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Zhang L, Zhu Y, Ren Y, Xu L, Liu X, Qi X, Jiao T, Sun G, Han H, Zhang J, Sun F, Yang Y, Zhao S. Genetic characterization of Tibetan pigs adapted to high altitude under natural selection based on a large whole-genome dataset. Sci Rep 2024; 14:17062. [PMID: 39048584 PMCID: PMC11269713 DOI: 10.1038/s41598-024-65559-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024] Open
Abstract
The Qinghai-Tibet Plateau is a valuable genetic resource pool, and the high-altitude adaptation of Tibetan pigs is a classic example of the adaptive evolution of domestic animals. Here, we report the presence of Darwinian positive selection signatures in Tibetan pigs (TBPs) using 348 genome-wide datasets (127 whole-genome sequence datasets (WGSs) and 221 whole-genome single-nucleotide polymorphism (SNP) chip datasets). We characterized a high-confidence list of genetic signatures related response to high-altitude adaptation in Tibetan pigs, including 4,598 candidate SNPs and 131 candidate genes. Functional annotation and enrichment analysis revealed that 131 candidate genes are related to multiple systems and organs in Tibetan pigs. Notably, eight of the top ten novel genes, RALB, NBEA, LIFR, CLEC17A, PRIM2, CDH7, GK5 and FAM83B, were highlighted and associated with improved adaptive heart functions in Tibetan pigs high-altitude adaptation. Moreover, genome-wide association analysis revealed that 29 SNPs were involved in 13 candidate genes associated with at least one adaptive trait. In particular, among the top ten candidate genes, CLEC17A is related to a reduction in hemoglobin (HGB) in Tibetan pigs. Overall, our study provides a robust SNP/gene list involving genetic adaptation for Tibetan pig high-altitude adaptation, and it will be a valuable resource for future Tibetan pig studies.
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Affiliation(s)
- Lingyun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yanbin Zhu
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, China
| | - Linna Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuanbo Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, China
| | - Ting Jiao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Guangming Sun
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, China
| | - Haiyu Han
- The Animal Husbandry Station in Changdu, Changdu, China
| | - Jian Zhang
- The Beast Prevention Station in Gongbujiangda County, Linzhi, China
| | - Fengbo Sun
- The Animal Husbandry Station in Tibet Autonomous Region, Lhasa, China
| | - Yanan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.
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2
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Liang X, Duan Q, Li B, Wang Y, Bu Y, Zhang Y, Kuang Z, Mao L, An X, Wang H, Yang X, Wan N, Feng Z, Shen W, Miao W, Chen J, Liu S, Storz JF, Liu J, Nevo E, Li K. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep. Proc Natl Acad Sci U S A 2024; 121:e2322291121. [PMID: 38913905 PMCID: PMC11228492 DOI: 10.1073/pnas.2322291121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over a relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish Tibetan sheep from closely related, low-altitude Hu sheep, and we examine associated changes in tissue-specific gene expression. We document differentiation between the two sheep breeds in frequencies of SVs associated with genes involved in cardiac function and circulation. In Tibetan sheep, we identified high-frequency SVs in a total of 462 genes, including EPAS1, PAPSS2, and PTPRD. Single-cell RNA-Seq data and luciferase reporter assays revealed that the SVs had cis-acting effects on the expression levels of these three genes in specific tissues and cell types. In Tibetan sheep, we identified a high-frequency chromosomal inversion that exhibited modified chromatin architectures relative to the noninverted allele that predominates in Hu sheep. The inversion harbors several genes with altered expression patterns related to heart protection, brown adipocyte proliferation, angiogenesis, and DNA repair. These findings indicate that SVs represent an important source of genetic variation in gene expression and may have contributed to high-altitude adaptation in Tibetan sheep.
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Affiliation(s)
- Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yueting Bu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yonglu Zhang
- Fengjia Town Health Center, Rushan City, Weihai City264200, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Wei Shen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Weilan Miao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jiaqi Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE68588
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa3498838, Israel
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
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3
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Fox JA, Hunt DAGA, Hendry AP, Chapman LJ, Barrett RDH. Counter-gradient variation in gene expression between fish populations facilitates colonization of low-dissolved oxygen environments. Mol Ecol 2024; 33:e17419. [PMID: 38808559 DOI: 10.1111/mec.17419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
The role of phenotypic plasticity during colonization remains unclear due to the shifting importance of plasticity across timescales. In the early stages of colonization, plasticity can facilitate persistence in a novel environment; but over evolutionary time, processes such as genetic assimilation may reduce variation in plastic traits such that species with a longer evolutionary history in an environment can show lower levels of plasticity than recent invaders. Therefore, comparing species in the early stages of colonization to long-established species provides a powerful approach for uncovering the role of phenotypic plasticity during different stages of colonization. We compared gene expression between low-dissolved oxygen (DO) and high-DO populations of two cyprinid fish: Enteromius apleurogramma, a species that has undergone a recent range expansion, and E. neumayeri, a long-established native species in the same region. We sampled tissue either immediately after capture from the field or after a 2-week acclimation under high-DO conditions, allowing us to test for both evolved and plastic differences in low-DO vs high-DO populations of each species. We found that most genes showing candidate-evolved differences in gene expression did not overlap with those showing plastic differences in gene expression. However, in the genes that did overlap, there was counter-gradient variation such that plastic and evolved gene expression responses were in opposite directions in both species. Additionally, E. apleurogramma had higher levels of plasticity and evolved divergence in gene expression between field populations. We suggest that the higher level of plasticity and counter-gradient variation may have allowed rapid genetic adaptation in E. apleurogramma and facilitated colonization. This study shows how counter-gradient variation may impact the colonization of divergent oxygen environments.
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Affiliation(s)
- Janay A Fox
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - David A G A Hunt
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Andrew P Hendry
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
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Kosch TA, Torres-Sánchez M, Liedtke HC, Summers K, Yun MH, Crawford AJ, Maddock ST, Ahammed MS, Araújo VLN, Bertola LV, Bucciarelli G, Carné A, Carneiro CM, Chan KO, Chen Y, Crottini A, da Silva JM, Denton RD, Dittrich C, Themudo GE, Farquharson KA, Forsdick NJ, Gilbert E, Jing C, Katzenback BA, Kotharambath R, Levis NA, Márquez R, Mazepa G, Mulder KP, Müller H, O’Connell MJ, Orozco-terWengel P, Palomar G, Petzold A, Pfennig DW, Pfennig KS, Reichert MS, Robert J, Scherz MD, Siu-Ting K, Snead AA, Stöck M, Stuckert AMM, Stynoski JL, Tarvin RD, Valero KCW. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601086. [PMID: 39005434 PMCID: PMC11244923 DOI: 10.1101/2024.06.27.601086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.
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Affiliation(s)
- Tiffany A. Kosch
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, Victoria, Australia
| | - María Torres-Sánchez
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Kyle Summers
- Biology Department, East Carolina University, Greenville, NC, USA 27858
| | - Maximina H. Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrew J. Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
- Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Simon T. Maddock
- School of Natural and Environmental Sciences, Newcastle University, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Seychelles
| | | | - Victor L. N. Araújo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Lorenzo V. Bertola
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, QLD 4810, Australia
| | - Gary Bucciarelli
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, USA
| | - Albert Carné
- Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Céline M. Carneiro
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kin O. Chan
- University of Kansas Biodiversity Institute and Natural History Museum, Lawrence, Kansas 66045, USA
| | - Ying Chen
- Biology Department, Queen’s University, Ontario, Canada
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169– 007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jessica M. da Silva
- Evolutionary Genomics and Wildlife Management, Foundatonal Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Newlands 7735, Cape Town, South Africa
- Centre for Evolutionary Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa
| | - Robert D. Denton
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Carolin Dittrich
- Rojas Lab, Konrad-Lorenz-Institute of Ethology, Department of Life Science, University of Veterinary Medicine, Vienna, Austria
| | - Gonçalo Espregueira Themudo
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos, Portugal
| | - Katherine A. Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Edward Gilbert
- School of Natural Sciences, The University of Hull, Hull, HU6 7RX, United Kingdom
- Energy and Environment Institute, The University of Hull, Hull, HU6 7RX, United Kingdom
| | - Che Jing
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | | | - Ramachandran Kotharambath
- Herpetology Lab, Dept. of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, 671320, India
| | - Nicholas A. Levis
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Roberto Márquez
- Department of Biological Sciences, Virginia Tech. Blacksburg, VA 24060, USA
| | - Glib Mazepa
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Switzerland
- Department of Ecology and Genetics, Evolutionary Biology, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Kevin P. Mulder
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Hendrik Müller
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, D-06108 Halle (Saale), Germany
| | - Mary J. O’Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Museum Avenue, CF10 3AX Cardiff, United Kingdom
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology; Faculty of Biological Sciences; Complutense University of Madrid, Madrid, Spain
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Alice Petzold
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str.24-25, 14476 Potsdam, Germany
| | - David W. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karin S. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael S. Reichert
- Department of Integrative Biology, Oklahoma State University, Stillwater OK, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Karen Siu-Ting
- School of Biological Sciences, Queen’s University Belfast, Belfast, BT7 1NN, Northern Ireland, United Kingdom
- Instituto Peruano de Herpetología, Ca. Augusto Salazar Bondy 136, Surco, Lima, Peru
- Herpetology Lab, The Natural History Museum, London, United Kingdom
| | - Anthony A Snead
- Department of Biology, New York University, New York, NY, USA
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany
| | - Adam M. M. Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA
| | | | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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Zhao M, Wu Q, Duanmu W, Shen J, Yuan W, Sun Y, Zhang X, Zhang J, He S. Clinical Analysis of Myocardial Injury in Highlanders with Pulmonary Hypertension. High Alt Med Biol 2024. [PMID: 38900692 DOI: 10.1089/ham.2023.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Background: Pulmonary hypertension (PH) is a prevalent adverse cardiovascular event at high-altitude environments. Prolonged exposure to high altitudes may result in myocardial injury, which is associated with poor clinical outcomes. This study aims to investigate the clinical characteristics of myocardial injury in patients with PH at high altitude. Methods: Consecutive patients admitted to a general tertiary hospital at the altitude of 3,650 m were selected into this retrospective study. Clinical and biochemical data were collected, as well as based on cardiac troponin I (cTnI) and echocardiography, patients were divided into myocardial injury group and non-myocardial injury group. Results: A total of 231 patients were enrolled, among whom 29 (12.6%) had myocardial injury. We found that body mass index, left ventricular end-diastolic dimension, and serum level of creatine kinase-MB (CK-MB) in myocardial injury group were significantly higher than non-myocardial injury group. Spearman correlation analysis revealed that cTnI has a significant positive correlation with CK-MB and lactic dehydrogenase instead of aspartate aminotransferase. A receiver operating characteristic curve was drawn to demonstrate that CK-MB could significantly predict the occurrence of myocardial injury with an area under the curve of 0.749, and a level of 3.035 (sensitivity = 59.3%, specificity = 90.5%) was optimal cutoff value. Conclusion: The incidence of myocardial injury in highlanders with PH is significant. CK-MB, as a convenient and efficient marker, has been found to be closely associated with cTnI and plays a predictive role in the occurrence of myocardial injury with PH in individuals exposed to high altitude.
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Affiliation(s)
- Maolin Zhao
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, The General Hospital of Western Theater Command, Chengdu, China
| | - Qianjin Wu
- Department of Health Service, Tibetan Military General Hospital, Lhasa, China
| | - Wangsheng Duanmu
- Department of Neurology, Tibetan Military General Hospital, Lhasa, China
| | - Junxian Shen
- Department of Neurology, Tibetan Military General Hospital, Lhasa, China
| | - Weixin Yuan
- Department of Neurology, Tibetan Military General Hospital, Lhasa, China
| | - Yingbin Sun
- Department of Cardiology, Tibetan Military General Hospital, Lhasa, China
| | - Xu Zhang
- Department of Cardiology, Tibetan Military General Hospital, Lhasa, China
| | - Jinbao Zhang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, The General Hospital of Western Theater Command, Chengdu, China
| | - Siyi He
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, The General Hospital of Western Theater Command, Chengdu, China
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Su R, Jia S, Zhang N, Wang Y, Li H, Zhang D, Ma H, Su Y. The effects of long-term high-altitude exposure on cognition: A meta-analysis. Neurosci Biobehav Rev 2024; 161:105682. [PMID: 38642865 DOI: 10.1016/j.neubiorev.2024.105682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
Long-term high altitudes (HA) exposure's impact on cognition has yielded inconsistent findings in previous research. To address this, we conducted a meta-analysis of 49 studies (6191 individuals) to comprehensively evaluate this effect. Moderating factors such as cognitive task type, altitude (1500-2500 m, 2500-4000 m, and above 4000 m), residential type (chronic and lifelong), adaptation level and demographic factors were analyzed. Cognitive tasks were classified into eight categories: perceptual processes, psychomotor function, long-term memory, working memory, inhibitory control, problem-solving, language, and others. Results revealed a moderate negative effect of HA on cognitive performance (g = -.40, SE =.18, 95% CI = -.76 to -.05). Psychomotor function and long-term memory notably experience the most pronounced decline, while working memory and language skills show moderate decreases due to HA exposure. However, perceptual processes, inhibitory control, and problem-solving abilities remain unaffected. Moreover, residing at altitudes above 4000 m and being a HA immigrant are associated with significant cognitive impairment. In summary, our findings indicate a selective adaptation of cognitive performance to HA conditions.
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Affiliation(s)
- Rui Su
- School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behavior and Mental Health, Peking University, Beijing 100871, China; Key Laboratory of High Altitudes Brain Science and Environmental Acclimation, Tibet University, Lhasa 85000, China
| | - Shurong Jia
- Key Laboratory of High Altitudes Brain Science and Environmental Acclimation, Tibet University, Lhasa 85000, China
| | - Niannian Zhang
- Key Laboratory of High Altitudes Brain Science and Environmental Acclimation, Tibet University, Lhasa 85000, China
| | - Yiyi Wang
- Department of Psychology, University of Chicago, Chicago, IL 60637, United States
| | - Hao Li
- Key Laboratory of High Altitudes Brain Science and Environmental Acclimation, Tibet University, Lhasa 85000, China
| | - Delong Zhang
- Key Laboratory of High Altitudes Brain Science and Environmental Acclimation, Tibet University, Lhasa 85000, China; School of Psychology, Center for Studies of Psychological Application, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
| | - Hailin Ma
- Key Laboratory of High Altitudes Brain Science and Environmental Acclimation, Tibet University, Lhasa 85000, China
| | - Yanjie Su
- School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behavior and Mental Health, Peking University, Beijing 100871, China.
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7
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Li X, Xu S, Li X, Wang Y, Sheng Y, Zhang H, Yang W, Yuan D, Jin T, He X. Novel insight into the genetic signatures of altitude adaptation related body composition in Tibetans. Front Public Health 2024; 12:1355659. [PMID: 38807991 PMCID: PMC11130355 DOI: 10.3389/fpubh.2024.1355659] [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: 12/20/2023] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Background The Tibetan population residing in high-altitude (HA) regions has adapted to extreme hypoxic environments. However, there is limited understanding of the genetic basis of body compositions in Tibetan population adapted to HA. Methods We performed a genome-wide association study (GWAS) to identify genetic variants associated with HA and HA-related body composition traits. A total of 755,731 single nucleotide polymorphisms (SNPs) were genotyped using the precision medicine diversity array from 996 Tibetan college students. T-tests and Pearson correlation analysis were used to estimate the association between body compositions and altitude. The mixed linear regression identified the SNPs significantly associated with HA and HA-related body compositions. LASSO regression was used to screen for important SNPs in HA and body compositions. Results Significant differences were observed in lean body mass (LBW), muscle mass (MM), total body water (TBW), standard weight (SBW), basal metabolic rate (BMR), total protein (TP), and total inorganic salt (Is) in different altitudes stratification. We identified three SNPs in EPAS1 (rs1562453, rs7589621 and rs7583392) that were significantly associated with HA (p < 5 × 10-7). GWAS analysis of 7 HA-related body composition traits, we identified 14 SNPs for LBM, 11 SNPs for TBW, 15 SNPs for MM, 16 SNPs for SBW, 9 SNPs for BMR, 12 SNPs for TP, and 26 SNPs for Is (p < 5.0 × 10-5). Conclusion These findings provide insight into the genetic basis of body composition in Tibetan college students adapted to HA, and lay the foundation for further investigation into the molecular mechanisms underlying HA adaptation.
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Affiliation(s)
- Xuguang Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
| | - Shilin Xu
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Xuemei Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
| | - Yuhe Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Healthcare, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
| | - Yemeng Sheng
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Hengxun Zhang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Healthcare, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
| | - Wei Yang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Emergency, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
| | - Dongya Yuan
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
| | - Tianbo Jin
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Xue He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi, China
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8
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Yan Z, Yang J, Wei WT, Zhou ML, Mo DX, Wan X, Ma R, Wu MM, Huang JH, Liu YJ, Lv FH, Li MH. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues. Nat Commun 2024; 15:3970. [PMID: 38730227 PMCID: PMC11087590 DOI: 10.1038/s41467-024-48261-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
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Affiliation(s)
- Ze Yan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen-Tian Wei
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ming-Liang Zhou
- Sichuan Academy of Grassland Science, Chengdu, 611743, China
| | - Dong-Xin Mo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing Wan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rui Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mei-Ming Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ya-Jing Liu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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9
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González-García M, Téllez LE. Adaptation to Living at High Altitude in Patients with COPD. Comparative Study of Exercise Capacity and Ventilatory Variables between Patients Residing at High and Low Altitudes in the Andes. High Alt Med Biol 2024. [PMID: 38526234 DOI: 10.1089/ham.2023.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
González-García, Mauricio and Luis Ernesto Téllez. Adaptation to living at high altitude in patients with COPD. Comparative study of exercise capacity and ventilatory variables between patients residing at high and low altitudes in the Andes. High Alt Med Biol. 00:000-000, 2024. Introduction: Although some variables related to oxygen transport and utilization such as ventilation, pulmonary vascular responses to hypoxia, heart rate (HR), cardiac output, hemoglobin (Hb), and oxygen saturation (SpO2) are used to compare adaptation to altitude between populations, peak oxygen consumption (VO2) constitutes an integrative measure of total oxygen transport that may reflect successful adaptation to altitude. We designed this study to make a direct comparison of VO2 in a cardiopulmonary exercise test (CPET) between chronic obstructive pulmonary disease (COPD) patients residing at high altitude (Bogotá, Colombia: 2,640 m) (COPD-HA) and those living at low altitude (Bucaramanga, Colombia: 959 m) (COPD-LA). Methods: All patients performed a CPET with measurements of VO2, minute ventilation (VE), HR, oxygen pulse (VO2/HR), ventilatory equivalents (VE/VCO2), and SpO2. Unpaired T-test or Mann-Whitney U test were used for comparisons between COPD-HA and COPD-LA. Results: We included 71 patients with COPD, 53 COPD-HA, and 18 COPD-LA. There were no differences between groups in age, sex, or forced expiratory volume in 1 second. The means ± SD of Hb, g/dl was slightly higher in COPD-HA (15.9 ± 1.9 vs. 14.7 ± 1.8, p = 0.048), without differences in VO2, % pred (71.6 ± 17.9 vs. 69.0 ± 17.0, p = 0.584), VO2/HR, % pred (92.1 ± 22.0 vs. 89.7 ± 19.8, p = 0.733) or VE/MVV, % (75.5 ± 14.1 vs. 76.5 ± 14.3, p = 0.790) at peak exercise between groups. Median (IQR) of VE/VCO2 nadir [38.0 (37.0-42.0) vs. 32.5 (31.0-39.0), p = 0.005] was significantly higher, and SpO2, % at rest [88.0 (86.0-91.0) vs. 95.0 (94.0-96.0), p < 0.001] and at peak exercise [84.0 (77.0-90.0) vs. 93.0 (92.0-95.0), p < 0.001] were significantly lower in COPD-HA. Conclusions: Despite higher desaturation at rest and during exercise in COPD-HA, there were no differences in VO2 peak between COPD-HA and COPD-LA, suggesting a potential altitude adaptation in those patients chronically exposed to hypoxia.
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Affiliation(s)
- Mauricio González-García
- Research Department, Fundación Neumologica Colombiana, Bogotá, Colombia
- Faculty of Medicine, Universidad de la Sabana, Chía, Colombia
- Postgraduate Program in Sports Medicine, Universidad El Bosque, Bogotá, Colombia
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10
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She H, Hao Y, Song G, Luo X, Lei F, Zhai W, Qu Y. Gene expression plasticity followed by genetic change during colonization in a high-elevation environment. eLife 2024; 12:RP86687. [PMID: 38470231 DOI: 10.7554/elife.86687] [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: 03/13/2024] Open
Abstract
Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called 'plasticity first.' Herein, we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage), and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscles, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associated with decreased hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increased hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e. 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.
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Affiliation(s)
- Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xu Luo
- Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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11
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An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, Qiao Z, Li B, Li F, Kuang Z, Wan N, Liang X, Duan Q, Feng Z, Yang X, Liu S, Nevo E, Liu J, Storz JF, Li K. Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors. Nat Ecol Evol 2024; 8:339-351. [PMID: 38195998 DOI: 10.1038/s41559-023-02275-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.
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Affiliation(s)
- Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qinqin Xu
- Department of Medical Oncology, Qinghai Provincial People's Hospital, Xining, China
| | - Xi Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhenglei Qiao
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Fang Li
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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12
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Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
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Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
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13
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Souchet J, Josserand A, Darnet E, Le Chevalier H, Trochet A, Bertrand R, Calvez O, Martinez-Silvestre A, Guillaume O, Mossoll-Torres M, Pottier G, Philippe H, Aubret F, Gangloff EJ. Embryonic and juvenile snakes (Natrix maura, Linnaeus 1758) compensate for high elevation hypoxia via shifts in cardiovascular physiology and metabolism. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:1102-1115. [PMID: 37723946 DOI: 10.1002/jez.2756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/30/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023]
Abstract
The colonization of novel environments requires a favorable response to conditions never, or rarely, encountered in recent evolutionary history. For example, populations colonizing upslope habitats must cope with lower atmospheric pressure at elevation, and thus reduced oxygen availability. The embryo stage in oviparous organisms is particularly susceptible, given its lack of mobility and limited gas exchange via diffusion through the eggshell and membranes. Especially little is known about responses of Lepidosaurian reptiles to reduced oxygen availability. To test the role of physiological plasticity during early development in response to high elevation hypoxia, we performed a transplant experiment with the viperine snake (Natrix maura, Linnaeus 1758). We maintained gravid females originating from low elevation populations (432 m above sea level [ASL]-normoxia) at both the elevation of origin and high elevation (2877 m ASL-extreme high elevation hypoxia; approximately 72% oxygen availability relative to sea level), then incubated egg clutches at both low and high elevation. Regardless of maternal exposure to hypoxia during gestation, embryos incubated at extreme high elevation exhibited altered developmental trajectories of cardiovascular function and metabolism across the incubation period, including a reduction in late-development egg mass. This physiological response may have contributed to the maintenance of similar incubation duration, hatching success, and hatchling body size compared to embryos incubated at low elevation. Nevertheless, after being maintained in hypoxia, juveniles exhibit reduced carbon dioxide production relative to oxygen consumption, suggesting altered energy pathways compared to juveniles maintained in normoxia. These findings highlight the role of physiological plasticity in maintaining rates of survival and fitness-relevant phenotypes in novel environments.
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Affiliation(s)
- Jérémie Souchet
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Alicia Josserand
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Elodie Darnet
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Hugo Le Chevalier
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Audrey Trochet
- Société Herpétologique de France, Muséum National d'Histoire Naturelle, Paris, France
| | - Romain Bertrand
- Laboratoire Évolution et Diversité Biologique (UMR CNRS 5174), Université de Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Olivier Calvez
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | | | - Olivier Guillaume
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | | | | | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
| | - Fabien Aubret
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
- School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Eric J Gangloff
- Station d'Ecologie Théorique et Expérimentale (UAR CNRS 2029), Moulis, France
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, Ohio, USA
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14
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He Y, Zheng W, Guo Y, Yue T, Cui C, Ouzhuluobu, Zhang H, Liu K, Yang Z, Wu T, Qu J, Jin ZB, Yang J, Lu F, Qi X, Su B. Deep phenotyping of 11,880 highlanders reveals novel adaptive traits in native Tibetans. iScience 2023; 26:107677. [PMID: 37680474 PMCID: PMC10481350 DOI: 10.1016/j.isci.2023.107677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/26/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
Tibetans are the ideal population to study genetic adaptation in extreme environments. Here, we performed systematic phenotyping of 11,880 highlanders, covering 133 quantitative traits of 13 organ systems. We provided a comprehensive phenotypic atlas by comparing altitude adaptation and altitude acclimatization. We found the differences between adaptation and acclimatization are quantitative rather than qualitative, with a whole-system "blunted effect" seen in the adapted Tibetans. We characterized twelve different functional changes between adaptation and acclimatization. More importantly, we established a landscape of adaptive phenotypes of indigenous Tibetans, including 45 newly identified Tibetan adaptation-nominated traits, involving specific changes of Tibetans in internal organ state, metabolism, eye morphology, and skin pigmentation. In addition, we observed a sex-biased pattern between altitude acclimatization and adaptation. The generated atlas of phenotypic landscape provides new insights into understanding of human adaptation to high-altitude environments, and it serves as a valuable blueprint for future medical and physiological studies.
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Affiliation(s)
- Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ouzhuluobu
- Tibetan Fukang Hospital, Lhasa 850000, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Academy of Medicine Science, Zhengzhou University, Zhengzhou 450052, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Jia Qu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Zi-Bing Jin
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing 100730, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Fan Lu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Tibetan Fukang Hospital, Lhasa 850000, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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15
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Jiang Y, Ping J, Lu H, Zhang H, Liu M, Li Y, Zhou G. Associations between high-altitude adaptation and risk of cardiovascular diseases: a bidirectional Mendelian randomization study. Mol Genet Genomics 2023; 298:1007-1021. [PMID: 37233799 DOI: 10.1007/s00438-023-02035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
High-altitude adaptation (HAA) was reported to be significantly associated with reduced risks for multiple cardiovascular diseases (CVDs). However, the causality and direction of the associations are largely uncharacterized. We aimed to examine the potential causal relationships between HAA and six types of CVD, including coronary artery disease (CAD), cerebral aneurysm, ischemic stroke, peripheral artery disease, arrhythmia and atrial fibrillation. We obtained the summary data from largest available genome-wide association study of HAA and six types of CVD. Two-sample bidirectional Mendelian randomization (MR) analyses were performed to infer the causality between them. In the sensitivity analyses, MR-Egger regression analyses and MR-Pleiotropy RESidual Sum and Outlier (MR-PRESSO) global analyses were used to assess the pleiotropic effects; Cochran's Q tests were used to test the heterogeneity by inverse variance-weighted (IVW) and MR-Egger methods; and the leave-one-out analyses were used to examine whether some single nucleotide polymorphisms (SNPs) could influence the results independently. The MR main analyses showed that the genetically instrumented HAA was significantly causally associated with the reduced risks of CAD (odds ratio [OR] = 0.029; 95% confidence interval [CI] = 0.004-0.234; P = 8.64 × 10-4). In contrast, there was no statistically significant relationship between CVDs and HAA. Our findings provide evidence for the causal effects of HAA on the reduced risks of CAD. However, there is no causality of CVDs on HAA. These findings might be helpful in developing the prevention and intervention strategies for CAD.
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Affiliation(s)
- Yuqing Jiang
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, 211166, People's Republic of China
| | - Jie Ping
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Hao Lu
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Haoxiang Zhang
- The No. 954 Hospital of PLA, Shannan City, 856100, People's Republic of China
| | - Mengyu Liu
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Yuanfeng Li
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Gangqiao Zhou
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, 211166, People's Republic of China.
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
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16
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Hao Y, Song G, Zhang YE, Zhai W, Jia C, Ji Y, Tang S, Lv H, Qu Y, Lei F. Divergent contributions of coding and noncoding sequences to initial high-altitude adaptation in passerine birds endemic to the Qinghai-Tibet Plateau. Mol Ecol 2023; 32:3524-3540. [PMID: 37000417 DOI: 10.1111/mec.16942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023]
Abstract
Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High-altitude adaptations have been extensively explored from the viewpoint of protein-coding genes; however, the contribution of noncoding regions remains relatively neglected. Here, we integrate genomic and transcriptomic data to investigate adaptive evolution in the ancestor of three high-altitude snowfinch species endemic to the Qinghai-Tibet Plateau. Our genome-wide scan for adaptation in the snowfinch ancestor identifies strong adaptation signals in functions of development and metabolism for the coding genes, but in functions of the nervous system development for noncoding regions. This pattern is exclusive to the snowfinch ancestor compared to a control ancestral lineage subject to weak selection. Changes in noncoding regions in the snowfinch ancestor, especially those nearest to coding genes, may be disproportionately associated with the differential expression of genes in the brain tissue compared to other tissues. Extensive gene expression in the brain tissue can be further altered via genetic regulatory networks of transcription factors harbouring potential accelerated regulatory regions (e.g., the development-related transcription factor YEATS4). Altogether, our study provides new evidence concerning how coding and noncoding sequences work through decoupled pathways in initial adaptation to the selective pressure of high-altitude environments. The analysis highlights the idea that noncoding sequences may be promising elements in facilitating the rapid evolution and adaptation to high altitudes.
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Affiliation(s)
- Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hongrui Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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17
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Patrician A, Willie C, Hoiland RL, Gasho C, Subedi P, Anholm JD, Tymko MM, Ainslie PN. Manipulation of iron status on cerebral blood flow at high altitude in lowlanders and adapted highlanders. J Cereb Blood Flow Metab 2023; 43:1166-1179. [PMID: 36883428 PMCID: PMC10291452 DOI: 10.1177/0271678x231152734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/27/2023] [Accepted: 12/05/2022] [Indexed: 03/09/2023]
Abstract
Cerebral blood flow (CBF) increases during hypoxia to counteract the reduction in arterial oxygen content. The onset of tissue hypoxemia coincides with the stabilization of hypoxia-inducible factor (HIF) and transcription of downstream HIF-mediated processes. It has yet to be determined, whether HIF down- or upregulation can modulate hypoxic vasodilation of the cerebral vasculature. Therefore, we examined whether: 1) CBF would increase with iron depletion (via chelation) and decrease with repletion (via iron infusion) at high-altitude, and 2) explore whether genotypic advantages of highlanders extend to HIF-mediated regulation of CBF. In a double-blinded and block-randomized design, CBF was assessed in 82 healthy participants (38 lowlanders, 20 Sherpas and 24 Andeans), before and after the infusion of either: iron(III)-hydroxide sucrose, desferrioxamine or saline. Across both lowlanders and highlanders, baseline iron levels contributed to the variability in cerebral hypoxic reactivity at high altitude (R2 = 0.174, P < 0.001). At 5,050 m, CBF in lowlanders and Sherpa were unaltered by desferrioxamine or iron. At 4,300 m, iron infusion led to 4 ± 10% reduction in CBF (main effect of time p = 0.043) in lowlanders and Andeans. Iron status may provide a novel, albeit subtle, influence on CBF that is potentially dependent on the severity and length-of-stay at high altitude.
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Affiliation(s)
- Alexander Patrician
- Centre for Heart, Lung, & Vascular Health, School of Health and Exercise Sciences, University of British Columbia – Okanagan, Kelowna, BC, Canada
| | - Christopher Willie
- Centre for Heart, Lung, & Vascular Health, School of Health and Exercise Sciences, University of British Columbia – Okanagan, Kelowna, BC, Canada
| | - Ryan L Hoiland
- Centre for Heart, Lung, & Vascular Health, School of Health and Exercise Sciences, University of British Columbia – Okanagan, Kelowna, BC, Canada
- Department of Anesthesiology, Pharmacology and Therapeutics, Faculty of Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC, Canada
- Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Gasho
- Pulmonary/Critical Care Section, VA Loma Linda Healthcare System and Department of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Prajan Subedi
- Pulmonary/Critical Care Section, VA Loma Linda Healthcare System and Department of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - James D Anholm
- Pulmonary/Critical Care Section, VA Loma Linda Healthcare System and Department of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Michael M Tymko
- Centre for Heart, Lung, & Vascular Health, School of Health and Exercise Sciences, University of British Columbia – Okanagan, Kelowna, BC, Canada
| | - Philip N Ainslie
- Centre for Heart, Lung, & Vascular Health, School of Health and Exercise Sciences, University of British Columbia – Okanagan, Kelowna, BC, Canada
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18
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Zheng W, He Y, Guo Y, Yue T, Zhang H, Li J, Zhou B, Zeng X, Li L, Wang B, Cao J, Chen L, Li C, Li H, Cui C, Bai C, Qi X, Su B. Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans. Genome Biol 2023; 24:73. [PMID: 37055782 PMCID: PMC10099689 DOI: 10.1186/s13059-023-02912-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes. RESULTS Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects. CONCLUSIONS Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.
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Affiliation(s)
- Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jun Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Liya Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Jingxin Cao
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Li Chen
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Chunxia Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Hongyan Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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19
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Macotela L, Naya DE, González-Morales JC, Anaya M, Fajardo V, Manjarrez J. Altitudinal variation in organ mass from three mountain systems: The case of mesquite lizard Sceloporus grammicus. Comp Biochem Physiol A Mol Integr Physiol 2023; 281:111426. [PMID: 37059292 DOI: 10.1016/j.cbpa.2023.111426] [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: 11/14/2022] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023]
Abstract
High altitude environments provide a fertile ground for investigating the benefits of phenotypic adjustments at several levels of biological organization. Low oxygen partial pressure and low environmental temperature are the main limiting factors that promote phenotypic variation in different organs, such as the lung and heart. Although high-altitude environments act like natural laboratories, most morphological studies conducted to date lack replication. Here, we evaluated organ mass variation in nine populations of Sceloporus grammicus, throughout three altitudinal gradients (mountains) from the Trans-Mexican volcanic belt. A total of 84 individuals from three different altitudes at three different mountains were collected. Then, we used generalized linear models to analyze the pattern of variation in internal organs mass as a function of altitude and temperature. We observed a striking pattern of altitudinal variation in the size of cardiorespiratory organs: while heart mass increased with altitude and decreased with temperature, the lung showed a significant statistical interaction between mountain transect and temperature. Overall, our results support the hypothesis that cardiorespiratory organs should be bigger in populations occurring at higher altitudes. Moreover, the study of different mountain systems allowed us to observe some differences in one mountain in relation to the other two.
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Affiliation(s)
- Luis Macotela
- Doctorado en Ciencias Agropecuarias y Recursos Naturales, Universidad Autónoma del Estado de México, Instituto Literario No. 100, Col. Centro, C. P. 5000 Toluca, Estado de Mexico, Mexico; Instituto para la Conservación de la Cordillera Neovolcánica ante el Cambio Climático, A.C. Calle Lago de Atitlán No. 502, C. P. 50100 Toluca, Estado de México, Mexico
| | - Daniel E Naya
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Juan C González-Morales
- Centro Universitario Amecameca, Universidad Autónoma del Estado de México, Instituto Literario 100, Col. Centro, CP 50000 Toluca, Estado de México, Mexico
| | - Mariluz Anaya
- Instituto para la Conservación de la Cordillera Neovolcánica ante el Cambio Climático, A.C. Calle Lago de Atitlán No. 502, C. P. 50100 Toluca, Estado de México, Mexico; Maestría en Ciencias Biológicas, Facultad de Ciencias, Universidad Autónoma del Estado de Mexico, Mexico
| | - Víctor Fajardo
- Instituto para la Conservación de la Cordillera Neovolcánica ante el Cambio Climático, A.C. Calle Lago de Atitlán No. 502, C. P. 50100 Toluca, Estado de México, Mexico
| | - Javier Manjarrez
- Facultad de Ciencias, Universidad Autónoma del Estado de México, Campus El Cerrillo, Carretera Toluca - Ixtlahuaca Km 15.5, Piedras Blancas, 50200 Toluca de Lerdo, Mexico.
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20
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Kanu FA, Jefferds MED, Williams AM, Addo OY, Suchdev PS, Sharma AJ. Association between hemoglobin and elevation among school-aged children: a verification of proposed adjustments. Am J Clin Nutr 2023:S0002-9165(23)46843-8. [PMID: 37059418 DOI: 10.1016/j.ajcnut.2023.04.014] [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: 02/07/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Anemia is defined by a hemoglobin (Hb) concentration lower than normal based on cutoffs specific to age, sex, and pregnancy status. Hemoglobin increases with elevation as an adaptive response to lower blood oxygen saturation, thus, adjusting Hb concentration for elevation is necessary before applying cutoffs. OBJECTIVE Recent evidence among preschool-aged children (PSC) and non-pregnant reproductive-aged women (WRA) suggests that current World Health Organization (WHO) recommended Hb adjustments for elevation need updating. To confirm these findings, we examined the cross-sectional association between Hb and elevation among non-pregnant school-age children (SAC). METHODS Using data from 9 population-based surveys, we examined 26,518 SAC 5-14 years (54.5% female) with data on Hb and elevation (-6 to 3,834 meters, m). We used generalized linear models to assess the association between Hb and elevation under varying conditions, including controlling for inflammation-corrected iron and vitamin A deficiency. Hemoglobin adjustments for each 500 m increase in elevation were estimated for SAC and compared to existing adjustments and those estimated for PSC and WRA. We evaluated the impact of adjustments on anemia prevalence. RESULTS Hemoglobin concentration (g/L) was positively associated with elevation (m). The SAC elevation adjustments were consistent with those reported among PSC and WRA and suggest current recommendations may under-adjust Hb for those residing at lower elevations (<3000 m) and over-adjust Hb for those residing at higher elevations (>3000 m). Among the surveys included, proposed elevation adjustments increased anemia prevalence among SAC by 0 (Ghana, United Kingdom) to 15 (Malawi) percentage points relative to current elevation adjustments. CONCLUSION Results confirm that current recommended Hb adjustments for elevation may need updating, and anemia prevalence in SAC may be higher than currently estimated. Findings will inform the WHO reexamination of global guidelines on the use of Hb adjustments for anemia assessment and may result in improved identification and treatment of anemia.
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Affiliation(s)
- Florence A Kanu
- Nutrition Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA; The U.S. Public Health Service Commissioned Corps, Atlanta, Georgia
| | | | - Anne M Williams
- Nutrition Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA; McKing, Atlanta, GA
| | - O Yaw Addo
- Nutrition Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA
| | - Parminder S Suchdev
- Nutrition Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA; Department of Pediatrics, Emory University, Atlanta, GA
| | - Andrea J Sharma
- Nutrition Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA; The U.S. Public Health Service Commissioned Corps, Atlanta, Georgia
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21
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Zuo XN, Dong W. Uncoiling the scroll of high-altitude population imaging: Native brains in Tibet. Neuroscience 2023; 520:132-133. [PMID: 37024068 DOI: 10.1016/j.neuroscience.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Affiliation(s)
- Xi-Nian Zuo
- Key Laboratory of Brain and Education, School of Education Sciences, Nanning Normal University, Nanning, Guangxi 530001, China; Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, and Faculty of Psychology, Beijing Normal University, Beijing 100875, China
| | - Weihua Dong
- Research Centre of Geospatial Cognition and Visual Analytics, State Key Laboratory of Remote Sensing Science, and Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
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22
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Zhang H, Zhang X, Liu Z, Mei Y, Liu Y, Wei X, Xiao C, Gao Y, Ma Z. Time-course effects and mechanisms of hypobaric hypoxia on nervous system in mice. Neurosci Lett 2023; 801:137163. [PMID: 36868397 DOI: 10.1016/j.neulet.2023.137163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023]
Abstract
OBJECTIVE The aim of this study was to investigate the effect of time course on neurological impairment after acute hypobaric hypoxia exposure in mice and clarify the mechanism of acclimatization, so as to provide a suitable mice model and identify potential target against hypobaric hypoxia for further drug research. METHOD Male C57BL/6J mice were exposed to hypobaric hypoxia at a simulated altitude of 7000 m for 1, 3, and 7 days (1HH, 3HH and 7HH respectively). The behavior of the mice was evaluated by novel object recognition (NOR) and morris water maze test (MWM), then, the pathological changes of mice brain tissues were observed by H&E and Nissl staining. In addition, RNA sequencing (RNA-Seq) was performed to characterize the transcriptome signatures, and enzyme-linked immunosorbent assay (ELISA), Real-time polymerase chain reaction (RT-PCR), and western blot (WB) were used to verify the mechanisms of neurological impairment induced by hypobaric hypoxia. RESULT The hypobaric hypoxia condition resulted in impaired learning and memory, decreased new object cognitive index, and increased escape latency to the hidden platform in mice, with significant changes seen in the 1HH and 3HH groups. Bioinformatic analysis of RNA-seq results of hippocampal tissue showed that 739 differentially expressed genes (DEGs) appeared in the 1HH group, 452 in the 3HH group, and 183 in the 7HH group compared to the control group. There were 60 key genes overlapping in three groups which represented persistent changes and closely related biological functions and regulatory mechanisms in hypobaric hypoxia-induced brain injuries. DEGs enrichment analysis showed that hypobaric hypoxia-induced brain injuries were associated with oxidative stress, inflammatory responses, and synaptic plasticity. ELISA and WB results confirmed that these responses occurred in all hypobaric hypoxic groups while attenuated in the 7HH group. VEGF-A-Notch signaling pathway was enriched by DEGs in hypobaric hypoxia groups and was validated by RT-PCR and WB. CONCLUSION The nervous system of mice exposed to hypobaric hypoxia exhibited stress followed by gradual habituation and thus acclimatization over time, which was reflected in the biological mechanism involving inflammation, oxidative stress, and synaptic plasticity, and accompanied by activation of the VEGF-A-Notch pathway.
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Affiliation(s)
- Huiting Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Xianxie Zhang
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Zuoxu Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Yu Mei
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Yufu Liu
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Xue Wei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Chengrong Xiao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Yue Gao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China.
| | - Zengchun Ma
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, PR China.
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23
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Samaja M, Ottolenghi S. The Oxygen Cascade from Atmosphere to Mitochondria as a Tool to Understand the (Mal)adaptation to Hypoxia. Int J Mol Sci 2023; 24:ijms24043670. [PMID: 36835089 PMCID: PMC9960749 DOI: 10.3390/ijms24043670] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Hypoxia is a life-threatening challenge for about 1% of the world population, as well as a contributor to high morbidity and mortality scores in patients affected by various cardiopulmonary, hematological, and circulatory diseases. However, the adaptation to hypoxia represents a failure for a relevant portion of the cases as the pathways of potential adaptation often conflict with well-being and generate diseases that in certain areas of the world still afflict up to one-third of the populations living at altitude. To help understand the mechanisms of adaptation and maladaptation, this review examines the various steps of the oxygen cascade from the atmosphere to the mitochondria distinguishing the patterns related to physiological (i.e., due to altitude) and pathological (i.e., due to a pre-existing disease) hypoxia. The aim is to assess the ability of humans to adapt to hypoxia in a multidisciplinary approach that correlates the function of genes, molecules, and cells with the physiologic and pathological outcomes. We conclude that, in most cases, it is not hypoxia by itself that generates diseases, but rather the attempts to adapt to the hypoxia condition. This underlies the paradigm shift that when adaptation to hypoxia becomes excessive, it translates into maladaptation.
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Affiliation(s)
- Michele Samaja
- MAGI GROUP, San Felice del Benaco, 25010 Brescia, Italy
- Correspondence:
| | - Sara Ottolenghi
- School of Medicine and Surgery, University of Milano Bicocca, 20126 Milan, Italy
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Mata-Greenwood E, Westenburg HCA, Zamudio S, Illsley NP, Zhang L. Decreased Vitamin D Levels and Altered Placental Vitamin D Gene Expression at High Altitude: Role of Genetic Ancestry. Int J Mol Sci 2023; 24:3389. [PMID: 36834800 PMCID: PMC9967090 DOI: 10.3390/ijms24043389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/14/2023] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
High-altitude hypoxia challenges reproduction; particularly in non-native populations. Although high-altitude residence is associated with vitamin D deficiency, the homeostasis and metabolism of vitamin D in natives and migrants remain unknown. We report that high altitude (3600 m residence) negatively impacted vitamin D levels, with the high-altitude Andeans having the lowest 25-OH-D levels and the high-altitude Europeans having the lowest 1α,25-(OH)2-D levels. There was a significant interaction of genetic ancestry with altitude in the ratio of 1α,25-(OH)2-D to 25-OH-D; with the ratio being significantly lower in Europeans compared to Andeans living at high altitude. Placental gene expression accounted for as much as 50% of circulating vitamin D levels, with CYP2R1 (25-hydroxylase), CYP27B1 (1α-hydroxylase), CYP24A1 (24-hydroxylase), and LRP2 (megalin) as the major determinants of vitamin D levels. High-altitude residents had a greater correlation between circulating vitamin D levels and placental gene expression than low-altitude residents. Placental 7-dehydrocholesterol reductase and vitamin D receptor were upregulated at high altitude in both genetic-ancestry groups, while megalin and 24-hydroxylase were upregulated only in Europeans. Given that vitamin D deficiency and decreased 1α,25-(OH)2-D to 25-OH-D ratios are associated with pregnancy complications, our data support a role for high-altitude-induced vitamin D dysregulation impacting reproductive outcomes, particularly in migrants.
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Affiliation(s)
- Eugenia Mata-Greenwood
- Lawrence D. Longo Center for Perinatal Biology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Hans C. A. Westenburg
- Lawrence D. Longo Center for Perinatal Biology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Stacy Zamudio
- Placental Research Group LLC, Maplewood, NJ 07040, USA
| | | | - Lubo Zhang
- Lawrence D. Longo Center for Perinatal Biology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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Lu CW, Huang ST, Cheng SJ, Lin CT, Hsu YC, Yao CT, Dong F, Hung CM, Kuo HC. Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Mol Ecol 2023; 32:2234-2251. [PMID: 36748940 DOI: 10.1111/mec.16875] [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: 11/04/2022] [Revised: 01/17/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023]
Abstract
Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.
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Affiliation(s)
- Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Ting Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shun-Jen Cheng
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Tau Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Liu S, Zhou C, Meng G, Wan T, Tang M, Yang C, Murphy RW, Fan Z, Liu Y, Zeng T, Zhao Y, Liu S. Evolution and diversification of Mountain voles (Rodentia: Cricetidae). Commun Biol 2022; 5:1417. [PMID: 36572770 PMCID: PMC9792541 DOI: 10.1038/s42003-022-04371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022] Open
Abstract
The systematics of the Cricetid genus Neodon have long been fraught with uncertainty due to sampling issues and a lack of comprehensive datasets. To gain better insights into the phylogeny and evolution of Neodon, we systematically sampled Neodon across the Hengduan and Himalayan Mountains, which cover most of its range in China. Analyses of skulls, teeth, and bacular structures revealed 15 distinct patterns corresponding to 15 species of Neodon. In addition to morphological analyses, we generated a high-quality reference genome for the mountain vole and generated whole-genome sequencing data for 47 samples. Phylogenomic analyses supported the recognition of six new species, revealing a long-term underestimation of Neodon diversity. We further identified positively selected genes potentially related to high-elevation adaptation. Together, our results illuminate how climate change caused the plateau to become the centre of Neodon origin and diversification and how mountain voles have adapted to the hypoxic high-altitude plateau environment.
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Affiliation(s)
- Shaoying Liu
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Chengran Zhou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 China ,grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Guanliang Meng
- grid.452935.c0000 0001 2216 5875Zoological Research Museum Alexander Koenig, D-53113 Bonn, Germany
| | - Tao Wan
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Mingkun Tang
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Chentao Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, 518083 China
| | - Robert W. Murphy
- Reptilia Sanctuary and Education Centre, Concord, ON L4K 2N6 Canada ,grid.421647.20000 0001 2197 9375Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON M5S 2C6 Canada
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Yang Liu
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry, No.18, Xinhui xilu, Chengdu, 610081 China
| | - Tao Zeng
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Yun Zhao
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
| | - Shanlin Liu
- grid.22935.3f0000 0004 0530 8290Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 China
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Townley IK, Babin CH, Murphy TE, Summa CM, Rees BB. Genomic analysis of hypoxia inducible factor alpha in ray-finned fishes reveals missing Ohnologs and evidence of widespread positive selection. Sci Rep 2022; 12:22312. [PMID: 36566251 PMCID: PMC9789988 DOI: 10.1038/s41598-022-26876-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
As aquatic hypoxia worsens on a global scale, fishes will become increasingly challenged by low oxygen, and understanding the molecular basis of their response to hypoxia may help to better define the capacity of fishes to cope with this challenge. The hypoxia inducible factor (HIF) plays a critical role in the molecular response to hypoxia by activating the transcription of genes that serve to improve oxygen delivery to the tissues or enhance the capacity of tissues to function at low oxygen. The current study examines the molecular evolution of genes encoding the oxygen-dependent HIFα subunit (HIFA) in the ray-finned fishes (Actinopterygii). Genomic analyses demonstrate that several lineages retain four paralogs of HIFA predicted from two rounds of genome duplication at the base of vertebrate evolution, broaden the known distribution of teleost-specific HIFA paralogs, and provide evidence for salmonid-specific HIFA duplicates. Evolution of the HIFA gene family is characterized by widespread episodic positive selection at amino acid sites that potentially mediate protein stability, protein-protein interactions, and transcriptional regulation. HIFA transcript abundance depends upon paralog, tissue, and fish lineage. A phylogenetically-informed gene nomenclature is proposed along with avenues for future research on this critical family of transcription factors.
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Affiliation(s)
- Ian K. Townley
- Science Department, Saint George’s School, Spokane, WA 99208 USA
| | - Courtney H. Babin
- grid.266835.c0000 0001 2179 5031Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148 USA
| | - Taylor E. Murphy
- grid.266835.c0000 0001 2179 5031Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148 USA
| | - Christopher M. Summa
- grid.266835.c0000 0001 2179 5031Department of Computer Sciences, University of New Orleans, New Orleans, LA 70148 USA
| | - Bernard B. Rees
- grid.266835.c0000 0001 2179 5031Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148 USA
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Terefe E, Belay G, Han J, Hanotte O, Tijjani A. Genomic adaptation of Ethiopian indigenous cattle to high altitude. Front Genet 2022; 13:960234. [PMID: 36568400 PMCID: PMC9780680 DOI: 10.3389/fgene.2022.960234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.
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Affiliation(s)
- Endashaw Terefe
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia,International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella, Ethiopia,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology (MCMB), College of Natural and Computational Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia,Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom,*Correspondence: Endashaw Terefe, Abdulfatai Tijjani,
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29
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The effects of normobaric and hypobaric hypoxia on cognitive performance and physiological responses: A crossover study. PLoS One 2022; 17:e0277364. [DOI: 10.1371/journal.pone.0277364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
This partially randomised controlled, crossover study sought to investigate the effects of normobaric hypoxia (NH) and hypobaric hypoxia (HH) on cognitive performance, the physiological response at rest and after a 3-min step-test. Twenty healthy participants (10 females and 10 males, 27.6±6.2yrs, 73.6±13.7kg, 175.3±8.9cm) completed a cognitive performance test, followed by the modified Harvard-step protocol, in four environments: normobaric normoxia (NN; PiO2: 146.0±1.5mmHg), NH (PiO2: 100.9±1.3mmHg), HH at the first day of ascent (HH1: PiO2 = 105.6±0.4mmHg) and HH after an overnight stay (HH2: PiO2 = 106.0±0.5mmHg). At rest and/or exercise, SpO2, NIRS, and cardiovascular and perceptual data were collected. The cerebral tissue oxygenation index and the cognitive performance (throughput, accuracy, and reaction time) were not different between the hypoxic conditions (all p>0.05). In NH, SpO2 was higher compared to HH1 (ΔSpO2 NH vs HH1: 1.7±0.5%, p = 0.003) whilst heart rate (ΔHR NH vs HH2: 5.8±2.6 bpm, p = 0.03) and sympathetic activation (ΔSNSi NH vs HH2: 0.8±0.4, p = 0.03) were lower in NH compared to HH2. Heart rate (ΔHR HH1 vs HH2: 6.9±2.6 bpm, p = 0.01) and sympathetic action (ΔSNSi HH1 vs HH2: 0.9±0.4, p = 0.02) were both lower in HH1 compared to HH2. In conclusion, cognitive performance and cerebral oxygenation didn’t differ between the hypoxic conditions. SpO2 was only higher in NH compared to HH1. In HH2, heart rate and sympathetic activation were higher compared to both NH and HH1. These conclusions account for a PiO2 between 100–106 mmHg.
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Zhong H, Kong X, Zhang Y, Su Y, Zhang B, Zhu L, Chen H, Gou X, Zhang H. Microevolutionary mechanism of high-altitude adaptation in Tibetan chicken populations from an elevation gradient. Evol Appl 2022; 15:2100-2112. [PMID: 36540645 PMCID: PMC9753841 DOI: 10.1111/eva.13503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 12/23/2022] Open
Abstract
As an indigenous breed, the Tibetan chicken is found in highland regions and shows physiological adaptations to high altitude; however, the genetic changes that determine these adaptations remain elusive. We assumed that the microevolution of the Tibetan chicken occurred from lowland to highland regions with a continuous elevation range. In this study, we analyzed the genome of 188 chickens from lowland areas to the high-altitude regions of the Tibetan plateau with four altitudinal levels. Phylogenetic analysis revealed that Tibetan chickens are significantly different from other altitude chicken populations. Reconstruction of the demographic history showed that the migration and admixture events of the Tibetan chicken occurred at different times. The genome of the Tibetan chicken was also used to analyze positive selection pressure that is associated with high-altitude adaptation, revealing the well-known candidate gene that participates in oxygen binding (HBAD), as well as other novel potential genes (e.g., HRG and ANK2) that are related to blood coagulation and cardiovascular efficiency. Our study provides novel insights regarding the evolutionary history and microevolution mechanisms of the high-altitude adaptation in the Tibetan chicken.
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Affiliation(s)
- Hai‐An Zhong
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Xiao‐Yan Kong
- School of Life Science and EngineeringFoshan UniversityGuangdongChina,College of Animal Science and TechnologyYunnan Agricultural UniversityKunmingChina
| | - Ya‐Wen Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Yan‐Kai Su
- Center for Computational GenomicsBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Li Zhu
- College of Animal Science and TechnologyYunnan Agricultural UniversityKunmingChina
| | - Hua Chen
- Center for Computational GenomicsBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
| | - Xiao Gou
- School of Life Science and EngineeringFoshan UniversityGuangdongChina
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
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Li B, Jia G, Wen D, Zhao X, Zhang J, Xu Q, Zhao X, Jiang N, Liu Z, Wang Y. Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai–Tibetan plateau. Front Microbiol 2022; 13:1027138. [PMID: 36299720 PMCID: PMC9589358 DOI: 10.3389/fmicb.2022.1027138] [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: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
The grassland in the Qinghai–Tibetan plateau provide habitat for many indigenous and introduced ruminants which perform important ecological functions that impact the whole Qinghai–Tibetan plateau ecosystem. These indigenous Tibetan ruminants have evolved several adaptive traits to withstand the severe environmental conditions, especially cold, low oxygen partial pressure, high altitude, strong UV radiation, and poor forage availability on the alpine rangelands. Despite the challenges to husbandry associated with the need for enhanced adaptation, several domesticated ruminants have also been successfully introduced to the alpine pasture regions to survive in the harsh environment. For ruminants, these challenging conditions affect not only the host, but also their commensal microbiota, especially the diversity and composition of the rumen microbiota; multiple studies have described tripartite interactions among host-environment-rumen microbiota. Thus, there are significant benefits to understanding the role of rumen microbiota in the indigenous and introduced ruminants of the Qinghai–Tibetan plateau, which has co-evolved with the host to ensure the availability of specific metabolic functions required for host survival, health, growth, and development. In this report, we systemically reviewed the dynamics of rumen microbiota in both indigenous and introduced ruminants (including gut microbiota of wild ruminants) as well as their structure, functions, and interactions with changing environmental conditions, especially low food availability, that enable survival at high altitudes. We summarized that three predominant driving factors including increased VFA production, enhanced fiber degradation, and lower methane production as indicators of higher efficiency energy harvest and nutrient utilization by microbiota that can sustain the host during nutrient deficit. These cumulative studies suggested alteration of rumen microbiota structure and functional taxa with genes that encode cellulolytic enzymes to potentially enhance nutrient and energy harvesting in response to low quality and quantity forage and cold environment. Future progress toward understanding ruminant adaptation to high altitudes will require the integration of phenotypic data with multi-omics analyses to identify host-microbiota co-evolutionary adaptations enabling survival on the Qinghai–Tibetan plateau.
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Affiliation(s)
- Bin Li
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Agricultural College, Ningxia University, Yinchuan, China
| | - Gaobin Jia
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- Colleges of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Dalian, China
| | - Dongxu Wen
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Xiuxin Zhao
- Agricultural College, Ningxia University, Yinchuan, China
| | - Junxing Zhang
- Agricultural College, Ningxia University, Yinchuan, China
| | - Qing Xu
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Xialing Zhao
- Institute of Animal Husbandry and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Nan Jiang
- Colleges of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Dalian, China
| | - Zhenjiang Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Yachun Wang
- Agricultural College, Ningxia University, Yinchuan, China
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Yin X, Zhang F, Sun P, Liu Y, Guo Y. The Multistage 20-Meter Shuttle Run Test Reference Values for Tibetan Children and Adolescents in Tibet, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12703. [PMID: 36232003 PMCID: PMC9565077 DOI: 10.3390/ijerph191912703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE Cardiorespiratory fitness (CRF) reference data for Tibetan (Zang ethnicity) children and adolescents at high altitudes in Tibet of China are lacking. The present study aimed to develop sex- and age-specific 20mSRT norms for Chinese Tibetan children and adolescents at high altitudes. METHOD A total of 4667 participants from Lhasa (3650 m), Nagqu (4500 m), and Amdo (4700 m) were selected by a stratified random cluster sampling method in two stages. The 20 m SRT test was used to estimate cardiorespiratory fitness. The 20 m SRT norms were developed by the lambda, mu, and sigma method (LMS). RESULTS The 20 m SRT laps, completed stages/minutes, and the speed at the last complete stage of Chinese Tibetan children and adolescents aged 7-18 years increased with age. CONCLUSION Given the importance of CRF for children and adolescents' health, the government should strengthen the monitoring of the CRF of Tibetan children and adolescents in high-altitude areas, strengthen physical education curriculum reform, and increase the level of physical activity in order to improve the level of CRF in children and adolescents.
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Affiliation(s)
- Xiaojian Yin
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Feng Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Pengwei Sun
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Yuan Liu
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Yaru Guo
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
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Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota. Appl Microbiol Biotechnol 2022; 106:6701-6711. [PMID: 36097173 DOI: 10.1007/s00253-022-12171-y] [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: 06/29/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/02/2022]
Abstract
Highland birds evolve multiple adaptive abilities to cope with the harsh environments; however, how they adapt to the high-altitude habitats via the gut microbiota remains understudied. Here we integrated evidences from comparative analysis of gut microbiota to explore the adaptive mechanism of black-necked crane, a typical highland bird in the Qinghai-Tibet Plateau. Firstly, the gut microbiota diversity and function was compared among seven crane species (one high-altitude species and six low-altitude species), and then among three populations of contrasting altitudes for the black-necked crane. Microbiota community diversity in black-necked crane was significantly lower than its low-altitude relatives, but higher microbiota functional diversity was observed in black-necked crane, suggesting that unique bacteria are developed and acquired due to the selection pressure of high-altitude environments. The functional microbial genes differed significantly between the low- and high-altitude black-necked cranes, indicating that altitude significantly impacted microbial communities' composition and structure. Adaptive changes in microbiota diversity and function are observed in response to high-altitude environments. These findings provide us a new insight into the adaptation mechanism to the high-altitude environment for birds via the gut microbiota. KEY POINTS: • The diversity and function of gut microbiota differed significantly between the low- and high-altitude crane species. • Black-necked crane adapts to the high-altitude environment via specific gut microbiota. • Altitude significantly impacted microbial communities' composition and structure.
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Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS. Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol 2022; 13:885295. [PMID: 36035495 PMCID: PMC9400701 DOI: 10.3389/fphys.2022.885295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.
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Affiliation(s)
- James J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Amy L. Non
- Department of Anthropology, Division of Social Sciences, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
| | - Erica C. Heinrich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, United States
| | - Wanjun Gu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, MX, United States
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Elijah S. Lawrence
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Michael S. Tift
- Department of Biology and Marine Biology, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Katie A. O'Brien
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Department of Physiology, Development and Neuroscience, Faculty of Biology, School of Biological Sciences, University of Cambridge, Cambridge, ENG, United Kingdom
| | - Jay F. Storz
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Anthony V. Signore
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | | | - Sean M. Wilson
- Lawrence D. Longo, MD Center for Perinatal Biology, Loma Linda, CA, United States
| | | | | | | | - Colleen G. Julian
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lorna G. Moore
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Aurora, CO, United States
| | - Mark M. Fuster
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jennifer A. Stokes
- Department of Kinesiology, Southwestern University, Georgetown, TX, United States
| | - Richard Milner
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - John B. West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jiao Zhang
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - John Y. Shyy
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José Pablo Vázquez-Medina
- Department of Integrative Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States
| | - Luu V. Pham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Omar A. Mesarwi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - James E. Hall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT, United States
| | - Jeremy Sieker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Arlin B. Blood
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Jason X. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Graham R. Scott
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Brinda K. Rana
- Moores Cancer Center, UC San Diego, La Jolla, CA, United States,Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - Paul J. Ponganis
- Center for Marine Biotechnology and Biomedicine, La Jolla, CA, United States
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Frank L. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, 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, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
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Yan Y, Zhang X, An X, Fan W, Liang J, Luo B, Ren H, Huang Y. The application and perspective of hyperbaric oxygen therapy in acute ischemic stroke: From the bench to a starter? Front Neurol 2022; 13:928802. [PMID: 35989933 PMCID: PMC9389005 DOI: 10.3389/fneur.2022.928802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Stroke has become a significant cause of death and disability globally. Along with the transition of the world's aging population, the incidence of acute ischemic stroke is increasing year by year. Even with effective treatment modalities, patients are not guaranteed to have a good prognosis. The treatment model combining intravenous thrombolysis/endovascular therapy and neuroprotection is gradually being recognized. After the clinical translation of pharmacological neuroprotective agents failed, non-pharmacological physical neuroprotective agents have rekindled hope. We performed a literature review using the National Center for Biotechnology Information (NCBI) PubMed database for studies that focused on the application of hyperbaric oxygen therapy in acute ischemic stroke. In this review, we present the history and mechanisms of hyperbaric oxygen therapy, focusing on the current status, outcomes, current challenges, perspective, safety, and complications of the application of hyperbaric oxygen in animal experiments and human clinical trials. Hyperbaric oxygen therapy, a non-pharmacological treatment, can improve the oxygenation level at the ischemic lesions in increased dissolved oxygen and oxygen diffusion radius to achieve salvage of neurological function, giving a new meaning to acute ischemic stroke.
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Affiliation(s)
- Yujia Yan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, China
| | - Xiqiang Zhang
- Department of Neurosurgery, Third People's Hospital of Xining City, Xining, China
| | - Xingwei An
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- Tianjin Center for Brain Science, Tianjin, China
| | - Wanpeng Fan
- Department of Neurosurgery, Third People's Hospital of Xining City, Xining, China
| | - Jingbo Liang
- Department of Neurosurgery, Third People's Hospital of Xining City, Xining, China
| | - Bin Luo
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, China
| | - Hecheng Ren
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, China
- *Correspondence: Hecheng Ren
| | - Ying Huang
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, China
- Ying Huang
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Kiselev AR, Arablinsky NA, Mironov SA, Umetov MA, Berns SA, Yavelov IS, Drapkina OM. Physiological and pathophysiological aspects of short-term middle-altitude adaptation in humans. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2022-3306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The review presents up-to-date information on the physiological and pathophysiological aspects of short-term middle-altitude adaptation in healthy individuals and patients with various chronic diseases. Unlike acute mountain sickness, which develops going to ≥3000, the physiological aspects of human adaptation to 2000-2500 m remain insufficiently studied. However, these altitudes are the most visited among tourist groups and individually.
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Affiliation(s)
- A. R. Kiselev
- National Medical Research Center for Therapy and Preventive Medicine
| | - N. A. Arablinsky
- National Medical Research Center for Therapy and Preventive Medicine
| | - S. A. Mironov
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. A. Umetov
- Kh. M. BerbekovKabardino-Balkarian State University
| | - S. A. Berns
- National Medical Research Center for Therapy and Preventive Medicine
| | - I. S. Yavelov
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Kiselev AR, Arablinsky NA, Mironov SA, Umetov MA, Berns SA, Yavelov IS, Drapkina OM. Physiological and pathophysiological aspects of short-term middle-altitude adaptation in humans. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-20223306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The review presents up-to-date information on the physiological and pathophysiological aspects of short-term middle-altitude adaptation in healthy individuals and patients with various chronic diseases. Unlike acute mountain sickness, which develops going to ≥3000, the physiological aspects of human adaptation to 2000-2500 m remain insufficiently studied. However, these altitudes are the most visited among tourist groups and individually.
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Affiliation(s)
- A. R. Kiselev
- National Medical Research Center for Therapy and Preventive Medicine
| | - N. A. Arablinsky
- National Medical Research Center for Therapy and Preventive Medicine
| | - S. A. Mironov
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. A. Umetov
- Kh. M. BerbekovKabardino-Balkarian State University
| | - S. A. Berns
- National Medical Research Center for Therapy and Preventive Medicine
| | - I. S. Yavelov
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Telemeco RS, Gangloff EJ, Cordero GA, Rodgers EM, Aubret F. From performance curves to performance surfaces: Interactive effects of temperature and oxygen availability on aerobic and anaerobic performance in the common wall lizard. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rory S. Telemeco
- Department of Biology California State University Fresno Fresno CA USA
| | - Eric J. Gangloff
- Department of Biological Sciences Ohio Wesleyan University Delaware OH USA
| | - G. Antonio Cordero
- Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology University of Lisbon Lisbon Portugal
| | - Essie M. Rodgers
- School of Biological Sciences, University of Canterbury Christchurch New Zealand
| | - Fabien Aubret
- Station d’Ecologie Théorique et Expérimentale du CNRS – UPR 2001 Moulis France
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Fount, fate, features, and function of renal erythropoietin-producing cells. Pflugers Arch 2022; 474:783-797. [PMID: 35750861 PMCID: PMC9338912 DOI: 10.1007/s00424-022-02714-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 12/19/2022]
Abstract
Renal erythropoietin (Epo)-producing (REP) cells represent a rare and incompletely understood cell type. REP cells are fibroblast-like cells located in close proximity to blood vessels and tubules of the corticomedullary border region. Epo mRNA in REP cells is produced in a pronounced “on–off” mode, showing transient transcriptional bursts upon exposure to hypoxia. In contrast to “ordinary” fibroblasts, REP cells do not proliferate ex vivo, cease to produce Epo, and lose their identity following immortalization and prolonged in vitro culture, consistent with the loss of Epo production following REP cell proliferation during tissue remodelling in chronic kidney disease. Because Epo protein is usually not detectable in kidney tissue, and Epo mRNA is only transiently induced under hypoxic conditions, transgenic mouse models have been developed to permanently label REP cell precursors, active Epo producers, and inactive descendants. Future single-cell analyses of the renal stromal compartment will identify novel characteristic markers of tagged REP cells, which will provide novel insights into the regulation of Epo expression in this unique cell type.
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Shang K, Xia Z, Ye X, Li Z, Gong C. Positive end-expiratory pressure and risk of postoperative pulmonary complications in patients living at high altitudes and undergoing surgery at low altitudes: a single-centre, retrospective observational study in China. BMJ Open 2022; 12:e057698. [PMID: 35701068 PMCID: PMC9198711 DOI: 10.1136/bmjopen-2021-057698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES To examine whether a high positive end-expiratory pressure (PEEP ≥5 cmH2O) has a protective effect on the risk of postoperative pulmonary complications (PPCs) in a cohort of patients living at high altitudes and undergoing general anaesthesia. DESIGN Retrospective, observational study. SETTING A tertiary hospital in China. PARTICIPANTS Adult Tibetan patients living at high altitudes (≥3000 m) and who went to the low-altitude plain to undergo non-cardiothoracic surgery under general anaesthesia, from January 2018 to April 2020. MEASUREMENTS This study included 1905 patients who were divided according to the application of an intraoperative PEEP: low PEEP (<5 cmH2O, including 0 cmH2O) or high PEEP (≥5 cmH2O). The primary outcome was a composite of PPCs within the first 7 postoperative days. The secondary outcomes included reintubation and unplanned intensive care unit (ICU) admission within the first 7 postoperative days and total hospital stays (day). RESULTS The study included 1032 patients in the low PEEP group and 873 in the high PEEP group. There were no differences in the incidence of PPCs between the high and low PEEP groups (relative risk (RR) 0.913; 95% CI 0.716 to 1.165; p=0.465). After propensity score matching, 643 patients remained in each group, and the incidence of PPCs in the low PEEP group (18.0%) was higher than in the high PEEP group (13.7%; RR 0.720; 95% CI 0.533 to 0.974; p=0.033). There were no differences in the incidence of reintubation, unplanned ICU admission or hospital stays. The risk factors of PPCs derived from multiple regression showed that the application of >5 cmH2O PEEP during intraoperative mechanical ventilation was associated with a significantly lower risk of PPCs in patients from a high altitude (OR=0.725, 95% CI 0.530 to 0.992; p=0.044). CONCLUSIONS The application of PEEP ≥5 cmH2O during intraoperative mechanical ventilation in patients living at high altitudes and undergoing surgery at low altitudes may be associated with a lower risk of PPCs. Prospective longitudinal studies are needed to further investigate perioperative lung protection ventilation strategies for patients from high altitudes. TRIAL REGISTRATION NUMBER Chinese Clinical Trial Registry (ChiCTR2100044260).
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Affiliation(s)
- Kaixi Shang
- Department of Anesthesiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (West China Hospital Sichuan University Tibet Chengdu Branch Hospital), Chengdu, China
| | - Zongjing Xia
- Department of Anesthesiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (West China Hospital Sichuan University Tibet Chengdu Branch Hospital), Chengdu, China
| | - Xiaoli Ye
- Department of Anesthesiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (West China Hospital Sichuan University Tibet Chengdu Branch Hospital), Chengdu, China
| | - Zhuoning Li
- Department of Anesthesiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (West China Hospital Sichuan University Tibet Chengdu Branch Hospital), Chengdu, China
| | - Chongcong Gong
- Department of Anesthesiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (West China Hospital Sichuan University Tibet Chengdu Branch Hospital), Chengdu, China
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王 金, 方 金, 谢 宇, 马 薇, 惠 培, 苏 晓, 郭 斌, 陈 雪, 王 旭, 范 杰, 赵 媛. [Analysis of related factors in secondary erythrocytosis of obstructive sleep apnea hypopnea syndrome in Gansu province]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2022; 36:338-342. [PMID: 35483682 PMCID: PMC10128252 DOI: 10.13201/j.issn.2096-7993.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Objective:To analyze the related factors of secondary erythrocytosis of obstructive sleep apnea(OSA) in Gansu province. Methods:Polysomnography recording and analysis from January 2013 to January 2021, A total of 448 OSA patients of long-resident Han nationality in Gansu province. Hemoglobin(Hb) values were divided into group A(Hb 120-160 g/L) 41 cases, B(Hb 161-179 g/L) 142 cases, C(Hb 180-199 g/L) 152 cases, D(Hb 200-219 g/L) 79 cases, and E(Hb ≥220 g/L) 30 cases. General clinical data, altitude of residence, disease course, apnea hypopnea index (AHI), and Lowest oxyhemoglobin(LSpO₂) were compared among these groups. Multivariate regression and ROC curves were used to analyze the influencing factors of OSA secondary erythrocytosis. Results:There were no significant differences in age, sex, and course of disease among groups A, B, C, D, and E (P>0.05).The altitude of group E was higher than that of groups A, B, C, and D (P<0.05), but there was no significant difference between groups A, B, C and D (P>0.05).AHI was significantly different among groups A, B, C, D, and E (P<0.05), groups C, D, and E were significantly higher than A; group D was significantly higher than B, C.LSpO₂ was significantly different among groups A, B, C, D, and E (P <0.05), groups B, C, D, and E was significantly lower than A; group D, E was significantly lower than B, C.MSpO₂ was significantly different among groups A, B, C, D, and E (P<0.05), groups B, C, D, and E was significantly lower A; groups D, E was significantly lower than B , C.Multivariate regression showed that the higher the altitude, the lower the MSpO₂, the more serious the secondary hyperhemoglobinemia.Age, course of the disease, AHI, and LSpO₂ were not the influencing factors of OSA secondary hemoglobin increase.The areas under the ROC curve for MSpO₂ and altitude to predict Hb≥180 g/L were 0.694(P<0.001) and 0.570(P=0.009), with statistically significant differences(Z=3.205, P=0.001). Conclusion:Altitude and MSpO₂ were independent risk factors for OSA secondary erythrocytosis; MSpO₂ predicted that Hb≥180 g/L in OSA patients was better than altitude.
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Affiliation(s)
- 金凤 王
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 金瑞 方
- 甘肃省人民医院日间诊疗中心Department of Day Care Center, Gansu Provincial Hospital
| | - 宇平 谢
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 薇 马
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 培林 惠
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 晓燕 苏
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 斌 郭
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 雪萍 陈
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 旭斌 王
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 杰 范
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - 媛 赵
- 甘肃省人民医院睡眠医学中心(兰州,730000)Department of Sleep Medicine Center, Gansu Provincial Hospital, Lanzhou, 730000, China
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Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol 2022; 6:630-643. [PMID: 35332281 PMCID: PMC9090980 DOI: 10.1038/s41559-022-01703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 01/31/2023]
Abstract
Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.
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Yan Y, Zhang X, Ren H, An X, Fan W, Liang J, Huang Y. Anterior Circulation Acute Ischemic Stroke in the Plateau of China: Risk Factors and Clinical Characteristics. Front Neurol 2022; 13:859616. [PMID: 35493834 PMCID: PMC9043326 DOI: 10.3389/fneur.2022.859616] [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: 01/21/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Purpose Acute ischemic stroke has a high incidence in the plateau of China. It has unique characteristics compared to the plains, and the specific relationship with altitude has not yet been appreciated. This study aimed to investigate the specificity of the plateau's anterior circulation acute ischemic stroke in China. Methods To retrospectively collect clinical data of patients with first-episode acute ischemic stroke in the anterior circulation in Tianjin and Xining city. The differences in clinical presentation, laboratory, and imaging examinations were compared. Results Patients at high altitudes showed a significant trend toward lower age (61.0 ± 10.2 vs. 64.8 ± 8.1, P = 0.010) and had a history of dyslipidemia, higher levels of inflammatory markers, erythrocytosis, and alcohol abuse. The main manifestations were higher diastolic blood pressure (85.5 ± 14.0 mmHg vs. 76.8 ± 11.6 mmHg, P < 0.001), triglycerides [2.0 (1.8) mmol/L vs. 1.3 (0.9) mmol/L, P < 0.001], CRP [4.7 (4.4) mg/L vs. 2.1 (1.9) mg/L, P < 0.001], homocysteine levels [14.5 (11.7) μmol/L vs. 11.2 (5.2) μmol/L, P < 0.001]; larger infarct volume [3.5 (4.8) cm3 vs. 9.0 (6.9) cm3, P < 0.001] and worse prognosis. Patients at high altitudes had higher atherosclerotic indexes in cIMT and plaque than those in plains. Conclusions The natural habituation and genetic adaptation of people to the particular geo-climatic environment of the plateau have resulted in significant differences in disease characteristics. Patients with the anterior circulation acute ischemic stroke in the plateau show more unfavorable clinical manifestations and prognosis. This study provides a preliminary interpretation of the effects of altitude and suggests developing preventive and therapeutic protocol measures that are more appropriate for the plateau of China.
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Affiliation(s)
- Yujia Yan
- Department of Neurosurgery, Tianjin University Huanhu Hospital, Tianjin, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xiqiang Zhang
- Department of Neurosurgery, Third People Hospital of Xining City, Xining, China
| | - Hecheng Ren
- Department of Neurosurgery, Tianjin University Huanhu Hospital, Tianjin, China
| | - Xingwei An
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- Tianjin Center for Brain Science, Tianjin, China
| | - Wanpeng Fan
- Department of Neurosurgery, Third People Hospital of Xining City, Xining, China
| | - Jingbo Liang
- Department of Neurosurgery, Third People Hospital of Xining City, Xining, China
| | - Ying Huang
- Department of Neurosurgery, Tianjin University Huanhu Hospital, Tianjin, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Ying Huang
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44
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Storz JF, Bautista NM. Altitude acclimatization, hemoglobin-oxygen affinity, and circulatory oxygen transport in hypoxia. Mol Aspects Med 2022; 84:101052. [PMID: 34879970 PMCID: PMC8821351 DOI: 10.1016/j.mam.2021.101052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 01/01/2023]
Abstract
In mammals and other air-breathing vertebrates that live at high altitude, adjustments in convective O2 transport via changes in blood hemoglobin (Hb) content and/or Hb-O2 affinity can potentially mitigate the effects of arterial hypoxemia. However, there are conflicting views about the optimal values of such traits in hypoxia, partly due to the intriguing observation that hypoxia-induced acclimatization responses in humans and other predominantly lowland mammals are frequently not aligned in the same direction as evolved phenotypic changes in high-altitude natives. Here we review relevant theoretical and empirical results and we highlight experimental studies of rodents and humans that provide insights into the combination of hematological changes that help attenuate the decline in aerobic performance in hypoxia. For a given severity of hypoxia, experimental results suggest that optimal values for hematological traits are conditional on the states of other interrelated phenotypes that govern different steps in the O2-transport pathway.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Naim M Bautista
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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45
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Barve S, Cadena CD. Variation in insulative feather structure in songbirds replacing each other along a tropical elevation gradient. Ecol Evol 2022; 12:e8698. [PMID: 35342618 PMCID: PMC8928881 DOI: 10.1002/ece3.8698] [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: 09/26/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
High-elevation organisms are expected to evolve physiological adaptations to cope with harsh environmental conditions. Yet, evidence for such adaptive differences, especially compared to closely related lowland taxa occurring along the same elevational gradient, is rare. Revisiting an anecdotal natural history observation by O. Bangs from 1899 and based on new measurements of museum specimens, we confirmed that the high-elevation hermit wood wren (Henicorhina anachoreta) from the Sierra Nevada de Santa Marta, Colombia, has longer, more insulative feathers on the chest and back, than its lower-elevation counterpart the grey-breasted wood wren (H. leucophrys). However, we did not find evidence for the same specializations in subspecies of H. leucophrys that live at high elevations on other elevational gradients in the Colombian Andes, although similar adaptive solutions have arisen in separate mountain systems like the Himalayas. Adaptations in plumage may be associated with the recurrence of elevational species replacements throughout the tropics.
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Affiliation(s)
- Sahas Barve
- Smithsonian National Museum of Natural HistoryWashingtonDistrict of ColumbiaUSA
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46
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Verma RK, Kalyakulina A, Mishra A, Ivanchenko M, Jalan S. Role of mitochondrial genetic interactions in determining adaptation to high altitude human population. Sci Rep 2022; 12:2046. [PMID: 35132109 PMCID: PMC8821606 DOI: 10.1038/s41598-022-05719-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.
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Affiliation(s)
- Rahul K Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Alena Kalyakulina
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ankit Mishra
- Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
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47
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Beckman EJ, Martins F, Suzuki TA, Bi K, Keeble S, Good JM, Chavez AS, Ballinger MA, Agwamba K, Nachman MW. The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics 2022; 220:iyab226. [PMID: 34897431 PMCID: PMC9097263 DOI: 10.1093/genetics/iyab226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.
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Affiliation(s)
- Elizabeth J Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felipe Martins
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Evolution, Ecology, and Organismal Biology and the Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Mallory A Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kennedy Agwamba
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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48
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Cas MD, Morano C, Ottolenghi S, Dicasillati R, Roda G, Samaja M, Paroni R. Inside the Alterations of Circulating Metabolome in Antarctica: The Adaptation to Chronic Hypoxia. Front Physiol 2022; 13:819345. [PMID: 35145434 PMCID: PMC8821919 DOI: 10.3389/fphys.2022.819345] [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: 11/21/2021] [Accepted: 01/04/2022] [Indexed: 11/21/2022] Open
Abstract
Although the human body may dynamically adapt to mild and brief oxygen shortages, there is a growing interest in understanding how the metabolic pathways are modified during sustained exposure to chronic hypoxia. Located at an equivalent altitude of approximately 3,800 m asl, the Concordia Station in Antarctica represents an opportunity to study the course of human adaption to mild hypoxia with reduced impact of potentially disturbing variables else than oxygen deprivation. We recruited seven healthy subjects who spent 10 months in the Concordia Station, and collected plasma samples at sea level before departure, and 90 days, 6 months, and 10 months during hypoxia. Samples were analyzed by untargeted liquid chromatography high resolution mass spectrometry to unravel how the non-polar and polar metabolomes are affected. Statistical analyses were performed by clustering the subjects into four groups according to the duration of hypoxia exposure. The non-polar metabolome revealed a modest decrease in the concentration of all the major lipid classes. By contrast, the polar metabolome showed marked alterations in several metabolic pathways, especially those related to amino acids metabolism, with a particular concern of arginine, glutamine, phenylalanine, tryptophan, and tyrosine. Remarkably, all the changes were evident since the first time point and remained unaffected by hypoxia duration (with the exception of a slight return of the non-polar metabolome after 6 months), highlighting a relative inability of the body to compensate them. Finally, we identified a few metabolic pathways that emerged as the main targets of chronic hypoxia.
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Affiliation(s)
- Michele Dei Cas
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Camillo Morano
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sara Ottolenghi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Department of Medicine and Surgery, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Roberto Dicasillati
- Department of General Surgery, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy
| | - Gabriella Roda
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy
| | - Michele Samaja
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- MAGI Group, Brescia, Italy
- *Correspondence: Michele Samaja,
| | - Rita Paroni
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
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49
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Webb KL, Dominelli PB, Baker SE, Klassen SA, Joyner MJ, Senefeld JW, Wiggins CC. Influence of High Hemoglobin-Oxygen Affinity on Humans During Hypoxia. Front Physiol 2022; 12:763933. [PMID: 35095551 PMCID: PMC8795792 DOI: 10.3389/fphys.2021.763933] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/22/2021] [Indexed: 01/11/2023] Open
Abstract
Humans elicit a robust series of physiological responses to maintain adequate oxygen delivery during hypoxia, including a transient reduction in hemoglobin-oxygen (Hb-O2) affinity. However, high Hb-O2 affinity has been identified as a beneficial adaptation in several species that have been exposed to high altitude for generations. The observed differences in Hb-O2 affinity between humans and species adapted to high altitude pose a central question: is higher or lower Hb-O2 affinity in humans more advantageous when O2 availability is limited? Humans with genetic mutations in hemoglobin structure resulting in high Hb-O2 affinity have shown attenuated cardiorespiratory adjustments during hypoxia both at rest and during exercise, providing unique insight into this central question. Therefore, the purpose of this review is to examine the influence of high Hb-O2 affinity during hypoxia through comparison of cardiovascular and respiratory adjustments elicited by humans with high Hb-O2 affinity compared to those with normal Hb-O2 affinity.
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Affiliation(s)
- Kevin L. Webb
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Sarah E. Baker
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Stephen A. Klassen
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Michael J. Joyner
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Jonathon W. Senefeld
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Chad C. Wiggins
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Chad C. Wiggins,
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50
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Ma J, Zhang T, Wang W, Chen Y, Cai W, Zhu B, Xu L, Gao H, Zhang L, Li J, Gao X. Comparative Transcriptome Analyses of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation. Front Genet 2022; 12:778788. [PMID: 35087567 PMCID: PMC8789257 DOI: 10.3389/fgene.2021.778788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Gayal and yak are well adapted to their local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analyses were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3,020 and 1,995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expressed regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found that UQCRC1 and COX5A are the shared differentially expressed hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differential hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expressed hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expressed hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Junya Li
- *Correspondence: Junya Li, ; Xue Gao,
| | - Xue Gao
- *Correspondence: Junya Li, ; Xue Gao,
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