half of these individuals were taking opioids for non-IBD pain and less than half had undergone an attempted opioid wean.In 324 hospitalised patients, 27% were prescribed opioids at discharge from hospital. At 12 months postdischarge, 11% were using opioids. Factors associated with opioid use in both cohorts included female sex, Crohn's disease and previous surgery., Conclusions: 1 in 10 patients with IBD attending outpatient appointments were opioid exposed in the past year while a quarter of inpatients were discharged with opioids, and 11% continued to use opioids 12 months after discharge. IBD services should aim to identify patients exposed to opioids, reduce exposure where possible and facilitate access to alternative pain management approaches., Competing Interests: Competing interests: SB has had speaker arrangements with Takeda and Dr Falk, has received travel grants from Galapagos, Celltrion and Dr Falk and has provided consultancy to Galapagos. JKL has received grants from Galapagos and Takeda and speaker and consultancy fees from Abbvie, Arena, Celltrion, Ferring, Galapagos, Janssen, MSD, Pfizer and Takeda. GP has had personal fees from AbbVie, Allergan, BMS, Celltrion, Ferring, Galapagos, Janssen, Takeda, Tillotts. Travel grants from—AbbVie, Celltrion, Ferring, Janssen, Takeda, Tillotts and is a Director and Shareholder in Ampersand Health. GS has had speaker arrangements with Takeda, Abbvie, Tillotts and Galapagos. TR has received research/educational grants and/or speaker/consultation fees from Abbvie, Arena, Aslan, AstraZeneca, Boehringer-Ingelheim, BMS, Celgene, Ferring, Galapagos, Gilead, GSK, Heptares, LabGenius, Janssen, Mylan, MSD, Novartis, Pfizer, Roche, Sandoz, Takeda and UCB. CAL reports grants from Genentech, grants and personal fees from Janssen, grants and personal fees from Takeda, grants from AbbVie, personal fees from Ferring, grants from Eli Lilly, grants from Pfizer, grants from Roche, grants from UCB Biopharma, grants from Sanofi Aventis, grants from Biogen IDEC, grants from Orion OYJ, personal fees from Dr Falk Pharma, grants from AstraZeneca, outside the submitted work. NAK has served as a speaker and/or advisory board member for AbbVie, Allergan, BMS, Falk, Ferring, Galapagos, Janssen, Mylan, Pharmacosmos, Sandoz, Takeda and Tillotts. IC has speaker arrangements with Celltrion and has received a travel grant from Galapagos. RP has provided consultancy to Galapagos. CS has received unrestricted research grants from Warner Chilcott, Janssen and AbbVie, has provided consultancy to Warner Chilcott, Dr Falk, AbbVie, Takeda, Fresenius Kabi, Galapagos, Ferring, Arena and Janssen, and had speaker arrangements with Warner Chilcott, Dr Falk, AbbVie, MSD, Pfizer, Celltrion and Takeda.The preparation of this paper was funded in part by Galapagos., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2023
- Full Text
- View/download PDF
31. Anti-TNF Biologicals Enhance the Anti-Inflammatory Properties of IgG N-Glycome in Crohn's Disease.
- Author
-
Hanić M, Vučković F, Deriš H, Bewshea C, Lin S, Goodhand JR, Ahmad T, Trbojević-Akmačić I, Kennedy NA, and Lauc G
- Subjects
- Humans, Tumor Necrosis Factor Inhibitors therapeutic use, Immunoglobulin G therapeutic use, Quality of Life, Anti-Inflammatory Agents pharmacology, Anti-Inflammatory Agents therapeutic use, Biological Factors therapeutic use, Tumor Necrosis Factor-alpha, Crohn Disease drug therapy, Biological Products therapeutic use
- Abstract
Crohn's disease (CD) is a chronic inflammation of the digestive tract that significantly impairs patients' quality of life and well-being. Anti-TNF biologicals revolutionised the treatment of CD, yet many patients do not adequately respond to such therapy. Previous studies have demonstrated a pro-inflammatory pattern in the composition of CD patients' immunoglobulin G (IgG) N-glycome compared to healthy individuals. Here, we utilised the high-throughput UHPLC method for N-glycan analysis to explore the longitudinal effect of the anti-TNF drugs infliximab and adalimumab on N-glycome composition of total serum IgG in 198 patients, as well as the predictive potential of IgG N-glycans at baseline to detect primary non-responders to anti-TNF therapy in 1315 patients. We discovered a significant decrease in IgG agalactosylation and an increase in monogalactosylation, digalactosylation and sialylation during the 14 weeks of anti-TNF treatment, regardless of therapy response, all of which suggested a diminished inflammatory environment in CD patients treated with anti-TNF therapy. Furthermore, we observed that IgG N-glycome might contain certain information regarding the anti-TNF therapy outcome before initiating the treatment. However, it is impossible to predict future primary non-responders to anti-TNF therapy based solely on IgG N-glycome composition at baseline.
- Published
- 2023
- Full Text
- View/download PDF
32. Establishing key performance indicators for inflammatory bowel disease in the UK.
- Author
-
Quraishi MN, Dobson E, Ainley R, Din S, Wakeman R, Cummings F, Sebastian S, Bloom S, Limdi JK, Dhar A, Speight RA, Bodger K, Kennedy NA, Lamb CA, Arnott ID, and Selinger CP
- Abstract
Background and Aims: Healthcare quality improvement (QI) is the systematic process to continuously improve the quality of care and outcomes for patients. The landmark Inflammatory Bowel Disease (IBD) UK National Audits provided a means to measure the variation in care, highlighting the need to define the standards of excellence in IBD care. Through a consensus approach, we aimed to establish key performance indicators (KPIs), providing reliable benchmarks for IBD care delivery in UK., Methods: KPIs that measure critical aspects of a patient journey within an IBD service were identified though stakeholder meetings. A two-stage Delphi consensus was then conducted. The first involved a multidisciplinary team of IBD clinicians and patients to refine definitions and methodology. The second stage assessed feasibility and utility of the proposed QI process by surveying gastroenterology services across UK., Results: First, the four proposed KPIs were refined and included time from primary care referral to diagnosis in secondary care, time to treatment recommendation following a diagnosis, appropriate use of steroids and advanced therapies prescreening and assessment. Second, the Delphi consensus reported >85% agreement on the feasibility of local adoption of the QI process and >75% agreement on the utility of benchmarking of the KPIs., Conclusions: Through a structured approach, we propose quantifiable KPIs for benchmarking to improve and reduce the individual variation in IBD care across the UK., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2023
- Full Text
- View/download PDF
33. Pretreatment Vitamin D Concentrations Do Not Predict Therapeutic Outcome to Anti-TNF Therapies in Biologic-Naïve Patients With Active Luminal Crohn's Disease.
- Author
-
Chanchlani N, Lin S, Smith R, Roberts C, Nice R, McDonald TJ, Hamilton B, Bishara M, Bewshea C, Kennedy NA, Goodhand JR, and Ahmad T
- Abstract
Background and Aims: Vitamin D has a regulatory role in innate and adaptive immune processes. Previous studies have reported that low pretreatment vitamin D concentrations are associated with primary non-response (PNR) and non-remission to anti-TNF therapy. This study aimed to assess whether pretreatment 25-hydroxyvitamin D concentrations predicted PNR and non-remission to infliximab and adalimumab in patients with active luminal Crohn's disease., Methods: 25-Hydroxyvitamin D concentrations were measured in stored baseline samples from 659 infliximab- and 448 adalimumab-treated patients in the Personalised Anti-TNF Therapy in Crohn's disease (PANTS) study. Cut-offs for vitamin D were deficiency <25 nmol/L, insufficiency 25-50 nmol/L, and adequacy/sufficiency >50 nmol/L., Results: About 17.1% (189/1107; 95% CI, 15.0-19.4) and 47.7% (528/1107; 95% CI, 44.8-50.6) of patients had vitamin D deficiency and insufficiency, respectively. 22.2% (246/1107) of patients were receiving vitamin D supplementation. Multivariable analysis confirmed that sampling during non-summer months, South Asian ethnicity, lower serum albumin concentrations, and non-treatment with vitamin D supplementation were independently associated with lower vitamin D concentrations. Pretreatment vitamin D status did not predict response or remission to anti-TNF therapy at week 14 (infliximab P
pnr = .89, adalimumab Ppnr = .18) or non-remission at week 54 (infliximab P = .13, adalimumab P = .58). Vitamin D deficiency was, however, associated with a longer time to immunogenicity in patients treated with infliximab, but not adalimumab., Conclusions: Vitamin D deficiency is common in patients with active Crohn's disease. Unlike previous studies, pretreatment vitamin D concentration did not predict PNR to anti-TNF treatment at week 14 or nonremission at week 54., Competing Interests: S.L. reports nonfinancial support from Pfizer outside the submitted work. N.A.K. reports grants from F. Hoffmann-La Roche AG, grants from Biogen Inc, grants from Celltrion Healthcare, grants from Galapagos NV, nonfinancial support from Immundiagnostik, grants and nonfinancial support from AbbVie, grants and personal fees from Celltrion, personal fees and nonfinancial support from Janssen, personal fees from Takeda, personal fees and nonfinancial support from Dr Falk, outside the submitted work. T.A. reports grants and nonfinancial support from F. Hoffmann-La Roche AG, grants from Biogen Inc, grants from Celltrion Healthcare, grants from Galapagos NV, nonfinancial support from Immundiagnostik, personal fees from Biogen inc, grants and personal fees from Celltrion Healthcare, personal fees and nonfinancial support from Immundiagnostik, personal fees from Takeda, personal fees from ARENA, personal fees from Gilead, personal fees from Adcock Ingram Healthcare, personal fees from Pfizer, personal fees from Genentech, nonfinancial support from Tillotts, outside the submitted work. J.R.G. reports grants from F. Hoffmann-La Roche AG, grants from Biogen Inc, grants from Celltrion Healthcare, grants from Galapagos NV, nonfinancial support from Immundiagnostik, outside the submitted work. The following authors have nothing to declare: N.C., R.S., C.R., R.N., T.J.M., C.B., B.H., and M.B., (© The Author(s) 2023. Published by Oxford University Press on behalf of Crohn's & Colitis Foundation.)- Published
- 2023
- Full Text
- View/download PDF
34. The gut microbiota and metabolome are associated with diminished COVID-19 vaccine-induced antibody responses in immunosuppressed inflammatory bowel disease patients.
- Author
-
Alexander JL, Mullish BH, Danckert NP, Liu Z, Olbei ML, Saifuddin A, Torkizadeh M, Ibraheim H, Blanco JM, Roberts LA, Bewshea CM, Nice R, Lin S, Prabhudev H, Sands C, Horneffer-van der Sluis V, Lewis M, Sebastian S, Lees CW, Teare JP, Hart A, Goodhand JR, Kennedy NA, Korcsmaros T, Marchesi JR, Ahmad T, and Powell N
- Subjects
- Humans, COVID-19 Vaccines, Antibody Formation, ChAdOx1 nCoV-19, BNT162 Vaccine, Infliximab, RNA, Ribosomal, 16S, Tumor Necrosis Factor Inhibitors therapeutic use, SARS-CoV-2, Metabolome, Gastrointestinal Microbiome, COVID-19, Inflammatory Bowel Diseases drug therapy
- Abstract
Background: Patients with inflammatory bowel disease (IBD) treated with anti-TNF therapy exhibit attenuated humoral immune responses to vaccination against SARS-CoV-2. The gut microbiota and its functional metabolic output, which are perturbed in IBD, play an important role in shaping host immune responses. We explored whether the gut microbiota and metabolome could explain variation in anti-SARS-CoV-2 vaccination responses in immunosuppressed IBD patients., Methods: Faecal and serum samples were prospectively collected from infliximab-treated patients with IBD in the CLARITY-IBD study undergoing vaccination against SARS-CoV-2. Antibody responses were measured following two doses of either ChAdOx1 nCoV-19 or BNT162b2 vaccine. Patients were classified as having responses above or below the geometric mean of the wider CLARITY-IBD cohort. 16S rRNA gene amplicon sequencing, nuclear magnetic resonance (NMR) spectroscopy and bile acid profiling with ultra-high-performance liquid chromatography mass spectrometry (UHPLC-MS) were performed on faecal samples. Univariate, multivariable and correlation analyses were performed to determine gut microbial and metabolomic predictors of response to vaccination., Findings: Forty-three infliximab-treated patients with IBD were recruited (30 Crohn's disease, 12 ulcerative colitis, 1 IBD-unclassified; 26 with concomitant thiopurine therapy). Eight patients had evidence of prior SARS-CoV-2 infection. Seventeen patients (39.5%) had a serological response below the geometric mean. Gut microbiota diversity was lower in below average responders (p = 0.037). Bilophila abundance was associated with better serological response, while Streptococcus was associated with poorer response. The faecal metabolome was distinct between above and below average responders (OPLS-DA R
2 X 0.25, R2 Y 0.26, Q2 0.15; CV-ANOVA p = 0.038). Trimethylamine, isobutyrate and omega-muricholic acid were associated with better response, while succinate, phenylalanine, taurolithocholate and taurodeoxycholate were associated with poorer response., Interpretation: Our data suggest that there is an association between the gut microbiota and variable serological response to vaccination against SARS-CoV-2 in immunocompromised patients. Microbial metabolites including trimethylamine may be important in mitigating anti-TNF-induced attenuation of the immune response., Funding: JLA is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-502), funded by Imperial College London and The Joyce and Norman Freed Charitable Trust. BHM is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-002). The Division of Digestive Diseases at Imperial College London receives financial and infrastructure support from the NIHR Imperial Biomedical Research Centre (BRC) based at Imperial College Healthcare NHS Trust and Imperial College London. Metabolomics studies were performed at the MRC-NIHR National Phenome Centre at Imperial College London; this work was supported by the Medical Research Council (MRC), the National Institute of Health Research (NIHR) (grant number MC_PC_12025) and infrastructure support was provided by the NIHR Imperial Biomedical Research Centre (BRC). The NIHR Exeter Clinical Research Facility is a partnership between the University of Exeter Medical School College of Medicine and Health, and Royal Devon and Exeter NHS Foundation Trust. This project is supported by the National Institute for Health Research (NIHR) Exeter Clinical Research Facility. The views expressed are those of the authors and not necessarily those of the NIHR or the UK Department of Health and Social Care., Competing Interests: Declaration of interests Dr Saifuddin has received travel expense support from Janssen. Dr Lin reports non-financial support from Pfizer, non-financial support from Ferring, outside the submitted work. Dr. Kennedy reports grants from AbbVie, Biogen, Celgene, Celtrion, Galapagos, MSD, Napp, Pfizer, Pharmacosmos, Roche and Takeda, consulting fees from Amgen, Bristol-Myers Squibb, Falk, Janssen, Mylan, Pharmacosmos, Galapagos, Takeda and Tillotts, personal fees from Allergan, Celltrion, Falk, Ferring, Janssen, Pharmacosmos, Takeda, Tilllotts, Galapagos, and support for attending meetings from AbbVie, Falk and Janssen outside the submitted work. Prof. Sebastian reports grants from Takeda, Abbvie, Tillots Pharma, Janssen, Pfizer, Biogen and personal fees from Takeda, Abbvie, Janssen, Pharmacocosmos, Biogen, Pfizer, Tillots Pharma and Falk Pharma, outside the submitted work. Dr Hart reports payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from AbbVie, AZ, Atlantic, Bristol-Myers Squibb, Celltrion, Falk, Galapogos, Janssen, MSD, Napp Pharmaceuticals, Pfizer, Pharmacosmos, Shire and Takeda and Global Steering Committee for Genentech, support for attending meetings from Abbvie, Takeda and Janssen, and Participation on a Data Safety Monitoring Board or Advisory Board for AbbVie, AZ, Atlantic, Bristol-Myers Squibb, Galapogos, Janssen, Pfizer and Takeda. Prof. Lees reports a Future Leaders Fellow award from UKRI, personal consulting fees from Galapagos, Abbvie, Takeda, Pfizer, Janssen, Iterative Scopes and institutional consulting fees from Trellus Health, personal fees from Galapagos, Abbvie, Takeda, Pfizer, Janssen, GSK, Gilead, Fresnius Kabi, Ferring and Dr Falk, and support for attending meetings from Galapagos, Abbvie, Takeda, Pfizer, Janssen, GSK, Gilead, Fresnius Kabi, Ferring and Dr Falk. Dr. Goodhand reports grants from F. Hoffmann-La Roche AG, grants from Biogen Inc, grants from Celltrion Healthcare, grants from Galapagos NV, non-financial support from Immundiagnostik, during the conduct of the study. Prof. Ahmad reports grant funding from Pfizer to his institution to deliver this study, grants from Celltrion, Roche, Takeda, Biogen and Galapagos and honoraria for lectures from Takeda and Roche, outside the submitted work. Dr Powell has received research grant(s) from Bristol Myers Squibb outside the submitted work. Dr. Powell reports personal fees from Takeda, Janssen, Pfizer, Bristol-Myers Squibb, Abbvie, Roche, Lilly, Allergan, and Celgene, outside the submitted work; Dr. Powell has served as a speaker/advisory board member for Abbvie, Allergan, Bristol Myers Squibb, Celgene, Falk, Ferring, Janssen, Pfizer, Tillotts, Takeda and Vifor Pharma. The following authors have nothing to declare: Dr Alexander, Dr Ibraheim, Claire Bewshea, Rachel Nice, Dr Liu, Dr Mullish, Dr Danckert, Melissa Torkizadeh, Jesús Miguéns Blanco, Lauren A Roberts, Hemanth Prabhudev, Caroline Sands, Verena Horneffer-van der Sluis, Matthew Lewis, Professor Teare, Martin Olbei, Tamas Korcsmaros and Professor Marchesi., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)- Published
- 2023
- Full Text
- View/download PDF
35. Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC).
- Author
-
Ventham NT, Kennedy NA, Kalla R, Adams AT, Noble A, Ennis H, Mowat C, Dunlop MG, and Satsangi J
- Subjects
- Adult, Humans, Child, Child, Preschool, DNA Methylation genetics, Genome-Wide Association Study methods, Epigenesis, Genetic, Membrane Proteins genetics, Crohn Disease genetics, Crohn Disease surgery, Inflammatory Bowel Diseases genetics
- Abstract
Background & Aims: DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn's disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts., Methods: TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198)., Results: CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P < .05), including probes mapping to WHSC1 (P = 4.1 × 10
-9 , Holm P = .002) and EFNA3 (P = 4.9 × 10-8 , Holm P = .02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10-5 ). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2-2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10-19 , SBNO2 = 1.2 × 10-11 ) and regions (TXK [false discovery rate, P = 3.6 × 10-14 ], WRAP73 [false discovery rate, P = 1.9 × 10-9 ], VMP1 [false discovery rate, P = 1.7 × 10-7 ], and ITGB2 [false discovery rate, P = 1.4 × 10-7 ])., Conclusions: We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2023
- Full Text
- View/download PDF
36. The importance of high-quality 'big data' in the application of artificial intelligence in inflammatory bowel disease.
- Author
-
Ashton JJ, Brooks-Warburton J, Allen PB, Tham TC, Hoque S, Kennedy NA, Dhar A, and Sebastian S
- Abstract
Competing Interests: Competing interests: JB-W holds research grants from AbbVie, and has received speaker fees from Dr Falk Pharma. JA no COI to declare. AD Advisory and consultancy for Pfizer UK, Tillotts Pharma UK, Dr Falk Pharma, Pharmacosmos, Takeda UK, Honoraria and Speaker Fees from Dr Falk Pharma, Pfizer, Janssen, Tillotts Pharma, Pharmacosmos, Takeda UK. PBA received research grants from Pfizer and speaker fees from Takaeda, AbbVie, GSK, Janssen, MSD and Tillotts. TCT no COI to declare. SH no COI to declare. SS holds research grants from Biogen, Takeda, AbbVie, TillottsPharma, Ferring and Biohit; served on the advisory boards of Takeda, AbbVie, Merck, Ferring, Pharmacocosmos, Warner Chilcott, Janssen, Falk Pharma, Biohit, TriGenix, Celgene and Tillots Pharma; and has received speaker fees from AbbVie, Biogen, AbbVie, Janssen, Merck, Warner Chilcott and Falk Pharma. NAK has served as a speaker and/or advisory board member for AbbVie, Allergan, BMS, Falk, Ferring, Janssen, Mylan, Pharmacosmos, Pfizer, Sandoz, Takeda and Tillotts. He is the director of a company that handles central reading of endoscopy. His department has received research funding from AbbVie, Biogen, Celgene, Celtrion, Galapagos, MSD, Napp, Pfizer, Pharmacosmos, Roche and Takeda.
- Published
- 2022
- Full Text
- View/download PDF
37. Real-world experience of intravenous ferric derisomaltose evaluated through safety and efficacy reporting in the UK.
- Author
-
Sinclair RCF, Nadaraja S, Kennedy NA, Wakatsuki M, and Bhandari S
- Subjects
- Adult, Pregnancy, Humans, Female, Male, Retrospective Studies, Ferric Compounds, Iron, Ferritins, Hemoglobins analysis, United Kingdom, Maltose therapeutic use, Anemia, Iron-Deficiency drug therapy, Anemia, Iron-Deficiency epidemiology
- Abstract
Ferric derisomaltose (FDI; Monofer) is used in clinical practice to treat iron deficiency, but the safety and efficacy of FDI has not been robustly evaluated in a large real-world study. This retrospective, multicentre, audit-based, observational study provides pragmatic information about safety and clinical responses with FDI across therapy areas and patient populations, helping to facilitate treatment decisions. Participating sites provided data from the medical records of adults who had received ≥ 1 FDI infusion. The primary outcome was the incidence of adverse reactions within 24 hours of the FDI infusion. Secondary outcomes included the change from baseline in haemoglobin and ferritin up to 12 months post infusion. In total, 19 sites provided data for a total of 7354 FDI-treated patients; 64.3% of patients were female, and 42.2% were aged ≥ 70 years. Surgery was the main hospital specialty (34.5%). The incidence of any recorded adverse reactions, hypersensitivity reactions, and anaphylaxis were 1.7%, 0.4%, and < 0.1%, respectively, regardless of baseline anaemia status. Statistically significant increases in haemoglobin and ferritin were observed between baseline and Month 4 following FDI treatment (p < 0.0001). Improvements in haemoglobin were more pronounced for hospital specialties where operative blood loss is expected (surgery/obstetrics) compared with those where blood loss is not expected. This study provides real-world clinical evidence for the low risk of adverse reactions with FDI across diverse patient populations, providing reassurance that intravenous iron is not associated with serious toxicity. These findings may inform changes in intravenous iron delivery to provide effective therapy to more patients in need., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
38. Treatment adaptations and outcomes of patients experiencing inflammatory bowel disease flares during the early COVID-19 pandemic: the PREPARE-IBD multicentre cohort study.
- Author
-
Saifuddin A, Kent AJ, Mehta SJ, Hicks LC, Gonzalez HA, Segal JP, Brookes MJ, Subramanian S, Bhala N, Conley TE, Patel KV, Lamb CA, Walker GJ, Kennedy NA, and Sebastian S
- Subjects
- Humans, Pandemics, Ustekinumab, State Medicine, Cohort Studies, Adrenal Cortex Hormones therapeutic use, Prednisolone, COVID-19, Inflammatory Bowel Diseases diagnosis, Inflammatory Bowel Diseases drug therapy, Inflammatory Bowel Diseases complications, Colitis, Ulcerative diagnosis, Colitis, Ulcerative drug therapy, Colitis, Ulcerative complications, Crohn Disease epidemiology
- Abstract
Background: The COVID-19 pandemic offered a unique opportunity to understand inflammatory bowel disease (IBD) management during unexpected disruption. This could help to guide practice overall., Aims: To compare prescribing behaviour for IBD flares and outcomes during the early pandemic with pre-pandemic findings METHODS: We performed an observational cohort study comprising patients who contacted IBD teams for symptomatic flares between March and June 2020 in 60 National Health Service trusts in the United Kingdom. Data were compared with a pre-pandemic cohort after propensity-matching for age and physician global assessment of disease activity., Results: We included 1864 patients in each of the pandemic and pre-pandemic cohorts. The principal findings were reduced systemic corticosteroid prescription during the pandemic in Crohn's disease (prednisolone: pandemic 26.5% vs. 37.1%; p < 0.001) and ulcerative colitis (UC) (prednisolone: pandemic 33.5% vs. 40.7%, p < 0.001), with increases in poorly bioavailable oral corticosteroids in Crohn's (pandemic 15.6% vs. 6.8%; p < 0.001) and UC (pandemic 11.8% vs. 5.2%; p < 0.001). Ustekinumab (Crohn's and UC) and vedolizumab (UC) treatment also significantly increased. Three-month steroid-free remission in each period was similar in Crohn's (pandemic 28.4% vs. 32.1%; p = 0.17) and UC (pandemic 36.4% vs. 40.2%; p = 0.095). Patients experiencing a flare and suspected COVID-19 were more likely to have moderately-to-severely active disease at 3 months than those with a flare alone., Conclusions: Despite treatment adaptations during the pandemic, steroid-free outcomes were comparable with pre-pandemic levels, although concurrent flare and suspected COVID-19 caused worse outcomes. These findings have implications for IBD management during future pandemics and for standard practice., (© 2022 John Wiley & Sons Ltd.)
- Published
- 2022
- Full Text
- View/download PDF
39. Implications for sequencing of biologic therapy and choice of second anti-TNF in patients with inflammatory bowel disease: results from the IMmunogenicity to Second Anti-TNF therapy (IMSAT) therapeutic drug monitoring study.
- Author
-
Chanchlani N, Lin S, Auth MK, Lee CL, Robbins H, Looi S, Murugesan SV, Riley T, Preston C, Stephenson S, Cardozo W, Sonwalkar SA, Allah-Ditta M, Mansfield L, Durai D, Baker M, London I, London E, Gupta S, Di Mambro A, Murphy A, Gaynor E, Jones KDJ, Claridge A, Sebastian S, Ramachandran S, Selinger CP, Borg-Bartolo SP, Knight P, Sprakes MB, Burton J, Kane P, Lupton S, Fletcher A, Gaya DR, Colbert R, Seenan JP, MacDonald J, Lynch L, McLachlan I, Shields S, Hansen R, Gervais L, Jere M, Akhtar M, Black K, Henderson P, Russell RK, Lees CW, Derikx LAAP, Lockett M, Betteridge F, De Silva A, Hussenbux A, Beckly J, Bendall O, Hart JW, Thomas A, Hamilton B, Gordon C, Chee D, McDonald TJ, Nice R, Parkinson M, Gardner-Thorpe H, Butterworth JR, Javed A, Al-Shakhshir S, Yadagiri R, Maher S, Pollok RCG, Ng T, Appiahene P, Donovan F, Lok J, Chandy R, Jagdish R, Baig D, Mahmood Z, Marsh L, Moss A, Abdulgader A, Kitchin A, Walker GJ, George B, Lim YH, Gulliver J, Bloom S, Theaker H, Carlson S, Cummings JRF, Livingstone R, Beale A, Carter JO, Bell A, Coulter A, Snook J, Stone H, Kennedy NA, Goodhand JR, and Ahmad T
- Subjects
- Adalimumab therapeutic use, Antibodies, Biological Therapy, Drug Monitoring, Humans, Immunologic Factors therapeutic use, Infliximab therapeutic use, Retrospective Studies, Tumor Necrosis Factor-alpha, Inflammatory Bowel Diseases drug therapy, Tumor Necrosis Factor Inhibitors therapeutic use
- Abstract
Background: Anti-drug antibodies are associated with treatment failure to anti-TNF agents in patients with inflammatory bowel disease (IBD)., Aim: To assess whether immunogenicity to a patient's first anti-TNF agent would be associated with immunogenicity to the second, irrespective of drug sequence METHODS: We conducted a UK-wide, multicentre, retrospective cohort study to report rates of immunogenicity and treatment failure of second anti-TNF therapies in 1058 patients with IBD who underwent therapeutic drug monitoring for both infliximab and adalimumab. The primary outcome was immunogenicity to the second anti-TNF agent, defined at any timepoint as an anti-TNF antibody concentration ≥9 AU/ml for infliximab and ≥6 AU/ml for adalimumab., Results: In patients treated with infliximab and then adalimumab, those who developed antibodies to infliximab were more likely to develop antibodies to adalimumab, than patients who did not develop antibodies to infliximab (OR 1.99, 95%CI 1.27-3.20, p = 0.002). Similarly, in patients treated with adalimumab and then infliximab, immunogenicity to adalimumab was associated with subsequent immunogenicity to infliximab (OR 2.63, 95%CI 1.46-4.80, p < 0.001). For each 10-fold increase in anti-infliximab and anti-adalimumab antibody concentration, the odds of subsequently developing antibodies to adalimumab and infliximab increased by 1.73 (95% CI 1.38-2.17, p < 0.001) and 1.99 (95%CI 1.34-2.99, p < 0.001), respectively. Patients who developed immunogenicity with undetectable drug levels to infliximab were more likely to develop immunogenicity with undetectable drug levels to adalimumab (OR 2.37, 95% CI 1.39-4.19, p < 0.001). Commencing an immunomodulator at the time of switching to the second anti-TNF was associated with improved drug persistence in patients with immunogenic, but not pharmacodynamic failure., Conclusion: Irrespective of drug sequence, immunogenicity to the first anti-TNF agent was associated with immunogenicity to the second, which was mitigated by the introduction of an immunomodulator in patients with immunogenic, but not pharmacodynamic treatment failure., (© 2022 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)
- Published
- 2022
- Full Text
- View/download PDF
40. Understanding anti-TNF treatment failure: does serum triiodothyronine-to-thyroxine (T3/T4) ratio predict therapeutic outcome to anti-TNF therapies in biologic-naïve patients with active luminal Crohn's disease?
- Author
-
Lin S, Chanchlani N, Carbery I, Janjua M, Nice R, McDonald TJ, Bewshea C, Kennedy NA, Ahmad T, Selinger CP, and Goodhand JR
- Subjects
- Adalimumab therapeutic use, Adult, Female, Humans, Infliximab therapeutic use, Male, Thyroid Function Tests, Thyroxine therapeutic use, Treatment Failure, Triiodothyronine, Tumor Necrosis Factor Inhibitors, Biological Products, Crohn Disease diagnosis, Crohn Disease drug therapy
- Abstract
Background: During illness, adaptations of the hypothalamic-pituitary-thyroid axis reduce energy expenditure, protein catabolism and modulate immune responses to promote survival. Lower serum free triiodothyronine-to-thyroxine (fT3/fT4) ratio has been linked to non-response to treatment in a range of diseases, including in biologic-treated patients with inflammatory bowel disease., Aim: To assess whether baseline serum fT3/fT4 ratio predicted primary non-response (PNR) and non-remission to infliximab and adalimumab in patients with Crohn's disease METHODS: Thyroid function tests were undertaken in stored serum from biologic-naïve adult patients with active luminal Crohn's disease immediately prior to treatment with infliximab (427 originator; 122 biosimilar) or adalimumab (448) in the Personalised Anti-TNF Therapy in Crohn's Disease study (PANTS)., Results: Baseline median [IQR] fT3/fT4 ratios were lower in women than men (0.30 [0.27-0.34] vs 0.32 [0.28-0.36], p < 0.001), in patients with more severe inflammatory disease, and in patients receiving corticosteroids (0.28 [0.25-0.33] vs. 0.32 [0.29-0.36], p < 0.001). Multivariable logistic regression analysis demonstrated that fT3/fT4 ratio was independently associated with PNR at week 14 (odds ratio [OR] 0.51, 95% confidence interval [CI] 0.31-0.85, p = 0.009), but not non-remission or changes in faecal calprotectin concentrations at week 54. The optimal threshold to determine PNR was 0.31 (area under the curve 0.57 [95% CI 0.54-0.61], sensitivity 0.62 [95% CI 0.41-0.74], and specificity 0.53 [95% CI 0.42-0.73])., Conclusions: Lower baseline serum fT3/fT4 ratio was associated with female sex, corticosteroid use and disease activity. It predicted PNR to anti-TNF treatment at week 14, but not non-remission at week 54., (© 2022 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)
- Published
- 2022
- Full Text
- View/download PDF
41. Prediction of Relapse After Anti-Tumor Necrosis Factor Cessation in Crohn's Disease: Individual Participant Data Meta-analysis of 1317 Patients From 14 Studies.
- Author
-
Pauwels RWM, van der Woude CJ, Nieboer D, Steyerberg EW, Casanova MJ, Gisbert JP, Kennedy NA, Lees CW, Louis E, Molnár T, Szántó K, Leo E, Bots S, Downey R, Lukas M, Lin WC, Amiot A, Lu C, Roblin X, Farkas K, Seidelin JB, Duijvestein M, D'Haens GR, and de Vries AC
- Subjects
- Adalimumab therapeutic use, Humans, Immunosuppressive Agents therapeutic use, Infliximab therapeutic use, Necrosis, Recurrence, Retrospective Studies, Crohn Disease drug therapy, Tumor Necrosis Factor Inhibitors therapeutic use
- Abstract
Background & Aims: Tools for stratification of relapse risk of Crohn's disease (CD) after anti-tumor necrosis factor (TNF) therapy cessation are needed. We aimed to validate a previously developed prediction model from the diSconTinuation in CrOhn's disease patients in stable Remission on combined therapy with Immunosuppressants (STORI) trial, and to develop an updated model., Methods: Cohort studies were selected that reported on anti-TNF cessation in 30 or more CD patients in remission. Individual participant data were requested for luminal CD patients and anti-TNF treatment duration of 6 months or longer. The discriminative ability (concordance-statistic [C-statistic]) and calibration (agreement between observed and predicted risks) were explored for the STORI model. Next, an updated prognostic model was constructed, with performance assessment by cross-validation., Results: This individual participant data meta-analysis included 1317 patients from 14 studies in 11 countries. Relapses after anti-TNF cessation occurred in 632 of 1317 patients after a median of 13 months. The pooled 1-year relapse rate was 38%. The STORI prediction model showed poor discriminative ability (C-statistic, 0.51). The updated model reached a moderate discriminative ability (C-statistic, 0.59), and included clinical symptoms at cessation (hazard ratio [HR], 2.2; 95% CI, 1.2-4), younger age at diagnosis (HR, 1.5 for A1 (age at diagnosis ≤16 years) vs A2 (age at diagnosis 17 - 40 years); 95% CI, 1.11-1.89), no concomitant immunosuppressants (HR, 1.4; 95% CI, 1.18-172), smoking (HR, 1.4; 95% CI, 1.15-1.67), second line anti-TNF (HR, 1.3; 95% CI, 1.01-1.69), upper gastrointestinal tract involvement (HR, 1.3 for L4 vs non-L4; 95% CI, 0.96-1.79), adalimumab (HR, 1.22 vs infliximab; 95% CI, 0.99-1.50), age at cessation (HR, 1.2 per 10 years younger; 95% CI, 1-1.33), C-reactive protein (HR, 1.04 per doubling; 95% CI, 1.00-1.08), and longer disease duration (HR, 1.07 per 5 years; 95% CI, 0.98-1.17). In subanalysis, the discriminative ability of the model improved by adding fecal calprotectin (C-statistic, 0.63)., Conclusions: This updated prediction model showed a reasonable discriminative ability, exceeding the performance of a previously published model. It might be useful to guide clinical decisions on anti-TNF therapy cessation in CD patients after further validation., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
42. Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in inflammatory bowel disease patients treated with infliximab and vedolizumab.
- Author
-
Lin S, Kennedy NA, Saifuddin A, Sandoval DM, Reynolds CJ, Seoane RC, Kottoor SH, Pieper FP, Lin KM, Butler DK, Chanchlani N, Nice R, Chee D, Bewshea C, Janjua M, McDonald TJ, Sebastian S, Alexander JL, Constable L, Lee JC, Murray CD, Hart AL, Irving PM, Jones GR, Kok KB, Lamb CA, Lees CW, Altmann DM, Boyton RJ, Goodhand JR, Powell N, and Ahmad T
- Subjects
- Antibodies, Monoclonal, Humanized therapeutic use, BNT162 Vaccine, COVID-19 Vaccines, ChAdOx1 nCoV-19, Humans, Infliximab therapeutic use, SARS-CoV-2, T-Lymphocytes, Tumor Necrosis Factor Inhibitors, COVID-19, Inflammatory Bowel Diseases drug therapy, Viral Vaccines
- Abstract
Anti tumour necrosis factor (anti-TNF) drugs increase the risk of serious respiratory infection and impair protective immunity following pneumococcal and influenza vaccination. Here we report SARS-CoV-2 vaccine-induced immune responses and breakthrough infections in patients with inflammatory bowel disease, who are treated either with the anti-TNF antibody, infliximab, or with vedolizumab targeting a gut-specific anti-integrin that does not impair systemic immunity. Geometric mean [SD] anti-S RBD antibody concentrations are lower and half-lives shorter in patients treated with infliximab than vedolizumab, following two doses of BNT162b2 (566.7 U/mL [6.2] vs 4555.3 U/mL [5.4], p <0.0001; 26.8 days [95% CI 26.2 - 27.5] vs 47.6 days [45.5 - 49.8], p <0.0001); similar results are also observed with ChAdOx1 nCoV-19 vaccination (184.7 U/mL [5.0] vs 784.0 U/mL [3.5], p <0.0001; 35.9 days [34.9 - 36.8] vs 58.0 days [55.0 - 61.3], p value < 0.0001). One fifth of patients fail to mount a T cell response in both treatment groups. Breakthrough SARS-CoV-2 infections are more frequent (5.8% (201/3441) vs 3.9% (66/1682), p = 0.0039) in patients treated with infliximab than vedolizumab, and the risk of breakthrough SARS-CoV-2 infection is predicted by peak anti-S RBD antibody concentration after two vaccine doses. Irrespective of the treatments, higher, more sustained antibody levels are observed in patients with a history of SARS-CoV-2 infection prior to vaccination. Our results thus suggest that adapted vaccination schedules may be required to induce immunity in at-risk, anti-TNF-treated patients., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
43. Ambulatory care management of 69 patients with acute severe ulcerative colitis in comparison to 695 inpatients: insights from a multicentre UK cohort study.
- Author
-
Sebastian S, Patel KV, Segal JP, Subramanian S, Conley TE, Gonzalez HA, Kent AJ, Saifuddin A, Hicks L, Mehta S, Bhala N, Brookes MJ, Lamb CA, Kennedy NA, and Walker GJ
- Subjects
- Adolescent, Ambulatory Care, Cohort Studies, Humans, Inpatients, SARS-CoV-2, United Kingdom epidemiology, COVID-19, Colitis, Ulcerative diagnosis, Colitis, Ulcerative epidemiology, Colitis, Ulcerative therapy
- Abstract
Introduction: Acute severe ulcerative colitis (ASUC) traditionally requires inpatient hospital management for intravenous therapies and/or colectomy. Ambulatory ASUC care has not yet been evaluated in large cohorts., Aims: We used data from PROTECT, a UK multicentre observational COVID-19 inflammatory bowel disease study, to report the extent, safety and effectiveness of ASUC ambulatory pathways., Methods: Adults (≥18 years old) meeting Truelove and Witts criteria between 1 January 2019-1 June 2019 and 1 March 2020-30 June 2020 were recruited to PROTECT. We used demographic, disease phenotype, treatment outcomes and 3-month follow-up data. Primary outcome was rate of colectomy during the index ASUC episode. Secondary outcomes included corticosteroid response, time to and rate of rescue or primary induction therapy, response to rescue or primary induction therapy, time to colectomy, mortality, duration of inpatient treatment and hospital readmission and colectomy within 3 months of index flare. We compared outcomes in three cohorts: (1) patients treated entirely in inpatient setting; ambulatory patients subdivided into; (2) patients managed as ambulatory from diagnosis and (3) patients hospitalised and subsequently discharged to ambulatory care for continued intravenous steroids., Results: 37% (22/60) participating hospitals used ambulatory pathways. Of 764 eligible patients, 695 (91%) patients received entirely inpatient care, 15 (2%) patients were managed as ambulatory from diagnosis and 54 (7%) patients were discharged to ambulatory pathways. Aside from younger age in patients treated as ambulatory from diagnosis, no significant differences in disease or patient phenotype were observed. The rate of colectomy (15.0% (104/695) vs 13.3% (2/15) vs 13.0% (7/54), respectively, p=0.96) and secondary outcomes were similar among all three cohorts. Stool culture and flexible sigmoidoscopy were less frequently performed in ambulatory cohorts. Forty per cent of patients treated as ambulatory from diagnosis required subsequent hospital admission., Conclusions: In a post hoc analysis of one of the largest ASUC cohorts collected to date, we report an emerging UK ambulatory practice which challenges treatment paradigms. However, our analysis remains underpowered to detect key outcome measures and further studies exploring clinical and cost-effectiveness as well as patient and physician acceptability are needed., Trial Registration Number: NCT04411784., Competing Interests: Competing interests: SS holds research grants from Biogen, Takeda, AbbVie, Tillotts Pharma, Ferring and Biohit; served on the advisory boards of Takeda, AbbVie, Merck, Ferring, Pharmacocosmos, Warner Chilcott, Janssen, Falk Pharma, Biohit, TriGenix, Celgene and Tillots Pharma; and has received speaker fees from AbbVie, Biogen, AbbVie, Janssen, Merck, Warner Chilcott and Falk Pharma. GW has served as a speaker and/or advisory board member for AbbVie, Falk and Janssen. He has had support to attend meetings from AbbVie, Falk, Janssen and Norgine. His department has received research funding from Tillotts. NAK has served as a speaker and/or advisory board member for Allergan, Falk, Janssen, Mylan, Pharmacosmos, Takeda and Tillotts. He has had support to attend meetings from AbbVie, Falk, Janssen and Norgine. His department has received research funding from AbbVie, Celgene, Celtrion, MSD, Napp, Pfizer, Pharmacosmos and Takeda. SSu has received speaker fees from MSD, Actavis, Abbvie, Dr Falk pharmaceuticals, Shire and received educational grants from MSD, Abbvie, Actavis and is an advisory board member for Celltrion, Dr Falk pharmaceuticals and Vifor pharmaceuticals. CAL has received research support and/or has received fees for delivery of non-promotional education from: Genentech, Janssen, Takeda, Abbvie, Dr Falk, AstraZeneca, Eli Lilly, Orion, Pfizer, Roche, Sanofi Aventis, Ferring, UCB and Biogen. MJBB has received research grants from Vifor International, Pharmacosmos and Tillots Pharma; has received speaker fee from Abbvie and Vifor International; has been an advisory board member for Tillots Pharma, Vifor International; and received travel/conference expenses from Vifor International, Abbvie and Tillots Pharma. AK has served on the advisory boards for Abbvie, Janssen and BMS Celgene and has received speaker fees from Takeda, Pfizer and Janssen; and received travel/conference expenses from Tillotts, Janssen, Abbvie and Shield Therapeutics. KVP has received honoraria for educational meetings and speaker fees from Abbvie, Janssen, Takeda, DrFalk and Ferring. KVP has received Advisory Board fees from Abbvie and Janssen., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2022
- Full Text
- View/download PDF
44. GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome.
- Author
-
Bonfiglio F, Liu X, Smillie C, Pandit A, Kurilshikov A, Bacigalupe R, Zheng T, Nim H, Garcia-Etxebarria K, Bujanda L, Andreasson A, Agreus L, Walter S, Abecasis G, Eijsbouts C, Jostins L, Parkes M, Hughes DA, Timpson N, Raes J, Franke A, Kennedy NA, Regev A, Zhernakova A, Simren M, Camilleri M, and D'Amato M
- Abstract
Gut dysmotility is associated with constipation, diarrhea, and functional gastrointestinal disorders like irritable bowel syndrome (IBS), although its molecular underpinnings are poorly characterized. We studied stool frequency (defined by the number of bowel movements per day, based on questionnaire data) as a proxy for gut motility in a GWAS meta-analysis including 167,875 individuals from UK Biobank and four smaller population-based cohorts. We identify 14 loci associated with stool frequency (p ≤ 5.0 × 10
-8 ). Gene set and pathway analyses detected enrichment for genes involved in neurotransmitter/neuropeptide signaling and preferentially expressed in enteric motor neurons controlling peristalsis. PheWAS identified pleiotropic associations with dysmotility syndromes and the response to their pharmacological treatment. The genetic architecture of stool frequency correlates with that of IBS, and UK Biobank participants from the top 1% of stool frequency polygenic score distribution were associated with 5× higher risk of IBS with diarrhea. These findings pave the way for the identification of actionable pathological mechanisms in IBS and the dysmotility syndromes., Competing Interests: A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics, and, until August 31, 2020, was a scientific advisory board member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov, and Thermo Fisher Scientific. A.R. is a member of the journal advisory board. From August 1, 2020, A.R. is an employee of Genentech., (© 2021 The Author(s).)- Published
- 2021
- Full Text
- View/download PDF
45. Systematic review with meta-analysis: effect of inflammatory bowel disease therapy on lipid levels.
- Author
-
Sleutjes JAM, Roeters van Lennep JE, Boersma E, Menchen LA, Laudes M, Farkas K, Molnár T, Kennedy NA, Pierik MJ, van der Woude CJ, and de Vries AC
- Subjects
- Humans, Lipids, Colitis, Inflammatory Bowel Diseases drug therapy
- Abstract
Background: Increase in lipid levels associated with the treatment of inflammatory bowel disease (IBD) has previously been reported. However, it is unknown if this effect is similar for all IBD drug classes., Aim: To precisely assess the effect of different IBD drug classes on lipid profiles METHODS: We performed a systematic literature search of randomised controlled trials and observational cohort studies that assessed lipid levels before and after induction (≤10 weeks) and maintenance (>10 weeks) of IBD treatment. Data of 11 studies (1663 patients) were pooled using random effects models. The influence of patient and disease characteristics on treatment effects on total cholesterol levels was analysed in 6 studies (1211 patients) for which individual data were available, using linear mixed models., Results: A statistically significant increase in total cholesterol was observed after induction treatment with corticosteroids (+1.19 mmol/L, 95% confidence interval [CI
95 ] +0.52 to +2.59), and tofacitinib (+0.66 mmol/L, CI95 +0.42 to +0.79), but not after anti-TNFα treatment (-0.11 mmol/L, CI95 -0.26 to +0.36 mmol/L). Similar differences were observed after maintenance treatment. Treatment effects were significantly related to age, but not with other factors. Lipid changes were inversely correlated with but not modified by CRP changes., Conclusions: Increase in total cholesterol levels was strongest for corticosteroids followed by tofacitinib but was not observed for anti-TNFα agents. Whether total cholesterol change associated with IBD treatment has an effect on cardiovascular risk requires further study., (© 2021 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)- Published
- 2021
- Full Text
- View/download PDF
46. Letter: risk of severe COVID-19 outcomes associated with inflammatory bowel disease medications-reassuring insights from the United Kingdom PREPARE-IBD multicentre cohort study.
- Author
-
Lamb CA, Sebastian S, Kent AJ, Segal JP, Gonzalez HA, Brookes MJ, Mehta SJ, Subramanian S, Bhala N, Hicks LC, Conley TE, Patel KV, Walker GJ, and Kennedy NA
- Subjects
- Cohort Studies, Humans, SARS-CoV-2, United Kingdom epidemiology, COVID-19, Inflammatory Bowel Diseases complications, Inflammatory Bowel Diseases drug therapy, Inflammatory Bowel Diseases epidemiology
- Published
- 2021
- Full Text
- View/download PDF
47. Hypophosphataemia after treatment of iron deficiency with intravenous ferric carboxymaltose or iron isomaltoside-a systematic review and meta-analysis.
- Author
-
Schaefer B, Tobiasch M, Viveiros A, Tilg H, Kennedy NA, Wolf M, and Zoller H
- Subjects
- Administration, Intravenous, Disaccharides, Ferric Compounds adverse effects, Fibroblast Growth Factor-23, Humans, Maltose analogs & derivatives, Prospective Studies, Anemia, Iron-Deficiency drug therapy, Anemia, Iron-Deficiency epidemiology, Hypophosphatemia chemically induced, Hypophosphatemia epidemiology
- Abstract
Aims: Hypophosphataemia is an increasingly recognized side-effect of ferric carboxymaltose (FCM) and possibly iron isomaltoside/ferric derisomaltose (IIM), which are used to treat iron deficiency. The aim of this study was to determine frequency, severity, duration and risk factors of incident hypophosphataemia after treatment with FCM and IIM., Methods: A systematic literature search for articles indexed in EMBASE, PubMed and Web of Science in years 2005-2020 was carried out using the search terms 'ferric carboxymaltose' OR 'iron isomaltoside'. Prospective clinical trials reporting outcomes on hypophosphataemia rate, mean nadir serum phosphate and/or change in mean serum phosphate from baseline were selected. Hypophosphataemia rate and severity were compared for studies on IIM vs. FCM after stratification for chronic kidney disease. Meta-regression analysis was used to investigate risk factors for hypophosphataemia., Results: Across the 42 clinical trials included in the meta-analysis, FCM induced a significantly higher incidence of hypophosphataemia than IIM (47%, 95% CI 36-58% vs. 4%, 95% CI 2-5%), and significantly greater mean decreases in serum phosphate (0.40 vs. 0.06 mmol/L). Hypophosphataemia persisted at the end of the study periods (maximum 3 months) in up to 45% of patients treated with FCM. Meta-regression analysis identified low baseline serum ferritin and transferrin saturation, and normal kidney function as significant predictors of hypophosphataemia., Conclusion: FCM is associated with a high risk of hypophosphataemia, which does not resolve for at least 3 months in a large proportion of affected patients. More severe iron deficiency and normal kidney function are risk factors for hypophosphataemia., (© 2020 The Authors. British Journal of Clinical Pharmacology published by John Wiley & Sons Ltd on behalf of British Pharmacological Society.)
- Published
- 2021
- Full Text
- View/download PDF
48. Validating the positivity thresholds of drug-tolerant anti-infliximab and anti-adalimumab antibody assays.
- Author
-
Nice R, Chanchlani N, Green H, Bewshea C, Ahmad T, Goodhand JR, McDonald TJ, Perry MH, and Kennedy NA
- Subjects
- Adalimumab therapeutic use, Adult, Humans, Infliximab, Treatment Outcome, Tumor Necrosis Factor-alpha, Crohn Disease drug therapy, Pharmaceutical Preparations
- Abstract
Background: When used proactively, drug-tolerant anti-tumour necrosis factor (TNF) antibody assays provide early opportunity to suppress immunogenicity., Aim: To validate positivity thresholds of IDKmonitor drug-tolerant anti-infliximab and -adalimumab antibody assays., Methods: We applied positivity thresholds, defined by testing sera from 498 anti-TNF naive healthy adults, from the Exeter Ten Thousand study to data from our therapeutic drug monitoring (TDM) service and Personalised Anti-TNF Therapy in Crohn's disease (PANTS) cohort to explore associations with drug level and treatment outcomes., Results: The 80% one-sided lower confidence interval of the 99th centile concentration for anti-infliximab and -adalimumab antibodies were lower than the manufacturers threshold of 10 arbitrary units (AU)/mL; 9 and 6 AU/mL, respectively. Using these new thresholds in the TDM cohort, more adalimumab- than infliximab- (11.2% [814/7272] vs 3.1% [390/12 683] P < 0.0001) treated patients were reclassified as antibody-positive. Adalimumab drug concentrations in this reclassified group (median 8.1, interquartile range [IQR] 5.5-11.0 mg/L) were lower than those below the new threshold (<5AU/mL) (median 9.9, IQR 7.1-13.0 mg/L; P < 0.0001), but higher than at the manufacturer's threshold (10-29 AU/mL) (median 5.9 mg/L, IQR 3.5-8.7; P < 0.0001). No difference in infliximab drug concentration was observed using the new or manufacturer's positivity threshold (P = 0.11). In the PANTS cohort, patients with anti-adalimumab antibody concentrations at or above the new threshold were more likely to be in primary non-response (25/68 [37%] vs. 64/332 [19%], P = 0.0035), and non-remission at week 54 (51/62 [82%] vs. 168/279 [60%], P = 0.0011), than patients with anti-drug antibody concentrations in the group below the new threshold (0-5 AU/mL); this was not seen for anti-infliximab antibodies., Conclusion: Laboratories should derive antibody positivity thresholds for assays they use. For adalimumab, low-concentration anti-drug antibodies were associated with lower drug levels and treatment failure., (© 2020 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
49. Root-cause analyses of missed opportunities for the diagnosis of colorectal cancer in patients with inflammatory bowel disease.
- Author
-
Gordon C, Chee D, Hamilton B, Heerasing NM, Hendy P, Chanchlani N, Lin S, Wesley E, Daniels IR, Silva N, Osborne M, Kennedy NA, Goodhand JR, and Ahmad T
- Subjects
- Colonoscopy, Humans, Risk Factors, Colitis, Colonic Neoplasms, Colorectal Neoplasms diagnosis, Colorectal Neoplasms epidemiology, Inflammatory Bowel Diseases complications, Inflammatory Bowel Diseases diagnosis
- Abstract
Background: Colonoscopic surveillance in patients with inflammatory bowel disease (IBD) leads to earlier detection of colorectal cancer (CRC) and reduces CRC-associated mortality. However, it is limited by poor adherence in practice., Aim: To identify missed opportunities to detect IBD-associated CRC at our hospital METHODS: We undertook root-cause analyses to identify patients with missed opportunities to diagnose IBD-associated CRC. We matched patients with IBD-associated CRC to patients with CRC in the general population to identify differences in staging at diagnosis and clinical outcomes., Results: Compared with the general population, patients with IBD were at increased risk of developing CRC (odds ratio 2.7 [95% CI 1.6-3.9], P < 0.001). The mean incidence of IBD-associated CRC between 1998 and 2019 was 165.4 (IQR 130.4-199.4) per 100 000 patients and has not changed over the last 20 years. Seventy-eight patients had IBD-associated CRC. Forty-two (54%) patients were eligible for CRC surveillance: 12% (5/42) and 10% (4/42) patients were diagnosed with CRC at an appropriately timed or overdue surveillance colonoscopy, respectively. Interval cancers occurred in 14% (6/42) of patients; 64% (27/42) of patients had a missed opportunity for colonoscopic surveillance where root-cause analyses demonstrated that 10/27 (37%) patients known to secondary care had not been offered surveillance. Four (15%) patients had a delayed diagnosis of CRC due to failure to account for previous colonoscopic findings. Seventeen (63%) patients were managed by primary care including seven patients discharged from secondary care without a surveillance plan. Matched case-control analysis did not show significant differences in cancer staging or 10-year survival outcomes., Conclusion: The incidence of IBD-associated CRC has remained static. Two-thirds of patients eligible for colonoscopic surveillance had missed opportunities to diagnose CRC. Surveillance programmes without comprehensive and fully integrated recall systems across primary and secondary care are set to fail., (© 2020 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
50. Editorial: missed opportunities to detect colorectal cancer in inflammatory bowel disease-getting to the root. Authors' reply.
- Author
-
Chee D, Kennedy NA, Goodhand JR, and Ahmad T
- Subjects
- Humans, Colitis, Colorectal Neoplasms diagnosis, Inflammatory Bowel Diseases diagnosis
- Published
- 2021
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.