73 results on '"Budden T"'
Search Results
2. Prognostic gene expression signature for high-grade serous ovarian cancer.
- Author
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Millstein, J, Budden, T, Goode, EL, Anglesio, MS, Talhouk, A, Intermaggio, MP, Leong, HS, Chen, S, Elatre, W, Gilks, B, Nazeran, T, Volchek, M, Bentley, RC, Wang, C, Chiu, DS, Kommoss, S, Leung, SCY, Senz, J, Lum, A, Chow, V, Sudderuddin, H, Mackenzie, R, George, J, AOCS Group, Fereday, S, Hendley, J, Traficante, N, Steed, H, Koziak, JM, Köbel, M, McNeish, IA, Goranova, T, Ennis, D, Macintyre, G, Silva De Silva, D, Ramón Y Cajal, T, García-Donas, J, Hernando Polo, S, Rodriguez, GC, Cushing-Haugen, KL, Harris, HR, Greene, CS, Zelaya, RA, Behrens, S, Fortner, RT, Sinn, P, Herpel, E, Lester, J, Lubiński, J, Oszurek, O, Tołoczko, A, Cybulski, C, Menkiszak, J, Pearce, CL, Pike, MC, Tseng, C, Alsop, J, Rhenius, V, Song, H, Jimenez-Linan, M, Piskorz, AM, Gentry-Maharaj, A, Karpinskyj, C, Widschwendter, M, Singh, N, Kennedy, CJ, Sharma, R, Harnett, PR, Gao, B, Johnatty, SE, Sayer, R, Boros, J, Winham, SJ, Keeney, GL, Kaufmann, SH, Larson, MC, Luk, H, Hernandez, BY, Thompson, PJ, Wilkens, LR, Carney, ME, Trabert, B, Lissowska, J, Brinton, L, Sherman, ME, Bodelon, C, Hinsley, S, Lewsley, LA, Glasspool, R, Banerjee, SN, Stronach, EA, Haluska, P, Ray-Coquard, I, Mahner, S, Winterhoff, B, Slamon, D, Levine, DA, Kelemen, LE, Benitez, J, and Chang-Claude, J
- Subjects
AOCS Group ,Humans ,Cystadenocarcinoma ,Serous ,Ovarian Neoplasms ,Prognosis ,Proportional Hazards Models ,Survival Analysis ,Female ,Transcriptome ,formalin-fixed paraffin-embedded ,gene expression ,high-grade serous ovarian cancer ,overall survival ,prognosis ,Rare Diseases ,Genetic Testing ,Cancer ,Ovarian Cancer ,Genetics ,4.4 Population screening ,4.2 Evaluation of markers and technologies ,Oncology & Carcinogenesis ,Oncology and Carcinogenesis - Abstract
BackgroundMedian overall survival (OS) for women with high-grade serous ovarian cancer (HGSOC) is ∼4 years, yet survival varies widely between patients. There are no well-established, gene expression signatures associated with prognosis. The aim of this study was to develop a robust prognostic signature for OS in patients with HGSOC.Patients and methodsExpression of 513 genes, selected from a meta-analysis of 1455 tumours and other candidates, was measured using NanoString technology from formalin-fixed paraffin-embedded tumour tissue collected from 3769 women with HGSOC from multiple studies. Elastic net regularization for survival analysis was applied to develop a prognostic model for 5-year OS, trained on 2702 tumours from 15 studies and evaluated on an independent set of 1067 tumours from six studies.ResultsExpression levels of 276 genes were associated with OS (false discovery rate < 0.05) in covariate-adjusted single-gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1 and PTGER3 (P < 0.001). The best performing prognostic signature included 101 genes enriched in pathways with treatment implications. Each gain of one standard deviation in the gene expression score conferred a greater than twofold increase in risk of death [hazard ratio (HR) 2.35, 95% confidence interval (CI) 2.02-2.71; P < 0.001]. Median survival [HR (95% CI)] by gene expression score quintile was 9.5 (8.3 to -), 5.4 (4.6-7.0), 3.8 (3.3-4.6), 3.2 (2.9-3.7) and 2.3 (2.1-2.6) years.ConclusionThe OTTA-SPOT (Ovarian Tumor Tissue Analysis consortium - Stratified Prognosis of Ovarian Tumours) gene expression signature may improve risk stratification in clinical trials by identifying patients who are least likely to achieve 5-year survival. The identified novel genes associated with the outcome may also yield opportunities for the development of targeted therapeutic approaches.
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- 2020
3. Australian children's physical activity and screen time while in grandparental care
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Jongenelis, MI, Budden, T, Jackson, B, Christian, H, Nathan, A, Coall, D, Glassenbury, E, Jongenelis, MI, Budden, T, Jackson, B, Christian, H, Nathan, A, Coall, D, and Glassenbury, E
- Abstract
OBJECTIVE: The objective of this study was to explore Australian children's engagement in physical activity and screen time while being cared for by their grandparents. METHOD: Grandparents (N = 1,190) providing ≥3 hours of weekly care to a grandchild aged 3-14 years completed an online survey assessing their grandchildren's movement behaviours while in their care. Descriptive statistics were computed for frequency of engagement in unstructured and structured physical activities, minutes spent playing outdoors, and minutes spent engaged in screen time. Regression analyses were conducted to assess socio-demographic predictors of movement behaviours. RESULTS: Playing in the yard was the most common form of physical activity in which grandchildren reportedly participated (77% 'usually' or 'always'), followed by playing with toys/equipment (62%). Few (14-36%) frequently engaged in active transport. Children spent an average of 181 minutes per week engaged in screen-based activities. CONCLUSIONS: There is an opportunity to improve children's movement behaviours while in grandparental care. Communicating to grandparents their importance in supporting an active lifestyle is warranted. IMPLICATIONS FOR PUBLIC HEALTH: Findings highlight the importance of creating environments that facilitate play-based, outdoor activities. Ensuring children have access to play equipment while in the care of grandparents and improving access to and quality of neighbourhood parks may assist with activity promotion.
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- 2024
4. Prognostic gene expression signature for high-grade serous ovarian cancer
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Bowtell, D., Chenevix-Trench, G., Green, A., Webb, P., DeFazio, A., Gertig, D., Traficante, N., Fereday, S., Moore, S., Hung, J., Harrap, K., Sadkowsky, T., Pandeya, N., Malt, M., Mellon, A., Robertson, R., Vanden Bergh, T., Jones, M., Mackenzie, P., Maidens, J., Nattress, K., Chiew, Y.E., Stenlake, A., Sullivan, H., Alexander, B., Ashover, P., Brown, S., Corrish, T., Green, L., Jackman, L., Ferguson, K., Martin, K., Martyn, A., Ranieri, B., White, J., Jayde, V., Mamers, P., Bowes, L., Galletta, L., Giles, D., Hendley, J., Alsop, K., Schmidt, T., Shirley, H., Ball, C., Young, C., Viduka, S., Tran, Hoa, Bilic, Sanela, Glavinas, Lydia, Brooks, Julia, Stuart-Harris, R., Kirsten, F., Rutovitz, J., Clingan, P., Glasgow, A., Proietto, A., Braye, S., Otton, G., Shannon, J., Bonaventura, T., Stewart, J., Begbie, S., Friedlander, M., Bell, D., Baron-Hay, S., Ferrier,a, A., Gard, G., Nevell, D., Pavlakis, N., Valmadre, S., Young, B., Camaris, C., Crouch, R., Edwards, L., Hacker, N., Marsden, D., Robertson, G., Beale, P., Beith, J., Carter, J., Dalrymple, C., Houghton, R., Russell, P., Links, M., Grygiel, J., Hill, J., Brand, A., Byth, K., Jaworski, R., Harnett, P., Sharma, R., Wain, G., Ward, B., Papadimos, D., Crandon, A., Cummings, M., Horwood, K., Obermair, A., Perrin, L., Wyld, D., Nicklin, J., Davy, M., Oehler, M.K., Hall, C., Dodd, T., Healy, T., Pittman, K., Henderson, D., Miller, J., Pierdes, J., Blomfield, P., Challis, D., McIntosh, R., Parker, A., Brown, B., Rome, R., Allen, D., Grant, P., Hyde, S., Laurie, R., Robbie, M., Healy, D., Jobling, T., Manolitsas, T., McNealage, J., Rogers, P., Susil, B., Sumithran, E., Simpson, I., Phillips, K., Rischin, D., Fox, S., Johnson, D., Lade, S., Loughrey, M., O’Callaghan, N., Murray, W., Waring, P., Billson, V., Pyman, J., Neesham, D., Quinn, M., Underhill, C., Bell, R., Ng, L.F., Blum, R., Ganju, V., Hammond, I., Leung, Y., McCartney, A., Buck, M., Haviv, I., Purdie, D., Whiteman, D., Zeps, N., Millstein, J., Budden, T., Goode, E.L., Anglesio, M.S., Talhouk, A., Intermaggio, M.P., Leong, H.S., Chen, S., Elatre, W., Gilks, B., Nazeran, T., Volchek, M., Bentley, R.C., Wang, C., Chiu, D.S., Kommoss, S., Leung, S.C.Y., Senz, J., Lum, A., Chow, V., Sudderuddin, H., Mackenzie, R., George, J., Steed, H., Koziak, J.M., Köbel, M., McNeish, I.A., Goranova, T., Ennis, D., Macintyre, G., Silva De Silva, D., Ramón y Cajal, T., García-Donas, J., Hernando Polo, S., Rodriguez, G.C., Cushing-Haugen, K.L., Harris, H.R., Greene, C.S., Zelaya, R.A., Behrens, S., Fortner, R.T., Sinn, P., Herpel, E., Lester, J., Lubiński, J., Oszurek, O., Tołoczko, A., Cybulski, C., Menkiszak, J., Pearce, C.L., Pike, M.C., Tseng, C., Alsop, J., Rhenius, V., Song, H., Jimenez-Linan, M., Piskorz, A.M., Gentry-Maharaj, A., Karpinskyj, C., Widschwendter, M., Singh, N., Kennedy, C.J., Harnett, P.R., Gao, B., Johnatty, S.E., Sayer, R., Boros, J., Winham, S.J., Keeney, G.L., Kaufmann, S.H., Larson, M.C., Luk, H., Hernandez, B.Y., Thompson, P.J., Wilkens, L.R., Carney, M.E., Trabert, B., Lissowska, J., Brinton, L., Sherman, M.E., Bodelon, C., Hinsley, S., Lewsley, L.A., Glasspool, R., Banerjee, S.N., Stronach, E.A., Haluska, P., Ray-Coquard, I., Mahner, S., Winterhoff, B., Slamon, D., Levine, D.A., Kelemen, L.E., Benitez, J., Chang-Claude, J., Gronwald, J., Wu, A.H., Menon, U., Goodman, M.T., Schildkraut, J.M., Wentzensen, N., Brown, R., Berchuck, A., deFazio, A., Gayther, S.A., García, M.J., Henderson, M.J., Rossing, M.A., Beeghly-Fadiel, A., Fasching, P.A., Orsulic, S., Karlan, B.Y., Konecny, G.E., Huntsman, D.G., Bowtell, D.D., Brenton, J.D., Doherty, J.A., Pharoah, P.D.P., and Ramus, S.J.
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- 2020
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5. The PI3K-AKT-mTOR axis persists as a therapeutic dependency in KRASG12D-driven non-small cell lung cancer
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McDaid, W. J., primary, Wilson, L., additional, Adderley, H., additional, Baker, M. J., additional, Searle, J., additional, Ginn, L., additional, Budden, T., additional, Aldea, M., additional, Marinello, A., additional, Aredo, J., additional, Viros, A., additional, Besse, B., additional, Wakelee, H. A., additional, Blackhall, F., additional, Lindsay, C. R., additional, and Malliri, A., additional
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- 2023
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6. Concurrent RB1 loss and BRCA-deficiency predicts enhanced immunological response and long-term survival in tubo-ovarian high-grade serous carcinoma.
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Saner, FAM, Takahashi, K, Budden, T, Pandey, A, Ariyaratne, D, Zwimpfer, TA, Meagher, NS, Fereday, S, Twomey, L, Pishas, KI, Hoang, T, Bolithon, A, Traficante, N, Alsop, K, Christie, EL, Kang, E-Y, Nelson, GS, Ghatage, P, Lee, C-H, Riggan, MJ, Alsop, J, Beckmann, MW, Boros, J, Brand, AH, Brooks-Wilson, A, Carney, ME, Coulson, P, Courtney-Brooks, M, Cushing-Haugen, KL, Cybulski, C, El-Bahrawy, MA, Elishaev, E, Erber, R, Gayther, SA, Gentry-Maharaj, A, Blake Gilks, C, Harnett, PR, Harris, HR, Hartmann, A, Hein, A, Hendley, J, AOCS Group, Hernandez, BY, Jakubowska, A, Jimenez-Linan, M, Jones, ME, Kaufmann, SH, Kennedy, CJ, Kluz, T, Koziak, JM, Kristjansdottir, B, Le, ND, Lener, M, Lester, J, Lubiński, J, Mateoiu, C, Orsulic, S, Ruebner, M, Schoemaker, MJ, Shah, M, Sharma, R, Sherman, ME, Shvetsov, YB, Singh, N, Rinda Soong, T, Steed, H, Sukumvanich, P, Talhouk, A, Taylor, SE, Vierkant, RA, Wang, C, Widschwendter, M, Wilkens, LR, Winham, SJ, Anglesio, MS, Berchuck, A, Brenton, JD, Campbell, I, Cook, LS, Doherty, JA, Fasching, PA, Fortner, RT, Goodman, MT, Gronwald, J, Huntsman, DG, Karlan, BY, Kelemen, LE, Menon, U, Modugno, F, Pharoah, PDP, Schildkraut, JM, Sundfeldt, K, Swerdlow, AJ, Goode, EL, DeFazio, A, Köbel, M, Ramus, SJ, Bowtell, DDL, Garsed, DW, Saner, FAM, Takahashi, K, Budden, T, Pandey, A, Ariyaratne, D, Zwimpfer, TA, Meagher, NS, Fereday, S, Twomey, L, Pishas, KI, Hoang, T, Bolithon, A, Traficante, N, Alsop, K, Christie, EL, Kang, E-Y, Nelson, GS, Ghatage, P, Lee, C-H, Riggan, MJ, Alsop, J, Beckmann, MW, Boros, J, Brand, AH, Brooks-Wilson, A, Carney, ME, Coulson, P, Courtney-Brooks, M, Cushing-Haugen, KL, Cybulski, C, El-Bahrawy, MA, Elishaev, E, Erber, R, Gayther, SA, Gentry-Maharaj, A, Blake Gilks, C, Harnett, PR, Harris, HR, Hartmann, A, Hein, A, Hendley, J, AOCS Group, Hernandez, BY, Jakubowska, A, Jimenez-Linan, M, Jones, ME, Kaufmann, SH, Kennedy, CJ, Kluz, T, Koziak, JM, Kristjansdottir, B, Le, ND, Lener, M, Lester, J, Lubiński, J, Mateoiu, C, Orsulic, S, Ruebner, M, Schoemaker, MJ, Shah, M, Sharma, R, Sherman, ME, Shvetsov, YB, Singh, N, Rinda Soong, T, Steed, H, Sukumvanich, P, Talhouk, A, Taylor, SE, Vierkant, RA, Wang, C, Widschwendter, M, Wilkens, LR, Winham, SJ, Anglesio, MS, Berchuck, A, Brenton, JD, Campbell, I, Cook, LS, Doherty, JA, Fasching, PA, Fortner, RT, Goodman, MT, Gronwald, J, Huntsman, DG, Karlan, BY, Kelemen, LE, Menon, U, Modugno, F, Pharoah, PDP, Schildkraut, JM, Sundfeldt, K, Swerdlow, AJ, Goode, EL, DeFazio, A, Köbel, M, Ramus, SJ, Bowtell, DDL, and Garsed, DW
- Abstract
BACKGROUND: Somatic loss of the tumour suppressor RB1 is a common event in tubo-ovarian high-grade serous carcinoma (HGSC), which frequently co-occurs with alterations in homologous recombination DNA repair genes including BRCA1 and BRCA2 (BRCA). We examined whether tumour expression of RB1 was associated with survival across ovarian cancer histotypes (HGSC, endometrioid (ENOC), clear cell (CCOC), mucinous (MOC), low-grade serous carcinoma (LGSC)), and how co-occurrence of germline BRCA pathogenic variants and RB1 loss influences long-term survival in a large series of HGSC. PATIENTS AND METHODS: RB1 protein expression patterns were classified by immunohistochemistry in epithelial ovarian carcinomas of 7436 patients from 20 studies participating in the Ovarian Tumor Tissue Analysis consortium and assessed for associations with overall survival (OS), accounting for patient age at diagnosis and FIGO stage. We examined RB1 expression and germline BRCA status in a subset of 1134 HGSC, and related genotype to survival, tumour infiltrating CD8+ lymphocyte counts and transcriptomic subtypes. Using CRISPR-Cas9, we deleted RB1 in HGSC cell lines with and without BRCA1 mutations to model co-loss with treatment response. We also performed genomic analyses on 126 primary HGSC to explore the molecular characteristics of concurrent homologous recombination deficiency and RB1 loss. RESULTS: RB1 protein loss was most frequent in HGSC (16.4%) and was highly correlated with RB1 mRNA expression. RB1 loss was associated with longer OS in HGSC (hazard ratio [HR] 0.74, 95% confidence interval [CI] 0.66-0.83, P = 6.8 ×10-7), but with poorer prognosis in ENOC (HR 2.17, 95% CI 1.17-4.03, P = 0.0140). Germline BRCA mutations and RB1 loss co-occurred in HGSC (P < 0.0001). Patients with both RB1 loss and germline BRCA mutations had a superior OS (HR 0.38, 95% CI 0.25-0.58, P = 5.2 ×10-6) compared to patients with either alteration alone, and their median OS was three times longer than non-carr
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- 2023
7. Time-Dependent Cell Release Rate And Gene Expression Profile In Human Articular Chondrocyte Isolation
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Zhang, M., primary, Liu, Z., additional, Budden, T., additional, Miller, A., additional, and Wang, J., additional
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- 2023
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8. 358: Role of methylthioadenosine in maintaining airway surface hydration in human bronchial epithelial cells
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Kamath, D., primary, Baumlin, N., additional, Kim, M., additional, Budden, T., additional, Salathe, M., additional, and Polineni, D., additional
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- 2021
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9. Melanoma exhibits defective nucleotide excision repair of UVB-induced DNA photoproducts: P038
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Budden, T. and Bowden, N.
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- 2014
10. Methylthioadenosine Improves Airway Surface Hydration in Human Bronchial Epithelial Cells
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Kamath, D., primary, Kim, M., additional, Baumlin, N., additional, Budden, T., additional, Salathe, M.A., additional, and Polineni, D., additional
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- 2021
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11. 081 Ultraviolet light-induced collagen degradation inhibits melanoma invasion
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Budden, T., primary, Gaudy, C., additional, Nagore, E., additional, and Viros, A., additional
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- 2021
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12. Cartilage-specific NFAT1 overexpression rescues osteoarthritic phenotypes in specific joint tissues of nfat1 knockout mice
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Wang, J., primary, Lu, Q., additional, Zhang, M., additional, and Budden, T., additional
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- 2021
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13. Molecular subtype, biological sex and age shape melanoma tumour evolution
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Lotz, M., primary, Budden, T., additional, Furney, S.J., additional, and Virós, A., additional
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- 2020
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14. 554 Skin ageing continues long after ultraviolet radiation damage
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Earnshaw, C.H., primary, Nagore, E., additional, Roeck, K., additional, Schneider, S., additional, Budden, T., additional, Craig, S., additional, Griffiths, C., additional, Furney, S., additional, Krutmann, J., additional, and Viros, A., additional
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- 2019
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15. NFAT1 protects articular cartilage against osteoarthritic degradation by directly regulating transcription of specific anabolic and catabolic genes
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Zhang, M., primary, Lu, Q., additional, Budden, T., additional, and Wang, J., additional
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- 2019
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16. Molecular subtype, biological sex and age shape melanoma tumour evolution.
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Lotz, M., Budden, T., Furney, S.J., and Virós, A.
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SEX (Biology) , *ENVIRONMENTAL degradation , *GENETIC load , *SOMATIC mutation , *CELL division , *RADIATION damage , *CYCLIN-dependent kinase inhibitor-2A , *MELANOMA - Abstract
Summary: Background: Many cancer types display sex and age disparity in incidence and outcome. The mutational load of tumours, including melanoma, varies according to sex and age. However, there are no tools to explore systematically whether clinical variables such as age and sex determine the genomic landscape of cancer. Objectives: To establish a mathematical approach using melanoma mutational data to analyse how sex and age shape the tumour genome. Methods: We model how age‐related (clock‐like) somatic mutations that arise during cell division, and extrinsic (environmental ultraviolet radiation) mutations accumulate in cancer genomes. Results: Melanoma is driven primarily by cell‐intrinsic age‐related mutations and extrinsic ultraviolet radiation‐induced mutations, and we show that these mutation types differ in magnitude and chronology and by sex in the distinct molecular melanoma subtypes. Our model confirms that age and sex are determinants of cellular mutation rate, shaping the final mutation composition. We show mathematically for the first time how, similarly to noncancer tissues, melanoma genomes reflect a decline in cell division during ageing. We find that clock‐like mutations strongly correlate with the acquisition of ultraviolet‐induced mutations, but critically, men present a higher number and rate of cell‐division‐linked mutations. Conclusions: These data indicate that the contribution of environmental damage to melanoma likely extends beyond genetic damage to affect cell division. Sex and age determine the final mutational composition of melanoma. What is already known about this topic? Cancer incidence and mortality are influenced by sex and age.Melanoma is more frequent in men, and the incidence and mortality rise with increasing age.The main mutations driving melanoma are linked predominantly to ultraviolet (UV) radiation damage and to errors accumulated in the DNA after each cell division, which are unrepaired.These clock‐like mutations linked to cell division accumulate steadily over time in both healthy tissue and cancers. What does this study add? Clock and UV mutations are tightly correlated and arise in melanoma as a function of age and sex.The molecular subtypes have a distinct pattern and rate of UV and clock mutations, and clock mutations depend on the amount of UV damage.The rate of clock mutations decreases as individuals age, reflecting a decrease in tissue proliferation during ageing.Men have more clock mutations, which reflect a distinct proliferation rate. What is the translational message? This study indicates that age and sex shape the rate of mutations observed in melanoma.The burden of mutation affects response to novel immunotherapies, so this work supports the rationale to stratify patients by their mutational landscape, age and sex to discriminate possible responders most easily.These data can better inform public health prevention campaigns. Linked Comment: Toland. Br J Dermatol 2021; 184:197–198. [ABSTRACT FROM AUTHOR]
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- 2021
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17. The principle of equivalence
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UCL, Ghins, Michel, Budden, T, UCL, Ghins, Michel, and Budden, T
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start from John Norton's analysis (1985) of the reach of Einstein's version of the principle of equivalence which is not a local principle but an extension of the relativity principle to reference frames in constant acceleration on the background of Minkowski spacetime. We examine how such a point of view implies a profound, and not generally recognised, reconsideration of the concepts of inertial system and field in physics. We then reevaluate the role that the infinitesimal principle, if adequately formulated, can legitimately be claimed to play in general relativity. We show that what we call the 'punctual equivalence principle' has significant physical content and that it permits the derivation of the geodesic law. (C) 2001 Elsevier Science Ltd. All rights reserved.
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- 2001
18. Geometric simultaneity and the continuity of special relativity
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UCL, Budden, T, UCL, and Budden, T
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In this note I briefly discuss some aspects of relative geometric-simultaneity in special relativity. After saying a. few words about the status and nature of Minkowski spacetime in special relativity I recall a uniqueness result due to David Malament concerning simultaneity relative to an inertial worldline and an extension of it due to Mark Hogarth and I prove an extension of it for simultaneity relative to an inertial frame in time-oriented spacetimes. Then I point out that the uniqueness results do not generalise to definitions of simultaneity relative to the rotating disk. Finally, I evaluate some recent claims of Selleri in the light of the results. Whilst some of his claims are supported by the approach taken here, the conclusion he draws from these claims, that special relativity harbours a discontinuity and so stands in need of replacement, does not follow and is rejected.
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- 1998
19. Galileo's ship and spacetime symmetry
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UCL, Budden, T, UCL, and Budden, T
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The empirical content of the modern definition of relativity given in the Andersonian approach to spacetime theory has been overestimated. It does not imply the empirical relativity Galileo illustrated in his famous ship thought experiment. I offer a number of arguments-some of which are in essential agreement with a recent analysis of Brown and Sypel [1995]-which make this plausible. Then I go on to present example spacetime theories which are modern relativistic but violate Galileo's relativity. I end by briefly discussing the prospects for improving on modern relativity.
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- 1997
20. Prognostic gene expression signature for high-grade serous ovarian cancer
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Millstein, J, Budden, T, Goode, EL, Anglesio, MS, Talhouk, A, Intermaggio, MP, Leong, HS, Chen, S, Elatre, W, Gilks, B, Nazeran, T, Volchek, M, Bentley, RC, Wang, C, Chiu, DS, Kommoss, S, Leung, SCY, Senz, J, Lum, A, Chow, V, Sudderuddin, H, Mackenzie, R, George, J, AOCS Group, Fereday, S, Hendley, J, Traficante, N, Steed, H, Koziak, JM, Köbel, M, McNeish, IA, Goranova, T, Ennis, D, Macintyre, G, Silva De Silva, D, Ramón Y Cajal, T, García-Donas, J, Hernando Polo, S, Rodriguez, GC, Cushing-Haugen, KL, Harris, HR, Greene, CS, Zelaya, RA, Behrens, S, Fortner, RT, Sinn, P, Herpel, E, Lester, J, Lubiński, J, Oszurek, O, Tołoczko, A, Cybulski, C, Menkiszak, J, Pearce, CL, Pike, MC, Tseng, C, Alsop, J, Rhenius, V, Song, H, Jimenez-Linan, M, Piskorz, AM, Gentry-Maharaj, A, Karpinskyj, C, Widschwendter, M, Singh, N, Kennedy, CJ, Sharma, R, Harnett, PR, Gao, B, Johnatty, SE, Sayer, R, Boros, J, Winham, SJ, Keeney, GL, Kaufmann, SH, Larson, MC, Luk, H, Hernandez, BY, Thompson, PJ, Wilkens, LR, Carney, ME, Trabert, B, Lissowska, J, Brinton, L, Sherman, ME, Bodelon, C, Hinsley, S, Lewsley, LA, Glasspool, R, Banerjee, SN, Stronach, EA, Haluska, P, Ray-Coquard, I, Mahner, S, Winterhoff, B, Slamon, D, Levine, DA, Kelemen, LE, Benitez, J, Chang-Claude, J, Gronwald, J, Wu, AH, Menon, U, Goodman, MT, Schildkraut, JM, Wentzensen, N, Brown, R, Berchuck, A, Chenevix-Trench, G, DeFazio, A, Gayther, SA, García, MJ, Henderson, MJ, Rossing, MA, Beeghly-Fadiel, A, Fasching, PA, Orsulic, S, Karlan, BY, Konecny, GE, Huntsman, DG, Bowtell, DD, Brenton, JD, Doherty, JA, Pharoah, PDP, and Ramus, SJ
- Subjects
Ovarian Neoplasms ,high-grade serous ovarian cancer ,overall survival ,gene expression ,Humans ,Female ,prognosis ,formalin-fixed paraffin-embedded ,Transcriptome ,Survival Analysis ,3. Good health ,Cystadenocarcinoma, Serous ,Proportional Hazards Models - Abstract
BACKGROUND: Median overall survival (OS) for women with high-grade serous ovarian cancer (HGSOC) is ∼4 years, yet survival varies widely between patients. There are no well-established, gene expression signatures associated with prognosis. The aim of this study was to develop a robust prognostic signature for OS in patients with HGSOC. PATIENTS AND METHODS: Expression of 513 genes, selected from a meta-analysis of 1455 tumours and other candidates, was measured using NanoString technology from formalin-fixed paraffin-embedded tumour tissue collected from 3769 women with HGSOC from multiple studies. Elastic net regularization for survival analysis was applied to develop a prognostic model for 5-year OS, trained on 2702 tumours from 15 studies and evaluated on an independent set of 1067 tumours from six studies. RESULTS: Expression levels of 276 genes were associated with OS (false discovery rate < 0.05) in covariate-adjusted single-gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1 and PTGER3 (P < 0.001). The best performing prognostic signature included 101 genes enriched in pathways with treatment implications. Each gain of one standard deviation in the gene expression score conferred a greater than twofold increase in risk of death [hazard ratio (HR) 2.35, 95% confidence interval (CI) 2.02-2.71; P < 0.001]. Median survival [HR (95% CI)] by gene expression score quintile was 9.5 (8.3 to -), 5.4 (4.6-7.0), 3.8 (3.3-4.6), 3.2 (2.9-3.7) and 2.3 (2.1-2.6) years. CONCLUSION: The OTTA-SPOT (Ovarian Tumor Tissue Analysis consortium - Stratified Prognosis of Ovarian Tumours) gene expression signature may improve risk stratification in clinical trials by identifying patients who are least likely to achieve 5-year survival. The identified novel genes associated with the outcome may also yield opportunities for the development of targeted therapeutic approaches.
21. Physical activity interventions for the promotion of mental health outcomes in at-risk children and adolescents: a systematic review.
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Simpson A, Teague S, Kramer B, Lin A, Thornton AL, Budden T, Furzer B, Jeftic I, Dimmock J, Rosenberg M, and Jackson B
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- Adolescent, Child, Humans, Basketball psychology, Bias, Internal-External Control, Martial Arts psychology, Resistance Training, Risk Factors, Soccer psychology, Water Sports psychology, Yoga psychology, Adolescent Health, Child Health, Exercise physiology, Mental Disorders prevention & control, Mental Disorders psychology, Mental Disorders therapy, Mental Health statistics & numerical data, Sports, Vulnerable Populations psychology, Health Promotion methods
- Abstract
Many young people are exposed to risk factors that increase their risk of mental illness. Physical activity provision is an increasingly popular approach to protect against mental illness in the face of these risk factors. We examined the effectiveness of physical activity interventions for the promotion of mental health outcomes in at-risk children and adolescents. We searched health databases for randomised and non-randomised intervention studies, with no date restriction, and assessed risk of bias using the Cochrane Risk of Bias tools. We present a narrative synthesis of our results accompanied with a summary of available effect sizes. Thirty-seven reports on 36 studies were included, with multi-sport or yoga interventions the most popular intervention approaches (a combined 50% of included studies). Outcomes measured included internalising, self-evaluative, wellbeing, overall symptomatology, resilience, externalising, and trauma outcomes. We found that 63% of between-groups effects favoured the intervention arm, and 83% of within-groups effects favoured an intervention effect. While recognising high risk of bias, our findings provide evidence in support of the effectiveness of physical activity interventions for promoting mental health outcomes in at-risk young people. We encourage further work designed to better understand the intervention characteristics that may lead to positive benefits.
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- 2024
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22. The Right Advice, from the Right Person, in the Right Way: Non-Engaged Consumer Families' Preferences for Lifestyle Intervention Design Relating to Severe Obesity in Childhood.
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Saunders LA, Dimmock JA, Jackson B, Gibson LY, Doust J, Davis EA, Price L, and Budden T
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- Humans, Female, Male, Child, Adolescent, Cross-Sectional Studies, Adult, Qualitative Research, Family psychology, Obesity, Morbid psychology, Obesity, Morbid therapy, Australia, Pediatric Obesity psychology, Pediatric Obesity therapy, Life Style, Parents psychology
- Abstract
Family-based lifestyle interventions for children/adolescents with severe levels of obesity are numerous, but evidence indicates programs fail to elicit short- or longer-term weight loss outcomes. Families with lived experience can provide valuable insight as we strive to improve outcomes from programs. Our aim was to explore elements that families desired in a program designed to treat severe levels of obesity in young people. We recruited a cross-sectional sample of 13 families (parents and young people) who had been referred but had not engaged with the state-wide Perth Children's Hospital, Healthy Weight Service (Perth, Australia), between 2016 and 2018. Utilizing semi-structured interviews and reflexive qualitative thematic analysis, we identified two broad themes, (1) bridging the gap between what to do and how to do it , and (2) peers doing it with you . The first theme reflected parents' and young people's feelings that programs ought to teach specialist-designed practical strategies utilizing non-generic information tailored to address the needs of the family, in a collaboratively supportive way, and encourage young people to learn for themselves. The second theme reflected the importance of social connection facilitated by peer support, and intervention programs should be offered in a group format to foster inclusion. Families indicated a willingness to engage in tertiary intervention programs but desired support from specialized health professionals/programs to be tailored to their needs, sensitive to their experiences and challenges and provide useful practical strategies that support the knowledge-to-action process.
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- 2024
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23. The Role of Grandparents in Facilitating Children's Physical Activity.
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Jongenelis MI, Budden T, Christian H, Coall DA, Jackson B, Nathan A, and Glassenbury E
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- Humans, Female, Child, Male, Adolescent, Child, Preschool, Australia, Middle Aged, Aged, Surveys and Questionnaires, Social Support, Grandparents psychology, Exercise psychology, Intergenerational Relations
- Abstract
Background: Research suggests there is considerable opportunity to improve children's movement behaviors while they are being cared for by their grandparents. An understanding of the extent to which grandparent practices facilitate children's engagement in physical activity is critical to the development of health interventions targeting grandparent caregivers. This study examined the activity-related beliefs and practices of grandparents and their association with grandchildren's engagement in various movement behaviors while in grandparental care., Methods: Australian grandparents (N = 1190; 60% women) who provided regular care to a grandchild aged 3-14 years were recruited via a web panel provider to complete an online survey. The survey assessed grandparents' physical activity-related beliefs (eg, perceived importance) and practices (eg, support and social control) and their grandchildren's engagement in physical activity (unstructured, structured, and outdoor play) and screen-based activities while in grandparental care., Results: The importance of grandchildren's physical activity was rated highly by grandparents. Grandparents' support for their grandchildren's physical activity was positively associated with their grandchildren's engagement in structured physical activity, unstructured physical activity, and outdoor play. Negative social control was associated with greater engagement in screen-based activities. Other correlates of grandchildren's physical activity and screen-based activities included grandparents' own engagement in these activities., Conclusions: Findings highlight the importance of reinforcing the beliefs and practices that positively influence children's movement behaviors and addressing those that have unintended consequences. Encouraging grandparents to support their grandchildren's physical activity and discouraging forms of negative social control are likely to be important in efforts to promote physical activity in children.
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- 2024
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24. Concurrent RB1 Loss and BRCA Deficiency Predicts Enhanced Immunologic Response and Long-term Survival in Tubo-ovarian High-grade Serous Carcinoma.
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Saner FAM, Takahashi K, Budden T, Pandey A, Ariyaratne D, Zwimpfer TA, Meagher NS, Fereday S, Twomey L, Pishas KI, Hoang T, Bolithon A, Traficante N, Alsop K, Christie EL, Kang EY, Nelson GS, Ghatage P, Lee CH, Riggan MJ, Alsop J, Beckmann MW, Boros J, Brand AH, Brooks-Wilson A, Carney ME, Coulson P, Courtney-Brooks M, Cushing-Haugen KL, Cybulski C, El-Bahrawy MA, Elishaev E, Erber R, Gayther SA, Gentry-Maharaj A, Gilks CB, Harnett PR, Harris HR, Hartmann A, Hein A, Hendley J, Hernandez BY, Jakubowska A, Jimenez-Linan M, Jones ME, Kaufmann SH, Kennedy CJ, Kluz T, Koziak JM, Kristjansdottir B, Le ND, Lener M, Lester J, Lubiński J, Mateoiu C, Orsulic S, Ruebner M, Schoemaker MJ, Shah M, Sharma R, Sherman ME, Shvetsov YB, Soong TR, Steed H, Sukumvanich P, Talhouk A, Taylor SE, Vierkant RA, Wang C, Widschwendter M, Wilkens LR, Winham SJ, Anglesio MS, Berchuck A, Brenton JD, Campbell I, Cook LS, Doherty JA, Fasching PA, Fortner RT, Goodman MT, Gronwald J, Huntsman DG, Karlan BY, Kelemen LE, Menon U, Modugno F, Pharoah PDP, Schildkraut JM, Sundfeldt K, Swerdlow AJ, Goode EL, DeFazio A, Köbel M, Ramus SJ, Bowtell DDL, and Garsed DW
- Subjects
- Humans, Female, Prognosis, Ubiquitin-Protein Ligases genetics, Neoplasm Grading, Lymphocytes, Tumor-Infiltrating immunology, Lymphocytes, Tumor-Infiltrating metabolism, Middle Aged, Germ-Line Mutation, Gene Expression Regulation, Neoplastic, Aged, Biomarkers, Tumor genetics, CD8-Positive T-Lymphocytes immunology, CD8-Positive T-Lymphocytes metabolism, Ovarian Neoplasms genetics, Ovarian Neoplasms mortality, Ovarian Neoplasms immunology, Ovarian Neoplasms pathology, BRCA2 Protein genetics, BRCA2 Protein deficiency, BRCA1 Protein genetics, BRCA1 Protein deficiency, Cystadenocarcinoma, Serous genetics, Cystadenocarcinoma, Serous pathology, Cystadenocarcinoma, Serous mortality, Cystadenocarcinoma, Serous immunology, Retinoblastoma Binding Proteins genetics
- Abstract
Purpose: The purpose of this study was to evaluate RB1 expression and survival across ovarian carcinoma histotypes and how co-occurrence of BRCA1 or BRCA2 (BRCA) alterations and RB1 loss influences survival in tubo-ovarian high-grade serous carcinoma (HGSC)., Experimental Design: RB1 protein expression was classified by immunohistochemistry in ovarian carcinomas of 7,436 patients from the Ovarian Tumor Tissue Analysis consortium. We examined RB1 expression and germline BRCA status in a subset of 1,134 HGSC, and related genotype to overall survival (OS), tumor-infiltrating CD8+ lymphocytes, and transcriptomic subtypes. Using CRISPR-Cas9, we deleted RB1 in HGSC cells with and without BRCA1 alterations to model co-loss with treatment response. We performed whole-genome and transcriptome data analyses on 126 patients with primary HGSC to characterize tumors with concurrent BRCA deficiency and RB1 loss., Results: RB1 loss was associated with longer OS in HGSC but with poorer prognosis in endometrioid ovarian carcinoma. Patients with HGSC harboring both RB1 loss and pathogenic germline BRCA variants had superior OS compared with patients with either alteration alone, and their median OS was three times longer than those without pathogenic BRCA variants and retained RB1 expression (9.3 vs. 3.1 years). Enhanced sensitivity to cisplatin and paclitaxel was seen in BRCA1-altered cells with RB1 knockout. Combined RB1 loss and BRCA deficiency correlated with transcriptional markers of enhanced IFN response, cell-cycle deregulation, and reduced epithelial-mesenchymal transition. CD8+ lymphocytes were most prevalent in BRCA-deficient HGSC with co-loss of RB1., Conclusions: Co-occurrence of RB1 loss and BRCA deficiency was associated with exceptionally long survival in patients with HGSC, potentially due to better treatment response and immune stimulation., (©2024 The Authors; Published by the American Association for Cancer Research.)
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- 2024
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25. Barriers and enablers to promoting grandchildren's physical activity and reducing screen time: a qualitative study with Australian grandparents.
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Budden T, Coall DA, Jackson B, Christian H, Nathan A, and Jongenelis MI
- Subjects
- Humans, Child, Female, Male, Aged, Adolescent, Child, Preschool, Australia, Middle Aged, Intergenerational Relations, Exercise psychology, Interviews as Topic, Motor Activity, Adult, Grandparents psychology, Focus Groups, Qualitative Research, Screen Time, Health Promotion methods
- Abstract
Background: With an increasing number of grandparents providing care to their grandchildren, calls have been made for these caregivers to be considered important stakeholders in encouraging children's engagement in health-promoting behaviors, such as physical activity. Understanding the perspectives of grandparents who provide care is crucial to informing efforts that aim to increase children's physical activity, yet little is understood about their perceptions of specific barriers and enablers to promoting children's physical activity and reducing screen time. The present study sought to explore these perceptions., Methods: Semi-structured focus groups and individual interviews were conducted with grandparents who reported providing care to a grandchild aged 3 to 14 years. A total of 20 grandparents were sampled (mean age = 67.8 years). Data were subjected to reflexive thematic analysis., Results: Key reported barriers to physical activity included (i) the effort (physical and logistical) and financial cost associated with organizing physical activities, (ii) grandparents' age and mobility issues (e.g., due to injury or illness), (iii) caring for children of different ages (e.g., older children having different physical activity interests than younger children), and (iv) a local environment that is not conducive to physical activity (e.g., lack of appropriate facilities). Barriers to reducing screen time included (i) parents sending children to care with electronic devices and (ii) children's fear of missing out on social connection that occurs electronically. Strategies and enablers of physical activity included (i) integrating activity into caregiving routines (e.g., walking the dog), (ii) involving grandchildren in decision making (e.g., asking them in which physical activities they wish to engage), (iii) encouraging grandchildren to engage in activity with other children, and (iv) creating a physical and social environment that supports activity (e.g., owning play equipment). A common strategy for reducing screen time was the creation of a home environment that is not conducive to this activity (e.g., removing electronic devices from view)., Conclusions: Findings suggest that grandparents may benefit from resources that assist them to identify activities that are inexpensive and require minimal effort to organize. Activities that account for grandparents' age and health status, as well as any environmental barriers, are likely to be well-received., (© 2024. The Author(s).)
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- 2024
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26. Australian children's physical activity and screen time while in grandparental care.
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Jongenelis MI, Budden T, Jackson B, Christian H, Nathan A, Coall D, and Glassenbury E
- Subjects
- Humans, Child, Female, Male, Australia, Adolescent, Child, Preschool, Middle Aged, Aged, Surveys and Questionnaires, Play and Playthings, Child Behavior psychology, Adult, Screen Time, Exercise, Grandparents psychology, Intergenerational Relations
- Abstract
Objective: The objective of this study was to explore Australian children's engagement in physical activity and screen time while being cared for by their grandparents., Method: Grandparents (N = 1,190) providing ≥3 hours of weekly care to a grandchild aged 3-14 years completed an online survey assessing their grandchildren's movement behaviours while in their care. Descriptive statistics were computed for frequency of engagement in unstructured and structured physical activities, minutes spent playing outdoors, and minutes spent engaged in screen time. Regression analyses were conducted to assess socio-demographic predictors of movement behaviours., Results: Playing in the yard was the most common form of physical activity in which grandchildren reportedly participated (77% 'usually' or 'always'), followed by playing with toys/equipment (62%). Few (14-36%) frequently engaged in active transport. Children spent an average of 181 minutes per week engaged in screen-based activities., Conclusions: There is an opportunity to improve children's movement behaviours while in grandparental care. Communicating to grandparents their importance in supporting an active lifestyle is warranted., Implications for Public Health: Findings highlight the importance of creating environments that facilitate play-based, outdoor activities. Ensuring children have access to play equipment while in the care of grandparents and improving access to and quality of neighbourhood parks may assist with activity promotion., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
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27. Understanding parent perspectives on engagement with online youth-focused mental health programs.
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Muller JL, Tomlin L, March S, Jackson B, Budden T, Law KH, and Dimmock JA
- Subjects
- Child, Humans, Adolescent, Australia, Health Promotion, Motivation, Mental Health, Parents psychology
- Abstract
Objective: Online youth-focused health programs often include parent modules-that equip parents with skills to assist their child in improving their health-alongside youth-specific content. BRAVE Self-Help, an evidence-based program designed for children and teenagers with early signs of anxiety, is a popular Australian program that includes six parent modules. Despite its popularity and proven efficacy, BRAVE Self-Help shares the same challenge as many online self-help programs-that of low participant engagement. Using parents registered in BRAVE Self-Help as 'information rich' participants, we explored (a) factors that influenced parent engagement in online health programs, and (b) their recommendations for enhancing parent engagement., Design and Outcome Measure: We conducted semi-structured interviews with 14 parents registered in BRAVE Self-Help. Data were analysed through reflexive thematic analysis., Results: Social-, family- and program-related factors drove parents' program engagement and recommendations. Social sub-themes related to the benefits of professional and community support in promoting more engagement. Family sub-themes included difficulties with program engagement due to competing priorities, perceptions that condition severity influenced engagement, and feelings that previously-acquired health knowledge reduced motivation to engage. Program sub-themes included perceived usefulness and ease-of-use., Conclusion: Program designers could target support systems, include flexible delivery options, and use iterative design processes to enhance parent engagement.
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- 2024
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28. Parents on the Concept of Physical Literacy: What Do They Know, What Do They Do, and What Do They Want?
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Simpson A, Jackson B, Thornton AL, Rosenberg M, Ward B, Roberts P, Derbyshire A, and Budden T
- Subjects
- Child, Humans, Child, Preschool, Australia, Exercise, Schools, Literacy, Parents
- Abstract
Physical literacy development in early childhood, viewed by many as the foundation for lifelong physical activity engagement, is significantly influenced by parents. Our aim was to explore parents' understanding of physical literacy and gain insight into their perspectives on physical literacy promotion. We recruited 18 parents of children between 5 and 8 years old in Australia. Using semistructured interviews and thematic analysis, we identified several key issues regarding parents' understanding and implementation of physical literacy. Parents expressed interest in improving their implementation of physical literacy practices and had (often unintentionally) provided support for physical literacy subcomponents in the past. However, they described difficulties prioritizing physical literacy above other parental demands and expressed conflicting perceptions regarding where the responsibility should lie for developing their child's physical literacy (e.g., at home or at school). To ensure that the physical literacy "message" reaches parents, we encourage physical literacy promoters to consider the target (e.g., responsibility, priorities, and awareness) of their promotional strategies. Further investigation into the influence of sociocultural and economic factors on parents' understanding and application of physical literacy is warranted.
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- 2024
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29. Concurrent RB1 loss and BRCA -deficiency predicts enhanced immunological response and long-term survival in tubo-ovarian high-grade serous carcinoma.
- Author
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Saner FAM, Takahashi K, Budden T, Pandey A, Ariyaratne D, Zwimpfer TA, Meagher NS, Fereday S, Twomey L, Pishas KI, Hoang T, Bolithon A, Traficante N, Alsop K, Christie EL, Kang EY, Nelson GS, Ghatage P, Lee CH, Riggan MJ, Alsop J, Beckmann MW, Boros J, Brand AH, Brooks-Wilson A, Carney ME, Coulson P, Courtney-Brooks M, Cushing-Haugen KL, Cybulski C, El-Bahrawy MA, Elishaev E, Erber R, Gayther SA, Gentry-Maharaj A, Blake Gilks C, Harnett PR, Harris HR, Hartmann A, Hein A, Hendley J, Hernandez BY, Jakubowska A, Jimenez-Linan M, Jones ME, Kaufmann SH, Kennedy CJ, Kluz T, Koziak JM, Kristjansdottir B, Le ND, Lener M, Lester J, Lubiński J, Mateoiu C, Orsulic S, Ruebner M, Schoemaker MJ, Shah M, Sharma R, Sherman ME, Shvetsov YB, Singh N, Rinda Soong T, Steed H, Sukumvanich P, Talhouk A, Taylor SE, Vierkant RA, Wang C, Widschwendter M, Wilkens LR, Winham SJ, Anglesio MS, Berchuck A, Brenton JD, Campbell I, Cook LS, Doherty JA, Fasching PA, Fortner RT, Goodman MT, Gronwald J, Huntsman DG, Karlan BY, Kelemen LE, Menon U, Modugno F, Pharoah PDP, Schildkraut JM, Sundfeldt K, Swerdlow AJ, Goode EL, DeFazio A, Köbel M, Ramus SJ, Bowtell DDL, and Garsed DW
- Abstract
Background: Somatic loss of the tumour suppressor RB1 is a common event in tubo-ovarian high-grade serous carcinoma (HGSC), which frequently co-occurs with alterations in homologous recombination DNA repair genes including BRCA1 and BRCA2 ( BRCA ). We examined whether tumour expression of RB1 was associated with survival across ovarian cancer histotypes (HGSC, endometrioid (ENOC), clear cell (CCOC), mucinous (MOC), low-grade serous carcinoma (LGSC)), and how co-occurrence of germline BRCA pathogenic variants and RB1 loss influences long-term survival in a large series of HGSC., Patients and Methods: RB1 protein expression patterns were classified by immunohistochemistry in epithelial ovarian carcinomas of 7436 patients from 20 studies participating in the Ovarian Tumor Tissue Analysis consortium and assessed for associations with overall survival (OS), accounting for patient age at diagnosis and FIGO stage. We examined RB1 expression and germline BRCA status in a subset of 1134 HGSC, and related genotype to survival, tumour infiltrating CD8+ lymphocyte counts and transcriptomic subtypes. Using CRISPR-Cas9, we deleted RB1 in HGSC cell lines with and without BRCA1 mutations to model co-loss with treatment response. We also performed genomic analyses on 126 primary HGSC to explore the molecular characteristics of concurrent homologous recombination deficiency and RB1 loss., Results: RB1 protein loss was most frequent in HGSC (16.4%) and was highly correlated with RB1 mRNA expression. RB1 loss was associated with longer OS in HGSC (hazard ratio [HR] 0.74, 95% confidence interval [CI] 0.66-0.83, P = 6.8 ×10
-7 ), but with poorer prognosis in ENOC (HR 2.17, 95% CI 1.17-4.03, P = 0.0140). Germline BRCA mutations and RB1 loss co-occurred in HGSC ( P < 0.0001). Patients with both RB1 loss and germline BRCA mutations had a superior OS (HR 0.38, 95% CI 0.25-0.58, P = 5.2 ×10-6 ) compared to patients with either alteration alone, and their median OS was three times longer than non-carriers whose tumours retained RB1 expression (9.3 years vs. 3.1 years). Enhanced sensitivity to cisplatin ( P < 0.01) and paclitaxel ( P < 0.05) was seen in BRCA1 mutated cell lines with RB1 knockout. Among 126 patients with whole-genome and transcriptome sequence data, combined RB1 loss and genomic evidence of homologous recombination deficiency was correlated with transcriptional markers of enhanced interferon response, cell cycle deregulation, and reduced epithelial-mesenchymal transition in primary HGSC. CD8+ lymphocytes were most prevalent in BRCA -deficient HGSC with co-loss of RB1 ., Conclusions: Co-occurrence of RB1 loss and BRCA mutation was associated with exceptionally long survival in patients with HGSC, potentially due to better treatment response and immune stimulation., Competing Interests: COMPETING INTERESTS DDLB is an Exo Therapeutics advisor and has received research grant funding from AstraZeneca, Genentech-Roche and BeiGene for unrelated work. SF, NT, KA, and ADeF received grant funding from AstraZeneca for unrelated work. AGM and UM report funded research collaborations for unrelated work with industry: Intelligent Lab on Fiber, RNA Guardian, Micronoma and Mercy BioAnalytics. UM had stock ownership (2011–2021) awarded by University College London (UCL) in Abcodia, which held the licence for the Risk of Ovarian Cancer Algorithm (ROCA). UM reports research collaboration contracts with Cambridge University and QIMR Berghofer Medical Research Institute. UM holds patent number EP10178345.4 for Breast Cancer Diagnostics. UM is a member of Tina’s Wish Scientific Advisory Board (USA) and Research Advisory Panel, Yorkshire Cancer Research (UK). The remaining authors declared no conflicts of interest.- Published
- 2023
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30. The Stride program: Feasibility and pre-to-post program change of an exercise service for university students experiencing mental distress.
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Jeftic I, Furzer B, Dimmock JA, Wright K, Budden T, Boyd C, Simpson A, Rosenberg M, Sabiston CM, deJonge M, and Jackson B
- Subjects
- Adult, Humans, Young Adult, Exercise, Feasibility Studies, Students, Universities, Mental Disorders, Quality of Life
- Abstract
Rates of mental illness are disproportionately high for young adult and higher education (e.g., university student) populations. As such, universities and tertiary institutions often devote significant efforts to services and programs that support and treat mental illness and/or mental distress. However, within that portfolio of treatment approaches, structured exercise has been relatively underutilised and greater research attention is needed to develop this evidence base. The Stride program is a structured 12-week exercise service for students experiencing mental distress. We aimed to explore the feasibility of the program and assess pre- and post-program change, through assessments of student health, lifestyle, and wellbeing outcomes. Drawing from feasibility and effectiveness-implementation hybrid design literatures, we conducted a non-randomised feasibility trial of the Stride program. Participants were recruited from the Stride program (N = 114, M
age = 24.21 years). Feasibility results indicated the program was perceived as acceptable and that participants reported positive perceptions of program components, personnel, and sessions. Participants' pre-to-post program change in depressive symptomatology, physical activity levels, mental health-related quality of life, and various behavioural outcomes were found to be desirable. Our results provide support for the feasibility of the Stride program, and more broadly for the delivery and potential effectiveness of structured exercise programs to support university students experiencing mental distress., Competing Interests: Declaration of competing interest As an author team, we declare one conflict of interest. Some of the authors of this manuscript were also involved in the design of the Stride program. However, this feasibility trial was conducted in adherence to CONSORT guidelines for feasibility trials, and we are highly confident that these stringent guidelines (e.g., reporting measures, providing access to data) will have ensured that any conflict of interest could not have interfered with the integrity of the study or its data., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)- Published
- 2023
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31. The Influence of Grandparents on Children's Dietary Health: A Narrative Review.
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Jongenelis MI and Budden T
- Subjects
- Child, Humans, Diet, Feeding Behavior, Meals, Intergenerational Relations, Grandparents
- Abstract
Purpose of Review: To examine and synthesise recent evidence on the role of grandparents in shaping children's dietary health., Recent Findings: The influence of grandparents on children's dietary health was evident across studies. Grandparents frequently provide their grandchildren with meals and snacks, and engage in many of the same feeding practices used by parents. Although grandparents report providing their grandchildren with healthy foods, the provision of treat foods high in sugar or fat was a common finding. This provision led to family conflict, with the indulgent behaviours of grandparents seen by parents as a barrier to healthy eating. Grandparents are exerting significant influence on child dietary health. Efforts are needed to ensure these care providers are considered key stakeholders in the promotion of healthy eating and are targeted in policies and programs addressing children's diets. Research that determines how to best support grandparents to foster healthy behaviours in children is critical., (© 2023. The Author(s).)
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- 2023
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32. 'It's been a lifelong thing for me': parents' experiences of facilitating a healthy lifestyle for their children with severe obesity.
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Saunders LA, Jackson B, Gibson LY, Doust J, Dimmock JA, Davis EA, Price L, and Budden T
- Subjects
- Adolescent, Child, Humans, Adult, Parents, Emotions, Healthy Lifestyle, Obesity, Morbid therapy, Pediatric Obesity prevention & control
- Abstract
Objective: For parents and guardians, assisting children/adolescents with severe obesity to lose weight is often a key objective but a complex and difficult challenge. Our aim in this study was to explore parents' (and guardians') perspectives on the challenges they have faced in assisting their children/adolescents with severe obesity to lead a healthy lifestyle., Methods: Thirteen parents/guardians were interviewed from a pool of families who had been referred but did not engage between 2016 and 2018 (N = 103), with the Perth Children's Hospital Healthy Weight Service, a clinical obesity program for children/adolescents (parent age M = 43.2 years, children age M = 10.3 years). Using semi-structured interviews and thematic analysis, we identified 3 broad themes., Results: Parental weight-related factors reflected parents' own lifelong obesity narrative and its effect on their own and their families' ability to live a healthy lifestyle. Perceived inevitability of obesity in their child reflected parents' feelings that the obesity weight status of their children/adolescent was a persistent and overwhelming problem that felt 'out of control'. Lastly, parents reported challenges getting medical help stemming from co-morbid medical diagnosis in their child/adolescent, and difficulties with medical professionals., Conclusion: This study demonstrates that parents face challenges in supporting healthy lifestyle for children/adolescents with severe obesity due to parents own internal weight biases and their negative experiences within the healthcare system when seeking help., (© 2023. The Author(s).)
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- 2023
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33. Support needs and experiences of young people living in families with mental illness.
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Budden T, Hafizuddin A, Dimmock JA, Law KH, Furzer BJ, and Jackson B
- Subjects
- Male, Child, Adolescent, Female, Humans, Australia, Family psychology, Qualitative Research, Social Support, Mental Disorders psychology
- Abstract
Introduction: Children and adolescents living in families affected by mental illness are at elevated risk of developing mental health problems. A range of interventions have been designed to help these young people; however, the effectiveness of these programs is, in some cases, mixed. Our aim was to understand in detail the support needs and experiences of a group of Australian children and adolescents living in families with mental illness., Methods: Our study is a qualitative in nature. In 2020-2021, we interviewed 25 Australian young people (M
age = 13.60, SD = 2.26, 20 females and 5 males) living with family members affected by mental illness to understand their (the young people's) experiences, and to identify the types of support that these young people considered important or effective. We conducted reflexive thematic analyses of interview data, underpinned by interpretivist assumptions., Results: We identified seven themes within two higher-order categories reflecting our aims to understand (1) lived experiences within families affected by mental illness (i.e., increased responsibilities, missing out, and stigmatization), and (2) support experiences, needs, and preferences (i.e., respite, shared experiences with like-minded others, education, and flexibility)., Conclusions: Our findings hold substantial practical value by informing services, interventions, and conversations that better support young people living in families affected by mental illness., (© 2023 2023 The Authors. Journal of Adolescence published by Wiley Periodicals LLC on behalf of Foundation for Professionals in Services to Adolescents.)- Published
- 2023
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34. Structured exercise programs for higher education students experiencing mental health challenges: background, significance, and implementation.
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Jeftic I, Furzer BJ, Dimmock JA, Wright K, Boyd C, Budden T, Rosenberg M, Kramer B, Buist B, Fitzpatrick I, Sabiston C, de Jonge M, and Jackson B
- Subjects
- Young Adult, Humans, Students psychology, Schools, Exercise Therapy, Mental Health, Mental Disorders therapy
- Abstract
The incidence of mental illness is greatest among young adults, and those enrolled in higher education may be particularly vulnerable compared to the general young adult population. Many higher education institutions employ student support staff tasked with implementing strategies to improve student wellbeing and mental illness. However, these strategies tend to be focused on clinical therapies and pharmacological interventions with limited lifestyle approaches. Exercise is an effective method for addressing mental illness and promoting wellbeing, yet widespread provision of structured exercise services to support treatment options for students with mental health challenges has not been fully realized. In an effort to guide exercise strategies for student mental health, we synthesize considerations for developing and delivering exercise programs in higher education settings. We draw directly from the evidence base on existing exercise programs in higher education; and the broader behavior change, exercise adherence, health psychology, implementation science, and exercise prescription literatures. Our broad considerations cover issues regarding program engagement and behavior change, exercise 'dose' and prescription, integration with other on-campus services, and robust research and evaluation. These considerations may provide impetus for widespread program development and implementation, as well as informing research focused on protecting and improving student mental health., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jeftic, Furzer, Dimmock, Wright, Boyd, Budden, Rosenberg, Kramer, Buist, Fitzpatrick, Sabiston, de Jonge and Jackson.)
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- 2023
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35. MAN v FAT Soccer: Feasibility Study and Preliminary Efficacy of a Sport-Based Weight-Loss Intervention for Overweight and Obese Men in Australia.
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Budden T, Dimmock JA, Rosenberg M, Beauchamp MR, Fitzpatrick I, and Jackson B
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- Australia, Feasibility Studies, Humans, Male, Obesity therapy, Weight Loss, Overweight psychology, Overweight therapy, Soccer
- Abstract
MAN v FAT Soccer is a sport-based weight-loss program for overweight and obese men that originated in the United Kingdom (i.e., as MAN v FAT Football) and appears to successfully engage men with weight loss. We sought to explore whether the program would work in an Australian context by (a) establishing a foundation for the implementation of the program on a larger scale and (b) determining how large-scale implementation is most feasible. We conducted a nonrandomized, single intervention group feasibility trial of MAN v FAT Soccer in Australia with 418 male participants with a body mass index greater than 27.50 kg/m2. Results indicate that the program is acceptable, with participants reporting positive perceptions of the various components of the program and a high proportion reporting intentions to recommend the program to others (95.9%). Furthermore, preliminary effectiveness results indicate positive changes in weight (4.6% reduction) and physical activity (88.5% increase) and improvements in psychological outcomes such as depression (17.6% decrease), stress (19.0% decrease), and body appreciation (19.1% increase). Our findings provide general support for the feasibility of MAN v FAT Soccer and the notion that leveraging competition and masculinity may help drive men's health behavior change.
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- 2022
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36. Perceptions of a family-based lifestyle intervention for children with overweight and obesity: a qualitative study on sustainability, self-regulation, and program optimization.
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Putter KC, Jackson B, Thornton AL, Willis CE, Goh KMB, Beauchamp MR, Benjanuvatra N, Dimmock JA, and Budden T
- Subjects
- Child, Exercise physiology, Humans, Life Style, Obesity therapy, Overweight psychology, Overweight therapy, Pediatric Obesity prevention & control, Pediatric Obesity psychology, Self-Control
- Abstract
Background: Family-based lifestyle interventions (FBLIs) are an important method for treating childhood weight problems. Despite being recognized as an effective intervention method, the optimal structure of these interventions for children's overweight and obesity has yet to be determined. Our aim was to better understand participants' (a) implementation of behaviour strategies and long-term outcomes, (b) perceptions regarding the optimal structure of FBLIs, and (c) insights into psychological concepts that may explain the success of these programs., Methods: Purposive sampling was used to recruit participants. We conducted focus groups as well as one-to-one interviews with parents (n = 53) and children (n = 50; aged 7-13, M = 9.4 yr, SD = 3.1) three months following their involvement in a 10-week, multi-component, FBLI involving education and activities relating to healthy nutrition, physical activity, and behavior modification. Using an interpretivist approach, a qualitative study design was employed to examine participant experiences., Results: We identified three higher-order categories: (a) participants' program experiences and perceptions (b) lifestyle changes post-program, and (c) recommendations for optimizing family-based programs. Themes identified within these categories included (a) support and structure & content, (b) diet and physical activity, and (c) in-program recommendations and post-program recommendations., Conclusions: We identified several challenges that can impair lasting behavior change (e.g., physical activity participation) following involvement in a FBLI. On optimizing these programs, participants emphasized fun, interactive content, interpersonal support, appropriate educational content, and behavior change techniques. Concepts rooted in motivational theory could help address calls for greater theoretical and mechanistic insight in FBLIs. Findings may support research advancement and assist health professionals to more consistently realize the potential of these interventions., (© 2022. The Author(s).)
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- 2022
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37. Molecular characterization of fast-growing melanomas.
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Gaudy-Marqueste C, Macagno N, Loundou A, Pellegrino E, Ouafik L, Budden T, Mundra P, Gremel G, Akhras V, Lin L, Cook M, Kumar R, Grob JJ, Nagore E, Marais R, and Virós A
- Subjects
- Humans, Mutation, Prognosis, Prospective Studies, Melanoma pathology, Skin Neoplasms pathology
- Abstract
Background: The rate of growth of primary melanoma is a robust predictor of aggressiveness, but the mutational profile of fast-growing melanomas (FGMM) and the potential to stratify patients at high risk of death has not been comprehensively studied., Objective: To investigate the epidemiologic, clinical, and mutational profile of primary cutaneous melanomas with a thickness ≥ 1 mm, stratified by rate of growth., Methods: Observational prospective study. Deep-targeted sequencing of 40 melanoma driver genes on formalin fixed, paraffin-embedded primary melanoma samples. Comparison of FGMM (rate of growth > 0.5 mm/month) and nonFGMM (rate of growth ≤ 0.5 mm/month)., Results: Two hundred patients were enrolled, among wom 70 had FGMM. The relapse-free survival was lower in the FGMM group (P = .014). FGMM had a higher number of predicted deleterious mutations within the 40 genes than nonFGMM (P = .033). Ulceration (P = .032), thickness (P = .006), lower sun exposure (P = .049), and fibroblast growth factor receptor 2 (FGFR2) mutations (P = .037) were significantly associated with fast growth., Limitations: Single-center study, cohort size, potential memory bias, number of investigated genes., Conclusion: Fast growth is linked to specific tumor biology and environmental factors. Ulceration, thickness, and FGFR2 mutations are associated with fast growth. Screening for FGFR2 mutations might provide an additional tool to better identify FGMM, which are probably good candidates for adjuvant therapies., Competing Interests: Conflicts of interest None disclosed., (Copyright © 2021 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.)
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- 2022
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38. Female Immunity Protects from Cutaneous Squamous Cell Carcinoma.
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Budden T, Gaudy-Marqueste C, Craig S, Hu Y, Earnshaw CH, Gurung S, Ra A, Akhras V, Shenjere P, Green R, Jamieson L, Lear J, Motta L, Caulín C, Oudit D, Furney SJ, and Virós A
- Subjects
- Animals, CD4-Positive T-Lymphocytes immunology, CD8-Positive T-Lymphocytes immunology, Carcinogens pharmacology, Carcinoma, Squamous Cell pathology, Carcinoma, Squamous Cell prevention & control, Cell Proliferation drug effects, Female, Humans, Male, Mice, Mitosis drug effects, Skin Neoplasms pathology, Skin Neoplasms prevention & control, Carcinoma, Squamous Cell immunology, Disease Susceptibility immunology, Sex Characteristics, Skin Neoplasms immunology
- Abstract
Purpose: Cancer susceptibility and mortality are higher in males, and the mutational and transcriptomic landscape of cancer differs by sex. The current assumption is that men are at higher risk of epithelial cancers as they expose more to carcinogens and accumulate more damage than women. We present data showing women present with less aggressive primary cutaneous squamous cell carcinoma (cSCC) and early strong immune activation., Experimental Design: We explored clinical and molecular sexual disparity in immunocompetent and immunosuppressed patients with primary cSCC ( N = 738, N = 160), advanced-stage cSCC ( N = 63, N = 20) and FVB/N mice exposed to equal doses of DMBA, as well as in human keratinocytes by whole-exome, bulk, and single-cell RNA sequencing., Results: We show cSCC is more aggressive in men, and immunocompetent women develop mild cSCC, later in life. To test whether sex drives disparity, we exposed male and female mice to equal doses of carcinogen, and found males present with more aggressive, metastatic cSCC than females. Critically, females activate cancer immune-related expression pathways and CD4 and CD8 T-cell infiltration independently of mutations, a response that is absent in prednisolone-treated animals. In contrast, males increase the rate of mitosis and proliferation in response to carcinogen. Women's skin and keratinocytes also activate immune-cancer fighting pathways and immune cells at UV radiation-damaged sites. Critically, a compromised immune system leads to high-risk, aggressive cSCC specifically in women., Conclusions: This work shows the immune response is sex biased in cSCC and highlights female immunity offers greater protection than male immunity., (©2021 American Association for Cancer Research.)
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- 2021
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39. Ultraviolet light-induced collagen degradation inhibits melanoma invasion.
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Budden T, Gaudy-Marqueste C, Porter A, Kay E, Gurung S, Earnshaw CH, Roeck K, Craig S, Traves V, Krutmann J, Muller P, Motta L, Zanivan S, Malliri A, Furney SJ, Nagore E, and Virós A
- Subjects
- Collagen Type I genetics, Collagen Type I metabolism, Collagen Type I, alpha 1 Chain, Enzyme-Linked Immunosorbent Assay, Fibroblasts metabolism, Fibroblasts radiation effects, Humans, Lentivirus genetics, Mass Spectrometry, Matrix Metalloproteinase 1 genetics, Matrix Metalloproteinase 1 metabolism, Microscopy, Atomic Force, Collagen metabolism, Melanoma metabolism, Melanoma therapy, Ultraviolet Rays
- Abstract
Ultraviolet radiation (UVR) damages the dermis and fibroblasts; and increases melanoma incidence. Fibroblasts and their matrix contribute to cancer, so we studied how UVR modifies dermal fibroblast function, the extracellular matrix (ECM) and melanoma invasion. We confirmed UVR-damaged fibroblasts persistently upregulate collagen-cleaving matrix metalloprotein-1 (MMP1) expression, reducing local collagen (COL1A1), and COL1A1 degradation by MMP1 decreased melanoma invasion. Conversely, inhibiting ECM degradation and MMP1 expression restored melanoma invasion. Primary cutaneous melanomas of aged humans show more cancer cells invade as single cells at the invasive front of melanomas expressing and depositing more collagen, and collagen and single melanoma cell invasion are robust predictors of poor melanoma-specific survival. Thus, primary melanomas arising over collagen-degraded skin are less invasive, and reduced invasion improves survival. However, melanoma-associated fibroblasts can restore invasion by increasing collagen synthesis. Finally, high COL1A1 gene expression is a biomarker of poor outcome across a range of primary cancers.
- Published
- 2021
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40. A pilot study of cystic fibrosis exacerbation response phenotypes reveals contrasting serum and sputum iron trends.
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Gifford AH, Polineni D, He J, D'Amico JL, Dorman DB, Williams MA, Nymon AB, Balwan A, Budden T, and Zuckerman JB
- Subjects
- Adult, Biomarkers blood, Female, Humans, Male, Middle Aged, Pilot Projects, Prospective Studies, Symptom Flare Up, Treatment Outcome, Young Adult, Anti-Bacterial Agents therapeutic use, Cystic Fibrosis drug therapy, Iron blood, Sputum chemistry
- Abstract
The cystic fibrosis (CF) community seeks to explain heterogeneous outcomes of pulmonary exacerbation (PEX) treatment. Serum and sputum inflammatory mediators may identify people with CF (PwCF) at risk for suboptimal responses. However, lack of an established association between response phenotypes and these mediators limits clinical application. In this pilot study, we prospectively characterized treatment response phenotypes by assessing health-related quality-of-life (HRQoL) during PEX. We also measured lung function and iron-related biochemical parameters in serum and sputum. We classified subjects as sustained symptom-responders (SRs) or non-sustained symptom-responders (NSRs) based on the absence or presence, respectively, of worsened symptom scores after initial improvement. We used linear mixed models (LMMs) to determine whether trends in lung function, hematologic, serum, and sputum indices of inflammation differed between response cohorts. In 20 PwCF, we identified 10 SRs and 10 NSRs with no significant differences in lung function at PEX onset and treatment durations. SRs had better model-predicted trends in lung function than NSRs during PEX. Non-linear trends in serum and sputum iron levels significantly differed between SRs and NSRs. In adults with cystic fibrosis, PEX treatment response phenotypes may be correlated with distinctive trends in serum and sputum iron concentrations.
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- 2021
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41. Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).
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Talhouk A, George J, Wang C, Budden T, Tan TZ, Chiu DS, Kommoss S, Leong HS, Chen S, Intermaggio MP, Gilks B, Nazeran TM, Volchek M, Elatre W, Bentley RC, Senz J, Lum A, Chow V, Sudderuddin H, Mackenzie R, Leong SCY, Liu G, Johnson D, Chen B, Group A, Alsop J, Banerjee SN, Behrens S, Bodelon C, Brand AH, Brinton L, Carney ME, Chiew YE, Cushing-Haugen KL, Cybulski C, Ennis D, Fereday S, Fortner RT, García-Donas J, Gentry-Maharaj A, Glasspool R, Goranova T, Greene CS, Haluska P, Harris HR, Hendley J, Hernandez BY, Herpel E, Jimenez-Linan M, Karpinskyj C, Kaufmann SH, Keeney GL, Kennedy CJ, Köbel M, Koziak JM, Larson MC, Lester J, Lewsley LA, Lissowska J, Lubiński J, Luk H, Macintyre G, Mahner S, McNeish IA, Menkiszak J, Nevins N, Osorio A, Oszurek O, Palacios J, Hinsley S, Pearce CL, Pike MC, Piskorz AM, Ray-Coquard I, Rhenius V, Rodriguez-Antona C, Sharma R, Sherman ME, De Silva D, Singh N, Sinn P, Slamon D, Song H, Steed H, Stronach EA, Thompson PJ, Tołoczko A, Trabert B, Traficante N, Tseng CC, Widschwendter M, Wilkens LR, Winham SJ, Winterhoff B, Beeghly-Fadiel A, Benitez J, Berchuck A, Brenton JD, Brown R, Chang-Claude J, Chenevix-Trench G, deFazio A, Fasching PA, García MJ, Gayther SA, Goodman MT, Gronwald J, Henderson MJ, Karlan BY, Kelemen LE, Menon U, Orsulic S, Pharoah PDP, Wentzensen N, Wu AH, Schildkraut JM, Rossing MA, Konecny GE, Huntsman DG, Huang RY, Goode EL, Ramus SJ, Doherty JA, Bowtell DD, and Anglesio MS
- Subjects
- Aged, Algorithms, Cystadenoma, Serous classification, Cystadenoma, Serous pathology, Female, Gene Expression Regulation, Neoplastic genetics, Humans, Lymphocytes, Tumor-Infiltrating pathology, Middle Aged, Neoplasm Grading, Neoplasm, Residual classification, Neoplasm, Residual genetics, Neoplasm, Residual pathology, Ovarian Neoplasms classification, Ovarian Neoplasms pathology, Cystadenoma, Serous genetics, Neoplasm Proteins genetics, Ovarian Neoplasms genetics, Transcriptome genetics
- Abstract
Purpose: Gene expression-based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features., Experimental Design: Adopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting., Results: Gene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations., Conclusions: We validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications. See related commentary by McMullen et al., p. 5271 ., (©2020 American Association for Cancer Research.)
- Published
- 2020
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42. Overweight and obese men's experiences in a sport-based weight loss intervention for men.
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Budden T, Dimmock JA, Smith B, Beauchamp M, Rosenberg M, and Jackson B
- Abstract
In Western countries, such as Australia and the UK, a significantly greater proportion of men (relative to women) are overweight and obese, yet relatively few weight loss interventions have been developed that sufficiently target men. This lack of male-focused programming may be in part because 'traditional' weight loss programs are unappealing for what is considered a 'hard-to-reach' population. One program that appears to have such appeal for men is the MAN v FAT Football (MVFF) program, based out of the United Kingdom, which is designed for men with a body mass index of (or greater than) 27.5. MVFF encourages men's participation in a community-based weight loss program that incentivizes weight loss through participation in a football league, and since 2016 MVFF has supported the weight loss efforts of several thousand men. Using MVFF as an exemplar, our aim was to derive insight into how men experience a male-only competitive, sport-based weight loss program. We recruited twenty-seven players ( Mage = 41.13 , SD = 9.93), and ten coaches ( Mage = 31.8, SD = 11.55) from program locations throughout the United Kingdom. Using semi-structured interviews and thematic analysis, we identified several appraisal aspects of the program that players and coaches considered important, including the appeal of sport, competition on a level playing field, being part of a team, camaraderie, accountability, men sharing issues with other men, gender-sensitized environment, likeminded and similar men, and perceptions that traditional weight loss programs are tailored towards women. Player experiences (i.e., competence and enjoyment) and functional supports in the program (e.g., player handbook, weight loss coach) were reported to drive outcomes of effective weight loss and program retention. Interventions aiming to target men may be more successful working with rather than against formulations of identity such as masculinities, and this can be achieved by tailoring program content (e.g., messaging), settings (e.g., among men sharing similar characteristics such as body-type or goals), and mode of delivery (e.g., through organized sports, and leveraging competition to drive healthy behaviours)., (© 2020 Elsevier Ltd. All rights reserved.)
- Published
- 2020
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43. Not All Promotion Is Good Promotion: The Pitfalls of Overexaggerated Claims and Controlling Language in Exercise Messaging.
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Dimmock J, Simich D, Budden T, Podlog L, Beauchamp M, and Jackson B
- Abstract
Across 2 studies, the authors explored reactance effects to overexaggerated claims and controlling language in exercise messaging. In Study 1, participants received either a message exaggerating the benefits of an upcoming exercise session or no message. They subsequently undertook a mundane exercise session led by an instructor, which was either need supportive or "realistically controlling." Relative to no-message participants, those who had read the message reported less positive evaluations of the session. These results were observed despite participants in the message condition holding more positive presession expectations, and the effect was apparent even for those who received need-supportive instruction. In Study 2, participants read an advertisement that was written in either autonomy-supportive language or controlling language. Despite reporting comparable expectations, participants who received a controlling-language message reported significantly greater anger and freedom threat-factors commonly linked to contrast effects. These studies highlight the operation of message-driven contrast effects in exercise.
- Published
- 2020
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44. MC1R CpG island regulates MC1R expression and is methylated in a subset of melanoma tumours.
- Author
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Budden T and Bowden NA
- Subjects
- Cell Line, Tumor, Enhancer Elements, Genetic genetics, Humans, RNA, Messenger genetics, RNA, Messenger metabolism, Receptor, Melanocortin, Type 1 metabolism, CpG Islands genetics, Gene Expression Regulation, Neoplastic, Melanoma genetics, Receptor, Melanocortin, Type 1 genetics
- Abstract
Melanocortin 1 receptor (MC1R) is a G protein-coupled receptor expressed in melanocytes where it plays an important role in skin pigmentation and in the UV response, and has implications in melanoma development. Here we show that methylation of a CpG island (CGI) within the MC1R gene can control expression of MC1R in melanoma. This CGI overlaps with a potential enhancer region, and is unmethylated in normal melanocytes but highly methylated in other skin cells, suggesting a melanocyte specific function. Analysis showed that MC1R was the only gene significantly differentially expressed by methylation of this region. Within several data sets, this region is methylated in a subset of melanoma tumours (55%-74% of tumours) and results in reduced MC1R expression and significantly longer overall survival., (© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2019
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45. Autophagy-lysosome pathway alterations and alpha-synuclein up-regulation in the subtype of neuronal ceroid lipofuscinosis, CLN5 disease.
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Adams J, Feuerborn M, Molina JA, Wilden AR, Adhikari B, Budden T, and Lee SY
- Subjects
- Autophagy, Fibroblasts pathology, HeLa Cells, Humans, Lysosomes metabolism, Up-Regulation, Fibroblasts metabolism, Lysosomal Membrane Proteins metabolism, Microtubule-Associated Proteins metabolism, Neuronal Ceroid-Lipofuscinoses metabolism, alpha-Synuclein metabolism
- Abstract
Neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative lysosomal storage disorders. CLN5 deficiency causes a subtype of NCL, referred to as CLN5 disease. CLN5 is a soluble lysosomal protein with an unclear function in the cell. Increased levels of the autophagy marker protein LC3-II have been reported in several subtypes of NCLs. In this report, we examine whether autophagy is altered in CLN5 disease. We found that the basal level of LC3-II was elevated in both CLN5 disease patient fibroblasts and CLN5-deficient HeLa cells. Further analysis using tandem fluorescent mRFP-GFP-LC3 showed the autophagy flux was increased. We found the alpha-synuclein (α-syn) gene SNCA was highly up-regulated in CLN5 disease patient fibroblasts. The aggregated form of α-syn is well known for its role in the pathogenicity of Parkinson's disease. Higher α-syn protein levels confirmed the SNCA up-regulation in both patient cells and CLN5 knockdown HeLa cells. Furthermore, α-syn was localized to the vicinity of lysosomes in CLN5 deficient cells, indicating it may have a lysosome-related function. Intriguingly, knocking down SNCA reversed lysosomal perinuclear clustering caused by CLN5 deficiency. These results suggest α-syn may affect lysosomal clustering in non-neuronal cells, similar to its role in presynaptic vesicles in neurons.
- Published
- 2019
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46. Does the primary site really matter? Profiling mucinous ovarian cancers of uncertain primary origin (MO-CUP) to personalise treatment and inform the design of clinical trials.
- Author
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Meagher NS, Schuster K, Voss A, Budden T, Pang CNI, deFazio A, Ramus SJ, and Friedlander ML
- Subjects
- Adenocarcinoma, Mucinous drug therapy, Biomarkers, Tumor genetics, Class I Phosphatidylinositol 3-Kinases genetics, Clinical Trials as Topic, DNA Mutational Analysis, DNA Topoisomerases, Type II genetics, Female, High-Throughput Nucleotide Sequencing, Humans, Molecular Targeted Therapy, Neoplasms, Unknown Primary drug therapy, Ovarian Neoplasms drug therapy, PTEN Phosphohydrolase genetics, Poly-ADP-Ribose Binding Proteins genetics, Precision Medicine, Proto-Oncogene Proteins B-raf genetics, Proto-Oncogene Proteins c-met, Proto-Oncogene Proteins p21(ras) genetics, Receptor, ErbB-2 genetics, Terminology as Topic, Thymidylate Synthase, Tubulin, Tumor Suppressor Protein p53 genetics, Uncertainty, Adenocarcinoma, Mucinous genetics, Adenocarcinoma, Mucinous metabolism, DNA, Neoplasm analysis, Neoplasms, Unknown Primary genetics, Ovarian Neoplasms genetics, Ovarian Neoplasms secondary
- Abstract
Objective: Advanced stage mucinous ovarian cancers are diagnostically and therapeutically challenging. Histotype specific trials have failed due to low recruitment after excluding non-ovarian primaries. Mucinous ovarian cancers are commonly metastatic from other sites however lack definitive diagnostic markers. We suggest a classification of mucinous ovarian cancers of uncertain primary origin 'MO-CUPs' in clinical trials. This study aims to identify drug targets to guide treatment and future trials., Methods: We analyzed a large de-identified, multi-platform tumor profiling dataset of MO-CUPs enriched for advanced stage and recurrent cases submitted to Caris Life Sciences. Available data included a 45-gene next-generation sequencing (NGS) panel, gene amplification of HER2 and cMET and 18 immunohistochemical (IHC) markers of drug sensitivity/resistance., Results: Mucinous tumors from 333 patients were analyzed, including 38 borderline tumors and 295 invasive cancers. The most common mutations in a subset (n = 128) of invasive cancers were KRAS (60%), TP53 (38%), PIK3CA (13%) and PTEN (9%). Borderline tumors had higher rates of BRAF mutations, and PGP and TOP2A overexpression than invasive cases. KRAS mutant invasive cancers had lower expression of thymidylate synthase (p = 0.01) and higher expression of TUBB3 (p = 0.01) than KRAS wildtype tumors., Conclusions: To our knowledge, this is the largest series profiling mucinous ovarian cancers and almost certainly includes cases of ovarian and non-ovarian origin. Given the difficulty recruiting patients to histotype-specific trials in rare subsets of ovarian cancer, it may be more important to focus on identifying potential treatment targets and to personalise treatment and design clinical trials in MO-CUPS agnostic of primary site to overcome these issues., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2018
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47. Sequential decitabine and carboplatin treatment increases the DNA repair protein XPC, increases apoptosis and decreases proliferation in melanoma.
- Author
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Budden T, van der Westhuizen A, and Bowden NA
- Subjects
- Apoptosis drug effects, Azacitidine administration & dosage, Azacitidine analogs & derivatives, Carboplatin administration & dosage, Cell Line, Tumor, Cell Proliferation drug effects, CpG Islands genetics, DNA Damage drug effects, DNA Repair genetics, Decitabine, Gene Expression Regulation, Neoplastic drug effects, Gene Knockdown Techniques, Humans, Melanoma genetics, Melanoma pathology, Promoter Regions, Genetic, Antineoplastic Agents administration & dosage, DNA Methylation genetics, DNA-Binding Proteins genetics, Melanoma drug therapy
- Abstract
Background: Melanoma has two key features, an over-representation of UV-induced mutations and resistance to DNA damaging chemotherapy agents. Both of these features may result from dysfunction of the nucleotide excision repair pathway, in particular the DNA damage detection branch, global genome repair (GGR). The key GGR component XPC does not respond to DNA damage in melanoma, the cause of this lack of response has not been investigated. In this study, we investigated the role of methylation in reduced XPC in melanoma., Methods: To reduce methylation and induce DNA-damage, melanoma cell lines were treated with decitabine and carboplatin, individually and sequentially. Global DNA methylation levels, XPC mRNA and protein expression and methylation of the XPC promoter were examined. Apoptosis, cell proliferation and senescence were also quantified. XPC siRNA was used to determine that the responses seen were reliant on XPC induction., Results: Treatment with high-dose decitabine resulted in global demethylation, including the the shores of the XPC CpG island and significantly increased XPC mRNA expression. Lower, clinically relevant dose of decitabine also resulted in global demethylation including the CpG island shores and induced XPC in 50% of cell lines. Decitabine followed by DNA-damaging carboplatin treatment led to significantly higher XPC expression in 75% of melanoma cell lines tested. Combined sequential treatment also resulted in a greater apoptotic response in 75% of cell lines compared to carboplatin alone, and significantly slowed cell proliferation, with some melanoma cell lines going into senescence. Inhibiting the increased XPC using siRNA had a small but significant negative effect, indicating that XPC plays a partial role in the response to sequential decitabine and carboplatin., Conclusions: Demethylation using decitabine increased XPC and apoptosis after sequential carboplatin. These results confirm that sequential decitabine and carboplatin requires further investigation as a combination treatment for melanoma.
- Published
- 2018
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48. Repair of UVB-induced DNA damage is reduced in melanoma due to low XPC and global genome repair.
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Budden T, Davey RJ, Vilain RE, Ashton KA, Braye SG, Beveridge NJ, and Bowden NA
- Subjects
- Age Factors, Biopsy, Cell Cycle, Cell Line, Tumor, Gene Expression Regulation, Neoplastic, Genome, Human, Humans, Light, Melanocytes metabolism, Mutation, Transcriptome, Tumor Suppressor Protein p53 genetics, Ultraviolet Rays, DNA Damage, DNA Repair, DNA-Binding Proteins genetics, Melanoma genetics, Skin Neoplasms genetics
- Abstract
UVB exposure leads to DNA damage, which when unrepaired induces C>T transitions. These mutations are found throughout the melanoma genome, particularly in non-transcribed regions. The global genome repair (GGR) branch of nucleotide excision repair (NER) is responsible for repairing UV-induced DNA damage across non-transcribed and silent regions of the genome. This study aimed to examine the relationship between UVB and GGR in melanoma. DNA repair capacity and relative expression of NER in melanocytes and melanoma cell lines before and after treatment with UVB was quantified. Transcript expression from 196 melanomas was compared to clinical parameters including solar elastosis and whole transcriptome data collected. Melanoma cell lines showed significantly reduced DNA repair when compared to melanocytes, most significantly in the S phase of the cell cycle. Expression of GGR components XPC, DDB1 and DDB2 was significantly lower in melanoma after UVB. In the melanoma tumours, XPC expression correlated with age of diagnosis and low XPC conferred significantly poorer survival. The same trend was seen in the TCGA melanoma dataset. Reduced GGR in melanoma may contribute to the UV mutation spectrum of the melanoma genome and adds further to the growing evidence of the link between UV, NER and melanoma., Competing Interests: The authors state no conflict of interest.
- Published
- 2016
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49. The role of N-glycosylation in folding, trafficking, and functionality of lysosomal protein CLN5.
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Moharir A, Peck SH, Budden T, and Lee SY
- Subjects
- Endosomes, Glycosylation, HeLa Cells, Humans, Lysosomal Membrane Proteins, Membrane Proteins chemistry, Mutant Proteins metabolism, Mutation genetics, Protein Stability, Protein Transport, Subcellular Fractions metabolism, rab5 GTP-Binding Proteins metabolism, Lysosomes metabolism, Membrane Proteins metabolism, Protein Folding
- Abstract
CLN5 is a soluble lysosomal protein with unknown function. Mutations in CLN5 lead to neuronal ceroid lipofuscinosis, a group of inherited neurodegenerative disorders that mainly affect children. CLN5 has eight potential N-glycosylation sites based on the Asn-X-Thr/Ser consensus sequence. Through site-directed mutagenesis of individual asparagine residues to glutamine on each of the N-glycosylation consensus sites, we showed that all eight putative N-glycosylation sites are utilized in vivo. Additionally, localization studies showed that the lack of N-glycosylation on certain sites (N179, N252, N304, or N320) caused CLN5 retention in the endoplasmic reticulum, indicating that glycosylation is important for protein folding. Interestingly, one particular mutant, N401Q, is mislocalized to the Golgi, suggesting that N401 is not important for protein folding but essential for CLN5 trafficking to the lysosome. Finally, we analyzed several patient mutations in which N-glycosylation is affected. The N192S patient mutant is localized to the lysosome, indicating that this mutant has a functional defect in the lysosome. Our results suggest that there are functional differences in various N-glycosylation sites of CLN5 which affect folding, trafficking, and lysosomal function of CLN5.
- Published
- 2013
- Full Text
- View/download PDF
50. Regulators of global genome repair do not respond to DNA damaging therapy but correlate with survival in melanoma.
- Author
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Bowden NA, Ashton KA, Vilain RE, Avery-Kiejda KA, Davey RJ, Murray HC, Budden T, Braye SG, Zhang XD, Hersey P, and Scott RJ
- Subjects
- Ataxia Telangiectasia Mutated Proteins genetics, BRCA1 Protein genetics, BRCA2 Protein genetics, Cell Line, Tumor, Cell Survival drug effects, Checkpoint Kinase 2 genetics, Cisplatin pharmacology, DNA Damage drug effects, DNA Damage genetics, DNA Repair drug effects, Humans, Melanoma genetics, DNA Repair genetics, Melanoma metabolism
- Abstract
Nucleotide excision repair (NER) orchestrates the repair of helix distorting DNA damage, induced by both ultraviolet radiation (UVR) and cisplatin. There is evidence that the global genome repair (GGR) arm of NER is dysfunctional in melanoma and it is known to have limited induction in melanoma cell lines after cisplatin treatment. The aims of this study were to examine mRNA transcript levels of regulators of GGR and to investigate the downstream effect on global transcript expression in melanoma cell lines after cisplatin treatment and in melanoma tumours. The GGR regulators, BRCA1 and PCNA, were induced in melanocytes after cisplatin, but not in melanoma cell lines. Transcripts associated with BRCA1, BRCA2, ATM and CHEK2 showed altered expression in melanoma cell lines after cisplatin treatment. In melanoma tumour tissue BRCA1 transcript expression correlated with poor survival and XPB expression correlated with solar elastosis levels. Taken together, these findings provide evidence of the mechanisms underlying NER deficiency in melanoma.
- Published
- 2013
- Full Text
- View/download PDF
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