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Pashinskaya KO, Samodova AV, Dobrodeeva LK. Features of the immune system and levels of blood transport components in residents of the arctic of the Russian Federation. Am J Hum Biol 2024:e24136. [PMID: 39032081 DOI: 10.1002/ajhb.24136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/22/2024] Open
Abstract
Changes in the immune status and the content of blood transport components reflect adaptations in the human body in response to adverse factors, showcasing the organism's adaptive capabilities and functional state. In this study, we aimed to determine the features of the immune system and levels of transport components of the blood system in residents of the Arctic of the Russian Federation. METHODS The peripheral venous blood of 191 residents of the Arctic of the Russian Federation (Murmansk Oblast) aged 21-55 analyzed comprehensively. Blood was sampled from the ulnar vein on an empty stomach in the morning. The hemogram, phagocytic activity of neutrophils, lymphocyte content with CD3, CD4, CD8, CD10, CD19, CD16, CD71, CD25, HLA-DR and CD95 phenotypes, concentrations of cytokines: TNF-α, IFN-γ, IL-6, IL-10, extracellular receptor pool: sCD71, sCD62L, sApo-1/Fas, sFasL, circulating immune complexes (CIC) and blood transport components: haptoglobin (Hp), transferrin, IgM, IgG, IgA, IgE (immunoglobulins M, G, A and E) low-density lipoproteins (LDL), and high density lipoprotein (HDL) were evaluated. The results were analyzed using descriptive statistics and comparative, factorial, and regression analyses. RESULTS Residents of the Murmansk Oblast exhibit a high prevalence of erythrocytosis (62.3%), thrombocytosis (25.0%), leukocytosis (20.1%), and increased hemoglobin (Hb) concentrations (42.5%), coupled with a significantly decreased level of active phagocytes (47.6%). A significantly decreased level of lymphocytes with phenotypes CD3 (92.4%), CD4 (40.4%), CD71 (62.3%) was revealed, coupled with the activation of lymphocytes with phenotypes CD16 (50.1%), CD8 (37.5%), CD19 (15.9%) and increased concentrations of pro-inflammatory IFN-γ (47.9%), IL-6 (33.3%), and TNF-α (20.1%). Elevated levels of sCD71 (56.6%), sCD62L (32.1%), sApo-1/Fas (22.1%), sFasL (10.2%), and autoantibodies to double-stranded DNA (57.1%), RNA (10.4%), and oLDL (oxidized-modified LDL) (16.3%) were recorded in residents of the Murmansk Oblast. Arctic residents showed elevated concentrations of Hp (63.3%), IgM (63.9%), IgA (42.4%), IgE (18.8%), LDL (24.9%), and a decreased level of HDL (21.1%) owing to an ApoA-I ligand deficiency (58.1%). Elevated levels of Hp in the blood are associated with increased erythrocyte aggregation frequency, T-lymphocyte activation, and increased concentration of free receptors of the extracellular pool. Increased IgM and IgA levels in the blood are attributed to the need to bind components of the extracellular receptor pool sCD71, sCD62L, sApo-1/Fas, sFasL and are associated with decreased levels lymphocyte with CD8 and CD16 phenotypes. The humoral immune response in Arctic residents is triggered when the cellular component of immunity is under strain which compounded by ineffective clearance of metabolic byproducts owing to imbalanced LDL and HDL lipid transport complexes. CONCLUSIONS The immune system of Arctic residents is characterized by excessive cytotoxic activity of lymphocytes and increased concentrations of pro-inflammatory cytokines, free forms of receptors of the extracellular pool, and autoantibodies. The change in the content of transport components of the blood system is directed at maintaining homeostasis by exhibiting antioxidant, anti-inflammatory, and immunoregulatory properties.
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Affiliation(s)
- Ksenya O Pashinskaya
- Institute of Physiology of Natural Adaptations, N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences (FECIAR UrB RAS), Arkhangelsk, Russian Federation
| | - Anna V Samodova
- Institute of Physiology of Natural Adaptations, N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences (FECIAR UrB RAS), Arkhangelsk, Russian Federation
| | - Liliya K Dobrodeeva
- Institute of Physiology of Natural Adaptations, N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences (FECIAR UrB RAS), Arkhangelsk, Russian Federation
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Guo Y, Hu M, Peng H, Zhang Y, Kuang R, Han Z, Wang D, Liao Y, Ma R, Xu Z, Sun J, Shen Y, Zhao C, Ma H, Liu D, Zhao S, Zhao Y. Epigenomic features associated with body temperature stabilize tissues during cold exposure in cold-resistant pigs. J Genet Genomics 2024:S1673-8527(24)00159-0. [PMID: 38969257 DOI: 10.1016/j.jgg.2024.06.017] [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: 03/27/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Cold stress in low-temperature environments can trigger changes in gene expression, but epigenomics regulation of temperature stability in vital tissues, including the fat and diencephalon, is still unclear. Here, we explore the cold-induced changes in epigenomic features in the diencephalon and fat tissues of two cold-resistant Chinese pig breeds, Min and Enshi black (ES) pigs, utilizing H3K27ac CUT&Tag, RNA-seq, and selective signature analysis. Our results show significant alterations in H3K27ac modifications in the diencephalon of Min pigs and the fat of ES pigs after cold exposure. Dramatic changes in H3K27ac modifications in Min pigs are primarily associated with genes involved in energy metabolism and hormone regulation, whereas those in ES pigs are primarily associated with immunity-related genes. Moreover, transcription factors PRDM1 and HSF1, which show evidence of selection, are enriched in genomic regions presenting cold-responsive alterations in H3K27ac modification in the Min pig diencephalon and ES pig fat, respectively. Our results indicate the diversity of epigenomic response mechanisms to cold exposure between Min and ES pigs, providing unique epigenetic resources for studies of low-temperature adaptation in large mammals.
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Affiliation(s)
- Yaping Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Mingyang Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China; Yazhouwan National Laboratory, 572000, Sanya, China
| | - Hao Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yan Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Renzhuo Kuang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zheyu Han
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Daoyuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yinlong Liao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China; Yazhouwan National Laboratory, 572000, Sanya, China
| | - Ruixian Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhixiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Jiahao Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yu Shen
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China; Yazhouwan National Laboratory, 572000, Sanya, China
| | - Hong Ma
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China.
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China; Yazhouwan National Laboratory, 572000, Sanya, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China; Yazhouwan National Laboratory, 572000, Sanya, China.
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Desgrouas C, Thalheim T, Cerino M, Badens C, Bonello-Palot N. Perilipin 1: a systematic review on its functions on lipid metabolism and atherosclerosis in mice and humans. Cardiovasc Res 2024; 120:237-248. [PMID: 38214891 DOI: 10.1093/cvr/cvae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 01/13/2024] Open
Abstract
The function of perilipin 1 in human metabolism was recently highlighted by the description of PLIN1 variants associated with various pathologies. These include severe familial partial lipodystrophy and early onset acute coronary syndrome. Additionally, certain variants have been reported to have a protective effect on cardiovascular diseases. The role of this protein remains controversial in mice and variant interpretation in humans is still conflicting. This literature review has two primary objectives (i) to clarify the function of the PLIN1 gene in lipid metabolism and atherosclerosis by examining functional studies performed in cells (adipocytes) and mice and (ii) to understand the impact of PLIN1 variants identified in humans based on the variant's location within the protein and the type of variant (missense or frameshift). To achieve these objectives, we conducted an extensive analysis of the relevant literature on perilipin 1, its function in cellular models and mice, and the consequences of its mutations in humans. We also utilized bioinformatics tools and consulted the Human Genetics Cardiovascular Disease Knowledge Portal to enhance the pathogenicity assessment of PLIN1 missense variants.
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Affiliation(s)
- Camille Desgrouas
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Faculte de médecine, 27 Bd Jean Moulin 13005 Marseille, France
| | - Tabea Thalheim
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Faculte de médecine, 27 Bd Jean Moulin 13005 Marseille, France
| | - Mathieu Cerino
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Faculte de médecine, 27 Bd Jean Moulin 13005 Marseille, France
- AP-HM, Service de Biochimie, Hôpital de la Timone 264 rue Saint Pierre 13005 Marseille, France
| | - Catherine Badens
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Faculte de médecine, 27 Bd Jean Moulin 13005 Marseille, France
- AP-HM, Service de Biochimie, Hôpital de la Timone 264 rue Saint Pierre 13005 Marseille, France
- Département de Génétique Médicale, APHM, Hôpital Timone Enfants, Hôpital de la Timone 264 rue Saint Pierre 13005 Marseille, France
| | - Nathalie Bonello-Palot
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Faculte de médecine, 27 Bd Jean Moulin 13005 Marseille, France
- Département de Génétique Médicale, APHM, Hôpital Timone Enfants, Hôpital de la Timone 264 rue Saint Pierre 13005 Marseille, France
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Lo RF, Sasaki JY. Lay Misperceptions of Culture as "Biological" and Suggestions for Reducing Them. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2024; 19:295-311. [PMID: 37493140 PMCID: PMC10790513 DOI: 10.1177/17456916231181139] [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] [Indexed: 07/27/2023]
Abstract
Culture is typically studied as socialized and learned. Yet lay intuitions may hold that culture is associated with biology via perceptions of race, presenting a problem for those who study culture: There may be a mismatch between how psychologists study culture and how their research is interpreted by lay audiences. This article is a call to researchers to recognize this mismatch as a problem and to critically evaluate the way we study culture. We first describe evidence that laypeople tend to associate culture with notions of folk biology. Next, we propose three suggestions for researchers: explicitly address whether biological processes are, or are not, relevant for studying culture in their work; consider using multiple methods because different methods for studying culture may come with assumptions about culture as more tied to socialization or biology; and represent all people as cultural by studying multiple forms of culture and by contextualizing all psychological research. Last, we provide an example for how researchers can implement these suggestions to encourage more accurate interpretations of findings.
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Affiliation(s)
| | - Joni Y. Sasaki
- Department of Psychology, University of Hawai‘i at Ma-noa
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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Ballinger MA, Mack KL, Durkin SM, Riddell EA, Nachman MW. Environmentally robust cis-regulatory changes underlie rapid climatic adaptation. Proc Natl Acad Sci U S A 2023; 120:e2214614120. [PMID: 37725649 PMCID: PMC10523592 DOI: 10.1073/pnas.2214614120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/26/2023] [Indexed: 09/21/2023] Open
Abstract
Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.
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Affiliation(s)
- Mallory A. Ballinger
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
- Department of Biology, Utah State University, Logan, UT84322
| | - Katya L. Mack
- Department of Biology, Stanford University, Stanford, CA94305
| | - Sylvia M. Durkin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Eric A. Riddell
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA50011
| | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
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Shu W, Wang Y, Li C, Zhang L, Zhuoma D, Yang P, Yan G, Chen C, Ba Y, Du P, Wang X. Single-cell Expression Atlas Reveals Cell Heterogeneity in the Creeping Fat of Crohn's Disease. Inflamm Bowel Dis 2023; 29:850-865. [PMID: 36715181 DOI: 10.1093/ibd/izac266] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Creeping fat (CrF) has been recognized to play a positive role in Crohn's disease (CD) progression, yet the cellular compositions within mesenteric adipose tissue (MAT) and their potential mechanism in CrF formation are poorly understood. METHODS Analysis of 10X single-cell RNA sequencing was performed on 67 064 cells from 3 pairs of surgically resected samples of CrF and their uninvolved MAT. The results were validated in another cohort with 6 paired MAT samples by immunofluorescence. RESULTS All samples manifested excellent consistency and repeatability in our study, and 10 cell types from the transcriptome atlas, including 20 clusters, were identified. In CrF, a specific vascular endothelial cell subpopulation highly expressing lipoprotein lipase was first identified, with a significantly increased proportion. This vascular endothelial cell subpopulation manifested robust peroxisome proliferator-activated receptor γ (PPARγ) transcription activity and an upregulated PPAR signaling pathway and was involved in lipid metabolism and the antibacterial response. A novel fibroblast subpopulation (FC3) with remarkable GREM1 and RFLNB expression was identified and validated to predominantly accumulate in the CrF. The FC3 was annotated as inflammation-associated fibroblasts, which are characterized by inflammatory responses and the regulation of Smad phosphorylation related to intestinal fibrosis. The trajectory of fibroblasts revealed their pro-inflammatory and profibrotic conversion tendency during CrF formation with corresponding gene dynamics. Additionally, we unprecedently dissected the different origins and functions of 6 macrophage subclusters within the myeloid compartment. CONCLUSIONS Our results uncover the cellular heterogeneity in the MAT of CD and the role of these various cellular compositions in CrF development. This comprehensive understanding of CrF provides future directions for in-depth research on and potential targets for MAT-based treatment.
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Affiliation(s)
- Weigang Shu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yongheng Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chuanding Li
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Lei Zhang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Deji Zhuoma
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Pengyu Yang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Guorong Yan
- Institute of Photomedicine, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai 200443, China
| | - Chunqiu Chen
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yongbing Ba
- OE Biotech Co., Ltd., Shanghai 201114, China
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200092, China
| | - Xiaolei Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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Balentine CM, Bolnick DA. Parallel evolution in human populations: A biocultural perspective. Evol Anthropol 2022; 31:302-316. [PMID: 36059181 DOI: 10.1002/evan.21956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/09/2022] [Accepted: 07/30/2022] [Indexed: 12/27/2022]
Abstract
Parallel evolution-where different populations evolve similar traits in response to similar environments-has been a topic of growing interest to biologists and biological anthropologists for decades. Parallel evolution occurs in human populations thanks to myriad biological and cultural mechanisms that permit humans to survive and thrive in diverse environments worldwide. Because humans shape and are shaped by their environments, biocultural approaches that emphasize the interconnections between biology and culture are key to understanding parallel evolution in human populations as well as the nuances of human biological variation and adaptation. In this review, we discuss how biocultural theory has been and can be applied to studies of parallel evolution and adaptation more broadly. We illustrate this through four examples of parallel evolution in humans: malaria resistance, lactase persistence, cold tolerance, and high-altitude adaptation.
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Affiliation(s)
- Christina M Balentine
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.,Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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Mörseburg A, Pagani L, Malyarchuk B, Derenko M, Kivisild T. Response to Wyckelsma et al.: Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation. Am J Hum Genet 2022; 109:967-972. [PMID: 35523147 PMCID: PMC9118108 DOI: 10.1016/j.ajhg.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
The common loss-of-function mutation R577X in the structural muscle protein ACTN3 emerged as a potential target of positive selection from early studies and has been the focus of insightful physiological work suggesting a significant impact on muscle metabolism. Adaptation to cold climates has been proposed as a key adaptive mechanism explaining its global allele frequency patterns. Here, we re-examine this hypothesis analyzing modern (n = 3,626) and ancient (n = 1,651) genomic data by using allele-frequency as well as haplotype homozygosity-based methods. The presented results are more consistent with genetic drift rather than selection in cold climates as the main driver of the ACTN3 R577X frequency distribution in human populations across the world. This Matters Arising paper is in response to Wyckelsma et al. (2021),1 published in The American Journal of Human Genetics. See also the response by Wyckelsma et al. (2022),2 published in this issue.
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Affiliation(s)
- Alexander Mörseburg
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, 35131 Padova, Italy
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 3000, Belgium.
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10
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Reconstructing Neanderthal diet: The case for carbohydrates. J Hum Evol 2021; 162:103105. [PMID: 34923240 DOI: 10.1016/j.jhevol.2021.103105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/22/2022]
Abstract
Evidence for plants rarely survives on Paleolithic sites, while animal bones and biomolecular analyses suggest animal produce was important to hominin populations, leading to the perspective that Neanderthals had a very-high-protein diet. But although individual and short-term survival is possible on a relatively low-carbohydrate diet, populations are unlikely to have thrived and reproduced without plants and the carbohydrates they provide. Today, nutritional guidelines recommend that around half the diet should be carbohydrate, while low intake is considered to compromise physical performance and successful reproduction. This is likely to have been the same for Paleolithic populations, highlighting an anomaly in that the basic physiological recommendations do not match the extensive archaeological evidence. Neanderthals had large, energy-expensive brains and led physically active lifestyles, suggesting that for optimal health they would have required high amounts of carbohydrates. To address this anomaly, we begin by outlining the essential role of carbohydrates in the human reproduction cycle and the brain and the effects on physical performance. We then evaluate the evidence for resource availability and the archaeological evidence for Neanderthal diet and investigate three ways that the anomaly between the archaeological evidence and the hypothetical dietary requirements might be explained. First, Neanderthals may have had an as yet unidentified genetic adaptation to an alternative physiological method to spare blood glucose and glycogen reserves for essential purposes. Second, they may have existed on a less-than-optimum diet and survived rather than thrived. Third, the methods used in dietary reconstruction could mask a complex combination of dietary plant and animal proportions. We end by proposing that analyses of Paleolithic diet and subsistence strategies need to be grounded in the minimum recommendations throughout the life course and that this provides a context for interpretation of the archaeological evidence from the behavioral and environmental perspectives.
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11
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Levy SB, Leonard WR. The evolutionary significance of human brown adipose tissue: Integrating the timescales of adaptation. Evol Anthropol 2021; 31:75-91. [PMID: 34910348 DOI: 10.1002/evan.21930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/14/2021] [Accepted: 11/19/2021] [Indexed: 12/20/2022]
Abstract
While human adaptability is regarded as a classical topic in anthropology, recent work provides new insight into metabolic adaptations to cold climates and the role of phenotypic plasticity in human evolution. A growing body of literature demonstrates that adults retain brown adipose tissue (BAT) which may play a role in non-shivering thermogenesis. In this narrative review, we apply the timescales of adaptation framework in order to explore the adaptive significance of human BAT. Human variation in BAT is shaped by multiple adaptive modes (i.e., allostasis, acclimatization, developmental adaptation, epigenetic inheritance, and genetic adaptation), and together the adaptive modes act as an integrated system. We hypothesize that plasticity in BAT facilitated the successful expansion of human populations into circumpolar regions, allowing for selection of genetic adaptations to cold climates to take place. Future research rooted in human energetics and biocultural perspectives is essential for understanding BAT's adaptive and health significance.
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Affiliation(s)
- Stephanie B Levy
- Department of Anthropology, CUNY Hunter College, New York, New York, USA.,New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - William R Leonard
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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12
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Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes. Sci Rep 2021; 11:21088. [PMID: 34702870 PMCID: PMC8548332 DOI: 10.1038/s41598-021-00123-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/01/2021] [Indexed: 11/15/2022] Open
Abstract
Evolutionary trends may underlie some aspects of the risk for common, non-communicable disorders, including psychiatric disease. We analyzed whole exome sequencing data from 80 unique individuals from India coming from families with two or more individuals with severe mental illness. We used Population Branch Statistics (PBS) to identify variants and genes under positive selection and identified 74 genes as candidates for positive selection. Of these, 20 were previously associated with Schizophrenia, Alzheimer’s disease and cognitive abilities in genome wide association studies. We then checked whether any of these 74 genes were involved in common biological pathways or related to specific cellular or molecular functions. We found that immune related pathways and functions related to innate immunity such as antigen binding were over-represented. We also evaluated for the presence of Neanderthal introgressed segments in these genes and found Neanderthal introgression in a single gene out of the 74 candidate genes. However, the introgression pattern indicates the region is unlikely to be the source for selection. Our findings hint at how selection pressures in individuals from families with a history of severe mental illness may diverge from the general population. Further, it also provides insights into the genetic architecture of severe mental illness, such as schizophrenia and its link to immune factors.
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13
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Kramer KL, Campbell BC, Achenbach A, Hackman JV. Sex differences in adipose development in a hunter-gatherer population. Am J Hum Biol 2021; 34:e23688. [PMID: 34655448 DOI: 10.1002/ajhb.23688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 09/09/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Humans are unusually sexually dimorphic in body composition, with adult females having on average nearly twice the fat mass as males. The development of adipose sex differences has been well characterized for children growing up in food-abundant environments, with less known about cross-cultural variation, particularly in populations without exposure to market foods, mechanized technologies, schooling, vaccination, or other medical interventions. METHODS To add to the existing cross-cultural data, we fit multiple growth curves to body composition and anthropometric data to describe adipose development for the Savanna Pumé, South American hunter-gatherers. RESULTS (1) Little evidence is found for an adiposity 'rebound' at the end of early childhood among either Savanna Pumé girls or boys. (2) Rather, fat deposition fluctuates during childhood, from age ~4 to ~9 years, with no appreciable accumulation until the onset of puberty, a pattern also observed among Congo Baka hunter-gatherers. (3) Body fat fluctuations are more pronounced for girls than boys. (4) The age of peak skeletal, weight, and adipose gains are staggered to a much greater extent among the Savanna Pumé compared to the National Health and Nutrition Examination Survey (NHANES III) reference, suggesting this is an important developmental strategy in lean populations. CONCLUSION Documenting growth patterns under diverse preindustrial energetic conditions provides an important baseline for understanding sex differences in body fat emerging today under food abundance.
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Affiliation(s)
- Karen L Kramer
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Benjamin C Campbell
- Department of Anthropology, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alan Achenbach
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Joseph V Hackman
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
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14
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Xu R, Li S, Li S, Wong EM, Southey MC, Hopper JL, Abramson MJ, Guo Y. Ambient temperature and genome-wide DNA methylation: A twin and family study in Australia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117700. [PMID: 34380236 DOI: 10.1016/j.envpol.2021.117700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Little is known about the association between ambient temperature and DNA methylation, which is a potential biological process through which ambient temperature affects health. This study aimed to evaluate the association between ambient temperature and DNA methylation across human genome. We included 479 Australian women, including 132 twin pairs and 215 sisters of these twins. Blood-derived DNA methylation was measured using the HumanMethylation450 BeadChip array. Data on average ambient temperature during eight different exposure windows [lag0d (the blood draw day), lag0-7d (the current day and previous seven days prior to blood draw), lag0-14d, lag0-21d, lag0-28d, lag0-90d, lag0-180d, and lag0-365d)] was linked to each participant's home address. For each cytosine-guanine dinucleotide (CpG), we evaluated the association between its methylation level and temperature using generalized estimating equations (GEE), adjusting for important covariates. We used comb-p and DMRcate to identify differentially methylated regions (DMRs). We identified 31 CpGs at which blood DNA methylation were significantly associated with ambient temperature with false discovery rate [FDR] < 0.05. There were 82 significant DMRs identified by both comb-p (Sidak p-value < 0.01) and DMRcate (FDR < 0.01). Most of these CpGs and DMRs only showed association with temperature during one specific exposure window. These CpGs and DMRs were mapped to 85 genes. These related genes have been related to many human chronic diseases or phenotypes (e.g., diabetes, arthritis, breast cancer, depression, asthma, body height) in previous studies. The signals of short-term windows (lag0d and lag0-21d) showed enrichment in biological processes related to cell adhesion. In conclusion, short-, medium-, and long-term exposures to ambient temperature were all associated with blood DNA methylation, but the target genomic loci varied by exposure window. These differential methylation signals may serve as potential biomarkers to understand the health impacts of temperature.
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Affiliation(s)
- Rongbin Xu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3800, Australia
| | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, 3010, Australia; Cancer Epidemiology Division, Cancer Council Victoria, VIC, 3004, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Michael J Abramson
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Yuming Guo
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia.
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15
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Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JT, Redondo SA, Prost S, Barsh G, Kaelin C, Phalke S, Chugani A, Gilbert M, Miquelle D, Zachariah A, Borthakur U, Reddy A, Louis E, Ryder OA, Jhala YV, Petrov D, Excoffier L, Hadly E, Ramakrishnan U. Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection. Mol Biol Evol 2021; 38:2366-2379. [PMID: 33592092 PMCID: PMC8136513 DOI: 10.1093/molbev/msab032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world’s wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.
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Affiliation(s)
| | - Anubhab Khan
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA.,End2End Genomics, LLC, Davis, CA, USA
| | - Alexandre Gouy
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gili Greenbaum
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Ecology, Evolution & Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexandre Thiéry
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jonathan T Kang
- Department of Biology, Stanford University, Stanford, CA, USA.,Genome Institute of Singapore, A*STAR, Singapore
| | | | - Stefan Prost
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Gregory Barsh
- Hudsonalpha Institute, Hunstville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | | | - Martin Gilbert
- Wildlife Conservation Society, Russia Program, New York, NY, USA.,College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Dale Miquelle
- Wildlife Conservation Society, Russia Program, New York, NY, USA
| | | | | | - Anuradha Reddy
- Laboratory for Conservation of Endangered Species, CCMB, Hyderabad, India
| | - Edward Louis
- Department of Genetics, Omaha Zoo, Omaha, NE, USA
| | - Oliver A Ryder
- San Diego Zoo, Institute for Conservation Research, Escondido, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Elizabeth Hadly
- Wildlife Conservation Society, Russia Program, New York, NY, USA
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16
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. Mol Biol Evol 2021; 38:3093-3110. [PMID: 33784744 PMCID: PMC8321547 DOI: 10.1093/molbev/msab078] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | | | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Andrey N Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Podolsk, Russia
| | - Oksana I Boronetskaya
- Moscow Agrarian Academy, Timiryazev Russian State Agrarian University, Moscow, Russia
| | | | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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17
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Xia T, Zhang L, Sun G, Yang X, Zhao C, Zhang H. Insights into cold tolerance in sable (Martes zibellina) from the adaptive evolution of lipid metabolism. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Tiis RP, Osipova LP, Galieva ER, Lichman DV, Voronina EN, Melikhova AV, Orlov YL, Filipenko ML. [N-aсetyltransferase (NAT2) gene polymorphism and gene network analysis]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2021; 67:213-221. [PMID: 34142528 DOI: 10.18097/pbmc20216703213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To search for new targets of therapy, it is necessary to reconstruct the gene network of the disease, and identify the interaction of genes, proteins, and drug compounds. Using the online bioinformatics tools we have analyzed the current data set related to the metabolism of xenobiotics, mediated by the N-acetyltransferase 2 (NAT2) gene. The study of allelic polymorphism of the NAT2 gene has a prognostic value, allowing to determine the risk of a number of oncological diseases, the degree of increased risk due to smoking and exposure to chemical carcinogens, including drugs. The aim of this study was to determine the frequencies of two important "slow" variants of the NAT2 gene (NAT2*5, rs1801280 and NAT2*7, rs1799931), which significantly affected the rate of xenobiotic acetylation among the indigenous Nenets population of Northern Siberia. The obtained frequencies of polymorphic variants among the Nenets occupy an intermediate value between those for Europeans and Asians, which might indicate specific features of adaptation. We present a model of the distribution of two polymorphic variants of the NAT2 gene involved in the biotransformation of xenobiotics to study the characteristics of their metabolism in the indigenous inhabitants of Yamal.
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Affiliation(s)
- R P Tiis
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - L P Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - E R Galieva
- Novosibirsk State University, Novosibirsk, Russia
| | - D V Lichman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - E N Voronina
- Novosibirsk State University, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Melikhova
- Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
| | - Y L Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia; I.M. Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
| | - M L Filipenko
- Novosibirsk State University, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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19
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Liu Q, Deng Y, Song A, Xiang Y, Chen D, Wei L. Comparative analysis of mite genomes reveals positive selection for diet adaptation. Commun Biol 2021; 4:668. [PMID: 34083730 PMCID: PMC8175442 DOI: 10.1038/s42003-021-02173-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
Diet is a powerful evolutionary force for species adaptation and diversification. Acari is one of the most abundant clades of Arachnida, exhibiting diverse dietary types, while the underlying genetic adaptive mechanisms are not fully understood. Based on comparative analyses of 15 Acari genomes, we found genetic bases for three specialized diets. Herbivores experienced stronger selection pressure than other groups; the olfactory genes and gene families involving metabolizing toxins showed strong adaptive signals. Genes and gene families related to anticoagulation, detoxification, and haemoglobin digestion were found to be under strong selection pressure or significantly expanded in the blood-feeding species. Lipid metabolism genes have a faster evolutionary rate and been subjected to greater selection pressures in fat-feeding species; one positively selected site in the fatty-acid amide hydrolases 2 gene was identified. Our research provides a new perspective for the evolution of Acari and offers potential target loci for novel pesticide development.
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Affiliation(s)
- Qiong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yuhua Deng
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - An Song
- ShaanXi JunDa Forensic Medicine Expertise Station, The Fourth Military Medical University, Xi'an, China
| | - Yifan Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
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20
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Hernandez M, Perry GH. Scanning the human genome for "signatures" of positive selection: Transformative opportunities and ethical obligations. Evol Anthropol 2021; 30:113-121. [PMID: 33788352 DOI: 10.1002/evan.21893] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/25/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over-assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying "signatures" of past positive selection from haplotype-based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome-wide "scans" for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome-wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross-application of the genome-wide scan approach to existing datasets, which we also discuss.
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Affiliation(s)
- Margarita Hernandez
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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21
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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22
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Fan Y, Gao Q, Guan JX, Liu L, Hong M, Jun L, Wang L, Ding HF, Jiang LH, Hou BY, Li M, Song ZQ, Sun DQ, Yan CQ, Ma L. DDAH2 (-449 G/C) G allele is positively associated with leukoaraiosis in northeastern China: a double-blind, intergroup comparison, case-control study. Neural Regen Res 2021; 16:1592-1597. [PMID: 33433489 PMCID: PMC8323672 DOI: 10.4103/1673-5374.303037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cerebrovascular endothelial dysfunction is involved in the progression of leukoaraiosis. Asymmetric dimethylarginine is a competitive inhibitor of nitric oxide, which is highly expressed in patients with leukoaraiosis. Dimethylarginine dimethylaminohydrolase (DDAH) is a hydrolytic enzyme that is primarily responsible for eliminating asymmetric dimethylarginine, and it plays a role in the pathogenesis of cardiovascular and cerebrovascular diseases. The DDAH2 subtype is expressed in organs rich in induced nitric oxide synthase, including the heart, the placenta, and the cerebral endothelium during cerebral ischemia, in the stress state, or under neurotoxicity. Overexpression of the DDAH2 gene can inhibit asymmetric dimethylarginine-induced peripheral circulating endothelial cell dysfunction. However, it is unknown whether this polymorphism regulates plasma asymmetric dimethylarginine levels in patients with leukoaraiosis. In this double-blind study, we recruited 46 patients with leukoaraiosis and 46 healthy, matched controls. Plasma asymmetric dimethylarginine levels were determined using enzyme-linked immunoassays. Genomic DNA was isolated from whole blood samples, and polymerase chain reaction, SmaI restriction enzyme digestion, restriction fragment length polymorphisms, and agarose electrophoresis were used to detect DDAH2 (-449 G/C) gene polymorphisms. The results revealed that 95.65% of leukoaraiosis patients had recessive genetic models (GG and CG), while 89.13% of healthy control subjects had dominant genetic models (CC and CG). There was a significant difference in the genotype composition ratio between leukoaraiosis patients and healthy controls (P = 0.0002). The frequency of G alleles in the leukoaraiosis patients (71.74%) was significantly higher than in healthy controls, whereas the frequency of C alleles was lower (χ2= 13.9580, P = 0.0002). Furthermore, asymmetric dimethylarginine concentrations in subjects with the GG genotype were significantly higher than in subjects with the CG and CC genotypes (Kruskal–Wallis H = 24.5955, P < 0.0001). In addition, the GG genotype of DDAH2 (-449 G/C) was more common in patients with leukoaraiosis. These findings suggest that the G allele of DDAH2 (-449 G/C) is a risk factor for leukoaraiosis morbidity and is correlated with high levels of asymmetric dimethylarginine. This study was approved by the Institutional Ethics Committee of the 2nd Affiliated Hospital of Harbin Medical University of China (approval No. KY2016-177) on July 28, 2016.
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Affiliation(s)
- Ying Fan
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Qiang Gao
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jia-Xin Guan
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lei Liu
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ming Hong
- Department of Geriatrics, Tongling Municipal Hospital, Tongling, Anhui Province, China
| | - Li Jun
- Department of Cardiovascular Medicine, Shanxi Cardiovascular Hospital, Taiyuan, Shanxi Province, China
| | - Li Wang
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hai-Feng Ding
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Li-Hong Jiang
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Bo-Yu Hou
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Mei Li
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhi-Qiang Song
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - De-Qin Sun
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chao-Qi Yan
- Physical Examination Center, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lan Ma
- Department of Geriatrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
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23
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Guo Y, Bian X, Liu J, Zhu M, Li L, Yao T, Tang C, Ravichandran V, Liao P, Papadimitriou K, Yin J. Dietary Components, Microbial Metabolites and Human Health: Reading between the Lines. Foods 2020; 9:E1045. [PMID: 32756378 PMCID: PMC7466307 DOI: 10.3390/foods9081045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Trillions of bacteria reside in the human gut and they metabolize dietary substances to obtain nutrients and energy while producing metabolites. Therefore, different dietary components could affect human health in various ways through microbial metabolism. Many such metabolites have been shown to affect human physiological activities, including short-chain fatty acids metabolized from carbohydrates; indole, kynurenic acid and para-cresol, metabolized from amino acids; conjugated linoleic acid and linoleic acid, metabolized from lipids. Here, we review the features of these metabolites and summarize the possible molecular mechanisms of their metabolisms by gut microbiota. We discuss the potential roles of these metabolites in health and diseases, and the interactions between host metabolism and the gut microbiota. We also show some of the major dietary patterns around the world and hope this review can provide insights into our eating habits and improve consumers' health conditions.
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Affiliation(s)
- Yao Guo
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha 410006, China
| | - Xiaohan Bian
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha 410006, China
| | - Jiali Liu
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha 410006, China
| | - Ming Zhu
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
| | - Lin Li
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
| | - Tingyu Yao
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
| | - Congjia Tang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
| | - Vinothkannan Ravichandran
- State Key Laboratory of Microbial Technology, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China;
| | - Peng Liao
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China;
| | - Konstantinos Papadimitriou
- Department of Food Science and Technology, School of Agriculture and Food, University of Peloponnese, 22131 Antikalamos, Greece;
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410006, China; (Y.G.); (X.B.); (J.L.); (M.Z.); (L.L.); (T.Y.); (C.T.)
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha 410006, China
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24
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Khrunin AV, Khvorykh GV, Fedorov AN, Limborska SA. Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia. PLoS One 2020; 15:e0228778. [PMID: 32023328 PMCID: PMC7001972 DOI: 10.1371/journal.pone.0228778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populations have hardly been analyzed. We searched for the genomic signatures of positive selection in (1) the genome-wide microarray data of 432 people from eight different northern Russian populations and (2) the whole-genome sequences of 250 people from Northern Eurasia from a public repository through testing the extended haplotype homozigosity (EHH) and direct comparison of allele frequency, respectively. The 20 loci with the strongest selection signals were characterized in detail. Among the top EHH hits were the NRG3 and NBEA genes, which are involved in the development and functioning of the neural system, the PTPRM gene, which mediates cell-cell interactions and adhesion, and a region on chromosome 4 (chr4:28.7-28.9 Mb) that contained several loci affiliated with different classes of non-coding RNAs (RN7SL101P, MIR4275, MESTP3, and LINC02364). NBEA and the region on chromosome 4 were novel selection targets that were identified for the first time in Western Siberian populations. Cross-population comparisons of EHH profiles suggested a particular role for the chr4:28.7-28.9 Mb region in the local adaptation of Western Siberians. The strongest selection signal identified in Siberian sequenced genomes was formed by six SNPs on chromosome 11 (chr11:124.9-125.2 Mb). This region included well-known genes SLC37A2 and PKNOX2. SLC37A2 is most-highly expressed in the gut. Its expression is regulated by vitamin D, which is often deficient in northern regions. The PKNOX2 gene is a transcription factor of the homeobox family that is expressed in the brain and many other tissues. This gene is associated with alcohol addiction, which is widespread in many Northern Eurasian populations.
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Affiliation(s)
- Andrey V. Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Gennady V. Khvorykh
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Alexei N. Fedorov
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
- Department of Medicine, University of Toledo, Toledo, Ohio, United States of America
| | - Svetlana A. Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
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25
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Tabikhanova LE, Osipova LP, Voronina EN, Bragin AO, Filipenko ML. Polymorphism of lipid exchange genes in some populations of South and East Siberia. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- L. E. Tabikhanova
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | - L. P. Osipova
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
| | - E. N. Voronina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS; Novosibirsk State University
| | | | - M. L. Filipenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS; Novosibirsk State University
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26
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Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift. Proc Natl Acad Sci U S A 2019; 116:13446-13451. [PMID: 31209046 DOI: 10.1073/pnas.1901093116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.
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27
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Karafet TM, Osipova LP, Savina OV, Hallmark B, Hammer MF. Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations. Am J Hum Biol 2018; 30:e23194. [PMID: 30408262 DOI: 10.1002/ajhb.23194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/26/2018] [Accepted: 09/23/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES We examined autosomal genome-wide SNPs and Y-chromosome data from 15 Siberian and 12 reference populations to study the affinities of Siberian populations, and to address hypotheses about the origin of the Samoyed peoples. METHODS Samples were genotyped for 567 096 autosomal SNPs and 147 Y-chromosome polymorphic sites. For several analyses, we used 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples. To examine genetic relatedness among populations, we applied PCA, FST , TreeMix, and ADMIXTURE analyses. To explore the potential effect of demography and evolutionary processes, the distribution of ROH and IBD sharing within population were studied. RESULTS Analyses of autosomal and Y-chromosome data reveal high differentiation of the Siberian groups. The Siberian populations have a large proportion of their genome in ROH and IBD segments. Several populations (ie, Nganasans, Evenks, Yukagirs, and Koryaks) do not appear to have experienced admixture with other Siberian populations (ie, producing only positive f3), while for the other tested populations the composition of mixing sources always included Nganasans or Evenks. The Nganasans from the Taymyr Peninsula demonstrate the greatest level of shared shorter ROH and IBD with nearly all other Siberian populations. CONCLUSIONS Autosomal SNP and Y-chromosome data demonstrate that Samoyedic populations differ significantly in their genetic composition. Genetic relationship is observed only between Forest and Tundra Nentsi. Selkups are affiliated with the Kets from the Yenisey River, while the Nganasans are separated from their linguistic neighbors, showing closer affinities with the Evenks and Yukagirs.
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Affiliation(s)
- Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Olga V Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona
| | - Brian Hallmark
- Interdisciplinary Program in Statistics, University of Arizona, Tucson, Arizona
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
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