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Sueangoen N, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Public neoantigens in breast cancer immunotherapy (Review). Int J Mol Med 2024; 54:65. [PMID: 38904202 PMCID: PMC11188978 DOI: 10.3892/ijmm.2024.5388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Among women globally, breast cancer is the most prevalent cancer and the leading cause of cancer‑related death. Interestingly, though genetic mutations contribute to the disease, <15% of women diagnosed with breast cancer have a family history of the disease, suggesting a prevalence of sporadic genetic mutations in breast cancer development. In the rapidly rising field of cancer genomics, neoantigen‑based immunotherapy has come to the fore. The investigation of novel proteins arising from unique somatic mutations or neoantigens have opened a new pathway for both individualized and public cancer treatments. Because they are shared among individuals with similar genetic changes, public neoantigens provide an opportunity for 'off‑the‑shelf' anticancer therapies, potentially extending the benefits to a wider patient group. The present review aimed to highlight the role of shared or public neoantigens as therapeutic targets for patients with breast cancer, emphasizing common hotspot mutations of certain genes identified in breast cancer. The clinical utilization of public neoantigen‑based therapies for breast cancer treatment were also discussed.
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Affiliation(s)
- Natthaporn Sueangoen
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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He J, Kou SH, Li J, Ding X, Wang SM. Pathogenic variants in human DNA damage repair genes mostly arose after the latest human out-of-Africa migration. Front Genet 2024; 15:1408952. [PMID: 38948361 PMCID: PMC11211533 DOI: 10.3389/fgene.2024.1408952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction The DNA damage repair (DDR) system in human genome is pivotal in maintaining genomic integrity. Pathogenic variation (PV) in DDR genes impairs their function, leading to genome instability and increased susceptibility to diseases, especially cancer. Understanding the evolution origin and arising time of DDR PV is crucial for comprehending disease susceptibility in modern humans. Methods We used big data approach to identify the PVs in DDR genes in modern humans. We mined multiple genomic databases derived from 251,214 modern humans of African and non-Africans. We compared the DDR PVs between African and non-African. We also mined the DDR PVs in the genomic data derived from 5,031 ancient humans. We used the DDR PVs from ancient humans as the intermediate to further the DDR PVs between African and non-African. Results and discussion We identified 1,060 single-base DDR PVs across 77 DDR genes in modern humans of African and non-African. Direct comparison of the DDR PVs between African and non-African showed that 82.1% of the non-African PVs were not present in African. We further identified 397 single-base DDR PVs in 56 DDR genes in the 5,031 ancient humans dated between 45,045 and 100 years before present (BP) lived in Eurasian continent therefore the descendants of the latest out-of-Africa human migrants occurred 50,000-60,000 years ago. By referring to the ancient DDR PVs, we observed that 276 of the 397 (70.3%) ancient DDR PVs were exclusive in non-African, 106 (26.7%) were shared between non-African and African, and only 15 (3.8%) were exclusive in African. We further validated the distribution pattern by testing the PVs in BRCA and TP53, two of the important genes in genome stability maintenance, in African, non-African, and Ancient humans. Our study revealed that DDR PVs in modern humans mostly emerged after the latest out-of-Africa migration. The data provides a foundation to understand the evolutionary basis of disease susceptibility, in particular cancer, in modern humans.
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Affiliation(s)
| | | | | | | | - San Ming Wang
- Department of Public Health and Medical Administration, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, University of Macau, Taipa, China
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Korneenko TV, Pestov NB. Oncogenic BRCA1,2 Mutations in the Human Lineage-A By-Product of Sexual Selection? Biomedicines 2023; 12:22. [PMID: 38275383 PMCID: PMC10813183 DOI: 10.3390/biomedicines12010022] [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: 10/31/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
In this review, we discuss the long-known problem of tissue-specific carcinogenesis in BRCA1 and BRCA2 mutation carriers: while the genes are expressed ubiquitously, increased cancer risk is observed mostly in the breast and ovaries, and to a much lesser extent, in some other tissues such as the prostate or pancreas. We reevaluate hypotheses on the evolutionary origin of these mutations in humans. Also, we align together the reports that at least some great apes have much lower risks of epithelial cancers in general and breast cancer in particular with the fact that humans have more voluminous breast tissue as compared to their closest extant relatives, particularly chimpanzees and bonobos. We conjecture that this disparity may be a consequence of sexual selection, augmented via selection for enhanced lactation. Further, we argue that there is an organ-specific enigma similar to the Peto paradox: breast cancer risk in humans is only minimally correlated with breast size. These considerations lead to the hypothesis that, along with the evolutionary development of larger breasts in humans, additional changes have played a balancing role in suppressing breast cancer. These yet-to-be-discovered mechanisms, while purely speculative, may be valuable to understanding human breast cancer, though they may not be exclusive to the mammary gland epithelial cells. Combining these themes, we review some anti-carcinogenesis preventive strategies and prospects of new interventions against breast cancer.
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Affiliation(s)
- Tatyana V. Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Nikolay B. Pestov
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Institute of Biomedical Chemistry, Moscow 119121, Russia
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow 108819, Russia
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4
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Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
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Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
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Wang SM. A global perspective on the ethnic-specific BRCA variation and its implication in clinical application. JOURNAL OF THE NATIONAL CANCER CENTER 2022. [DOI: 10.1016/j.jncc.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Li J, Zhao B, Huang T, Qin Z, Wang SM. Human BRCA pathogenic variants were originated during recent human history. Life Sci Alliance 2022; 5:5/5/e202101263. [PMID: 35165121 PMCID: PMC8860097 DOI: 10.26508/lsa.202101263] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/05/2023] Open
Abstract
BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.
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Affiliation(s)
- Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Bojin Zhao
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Teng Huang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Zixin Qin
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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Nunney L. Resolving Peto's paradox: Modeling the potential effects of size-related metabolic changes, and of the evolution of immune policing and cancer suppression. Evol Appl 2020; 13:1581-1592. [PMID: 32821274 PMCID: PMC7428811 DOI: 10.1111/eva.12993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
The intrinsic risk of cancer increases with body size and longevity; however, big long-lived species do not exhibit this increase, a contradiction named Peto's paradox. Five hypotheses potentially resolving this paradox were modeled using the multistage model of carcinogenesis. The five hypotheses were based on (1) intrinsic changes in metabolic rate with body size; adaptive increase in immune policing of (2) cancer cells or (3) cells with driver mutations; or adaptive increase in cancer suppression via (4) decreased somatic mutation rate, or (5) increased genetic control. Parameter changes needed to stabilize cancer risk in three types of cancer were estimated for tissues scaled from mouse size and longevity to human and blue whale levels. The metabolic rate hypothesis alone was rejected due to a conflict between the required interspecific effect with the observed intraspecific effect of size on cancer risk, but some metabolic change was optionally incorporated in the other models. Necessary parameter changes in immune policing and somatic mutation rate far exceeded values observed; however, natural selection increasing the genetic suppression of cancer was generally consistent with data. Such adaptive increases in genetic control of cancers in large and/or long-lived animals raise the possibility that nonmodel animals will reveal novel anticancer mechanisms.
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Affiliation(s)
- Leonard Nunney
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California RiversideRiversideCAUSA
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8
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Vicens A, Posada D. Selective Pressures on Human Cancer Genes along the Evolution of Mammals. Genes (Basel) 2018; 9:genes9120582. [PMID: 30487452 PMCID: PMC6316132 DOI: 10.3390/genes9120582] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Cancer is a disease driven by both somatic mutations that increase survival and proliferation of cell lineages and the evolution of genes associated with cancer risk in populations. Several genes associated with cancer in humans, hereafter cancer genes, show evidence of germline positive selection among species. Taking advantage of a large collection of mammalian genomes, we systematically looked for signatures of germline positive selection in 430 cancer genes available in COSMIC. We identified 40 cancer genes with a robust signal of positive selection in mammals. We found evidence for fewer selective constraints—higher number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site (dN/dS)—and higher incidence of positive selection—more positively selected sites—in cancer genes bearing germline and recessive mutations that predispose to cancer. This finding suggests a potential association between relaxed selection, positive selection, and risk of hereditary cancer. On the other hand, we did not find significant differences in terms of tissue or gene type. Human cancer genes under germline positive selection in mammals are significantly enriched in the processes of DNA repair, with high presence of Fanconi anaemia/Breast Cancer A (FA/BRCA) pathway components and T cell proliferation genes. We also show that the inferred positively selected sites in the two genes with the strongest signal of positive selection, i.e., BRCA2 and PTPRC, are in regions of functional relevance, which could be relevant to cancer susceptibility.
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Affiliation(s)
- Alberto Vicens
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
- Galicia Sur Health Research Institute, 36310 Vigo, Spain.
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9
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Orlenko A, Chi PB, Liberles DA. Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. BMC Evol Biol 2017; 17:117. [PMID: 28545395 PMCID: PMC5445498 DOI: 10.1186/s12862-017-0962-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 05/09/2017] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Results Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Conclusions Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0962-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alena Orlenko
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, 19426, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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Orlenko A, Teufel AI, Chi PB, Liberles DA. Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biol Direct 2016; 11:31. [PMID: 27393343 PMCID: PMC4938953 DOI: 10.1186/s13062-016-0133-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/02/2016] [Indexed: 11/15/2022] Open
Abstract
Background While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily stable rate limiting (flux controlling) steps. Results A set of evolutionary simulations using a kinetic model of a metabolic pathway was performed under different conditions to evaluate the evolutionary stability of rate limiting steps. Simulations used combinations of selection for steady state flux, selection against the cost of molecular biosynthesis, and selection against the accumulation of high concentrations of a deleterious intermediate. Two mutational regimes were used, one with mutations that on average were neutral to molecular phenotype and a second with a preponderance of activity-destroying mutations. The evolutionary stability of rate limiting steps was low in all simulations with non-neutral mutational processes. Clustering of parameter co-evolution showed divergent inter-molecular evolutionary patterns under different evolutionary regimes. Conclusions This study provides a null model for pathway evolution when compensatory processes dominate with potential applications to predicting pathway functional change. This result also suggests a possible mechanism in which studies in statistical genetics that aim to associate a genotype to a phenotype assuming independent action of variants may be mis-specified through a mis-characterization of the link between individual gene function and pathway function. A better understanding of the genotype-phenotype map has potential applications in differentiating between compensatory changes and directional selection on pathways as well as detecting SNPs and fixed differences that might have phenotypic effects. Reviewers This article was reviewed by Arne Elofsson, David Ardell, and Shamil Sunyaev. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0133-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alena Orlenko
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Ashley I Teufel
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Peter B Chi
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, 19426, USA
| | - David A Liberles
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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Orlenko A, Hermansen RA, Liberles DA. Flux Control in Glycolysis Varies Across the Tree of Life. J Mol Evol 2016; 82:146-61. [PMID: 26920685 DOI: 10.1007/s00239-016-9731-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/29/2022]
Abstract
Biochemical thought posits that rate-limiting steps (defined here as points of flux control) are strongly selected as points of pathway regulation and control and are thus expected to be evolutionarily conserved. Conversely, population genetic thought based upon the concepts of mutation-selection-drift balance at the pathway level might suggest variation in flux controlling steps over evolutionary time. Glycolysis, as one of the most conserved and best characterized pathways, was studied to evaluate its evolutionary conservation. The flux controlling step in glycolysis was found to vary over the tree of life. Further, phylogenetic analysis suggested at least 60 events of gene duplication and additional events of putative positive selection that might alter pathway kinetic properties. Together, these results suggest that even with presumed largely negative selection on pathway output on glycolysis, the co-evolutionary process under the hood is dynamic.
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Affiliation(s)
- Alena Orlenko
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Russell A Hermansen
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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Lou DI, McBee RM, Le UQ, Stone AC, Wilkerson GK, Demogines AM, Sawyer SL. Rapid evolution of BRCA1 and BRCA2 in humans and other primates. BMC Evol Biol 2014; 14:155. [PMID: 25011685 PMCID: PMC4106182 DOI: 10.1186/1471-2148-14-155] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/27/2014] [Indexed: 12/04/2022] Open
Abstract
Background The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected that DNA repair proteins would be evolutionarily conserved, exhibiting very minimal sequence change over time. However, BRCA1, an essential gene involved in DNA repair, has been reported to be evolving rapidly despite the fact that many protein-altering mutations within this gene convey a significantly elevated risk for breast and ovarian cancers. Results To obtain a deeper understanding of the evolutionary trajectory of BRCA1, we analyzed complete BRCA1 gene sequences from 23 primate species. We show that specific amino acid sites have experienced repeated selection for amino acid replacement over primate evolution. This selection has been focused specifically on humans and our closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). After examining BRCA1 polymorphisms in 7 bonobo, 44 chimpanzee, and 44 rhesus macaque (Macaca mulatta) individuals, we find considerable variation within each of these species and evidence for recent selection in chimpanzee populations. Finally, we also sequenced and analyzed BRCA2 from 24 primate species and find that this gene has also evolved under positive selection. Conclusions While mutations leading to truncated forms of BRCA1 are clearly linked to cancer phenotypes in humans, there is also an underlying selective pressure in favor of amino acid-altering substitutions in this gene. A hypothesis where viruses are the drivers of this natural selection is discussed.
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Affiliation(s)
| | | | | | | | | | | | - Sara L Sawyer
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
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Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
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