1
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Oswald LB, Bloomer A, Li X, Jean-Baptiste E, Trujillo G, Felder S, Small BJ, Ose J, Hardikar S, Strehli I, Huang LC, Mooney K, Mutch MG, Chao D, Cohen SA, Karchi M, Wood EH, Damerell V, Loroña NC, Gong J, Toriola AT, Li CI, Shibata D, Schneider M, Gigic B, Figueiredo JC, Jim HSL, Ulrich CM, Siegel EM. Functional quality of life among newly diagnosed young adult colorectal cancer survivors compared to older adults: results from the ColoCare Study. Support Care Cancer 2024; 32:298. [PMID: 38639810 DOI: 10.1007/s00520-024-08511-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024]
Abstract
PURPOSE Colorectal cancer (CRC) incidence and mortality are increasing among young adults (YAs) aged 18-39. This study compared quality of life (QOL) between YA and older adult CRC survivors in the ColoCare Study. METHODS Participants were grouped by age (years) as follows: 18-39 (YA), 40-49, 50-64, and 65 + . Functional QOL (physical, social, role, emotional, cognitive) and global QOL were assessed with the EORTC-QLQ-C30 at enrollment, 3, 6, and 12 months. Average scores were compared between groups over time using longitudinal mixed-effect modeling. Proportions with clinically meaningful QOL impairment were calculated using age-relevant thresholds and compared between groups over time using logistic regression with mixed effects. RESULTS Participants (N = 1590) were n = 81 YAs, n = 196 aged 40-49, n = 627 aged 50-64, and n = 686 aged 65 + . Average physical function was better among YAs than participants aged 50-64 (p = 0.010) and 65 + (p < 0.001), and average social function was worse among YAs than aged 65 + (p = 0.046). Relative to YAs, all age groups were less likely to report clinically meaningful social dysfunction (aged 40-49 OR = 0.13, 95%CI = 0.06-0.29; aged 50-64 OR = 0.10, 95%CI = 0.05-0.21; aged 65 + OR = 0.07, 95%CI = 0.04-0.15) and role dysfunction (aged 40-49 OR = 0.36, 95%CI = 0.18-0.75; aged 50-64 OR = 0.41, 95%CI = 0.22-0.78; aged 65 + OR = 0.32, 95%CI = 0.17-0.61). Participants aged 40-49 were also less likely to report physical dysfunction (OR = 0.42, 95%CI = 0.19-0.93). CONCLUSION YA CRC survivors reported better physical and worse social function compared to older CRC survivors, and YA CRC survivors were more likely to report clinically meaningful social, role, and physical disfunction. Future work should further investigate QOL using age-relevant benchmarks to inform best practices for CRC survivorship care. TRIAL REGISTRATION NCT02328677, registered December 2014.
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Affiliation(s)
- Laura B Oswald
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA.
| | - Amanda Bloomer
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA
| | - Xiaoyin Li
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA
| | | | - Gillian Trujillo
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA
| | - Seth Felder
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA
| | - Brent J Small
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer Ose
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah, Salt Lake City, UT, USA
- University of Applied Sciences and Arts, Hanover, Germany
| | - Sheetal Hardikar
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah, Salt Lake City, UT, USA
| | | | - Lyen C Huang
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah, Salt Lake City, UT, USA
| | - Kathi Mooney
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah, Salt Lake City, UT, USA
| | | | - Dante Chao
- Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, St. Louis, MO, USA
| | | | - Meghana Karchi
- University of Tennessee Health Science Center, Memphis, TN, USA
| | | | | | - Nicole C Loroña
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jun Gong
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Adetunji T Toriola
- Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, St. Louis, MO, USA
| | | | - David Shibata
- University of Tennessee Health Science Center, Memphis, TN, USA
| | | | | | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heather S L Jim
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah, Salt Lake City, UT, USA
| | - Erin M Siegel
- Moffitt Cancer Center, 12902 USF Magnolia Drive, MRC-HOB, Tampa, FL, 33612, USA
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2
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Li X, Hoogland AI, Small BJ, Crowder SL, Gonzalez BD, Oswald LB, Sleight AG, Nguyen N, Lorona NC, Damerell V, Komrokji KR, Mooney K, Playdon MC, Ulrich CM, Li CI, Shibata D, Toriola AT, Ose J, Peoples AR, Siegel EM, Bower JE, Schneider M, Gigic B, Figueiredo JC, Jim HSL. Trajectories and risk factors of fatigue following colorectal cancer diagnosis. Colorectal Dis 2023; 25:2054-2063. [PMID: 37700526 PMCID: PMC10815933 DOI: 10.1111/codi.16746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/08/2023] [Accepted: 08/02/2023] [Indexed: 09/14/2023]
Abstract
AIM This study sought to identify groups of colorectal cancer patients based upon trajectories of fatigue and examine how demographic, clinical and behavioural risk factors differentiate these groups. METHOD Patients were from six cancer centres in the United States and Germany. Fatigue was measured using the fatigue subscale of the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30) at five time points (baseline/enrolment and 3, 6, 12 and 24 months after diagnosis). Piecewise growth mixture models identified latent trajectories of fatigue. Logistic regression models examined differences in demographic, clinical and behavioural characteristics between fatigue trajectory groups. RESULTS Among 1615 participants (57% men, 86% non-Hispanic White, mean age 61 ± 13 years at diagnosis), three distinct groups were identified. In the high fatigue group (36%), fatigue significantly increased in the first 6 months after diagnosis and then showed statistically and clinically significant improvement from 6 to 24 months (P values < 0.01). Throughout the study period, average fatigue met or exceeded cutoffs for clinical significance. In the moderate (34%) and low (30%) fatigue groups, fatigue levels remained below or near population norms across the study period. Patients who were diagnosed with Stage II-IV disease and/or current smokers were more likely to be in the high fatigue than in the moderate fatigue group (P values < 0.05). CONCLUSION A large proportion of colorectal cancer patients experienced sustained fatigue after initiation of cancer treatment. Patients with high fatigue at the time of diagnosis may benefit from early supportive care.
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Affiliation(s)
- Xiaoyin Li
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Aasha I Hoogland
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Brent J Small
- School of Aging Studies, University of South Florida, Tampa, Florida, USA
| | - Sylvia L Crowder
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Brian D Gonzalez
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Laura B Oswald
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Alix G Sleight
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nathalie Nguyen
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nicole C Lorona
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Victoria Damerell
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Khaled R Komrokji
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Kathi Mooney
- College of Nursing, University of Utah, Salt Lake City, Utah, USA
- Cancer Control and Population Sciences Program, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Mary C Playdon
- Cancer Control and Population Sciences Program, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Nutrition and Integrative Physiology, College of Health, University of Utah, Salt Lake City, Utah, USA
| | - Cornelia M Ulrich
- Cancer Control and Population Sciences Program, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
- Population Health Sciences, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Adetunji T Toriola
- Department of Surgery, Washington University St. Louis, St. Louis, Missouri, USA
| | - Jennifer Ose
- Cancer Control and Population Sciences Program, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
- Population Health Sciences, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Anita R Peoples
- Cancer Control and Population Sciences Program, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
- Population Health Sciences, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Erin M Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Biljana Gigic
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Heather S L Jim
- Department of Health Outcomes and Behavior, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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3
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Gigic B, Ose J, Brezina S, Geijsen AJMR, Ulvik A, van Roekel EH, Holowatyj AN, Kok DE, van Duijnhoven FJB, Damerell V, Li CI, Habermann N, Ulrich AB, Weijenberg MP, Gsur A, Ueland PM, Kampman E, Schneider M, Ulrich CM. Abstract 1010: Circulating biomarkers of vitamin B1, B2, and B3 status and their associations with clinical outcomes among non-metastatic colorectal cancer patients: results from the FOCUS Consortium. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: Circulating levels of biomarkers indicating better B vitamin status appear to have a protective effect on various medical conditions, while they also contribute to the reduction in risk of some cancer entities, e.g. colorectal cancer (CRC). However, little is known about the associations of circulating vitamin B biomarkers with clinical outcomes among CRC patients, such as overall survival (OS), disease-free survival (DFS), and risk of recurrence. Recently, we showed that higher vitamin B6 status is associated with improved OS and DFS. In the present study, we further investigated associations of vitamin B1, B2, and B3 status with clinical outcomes in a prospective cohort of non-metastatic CRC patients.
Materials and Methods: A total of 2,102 patients with stage I-III CRC participated in six cohorts in the international FOCUS Consortium. Circulating concentrations of vitamin B biomarkers (thiamine and thiamine monophosphate (representing vitamin B1), riboflavin (vitamin B2), and vitamin B3 markers N1-methylnicotinamide and nicotinamide were measured by liquid chromatography-tandem mass spectrometry in preoperative blood samples. Using Cox proportional hazards regression, we examined associations of vitamin B1, B2, B3 status, and related biomarkers with OS, DFS, and risk of recurrence. Models were adjusted for patient age, sex, circulating creatinine levels, tumor site, tumor stage, and study site.
Results and Discussion: After a median follow-up of 3.2 years for OS, higher levels of thiamine monophosphate were associated with lower risk of all-cause mortality (HROS: 0.82; 95% CI, 0.71-0.95, p=0.008). Furthermore, higher riboflavin levels were associated with improved OS (HROS: 0.88; 95% CI, 0.78-0.98, p=0.03) and DFS (HRDFS: 0.91; 95% CI, 0.83-0.99, p=0.04). We did not observe any associations of thiamine, N1-methylnicotinamide, and nicotinamide with clinical outcomes among CRC patients.
Conclusion: Findings from this multi-centre study of non-metastatic CRC patients yield important clinical information. We observed significantly improved OS among patients with higher levels of thiamine monophosphate after CRC diagnosis. Further, higher preoperative riboflavin may represent a promising predictor for OS and DFS among non-metastatic CRC patients.
Citation Format: Biljana Gigic, Jennifer Ose, Stefanie Brezina, Anne JMR Geijsen, Arve Ulvik, Eline H. van Roekel, Andreana N. Holowatyj, Dieuwertje E. Kok, Fränzel JB van Duijnhoven, Victoria Damerell, Christopher I. Li, Nina Habermann, Alexis B. Ulrich, Matty P. Weijenberg, Andrea Gsur, Per M. Ueland, Ellen Kampman, Martin Schneider, Cornelia M. Ulrich. Circulating biomarkers of vitamin B1, B2, and B3 status and their associations with clinical outcomes among non-metastatic colorectal cancer patients: results from the FOCUS Consortium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1010.
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Affiliation(s)
- Biljana Gigic
- 1Heidelberg University Hospital (UKHD), Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | | - Nina Habermann
- 9European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | - Andrea Gsur
- 3Medical University of Vienna, Vienna, Austria
| | | | - Ellen Kampman
- 4Wageningen University & Research, Wageningen, Netherlands
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4
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Himbert C, Ose J, Gigic B, Viskochil R, Santuci K, Lin T, Ashworth A, Cohan JN, Scaife CL, Jedrzkiewicz J, Damerell V, Atkins KM, Gong J, Mutch MG, Bernadt C, Felder S, Sanchez J, Cohen SA, Krane MK, Hinkle N, Wood E, Peoples AR, Figueiredo JC, Toriola AT, Siegel EM, Li CI, Shibata D, Boucher K, Round JL, Ulrich AB, Schneider M, Huang LC, Hardikar S, Ulrich CM. Associations of combined physical activity and body mass index groups with colorectal cancer survival outcomes. BMC Cancer 2023; 23:300. [PMID: 37013476 PMCID: PMC10069054 DOI: 10.1186/s12885-023-10695-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Physical activity and BMI have been individually associated with cancer survivorship but have not yet been studied in combinations in colorectal cancer patients. Here, we investigate individual and combined associations of physical activity and BMI groups with colorectal cancer survival outcomes. METHODS Self-reported physical activity levels (MET hrs/wk) were assessed using an adapted version of the International Physical Activity Questionnaire (IPAQ) at baseline in 931 patients with stage I-III colorectal cancer and classified into 'highly active' and'not-highly active'(≥ / < 18 MET hrs/wk). BMI (kg/m2) was categorized into 'normal weight', 'overweight', and 'obese'. Patients were further classified into combined physical activity and BMI groups. Cox-proportional hazard models with Firth correction were computed to assess associations [hazard ratio (HR), 95% profile HR likelihood confidence interval (95% CI) between individual and combined physical activity and BMI groups with overall and disease-free survival in colorectal cancer patients. RESULTS 'Not-highly active' compared to 'highly active' and 'overweight'/ 'obese' compared to 'normal weight' patients had a 40-50% increased risk of death or recurrence (HR: 1.41 (95% CI: 0.99-2.06), p = 0.03; HR: 1.49 (95% CI: 1.02-2.21) and HR: 1.51 (95% CI: 1.02-2.26), p = 0.04, respectively). 'Not-highly active' patients had worse disease-free survival outcomes, regardless of their BMI, compared to 'highly active/normal weight' patients. 'Not-highly active/obese' patients had a 3.66 times increased risk of death or recurrence compared to 'highly active/normal weight' patients (HR: 4.66 (95% CI: 1.75-9.10), p = 0.002). Lower activity thresholds yielded smaller effect sizes. CONCLUSION Physical activity and BMI were individually associated with disease-free survival among colorectal cancer patients. Physical activity seems to improve survival outcomes in patients regardless of their BMI.
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Affiliation(s)
- Caroline Himbert
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Jennifer Ose
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | | | - Richard Viskochil
- University of Utah, Salt Lake City, UT, USA
- University of Massachusetts Boston, Boston, MA, USA
| | | | - Tengda Lin
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | | | - Jessica N Cohan
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Courtney L Scaife
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Jolanta Jedrzkiewicz
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | | | | | - Jun Gong
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew G Mutch
- Washington University School of Medicine, St. Louis, MO, USA
| | - Corey Bernadt
- Washington University School of Medicine, St. Louis, MO, USA
| | - Seth Felder
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Julian Sanchez
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stacey A Cohen
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | - Mukta K Krane
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | - Nathan Hinkle
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Elizabeth Wood
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Anita R Peoples
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | | | | | - Erin M Siegel
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Christopher I Li
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | - David Shibata
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kenneth Boucher
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | | | | | | | - Lyen C Huang
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sheetal Hardikar
- University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Cornelia M Ulrich
- University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, Salt Lake City, UT, USA.
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5
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Gigic B, van Roekel E, Holowatyj AN, Brezina S, Geijsen AJMR, Ulvik A, Ose J, Koole JL, Damerell V, Kiblawi R, Gumpenberger T, Lin T, Kvalheim G, Koelsch T, Kok DE, van Duijnhoven FJ, Bours MJ, Baierl A, Li CI, Grady W, Vickers K, Habermann N, Schneider M, Kampman E, Ueland PM, Ulrich A, Weijenberg M, Gsur A, Ulrich C. Cohort profile: Biomarkers related to folate-dependent one-carbon metabolism in colorectal cancer recurrence and survival - the FOCUS Consortium. BMJ Open 2022; 12:e062930. [PMID: 36549742 PMCID: PMC9772678 DOI: 10.1136/bmjopen-2022-062930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The overarching goal of the FOCUS (biomarkers related to folate-dependent one-carbon metabolism in colorectal cancer (CRC) recurrence and survival) Consortium is to unravel the effect of folate and folate-mediated one-carbon metabolism (FOCM) biomarkers on CRC prognosis to provide clinically relevant advice on folate intake to cancer patients and define future tertiary prevention strategies. PARTICIPANTS The FOCUS Consortium is an international, prospective cohort of 2401 women and men above 18 years of age who were diagnosed with a primary invasive non-metastatic (stages I-III) CRC. The consortium comprises patients from Austria, two sites from the Netherlands, Germany and two sites from the USA. Patients are recruited after CRC diagnosis and followed at 6 and 12 months after enrolment. At each time point, sociodemographic data, data on health behaviour and clinical data are collected, blood samples are drawn. FINDINGS TO DATE An increased risk of cancer recurrences was observed among patients with higher compared with lower circulating folic acid concentrations. Furthermore, specific folate species within the FOCM pathway were associated with both inflammation and angiogenesis pathways among patients with CRC. In addition, higher vitamin B6 status was associated with better quality of life at 6 months post-treatment. FUTURE PLANS Better insights into the research on associations between folate and FOCM biomarkers and clinical outcomes in patients with CRC will facilitate the development of guidelines regarding folate intake in order to provide clinically relevant advice to patients with cancer, health professionals involved in patient care, and ultimately further tertiary prevention strategies in the future. The FOCUS Consortium offers an excellent infrastructure for short-term and long-term research projects and for combining additional biomarkers and data resulting from the individual cohorts within the next years, for example, microbiome data, omics and multiomics data or CT-quantified body composition data.
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Affiliation(s)
- Biljana Gigic
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Eline van Roekel
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Andreana N Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Stefanie Brezina
- Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Anne J M R Geijsen
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jennifer Ose
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Janna L Koole
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Victoria Damerell
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Rama Kiblawi
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Tengda Lin
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Torsten Koelsch
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Franzel J van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn J Bours
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Wien, Austria
| | - Christopher I Li
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - William Grady
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kathy Vickers
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nina Habermann
- Genome Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Surgical Department I, Städtische Kliniken Neuss, Lukaskrankenhaus GmbH, Neuss, Germany
| | - Matty Weijenberg
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Andrea Gsur
- Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Cornelia Ulrich
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
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6
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Harrison V, Khan SF, Damerell V, Bleloch J, ArulJothi KN, Sinkala M, Lennard K, Mulder N, Calder B, Blackburn J, Prince S. Strongylopus grayii tadpole blastema extract exerts cytotoxic effects on embryonal rhabdomyosarcoma cells. In Vitro Cell Dev Biol Anim 2022; 58:679-692. [PMID: 35947290 DOI: 10.1007/s11626-022-00714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022]
Abstract
Amphibians have regenerative capacity and are resistant to developing cancer. This suggests that the developing blastema, located at the tissue regeneration site, may secrete anti-cancer factors. Here, we investigate the anti-cancer potential of tadpole tail blastema extracts (TAD) from the stream frog, Strongylopus grayii, in embryonal rhabdomyosarcoma (ERMS) cells. ERMS originates in skeletal muscle tissue and is a common pediatric soft tissue sarcoma. We show using MTT assays that TAD inhibited ERMS cell viability in a concentration-dependent manner, and phase contrast/fluorescent microscopy revealed that it induced morphological markers of senescence and apoptosis. Western blotting showed that this was associated with DNA damage (γH2AX) and activation of the p38/MAPK stress signaling pathway as well as molecular markers of senescence (p16INK4a), apoptosis (cleaved PARP), and inhibition of cell cycle promoters (cyclin A, CDK2, and cyclin B1). Furthermore, proteomics followed by gene ontology analyses showed that TAD treatment inhibited known tumor promoters and proteins required for cancer cell survival. Lastly, using the LINCS drug perturbation library, we show that there is an overlap between the proteomics signature induced by TAD and common anti-cancer drugs. Taken together, this study provides novel evidence that TAD exhibits cytotoxicity in ERMS cells.
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Affiliation(s)
| | - Saif F Khan
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Victoria Damerell
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Jenna Bleloch
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - K N ArulJothi
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, India
| | - Musalula Sinkala
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Bridget Calder
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Jonathan Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Sharon Prince
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
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7
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Damerell V, Ambele MA, Salisbury S, Neumann-Mufweba A, Durandt C, Pepper MS, Prince S. The c-Myc/TBX3 Axis Promotes Cellular Transformation of Sarcoma-Initiating Cells. Front Oncol 2022; 11:801691. [PMID: 35145908 PMCID: PMC8821881 DOI: 10.3389/fonc.2021.801691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/30/2021] [Indexed: 11/23/2022] Open
Abstract
Sarcomas are highly aggressive cancers of mesenchymal origin whose clinical management is highly complex. This is partly due to a lack of understanding of the molecular mechanisms underpinning the transformation of mesenchymal stromal/stem cells (MSCs) which are presumed to be the sarcoma-initiating cells. c-Myc is amplified/overexpressed in a range of sarcomas where it has an established oncogenic role and there is evidence that it contributes to the malignant transformation of MSCs. T-box transcription factor 3 (TBX3) is upregulated by c-Myc in a host of sarcoma subtypes where it promotes proliferation, tumor formation, migration, and invasion. This study investigated whether TBX3 is a c-Myc target in human MSCs (hMSCs) and whether overexpressing TBX3 in hMSCs can phenocopy c-Myc overexpression to promote malignant transformation. Using siRNA, qRT-PCR, luciferase reporter and chromatin-immunoprecipitation assays, we show that c-Myc binds and directly activates TBX3 transcription in hMSCs at a conserved E-box motif. When hMSCs were engineered to stably overexpress TBX3 using lentiviral gene transfer and the resulting cells characterised in 2D and 3D, the overexpression of TBX3 was shown to promote self-renewal, bypass senescence, and enhance proliferation which corresponded with increased levels of cell cycle progression markers (cyclin A, cyclin B1, CDK2) and downregulation of the p14ARF/MDM2/p53 tumor suppressor pathway. Furthermore, TBX3 promoted the migratory and invasive ability of hMSCs which associated with increased levels of markers of migration (Vimentin, SLUG, SNAIL, TWIST1) and invasion (MMP2, MMP9). Transcriptomic analysis revealed that genes upregulated upon TBX3 overexpression overlapped with c-myc targets, were involved in cell cycle progression, and were associated with sarcomagenesis. Together, the data described indicate that the c-Myc/TBX3 oncogenic molecular pathway may be a key mechanism that transforms hMSCs into sarcomas.
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Affiliation(s)
- Victoria Damerell
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Melvin Anyasi Ambele
- Department of Immunology and SAMRC Extramural Unit for Stem Research and Therapy, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- Department of Oral Pathology and Oral Biology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Shanel Salisbury
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alexis Neumann-Mufweba
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Chrisna Durandt
- Department of Immunology and SAMRC Extramural Unit for Stem Research and Therapy, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
| | - Michael Sean Pepper
- Department of Immunology and SAMRC Extramural Unit for Stem Research and Therapy, Faculty of Health Sciences, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- *Correspondence: Sharon Prince,
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8
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Willmer T, Damerell V, Smyly S, Sims D, Du Toit M, Ncube S, Sinkala M, Govender D, Sturrock E, Blackburn JM, Prince S. Targeting the oncogenic TBX3:nucleolin complex to treat multiple sarcoma subtypes. Am J Cancer Res 2021; 11:5680-5700. [PMID: 34873487 PMCID: PMC8640805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023] Open
Abstract
Sarcomas are diverse cancers of mesenchymal origin, with compromised clinical management caused by insufficient diagnostic biomarkers and limited treatment options. The transcription factor TBX3 is upregulated in a diverse range of sarcoma subtypes, where it plays a direct oncogenic role, and it may thus represent a novel therapeutic target. To identify versatile ways to target TBX3, we performed affinity purification coupled by mass spectrometry to identify putative TBX3 protein cofactors that regulate its oncogenic activity in sarcomas. Here we identify and validate the multifunctional phosphoprotein nucleolin as a TBX3 cofactor. We show that nucleolin is co-expressed with TBX3 in several sarcoma subtypes and their expression levels positively correlate in sarcoma patients which are associated with poor prognosis. Furthermore, we demonstrate that nucleolin and TBX3 interact in chondrosarcoma, liposarcoma and rhabdomyosarcoma cells where they act together to enhance proliferation and migration and regulate a common set of tumor suppressor genes. Importantly, the nucleolin targeting aptamer, AS1411, exhibits selective anti-cancer activity in these cells and mislocalizes TBX3 and nucleolin to the cytoplasm which correlates with the re-expression of the TBX3/nucleolin target tumor suppressors CDKN1A (p21CIP1) and CDKN2A (p14ARF). Our findings provide the first evidence that TBX3 requires nucleolin to promote features of sarcomagenesis and that disruption of the oncogenic TBX3-nucleolin interaction by AS1411 may be a novel approach for treating sarcomas.
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Affiliation(s)
- Tarryn Willmer
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research CouncilTygerberg 7505, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch UniversityTygerberg 7505, South Africa
| | - Victoria Damerell
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
| | - Shannon Smyly
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
| | - Danica Sims
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
| | - Michelle Du Toit
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
| | - Stephanie Ncube
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
| | - Musalula Sinkala
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town 7925, South Africa
| | - Dhirendra Govender
- Anatomical Pathology, PathcareCape Town 7925, South Africa
- Division of Anatomical Pathology, Faculty of Health Sciences, University of Cape Town, NHLS-Groote Schuur HospitalCape Town 7925, South Africa
| | - Edward Sturrock
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town 7925, South Africa
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town 7925, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape TownCape Town 7925, South Africa
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9
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Damerell V, Pepper MS, Prince S. Molecular mechanisms underpinning sarcomas and implications for current and future therapy. Signal Transduct Target Ther 2021; 6:246. [PMID: 34188019 PMCID: PMC8241855 DOI: 10.1038/s41392-021-00647-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/18/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
Sarcomas are complex mesenchymal neoplasms with a poor prognosis. Their clinical management is highly challenging due to their heterogeneity and insensitivity to current treatments. Although there have been advances in understanding specific genomic alterations and genetic mutations driving sarcomagenesis, the underlying molecular mechanisms, which are likely to be unique for each sarcoma subtype, are not fully understood. This is in part due to a lack of consensus on the cells of origin, but there is now mounting evidence that they originate from mesenchymal stromal/stem cells (MSCs). To identify novel treatment strategies for sarcomas, research in recent years has adopted a mechanism-based search for molecular markers for targeted therapy which has included recapitulating sarcomagenesis using in vitro and in vivo MSC models. This review provides a comprehensive up to date overview of the molecular mechanisms that underpin sarcomagenesis, the contribution of MSCs to modelling sarcomagenesis in vivo, as well as novel topics such as the role of epithelial-to-mesenchymal-transition (EMT)/mesenchymal-to-epithelial-transition (MET) plasticity, exosomes, and microRNAs in sarcomagenesis. It also reviews current therapeutic options including ongoing pre-clinical and clinical studies for targeted sarcoma therapy and discusses new therapeutic avenues such as targeting recently identified molecular pathways and key transcription factors.
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Affiliation(s)
- Victoria Damerell
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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10
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Peres J, Damerell V, Chauhan J, Popovic A, Desprez PY, Galibert MD, Goding CR, Prince S. TBX3 Promotes Melanoma Migration by Transcriptional Activation of ID1, which Prevents Activation of E-Cadherin by MITF. J Invest Dermatol 2021; 141:2250-2260.e2. [PMID: 33744299 DOI: 10.1016/j.jid.2021.02.740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/22/2021] [Accepted: 02/09/2021] [Indexed: 01/22/2023]
Abstract
In melanoma, a phenotype switch from proliferation to invasion underpins metastasis, the major cause of melanoma-associated death. The transition from radial to vertical growth phase (invasive) melanoma is characterized by downregulation of both E-cadherin (CDH1) and MITF and upregulation of the key cancer-associated gene TBX3 and the phosphatidylinositol 3 kinase signaling pathway. Yet, whether and how these diverse events are linked remains poorly understood. Here, we show that TBX3 directly promotes expression of ID1, a dominant-negative regulator of basic helix-loop-helix transcription factors, and that ID1 decreases MITF binding and upregulation of CDH1. Significantly, we show that TBX3 activation of ID1 is necessary for TBX3 to enhance melanoma cell migration, and the mechanistic links between TBX3, ID1, MITF, and invasion revealed here are reflected in their expression in human melanomas. Our results reveal that melanoma migration is promoted through a TBX3-ID1-MITF-E-cadherin axis and that ID1-mediated repression of MITF activity may reinforce maintenance of an MITFLow phenotype associated with disease progression and therapy resistance.
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Affiliation(s)
- Jade Peres
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Victoria Damerell
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford United Kingdom
| | - Ana Popovic
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Pierre-Yves Desprez
- California Pacific Medical Center, Research Institute, San Francisco, California, USA
| | - Marie-Dominique Galibert
- IGDR (Institut de Génétique et Développement de Rennes) - UMR6290, CNRS, University of Rennes, Rennes, France; Department of Molecular Genetics and Genomics, Hospital University of Rennes (CHU Rennes), Rennes, France
| | - Colin R Goding
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford United Kingdom
| | - Sharon Prince
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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11
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Khan SF, Damerell V, Omar R, Du Toit M, Khan M, Maranyane HM, Mlaza M, Bleloch J, Bellis C, Sahm BDB, Peres J, ArulJothi KN, Prince S. The roles and regulation of TBX3 in development and disease. Gene 2020; 726:144223. [PMID: 31669645 PMCID: PMC7108957 DOI: 10.1016/j.gene.2019.144223] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022]
Abstract
TBX3, a member of the ancient and evolutionary conserved T-box transcription factor family, is a critical developmental regulator of several structures including the heart, mammary glands, limbs and lungs. Indeed, mutations in the human TBX3 lead to ulnar mammary syndrome which is characterized by several clinical malformations including hypoplasia of the mammary and apocrine glands, defects of the upper limb, areola, dental structures, heart and genitalia. In contrast, TBX3 has no known function in adult tissues but is frequently overexpressed in a wide range of epithelial and mesenchymal derived cancers. This overexpression greatly impacts several hallmarks of cancer including bypass of senescence, apoptosis and anoikis, promotion of proliferation, tumour formation, angiogenesis, invasion and metastatic capabilities as well as cancer stem cell expansion. The debilitating consequences of having too little or too much TBX3 suggest that its expression levels need to be tightly regulated. While we have a reasonable understanding of the mutations that result in low levels of functional TBX3 during development, very little is known about the factors responsible for the overexpression of TBX3 in cancer. Furthermore, given the plethora of oncogenic processes that TBX3 impacts, it must be regulating several target genes but to date only a few have been identified and characterised. Interestingly, while there is compelling evidence to support oncogenic roles for TBX3, a few studies have indicated that it may also have tumour suppressor functions in certain contexts. Together, the diverse functional elasticity of TBX3 in development and cancer is thought to involve, in part, the protein partners that it interacts with and this area of research has recently received some attention. This review provides an insight into the significance of TBX3 in development and cancer and identifies research gaps that need to be explored to shed more light on this transcription factor.
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Affiliation(s)
- Saif F Khan
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Victoria Damerell
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Rehana Omar
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Michelle Du Toit
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Mohsin Khan
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Hapiloe Mabaruti Maranyane
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Mihlali Mlaza
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Jenna Bleloch
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Claire Bellis
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Bianca D B Sahm
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa; Department of Pharmacology, Institute of Biomedical Science, University of São Paulo, São Paulo, SP 11030-400, Brazil
| | - Jade Peres
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - K N ArulJothi
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa.
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12
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Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ. ELM 2016--data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Res 2016; 44:D294-300. [PMID: 26615199 PMCID: PMC4702912 DOI: 10.1093/nar/gkv1291] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/18/2023] Open
Abstract
The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to this resource, along with more improvements to the web interface. ELM 2016 contains more than 240 different motif classes with over 2700 experimentally validated instances, manually curated from more than 2400 scientific publications. In addition, more data have been made available as individually searchable pages and are downloadable in various formats.
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Affiliation(s)
- Holger Dinkel
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kim Van Roey
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sushama Michael
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Manjeet Kumar
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Vladislava Milchevskaya
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Helen Kühn
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | | | | | | | | | - Sara Kalman
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | | | | | | | | | | | - Vera Thiel
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Lukas Welti
- Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Francesca Diella
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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