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Hussein AA, Hamad R, Newport MJ, Ibrahim ME. Individualized Medicine in Africa: Bringing the Practice Into the Realms of Population Heterogeneity. Front Genet 2022; 13:853969. [PMID: 35495155 PMCID: PMC9047898 DOI: 10.3389/fgene.2022.853969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
The declared aim of “personalized”, “stratified” or “precision” approaches is to place individual variation, as ascertained through genomic and various other biomarkers, at the heart of Scientific Medicine using it to predict risk of disease or response to therapy and to tailor interventions and target therapies so as to maximize benefit and minimize risk for individual patients and efficiency for the health care system overall. It is often contrasted to current practices for which the scientific base is rooted in concepts of a “universal biology” and a “typical” or “average patient” and in which variation is ignored. Yet both approaches equally overlook the hierarchical nature of human variation and the critical importance of differences between populations. Impact of genetic heterogeneity has to be seen within that context to be meaningful and subsequently useful. In Africa such complexity is compounded by the high effective size of its populations, their diverse histories and the diversity of the environmental terrains they occupy, rendering analysis of gene environment interactions including the establishment of phenotype genotype correlations even more cumbersome. Henceforth “Individualized” methods and approaches can only magnify the shortcomings of universal approaches if adopted without due regard to these complexities. In the current perspective we review examples of potential hurdles that may confront biomedical scientists and analysts in genomic medicine in clinical and public health genomics in Africa citing specific examples from the current SARS-COV2 pandemic and the challenges of establishing reference biobanks and pharmacogenomics reference values.
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Affiliation(s)
- Ayman A. Hussein
- Unit of Diseases and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Reem Hamad
- Unit of Diseases and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Melanie J. Newport
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Muntaser E. Ibrahim
- Unit of Diseases and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- *Correspondence: Muntaser E. Ibrahim,
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Zhao S, Wu W, Jiang Z, Tang F, Ding L, Xu W, Ruan L. Roles of ARID1A variations in colorectal cancer: a collaborative review. Mol Med 2022; 28:42. [PMID: 35421925 PMCID: PMC9009033 DOI: 10.1186/s10020-022-00469-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
AbstractColorectal cancer (CRC), a common malignancy, is one of the leading cause of cancer death in adults. AT-rich interaction domain 1A (ARID1A), a critical portion of the SWItch/sucrose non-fermentation (SWI/SNF) chromatin remodeling complexes, shows one of the most frequent mutant genes across different human cancer types. Deleterious variations of ARID1A has been recognized to be correlated the tumorigenesis and the poor prognosis of CRC. Here, we summarize recent advances in the clinical implications and molecular pathogenesis of ARID1A variations in CRC. According to independent data of 23 included studies, ARID1A is mutated in 3.6–66.7%. Consistently, all of the 23 relevant studies report that ARID1A functions as a specific tumor suppressor in CRC. Clinically, ARID1A variation status serves as a biomarker for survival prognosis and various therapies for CRC. Mechanistically, the pathophysiologic impacts of ARID1A variations on CRC may be associated with the co-occurrence variations of other genes (i.e., TP53, KRAS, APC, FBXW7, and PIK3CA) and the regulation of several signaling pathways being affected (i.e., WNT signaling, Akt signaling, and MEK/ERK pathway), leading to cell cycle arrest, chromatin remodeling, chromosome organization, and DNA hypermethylation of the cancer cells. The present review highlights ARID1A serving as a potent tumor suppressor and an important prognostic factor in CRC. ARID1A variations hint towards a promising tool for diagnostic tumor profiling and individualized therapeutic targets for CRC in the future.
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Ibrahim ME. Genetic diversity of the Sudanese: insights on origin and implications for health. Hum Mol Genet 2021; 30:R37-R41. [PMID: 33864377 PMCID: PMC8223596 DOI: 10.1093/hmg/ddab028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 11/21/2022] Open
Abstract
By virtue of their cultural, linguistic and genetic legacies, many populations from Sudan have deep histories in the region and retain high genetic diversities. Sudan’s location in north east Africa, a unique spot believed to act as a climatic refuge during periods of climate extremes, might have dictated that fate. Among the marked consequences of this diversity is the potential to provide information on the origin and structure of human populations within and outside the continent, as well as migration patterns towards various parts of the African continent, and out of Africa. The diverse Sudanese gene pool further has the potential to inform on genetic adaptations driven by culture and the environment resulting in unique and interesting traits, some of which are yet to be investigated. In addition, these genomes could offer clues to complex issues of causation amidst the challenge of new paradigms in biology underpinned by the genomic revolution.
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Intarajak T, Udomchaiprasertkul W, Bunyoo C, Yimnoon J, Soonklang K, Wiriyaukaradecha K, Lamlertthon W, Sricharunrat T, Chaiwiriyawong W, Siriphongpreeda B, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Jenjaroenpun P, Wongsurawat T, Nookaew I, Auewarakul C, Cheevadhanarak S. Genetic Aberration Analysis in Thai Colorectal Adenoma and Early-Stage Adenocarcinoma Patients by Whole-Exome Sequencing. Cancers (Basel) 2019; 11:E977. [PMID: 31336886 PMCID: PMC6679221 DOI: 10.3390/cancers11070977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal adenomas are precursor lesions of colorectal adenocarcinoma. The transition from adenoma to carcinoma in patients with colorectal cancer (CRC) has been associated with an accumulation of genetic aberrations. However, criteria that can screen adenoma progression to adenocarcinoma are still lacking. This present study is the first attempt to identify genetic aberrations, such as the somatic mutations, copy number variations (CNVs), and high-frequency mutated genes, found in Thai patients. In this study, we identified the genomic abnormality of two sample groups. In the first group, five cases matched normal-colorectal adenoma-colorectal adenocarcinoma. In the second group, six cases matched normal-colorectal adenomas. For both groups, whole-exome sequencing was performed. We compared the genetic aberration of the two sample groups. In both normal tissues compared with colorectal adenoma and colorectal adenocarcinoma analyses, somatic mutations were observed in the tumor suppressor gene APC (Adenomatous polyposis coli) in eight out of ten patients. In the group of normal tissue comparison with colorectal adenoma tissue, somatic mutations were also detected in Catenin Beta 1 (CTNNB1), Family With Sequence Similarity 123B (FAM123B), F-Box And WD Repeat Domain Containing 7 (FBXW7), Sex-Determining Region Y-Box 9 (SOX9), Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5), Frizzled Class Receptor 10 (FZD10), and AT-Rich Interaction Domain 1A (ARID1A) genes, which are involved in the Wingless-related integration site (Wnt) signaling pathway. In the normal tissue comparison with colorectal adenocarcinoma tissue, Kirsten retrovirus-associated DNA sequences (KRAS), Tumor Protein 53 (TP53), and Ataxia-Telangiectasia Mutated (ATM) genes are found in the receptor tyrosine kinase-RAS (RTK-RAS) signaling pathway and p53 signaling pathway, respectively. These results suggest that APC and TP53 may act as a potential screening marker for colorectal adenoma and early-stage CRC. This preliminary study may help identify patients with adenoma and early-stage CRC and may aid in establishing prevention and surveillance strategies to reduce the incidence of CRC.
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Affiliation(s)
- Thoranin Intarajak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Bioinformatics Unit for Genomic Analysis, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Wandee Udomchaiprasertkul
- Molecular Biology and Genomic Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Chakrit Bunyoo
- Bioinformatics Unit for Genomic Analysis, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Jutamas Yimnoon
- Cytogenetics Unit, Central Research Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kamonwan Soonklang
- Data Management Unit, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kriangpol Wiriyaukaradecha
- Molecular Biology and Genomic Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Wisut Lamlertthon
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Thaniya Sricharunrat
- Pathology Laboratory Unit, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Worawit Chaiwiriyawong
- Department of Medical Oncology, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Bunchorn Siriphongpreeda
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Sawannee Sutheeworapong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Weerayuth Kittichotirat
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Systems Biology research group, National Center for Genetic Engineering and Biotechnology (BIOTEC) at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Chirayu Auewarakul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand.
| | - Supapon Cheevadhanarak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
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Jiang Y, Sun Y, Hu J, Yu N, Liu H, Fan J, Ning X, Li Y, Liu B, Sun Y, Zhang J, Qiu X, Fu S, Zhou C, Xu H. A germline mutation in Rab43 gene identified from a cancer family predisposes to a hereditary liver-colon cancer syndrome. BMC Cancer 2019; 19:613. [PMID: 31226964 DOI: 10.1186/s12885-019-5845-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/16/2019] [Indexed: 12/18/2022] Open
Abstract
Background Hereditary cancer syndromes have inherited germline mutations which predispose to benign and malignant tumors. Understanding of the molecular causes in hereditary cancer syndromes has advanced cancer treatment and prevention. However, the causal genes of many hereditary cancer syndromes remain unknown due to their rare frequency of mutation. Methods A large Chinese family with a history of hereditary liver-colon cancer syndrome was studied. The genomic DNA was extracted from the blood samples of involved family members, whole-exome sequencing was performed to identify genetic variants. Functional validation of a candidate variant was carried out using gene expression, gene knockout and immunohistochemistry. Results The whole-exome of the proband diagnosed with colon cancer was sequenced in comparison with his mother. A total of 13 SNVs and 16 InDels were identified. Among these variants, we focused on a mutation of Rab43 gene, a GTPase family member involving in protein trafficking, for further validation. Sanger DNA sequencing confirmed a mutation (c: 128810106C > T, p: A158T) occurred in one allele of Rab43 gene from the proband, that heterozygous mutation also was verified in the genome of the proband’s deceased father with liver cancer, but not in his healthy mother and sister. Ectopic expression of the Rab43 A158T mutant in Huh7 cells led to more enhanced cell growth, proliferation and migration compared to the expression of wild type Rab43. Conversely, knockout of Rab43 in HepG2 cells resulted in slow cell growth and multiple nuclei formation and impaired activation of Akt. Finally, a positive correlation between the expression levels of Rab43 protein and cancer development in that family was confirmed. Conclusions A germline mutation of Rab43 gene is identified to be associated with the onset of a familial liver-colon cancer syndrome. Our finding points to a potential role of protein trafficking in the tumorigenesis of the familial cancer syndrome, and helps the genetic counseling to the affected family members. Electronic supplementary material The online version of this article (10.1186/s12885-019-5845-4) contains supplementary material, which is available to authorized users.
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Burns MB, Montassier E, Abrahante J, Priya S, Niccum DE, Khoruts A, Starr TK, Knights D, Blekhman R. Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PLoS Genet 2018; 14:e1007376. [PMID: 29924794 PMCID: PMC6028121 DOI: 10.1371/journal.pgen.1007376] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/02/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. In conclusion, our study shows that CRC microbiomes are correlated with tumor mutational profiles, pointing towards possible mechanisms of molecular interaction.
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Affiliation(s)
- Michael B. Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- * E-mail: (MBB); (RB)
| | - Emmanuel Montassier
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- MiHAR lab, Université de Nantes, 44000 Nantes, France
| | - Juan Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - David E. Niccum
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Timothy K. Starr
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail: (MBB); (RB)
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