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Koloi S, Ganguly I, Singh S, Dixit S. Whole genome re-sequencing reveals high altitude adaptation signatures and admixture in Ladakhi cattle. Gene 2024; 933:148957. [PMID: 39306203 DOI: 10.1016/j.gene.2024.148957] [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: 09/14/2023] [Revised: 08/19/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024]
Abstract
Ladakhi cattle, native to the high-altitude region of Ladakh in northern India (ranging from 3,000 to 5,000 m above sea level), have evolved unique genetic adaptations to thrive in harsh environmental conditions, such as hypoxia, extreme cold, and low humidity. This study explored the genome of Ladakhi cattle to investigate genetic structure, selection signatures, and adaptive mechanisms. Whole genome sequencing reads, generated on Illumina NovaSeq 6000 platform, were aligned to the Bos taurus reference genome with BWA-MEM. SNPs were identified and filtered using GATK and bcftools, and functionally annotated with SnpEff. For population genomic analysis, PCA and admixture modeling assessed genetic structure, while Neighbor-Joining trees, LD decay, nucleotide diversity (π), and FST evaluated phylogenetic relationships and genetic variation. Selective sweeps were detected using RAiSD, and gene-set enrichment and protein-protein interaction analyses were conducted to explore functional pathways related to adaptation. The study revealed 3,759,279 unique SNPs and demonstrated that Ladakhi cattle form a distinct genetic cluster with an estimated admixture of 68 % Bos indicus and 32 % Bos taurus ancestry. Key findings include rapid linkage disequilibrium decay, low inbreeding level, and the identification of selection signatures and genes associated with hypoxia response, energy metabolism, and cold adaptation. Mean nucleotide diversity (π, 0.0037) and FST values indicated moderate genetic differentiation from other breeds. The analysis highlighted selection signatures for genes like HIF1A, ENO4, ANGPT1, EPO, NOS3, MAPK3, HMOX1, BCL2,CAMK2D, MTOR, AKT2,PIK3CB, and MAP2K1, among others, including various keratin and heat shock proteins. The interaction between genes associated with hypoxia signaling (HIF-1) and other enriched pathways such as PI3K, mTOR, NFκB, ERK, and ER stress, reveals a complex mechanism for managing hypoxic stress in Ladakhi cattle. These findings offer valuable insights for breeding programs aimed at enhancing livestock resilience in extreme environments and enhance understanding of mammalian adaptation to high-altitude conditions.
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Affiliation(s)
- Subrata Koloi
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India; Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, India
| | - Indrajit Ganguly
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India.
| | - Sanjeev Singh
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India
| | - Satpal Dixit
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, India.
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Wang Z, Song B, Yao J, Li X, Zhang Y, Tang Z, Yi G. Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs. J Anim Sci Biotechnol 2024; 15:97. [PMID: 38982489 PMCID: PMC11234542 DOI: 10.1186/s40104-024-01053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear. RESULTS Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments. CONCLUSIONS In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.
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Affiliation(s)
- Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Jianyu Yao
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Yan Zhang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
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Sunwoo BY, Malhotra A. Mechanical Interactions Between the Upper Airway and the Lungs that Affect the Propensity to Obstructive Sleep Apnea in Health and Chronic Lung Disease. Sleep Med Clin 2024; 19:211-218. [PMID: 38692746 PMCID: PMC11168246 DOI: 10.1016/j.jsmc.2024.02.001] [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] [Indexed: 05/03/2024]
Abstract
Obstructive sleep apnea (OSA) is a common disorder characterized by repetitive narrowing and collapse of the upper airways during sleep. It is caused by multiple anatomic and nonanatomic factors but end-expiratory lung volume (EELV) is an important factor as increased EELV can stabilize the upper airway via caudal traction forces. EELV is impacted by changes in sleep stages, body position, weight, and chronic lung diseases, and this article reviews the mechanical interactions between the lungs and upper airway that affect the propensity to OSA. In doing so, it highlights the need for additional research in this area.
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Affiliation(s)
- Bernie Y Sunwoo
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, San Diego, CA, USA.
| | - Atul Malhotra
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, San Diego, CA, USA
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Liu B, Yuan M, Yang M, Zhu H, Zhang W. The Effect of High-Altitude Hypoxia on Neuropsychiatric Functions. High Alt Med Biol 2024; 25:26-41. [PMID: 37815821 DOI: 10.1089/ham.2022.0136] [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: 10/11/2023] Open
Abstract
Liu, Bo, Minlan Yuan, Mei Yang, Hongru Zhu, and Wei Zhang. The effect of high-altitude hypoxia on neuropsychiatric functions. High Alt Med Biol. 25:26-41, 2024. Background: In recent years, there has been a growing popularity in engaging in activities at high altitudes, such as hiking and work. However, these high-altitude environments pose risks of hypoxia, which can lead to various acute or chronic cerebral diseases. These conditions include common neurological diseases such as acute mountain sickness (AMS), high-altitude cerebral edema, and altitude-related cerebrovascular diseases, as well as psychiatric disorders such as anxiety, depression, and psychosis. However, reviews of altitude-related neuropsychiatric conditions and their potential mechanisms are rare. Methods: We conducted searches on PubMed and Google Scholar, exploring existing literature encompassing preclinical and clinical studies. Our aim was to summarize the prevalent neuropsychiatric diseases induced by altitude hypoxia, the potential pathophysiological mechanisms, as well as the available pharmacological and nonpharmacological strategies for prevention and intervention. Results: The development of altitude-related cerebral diseases may arise from various pathogenic processes, including neurovascular alterations associated with hypoxia, cytotoxic responses, activation of reactive oxygen species, and dysregulation of the expression of hypoxia inducible factor-1 and nuclear factor erythroid 2-related factor 2. Furthermore, the interplay between hypoxia-induced neurological and psychiatric changes is believed to play a role in the progression of brain damage. Conclusions: While there is some evidence pointing to pathophysiological changes in hypoxia-induced brain damage, the precise mechanisms responsible for neuropsychiatric alterations remain elusive. Currently, the range of prevention and intervention strategies available is primarily focused on addressing AMS, with a preference for prevention rather than treatment.
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Affiliation(s)
- Bo Liu
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China
- Zigong Mental Health Center, Zigong, China
| | - Minlan Yuan
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China
| | - Mei Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Basic Medical Sciences and Forensic Medicine, Chengdu, Sichuan
| | - Hongru Zhu
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China
| | - Wei Zhang
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
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Cui J, Nima O, Zhaxi D, Jin C, Wang R, Diao Y, Chen Y, Xu X, Li X. Health status of the population in Naqu, Tibet and its latent class analysis: a cross-sectional survey. Front Public Health 2023; 11:1223382. [PMID: 38026270 PMCID: PMC10654740 DOI: 10.3389/fpubh.2023.1223382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Through a survey and analysis of the population's present state of health, it is possible to give data support for improving the health status of inhabitants in Naqu, Tibet. Additionally, it is possible to provide specific recommendations for the development of medical and healthcare facilities in Tibet. Methods The health scores of the participants were based on their responses to the four main sections of the questionnaire: dietary habits, living habits, health knowledge, and clinical disease history, and the variability of health status among groups with different characteristics was analyzed based on the scores. The four major sections were used to create classes of participants using latent class analysis (LCA). Using logistic regression, the factors influencing the classification of latent classes of health status were investigated. Results A total of 995 residents from 10 counties in Naqu were selected as the study subjects. And their demographic characteristics were described. The mean health score of residents after standardization was 81.59 ± 4.68. With the exception of gender, health scores differed between groups by age, education level, different occupations, marital status, and monthly income. The health status in Naqu, Tibet, was divided into two groups (entropy = 0.29, BLRT = 0.001, LMRT = 0.001) defined as the "good health group" and the "general health group." A monthly income of more than ¥5000 adverse to good health in Naqu, Tibet. Discussion Single, well-educated young adults in Naqu, Tibet, have outstanding health. The vast majority of people in Tibet's Naqu region were in good health. Furthermore, the population's latent health status was divided into two classes, each with good dietary and living habits choices, low health knowledge, and a history of several clinical diseases. Univariate and multivariate logistic regression analysis showed that monthly income more than ¥5000 was an independent risk factor for poor health status.
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Affiliation(s)
- Jiaxue Cui
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Ouzhu Nima
- Institute of High Altitude Medicine, People’s Hospital of Naqu Affiliated to Dalian Medical University, Naqu, China
| | - Duoji Zhaxi
- Institute of High Altitude Medicine, People’s Hospital of Naqu Affiliated to Dalian Medical University, Naqu, China
| | - Chenxin Jin
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Ruiqi Wang
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Yizhuo Diao
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Yongxing Chen
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Xiaoguang Xu
- Institute of High Altitude Medicine, People’s Hospital of Naqu Affiliated to Dalian Medical University, Naqu, China
- Department of Neurosurgery, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaofeng Li
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
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Meng J, Huang F, Shi J, Zhang C, Feng L, Wang S, Li H, Guo Y, Hu X, Li X, He W, Cheng J, Wu Y. Integrated biomarker profiling of the metabolome associated with type 2 diabetes mellitus among Tibetan in China. Diabetol Metab Syndr 2023; 15:146. [PMID: 37393287 DOI: 10.1186/s13098-023-01124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023] Open
Abstract
INTRODUCTION Metabolomic signatures of type 2 diabetes mellitus (T2DM) in Tibetan Chinese population, a group with high diabetes burden, remain largely unclear. Identifying the serum metabolite profile of Tibetan T2DM (T-T2DM) individuals may provide novel insights into early T2DM diagnosis and intervention. METHODS Hence, we conducted untargeted metabolomics analysis of plasma samples from a retrospective cohort study with 100 healthy controls and 100 T-T2DM patients by using liquid chromatography-mass spectrometry. RESULTS The T-T2DM group had significant metabolic alterations that are distinct from known diabetes risk indicators, such as body mass index, fasting plasma glucose, and glycosylated hemoglobin levels. The optimal metabolite panels for predicting T-T2DM were selected using a tenfold cross-validation random forest classification model. Compared with the clinical features, the metabolite prediction model provided a better predictive value. We also analyzed the correlation of metabolites with clinical indices and found 10 metabolites that were independently predictive of T-T2DM. CONCLUSION By using the metabolites identified in this study, we may provide stable and accurate biomarkers for early T-T2DM warning and diagnosis. Our study also provides a rich and open-access data resource for optimizing T-T2DM management.
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Affiliation(s)
- Jinli Meng
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Fangfang Huang
- Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Jing Shi
- Department of Science and Education Section, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Chenghui Zhang
- Department of Endocrinology and Metabolism, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Li Feng
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Suyuan Wang
- Department of Endocrinology and Metabolism, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Hengyan Li
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Yongyue Guo
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Xin Hu
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Xiaomei Li
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Wanlin He
- Department of Radiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China
| | - Jian Cheng
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China.
| | - Yunhong Wu
- Department of Endocrinology and Metabolism, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital. C.T.), No. 20, Xi Mian Qiao Heng Jie, Wuhou District, Chengdu, Sichuan, China.
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Abbasi BA, Chanana N, Palmo T, Pasha Q. Disparities in COVID-19 incidence and fatality rates at high-altitude. PeerJ 2023; 11:e14473. [PMID: 36788813 PMCID: PMC9922493 DOI: 10.7717/peerj.14473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/06/2022] [Indexed: 02/11/2023] Open
Abstract
Background SARS-CoV-2 has affected every demography disproportionately, including even the native highland populations. Hypobaric-hypoxic settings at high-altitude (HA, >2,500 masl) present an extreme environment that impacts the survival of permanent residents, possibly including SARS-CoV-2. Conflicting hypotheses have been presented for COVID-19 incidence and fatality at HA. Objectives To evaluate protection or risk against COVID-19 incidence and fatality in humans under hypobaric-hypoxic environment of high-altitude (>2,501 masl). Methods Global COVID-19 data of March 2020-21, employed from official websites of the Indian Government, John Hopkins University, and Worldometer were clustered into 6 altitude categories. Clinical cofactors and comorbidities data were evaluated with COVID-19 incidence and fatality. Extensive comparisons and correlations using several statistical tools estimated the risk and protection. Results Of relevance, data analyses revealed four distinct responses, namely, partial risk, total risk, partial protection, and total protection from COVID-19 at high-altitude indicating a mixed baggage and complexity of the infection. Surprisingly, it included the countries within the same geographic region. Moreover, body mass index, hypertension, and diabetes correlated significantly with COVID-19 incidence and fatality rate (P ≤ 0.05). Conclusions Varied patterns of protection and risk against COVID-19 incidence and fatality were observed among the high-altitude populations. It is though premature to generalize COVID-19 effects on any particular demography without further extensive studies.
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Affiliation(s)
- Bilal Ahmed Abbasi
- CSIR-Institute of Genomics and Integrative Biology, Genomics and Molecular Medicine, Delhi, India
| | - Neha Chanana
- CSIR-Institute of Genomics and Integrative Biology, Genomics and Molecular Medicine, Delhi, India
| | - Tsering Palmo
- CSIR-Institute of Genomics and Integrative Biology, Genomics and Molecular Medicine, Delhi, India
| | - Qadar Pasha
- CSIR-Institute of Genomics and Integrative Biology, Genomics and Molecular Medicine, Delhi, India
- Institute of Hypoxia Research, New Delhi, India
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Cui J, Zhaxi D, Sun X, Teng N, Wang R, Diao Y, Jin C, Chen Y, Xu X, Li X. Association of dietary pattern and Tibetan featured foods with high-altitude polycythemia in Naqu, Tibet: A 1:2 individual-matched case-control study. Front Nutr 2022; 9:946259. [PMID: 36211499 PMCID: PMC9538783 DOI: 10.3389/fnut.2022.946259] [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: 05/17/2022] [Accepted: 09/01/2022] [Indexed: 12/01/2022] Open
Abstract
This study focused on the association of dietary patterns and Tibetan featured foods with high-altitude polycythemia (HAPC) in Naqu, Tibet, to explore the risk factors of HAPC in Naqu, Tibet, to raise awareness of the disease among the population and provide evidence for the development of prevention and treatment interventions. A 1:2 individual-matched case-control study design was used to select residents of three villages in the Naqu region of Tibet as the study population. During the health examination and questionnaire survey conducted from December 2020 to December 2021, a sample of 1,171 cases was collected. And after inclusion and exclusion criteria and energy intake correction, 100 patients diagnosed with HAPC using the “Qinghai criteria” were identified as the case group, while 1,059 patients without HAPC or HAPC -related diseases were identified as the control group. Individuals were matched by a 1:2 propensity score matching according to gender, age, body mass index (BMI), length of residence, working altitude, smoking status, and alcohol status. Dietary patterns were determined by a principal component analysis, and the scores of study subjects for each dietary pattern were calculated. The effect of dietary pattern scores and mean daily intake (g/day) of foods in the Tibetan specialty diet on the prevalence of HAPC was analyzed using conditional logistic regression. After propensity score matching, we found three main dietary patterns among residents in Naqu through principal component analysis, which were a “high protein pattern,” “snack food pattern,” and “vegetarian food pattern.” All three dietary patterns showed a high linear association with HAPC (p < 0.05) and were risk factors for HAPC. In the analysis of the relationship between Tibetan featured foods and the prevalence of HAPC, the results of the multifactorial analysis following adjustment for other featured foods showed that there was a positive correlation between the average daily intake of tsampa and the presence of HAPC, which was a risk factor. Additionally, there was an inverse correlation between the average daily intake of ghee tea and the presence of HAPC, which was a protective factor.
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Affiliation(s)
- Jiaxue Cui
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Duoji Zhaxi
- Institute of High Altitude Medicine, People’s Hospital of Naqu Affiliated to Dalian Medical University, Naqu, China
| | - Xianzhi Sun
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Nan Teng
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Ruiqi Wang
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Yizhuo Diao
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Chenxin Jin
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Yongxing Chen
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
| | - Xiaoguang Xu
- Institute of High Altitude Medicine, People’s Hospital of Naqu Affiliated to Dalian Medical University, Naqu, China
- Department of Neurosurgery, Second Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Xiaoguang Xu,
| | - Xiaofeng Li
- Department of Epidemiology and Health Statistics, Dalian Medical University, Dalian, China
- Xiaofeng Li,
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9
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Melanson G, Du Bois AC, Webster C, Uniacke J. ISGylation
directly modifies hypoxia‐inducible factor‐2α and enhances its polysome association. FEBS Lett 2022; 596:2834-2850. [DOI: 10.1002/1873-3468.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Gaelan Melanson
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
| | - Antonia C. Du Bois
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
| | - Caroline Webster
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
| | - James Uniacke
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
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Ma L, Wang R, Feng S, Yang X, Li J, Zhang Z, Zhan H, Wang Y, Xia Z, Wang CC, Kang L. Genomic insight into the population history and biological adaptations of high-altitude Tibetan highlanders in Nagqu. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tibetan, one of the largest indigenous populations living in the high-altitude region of the Tibetan Plateau (TP), has developed a suite of physiological adaptation strategies to cope with the extreme highland environment in TP. Here, we reported genome-wide SNP data from 48 Kham-speaking Nagqu Tibetans and analyzed it with published data from 1,067 individuals in 167 modern and ancient populations to characterize the detailed Tibetan subgroup history and population substructure. Overall, the patterns of allele sharing and haplotype sharing suggested (1) the relatively genetic homogeny between the studied Nagqu Tibetans and ancient Nepalese as well as present-day core Tibetans from Lhasa, Nagqu, and Shigatse; and (2) the close relationship between our studied Kham-speaking Nagqu Tibetans and Kham-speaking Chamdo Tibetans. The fitted qpAdm models showed that the studied Nagqu Tibetans could be fitted as having the main ancestry from late Neolithic upper Yellow River millet farmers and deeply diverged lineages from Southern East Asians (represented by Upper Paleolithic Guangxi_Longlin and Laos_Hoabinhian), and a non-neglectable western Steppe herder-related ancestry (∼3%). We further scanned the candidate genomic regions of natural selection for our newly generated Nagqu Tibetans and the published core Tibetans via FST, iHS, and XP-EHH tests. The genes overlapping with these regions were associated with essential human biological functions such as immune response, enzyme activity, signal transduction, skin development, and energy metabolism. Together, our results shed light on the admixture and evolutionary history of Nagqu Tibetan populations.
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Shang P, Zhang B, Li P, Ahmed Z, Hu X, Chamba Y, Zhang H. Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs. Animals (Basel) 2022; 12:ani12151919. [PMID: 35953907 PMCID: PMC9367445 DOI: 10.3390/ani12151919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/29/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Elevated environments such as plateaus are often classified as low oxygen environments. The hypoxic adaptation mechanisms utilized by organisms in these conditions are not well understood. To address this, the differentially expressed genes (DEGs) involved in hypoxia adaptation were assessed using two pig breeds (Tibetan pig [TP] and Yorkshire sow [YY]). Genes related to lung tissue responses to hypoxia were assessed using transcriptomic (using RNA-seq) and proteomic (using iTRAQ) analysis. A total of 1021 DEGs were screened out. In the iTRAQ omics data, a total of 22,100 peptides were obtained and 4518 proteins were found after filtering. A total of 271 differentially expressed proteins [DEPs] were screened using the conditions of p < 0.05; FC ≤ 0.833; and FC ≥ 1.2. A total of 14 DEGs at the mRNA and protein levels were identified and found to be associated with regulation of the inflammatory response; blood particles; and MAPK cascade response regulation. Among the DEGs, six were associated with hypoxia adaptation function (mitochondria and glycolysis) in pigs. The results of this study identify novel candidate genes involved in porcine hypoxia adaptation mechanisms.
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Affiliation(s)
- Peng Shang
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
- Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Bo Zhang
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
| | - Pan Li
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot 12350, Pakistan;
| | - Xiaoxiang Hu
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
| | - Yangzom Chamba
- Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
- Correspondence: (Y.C.); (H.Z.)
| | - Hao Zhang
- Laboratory National Engineering for Animal Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China; (P.S.); (B.Z.); (P.L.); (X.H.)
- Correspondence: (Y.C.); (H.Z.)
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12
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Ivy CM, Velotta JP, Cheviron ZA, Scott GR. Genetic variation in HIF-2α attenuates ventilatory sensitivity and carotid body growth in chronic hypoxia in high-altitude deer mice. J Physiol 2022; 600:4207-4225. [PMID: 35797482 DOI: 10.1113/jp282798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/27/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS High-altitude natives of many species have experienced natural selection on the gene encoding HIF-2α, Epas1, including high-altitude populations of deer mice. HIF-2α regulates ventilation and carotid body growth in hypoxia, so the genetic variants in Epas1 in high-altitude natives may underlie evolved changes in control of breathing. Deer mice from controlled crosses between high- and low-altitude populations were used to examine the effects of Epas1 genotype on an admixed genomic background. The high-altitude variant was associated with reduced ventilatory chemosensitivity and carotid body growth in chronic hypoxia, but had no effects on haematology. The results help us better understand the genetic basis for the unique physiological phenotype of high-altitude natives. ABSTRACT The gene encoding HIF-2α, Epas1, has experienced a history of natural selection in many high-altitude taxa, but the functional role of mutations in this gene are still poorly understood. We investigated the influence of the high-altitude variant of Epas1 in North American deer mice (Peromyscus maniculatus) on control of breathing and carotid body growth during chronic hypoxia. We created hybrids between high- and low-altitude populations of deer mice to disrupt linkages between genetic loci so physiological effects of Epas1 alleles (Epas1H and Epas1L , respectively) could be examined on an admixed genomic background. In general, chronic hypoxia (4 weeks at 12 kPa O2 ) enhanced ventilatory chemosensitivity (assessed as the acute ventilatory response to hypoxia), increased total ventilation and arterial O2 saturation during progressive poikilocapnic hypoxia, and increased haematocrit and blood haemoglobin content across genotypes. However, effects of chronic hypoxia on ventilatory chemosensitivity were attenuated in mice that were homozygous for the high-altitude Epas1 allele (Epas1H/H ). Carotid body growth and glomus cell hyperplasia, which was strongly induced in Epas1L/L mice in chronic hypoxia, was not observed in Epas1H/H mice. Epas1 genotype also modulated the effects of chronic hypoxia on metabolism and body temperature depression in hypoxia, but had no effects on haematological traits. These findings confirm the important role of HIF-2α in modulating ventilatory sensitivity and carotid body growth in chronic hypoxia, and show that genetic variation in Epas1 is responsible for evolved changes in the control of breathing and metabolism in high-altitude deer mice. Abstract figure legend ventilation and carotid body growth in hypoxia, so we investigated the role genetic variants in Epas1 in highaltitude deer mice on the control of breathing. In the lab, hybrids between high- and lowaltitude populations of deer mice were created to disrupt linkages between genetic loci so physiological effects of Epas1 alleles (Epas1H and Epas1L, respectively) could be examined on an admixed genomic background. The high-altitude variant was associated with reduced ventilatory chemosensitivity and carotid body growth after 4 weeks of chronic hypoxia, compared to mice homozygous for the low-altitude allele (Epas1LL). These results help us better understand the genetic basis for the unique physiological phenotype of high-altitude natives. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Catherine M Ivy
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Jonathan P Velotta
- Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
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13
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Zhang P, Zhang X, Zhang X, Gao X, Huerta-Sanchez E, Zwyns N. Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations. Trends Ecol Evol 2022; 37:257-267. [PMID: 34863581 PMCID: PMC9140327 DOI: 10.1016/j.tree.2021.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Recent archaeological discoveries suggest that both archaic Denisovans and Homo sapiens occupied the Tibetan Plateau earlier than expected. Genetic studies show that a pulse of Denisovan introgression was involved in the adaptation of Tibetan populations to high-altitude hypoxia. These findings challenge the traditional view that the plateau was one of the last places on earth colonized by H. sapiens and warrant a reappraisal of the population history of this highland. Here, we integrate archaeological and genomic evidence relevant to human dispersal, settlement, and adaptation in the region. We propose two testable models to address the peopling of the plateau in the broader context of H. sapiens dispersal and their encounters with Denisovans in Asia.
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Affiliation(s)
- Peiqi Zhang
- Department of Anthropology, University of California, Davis, CA 95616, USA.
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Nicolas Zwyns
- Department of Anthropology, University of California, Davis, CA 95616, USA; Department of Human Evolution, Max Planck Insititute for Evolutionary Anthropology, Leipzig 04103, Germany
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14
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Ivy CM, Wearing OH, Natarajan C, Schweizer RM, Gutiérrez-Pinto N, Velotta JP, Campbell-Staton SC, Petersen EE, Fago A, Cheviron ZA, Storz JF, Scott GR. Genetic variation in haemoglobin is associated with evolved changes in breathing in high-altitude deer mice. J Exp Biol 2022; 225:273749. [PMID: 34913467 PMCID: PMC8917448 DOI: 10.1242/jeb.243595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/09/2021] [Indexed: 01/21/2023]
Abstract
Physiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated whether genetic variants in haemoglobin (Hb) that contribute to high-altitude adaptation in deer mice (Peromyscus maniculatus) are associated with evolved changes in the control of breathing. We created F2 inter-population hybrids of highland and lowland deer mice to test for phenotypic associations of α- and β-globin variants on a mixed genetic background. Hb genotype had expected effects on Hb-O2 affinity that were associated with differences in arterial O2 saturation in hypoxia. However, high-altitude genotypes were also associated with breathing phenotypes that should contribute to enhancing O2 uptake in hypoxia. Mice with highland α-globin exhibited a more effective breathing pattern, with highland homozygotes breathing deeper but less frequently across a range of inspired O2, and this difference was comparable to the evolved changes in breathing pattern in deer mouse populations native to high altitude. The ventilatory response to hypoxia was augmented in mice that were homozygous for highland β-globin. The association of globin variants with variation in breathing phenotypes could not be recapitulated by acute manipulation of Hb-O2 affinity, because treatment with efaproxiral (a synthetic drug that acutely reduces Hb-O2 affinity) had no effect on breathing in normoxia or hypoxia. Therefore, adaptive variation in Hb may have unexpected effects on physiology in addition to the canonical function of this protein in circulatory O2 transport.
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Affiliation(s)
- Catherine M. Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1,Author for correspondence ()
| | - Oliver H. Wearing
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | | | - Rena M. Schweizer
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Jonathan P. Velotta
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Shane C. Campbell-Staton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Elin E. Petersen
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Angela Fago
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Zachary A. Cheviron
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
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15
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Jin Y, Tong H, Shao G, Li J, Lv Y, Wo Y, Brown RP, Fu C. Dorsal Pigmentation and Its Association with Functional Variation in MC1R in a Lizard from Different Elevations on the Qinghai-Tibetan Plateau. Genome Biol Evol 2021; 12:2303-2313. [PMID: 33095228 PMCID: PMC7719228 DOI: 10.1093/gbe/evaa225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/27/2022] Open
Abstract
Identification of the role of the MC1R gene has provided major insights into variation in skin pigmentation in several organisms, including humans, but the evolutionary genetics of this variation is less well established. Variation in this gene and its relationship with degree of melanism was analyzed in one of the world’s highest-elevation lizards, Phrynocephalus theobaldi from the Qinghai–Tibetan Plateau. Individuals from the low-elevation group were shown to have darker dorsal pigmentation than individuals from a high-elevation group. The existence of climatic variation across these elevations was quantified, with lower elevations exhibiting higher air pressure, temperatures, and humidity, but less wind and insolation. Analysis of the MC1R gene in 214 individuals revealed amino acid differences at five sites between intraspecific sister lineages from different elevations, with two sites showing distinct fixed residues at low elevations. Three of the four single-nucleotide polymorphisms that underpinned these amino acid differences were highly significant outliers, relative to the generalized MC1R population structuring, suggestive of selection. Transfection of cells with an MC1R allele from a lighter high-elevation population caused a 43% reduction in agonist-induced cyclic AMP accumulation, and hence lowered melanin synthesis, relative to transfection with an allele from a darker low-elevation population. The high-elevation allele led to less efficient integration of the MC1R protein into melanocyte membranes. Our study identifies variation in the degree of melanism that can be explained by four or fewer MC1R substitutions. We establish a functional link between these substitutions and melanin synthesis and demonstrate elevation-associated shifts in their frequencies.
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Affiliation(s)
- Yuanting Jin
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Haojie Tong
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Gang Shao
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Jiasheng Li
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Yudie Lv
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Yubin Wo
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Richard P Brown
- College of Life Sciences, China Jiliang University, Hangzhou, China.,School of Biological & Environmental Sciences, Liverpool John Moores University, United Kingdom
| | - Caiyun Fu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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16
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Liu K, Yang J, Yuan H. Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau. J Evol Biol 2021; 34:1514-1530. [PMID: 34473899 DOI: 10.1111/jeb.13924] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/05/2021] [Accepted: 08/30/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities that inhabit the host's intestine influence many aspects of the host's health and bear the adaptive potential to alterations in harsh environments and diets. The Qinghai-Tibet Plateau represents one of the harshest environments in the world. Preliminary progress has been made in identifying the communities of gut microbes in Indigenous Tibetans and non-human animals. However, due to the complexity of microbial communities, the effects of gut microbes on the host's health and high-plateau adaptation remain unexplained. Herein, we review the latest progress in identifying factors affecting the gut microbiota of native Tibetans and non-human animals and highlight the complex interactions between the gut microbiota, health and highland adaptation, which provides a basis for exploring the correlations between the gut microbiota and clinical indexes in native highland residents and travellers, as well as developing microbiota-based strategies to mitigate health risks for tourists and treatments for mountain sickness during high-altitude travel in the future.
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Affiliation(s)
- Kui Liu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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17
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Lucero García Rojas EY, Villanueva C, Bond RA. Hypoxia Inducible Factors as Central Players in the Pathogenesis and Pathophysiology of Cardiovascular Diseases. Front Cardiovasc Med 2021; 8:709509. [PMID: 34447792 PMCID: PMC8382733 DOI: 10.3389/fcvm.2021.709509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/09/2021] [Indexed: 01/01/2023] Open
Abstract
Cardiovascular (CV) diseases are the major cause of death in industrialized countries. The main function of the CV system is to deliver nutrients and oxygen to all tissues. During most CV pathologies, oxygen and nutrient delivery is decreased or completely halted. Several mechanisms, including increased oxygen transport and delivery, as well as increased blood flow are triggered to compensate for the hypoxic state. If the compensatory mechanisms fail to sufficiently correct the hypoxia, irreversible damage can occur. Thus, hypoxia plays a central role in the pathogenesis and pathophysiology of CV diseases. Hypoxia inducible factors (HIFs) orchestrate the gene transcription for hundreds of proteins involved in erythropoiesis, glucose transport, angiogenesis, glycolytic metabolism, reactive oxygen species (ROS) handling, cell proliferation and survival, among others. The overall regulation of the expression of HIF-dependent genes depends on the severity, duration, and location of hypoxia. In the present review, common CV diseases were selected to illustrate that HIFs, and proteins derived directly or indirectly from their stabilization and activation, are related to the development and perpetuation of hypoxia in these pathologies. We further classify CV diseases into acute and chronic hypoxic states to better understand the temporal relevance of HIFs in the pathogenesis, disease progression and clinical outcomes of these diseases. We conclude that HIFs and their derived factors are fundamental in the genesis and progression of CV diseases. Understanding these mechanisms will lead to more effective treatment strategies leading to reduced morbidity and mortality.
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Affiliation(s)
| | - Cleva Villanueva
- Instituto Politecnico Nacional, Escuela Superior de Medicina, Mexico City, Mexico
| | - Richard A Bond
- Department of Pharmacology and Pharmaceutical Sciences, University of Houston, Houston, TX, United States
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18
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Fan C, Sun R, Nie M, Wang M, Yao Z, Feng Q, Xu W, Yuan R, Gao Z, Cheng Q, Wang J. The Cardiorespiratory fitness of children and adolescents in Tibet at altitudes over 3,500 meters. PLoS One 2021; 16:e0256258. [PMID: 34411164 PMCID: PMC8375997 DOI: 10.1371/journal.pone.0256258] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cardiorespiratory fitness (CRF) is the core element of health-related physical fitness evaluation. High pressure and low oxygen in Tibet (over 3,500 m above sea level) may negatively impact the residents' CRF. The 20-m shuttle run test (20mSRT) is the most popular field-based assessment and estimate of CRF in children and adolescents worldwide. However, normative CRF data for the children and adolescents residing in China's plateau region are unavailable, which prevents comparability among those living at high-altitudes around the world. PURPOSE To measure the CRF of Chinese children and adolescents aged 9-18 years living in Tibet at altitudes exceeding 3,500 m, and to identify correlations between this metric and demographic characteristics (age, sex, and ethnicity). These data were then compared with those generated in the lowland (Shanghai, China) and various global regions. METHODS 20mSRT performance (number of completed laps) and predicted peak oxygen consumption (VO2peak) were used as indicators of CRF. We measured the CRF of 1,717 healthy children and adolescents aged 9-18 years living in Tibet. The CRF data from school-age subjects in Shanghai (2,437 boys and 2,396 girls) and worldwide (1,142,026 students from 50 countries/regions in Africa, Asia, Europe, Latin America, North America, and Oceania) were collated from published papers. RESULTS The average CRF of the participants from Tibet was 39.8 mL/kg/min. The male subjects (n = 876; 41.1 ± 4.42 mL/kg/min) had a higher average CRF than their female counterparts (n = 841; 37.8 ± 5.40 mL/kg/min). CRF decreased with age in both sexes at statistical significance (F = 1249.9, p for trend 0.05). The indigenous Tibetans (n = 1289; 40.1 ± 3.71 mL/kg/min) had a significant higher average CRF than those of Han descent (n = 394; 38.9 ± 4.70 mL/kg/min) (p < 0.05). CONCLUSIONS Children and adolescents aged 7-18 years residing above 3,500 m in Tibet displayed lower CRF traits compared with their counterparts from the plains area and other high altitude places. CRF varied according to age, sex, and ethnic group. Given the importance of CRF in children and adolescents, effective intervention strategies should be implemented to improve CRF in children and adolescents on the plateau.
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Affiliation(s)
- Chaoqun Fan
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
| | - Ruizhe Sun
- Physical Fitness Research Center, Tibet Institute of Sport Science, Lhasa, Tibet, China
| | - Mingjian Nie
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
- Beijing Sport University, Haidian, Beijing, China
| | - Mei Wang
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
| | - Zhi Yao
- Physical Fitness Research Center, Tibet Institute of Sport Science, Lhasa, Tibet, China
| | - Qiang Feng
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
| | - Wenfeng Xu
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
| | - Runzi Yuan
- College of Physical Education, Qufu Normal University, Qufu, Shangdong Province, China
| | - Zhongfang Gao
- College of Physical Education, Qufu Normal University, Qufu, Shangdong Province, China
| | - Qiaorui Cheng
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
| | - Jingjing Wang
- National Physical Fitness Research Center, China Institute of Sport Science, Dongcheng, Beijing, China
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19
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Graham AM, Peters JL, Wilson RE, Muñoz-Fuentes V, Green AJ, Dorfsman DA, Valqui TH, Winker K, McCracken KG. Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity (Edinb) 2021; 127:107-123. [PMID: 33903741 PMCID: PMC8249413 DOI: 10.1038/s41437-021-00437-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/04/2021] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Abstract
Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb β-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the β-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these β-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.
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Affiliation(s)
- Allie M Graham
- Eccles Institute for Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Robert E Wilson
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Daniel A Dorfsman
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Thomas H Valqui
- Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima, Perú
- Universidad Nacional Agraria, La Molina, Perú
| | - Kevin Winker
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kevin G McCracken
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima, Perú.
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Department of Biology, University of Miami, Coral Gables, FL, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.
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20
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Babitt JL, Eisenga MF, Haase VH, Kshirsagar AV, Levin A, Locatelli F, Małyszko J, Swinkels DW, Tarng DC, Cheung M, Jadoul M, Winkelmayer WC, Drüeke TB. Controversies in optimal anemia management: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Conference. Kidney Int 2021; 99:1280-1295. [PMID: 33839163 DOI: 10.1016/j.kint.2021.03.020] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
In chronic kidney disease, anemia and disordered iron homeostasis are prevalent and associated with significant adverse consequences. In 2012, Kidney Disease: Improving Global Outcomes (KDIGO) issued an anemia guideline for managing the diagnosis, evaluation, and treatment of anemia in chronic kidney disease. Since then, new data have accrued from basic research, epidemiological studies, and randomized trials that warrant a re-examination of previous recommendations. Therefore, in 2019, KDIGO decided to convene 2 Controversies Conferences to review the latest evidence, explore new and ongoing controversies, assess change implications for the current KDIGO anemia guideline, and propose a research agenda. The first conference, described here, focused mainly on iron-related issues, including the contribution of disordered iron homeostasis to the anemia of chronic kidney disease, diagnostic challenges, available and emerging iron therapies, treatment targets, and patient outcomes. The second conference will discuss issues more specifically related to erythropoiesis-stimulating agents, including epoetins, and hypoxia-inducible factor-prolyl hydroxylase inhibitors. Here we provide a concise overview of the consensus points and controversies resulting from the first conference and prioritize key questions that need to be answered by future research.
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Affiliation(s)
- Jodie L Babitt
- Nephrology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| | - Michele F Eisenga
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Volker H Haase
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics and Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Medical Cell Biology, Division of Integrative Physiology, Uppsala University, Uppsala, Sweden
| | - Abhijit V Kshirsagar
- UNC Kidney Center and Division of Nephrology & Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adeera Levin
- Department of Medicine, Division of Nephrology, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Francesco Locatelli
- Department of Nephrology and Dialysis, Alessandro Manzoni Hospital, ASST Lecco, Lecco, Italy
| | - Jolanta Małyszko
- Department of Nephrology, Dialysis, and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Dorine W Swinkels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Der-Cherng Tarng
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | - Michel Jadoul
- Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Wolfgang C Winkelmayer
- Department of Medicine, Section of Nephrology, Selzman Institute for Kidney Health, Baylor College of Medicine, Houston, Texas, USA
| | - Tilman B Drüeke
- Inserm Unit 1018, Team 5, CESP, Hôpital Paul Brousse, Paris-Sud University (UPS), Villejuif, France; Versailles Saint-Quentin-en-Yvelines University (Paris-Ile-de-France-Ouest University, UVSQ), Villejuif, France.
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21
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Velotta JP, Robertson CE, Schweizer RM, McClelland GB, Cheviron ZA. Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. Mol Biol Evol 2021; 37:2309-2321. [PMID: 32243546 DOI: 10.1093/molbev/msaa086] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aerobic performance is tied to fitness as it influences an animal's ability to find food, escape predators, or survive extreme conditions. At high altitude, where low O2 availability and persistent cold prevail, maximum metabolic heat production (thermogenesis) is an aerobic performance trait that is closely linked to survival. Understanding how thermogenesis evolves to enhance survival at high altitude will yield insight into the links between physiology, performance, and fitness. Recent work in deer mice (Peromyscus maniculatus) has shown that adult mice native to high altitude have higher thermogenic capacities under hypoxia compared with lowland conspecifics, but that developing high-altitude pups delay the onset of thermogenesis. This finding suggests that natural selection on thermogenic capacity varies across life stages. To determine the mechanistic cause of this ontogenetic delay, we analyzed the transcriptomes of thermoeffector organs-brown adipose tissue and skeletal muscle-in developing deer mice native to low and high altitude. We demonstrate that the developmental delay in thermogenesis is associated with adaptive shifts in the expression of genes involved in nervous system development, fuel/O2 supply, and oxidative metabolism pathways. Our results demonstrate that selection has modified the developmental trajectory of the thermoregulatory system at high altitude and has done so by acting on the regulatory systems that control the maturation of thermoeffector tissues. We suggest that the cold and hypoxic conditions of high altitude force a resource allocation tradeoff, whereby limited energy is allocated to developmental processes such as growth, versus active thermogenesis, during early development.
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Affiliation(s)
| | | | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
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22
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Lim MCW, Bi K, Witt CC, Graham CH, Dávalos LM. Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations. J Hered 2021; 112:229-240. [PMID: 33631009 DOI: 10.1093/jhered/esab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/23/2021] [Indexed: 01/28/2023] Open
Abstract
Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them "taller" biogeographic barriers.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, CA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA (Bi)
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY
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23
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Werren EA, Garcia O, Bigham AW. Identifying adaptive alleles in the human genome: from selection mapping to functional validation. Hum Genet 2020; 140:241-276. [PMID: 32728809 DOI: 10.1007/s00439-020-02206-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI, USA
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed Garcia
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California Los Angeles, 341 Haines Hall, Los Angeles, CA, 90095, USA.
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24
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Zhang JH, Shen Y, Liu C, Yang J, Yang YQ, Zhang C, Bian SZ, Yu J, Gao XB, Zhang LP, Ke JB, Yuan FZY, Pan WX, Guo ZN, Huang L. EPAS1 and VEGFA gene variants are related to the symptoms of acute mountain sickness in Chinese Han population: a cross-sectional study. Mil Med Res 2020; 7:35. [PMID: 32718338 PMCID: PMC7385974 DOI: 10.1186/s40779-020-00264-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/14/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND More people ascend to high altitude (HA) for various activities, and some individuals are susceptible to HA illness after rapidly ascending from plains. Acute mountain sickness (AMS) is a general complaint that affects activities of daily living at HA. Although genomic association analyses suggest that single nucleotide polymorphisms (SNPs) are involved in the genesis of AMS, no major gene variants associated with AMS-related symptoms have been identified. METHODS In this cross-sectional study, 604 young, healthy Chinese Han men were recruited in June and July of 2012 in Chengdu, and rapidly taken to above 3700 m by plane. Basic demographic parameters were collected at sea level, and heart rate, pulse oxygen saturation (SpO2), systolic and diastolic blood pressure and AMS-related symptoms were determined within 18-24 h after arriving in Lhasa. AMS patients were identified according to the latest Lake Louise scoring system (LLSS). Potential associations between variant genotypes and AMS/AMS-related symptoms were identified by logistic regression after adjusting for potential confounders (age, body mass index and smoking status). RESULTS In total, 320 subjects (53.0%) were diagnosed with AMS, with no cases of high-altitude pulmonary edema or high-altitude cerebral edema. SpO2 was significantly lower in the AMS group than that in the non-AMS group (P = 0.003). Four SNPs in hypoxia-inducible factor-related genes were found to be associated with AMS before multiple hypothesis testing correction. The rs6756667 (EPAS1) was associated with mild gastrointestinal symptoms (P = 0.013), while rs3025039 (VEGFA) was related to mild headache (P = 0.0007). The combination of rs6756667 GG and rs3025039 CT/TT further increased the risk of developing AMS (OR = 2.70, P < 0.001). CONCLUSIONS Under the latest LLSS, we find that EPAS1 and VEGFA gene variants are related to AMS susceptibility through different AMS-related symptoms in the Chinese Han population; this tool might be useful for screening susceptible populations and predicting clinical symptoms leading to AMS before an individual reaches HA. TRIAL REGISTRATION Chinese Clinical Trial Registration, ChiCTR-RCS-12002232 . Registered 31 May 2012.
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Affiliation(s)
- Ji-Hang Zhang
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yang Shen
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Chuan Liu
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jie Yang
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yuan-Qi Yang
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Chen Zhang
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Shi-Zhu Bian
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jie Yu
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xu-Bin Gao
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Lai-Ping Zhang
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jing-Bin Ke
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Fang-Zheng-Yuan Yuan
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Wen-Xu Pan
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Zhi-Nian Guo
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Lan Huang
- Institute of Cardiovascular Diseases, Department of Cardiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
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25
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Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-Species Insights Into Genomic Adaptations to Hypoxia. Front Genet 2020; 11:743. [PMID: 32849780 PMCID: PMC7387696 DOI: 10.3389/fgene.2020.00743] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia today. Of particular interest are species that inhabit high-altitude niches, which experience chronic hypobaric hypoxia throughout their lives. Physiological and molecular aspects of adaptation to hypoxia have long been the focus of high-altitude populations and, within the past decade, genomic information has become increasingly accessible. These data provide an opportunity to search for common genetic signatures of selection across uniquely informative populations and thereby augment our understanding of the mechanisms underlying adaptations to hypoxia. In this review, we synthesize the available genomic findings across hypoxia-tolerant species to provide a comprehensive view of putatively hypoxia-adaptive genes and pathways. In many cases, adaptive signatures across species converge on the same genetic pathways or on genes themselves [i.e., the hypoxia inducible factor (HIF) pathway). However, specific variants thought to underlie function are distinct between species and populations, and, in most cases, the precise functional role of these genomic differences remains unknown. Efforts to standardize these findings and explore relationships between genotype and phenotype will provide important clues into the evolutionary and mechanistic bases of physiological adaptations to environmental hypoxia.
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Affiliation(s)
- Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - James E. Hall
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yuuka Tanabe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
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26
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Association of EPAS1 and PPARA Gene Polymorphisms with High-Altitude Headache in Chinese Han Population. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1593068. [PMID: 32185192 PMCID: PMC7060407 DOI: 10.1155/2020/1593068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 11/17/2022]
Abstract
Background High-altitude headache (HAH) is the most common complication after high-altitude exposure. Hypoxia-inducible factor- (HIF-) related genes have been confirmed to contribute to high-altitude acclimatization. We aim to investigate a possible association between HIF-related genes and HAH in the Chinese Han population. Methods In total, 580 healthy Chinese Han volunteers were recruited in Chengdu (500 m) and carried to Lhasa (3700 m) by plane in 2 hours. HAH scores and basic physiological parameters were collected within 18-24 hours after the arrival. Thirty-five single nucleotide polymorphisms (SNPs) in HIF-related genes were genotyped, and linkage disequilibrium (LD) was evaluated by Haploview software. The functions of SNPs/haplotypes for HAH were developed by using logistic regression analysis. Results In comparison with wild types, the rs4953354 "G" allele (P=0.013), rs6756667 "A" allele (P=0.013), rs6756667 "A" allele (EPAS1, and rs6520015 "C" allele in PPARA (P=0.013), rs6756667 "A" allele (PPARA (P=0.013), rs6756667 "A" allele (EPAS1, and rs6520015 "C" allele in PPARA (P=0.013), rs6756667 "A" allele (. Conclusions EPAS1 and PPARA polymorphisms were associated with HAH in the Chinese Han population. Our findings pointed out potentially predictive gene markers, provided new insights into understanding pathogenesis, and may further provide prophylaxis and treatment strategies for HAH.EPAS1, and rs6520015 "C" allele in PPARA (.
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27
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Huang M, Yang B, Chen H, Zhang H, Wu Z, Ai H, Ren J, Huang L. The fine-scale genetic structure and selection signals of Chinese indigenous pigs. Evol Appl 2020; 13:458-475. [PMID: 31993089 PMCID: PMC6976964 DOI: 10.1111/eva.12887] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 01/24/2023] Open
Abstract
Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well-characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
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Affiliation(s)
- Min Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hui Zhang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
- Present address:
College of Animal ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
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28
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Zhang S, Liu D, Gesang DZ, Lv M. Characteristics of Cerebral Stroke in the Tibet Autonomous Region of China. Med Sci Monit 2020; 26:e919221. [PMID: 31917778 PMCID: PMC6977622 DOI: 10.12659/msm.919221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/03/2019] [Indexed: 11/09/2022] Open
Abstract
It is well known that cerebrovascular disease has become an important cause of adult death and disability. Strikingly, the Tibet Autonomous Region (TAR) ranks on the top in China for the incidence of stroke. To help explain this phenomenon, we have searched for and analyzed stroke-related literature for the TAR in the past 2 decades and have referenced reports from other regions at similar altitudes. This article focuses on epidemiology features, risk factors, and pathogenesis of stroke in the TAR in an effort to generate a better understanding of the characteristics of stroke in this region. The special plateau-related factors such as its high elevation, limited oxygen, the high incidence of hypertension, smoking, and the unique dietary habits of the region are correlated with the high incidence of stroke. In addition to these factors, the pathogenesis of stroke in this high-altitude area is also unique. However, there is no established explanation for the unique occurrence and high incidence of stroke in the TAR. Our study provides an important rationale not only for the clinic to prevent and treat this disease, but also for the government to develop appropriate health policies for the prevention of stroke in the TAR.
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Affiliation(s)
- Shuai Zhang
- Department of Neurosurgery, Beijing Aerospace General Hospital, Beijing, P.R. China
| | - Dong Liu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, P.R. China
| | - Dun Zhu Gesang
- Department of Neurosurgery, Second People’s Hospital of Tibet Autonomous Region, Lhasa, Tibet Autonomous Region, P.R. China
| | - Ming Lv
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
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29
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Now a Nobel gas: oxygen. Pflugers Arch 2019; 471:1343-1358. [PMID: 31754831 DOI: 10.1007/s00424-019-02334-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023]
Abstract
The recent bestowal of the Nobel Prize 2019 in Physiology or Medicine to Gregg L. Semenza, Sir Peter J. Ratcliffe, and William G. Kaelin Jr. celebrates a series of remarkable discoveries that span from the physiological research question on how oxygen deficiency (hypoxia) induces the red blood cell forming hormone erythropoietin (Epo) to the first clinical application of a novel family of Epo-inducing drugs to treat patients suffering from renal anemia. This review looks back at the most important findings made by the three Nobel laureates, highlights current research trends, and sheds an eye on future perspectives of hypoxia research, including emerging and potential clinical applications.
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30
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Chronic Exposure to High Altitude: Synaptic, Astroglial and Memory Changes. Sci Rep 2019; 9:16406. [PMID: 31712561 PMCID: PMC6848138 DOI: 10.1038/s41598-019-52563-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022] Open
Abstract
Long-term operations carried out at high altitude (HA) by military personnel, pilots, and astronauts may trigger health complications. In particular, chronic exposure to high altitude (CEHA) has been associated with deficits in cognitive function. In this study, we found that mice exposed to chronic HA (5000 m for 12 weeks) exhibited deficits in learning and memory associated with hippocampal function and were linked with changes in the expression of synaptic proteins across various regions of the brain. Specifically, we found decreased levels of synaptophysin (SYP) (p < 0.05) and spinophilin (SPH) (p < 0.05) in the olfactory cortex, post synaptic density−95 (PSD-95) (p < 0.05), growth associated protein 43 (GAP43) (p < 0.05), glial fibrillary acidic protein (GFAP) (p < 0.05) in the cerebellum, and SYP (p < 0.05) and PSD-95 (p < 0.05) in the brainstem. Ultrastructural analyses of synaptic density and morphology in the hippocampus did not reveal any differences in CEHA mice compared to SL mice. Our data are novel and suggest that CEHA exposure leads to cognitive impairment in conjunction with neuroanatomically-based molecular changes in synaptic protein levels and astroglial cell marker in a region specific manner. We hypothesize that these new findings are part of highly complex molecular and neuroplasticity mechanisms underlying neuroadaptation response that occurs in brains when chronically exposed to HA.
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31
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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32
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Sanghani NS, Haase VH. Hypoxia-Inducible Factor Activators in Renal Anemia: Current Clinical Experience. Adv Chronic Kidney Dis 2019; 26:253-266. [PMID: 31477256 PMCID: PMC7318915 DOI: 10.1053/j.ackd.2019.04.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
Prolyl hydroxylase domain oxygen sensors are dioxygenases that regulate the activity of hypoxia-inducible factor (HIF), which controls renal and hepatic erythropoietin production and coordinates erythropoiesis with iron metabolism. Small molecule inhibitors of prolyl hydroxylase domain dioxygenases (HIF-PHI [prolyl hydroxylase inhibitor]) stimulate the production of endogenous erythropoietin and improve iron metabolism resulting in efficacious anemia management in patients with CKD. Three oral HIF-PHIs-daprodustat, roxadustat, and vadadustat-have now advanced to global phase III clinical development culminating in the recent licensing of roxadustat for oral anemia therapy in China. Here, we survey current clinical experience with HIF-PHIs, discuss potential therapeutic advantages, and deliberate over safety concerns regarding long-term administration in patients with renal anemia.
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Affiliation(s)
- Neil S Sanghani
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Volker H Haase
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Department of Medical Cell Biology, Uppsala Universitet, Uppsala, Sweden; Department of Molecular Physiology & Biophysics and Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN.
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Gassmann M, Mairbäurl H, Livshits L, Seide S, Hackbusch M, Malczyk M, Kraut S, Gassmann NN, Weissmann N, Muckenthaler MU. The increase in hemoglobin concentration with altitude varies among human populations. Ann N Y Acad Sci 2019; 1450:204-220. [PMID: 31257609 DOI: 10.1111/nyas.14136] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 02/06/2023]
Abstract
Decreased oxygen availability at high altitude requires physiological adjustments allowing for adequate tissue oxygenation. One such mechanism is a slow increase in the hemoglobin concentration ([Hb]) resulting in elevated [Hb] in high-altitude residents. Diagnosis of anemia at different altitudes requires reference values for [Hb]. Our aim was to establish such values based on published data of residents living at different altitudes by applying meta-analysis and multiple regressions. Results show that [Hb] is increased in all high-altitude residents. However, the magnitude of increase varies among the regions analyzed and among ethnic groups within a region. The highest increase was found in residents of the Andes (1 g/dL/1000 m), but this increment was smaller in all other regions of the world (0.6 g/dL/1000 m). While sufficient data exist for adult males and females showing that sex differences in [Hb] persist with altitude, data for infants, children, and pregnant women are incomplete preventing such analyses. Because WHO reference values were originally based on [Hb] of South American people, we conclude that individual reference values have to be defined for ethnic groups to reliably diagnose anemia and erythrocytosis in high-altitude residents. Future studies need to test their applicability for children of different ages and pregnant women.
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Affiliation(s)
- Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland.,Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | - Heimo Mairbäurl
- Translational Lung Research Center Heidelberg (TLRC), the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Leonid Livshits
- Institute of Veterinary Physiology, Vetsuisse Faculty and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Svenja Seide
- Institute of Medical Biometry and Informatics (IMBI), University Hospital Heidelberg, Heidelberg, Germany
| | - Matthes Hackbusch
- Institute of Medical Biometry and Informatics (IMBI), University Hospital Heidelberg, Heidelberg, Germany
| | - Monika Malczyk
- Excellence Cluster Cardiopulmonary System, Justus-Liebig-University Giessen, University of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Simone Kraut
- Excellence Cluster Cardiopulmonary System, Justus-Liebig-University Giessen, University of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Norina N Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Norbert Weissmann
- Excellence Cluster Cardiopulmonary System, Justus-Liebig-University Giessen, University of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Martina U Muckenthaler
- Pediatric Hematology, Oncology and Immunology, University Hospital Heidelberg, Molecular Medicine Partnership Unit, University of Heidelberg, Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research, Heidelberg, Germany
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Richardson MF, Munyard K, Croft LJ, Allnutt TR, Jackling F, Alshanbari F, Jevit M, Wright GA, Cransberg R, Tibary A, Perelman P, Appleton B, Raudsepp T. Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. Front Genet 2019; 10:586. [PMID: 31293619 PMCID: PMC6598621 DOI: 10.3389/fgene.2019.00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.
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Affiliation(s)
- Mark F Richardson
- Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Kylie Munyard
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Larry J Croft
- Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Theodore R Allnutt
- Bioinformatics Core Research Group, Deakin University, Geelong, VIC, Australia
| | - Felicity Jackling
- Department of Genetics, The University of Melbourne, Melbourne, VIC, Australia
| | - Fahad Alshanbari
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Matthew Jevit
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Gus A Wright
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Rhys Cransberg
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Ahmed Tibary
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Polina Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Belinda Appleton
- Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Terje Raudsepp
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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Heinrich EC, Wu L, Lawrence ES, Cole AM, Anza-Ramirez C, Villafuerte FC, Simonson TS. Genetic variants at the EGLN1 locus associated with high-altitude adaptation in Tibetans are absent or found at low frequency in highland Andeans. Ann Hum Genet 2019; 83:171-176. [PMID: 30719713 PMCID: PMC7920394 DOI: 10.1111/ahg.12299] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
EGLN1 encodes the hypoxia-inducible factor (HIF) pathway prolyl hydroxylase 2 (PHD2) that serves as an oxygen-sensitive regulator of HIF activity. The EGLN1 locus exhibits a signature of positive selection in Tibetan and Andean populations and is associated with hemoglobin concentration in Tibetans. Recent reports provide evidence for functional roles of protein-coding variants within the first exon of EGLN1 (rs186996510, rs12097901) that are linked to an adaptive signal in Tibetans, yet whether these same variants are present and contribute to adaptation in Andean highlanders is unknown. We determined the frequencies of these adaptive Tibetan alleles in Quechua Andeans resident at high altitude (4,350 m) in addition to individuals of Nepali ancestry resident at sea level. The rs186996510 C (minor) allele previously found at high frequency in Tibetans is absent in Andean (G: 100%) and rare among Nepali (C: 11.8%, G: 88.2%) cohorts. The minor G allele of rs12097901 is found at similarly low frequencies in Andeans (G: 12.7%, C: 87.3%) and Nepalis (G: 23.5%, C: 76.5%) compared to Tibetans. These results suggest that adaptation involving EGLN1 in Andeans involves different mechanisms than those described in Tibetans. The precise Andean adaptive variants remain to be determined.
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Affiliation(s)
- Erica C. Heinrich
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Lu Wu
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Elijah S. Lawrence
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Amy M. Cole
- Department of Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Cecilia Anza-Ramirez
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | | | - Tatum S. Simonson
- Division of Physiology, Department of Medicine, University of California, San Diego, La Jolla, California
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37
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Congenital and evolutionary modulations of hypoxia sensing and their erythroid phenotype. CURRENT OPINION IN PHYSIOLOGY 2019. [DOI: 10.1016/j.cophys.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Convergent evolution on the hypoxia-inducible factor (HIF) pathway genes EGLN1 and EPAS1 in high-altitude ducks. Heredity (Edinb) 2019; 122:819-832. [PMID: 30631144 PMCID: PMC6781116 DOI: 10.1038/s41437-018-0173-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
During periods of reduced O2 supply, the most profound changes in gene expression are mediated by hypoxia-inducible factor (HIF) transcription factors that play a key role in cellular responses to low-O2 tension. Using target-enrichment sequencing, we tested whether variation in 26 genes in the HIF signaling pathway was associated with high altitude and therefore corresponding O2 availability in three duck species that colonized the Andes from ancestral low-altitude habitats in South America. We found strong support for convergent evolution in the case of two of the three duck species with the same genes (EGLN1, EPAS1), and even the same exons (exon 12, EPAS1), exhibiting extreme outliers with a high probability of directional selection in the high-altitude populations. These results mirror patterns of adaptation seen in human populations, which showed mutations in EPAS1, and transcriptional regulation differences in EGLN1, causing changes in downstream target transactivation, associated with a blunted hypoxic response.
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Shimoda LA, Yun X, Sikka G. Revisiting the role of hypoxia-inducible factors in pulmonary hypertension. CURRENT OPINION IN PHYSIOLOGY 2019; 7:33-40. [PMID: 33103021 DOI: 10.1016/j.cophys.2018.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pulmonary hypertension (PH) is a deadly condition with limited treatment options. Early studies implicated hypoxia-inducible factors as contributing to the development of hypoxia-induced PH. Recently, the use of cells derived from patients and transgenic animals with cell specific deletions for various parts of the HIF system have furthered our understanding of the mechanisms by which HIFs control pulmonary vascular tone and remodeling to promote PH. Additionally, identification of HIF inhibitors further allows assessment of the potential for targeting HIFs to prevent and/or reverse PH. In this review, recent findings exploring the role of HIFs as potential mediators and therapeutic targets for PH are discussed.
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Affiliation(s)
- Larissa A Shimoda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Xin Yun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Gautam Sikka
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224
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40
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Abstract
People living at sea level experience intermittent hypoxia (IH) as a consequence of sleep apnea, which is a highly prevalent respiratory disorder. Sleep apnea patients and rodents exposed to IH exhibit autonomic dysfunction manifested as increased sympathetic nerve activity and hypertension. This article highlights physiologic basis of autonomic disturbances by IH, which involves abnormal activation of the carotid body (CB) chemo reflex by reactive oxygen species (ROS).We further evaluate major molecular mechanisms underlying IH-induced ROS generation including transcriptional activation of genes encoding pro-oxidant enzymes by hypoxia-inducible factor (HIF)-1 and transcriptional repression of anti-oxidant enzyme genes by DNA methylation. Lastly, evidence is presented for CB neural activity as a major regulator of HIF-1 activation and DNA methylation by IH in the chemo reflex pathway.
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41
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Verma P, Sharma A, Sodhi M, Thakur K, Kataria RS, Niranjan SK, Bharti VK, Kumar P, Giri A, Kalia S, Mukesh M. Transcriptome Analysis of Circulating PBMCs to Understand Mechanism of High Altitude Adaptation in Native Cattle of Ladakh Region. Sci Rep 2018; 8:7681. [PMID: 29769561 PMCID: PMC5955995 DOI: 10.1038/s41598-018-25736-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/03/2018] [Indexed: 12/19/2022] Open
Abstract
Ladakhi cattle is native population of Leh and Ladakh region and constantly exposed to hypobaric hypoxia over many generations. In present study, transcriptome signatures of cattle from Ladakh region (~5500 m) and Sahiwal cattle from tropical regions were evaluated using Agilent 44 K microarray chip. The top up-regulated genes in Ladakhi cows were INHBC, ITPRI, HECA, ABI3, GPR171, and HIF-1α involved in hypoxia and stress response. In Sahiwal cows, the top up-regulated genes eEF1A1, GRO1, CXCL2, DEFB3 and BOLA-DQA3 were associated with immune function and inflammatory response indicating their strong immune potential to combat the pathogens prevalent in the tropical conditions. The molecular pathways highly impacted were MAPK signaling, ETC, apoptosis, TLR signaling and NF- kB signaling pathway indicating signatures of adaptive evolution of these two cattle types in response to diverse environments. Further, qPCR analysis revealed increased expression of DEGs such as HIF-1, EPAS-1, VEGFA, NOS2, and GLUT-1/SLC2A1 in cattle types from high altitude suggesting their pivotal role in association with high altitude adaptation. Based on data generated, native cattle of Ladakh region was found to be genetically distinct from native cattle adapted to the tropical region of India.
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Affiliation(s)
- Preeti Verma
- Singhania University, Jhunjhunu, Rajasthan, India
| | - Ankita Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Kiran Thakur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Ranjit S Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Saket K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | | | - Prabhat Kumar
- Defence Institute of High Altitude Research, Leh, India
| | - Arup Giri
- Defence Institute of High Altitude Research, Leh, India
| | - Sahil Kalia
- Defence Institute of High Altitude Research, Leh, India
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
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42
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Shih HM, Wu CJ, Lin SL. Physiology and pathophysiology of renal erythropoietin-producing cells. J Formos Med Assoc 2018; 117:955-963. [PMID: 29655605 DOI: 10.1016/j.jfma.2018.03.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 02/05/2023] Open
Abstract
Anemia is a common complication and contributes to increased morbidity and mortality in chronic kidney disease (CKD) patients. Whereas there has been a significant improvement of understanding the underlying mechanism of erythropoiesis, the treatment of renal anemia is still restricted to erythropoietin (EPO)-stimulating agents. The purpose of this article is to review the physiology of erythropoiesis, functional role of EPO and underlying molecular and cellular basis that regulate EPO production. Regulation of EPO production is at mRNA level. When anemia or hypoxia occurs, transcriptional factor, hypoxia-inducible factor (HIF), binds to EPO 5' hypoxic response element and EPO gene transcription increases. The renal EPO is mainly produced by pericytes. In CKD, pericytes transdifferentiate to myofibroblasts, and subsequently the ability of EPO production decreases, leading to renal anemia. Recent experimental and clinical studies show the promising efficacy of prolyl hydroxylase inhibitors in renal anemia through increasing EPO production by stabilizing HIF. Recent advances on epigenetics create a new field to study EPO gene expression at chromatin level. We will discuss the role of demethylating agent on restoring EPO expression, providing a novel approach to the treatment of renal anemia.
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Affiliation(s)
- Hong-Mou Shih
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Nephrology, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chih-Jen Wu
- Division of Nephrology, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, Taipei, Taiwan; Graduate Institute of Medical Sciences and Department of Pharmacology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shuei-Liong Lin
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan; Renal Division, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Integrated Diagnostics &Therapeutics, National Taiwan University Hospital, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan.
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43
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Shattuck EC. Ecological Context and Human Variation: Applying the Principles of Biological Anthropology to Psychoneuroimmunology. Methods Mol Biol 2018; 1781:55-76. [PMID: 29705842 DOI: 10.1007/978-1-4939-7828-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is considerable research interest overlap between biological anthropology and psychoneuroimmunology (PNI), particularly given recent anthropological interest in endocrine and immune system functioning over the life span and in different environmental contexts. In this chapter, I argue that conducting research on non-WEIRD populations and applying an anthropological, evolutionary approach to PNI can greatly strengthen our understanding of immune-endocrine-behavior connections. This chapter reviews population-level variation in the human immune and endocrine systems, as well as genetic and environmental contributions to this variation. The effects of culture on shaping health outcomes and stress responses are also considered. Finally, this chapter discusses some noninvasive sampling methodologies appropriate to field research and alternatives to laboratory-based research designs. By confronting variable social and environmental contexts, PNI can greatly expand on its existing contributions to the treatment and understanding of depression, mood disorders, stress, and other aspects of health and well-being.
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Affiliation(s)
- Eric C Shattuck
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
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44
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Affiliation(s)
- W. K. Milsom
- Department of Zoology; University of British Columbia; Vancouver BC Canada
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45
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Evidence of Early-Stage Selection on EPAS1 and GPR126 Genes in Andean High Altitude Populations. Sci Rep 2017; 7:13042. [PMID: 29026132 PMCID: PMC5638799 DOI: 10.1038/s41598-017-13382-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/22/2017] [Indexed: 11/21/2022] Open
Abstract
The aim of this study is to identify genetic variants that harbour signatures of recent positive selection and may facilitate physiological adaptations to hypobaric hypoxia. To achieve this, we conducted whole genome sequencing and lung function tests in 19 Argentinean highlanders (>3500 m) comparing them to 16 Native American lowlanders. We developed a new statistical procedure using a combination of population branch statistics (PBS) and number of segregating sites by length (nSL) to detect beneficial alleles that arose since the settlement of the Andes and are currently present in 15–50% of the population. We identified two missense variants as significant targets of selection. One of these variants, located within the GPR126 gene, has been previously associated with the forced expiratory volume/forced vital capacity ratio. The other novel missense variant mapped to the EPAS1 gene encoding the hypoxia inducible factor 2α. EPAS1 is known to be the major selection candidate gene in Tibetans. The derived allele of GPR126 is associated with lung function in our sample of highlanders (p < 0.05). These variants may contribute to the physiological adaptations to hypobaric hypoxia, possibly by altering lung function. The new statistical approach might be a useful tool to detect selected variants in population studies.
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46
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Lanikova L, Reading NS, Hu H, Tashi T, Burjanivova T, Shestakova A, Siwakoti B, Thakur BK, Pun CB, Sapkota A, Abdelaziz S, Feng BJ, Huff CD, Hashibe M, Prchal JT. Evolutionary selected Tibetan variants of HIF pathway and risk of lung cancer. Oncotarget 2017; 8:11739-11747. [PMID: 28036300 PMCID: PMC5355300 DOI: 10.18632/oncotarget.14340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/16/2016] [Indexed: 01/09/2023] Open
Abstract
Tibetans existed in high altitude for ~25 thousand years and have evolutionary selected unique haplotypes assumed to be beneficial to hypoxic adaptation. EGLN1/PHD2 and EPAS1/HIF-2α, both crucial components of hypoxia sensing, are the two best-established loci contributing to high altitude adaptation. The co-adapted Tibetan-specific haplotype encoding for PHD2:p.[D4E/C127S] promotes increased HIF degradation under hypoxic conditions. The Tibetan-specific 200 kb EPAS1 haplotype introgressed from an archaic human population related to Denisovans which underwent evolutionary decay; however, the functional variant(s) responsible for high-altitude adaptation at EPAS1/HIF-2α have not yet been identified. Since HIF modulates the behavior of cancer cells, we hypothesized that these Tibetan selected genomic variants may modify cancer risk predisposition. Here, we ascertained the frequencies of EGLN1D4E/C127S and EGLN1C127S variants and ten EPAS1/HIF-2α variants in lung cancer patients and controls in Nepal, whose population consists of people with Indo-Aryan origin and Tibetan-related Mongoloid origin. We observed a significant association between the selected Tibetan EGLN1/PHD2 haplotype and lung cancer (p=0.0012 for D4E, p=0.0002 for C127S), corresponding to a two-fold increase in lung cancer risk. We also observed a two-fold or greater increased risk for two of the ten EPAS1/HIF-2α variants, although the association was not significant after correcting for multiple comparisons (p=0.12). Although these data cannot address the role of these genetic variants on lung cancer initiation or progression, we conclude that some selected Tibetan variants are strongly associated with a modified risk of lung cancer.
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Affiliation(s)
- Lucie Lanikova
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Institute of Molecular Genetics, Academy of Sciences, Prague, Czech Republic
| | - N Scott Reading
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Hao Hu
- University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Tsewang Tashi
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tatiana Burjanivova
- Department of Molecular Biology, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Slovak Republic
| | - Anna Shestakova
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bhola Siwakoti
- B.P. Koirala Memorial Cancer Hospital, Bharatpur, Chitwan, Nepal
| | | | - Chin Bahadur Pun
- B.P. Koirala Memorial Cancer Hospital, Bharatpur, Chitwan, Nepal
| | - Amir Sapkota
- Maryland Institute for Applied Environmental Health, and University of Maryland College Park School of Public Health, Maryland, USA
| | - Sarah Abdelaziz
- Division of Public Health, Department of Family & Preventive Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Chad D Huff
- University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Mia Hashibe
- Division of Public Health, Department of Family & Preventive Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Josef T Prchal
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Department of Pathophysiology and 1st Department of Medicine, 1st Faculty of Medicine, Charles University in Prague, Czech Republic
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Gonggalanzi, Labasangzhu, Bjertness E, Wu T, Stigum H, Nafstad P. Acute mountain sickness, arterial oxygen saturation and heart rate among Tibetan students who reascend to Lhasa after 7 years at low altitude: a prospective cohort study. BMJ Open 2017; 7:e016460. [PMID: 28698346 PMCID: PMC5726117 DOI: 10.1136/bmjopen-2017-016460] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objectives The aim of the present study was to estimate the incidence of acute mountain sickness (AMS) and address the changes in arterial oxygen saturation (SaO2) and heart rate (HR) in native Tibetans who reascend to the high-altitude city of Lhasa (3658 m) after a 7-year stay at low altitude. Methods We followed two cohorts of students aged 17–21 years (859 Native Tibetan and 801 Han Chinese), travelling from lowland China until 3 days after their arrival in highland city of Lhasa. Questionnaire information of the symptoms of AMS using the Lake Louise Scoring System, resting SaO2 and HR were assessed both before leaving the lowland and after arriving in Lhasa. Linear regression was performed to compare changes in SaO2 and HR levels from low to high altitude in Tibetan and Han Chinese. Results New cases of AMS occurred in only 1.2% (95% CI 0.4% to 2.0%) of the Tibetan students who came to Lhasa by train compared with 32.7% (95% CI 28.0% to 37.3%) and 42.9% (95% CI 38.0% to 47.7%) of the Han Chinese students who came to Lhasa by train and by air, respectively. Tibetan students had less changes in SaO2 (−2.95 percentage points, 95% CI −3.24% to −2.65%) and HR (10.89 beats per minute (bpm), 95% CI 9.62 to 12.16 bpm) from low to high altitude compared with Han Chinese students, although measurements did not differ between the two groups when measured at low altitude. Conclusions Healthy Tibetans are mostly protected against AMS and primarily maintain their good adaptation to high altitude, even after a long period of stay at low altitude.
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Affiliation(s)
- Gonggalanzi
- Tibet University Medical College, Tibet, China
| | - Labasangzhu
- Tibet University Medical College, Tibet, China
| | - Espen Bjertness
- Tibet University Medical College, Tibet, China.,Faculty of Medicine,University of Oslo, Oslo, Norway
| | - Tianyi Wu
- Tibet University Medical College, Tibet, China.,National Key Laboratory of High-Altitude Medicine, Xining, Qinghai, China
| | - Hein Stigum
- Faculty of Medicine,University of Oslo, Oslo, Norway.,Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Nafstad
- Faculty of Medicine,University of Oslo, Oslo, Norway.,Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
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Zhang B, Chamba Y, Shang P, Wang Z, Ma J, Wang L, Zhang H. Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig. Sci Rep 2017. [PMID: 28623314 PMCID: PMC5473931 DOI: 10.1038/s41598-017-03976-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan pigs that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from lowland pigs, and have adapted well to extreme conditions. However, the mechanisms involved in regulating gene expression at high altitude in these animals are not fully understood. In this study, we obtained transcriptomic and proteomic data from the heart tissues of Tibetan and Yorkshire pigs raised in the highlands (TH and YH) and lowlands (TL and YL) via RNA-seq and iTRAQ (isobaric tags for relative and absolute quantitation) analyses, respectively. Comparative analyses of TH vs. YH, TH vs.TL, TL vs. YL, and YH vs. YL yielded 299, 169, 242, and 368 differentially expressed genes (DEGs), and 473, 297, 394, and 297 differentially expressed proteins (DEPs), respectively. By functional annotation of these DEGs and DEPs, genes that were enriched in the HIF-1 signaling pathway (NPPA, ERK2, ENO3, and EGLN3), VEGF signaling pathway (ERK2, A2M, FGF1, CTGF, and DPP4), and hypoxia-related processes (CRYAB, EGLN3, TGFB2, DPP4, and ACE) were identified as important candidate genes for high-altitude adaptation in the Tibetan pig. This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in pigs, and furthers our understanding of human hypoxic diseases.
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Affiliation(s)
- Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Peng Shang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.,Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, 860000, China
| | - Zhixiu Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Jun Ma
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Liyuang Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, China.
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49
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Tashi T, Scott Reading N, Wuren T, Zhang X, Moore LG, Hu H, Tang F, Shestakova A, Lorenzo F, Burjanivova T, Koul P, Guchhait P, Wittwer CT, Julian CG, Shah B, Huff CD, Gordeuk VR, Prchal JT, Ge R. Gain-of-function EGLN1 prolyl hydroxylase (PHD2 D4E:C127S) in combination with EPAS1 (HIF-2α) polymorphism lowers hemoglobin concentration in Tibetan highlanders. J Mol Med (Berl) 2017; 95:665-670. [PMID: 28233034 DOI: 10.1007/s00109-017-1519-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/14/2016] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
Tibetans have lived at high altitude for generations and are thought to be genetically adapted to hypoxic environments. Most are protected from hypoxia-induced polycythemia, and a haplotype of EPAS1, encoding hypoxia-inducible factor (HIF-2α), has been associated with lower hemoglobin levels. We earlier reported a Tibetan-specific EGLN1 haplotype encoding PHD2 which abrogates HIF augmentation in hypoxia. We genotyped 347 Tibetan individuals from varying altitudes for both the Tibetan-specific EGLN1 haplotype and 10 candidate SNPs in the EPAS1 haplotype and correlated their association with hemoglobin levels. The effect of the EGLN1 haplotype on hemoglobin exhibited age dependency at low altitude, while at higher altitudes, it showed a trend to lower hemoglobin levels in the presence of the Tibetan-selected EPAS1 rs142764723 C/C allele. The observed gene-environment and gene-gene interactions and the moderate effect of the EGLN1 and EPAS1 haplotypes on hemoglobin indicate that other modifiers exist. It remains to be determined whether a blunting of erythropoiesis or other physiological consequences of HIF downregulation are the primary drivers of these genetic adaptations among Tibetans. KEY MESSAGE Most Tibetans are protected from polycythemia while living in high altitude. An EGLN1 co-adapted haplotype, EGLN1 c.12C>G, c.380G>C is uniquely Tibetan. The Tibetan EPAS1 haplotype has introgressed from the Denisovan genome. While EGLN1 and EPAS1 genotypes lower Hb, this study indicates additional Hb modifiers.
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Affiliation(s)
- Tsewang Tashi
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
| | - N Scott Reading
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Tanna Wuren
- Research Center for High-Altitude Medicine, Qinghai University, Xining, China
| | - Xu Zhang
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Lorna G Moore
- Departments of Medicine and Obstetrics/Gynecology, University of Colorado Denver, Aurora, CO, USA
| | - Hao Hu
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Feng Tang
- Research Center for High-Altitude Medicine, Qinghai University, Xining, China
| | - Anna Shestakova
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Felipe Lorenzo
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
| | - Tatiana Burjanivova
- Division of Hematology, University of Utah, Salt Lake City, UT, USA
- Department of Molecular Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Bratislava, Slovakia
| | - Parvaiz Koul
- Sher-i-Kashmir Institute of Medical Sciences, Srinagar, India
| | | | - Carl T Wittwer
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Colleen G Julian
- Departments of Medicine and Obstetrics/Gynecology, University of Colorado Denver, Aurora, CO, USA
| | - Binal Shah
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Chad D Huff
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Victor R Gordeuk
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Josef T Prchal
- Division of Hematology, University of Utah, Salt Lake City, UT, USA.
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, UT, USA.
- Department of Pathophysiology and 1st Department of Medicine, 1st Faculty Medicine, Charles University in Prague, Prague, Czech Republic.
- Hematology, SOM 5C310, University of Utah School of Medicine, Salt Lake City, UT, 84132-2408, USA.
| | - RiLi Ge
- Research Center for High-Altitude Medicine, Qinghai University, Xining, China.
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50
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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