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1. A Bayesian factor analysis model for high-dimensional microbiome count data

Author

Ba, Ismaïla, Turgeon, Maxime, Veniamin, Simona, Joel, Juan, Miller, Richard, Graham, Morag, Bonner, Christine, Bernstein, Charles N., Arnold, Douglas L., Bar-Or, Amit, Marrie, Ruth Ann, O'Mahony, Julia, Yeh, E. Ann, Banwell, Brenda, Waubant, Emmanuelle, Knox, Natalie, Van Domselaar, Gary, Mirza, Ali I., Armstrong, Heather, Muthukumarana, Saman, and McGregor, Kevin

Subjects
Statistics - Methodology
Abstract

Dimension reduction techniques are among the most essential analytical tools in the analysis of high-dimensional data. Generalized principal component analysis (PCA) is an extension to standard PCA that has been widely used to identify low-dimensional features in high-dimensional discrete data, such as binary, multi-category and count data. For microbiome count data in particular, the multinomial PCA is a natural counterpart of the standard PCA. However, this technique fails to account for the excessive number of zero values, which is frequently observed in microbiome count data. To allow for sparsity, zero-inflated multivariate distributions can be used. We propose a zero-inflated probabilistic PCA model for latent factor analysis. The proposed model is a fully Bayesian factor analysis technique that is appropriate for microbiome count data analysis. In addition, we use the mean-field-type variational family to approximate the marginal likelihood and develop a classification variational approximation algorithm to fit the model. We demonstrate the efficiency of our procedure for predictions based on the latent factors and the model parameters through simulation experiments, showcasing its superiority over competing methods. This efficiency is further illustrated with two real microbiome count datasets. The method is implemented in R., Comment: 2 figures, 3 tables

Published
2024

4. Stability of the gut microbiota in persons with paediatric-onset multiple sclerosis and related demyelinating diseases

Author

Liang, Geoffrey, Zhu, Feng, Mirza, Ali I, Bar-Or, Amit, Bernstein, Charles N, Bonner, Christine, Forbes, Jessica D, Graham, Morag, Hart, Janace, Knox, Natalie C, Marrie, Ruth Ann, O’Mahony, Julia, Van Domselaar, Gary, Yeh, E Ann, Zhao, Yinshan, Banwell, Brenda, Waubant, Emmanuelle, Tremlett, Helen, and Network, the Canadian Paediatric Demyelinating Disease

Subjects
Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Brain Disorders, Autoimmune Disease, Multiple Sclerosis, Neurodegenerative, Child, Gastrointestinal Microbiome, Humans, Syndrome, Multiple sclerosis, demyelinating disease, gut microbiota, stability, paediatric, monophasic acquired demyelinating syndrome, Canadian Paediatric Demyelinating Disease Network, Neurology & Neurosurgery, Clinical sciences, Biological psychology
Abstract

ObjectiveExamine if the gut microbiota composition changes across repeated samples in paediatric-onset multiple sclerosis (MS) or monophasic-acquired demyelinating syndromes (monoADS).MethodsA total of 36 individuals (18 MS/18 monoADS) with ⩾2 stool samples were included. Stool sample-derived DNA was sequenced. Alpha/beta diversities and genus-level taxa were analysed.ResultsMean ages at first sample procurement (MS/monoADS) = 18.0/13.8 years. Median time (months) between first/second samples = 11.2 and second/third = 10.3. Alpha/beta diversities did not differ between stool samples (p > 0.09), while one genus - Solobacterium did (p = 0.001).ConclusionsThe gut microbiota composition in paediatric-onset MS and monoADS exhibited stability, suggesting that single stool sample procurement is a reasonable first approach.

Published
2022

5. Comparison of Patient Health Questionnaire-9, Edinburgh Postnatal Depression Scale and Hospital Anxiety and Depression – Depression subscale scores by administration mode: An individual participant data differential item functioning meta-analysis

Author

Azar, Marleine, Bhandari, Parash Mani, Chiovitti, Matthew J., He, Chen, Imran, Mahrukh, Krishnan, Ankur, Negeri, Zelalem, Neupane, Dipika, Riehm, Kira E., Yan, Xin Wei, Kloda, Lorie A., Henry, Melissa, Ismail, Zahinoor, Loiselle, Carmen G., Mitchell, Nicholas D., Al-Adawi, Samir, Alvarado, Rubén, Amtmann, Dagmar, Arroll, Bruce, Ayalon, Liat, Baradaran, Hamid R., Barnes, Jacqueline, Beck, Kevin R., Beck, Cheryl Tatano, Bernstein, Charles N., Bindt, Carola, Bombardier, Charles H., Boye, Birgitte, Büel-Drabe, Natalie, Buji, Ryna Imma, Bunevicius, Adomas, Butterworth, Peter, Can, Ceyhun, Carter, Gregory, Chagas, Marcos H., Chan, Juliana C.N., Chan, Lai Fong, Chen, Chih-Ken, Chibanda, Dixon, Chorwe-Sungani, Genesis, Clover, Kerrie, Conroy, Ronán M., Conway, Aaron, Conwell, Yeates, Correa, Humberto, Couto, Thiago Castro e, Cukor, Daniel, Daray, Federico M., de Man-van Ginkel, Janneke M., De Souza, Jennifer, Downing, Marina G., Eapen, Valsamma, Fann, Jesse R., Favez, Nicolas, Felice, Ethel, Fellmeth, Gracia, Ferentinos, Panagiotis P., Fernandes, Michelle, Field, Sally, Figueiredo, Barbara, Fischer, Felix H., Fisher, Jane R.W., Flint, Alastair J., Fujimori, Maiko, Fung, Daniel S.S., Gallagher, Pamela, Gandy, Milena, Gelaye, Bizu, Gholizadeh, Leila, Gibson, Lorna J., Goodyear-Smith, Felicity, Grassi, Luigi, Green, Eric P., Greeno, Catherine G., Hall, Brian J., Hantsoo, Liisa, Haroz, Emily E., Härter, Martin, Hegerl, Ulrich, Helle, Nadine, Hernando, Asuncion, Hides, Leanne, Hobfoll, Stevan E., Honikman, Simone, Howard, Louise M., Hyphantis, Thomas, Iglesias-González, Maria, Inagaki, Masatoshi, Jenewein, Josef, Jeon, Hong Jin, Jetté, Nathalie, Julião, Miguel, Kettunen, Pirjo A., Khamseh, Mohammad E., Kiely, Kim M., Kim, Sung-Wan, Kjærgaard, Marie, Kohlhoff, Jane, Kohrt, Brandon A., König, Hans-Helmut, Kozinszky, Zoltán, Kwan, Yunxin, Lamers, Femke, Lara, María Asunción, Leonardou, Angeliki A., Levin-Aspenson, Holly F., Liu, Shen-Ing, Löbner, Margrit, Loosman, Wim L., Lotrakul, Manote, Loureiro, Sonia R., Love, Anthony W., Löwe, Bernd, Luitel, Nagendra P., Lund, Crick, Maes, Michael, Malt, Ulrik F., Marrie, Ruth Ann, Marsh, Laura, Martínez, Pablo, Marx, Brian P., Matsuoka, Yutaka, McGuire, Anthony, Mehnert, Anja, Michopoulos, Ioannis, Sidik, Sherina Mohd, Müller-Nordhorn, Jacqueline, Muramatsu, Kumiko, Radoš, Sandra Nakić, Navarrete, Laura, Nelson, Christian J., Ng, Chong Guan, Nishi, Daisuke, O'Donnell, Meaghan L., O'Rourke, Suzanne J., Osório, Flávia L., Pabst, Alexander, Pasco, Julie A., Pawlby, Susan J., Peceliuniene, Jurate, Pence, Brian W., Persoons, Philippe, Petersen, Inge, Picardi, Angelo, Ponsford, Jennie L., Pugh, Stephanie L., Pulido, Federico, Quinn, Terence J., Quispel, Chantal, Rathod, Sujit D., Reme, Silje E., Reuter, Katrin, Riedel-Heller, Steffi G., Rooney, Alasdair G., Santos, Iná S., Saracino, Rebecca M., Schellekens, Melanie P.J., Schwarzbold, Marcelo L., Cankorur, Vesile Senturk, Shaaban, Juwita, Sharp, Deborah J., Sharpe, Louise, Shinn, Eileen H., Sidebottom, Abbey, Simard, Sébastien, Singer, Susanne, Skalkidou, Alkistis, Smith-Nielsen, Johanne, Spangenberg, Lena, Stafford, Lesley, Stein, Alan, Stewart, Robert C., Strobel, Natalie A., Su, Kuan-Pin, Sultan, Serge, Sundström-Poromaa, Inger, Sung, Sharon C., Suzuki, Keiko, Tadinac, Meri, Tan, Pei Lin Lynnette, Tandon, S. Darius, Taylor-Rowan, Martin, Teixeira, Antonio L., Tendais, Iva, Tiringer, Istvan, Töreki, Annamária, Tran, Thach D., Trevillion, Kylee, Tschorn, Mira, Turner, Alyna, Væver, Mette S., van der Feltz-Cornelis, Christina M., van Heyningen, Thandi, Vega-Dienstmaier, Johann M., Wagner, Michael, Wagner, Lynne I., Wang, Liang-Jen, Wang, Jian Li, Watson, David, Weyerer, Siegfried B., White, Jennifer, Whooley, Mary A., Wiese, Birgitt, Williams, Lana J., Winkley, Kirsty, Wynter, Karen, Yamada, Mitsuhiko, Yonkers, Kimberly A., Zeng, Qing Zhi, Zhang, Yuying, Harel, Daphna, Wu, Yin, Levis, Brooke, Fan, Suiqiong, Sun, Ying, Xu, Mingyao, Rice, Danielle B., Boruff, Jill, Markham, Sarah, Ioannidis, John P.A., Takwoingi, Yemisi, Patten, Scott B., Ziegelstein, Roy C., Cuijpers, Pim, Gilbody, Simon, Vigod, Simone, Akena, Dickens, Benedetti, Andrea, and Thombs, Brett D.

Published
2024
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6. Environmental Factors Associated With Risk of Crohn’s Disease Development in the Crohn’s and Colitis Canada - Genetic, Environmental, Microbial Project

Author

Abreu, Maria, Beck, Paul, Bernstein, Charles, Croitoru, Kenneth, Dieleman, Levinus A., Feagan, Brian, Griffiths, Anne, Guttman, David, Jacobson, Kevan, Kaplan, Gilaad, Krause, Denis O., Madsen, Karen, Marshall, John, Moayyedi, Paul, Ropeleski, Mark, Seidman, Ernest, Silverberg, Mark, Snapper, Scott, Stadnyk, Andy, Steinhart, Hillary, Surette, Michael, Turner, Dan, Walters, Thomas, Vallance, Bruce, Aumais, Guy, Bitton, Alain, Cino, Maria, Critch, Jeff, Denson, Lee, Deslandres, Colette, El-Matary, Wael, Herfarth, Hans, Higgins, Peter, Huynh, Hien, Hyams, Jeffrey S., Mack, David, McGrath, Jerry, Otley, Anthony, Panancionne, Remo, Xue, Mingyue, Leibovitzh, Haim, Jingcheng, Shao, Neustaeter, Anna, Dong, Mei, Xu, Wei, Espin-Garcia, Osvaldo, Griffiths, Anne M., Steinhart, A. Hillary, Huynh, Hien Q., Panaccione, Remo, Bressler, Brian, Murthy, Sanjay, Marshall, John K., Bernstein, Charles N., Fich, Alexander, Denson, Lee A., Ropeleski, Mark J., Abreu, Maria T., Avni-Biron, Irit, Lee, Sun-Ho, and Turpin, Williams

Published
2024
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8. Dynamic Prediction of Advanced Colorectal Neoplasia in Inflammatory Bowel Disease

Author

van Bodegraven, Adriaan A., Fidder, Herma H., Hirdes, Meike M.C., Hoentjen, Frank, Jansen, Jeroen M., Mahmmod, Nofel, van der Meulen-de Jong, Andrea E., Ponsioen, Cyriel Y., van Schaik, Fiona D.M., van der Woude, C. Janneke, Wijnands, Anouk M., Penning de Vries, Bas B.L., Lutgens, Maurice W.M.D., Bakhshi, Zeinab, Al Bakir, Ibrahim, Beaugerie, Laurent, Bernstein, Charles N., Chang-ho Choi, Ryan, Coelho-Prabhu, Nayantara, Graham, Trevor A., Hart, Ailsa L., ten Hove, Joren R., Itzkowitz, Steven H., Kirchgesner, Julien, Mooiweer, Erik, Shaffer, Seth R., Shah, Shailja C., Elias, Sjoerd G., and Oldenburg, Bas

Published
2024
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9. Interim Analysis of a Trial Evaluating the Utility of Non-Targeted Biopsies for Colorectal Neoplasia Detection in Inflammatory Bowel Disease

Author

Conner, James, Ramsay, Tim, Castelli, Jane M., Ahmed, Faria, Narula, Neeraj, Bessissow, Talat, Bressler, Brian, Borgaonkar, Mark, Jones, Jennifer, Loomes, Dustin, Hoentjen, Frank, Baumgart, Daniel C., Zezos, Petros, Moyana, Terrance, Ramsay, Jennifer, Murthy, Sanjay K., Bernstein, Charles N., Nguyen, Geoffrey C., Jairath, Vipul, Riddell, Robert, and Fergusson, Dean

Published
2024
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11. Development of the global inflammatory bowel disease visualization of epidemiology studies in the 21st century (GIVES-21)

Author

Mak, Joyce W. Y., Sun, Yang, Limsrivilai, Julajak, Abdullah, Murdani, Kaibullayeva, Jamilya, Balderramo, Domingo, Vergara, Beatriz Iade, Paudel, Mukesh Sharma, Banerjee, Rupa, Hilmi, Ida, Ali, Raja Affendi Raja, Wei, Shu Chen, Ng, Ka Kei, Altuwaijri, Mansour, Kelly, Paul, Yamamoto-Furusho, Jesus K., Kotze, Paulo Gustavo, Ahuja, Vineet, Chong, Vui Heng, Dao, Hang Viet, Abbey, Yvonne, Ching, Jessica Y. L., Ho, Agnes, Chan, Alicia K. W., Bernstein, Charles N., Gearry, Richard B., Abreu, Maria, Rubin, David T., Dotan, Iris, Hracs, Lindsay, Kaplan, Gilaad G., and Ng, Siew C.

Published
2023
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13. Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome

Author

Mirza, Ali I, Zhu, Feng, Knox, Natalie, Forbes, Jessica D, Van Domselaar, Gary, Bernstein, Charles N, Graham, Morag, Marrie, Ruth Ann, Hart, Janace, Yeh, E Ann, Arnold, Douglas L, Bar-Or, Amit, O'Mahony, Julia, Zhao, Yinshan, Hsiao, William, Banwell, Brenda, Waubant, Emmanuelle, and Tremlett, Helen

Subjects
Pediatric, Neurodegenerative, Clinical Research, Autoimmune Disease, Digestive Diseases, Neurosciences, Brain Disorders, Genetics, Multiple Sclerosis, Neurological, Adolescent, Adult, Canada, Child, Female, Gastrointestinal Microbiome, Humans, Young Adult, Clinical Sciences, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Background and objectivesLittle is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.MethodsPersons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty patients with MS (McDonald criteria) with symptom onset 0.20), but metabolic pathways, gene annotations, and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio 10, p = 0.044) and Methanobrevibacter abundance (log2 fold change [LFC] 1.7, p = 0.0014), but lower homolactic fermentation abundance (LFC -0.48, p = 0.039). Differences by DMD status included lower phosphate butyryl transferase for DMD-naive vs exposed patients with MS (LFC -1.0, p = 0.033).DiscussionThe gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS vs controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.

Published
2022

14. Functional brain rewiring and altered cortical stability in ulcerative colitis

Author

Wang, Hao, Labus, Jennifer S, Griffin, Fiona, Gupta, Arpana, Bhatt, Ravi R, Sauk, Jenny S, Turkiewicz, Joanna, Bernstein, Charles N, Kornelsen, Jennifer, and Mayer, Emeran A

Subjects
Behavioral and Social Science, Digestive Diseases, Inflammatory Bowel Disease, Clinical Research, Neurosciences, Mental Health, Basic Behavioral and Social Science, Autoimmune Disease, 2.1 Biological and endogenous factors, Underpinning research, 1.1 Normal biological development and functioning, Aetiology, Neurological, Mental health, Oral and gastrointestinal, Brain, Colitis, Ulcerative, Connectome, Humans, Inflammation, Irritable Bowel Syndrome, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

Despite recent advances, there is still a major need to better understand the interactions between brain function and chronic gut inflammation and its clinical implications. Alterations in executive function have previously been identified in several chronic inflammatory conditions, including inflammatory bowel diseases. Inflammation-associated brain alterations can be captured by connectome analysis. Here, we used the resting-state fMRI data from 222 participants comprising three groups (ulcerative colitis (UC), irritable bowel syndrome (IBS), and healthy controls (HC), N = 74 each) to investigate the alterations in functional brain wiring and cortical stability in UC compared to the two control groups and identify possible correlations of these alterations with clinical parameters. Globally, UC participants showed increased functional connectivity and decreased modularity compared to IBS and HC groups. Regionally, UC showed decreased eigenvector centrality in the executive control network (UC  IBS > HC). UC also showed increased connectivity in dorsal attention, somatomotor network, and visual networks, and these enhanced subnetwork connectivities were able to distinguish UC participants from HCs and IBS with high accuracy. Dynamic functional connectome analysis revealed that UC showed enhanced cortical stability in the medial prefrontal cortex (mPFC), which correlated with severe depression and anxiety-related measures. None of the observed brain changes were correlated with disease duration. Together, these findings are consistent with compromised functioning of networks involved in executive function and sensory integration in UC.

Published
2022

18. Gut Microbiome Composition Is Associated With Future Onset of Crohn’s Disease in Healthy First-Degree Relatives

Author

Abreu, Maria, Beck, Paul, Bernstein, Charles, Croitoru, Kenneth, Dieleman, Levinus A., Feagan, Brian, Griffiths, Anne, Guttman, David, Jacobson, Kevan, Kaplan, Gilaad, Krause, Denis O., Madsen, Karen, Marshall, John, Moayyedi, Paul, Ropeleski, Mark, Seidman, Ernest, Silverberg, Mark, Snapper, Scott, Stadnyk, Andy, Steinhart, Hillary, Surette, Michael, Turner, Dan, Walters, Thomas, Vallance, Bruce, Aumais, Guy, Bitton, Alain, Cino, Maria, Critch, Jeff, Denson, Lee, Deslandres, Colette, El-Matary, Wael, Herfarth, Hans, Higgins, Peter, Huynh, Hien, Hyams, Jeffrey S., Mack, David, McGrath, Jerry, Otley, Anthony, Panancionne, Remo, Raygoza Garay, Juan Antonio, Turpin, Williams, Lee, Sun-Ho, Smith, Michelle I., Goethel, Ashleigh, Griffiths, Anne M., Espin-Garcia, Osvaldo, Aumais, Guy L., Bernstein, Charles N., Biron, Irit A., Dotan, Iris, Guttman, David S., Marshall, John K., Panaccione, Remo, Silverberg, Mark S., Steinhart, A. Hillary, Yerushalmi, Baruch, Paterson, Andrew D., and Xu, Wei

Published
2023
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19. Altered brain structural connectivity in patients with longstanding gut inflammation is correlated with psychological symptoms and disease duration

Author

Turkiewicz, Joanna, Bhatt, Ravi R, Wang, Hao, Vora, Priten, Krause, Beatrix, Sauk, Jenny S, Jacobs, Jonathan P, Bernstein, Charles N, Kornelsen, Jennifer, Labus, Jennifer S, Gupta, Arpana, and Mayer, Emeran A

Subjects
Biological Psychology, Psychology, Autoimmune Disease, Mental Health, Pain Research, Behavioral and Social Science, Chronic Pain, Digestive Diseases, Neurosciences, Clinical Research, Inflammatory Bowel Disease, Oral and gastrointestinal, Mental health, Brain, Humans, Inflammation, Irritable Bowel Syndrome, Neuronal Plasticity, Somatosensory Cortex, IBD, Brain imaging, Ulcerative colitis, Centrality, Graph theory, Diffusion weighted imaging, Biological psychology, Clinical and health psychology
Abstract

ObjectiveWe aimed to identify differences in network properties of white matter microstructure between asymptomatic ulcerative colitis (UC) participants who had a history of chronic gut inflammation, healthy controls (HCs) and a disease control group without gut inflammation (irritable bowel syndrome; IBS).DesignDiffusion weighted imaging was conducted in age and sex-matched participants with UC, IBS, and HCs (N = 74 each), together with measures of gastrointestinal and psychological symptom severity. Using streamline connectivity matrices and graph theory, we aimed to quantify group differences in brain network connectivity. Regions showing group connectivity differences were correlated with measures showing group behavioral and clinical differences.ResultsUC participants exhibited greater centrality in regions of the somatosensory network and default mode network, but lower centrality in the posterior insula and globus pallidus compared to HCs (q

Published
2021

21. Global Hospitalization Trends for Crohn’s Disease and Ulcerative Colitis in the 21st Century: A Systematic Review With Temporal Analyses

Author

Buie, Michael J., Quan, Joshua, Windsor, Joseph W., Coward, Stephanie, Hansen, Tawnya M., King, James A., Kotze, Paulo G., Gearry, Richard B., Ng, Siew C., Mak, Joyce W.Y., Abreu, Maria T., Rubin, David T., Bernstein, Charles N., Banerjee, Rupa, Yamamoto-Furusho, Jesus K., Panaccione, Remo, Seow, Cynthia H., Ma, Christopher, Underwood, Fox E., Ahuja, Vineet, Panaccione, Nicola, Shaheen, Abdel-Aziz, Holroyd-Leduc, Jayna, Kaplan, Gilaad G., Balderramo, Domingo, Chong, Vui Heng, Juliao-Baños, Fabián, Dutta, Usha, Simadibrata, Marcellus, Kaibullayeva, Jamilya, Sun, Yang, Hilmi, Ida, Raja Ali, Raja Affendi, Paudel, Mukesh Sharma, Altuwaijri, Mansour, Hartono, Juanda Leo, Wei, Shu Chen, Limsrivilai, Julajak, El Ouali, Sara, Vergara, Beatriz Iade, Dao, Viet Hang, Kelly, Paul, Hodges, Phoebe, Miao, Yinglei, and Li, Maojuan

Published
2023
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22. Transition Readiness in Youth with Inflammatory Bowel Disease

Author

Foster, Alice, Chan, Justin M., Wine, Eytan, El-Matary, Wael, Carroll, Matthew W., Kroeker, Karen I., deBruyn, Jennifer C., Seow, Cynthia H., Lawrence, Sally, Evans, Kathy, Kluthe, Cheryl, Sharifi, Nastaran, Pears, Christina, Nicol, Simone, Olayinka, Lily, Fu, Nancy, Huynh, Hien Q., Bressler, Brian, Bernstein, Charles N., and Jacobson, Kevan

Published
2023
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23. The cost of inflammatory bowel disease in high-income settings: a Lancet Gastroenterology & Hepatology Commission

Author

Burisch, Johan, Zhao, Mirabella, Odes, Selwyn, De Cruz, Peter, Vermeire, Severine, Bernstein, Charles N, Kaplan, Gilaad G, Duricova, Dana, Greenberg, Dan, Melberg, Hans O, Watanabe, Mamoru, Ahn, Hyeong Sik, Targownik, Laura, Pittet, Valérie E H, Annese, Vito, Park, KT, Katsanos, Konstantinos H, Høivik, Marte L, Krznaric, Zeljko, Chaparro, María, Loftus, Edward V, Jr, Lakatos, Peter L, Gisbert, Javier P, Bemelman, Willem, Moum, Bjorn, Gearry, Richard B, Kappelman, Michael D, Hart, Ailsa, Pierik, Marieke J, Andrews, Jane M, Ng, Siew C, D'Inca, Renata, and Munkholm, Pia

Published
2023
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24. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

Author

Sazonovs, Aleksejs, Stevens, Christine R., Venkataraman, Guhan R., Yuan, Kai, Avila, Brandon, Abreu, Maria T., Ahmad, Tariq, Allez, Matthieu, Ananthakrishnan, Ashwin N., Atzmon, Gil, Baras, Aris, Barrett, Jeffrey C., Barzilai, Nir, Beaugerie, Laurent, Beecham, Ashley, Bernstein, Charles N., Bitton, Alain, Bokemeyer, Bernd, Chan, Andrew, Chung, Daniel, Cleynen, Isabelle, Cosnes, Jacques, Cutler, David J., Daly, Allan, Damas, Oriana M., Datta, Lisa W., Dawany, Noor, Devoto, Marcella, Dodge, Sheila, Ellinghaus, Eva, Fachal, Laura, Farkkila, Martti, Faubion, William, Ferreira, Manuel, Franchimont, Denis, Gabriel, Stacey B., Ge, Tian, Georges, Michel, Gettler, Kyle, Giri, Mamta, Glaser, Benjamin, Goerg, Siegfried, Goyette, Philippe, Graham, Daniel, Hämäläinen, Eija, Haritunians, Talin, Heap, Graham A., Hiltunen, Mikko, Hoeppner, Marc, Horowitz, Julie E., Irving, Peter, Iyer, Vivek, Jalas, Chaim, Kelsen, Judith, Khalili, Hamed, Kirschner, Barbara S., Kontula, Kimmo, Koskela, Jukka T., Kugathasan, Subra, Kupcinskas, Juozas, Lamb, Christopher A., Laudes, Matthias, Lévesque, Chloé, Levine, Adam P., Lewis, James D., Liefferinckx, Claire, Loescher, Britt-Sabina, Louis, Edouard, Mansfield, John, May, Sandra, McCauley, Jacob L., Mengesha, Emebet, Mni, Myriam, Moayyedi, Paul, Moran, Christopher J., Newberry, Rodney D., O’Charoen, Sirimon, Okou, David T., Oldenburg, Bas, Ostrer, Harry, Palotie, Aarno, Paquette, Jean, Pekow, Joel, Peter, Inga, Pierik, Marieke J., Ponsioen, Cyriel Y., Pontikos, Nikolas, Prescott, Natalie, Pulver, Ann E., Rahmouni, Souad, Rice, Daniel L., Saavalainen, Päivi, Sands, Bruce, Sartor, R. Balfour, Schiff, Elena R., Schreiber, Stefan, Schumm, L. Philip, Segal, Anthony W., Seksik, Philippe, Shawky, Rasha, Sheikh, Shehzad Z., Silverberg, Mark S., Simmons, Alison, Skeiceviciene, Jurgita, Sokol, Harry, Solomonson, Matthew, Somineni, Hari, Sun, Dylan, Targan, Stephan, Turner, Dan, Uhlig, Holm H., van der Meulen, Andrea E., Vermeire, Séverine, Verstockt, Sare, Voskuil, Michiel D., Winter, Harland S., Young, Justine, Duerr, Richard H., Franke, Andre, Brant, Steven R., Cho, Judy, Weersma, Rinse K., Parkes, Miles, Xavier, Ramnik J., Rivas, Manuel A., Rioux, John D., McGovern, Dermot P. B., Huang, Hailiang, Anderson, Carl A., and Daly, Mark J.

Published
2022
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25. Exploring the Relationship Between Self-Isolation and Distress Among People with Gastrointestinal Disorders During the COVID-19 Pandemic

Author

Mikocka-Walus, Antonina, Skvarc, David, de Acosta, Manuel Barreiro, Evertsz, Floor Bennebroek, Bernstein, Charles N., Burisch, Johan, Ferreira, Nuno, Gearry, Richard B., Graff, Lesley A., Jedel, Sharon, Mokrowiecka, Anna, Stengel, Andreas, Trindade, Inês A., van Tilburg, Miranda A. L., and Knowles, Simon R.

Published
2022
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26. Extending the Common Sense Model to Explore the Impact of the Fear of COVID-19 on Quality of Life in an International Inflammatory Bowel Disease Cohort

Author

Hayes, Bree, Apputhurai, Pragalathan, Mikocka-Walus, Antonina, Barreiro-de Acosta, Manuel, Bernstein, Charles N., Burgell, Rebecca, Burisch, Johan, Bennebroek Evertsz, Floor, Ferreira, Nuno, Graff, Lesley A., Trindade, Inês A., Gearry, Richard, Lo, Bobby, Mokrowiecka, Anna, Moser, Gabriele, Petrik, Megan, Stengel, Andreas, and Knowles, Simon R.

Published
2022
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27. Unfermented β-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients

Author

Armstrong, Heather K., Bording-Jorgensen, Michael, Santer, Deanna M., Zhang, Zhengxiao, Valcheva, Rosica, Rieger, Aja M., Sung-Ho Kim, Justin, Dijk, Stephanie I., Mahmood, Ramsha, Ogungbola, Olamide, Jovel, Juan, Moreau, France, Gorman, Hayley, Dickner, Robyn, Jerasi, Jeremy, Mander, Inderdeep K., Lafleur, Dawson, Cheng, Christopher, Petrova, Alexandra, Jeanson, Terri-Lyn, Mason, Andrew, Sergi, Consolato M., Levine, Arie, Chadee, Kris, Armstrong, David, Rauscher, Sarah, Bernstein, Charles N., Carroll, Matthew W., Huynh, Hien Q., Walter, Jens, Madsen, Karen L., Dieleman, Levinus A., and Wine, Eytan

Published
2023
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30. Challenges in IBD Research: Environmental Triggers

Author

Ho, Shuk-Mei, Lewis, James D, Mayer, Emeran A, Bernstein, Charles N, Plevy, Scott E, Chuang, Emil, Rappaport, Stephen M, Croitoru, Kenneth, Korzenik, Joshua R, Krischer, Jeffrey, Hyams, Jeffrey S, Judson, Richard, Kellis, Manolis, Jerrett, Michael, Miller, Gary W, Grant, Melanie L, Shtraizent, Nataly, Honig, Gerard, Hurtado-Lorenzo, Andrés, and Wu, Gary D

Subjects
Crohn's Disease, Clinical Research, Digestive Diseases, Autoimmune Disease, Inflammatory Bowel Disease, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Diet, Environmental Exposure, Gastrointestinal Microbiome, Gene-Environment Interaction, Humans, Inflammatory Bowel Diseases, Life Style, Risk Factors, Crohn's disease, ulcerative colitis, environment, exposome, smoking, antibiotic, virus, pollutant, diet, epidemiology, in silico modeling, Crohn’s disease, Clinical Sciences, Gastroenterology & Hepatology
Abstract

Environmental triggers is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, novel technologies, precision medicine and pragmatic clinical research. The Challenges in IBD research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the environmental triggers section is focused on the main research gaps in elucidating causality of environmental factors in IBD. Research gaps were identified in: 1) epidemiology of exposures; 2) identification of signatures of biological response to exposures; and 3) mechanisms of how environmental exposures drive IBD. To address these gaps, the implementation of longitudinal prospective studies to determine disease evolution and identify sub-clinical changes in response to exposures is proposed. This can help define critical windows of vulnerability and risk prediction. In addition, systems biology analysis and in silico modeling were proposed as approaches to integrate the IBD exposome for the identification of biological signatures of response to exposures, and to develop prediction models of the effects of environmental factors in driving disease activity and response to therapy. This research could lead to identification of biomarkers of exposures and new modalities for therapeutic intervention. Finally, hypothesis-driven mechanistic studies to understand gene-environment interactions and to validate causality of priority factors should be performed to determine how environment influences clinical outcomes.

Published
2019

32. Management of pouch neoplasia: consensus guidelines from the International Ileal Pouch Consortium

Author

Kiran, Ravi P, Kochhar, Gursimran S, Kariv, Revital, Rex, Douglas K, Sugita, Akira, Rubin, David T, Navaneethan, Udayakumar, Hull, Tracy L, Ko, Huaibin Mabel, Liu, Xiuli, Kachnic, Lisa A, Strong, Scott, Iacucci, Marietta, Bemelman, Willem, Fleshner, Philip, Safyan, Rachael A, Kotze, Paulo G, D'Hoore, André, Faiz, Omar, Lo, Simon, Ashburn, Jean H, Spinelli, Antonino, Bernstein, Charles N, Kane, Sunanda V, Cross, Raymond K, Schairer, Jason, McCormick, James T, Farraye, Francis A, Chang, Shannon, Scherl, Ellen J, Schwartz, David A, Bruining, David H, Philpott, Jessica, Bentley-Hibbert, Stuart, Tarabar, Dino, El-Hachem, Sandra, Sandborn, William J, Silverberg, Mark S, Pardi, Darrell S, Church, James M, and Shen, Bo

Published
2022
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34. Lifestyle, behaviour, and environmental modification for the management of patients with inflammatory bowel diseases: an International Organization for Study of Inflammatory Bowel Diseases consensus

Author

Abreu, M, Ahuja, V, Allez, M, Ananthakrishnan, A, Bemelman, W, Bernstein, C, Braun, J, Chowers, Y, Colombel, J-F, Danese, S, D'Haens, G, D'Hoore, A, Dignass, A, Dotan, I, Dubinsky, M, Ekbom, A, Fleshner, P, Gasche, C, Gassull, MA, Gearry, R, Ghosh, S, Gibson, P, Griffiths, A, Halfvarson, J, Hanauer, S, Harpaz, N, Hart, A, Hibi, T, Kamm, M, Kaplan, G, Kaser, A, Korelitz, B, Kotze, P, Koutroubakis, I, Kruis, W, Lakatos, P, Lewis, J, Lindsay, J, Loftus, E, Louis, E, Lukas, M, Magro, F, Mahadevan, U, Mantzaris, G, Mary, J-Y, McGovern, D, Moum, B, Munkholm, P, Neurath, M, Ng, S, O'Morain, C, Oresland, T, Panaccione, R, Panes, J, Panis, Y, Pemberton, J, Peyrin-Biroulet, L, Prantera, C, Rachmilewitz, D, Ran, Z, Reinisch, W, Remzi, F, Rhodes, J, Riddell, R, Rogler, G, Rubin, D, Sachar, D, Sandborn, W, Sands, B, Sartor, B, Schoelmerich, J, Schreiber, S, Siegel, C, Siegmund, B, Silverberg, M, Söderholm, J, Sood, A, Spinelli, A, Stange, E, Steinwurz, F, Targan, S, Travis, S, Turner, D, Tysk, C, Vatn, M, Vermeire, S, Watanabe, M, Yamamoto, T, Yamamoto-Furusho, J, Ananthakrishnan, Ashwin N, Kaplan, Gilaad G, Bernstein, Charles N, Burke, Kristin E, Lochhead, Paul J, Sasson, Alexa N, Agrawal, Manasi, Tiong, Jimmy Ho Tuan, Steinberg, Joshua, Kruis, Wolfgang, Steinwurz, Flavio, Ahuja, Vineet, Ng, Siew C, Rubin, David T, Colombel, Jean-Frederic, and Gearry, Richard

Published
2022
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41. Duration of Postvaccination Neutralizing Antibodies to SARS‐CoV‐2 and Medication Effects: Results from the Safety and Immunogenicity of COVID‐19 Vaccination in Systemic Immune‐Mediated Inflammatory Diseases Cohort Study.

Author

Habib, Rami, Dayam, Roya M., Hitchon, Carol, Chandran, Vinod, Fortin, Paul R., Boire, Gilles, Bowdish, Dawn M. E., Gingras, Anne‐Claude, Flamand, Louis, Larché, Maggie J., Colmegna, Ines, Lukusa, Luck, Lee, Jennifer L. F., Pereira, Daniel, Bernstein, Charles N., Lalonde, Nadine, Turnbull, Elizabeth, and Bernatsky, Sasha

Abstract

Objective: In the face of the ongoing circulation of SARS‐CoV‐2, the durability of neutralization post–COVID‐19 vaccination in immune‐mediated inflammatory disease (IMID) is a key issue, as are the effects of medications. Methods: Adults (n = 112) with inflammatory bowel disease, psoriasis/psoriatic arthritis, rheumatoid arthritis, spondylarthritis, and systemic lupus were recruited from participating Canadian medical centers from 2021 to 2023. We focused on log‐transformed neutralization (lentivirus methods) as a continuous outcome, with separate models for wild‐type and Omicron strains BA.1 and BA.5. Results: Compared with 30 to 120 days postvaccination, subsequent periods were associated with greater neutralization in unadjusted models for wild‐type, BA.1, and BA.5 strains and against the BA.1 strain in adjusted models. Rituximab was associated with lower neutralization for the BA.1 strain in adjusted models, with a similar trend for BA.5. In methotrexate users, there were trends for less neutralization of BA.1 and BA.5 in all unadjusted models, whereas in adjusted models, there was significantly lower neutralization only for the wild type. Three or more doses and Omicron‐specific vaccines were both independently associated with better neutralization ability for all three strains. A COVID‐19 infection within six months before sampling was associated with higher neutralization of wild type and BA.1 in adjusted analyses. Anti–tumor necrosis factor agents were associated with lower neutralization ability for BA.5 in adjusted analyses. Conclusion: Neutralization responses in immunosuppressed individuals with IMID were durable over time and were augmented by more than three doses and Omicron‐specific vaccines. Less neutralization was seen with certain medications. Our work clarifies the joint effects of vaccine history, infection, and medications on COVID‐19 immunity. [ABSTRACT FROM AUTHOR]

Published
2024
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42. The 5-year pre- and post-hospitalization treated prevalence of mental disorders and psychotropic medication use in critically ill patients: a Canadian population-based study

Author

Olafson, Kendiss, Marrie, Ruth Ann, Bolton, James M., Bernstein, Charles N., Bienvenu, O. Joseph, Kredentser, Maia S., and Logsetty, Sarvesh

Subjects
Medical research -- Comparative analysis, Medicine, Experimental -- Comparative analysis, Antidepressants -- Comparative analysis, Tranquilizing drugs -- Comparative analysis, Hospital patients -- Care and treatment, Mental illness -- Care and treatment, Health care industry
Abstract

Purpose The interplay between critical illness and mental disorders is poorly understood. The purpose of this study is to measure both the treated prevalence of mental disorders and psychotropic medication use before and after hospitalization and the impact of intensive care unit (ICU) admission on these outcomes. Methods Using a population-based administrative database in Manitoba, Canada, 49,439 ICU patients admitted between 2000 and 2012 were compared to two matched comparison groups (hospitalized; n = 146,968 and general population; n = 141,937). Treated prevalence of mental disorders and psychotropic medication prescriptions were measured in the 5-year periods before and after the hospitalization. Multivariable models compared adjusted prevalence ratios (APRs) between populations. Results The 5-year treated mental disorder prevalence in the ICU population increased from 41.5% pre-hospitalization to 55.6% post-hospitalization. Compared to non-ICU hospitalized patients, the adjusted treated mental disorder prevalence in ICU patients was lower prior to hospitalization (1-year APR 0.94, 95% CI 0.92-0.97, p < 0.0001; 5-year APR 0.99, 95% CI 0.98-1.00, p = 0.1), but higher following discharge (1-year APR 1.08, 95% CI 1.05-1.11, p < 0.0001, 5-year APR 1.03, 95% CI 1.01-1.05, p < 0.0001). A high proportion of ICU patients received antidepressant, anxiolytic and sedative-hypnotic prescriptions before and after their hospitalization. In multivariable analyses, ICU exposure was associated with an increase in mood, anxiety and psychotic disorders, and sedative-hypnotics use (p < 0.0001 for all Time x Group interactions). Conclusions During the 5 years after admission to ICU, there is a significant increase in treated prevalence of mental disorders and psychotropic medication use compared to the 5 years prior to ICU and compared to general population and hospital cohorts. Prevention and intervention programs that identify and treat mental disorders among survivors of critical illness warrant further study., Author(s): Kendiss Olafson [sup.1], Ruth Ann Marrie [sup.1] [sup.2], James M. Bolton [sup.2] [sup.3] [sup.4], Charles N. Bernstein [sup.1], O. Joseph Bienvenu [sup.5], Maia S. Kredentser [sup.6], Sarvesh Logsetty [sup.3] [...]

Published
2021
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43. Treatment of pouchitis, Crohn's disease, cuffitis, and other inflammatory disorders of the pouch: consensus guidelines from the International Ileal Pouch Consortium

Author

Shen, Bo, Kochhar, Gursimran S, Rubin, David T, Kane, Sunanda V, Navaneethan, Udayakumar, Bernstein, Charles N, Cross, Raymond K, Sugita, Akira, Schairer, Jason, Kiran, Ravi P, Fleshner, Philip, McCormick, James T, D’Hoore, André, Shah, Samir A, Farraye, Francis A, Kariv, Revital, Liu, Xiuli, Rosh, Joel, Chang, Shannon, Scherl, Ellen, Schwartz, David A, Kotze, Paulo Gustavo, Bruining, David H, Philpott, Jessica, Abraham, Bincy, Segal, Jonathan, Sedano, Rocio, Kayal, Maia, Bentley-Hibbert, Stuart, Tarabar, Dino, El-Hachem, Sandra, Sehgal, Priya, Picoraro, Joseph A, Vermeire, Séverine, Sandborn, William J, Silverberg, Mark S, and Pardi, Darrell S

Published
2022
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46. Polygenic liability for anxiety in association with comorbid anxiety in multiple sclerosis

Author

Kowalec, Kaarina, primary, Harder, Arvid, additional, Dolovich, Casandra, additional, Fitzgerald, Kathryn C., additional, Salter, Amber, additional, Lu, Yi, additional, Bernstein, Charles N., additional, Bolton, James M., additional, Cutter, Gary, additional, Fisk, John D., additional, Gelernter, Joel, additional, Graff, Lesley A., additional, Hägg, Sara, additional, Hitchon, Carol A., additional, Levey, Daniel F., additional, Lublin, Fred D., additional, McKay, Kyla A., additional, Patten, Scott, additional, Patki, Amit, additional, Stein, Murray B., additional, Tiwari, Hemant K., additional, Wolinsky, Jerry S., additional, and Marrie, Ruth A., additional

Published
2024
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47. Crohn’s Disease Phenotypes and Associations With Comorbidities, Surgery Risk, Medications and Nonmedication Approaches: The MAGIC in IMAGINE Study

Author

Bernstein, Charles N, primary, Panaccione, Remo, additional, Nugent, Zoann, additional, Marshall, Deborah A, additional, Kaplan, Gilaad G, additional, Vanner, Stephen, additional, Dieleman, Levinus A, additional, Graff, Lesley A, additional, Otley, Anthony, additional, Jones, Jennifer, additional, Buresi, Michelle, additional, Murthy, Sanjay, additional, Borgaonkar, Mark, additional, Bressler, Brian, additional, Bitton, Alain, additional, Croitoru, Kenneth, additional, Sidani, Sacha, additional, Fernandes, Aida, additional, and Moayyedi, Paul, additional

Published
2024
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48. Diagnosis and classification of ileal pouch disorders: consensus guidelines from the International Ileal Pouch Consortium

Author

Shen, Bo, Kochhar, Gursimran S, Kariv, Revital, Liu, Xiuli, Navaneethan, Udayakumar, Rubin, David T, Cross, Raymond K, Sugita, Akira, D'Hoore, André, Schairer, Jason, Farraye, Francis A, Kiran, Ravi P, Fleshner, Philip, Rosh, Joel, Shah, Samir A, Chang, Shannon, Scherl, Ellen, Pardi, Darrell S, Schwartz, David A, Kotze, Paulo G, Bruining, David H, Kane, Sunanda V, Philpott, Jessica, Abraham, Bincy, Segal, Jonathan, Sedano, Rocio, Kayal, Maia, Bentley-Hibbert, Stuart, Tarabar, Dino, El-Hachem, Sandra, Sehgal, Priya, McCormick, James T, Picoraro, Joseph A, Silverberg, Mark S, Bernstein, Charles N, Sandborn, William J, and Vermeire, Séverine

Published
2021
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50. The impact of the coronavirus (COVID-19) pandemic on individuals with gastrointestinal disorders: A protocol of an international collaborative study

Author

Ferreira, Nuno, Mikocka-Walus, Antonina, van Tilburg, Miranda A.L., Graff, Lesley A., Apputhurai, Pragalathan, Barreiro-de Acosta, Manuel, Bennebroek Evertsz, Floor, Burisch, Johan, Lo, Bobby, Petrik, Megan, Trindade, Inês A., Jedel, Sharon, Moser, Gabriele, Mokrowiecka, Anna, Bernstein, Charles N., Dumitrascu, Dan, Ford, Alexander C., Stengel, Andreas, Gearry, Richard, and Knowles, Simon R.

Published
2021
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