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Zhang M, Wang X, Yang N, Zhu X, Lu Z, Cai Y, Li B, Zhu Y, Li X, Wei Y, Zhang S, Tian J, Miao X. Prioritization of risk genes in colorectal cancer by integrative analysis of multi-omics data and gene networks. SCIENCE CHINA. LIFE SCIENCES 2024; 67:132-148. [PMID: 37747674 DOI: 10.1007/s11427-023-2439-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/26/2023] [Indexed: 09/26/2023]
Abstract
Genome-wide association studies (GWASs) have identified over 140 colorectal cancer (CRC)-associated loci; however, target genes at the majority of loci and underlying molecular mechanisms are poorly understood. Here, we utilized a Bayesian approach, integrative risk gene selector (iRIGS), to prioritize risk genes at CRC GWAS loci by integrating multi-omics data. As a result, a total of 105 high-confidence risk genes (HRGs) were identified, which exhibited strong gene dependencies for CRC and enrichment in the biological processes implicated in CRC. Among the 105 HRGs, CEBPB, located at the 20q13.13 locus, acted as a transcription factor playing critical roles in cancer. Our subsequent assays indicated the tumor promoter function of CEBPB that facilitated CRC cell proliferation by regulating multiple oncogenic pathways such as MAPK, PI3K-Akt, and Ras signaling. Next, by integrating a fine-mapping analysis and three independent case-control studies in Chinese populations consisting of 8,039 cases and 12,775 controls, we elucidated that rs1810503, a putative functional variant regulating CEBPB, was associated with CRC risk (OR=0.90, 95%CI=0.86-0.93, P=1.07×10-7). The association between rs1810503 and CRC risk was further validated in three additional multi-ancestry populations consisting of 24,254 cases and 58,741 controls. Mechanistically, the rs1810503 A to T allele change weakened the enhancer activity in an allele-specific manner to decrease CEBPB expression via long-range promoter-enhancer interactions, mediated by the transcription factor, REST, and thus decreased CRC risk. In summary, our study provides a genetic resource and a generalizable strategy for CRC etiology investigation, and highlights the biological implications of CEBPB in CRC tumorigenesis, shedding new light on the etiology of CRC.
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Affiliation(s)
- Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Cancer Epidemiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Zhengzhou, 450008, China
| | - Nan Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiangpan Li
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430062, China
| | - Shaokai Zhang
- Department of Cancer Epidemiology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Zhengzhou, 450008, China.
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China.
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China.
- Research Center of Public Health, Renmin hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430073, China.
- Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
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2
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Palmer JR, Cozier YC, Rosenberg L. Research on Health Disparities: Strategies and Findings From the Black Women's Health Study. Am J Epidemiol 2023; 192:1806-1810. [PMID: 35136921 PMCID: PMC11004793 DOI: 10.1093/aje/kwac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 01/10/2023] Open
Abstract
The American Journal of Epidemiology has been a platform for findings from the Black Women's Health Study (BWHS) that are relevant to health disparities. Topics addressed have included methods of follow-up of a large cohort of Black women, disparities in health-care delivery, modifiable risk factors for health conditions that disproportionately affect Black women, associations with exposures that are highly prevalent in Black women, and methods for genetic research. BWHS papers have also highlighted the importance of considering social context, including perceived experiences of racism, in understanding health disparities. In the future, BWHS investigators will contribute to documentation of the role that structural racism plays in health disparities.
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Affiliation(s)
| | | | - Lynn Rosenberg
- Correspondence to Dr. Lynn Rosenberg, Slone Epidemiology Center at Boston University, 72 East Concord Street L7, Boston, MA 02118 (e-mail: )
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3
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Boudeau S, Ramakodi MP, Zhou Y, Liu JC, Ragin C, Kulathinal RJ. Extensive set of African ancestry-informative markers (AIMs) to study ancestry and population health. Front Genet 2023; 14:1061781. [PMID: 36911410 PMCID: PMC9997643 DOI: 10.3389/fgene.2023.1061781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/20/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction: Human populations are often highly structured due to differences in genetic ancestry among groups, posing difficulties in associating genes with diseases. Ancestry-informative markers (AIMs) aid in the detection of population stratification and provide an alternative approach to map population-specific alleles to disease. Here, we identify and characterize a novel set of African AIMs that separate populations of African ancestry from other global populations including those of European ancestry. Methods: Using data from the 1000 Genomes Project, highly informative SNP markers from five African subpopulations were selected based on estimates of informativeness (In) and compared against the European population to generate a final set of 46,737 African ancestry-informative markers (AIMs). The AIMs identified were validated using an independent set and functionally annotated using tools like SIFT, PolyPhen. They were also investigated for representation of commonly used SNP arrays. Results: This set of African AIMs effectively separates populations of African ancestry from other global populations and further identifies substructure between populations of African ancestry. When a subset of these AIMs was studied in an independent dataset, they differentiated people who self-identify as African American or Black from those who identify their ancestry as primarily European. Most of the AIMs were found to be in their intergenic and intronic regions with only 0.6% in the coding regions of the genome. Most of the commonly used SNP array investigated contained less than 10% of the AIMs. Discussion: While several functional annotations of both coding and non-coding African AIMs are supported by the literature and linked these high-frequency African alleles to diseases in African populations, more effort is needed to map genes to diseases in these genetically diverse subpopulations. The relative dearth of these African AIMs on current genotyping platforms (the array with the highest fraction, llumina's Omni 5, harbors less than a quarter of AIMs), further demonstrates a greater need to better represent historically understudied populations.
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Affiliation(s)
- Samantha Boudeau
- Department of Biology, Temple University, Philadelphia, PA, United States.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Meganathan P Ramakodi
- Department of Biology, Temple University, Philadelphia, PA, United States.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jeffrey C Liu
- Department of Otolaryngology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.,Department of Surgical Oncology, Fox chase Cancer center, Philadelphia, PA, United States
| | - Camille Ragin
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Rob J Kulathinal
- Department of Biology, Temple University, Philadelphia, PA, United States.,African Caribbean Cancer Consortium, Fox Chase Cancer Center, Philadelphia, PA, United States
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4
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Forgacova N, Gazdarica J, Budis J, Radvanszky J, Szemes T. Repurposing non-invasive prenatal testing data: Population study of single nucleotide variants associated with colorectal cancer and Lynch syndrome. Oncol Lett 2021; 22:779. [PMID: 34594420 PMCID: PMC8456492 DOI: 10.3892/ol.2021.13040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
In our previous work, genomic data generated through non-invasive prenatal testing (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA of pregnant women in Slovakia was described as a valuable source of population specific data. In the present study, these data were used to determine the population allele frequency of common risk variants located in genes associated with colorectal cancer (CRC) and Lynch syndrome (LS). Allele frequencies of identified variants were compared with six world populations to detect significant differences between populations. Finally, variants were interpreted, functional consequences were searched for and clinical significance of variants was investigated using publicly available databases. Although the present study did not identify any pathogenic variants associated with CRC or LS in the Slovak population using NIPT data, significant differences were observed in the allelic frequency of risk CRC variants previously reported in genome-wide association studies and common variants located in genes associated with LS. As Slovakia is one of the leading countries with the highest incidence of CRC among male patients in the world, there is a need for studies dedicated to investigating the cause of such a high incidence of CRC in Slovakia. The present study also assumed that extensive cross-country data aggregation of NIPT results would represent an unprecedented source of information concerning human genome variation in cancer research.
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Affiliation(s)
- Natalia Forgacova
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Juraj Gazdarica
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia.,Science Support Section, Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia.,Science Support Section, Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Jan Radvanszky
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia
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5
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Ability of known colorectal cancer susceptibility SNPs to predict colorectal cancer risk: A cohort study within the UK Biobank. PLoS One 2021; 16:e0251469. [PMID: 34525106 PMCID: PMC8443076 DOI: 10.1371/journal.pone.0251469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer risk stratification is crucial to improve screening and risk-reducing recommendations, and consequently do better than a one-size-fits-all screening regimen. Current screening guidelines in the UK, USA and Australia focus solely on family history and age for risk prediction, even though the vast majority of the population do not have any family history. We investigated adding a polygenic risk score based on 45 single-nucleotide polymorphisms to a family history model (combined model) to quantify how it improves the stratification and discriminatory performance of 10-year risk and full lifetime risk using a prospective population-based cohort within the UK Biobank. For both 10-year and full lifetime risk, the combined model had a wider risk distribution compared with family history alone, resulting in improved risk stratification of nearly 2-fold between the top and bottom risk quintiles of the full lifetime risk model. Importantly, the combined model can identify people (n = 72,019) who do not have family history of colorectal cancer but have a predicted risk that is equivalent to having at least one affected first-degree relative (n = 44,950). We also confirmed previous findings by showing that the combined full lifetime risk model significantly improves discriminatory accuracy compared with a simple family history model 0.673 (95% CI 0.664–0.682) versus 0.666 (95% CI 0.657–0.675), p = 0.0065. Therefore, a combined polygenic risk score and first-degree family history model could be used to improve risk stratified population screening programs.
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6
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Baidoun F, Elshiwy K, Elkeraie Y, Merjaneh Z, Khoudari G, Sarmini MT, Gad M, Al-Husseini M, Saad A. Colorectal Cancer Epidemiology: Recent Trends and Impact on Outcomes. Curr Drug Targets 2021; 22:998-1009. [PMID: 33208072 DOI: 10.2174/1389450121999201117115717] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/30/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related deaths in the world with an estimated number of 1.8 million new cases and about 881,000 deaths worldwide in 2018. The epidemiology of CRC varies significantly between different regions in the world as well as between different age, gender and racial groups. Multiple factors are involved in this variation, including risk factor exposure, demographic variations in addition to genetic susceptibility and genetic mutations and their effect on the prognosis and treatment response. In this mini-review, we discuss the recent epidemiological trend including the incidence and mortality of colorectal cancer worldwide and the factors affecting these trends.
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Affiliation(s)
- Firas Baidoun
- Department of Hospital Medicine, Cleveland Clinic Foundation, Cleveland, OH, United States
| | | | - Yasmine Elkeraie
- High institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Zahi Merjaneh
- Department of Hospital Medicine, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - George Khoudari
- Department of Hospital Medicine, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Muhammad Talal Sarmini
- Department of Hospital Medicine, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Mohamed Gad
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Muneer Al-Husseini
- Department of Medicine, Ascension St John Hospital, Detroit, Michigan, United States
| | - Anas Saad
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
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7
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Hennig EE, Kluska A, Piątkowska M, Kulecka M, Bałabas A, Zeber-Lubecka N, Goryca K, Ambrożkiewicz F, Karczmarski J, Olesiński T, Zyskowski Ł, Ostrowski J. GWAS Links New Variant in Long Non-Coding RNA LINC02006 with Colorectal Cancer Susceptibility. BIOLOGY 2021; 10:biology10060465. [PMID: 34070617 PMCID: PMC8229782 DOI: 10.3390/biology10060465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023]
Abstract
Simple Summary Identifying risk factors for cancer development can allow for appropriate stratification and surveillance of individuals at risk, increasing their chances of benefiting from early disease detection; however, most of the genetic factors contributing to the risk of colorectal cancer (CRC) remain undetermined. Here, we adopted a new approach for selecting index polymorphism for further validation in combination with a genome-wide association study of pooled DNA samples for CRC susceptibility variants in the Polish population. This study, including 2013 patients and controls, uncovered five susceptibility loci not previously reported for CRC. Four of identified variants were located within genes likely involved in tumor invasiveness and metastasis, suggesting that they could be markers of poor prognosis in CRC patients. Our results provide evidence that conducting association studies on small but homogenous populations can help us discover new common risk variants specific to the studied population. Abstract Despite great efforts, most of the genetic factors contributing to the risk of colorectal cancer (CRC) remain undetermined. Including small but homogenous populations in genome-wide association studies (GWAS) can help us discover new common risk variants specific to the studied population. In this study, including 465 CRC patients and 1548 controls, a pooled DNA samples-based GWAS was conducted in search of genetic variants associated with CRC in a Polish population. Combined with a new method of selecting single-nucleotide polymorphisms (SNPs) for verification in individual DNA samples, this approach allowed the detection of five new susceptibility loci not previously reported for CRC. The discovered loci were found to explain 10% of the overall risk of developing CRC. The strongest association was observed for rs10935945 in long non-coding RNA LINC02006 (3q25.2). Three other SNPs were also located within genes (rs17575184 in NEGR1, rs11060839 in PIWIL1, rs12935896 in BCAS3), while one was intergenic (rs9927668 at 16p13.2). An expression quantitative trait locus (eQTL) bioinformatic analysis suggested that these polymorphisms may affect transcription factor binding sites. In conclusion, four of the identified variants were located within genes likely involved in tumor invasiveness and metastasis. Therefore, they could possibly be markers of poor prognosis in CRC patients.
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Affiliation(s)
- Ewa E. Hennig
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
- Correspondence:
| | - Anna Kluska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Magdalena Piątkowska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Aneta Bałabas
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Krzysztof Goryca
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Jakub Karczmarski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Tomasz Olesiński
- Department of Gastroenterological Oncology, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (T.O.); (Ł.Z.)
| | - Łukasz Zyskowski
- Department of Gastroenterological Oncology, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (T.O.); (Ł.Z.)
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
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8
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Al Abo M, Hyslop T, Qin X, Owzar K, George DJ, Patierno SR, Freedman JA. Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas. Genomics 2021; 113:1234-1246. [PMID: 33705884 DOI: 10.1016/j.ygeno.2021.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 11/26/2022]
Abstract
Individuals of African ancestry suffer disproportionally from higher incidence, aggressiveness, and mortality for particular cancers. This disparity likely results from an interplay among differences in multiple determinants of health, including differences in tumor biology. We used The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA aggregate expression datasets and identified differential alternative RNA splicing and transcription events (ARS/T) in cancers between self-identified African American (AA) and White (W) patients. We found that retained intron events were enriched among race-related ARS/T. In addition, on average, 12% of the most highly ranked race-related ARS/T overlapped between any two analyzed cancers. Moreover, the genes undergoing race-related ARS/T functioned in cancer-promoting pathways, and a number of race-related ARS/T were associated with patient survival. We built a web-application, CanSplice, to mine genomic datasets by self-identified race. The race-related targets have the potential to aid in the development of new biomarkers and therapeutics to mitigate cancer disparity.
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Affiliation(s)
- Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Terry Hyslop
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xiaodi Qin
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Daniel J George
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Steven R Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jennifer A Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA.
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9
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Jonaitis P, Kiudelis V, Streleckiene G, Gedgaudas R, Skieceviciene J, Kupcinskas J. Novel Biomarkers in the Diagnosis of Benign and Malignant Gastrointestinal Diseases. Dig Dis 2021; 40:1-13. [PMID: 33647906 DOI: 10.1159/000515522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/26/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Various noninvasive biomarkers have been used in the diagnosis, prognosis, and treatment of different gastrointestinal (GI) diseases for years. Novel technological developments and profound perception of molecular processes related to GI diseases over the last decade have allowed researchers to evaluate genetic, epigenetic, and many other potential molecular biomarkers in different diseases and clinical settings. Here, we present a review of recent and most relevant articles in order to summarize major findings on novel biomarkers in the diagnosis of benign and malignant GI diseases. SUMMARY Genetic variations, noncoding RNAs (ncRNAs), cell-free DNA (cfDNA), and microbiome-based biomarkers have been extensively analyzed as potential biomarkers in benign and malignant GI diseases. Multiple single-nucleotide polymorphisms have been linked with a number of GI diseases, and these observations are further being used to build up disease-specific genetic risk scores. Micro-RNAs and long ncRNAs have a large potential as noninvasive biomarkers in the management of inflammatory bowel diseases and GI tumors. Altered microbiome profiles were observed in multiple GI diseases, but most of the findings still lack translational clinical application. As of today, cfDNA appears to be the most potent biomarker for early detection and screening of GI cancers. Key Messages: Novel noninvasive molecular biomarkers show huge potential as useful tools in the diagnostics and management of different GI diseases. However, the use of these biomarkers in real-life clinical practice still remains limited, and further large studies are needed to elucidate the ultimate role of these potential noninvasive clinical tools.
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Affiliation(s)
- Paulius Jonaitis
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Greta Streleckiene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rolandas Gedgaudas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
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10
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Pirim D. Integrative analyses of molecular pathways and key candidate biomarkers associated with colorectal cancer. Cancer Biomark 2020; 27:555-568. [PMID: 32176635 DOI: 10.3233/cbm-191263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths and mining the molecular factors underlying CRC pathogenesis is imperative for alleviating the disease burden. OBJECTIVE To highlight key molecular pathways, prioritize hub genes and their regulators related to CRC. METHODS Data sets of TCGA-COAD and GTEx were used to identify differentially expressed genes (DEGs) and their functional enrichments in pathways and biological processes were analyzed using bioinformatics tools. Protein-protein interaction network was constructed and hub genes were identified using Cytoscape. Ingenuity Pathway Analysis was used to analyze the relations of the hub genes with diseases and canonical pathways. Key regulators targeting the hub genes such as TFs, miRNAs and their interactions were identified using in silico tools. RESULTS AURKA, CDK1, MYC, CDH1, CCNB1, CDC20, UBE2C, PLK1, KIF11, and CCNA2 were prioritized as hub genes based on their topological properties. Enrichment analyses emphasized the roles of DEGs and hub genes in the cell cycle process. Interactions of the hub genes with TFs and miRNAs suggested TP53, EZH2 and KLF4 as being promising candidate biomarkers for CRC. CONCLUSIONS Our results provide in silico evidence for candidate biomolecules that may have strong biomarker potential for CRC-related translational strategies.
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11
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Paredes J, Zabaleta J, Garai J, Ji P, Imtiaz S, Spagnardi M, Alvarado J, Li L, Akadri M, Barrera K, Munoz-Sagastibelza M, Gupta R, Alshal M, Agaronov M, Talus H, Wang X, Carethers JM, Williams JL, Martello LA. Immune-Related Gene Expression and Cytokine Secretion Is Reduced Among African American Colon Cancer Patients. Front Oncol 2020; 10:1498. [PMID: 32983990 PMCID: PMC7492388 DOI: 10.3389/fonc.2020.01498] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Colorectal cancer is the third most deadly cancer among African Americans (AA). When compared to Caucasian Americans (CA), AA present with more advanced disease and lower survival rates. Here, we investigated if differences in tumor immunology could be contributive to disparities observed between these populations. Methods: We examined gene expression of tumor and non-tumor adjacent tissues from AA and CA by whole transcriptome sequencing, and generated scores for immune cell populations by NanoString. In addition, we utilized “The Cancer Genome Atlas” (TCGA) database from AA and CA as a validation cohort. Finally, we measured the secretion of cytokines characteristic of effector T helper cell (Th) subsets by ELISA using plasma from each AA and CA participant. Results: Colon tumors from AA patients showed significant fold-change increase in gene expression when compared to CA for FOXP3 (6.22 vs. 3.22), IL1B (103 vs. 11.4) and IL8 (220 vs. 28.9) (p < 0.05). In contrast, among CA we observed statistically higher gene expression of markers associated with antitumor activity such as GZMB (Granzyme B), IFNG and the immunotherapy targets PDL1 (CD274) and CTLA4 (p < 0.05). TCGA data validated our observed higher gene expression of GZMB and PDL1 in CA patients when compared to AA. Notably, our observations on immune cell populations show that AA tumors have significantly higher number of exhausted CD8+ cells (p < 0.01), mast cells (p < 0.02) and increased T regulatory cells when compared to CA. AA colon cancer patients differed from CA in cytokine production patterns in plasma (i.e., reduced IL-12). Conclusions: Our study demonstrates significant differences of the immunological profiles of colon tumors from AA compared to CA that suggest a deficiency of appropriate immune defense mechanisms in terms of gene expression, recruitment of immune cells and systemic secretion of cytokines. As such, these immune differences could be mitigated through population-specific therapeutic approaches.
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Affiliation(s)
- Jenny Paredes
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Jovanny Zabaleta
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jone Garai
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Ping Ji
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Sayed Imtiaz
- Department of Surgery, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Marzia Spagnardi
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Joussette Alvarado
- Department of Genetics, Louisiana State University Health Sciences Center, Loyola University New Orleans, New Orleans, LA, United States
| | - Li Li
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Mubarak Akadri
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Kaylene Barrera
- Department of Surgery, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Maria Munoz-Sagastibelza
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Raavi Gupta
- Department of Pathology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Mohamed Alshal
- Department of Pathology, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Maksim Agaronov
- Department of Pathology, Kings County Hospital, Brooklyn, NY, United States
| | - Henry Talus
- Department of Surgery, Kings County Hospital, Brooklyn, NY, United States
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - John M Carethers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jennie L Williams
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Laura A Martello
- Division of Gastroenterology and Hepatology, Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
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12
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Shahamatdar S, He MX, Reyna MA, Gusev A, AlDubayan SH, Van Allen EM, Ramachandran S. Germline Features Associated with Immune Infiltration in Solid Tumors. Cell Rep 2020; 30:2900-2908.e4. [PMID: 32130895 PMCID: PMC7082123 DOI: 10.1016/j.celrep.2020.02.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/12/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
The immune composition of the tumor microenvironment influences response and resistance to immunotherapies. While numerous studies have identified somatic correlates of immune infiltration, germline features that associate with immune infiltrates in cancers remain incompletely characterized. We analyze seven million autosomal germline variants in the TCGA cohort and test for association with established immune-related phenotypes that describe the tumor immune microenvironment. We identify one SNP associated with the amount of infiltrating follicular helper T cells; 23 candidate genes, some of which are involved in cytokine-mediated signaling and others containing cancer-risk SNPs; and networks with genes that are part of the DNA repair and transcription elongation pathways. In addition, we find a positive association between polygenic risk for rheumatoid arthritis and amount of infiltrating CD8+ T cells. Overall, we identify multiple germline genetic features associated with tumor-immune phenotypes and develop a framework for probing inherited features that contribute to differences in immune infiltration.
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Affiliation(s)
- Sahar Shahamatdar
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Meng Xiao He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Boston, MA 02115, USA
| | - Matthew A Reyna
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322, USA; Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Saud H AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
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13
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Keum N, Giovannucci E. Global burden of colorectal cancer: emerging trends, risk factors and prevention strategies. Nat Rev Gastroenterol Hepatol 2019; 16:713-732. [PMID: 31455888 DOI: 10.1038/s41575-019-0189-8] [Citation(s) in RCA: 1221] [Impact Index Per Article: 244.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/11/2019] [Indexed: 02/06/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the second leading cause of cancer death. Arising through three major pathways, including adenoma-carcinoma sequence, serrated pathway and inflammatory pathway, CRC represents an aetiologically heterogeneous disease according to subtyping by tumour anatomical location or global molecular alterations. Genetic factors such as germline MLH1 and APC mutations have an aetiologic role, predisposing individuals to CRC. Yet, the majority of CRC is sporadic and largely attributable to the constellation of modifiable environmental risk factors characterizing westernization (for example, obesity, physical inactivity, poor diets, alcohol drinking and smoking). As such, the burden of CRC is shifting towards low-income and middle-income countries as they become westernized. Furthermore, the rising incidence of CRC at younger ages (before age 50 years) is an emerging trend. This Review provides a comprehensive summary of CRC epidemiology, with emphasis on modifiable lifestyle and nutritional factors, chemoprevention and screening. Overall, the optimal reduction of CRC incidence and mortality will require concerted efforts to reduce modifiable risk factors, to leverage chemoprevention research and to promote population-wide and targeted screening.
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Affiliation(s)
- NaNa Keum
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Food Science and Biotechnology, Dongguk University, Goyang, South Korea
| | - Edward Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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14
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Lara OD, Wang Y, Asare A, Xu T, Chiu HS, Liu Y, Hu W, Sumazin P, Uppal S, Zhang L, Rauh-Hain JA, Sood AK. Pan-cancer clinical and molecular analysis of racial disparities. Cancer 2019; 126:800-807. [PMID: 31730714 DOI: 10.1002/cncr.32598] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Racial disparities in cancer outcomes are increasingly recognized, but comprehensive analyses, including molecular studies, are limited. The objective of the current study was to perform a pan-cancer clinical and epigenetic molecular analysis of outcomes in African American (AA) and European American (EA) patients. METHODS Cross-platform analyses using cancer databases (the Surveillance, Epidemiology, and End Results program database and the National Cancer Data Base) and a molecular database (The Cancer Genome Ancestry Atlas) were performed to evaluate clinical and epigenetic molecular differences between AA and EA patients based on genetic ancestry. RESULTS In the primary pan-cancer survival analysis using the Surveillance, Epidemiology, and End Results database (2,045,839 patients; 87.5% EA and 12.5% AA), AA patients had higher mortality rates for 28 of 42 cancer types analyzed (hazard ratio, >1.0). AAs continued to have higher mortality in 13 cancer types after adjustment for socioeconomic variables using the National Cancer Database (5,150,023 patients; 11.6% AA and 88.4% EA). Then, molecular features of 5,283 tumors were analyzed in patients who had genetic ancestry data available (87.2% EA and 12.8% AA). Genes were identified with altered DNA methylation along with increased microRNA expression levels unique to AA patients that are associated with cancer drug resistance. Increased miRNAs (miR-15a, miR-17, miR-130-3p, miR-181a) were noted in common among AAs with breast, kidney, thyroid, or prostate carcinomas. CONCLUSIONS The current results identified epigenetic features in AA patients who have cancer that may contribute to higher mortality rates compared with EA patients who have cancer. Therefore, a focus on molecular signatures unique to AAs may identify actionable molecular abnormalities.
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Affiliation(s)
- Olivia D Lara
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ying Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amma Asare
- Baylor College of Medicine, Houston, Texas
| | - Tao Xu
- Department of Gynecologic Oncology, University of Michigan, Ann Arbor, Michigan
| | | | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Hu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Shitanshu Uppal
- Department of Gynecologic Oncology, University of Michigan, Ann Arbor, Michigan
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - J Alejandro Rauh-Hain
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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15
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Bien SA, Su YR, Conti DV, Harrison TA, Qu C, Guo X, Lu Y, Albanes D, Auer PL, Banbury BL, Berndt SI, Bézieau S, Brenner H, Buchanan DD, Caan BJ, Campbell PT, Carlson CS, Chan AT, Chang-Claude J, Chen S, Connolly CM, Easton DF, Feskens EJM, Gallinger S, Giles GG, Gunter MJ, Hampe J, Huyghe JR, Hoffmeister M, Hudson TJ, Jacobs EJ, Jenkins MA, Kampman E, Kang HM, Kühn T, Küry S, Lejbkowicz F, Le Marchand L, Milne RL, Li L, Li CI, Lindblom A, Lindor NM, Martín V, McNeil CE, Melas M, Moreno V, Newcomb PA, Offit K, Pharaoh PDP, Potter JD, Qu C, Riboli E, Rennert G, Sala N, Schafmayer C, Scacheri PC, Schmit SL, Severi G, Slattery ML, Smith JD, Trichopoulou A, Tumino R, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Casey G, Nickerson DA, Gruber SB, Hsu L, Zheng W, Peters U. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer. Hum Genet 2019; 138:307-326. [PMID: 30820706 PMCID: PMC6483948 DOI: 10.1007/s00439-019-01989-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10- 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10- 4, replication P = 6.7 × 10- 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David V Conti
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tabitha A Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Xingyi Guo
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Yingchang Lu
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53205, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Barbara L Banbury
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stéphane Bézieau
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Colorectal Oncogenomics Group, Department of Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, 94612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Genetic Tumour Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, 20246, Hamburg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sai Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Charles M Connolly
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care School of Clinical Medicine, University of Cambridge, Cambridge, England, 01223, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, 1X5, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marc J Gunter
- Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, 01307, Dresden, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeroen R Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- AbbVie Inc, 1500 Seaport Blvd, Redwood City, CA, 94063, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sébastien Küry
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Flavio Lejbkowicz
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Loic Le Marchand
- University of Hawai'i Cancer Center, Honolulu, Hawaii, 96813, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Li
- Department of Family Medicine and Community Health, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital Solna, 171 77, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, 171 77, Stockholm, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Vicente Martín
- Biomedicine Institute (IBIOMED), University of León, León, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08028, Barcelona, Spain
- University of Barcelona, 08007, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul D P Pharaoh
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB2 1TN, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, 24118, Kiel, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Joshua D Smith
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, 13 Kaisareias & Alexandroupoleos, 115 27, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 115 27, Athens, Greece
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Rosario Tumino
- Affiliation Cancer Registry, Department of Prevention, Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Cornelia M Ulrich
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Fränzel J B van Duijnhoven
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bethany Van Guelpen
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet Solna, 17177, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, 75121, Uppsala, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, Saint John's, NL, A1B 3V6, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Anna H Wu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham Casey
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Deborah A Nickerson
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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16
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Robertson DJ, Ladabaum U. Opportunities and Challenges in Moving From Current Guidelines to Personalized Colorectal Cancer Screening. Gastroenterology 2019; 156:904-917. [PMID: 30593801 DOI: 10.1053/j.gastro.2018.12.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Douglas J Robertson
- Department of Veterans Affairs Medical Center, White River Junction, Vermont; Geisel School of Medicine at Dartmouth and The Dartmouth Institute, Hanover, New Hampshire.
| | - Uri Ladabaum
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, California
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17
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Pérez-Mayoral J, Soto-Salgado M, Shah E, Kittles R, Stern MC, Olivera MI, Gonzalez-Pons M, Rodriguez-Quilichinni S, Torres M, Reyes JS, Tous L, López N, Chevere VC, Cruz-Correa M. Association of genetic ancestry with colorectal tumor location in Puerto Rican Latinos. Hum Genomics 2019; 13:12. [PMID: 30786938 PMCID: PMC6383234 DOI: 10.1186/s40246-019-0196-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/03/2019] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) is the first cause of cancer deaths among Puerto Ricans. The incidence and mortality of CRC in Puerto Rico continue to be on the rise. The burden of CRC in Puerto Rico is higher than among US Hispanics and is second only to African Americans, thus supporting the importance of studying this CRC health disparity. The genetic background of the Puerto Rican population is a mix of European, African, and Amerindian races, which may account, in part, for the differences observed in the CRC mortality rates among Puerto Ricans. The objective of the study was to assess the role of genetic ancestry in CRC risk and its association with clinicopathological features of CRC tumors in Puerto Ricans. Results We used a validated panel of 105 ancestry informative markers (AIMs) to estimate genetic ancestry in 406 Puerto Rican CRC cases and 425 Puerto Rican controls. We examined the association of genetic ancestry with CRC risk and tumor clinicopathological characteristics. Conclusions The mean ancestry proportions in the study population were 61% European, 21% African, and 18% Amerindian. No association was observed between genetic ancestry and risk of CRC. However, African ancestry was associated with an increased risk of developing rectal tumors (OR = 1.55, 95% CI 1.04–2.31). Additional studies are needed to fully elucidate the role of African ancestry in CRC carcinogenesis.
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Affiliation(s)
- Julyann Pérez-Mayoral
- Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, PMB 711 Ave. De Diego 89 Ste. 105, San Juan, PR, 00927-6346, USA
| | | | - Ebony Shah
- Department of Surgery, Division of Urology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Rick Kittles
- Department of Population Sciences, Division of Health Equities, City of Hope Comprehensive Center, Duarte, CA, USA
| | - Mariana C Stern
- Department of Preventive Medicine and Urology, Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Myrta I Olivera
- Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, PMB 711 Ave. De Diego 89 Ste. 105, San Juan, PR, 00927-6346, USA
| | - María Gonzalez-Pons
- Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, PMB 711 Ave. De Diego 89 Ste. 105, San Juan, PR, 00927-6346, USA
| | - Segundo Rodriguez-Quilichinni
- Department of Biochemistry and Medicine, School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
| | - Marla Torres
- Colorectal Surgery Clinic, Ashford Presbyterian Hospital, San Juan, PR, USA
| | - Jose S Reyes
- Colorectal Surgery Clinic, Ashford Presbyterian Hospital, San Juan, PR, USA
| | - Luis Tous
- Colorectal Surgery Clinic, Ashford Presbyterian Hospital, San Juan, PR, USA
| | - Nicolas López
- Colorectal Surgery Clinic, Ashford Presbyterian Hospital, San Juan, PR, USA
| | - Victor Carlo Chevere
- Department of Biochemistry and Medicine, School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
| | - Marcia Cruz-Correa
- Division of Cancer Biology, University of Puerto Rico Comprehensive Cancer Center, PMB 711 Ave. De Diego 89 Ste. 105, San Juan, PR, 00927-6346, USA. .,Department of Biochemistry and Medicine, School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA.
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18
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Yu Y, Cheng D, Parfrey P, Liu G, Savas S. Two functional indel polymorphisms in the promoter region of the Brahma gene (BRM) and disease risk and progression-free survival in colorectal cancer. PLoS One 2018; 13:e0198873. [PMID: 29894502 PMCID: PMC5997361 DOI: 10.1371/journal.pone.0198873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/25/2018] [Indexed: 01/28/2023] Open
Abstract
Background and objective The Brahma gene (BRM) encodes a catalytic ATPase subunit of the Switch/Sucrose non-fermentable (SWI/SNF) complex, which modulates gene expression and many important cellular processes. Two indel polymorphisms in the promoter region of BRM (BRM-741 and BRM-1321) are associated with its reduced expression and the risk of susceptibility or survival outcomes in multiple solid cancers. In this study, we have examined these variants in relation to susceptibility and survival outcomes in colorectal cancer. Methods Genotypes were obtained using TaqMan assays in 427 cases and 408 controls. Multivariate logistic and Cox regression models were fitted to examine the associations of the BRM-741 and BRM-1321 genotypes adjusting for relevant covariates. Sub-group analyses based on tumor location and patient sex were also performed. In all analyses, indels were examined individually as well as in combination. Results Our results showed that there was no association between the BRM polymorphisms and the risk of colorectal cancer. However, genotype combinations of the BRM-741 and BRM-1321 variants were associated with the risk of colon cancer. Particularly, patients having at least one variant allele had increased risk of colon cancer when compared to patients with the double wild-type genotype. In the survival analyses, BRM-741 heterozygosity was associated with longer progression-free survival time in the colorectal cancer patients. A stronger association was detected in the male patients under the recessive genetic model where the homozygosity for the variant allele of BRM-741 was associated with shorter progression-free survival time. Conclusions Our analyses suggest that BRM-741 and BRM-1321 indels are associated with the risk of developing colon cancer and the BRM-741 indel is associated with the disease progression in colorectal cancer patients, especially in the male patients. Although our results show a different relationship between these indels and colorectal cancer compared to other cancer sites, they also suggest that BRM and its promoter variants may have biological roles in susceptibility and survival outcomes in colorectal cancers. Performing further analyses in additional and larger cohorts are needed to confirm our conclusions.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Dangxiao Cheng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Geoffrey Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada
- Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
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19
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Tanskanen T, van den Berg L, Välimäki N, Aavikko M, Ness-Jensen E, Hveem K, Wettergren Y, Bexe Lindskog E, Tõnisson N, Metspalu A, Silander K, Orlando G, Law PJ, Tuupanen S, Gylfe AE, Hänninen UA, Cajuso T, Kondelin J, Sarin AP, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Al-Tassan NA, Palles C, Martin L, Barclay E, Tenesa A, Farrington S, Timofeeva MN, Meyer BF, Wakil SM, Campbell H, Smith CG, Idziaszczyk S, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper J, Jenkins M, Newcomb PA, Gallinger S, Conti D, Schumacher FR, Casey G, Cheadle JP, Dunlop MG, Tomlinson IP, Houlston RS, Palin K, Aaltonen LA. Genome-wide association study and meta-analysis in Northern European populations replicate multiple colorectal cancer risk loci. Int J Cancer 2018; 142:540-546. [PMID: 28960316 PMCID: PMC6383773 DOI: 10.1002/ijc.31076] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/04/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies have been successful in elucidating the genetic basis of colorectal cancer (CRC), but there remains unexplained variability in genetic risk. To identify new risk variants and to confirm reported associations, we conducted a genome-wide association study in 1,701 CRC cases and 14,082 cancer-free controls from the Finnish population. A total of 9,068,015 genetic variants were imputed and tested, and 30 promising variants were studied in additional 11,647 cases and 12,356 controls of European ancestry. The previously reported association between the single-nucleotide polymorphism (SNP) rs992157 (2q35) and CRC was independently replicated (p = 2.08 × 10-4 ; OR, 1.14; 95% CI, 1.06-1.23), and it was genome-wide significant in combined analysis (p = 1.50 × 10-9 ; OR, 1.12; 95% CI, 1.08-1.16). Variants at 2q35, 6p21.2, 8q23.3, 8q24.21, 10q22.3, 10q24.2, 11q13.4, 11q23.1, 14q22.2, 15q13.3, 18q21.1, 20p12.3 and 20q13.33 were associated with CRC in the Finnish population (false discovery rate < 0.1), but new risk loci were not found. These results replicate the effects of multiple loci on the risk of CRC and identify shared risk alleles between the Finnish population isolate and outbred populations.
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Affiliation(s)
- Tomas Tanskanen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Linda van den Berg
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Eivind Ness-Jensen
- HUNT Research Centre, Department of Public Health, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Elinor Bexe Lindskog
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Neeme Tõnisson
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Kaisa Silander
- National Institute for Health and Welfare, Helsinki, Finland
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Philip J. Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Sari Tuupanen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Alexandra E. Gylfe
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Ulrika A. Hänninen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | | | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Heikki Järvinen
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | | | - Anna Lepistö
- Department of Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Nada A. Al-Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Easter Bush, Roslin, UK
| | - Susan Farrington
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - Maria N. Timofeeva
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - Brian F. Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M. Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Christopher G. Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Shelley Idziaszczyk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Tim S. Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Rachel Kerr
- Oxford Cancer Centre, Department of Oncology, University of Oxford, Churchill Hospital, Oxford, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Aung K. Win
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - John Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Mark Jenkins
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, Australia
| | - Polly A. Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steve Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick R. Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jeremy P. Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Malcolm G. Dunlop
- Colon Cancer Genetics Group, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - Ian P. Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A. Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
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20
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Augustus GJ, Ellis NA. Colorectal Cancer Disparity in African Americans: Risk Factors and Carcinogenic Mechanisms. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:291-303. [PMID: 29128568 DOI: 10.1016/j.ajpath.2017.07.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/01/2017] [Accepted: 07/20/2017] [Indexed: 12/13/2022]
Abstract
African Americans have the highest incidence and mortality rates of colorectal cancer (CRC) of any ethnic group in the United States. Although some of these disparities can be explained by differences in access to care, cancer screening, and other socioeconomic factors, disparities remain after adjustment for these factors. Consequently, an examination of recent advances in the understanding of ethnicity-specific factors, including genetic and environmental factors relating to risk of CRC, the biology of CRC progression, and the changes in screening and mortality, is important for evaluating our progress toward eliminating the disparities. An overarching limitation in this field is the number and sample size of studies performed to characterize the etiological bases of CRC incidence and mortality in African Americans. Despite this limitation, significant differences in etiology are manifest in many studies. These differences need validation, and their impacts on disparities need more detailed investigation. Perhaps most heartening, improvements in CRC screening can be attributed to the smallest difference in CRC incidence between African Americans and whites since the late 1980s. Cancer mortality, however, remains a persistent difference.
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Affiliation(s)
- Gaius J Augustus
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona.
| | - Nathan A Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona.
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