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Tang N, Zheng YT, Zhao H, Chan WY, Yao YG. Jump further, leap higher, and consolidate stronger: A brief review of the long-term partnership between Kunming Institute of Zoology (KIZ) and the Chinese University of Hong Kong (CUHK) in bioresources and molecular research. Zool Res 2023; 44:556-558. [PMID: 37070588 PMCID: PMC10236301 DOI: 10.24272/j.issn.2095-8137.2023.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Affiliation(s)
- Nelson Tang
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China. E-mail:
| | - Yong-Tang Zheng
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China. E-mail:
| | - Hui Zhao
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China. E-mail:
| | - Wai-Yee Chan
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China. E-mail:
| | - Yong-Gang Yao
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China. E-mail:
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Mallet RT, Burtscher J, Pialoux V, Pasha Q, Ahmad Y, Millet GP, Burtscher M. Molecular Mechanisms of High-Altitude Acclimatization. Int J Mol Sci 2023; 24:ijms24021698. [PMID: 36675214 PMCID: PMC9866500 DOI: 10.3390/ijms24021698] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
High-altitude illnesses (HAIs) result from acute exposure to high altitude/hypoxia. Numerous molecular mechanisms affect appropriate acclimatization to hypobaric and/or normobaric hypoxia and curtail the development of HAIs. The understanding of these mechanisms is essential to optimize hypoxic acclimatization for efficient prophylaxis and treatment of HAIs. This review aims to link outcomes of molecular mechanisms to either adverse effects of acute high-altitude/hypoxia exposure or the developing tolerance with acclimatization. After summarizing systemic physiological responses to acute high-altitude exposure, the associated acclimatization, and the epidemiology and pathophysiology of various HAIs, the article focuses on molecular adjustments and maladjustments during acute exposure and acclimatization to high altitude/hypoxia. Pivotal modifying mechanisms include molecular responses orchestrated by transcription factors, most notably hypoxia inducible factors, and reciprocal effects on mitochondrial functions and REDOX homeostasis. In addition, discussed are genetic factors and the resultant proteomic profiles determining these hypoxia-modifying mechanisms culminating in successful high-altitude acclimatization. Lastly, the article discusses practical considerations related to the molecular aspects of acclimatization and altitude training strategies.
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Affiliation(s)
- Robert T. Mallet
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Johannes Burtscher
- Department of Biomedical Sciences, University of Lausanne, CH-1005 Lausanne, Switzerland
- Institute of Sport Sciences, University of Lausanne, CH-1005 Lausanne, Switzerland
| | - Vincent Pialoux
- Inter-University Laboratory of Human Movement Biology EA7424, University Claude Bernard Lyon 1, University of Lyon, FR-69008 Lyon, France
| | - Qadar Pasha
- Institute of Hypoxia Research, New Delhi 110067, India
| | - Yasmin Ahmad
- Defense Institute of Physiology & Allied Sciences (DIPAS), Defense Research & Development Organization(DRDO), New Delhi 110054, India
| | - Grégoire P. Millet
- Department of Biomedical Sciences, University of Lausanne, CH-1005 Lausanne, Switzerland
- Institute of Sport Sciences, University of Lausanne, CH-1005 Lausanne, Switzerland
| | - Martin Burtscher
- Department of Sport Science, University of Innsbruck, A-6020 Innsbruck, Austria
- Austrian Society for Alpine and High-Altitude Medicine, A-6020 Innsbruck, Austria
- Correspondence:
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Volkova YL, Pickel C, Jucht AE, Wenger RH, Scholz CC. The Asparagine Hydroxylase FIH: A Unique Oxygen Sensor. Antioxid Redox Signal 2022; 37:913-935. [PMID: 35166119 DOI: 10.1089/ars.2022.0003] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Limited oxygen availability (hypoxia) commonly occurs in a range of physiological and pathophysiological conditions, including embryonic development, physical exercise, inflammation, and ischemia. It is thus vital for cells and tissues to monitor their local oxygen availability to be able to adjust in case the oxygen supply is decreased. The cellular oxygen sensor factor inhibiting hypoxia-inducible factor (FIH) is the only known asparagine hydroxylase with hypoxia sensitivity. FIH uniquely combines oxygen and peroxide sensitivity, serving as an oxygen and oxidant sensor. Recent Advances: FIH was first discovered in the hypoxia-inducible factor (HIF) pathway as a modulator of HIF transactivation activity. Several other FIH substrates have now been identified outside the HIF pathway. Moreover, FIH enzymatic activity is highly promiscuous and not limited to asparagine hydroxylation. This includes the FIH-mediated catalysis of an oxygen-dependent stable (likely covalent) bond formation between FIH and selected substrate proteins (called oxomers [oxygen-dependent stable protein oligomers]). Critical Issues: The (patho-)physiological function of FIH is only beginning to be understood and appears to be complex. Selective pharmacologic inhibition of FIH over other oxygen sensors is possible, opening new avenues for therapeutic targeting of hypoxia-associated diseases, increasing the interest in its (patho-)physiological relevance. Future Directions: The contribution of FIH enzymatic activity to disease development and progression should be analyzed in more detail, including the assessment of underlying molecular mechanisms and relevant FIH substrate proteins. Also, the molecular mechanism(s) involved in the physiological functions of FIH remain(s) to be determined. Furthermore, the therapeutic potential of recently developed FIH-selective pharmacologic inhibitors will need detailed assessment. Antioxid. Redox Signal. 37, 913-935.
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Affiliation(s)
- Yulia L Volkova
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Christina Pickel
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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Association of EPAS1 and PPARA Gene Polymorphisms with High-Altitude Headache in Chinese Han Population. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1593068. [PMID: 32185192 PMCID: PMC7060407 DOI: 10.1155/2020/1593068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 11/17/2022]
Abstract
Background High-altitude headache (HAH) is the most common complication after high-altitude exposure. Hypoxia-inducible factor- (HIF-) related genes have been confirmed to contribute to high-altitude acclimatization. We aim to investigate a possible association between HIF-related genes and HAH in the Chinese Han population. Methods In total, 580 healthy Chinese Han volunteers were recruited in Chengdu (500 m) and carried to Lhasa (3700 m) by plane in 2 hours. HAH scores and basic physiological parameters were collected within 18-24 hours after the arrival. Thirty-five single nucleotide polymorphisms (SNPs) in HIF-related genes were genotyped, and linkage disequilibrium (LD) was evaluated by Haploview software. The functions of SNPs/haplotypes for HAH were developed by using logistic regression analysis. Results In comparison with wild types, the rs4953354 "G" allele (P=0.013), rs6756667 "A" allele (P=0.013), rs6756667 "A" allele (EPAS1, and rs6520015 "C" allele in PPARA (P=0.013), rs6756667 "A" allele (PPARA (P=0.013), rs6756667 "A" allele (EPAS1, and rs6520015 "C" allele in PPARA (P=0.013), rs6756667 "A" allele (. Conclusions EPAS1 and PPARA polymorphisms were associated with HAH in the Chinese Han population. Our findings pointed out potentially predictive gene markers, provided new insights into understanding pathogenesis, and may further provide prophylaxis and treatment strategies for HAH.EPAS1, and rs6520015 "C" allele in PPARA (.
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Ray K, Kishore K, Vats P, Bhattacharyya D, Akunov A, Maripov A, Sarybaev A, Singh SB, Kumar B. A Temporal Study on Learning and Memory at High Altitude in Two Ethnic Groups. High Alt Med Biol 2019; 20:236-244. [PMID: 31210541 DOI: 10.1089/ham.2018.0139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introduction: Cognitive function has been compromised during high-altitude (HA) exposure due to slowing of mental processing. Materials and Methods: A total of 20 Indian and 20 Kyrgyz soldiers were studied at 4111 m to assess cognitive function in two different ethnic groups. Paired associate learning, pattern recognition memory, spatial span (SSP), spatial working memory (SWM), choice reaction time (CRT), and simple reaction time (SRT) were evaluated at sea level and on days 3, 7, 14, and 21 of HA stay and on day 3 of deinduction. Results: All the parameters were significantly affected at HA. Indian soldiers were acclimatized by 7 days but Kyrgyz soldiers required 21 days for acclimatization. A slow impairment in SWM, CRT, and SRT was observed in Kyrgyz soldiers than in Indian soldiers and it continues throughout 21 days of HA stay, but for Indian soldiers the deterioration was maximum on day 7 and improvement in SWM, CRT, and SRT was observed on day 14 and close to baseline value on day 21. After deinduction, although Indian soldiers attained the normal value, Kyrgyz soldiers had higher value than baseline in SSP, SWM, CRT, and SRT. Conclusion: Difference in the cognitive performances of Indian and Kyrgyz soldiers may be due to the ethnogenetic diversity of these two groups.
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Affiliation(s)
- Koushik Ray
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Delhi, India
| | - Krishna Kishore
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Delhi, India
| | - Praveen Vats
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Delhi, India
| | - Debojyoti Bhattacharyya
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Delhi, India
| | - Almaz Akunov
- Kyrgyz-Indian Mountain Biomedical Research Centre, Bishkek, Kyrgyzstan
| | | | - Akpay Sarybaev
- Kyrgyz-Indian Mountain Biomedical Research Centre, Bishkek, Kyrgyzstan
| | - Shashi Bala Singh
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Delhi, India
| | - Bhuvnesh Kumar
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Delhi, India
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Meng K, Wu Y. Footprints of divergent evolution in two Na+/H+ type antiporter gene families (NHX and SOS1) in the genus Populus. TREE PHYSIOLOGY 2018; 38:813-824. [PMID: 29394412 DOI: 10.1093/treephys/tpx173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/19/2017] [Indexed: 05/19/2023]
Abstract
Populus, a deciduous tree species of major economic and ecological value, grows across the range in which trees are distributed in the Northern Hemisphere. Patterns of DNA variation are often used to identify the evolutionary forces shaping the genotypes of distinctive species lineages. Sodium/hydrogen (Na+/H+) antiporter genes have been shown to play a central role in plant salt tolerance. Here, we analyzed DNA nucleotide polymorphisms in the Na+/H+ antiporter (NHX and SOS1) gene families across 30 different Populus species using several methods of phylogenetic analysis and functional verification. NHX and SOS1 gene families in the genus Populus have expanded from the state in their common ancestors by duplication events, and their distinct lineages have been retained. Signals of positive selection at certain amino acid sites in different members of the Na/H antiporter gene families show that the dynamics that drive the evolution of each gene vary. SOS1 has undergone duplication in Populus euphratica and been subjected to adaptive evolution in section Turanga; the paralog of PeSOS1 (PeSOS1.2) can complement the Escherichia coli mutant EP432; and the expression pattern of PeSOS1.2 is different from that of PeSOS1, a fact which may have been beneficial for P. euphratica, conferring a fitness advantage in saline habitats. The divergent evolution of the individual members of the NHX and SOS1 gene families is likely to have been influenced by the varied ecological and environmental niches occupied by the different poplar species, giving rise to evolutionary footprints that reflect the specific functions and subcellular localizations of the proteins encoded by these genes.
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Affiliation(s)
- Kuibin Meng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yuxia Wu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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The Factor Inhibiting HIF Asparaginyl Hydroxylase Regulates Oxidative Metabolism and Accelerates Metabolic Adaptation to Hypoxia. Cell Metab 2018; 27:898-913.e7. [PMID: 29617647 PMCID: PMC5887987 DOI: 10.1016/j.cmet.2018.02.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/29/2017] [Accepted: 02/20/2018] [Indexed: 01/16/2023]
Abstract
Animals require an immediate response to oxygen availability to allow rapid shifts between oxidative and glycolytic metabolism. These metabolic shifts are highly regulated by the HIF transcription factor. The factor inhibiting HIF (FIH) is an asparaginyl hydroxylase that controls HIF transcriptional activity in an oxygen-dependent manner. We show here that FIH loss increases oxidative metabolism, while also increasing glycolytic capacity, and that this gives rise to an increase in oxygen consumption. We further show that the loss of FIH acts to accelerate the cellular metabolic response to hypoxia. Skeletal muscle expresses 50-fold higher levels of FIH than other tissues: we analyzed skeletal muscle FIH mutants and found a decreased metabolic efficiency, correlated with an increased oxidative rate and an increased rate of hypoxic response. We find that FIH, through its regulation of oxidation, acts in concert with the PHD/vHL pathway to accelerate HIF-mediated metabolic responses to hypoxia.
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Xiao J, Li X, Liu J, Fan X, Lei H, Li C. Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies. PeerJ 2017; 5:e3726. [PMID: 28970964 PMCID: PMC5622608 DOI: 10.7717/peerj.3726] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes. RESULTS The expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions. CONCLUSION These results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings.
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Affiliation(s)
- Jun Xiao
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiaowei Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Juan Liu
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiu Fan
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Huifen Lei
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
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Su Y, Li D, Gaur U, Chen B, Zhao X, Wang Y, Yin H, Zhu Q. The comparison of blood characteristics in low- and high-altitude chickens. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1355272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yuan Su
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Uma Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Binlong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Xiaoling Zhao
- Department of Animal Science, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Qing Zhu
- Department of Animal Science, Sichuan Agricultural University, Chengdu, Sichuan Province, China
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GUO LI, ZHANG JIHANG, JIN JUN, GAO XUBIN, YU JIE, GENG QIANWEN, LI HUIJIE, HUANG LAN. Genetic variants of endothelial PAS domain protein 1 are associated with susceptibility to acute mountain sickness in individuals unaccustomed to high altitude: A nested case-control study. Exp Ther Med 2015; 10:907-914. [PMID: 26622413 PMCID: PMC4533176 DOI: 10.3892/etm.2015.2611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/15/2015] [Indexed: 01/25/2023] Open
Abstract
The endothelial PAS domain protein 1 (EPAS1) gene functions to sense the blood oxygen level by regulating the hypoxia-inducible transcription factor pathway, and single nucleotide polymorphisms (SNPs) of EPAS1 have been found to have a strong and positive selection in the adaptation of the native Tibetan highland population to high-altitude hypoxia. The aim of the present study was to investigate the effect of EPAS1 SNPs on the risk of acute mountain sickness (AMS) and the physiological responses to acute high-altitude hypoxia in lowland humans. Three tag SNPs (rs6756667, rs13419896 and rs4953354; minor allele frequency, ≥5%) were selected and genotyped in 603 unrelated Han Chinese men, who had traveled to Lhasa (a high-altitude hypoxia environment) by plane, using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry method. The data showed that the EPAS1 rs6756667 wild-type GG homozygous genotype was associated with elevated AMS risk compared with the AA and AG genotypes (odds ratio, 1.815; 95% confidence interval, 1.233-2.666; P=0.0023) using the dominant-model analysis. EPAS1 rs6756667 GG genotypes were also associated with higher levels of hemoglobin, red blood cells and hematocrit than those carrying the AG heterozygote during AMS development. These findings indicate that EPAS1 SNPs play a role in the physiological effects of AMS, and these effects could be further evaluated as a therapeutic strategy to control acute hypoxia-related human diseases.
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Affiliation(s)
- LI GUO
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - JIHANG ZHANG
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - JUN JIN
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - XUBIN GAO
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - JIE YU
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - QIANWEN GENG
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - HUIJIE LI
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
| | - LAN HUANG
- Institute of Cardiovascular Diseases of PLA, Department of Cardiology, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, P.R. China
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Mishra A, Mohammad G, Norboo T, Newman JH, Pasha MAQ. Lungs at high-altitude: genomic insights into hypoxic responses. J Appl Physiol (1985) 2015; 119:1-15. [DOI: 10.1152/japplphysiol.00513.2014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 04/20/2015] [Indexed: 11/22/2022] Open
Abstract
Hypobaric hypoxia at high altitude (HA) results in reduced blood arterial oxygen saturation, perfusion of organs with hypoxemic blood, and direct hypoxia of lung tissues. The pulmonary complications in the cells of the pulmonary arterioles due to hypobaric hypoxia are the basis of the pathophysiological mechanisms of high-altitude pulmonary edema (HAPE). Some populations that have dwelled at HA for thousands of years have evolutionarily adapted to this environmental stress; unadapted populations may react with excessive physiological responses that impair health. Individual variations in response to hypoxia and the mechanisms of HA adaptation provide insight into physiological responses. Adaptive and maladaptive responses include alterations in pathways such as oxygen sensing, hypoxia signaling, K+- and Ca2+-gated channels, redox balance, and the renin-angiotensin-aldosterone system. Physiological imbalances are linked with genetic susceptibilities, and nonhomeostatic responses in gene regulation that occur by small RNAs, histone modification, and DNA methylation predispose susceptible humans to these HA illnesses. Elucidation of the interaction of these factors will lead to a more comprehensive understanding of HA adaptations and maladaptations and will lead to new therapeutics for HA disorders related to hypoxic lungs.
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Affiliation(s)
- Aastha Mishra
- Department of Genomics and Molecular Medicine, Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Department of Biotechnology, University of Pune, Pune, India
| | - Ghulam Mohammad
- Department of Medicine, SNM Hospital, Leh, Ladakh, J&K, India
| | - Tsering Norboo
- Ladakh Institute of Prevention, Leh, Ladakh, J&K, India; and
| | - John H. Newman
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - M. A. Qadar Pasha
- Department of Genomics and Molecular Medicine, Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
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Wang GD, Fan RX, Zhai W, Liu F, Wang L, Zhong L, Wu H, Yang HC, Wu SF, Zhu CL, Li Y, Gao Y, Ge RL, Wu CI, Zhang YP. Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau. Genome Biol Evol 2015; 6:2122-8. [PMID: 25091388 PMCID: PMC4231634 DOI: 10.1093/gbe/evu162] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ruo-Xi Fan
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Weiwei Zhai
- Center for Computational Biology and Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Fei Liu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Hong Wu
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - He-Chuan Yang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yan Li
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ri-Li Ge
- Key Laboratory for High Altitude Medicine of Ministry of Chinese Education and Research Center for High Altitude Medicine, Qinghai University, Xining, China
| | - Chung-I Wu
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China Department of Ecology and Evolution, University of Chicago
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
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Fan R, Liu F, Wu H, Wu S, Zhu C, Li Y, Wang G, Zhang Y. A Positive Correlation between Elevated Altitude and Frequency of Mutant Alleles at the EPAS1 and HBB Loci in Chinese Indigenous Dogs. J Genet Genomics 2015; 42:173-7. [PMID: 25953356 DOI: 10.1016/j.jgg.2015.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/20/2015] [Accepted: 02/26/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Ruoxi Fan
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
| | - Fei Liu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong Wu
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
| | - Shifang Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chunling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yan Li
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guodong Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China; State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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14
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Wilkins MR, Ghofrani HA, Weissmann N, Aldashev A, Zhao L. Pathophysiology and Treatment of High-Altitude Pulmonary Vascular Disease. Circulation 2015; 131:582-90. [DOI: 10.1161/circulationaha.114.006977] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Martin R. Wilkins
- From Experimental Medicine, Imperial College London, Hammersmith Hospital, United Kingdom (M.R.W., H.-A.G., L.Z.); Excellence Cluster Cardio-Pulmonary System, Universities of Giessen, Germany (M.R.W., H.-A.G., N.W., L.Z.); University of Giessen Marburg Lung Center, Justus-Liebig-University, Germany (M.R.W., H.-A.G., N.W., L.Z.); Kerckhoff Clinic, Bad Nauheim, Germany (H.-A.G.); Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan (A.A.)
| | - Hossein-Ardeschir Ghofrani
- From Experimental Medicine, Imperial College London, Hammersmith Hospital, United Kingdom (M.R.W., H.-A.G., L.Z.); Excellence Cluster Cardio-Pulmonary System, Universities of Giessen, Germany (M.R.W., H.-A.G., N.W., L.Z.); University of Giessen Marburg Lung Center, Justus-Liebig-University, Germany (M.R.W., H.-A.G., N.W., L.Z.); Kerckhoff Clinic, Bad Nauheim, Germany (H.-A.G.); Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan (A.A.)
| | - Norbert Weissmann
- From Experimental Medicine, Imperial College London, Hammersmith Hospital, United Kingdom (M.R.W., H.-A.G., L.Z.); Excellence Cluster Cardio-Pulmonary System, Universities of Giessen, Germany (M.R.W., H.-A.G., N.W., L.Z.); University of Giessen Marburg Lung Center, Justus-Liebig-University, Germany (M.R.W., H.-A.G., N.W., L.Z.); Kerckhoff Clinic, Bad Nauheim, Germany (H.-A.G.); Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan (A.A.)
| | - Almaz Aldashev
- From Experimental Medicine, Imperial College London, Hammersmith Hospital, United Kingdom (M.R.W., H.-A.G., L.Z.); Excellence Cluster Cardio-Pulmonary System, Universities of Giessen, Germany (M.R.W., H.-A.G., N.W., L.Z.); University of Giessen Marburg Lung Center, Justus-Liebig-University, Germany (M.R.W., H.-A.G., N.W., L.Z.); Kerckhoff Clinic, Bad Nauheim, Germany (H.-A.G.); Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan (A.A.)
| | - Lan Zhao
- From Experimental Medicine, Imperial College London, Hammersmith Hospital, United Kingdom (M.R.W., H.-A.G., L.Z.); Excellence Cluster Cardio-Pulmonary System, Universities of Giessen, Germany (M.R.W., H.-A.G., N.W., L.Z.); University of Giessen Marburg Lung Center, Justus-Liebig-University, Germany (M.R.W., H.-A.G., N.W., L.Z.); Kerckhoff Clinic, Bad Nauheim, Germany (H.-A.G.); Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan (A.A.)
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15
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Stevens CW. Bioinformatics and evolution of vertebrate nociceptin and opioid receptors. VITAMINS AND HORMONES 2015; 97:57-94. [PMID: 25677768 DOI: 10.1016/bs.vh.2014.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G protein-coupled receptors (GPCRs) are ancestrally related membrane proteins on cells that mediate the pharmacological effect of most drugs and neurotransmitters. GPCRs are the largest group of membrane receptor proteins encoded in the human genome. One of the most famous types of GPCRs is the opioid receptors. Opioid family receptors consist of four closely related proteins expressed in all vertebrate brains and spinal cords examined to date. The three classical types of opioid receptors shown unequivocally to mediate analgesia in animal models and in humans are the mu- (MOR), delta- (DOR), and kappa-(KOR) opioid receptor proteins. The fourth and most recent member of the opioid receptor family discovered is the nociceptin or orphanin FQ receptor (ORL). The role of ORL and its ligands in producing analgesia is not as clear, with both analgesic and hyperalgesic effects reported. All four opioid family receptor genes were cloned from expressed mRNA in a number of vertebrate species, and there are enough sequences presently available to carry out bioinformatic analysis. This chapter presents the results of a comparative analysis of vertebrate opioid receptors using pharmacological studies, bioinformatics, and the latest data from human whole-genome studies. Results confirm our initial hypotheses that the four opioid receptor genes most likely arose by whole-genome duplication, that there is an evolutionary vector of opioid receptor type divergence in sequence and function, and that the hMOR gene shows evidence of positive selection or adaptive evolution in Homo sapiens.
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Affiliation(s)
- Craig W Stevens
- Department of Pharmacology and Physiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA.
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16
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Variants of the low oxygen sensors EGLN1 and HIF-1AN associated with acute mountain sickness. Int J Mol Sci 2014; 15:21777-87. [PMID: 25431923 PMCID: PMC4284677 DOI: 10.3390/ijms151221777] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 02/06/2023] Open
Abstract
Two low oxygen sensors, Egl nine homolog 1 (EGLN1) and hypoxia-inducible factor 1-α inhibitor (HIF-1AN), play pivotal roles in the regulation of HIF-1α, and high altitude adaption may be involved in the pathology of acute mountain sickness (AMS). Here, we aimed to analyze single nucleotide polymorphisms (SNPs) in the untranslated regions of the EGLN1 and HIF-1AN genes and SNPs chosen from a genome-wide adaptation study of the Han Chinese population. To assess the association between EGLN1 and HIF-1AN SNPs and AMS in a Han Chinese population, a case-control study was performed including 190 patients and 190 controls. In total, thirteen SNPs were genotyped using the MassARRAY® MALDI-TOF system. Multiple genetic models were tested; The Akaike's information criterion (AIC) and Bayesian information criterion (BIC) values indicated that the dominant model may serve as the best-fit model for rs12406290 and rs2153364 of significant difference. However, these data were not significant after Bonferroni correction. No significant association was noted between AMS and rs12757362, rs1339894, rs1361384, rs2009873, rs2739513 or rs2486729 before and after Bonferroni correction. Further haplotype analyses indicated the presence of two blocks in EGLN1; one block consists of rs12406290-rs2153364, located upstream of the EGLN1 gene. Carriers of the "GG" haplotype of rs12406290-rs2153364 exhibited an increased risk of AMS after adjustments for age and smoking status. However, no significant association was observed among HIF-1AN 3'-untranslated region (3'-UTR) polymorphisms, haplotype and AMS. Our study indicates that variants in the EGLN1 5'-UTR influence the susceptibility to AMS in a Han Chinese population.
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17
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Wilkins MR, Aldashev AA, Wharton J, Rhodes CJ, Vandrovcova J, Kasperaviciute D, Bhosle SG, Mueller M, Geschka S, Rison S, Kojonazarov B, Morrell NW, Neidhardt I, Surmeli NB, Surmeli NB, Aitman TJ, Stasch JP, Behrends S, Marletta MA. α1-A680T variant in GUCY1A3 as a candidate conferring protection from pulmonary hypertension among Kyrgyz highlanders. ACTA ACUST UNITED AC 2014; 7:920-9. [PMID: 25373139 DOI: 10.1161/circgenetics.114.000763] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Human variation in susceptibility to hypoxia-induced pulmonary hypertension is well recognized. High-altitude residents who do not develop pulmonary hypertension may host protective gene mutations. METHODS AND RESULTS Exome sequencing was conducted on 24 unrelated Kyrgyz highlanders living 2400 to 3800 m above sea level, 12 (10 men; mean age, 54 years) with an elevated mean pulmonary artery pressure (mean±SD, 38.7±2.7 mm Hg) and 12 (11 men; mean age, 52 years) with a normal mean pulmonary artery pressure (19.2±0.6 mm Hg) to identify candidate genes that may influence the pulmonary vascular response to hypoxia. A total of 140 789 exomic variants were identified and 26 116 (18.5%) were classified as novel or rare. Thirty-three novel or rare potential pathogenic variants (frameshift, essential splice-site, and nonsynonymous) were found exclusively in either ≥3 subjects with high-altitude pulmonary hypertension or ≥3 highlanders with a normal mean pulmonary artery pressure. A novel missense mutation in GUCY1A3 in 3 subjects with a normal mean pulmonary artery pressure encodes an α1-A680T soluble guanylate cyclase (sGC) variant. Expression of the α1-A680T sGC variant in reporter cells resulted in higher cyclic guanosine monophosphate production compared with the wild-type enzyme and the purified α1-A680T sGC exhibited enhanced sensitivity to nitric oxide in vitro. CONCLUSIONS The α1-A680T sGC variant may contribute to protection against high-altitude pulmonary hypertension and supports sGC as a pharmacological target for reducing pulmonary artery pressure in humans at altitude.
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Affiliation(s)
- Martin R Wilkins
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.).
| | - Almaz A Aldashev
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - John Wharton
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Christopher J Rhodes
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Jana Vandrovcova
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Dalia Kasperaviciute
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Shriram G Bhosle
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Michael Mueller
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Sandra Geschka
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Stuart Rison
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Baktybek Kojonazarov
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Nicholas W Morrell
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Inga Neidhardt
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | | | - Nur Basek Surmeli
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Tim J Aitman
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Johannes-Peter Stasch
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Soenke Behrends
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
| | - Michael A Marletta
- From the Department of Medicine, Imperial College London, London, United Kingdom (M.R.W., J.W., C.J.R., S.R.); National Academy of Sciences of Kyrgyz Republic, Bishkek, Kyrgyz Republic (A.A.A.); Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom (J.V., T.J.A.); NIHR BRC Clinical Genome Informatics Facility, Imperial College London, London, United Kingdom (D.K., S.G.B., M.M.); Cardiology Research, Bayer Pharma AG, Wuppertal, Germany (S.G., J.-P.S.); Department of Pharmacology, The School of Pharmacy, Martin-Luther-University, Halle, Germany (J.-P.S.); Department of Pulmonary Pharmacotherapy, University of Giessen and Marburg Lung Center, Giessen, Germany (B.K.); Department of Medicine, University of Cambridge, Cambridge, United Kingdom (N.W.M.); Department of Pharmacology, Toxicology, and Clinical Pharmacy, University of Braunschweig-Center of Pharmaceutical Engineering, Braunschweig, Germany (I.N., S.B.); and Department of Chemistry, The Scripps Research Institute, La Jolla, CA (N.B.S., M.A.M.)
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18
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Abstract
Populations residing for millennia on the high-altitude plateaus of the world started natural experiments that we can evaluate to address questions about the processes of evolution and adaptation. A 2001 assessment in this journal summarized abundant evidence that Tibetan and Andean high-altitude natives had different phenotypes, and the article made a case for the hypothesis that different genetic bases underlie traits in the two populations. Since then, knowledge of the prehistory of high-altitude populations has grown, information about East African highlanders has become available, genomic science has grown exponentially, and the genetic and molecular bases of oxygen homeostasis have been clarified. Those scientific advances have transformed the study of high-altitude populations. The present review aims to summarize recent advances in understanding with an emphasis on the genetic bases of adaptive phenotypes, particularly hemoglobin concentration among Tibetan highlanders. EGLN1 and EPAS1 encode two crucial proteins contributing to oxygen homeostasis, the oxygen sensor PHD2 and the transcription factor subunit HIF-2α, respectively; they show signals of natural selection such as marked allele frequency differentiation between Tibetans and lowland populations. EPAS1 genotypes associated in several studies with the dampened hemoglobin phenotype that is characteristic of Tibetans at high altitude but did not associate with the dampened response among Amhara from Ethiopia or the vigorous elevation of hemoglobin concentration among Andean highlanders. Future work will likely develop understanding of the integrative biology leading from genotype to phenotype to population in all highland areas.
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Affiliation(s)
- Cynthia M. Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106–7125
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19
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Dong K, Yao N, Pu Y, He X, Zhao Q, Luan Y, Guan W, Rao S, Ma Y. Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs. PLoS One 2014; 9:e110520. [PMID: 25329542 PMCID: PMC4201535 DOI: 10.1371/journal.pone.0110520] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 09/16/2014] [Indexed: 01/04/2023] Open
Abstract
High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP) that is well adapted to the high altitude and Dahe pig (DHP) that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP) as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19) for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG) for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16) were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9) were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.
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Affiliation(s)
- Kunzhe Dong
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Na Yao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohong He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yizhao Luan
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, Guangdong Medical College, Dongguan, China
| | - Weijun Guan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoqi Rao
- Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology, Guangdong Medical College, Dongguan, China
- * E-mail: (YHM); (SQR)
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (YHM); (SQR)
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20
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Foll M, Gaggiotti O, Daub J, Vatsiou A, Excoffier L. Widespread signals of convergent adaptation to high altitude in Asia and america. Am J Hum Genet 2014; 95:394-407. [PMID: 25262650 DOI: 10.1016/j.ajhg.2014.09.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023] Open
Abstract
Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low- and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia.
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21
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Zhang W, Fan Z, Han E, Hou R, Zhang L, Galaverni M, Huang J, Liu H, Silva P, Li P, Pollinger JP, Du L, Zhang X, Yue B, Wayne RK, Zhang Z. Hypoxia adaptations in the grey wolf (Canis lupus chanco) from Qinghai-Tibet Plateau. PLoS Genet 2014; 10:e1004466. [PMID: 25078401 PMCID: PMC4117439 DOI: 10.1371/journal.pgen.1004466] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/14/2014] [Indexed: 12/11/2022] Open
Abstract
The Tibetan grey wolf (Canis lupus chanco) occupies habitats on the Qinghai-Tibet Plateau, a high altitude (>3000 m) environment where low oxygen tension exerts unique selection pressure on individuals to adapt to hypoxic conditions. To identify genes involved in hypoxia adaptation, we generated complete genome sequences of nine Chinese wolves from high and low altitude populations at an average coverage of 25× coverage. We found that, beginning about 55,000 years ago, the highland Tibetan grey wolf suffered a more substantial population decline than lowland wolves. Positively selected hypoxia-related genes in highland wolves are enriched in the HIF signaling pathway (P = 1.57E-6), ATP binding (P = 5.62E-5), and response to an oxygen-containing compound (P≤5.30E-4). Of these positively selected hypoxia-related genes, three genes (EPAS1, ANGPT1, and RYR2) had at least one specific fixed non-synonymous SNP in highland wolves based on the nine genome data. Our re-sequencing studies on a large panel of individuals showed a frequency difference greater than 58% between highland and lowland wolves for these specific fixed non-synonymous SNPs and a high degree of LD surrounding the three genes, which imply strong selection. Past studies have shown that EPAS1 and ANGPT1 are important in the response to hypoxic stress, and RYR2 is involved in heart function. These three genes also exhibited significant signals of natural selection in high altitude human populations, which suggest similar evolutionary constraints on natural selection in wolves and humans of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Wenping Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu research base of giant panda breeding, Chengdu, Sichuan Province, P. R. China
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Zhenxin Fan
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Eunjung Han
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu research base of giant panda breeding, Chengdu, Sichuan Province, P. R. China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu research base of giant panda breeding, Chengdu, Sichuan Province, P. R. China
| | | | - Jie Huang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Hong Liu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu research base of giant panda breeding, Chengdu, Sichuan Province, P. R. China
| | - Pedro Silva
- CIBIO-UP, University of Porto, Vairão, Portugal
| | - Peng Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - John P. Pollinger
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Lianming Du
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - XiuyYue Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu research base of giant panda breeding, Chengdu, Sichuan Province, P. R. China
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22
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Gardie B, Percy MJ, Hoogewijs D, Chowdhury R, Bento C, Arsenault PR, Richard S, Almeida H, Ewing J, Lambert F, McMullin MF, Schofield CJ, Lee FS. The role of PHD2 mutations in the pathogenesis of erythrocytosis. HYPOXIA 2014; 2:71-90. [PMID: 27774468 PMCID: PMC5045058 DOI: 10.2147/hp.s54455] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transcription of the erythropoietin (EPO) gene is tightly regulated by the hypoxia response pathway to maintain oxygen homeostasis. Elevations in serum EPO level may be reflected in an augmentation in the red cell mass, thereby causing erythrocytosis. Studies on erythrocytosis have provided insights into the function of the oxygen-sensing pathway and the critical proteins involved in the regulation of EPO transcription. The α subunits of the hypoxia-inducible transcription factor are hydroxylated by three prolyl hydroxylase domain (PHD) enzymes, which belong to the iron and 2-oxoglutarate-dependent oxygenase superfamily. Sequence analysis of the genes encoding the PHDs in patients with erythrocytosis has revealed heterozygous germline mutations only occurring in Egl nine homolog 1 (EGLN1, also known as PHD2), the gene that encodes PHD2. To date, 24 different EGLN1 mutations comprising missense, frameshift, and nonsense mutations have been described. The phenotypes associated with the patients carrying these mutations are fairly homogeneous and typically limited to erythrocytosis with normal to elevated EPO. However, exceptions exist; for example, there is one case with development of concurrent paraganglioma (PHD2-H374R). Analysis of the erythrocytosis-associated PHD2 missense mutations has shown heterogeneous results. Structural studies reveal that mutations can affect different domains of PHD2. Some are close to the hypoxia-inducible transcription factor α/2-oxoglutarate or the iron binding sites for PHD2. In silico studies demonstrate that the mutations do not always affect fully conserved residues. In vitro and in cellulo studies showed varying effects of the mutations, ranging from mild effects to severe loss of function. The exact mechanism of a potential tumor-suppressor role for PHD2 still needs to be elucidated. A knockin mouse model expressing the first reported PHD2-P317R mutation recapitulates the phenotype observed in humans (erythrocytosis with inappropriately normal serum EPO levels) and demonstrates that haploinsufficiency and partial deregulation of PHD2 is sufficient to cause erythrocytosis.
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Affiliation(s)
- Betty Gardie
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes, Villejuif; Unité Mixte de Recherche, Institut national de la santé et de la recherche médicale U892, Centre national de la recherche scientifique 6299, Centre de Recherche en Cancérologie Nantes/Angers, Université de Nantes, Nantes, France
| | - Melanie J Percy
- Department of Haematology, Belfast City Hospital, Belfast, UK
| | - David Hoogewijs
- Institute of Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland
| | - Rasheduzzaman Chowdhury
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Celeste Bento
- Department of Hematology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Patrick R Arsenault
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stéphane Richard
- Laboratoire de Génétique Oncologique de l'Ecole Pratique des Hautes Etudes, Villejuif; Institut national de la santé et de la recherche médicale U753, Institut de cancérologie Gustave Roussy (IGR), Villejuif, France; Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, France
| | - Helena Almeida
- Department of Hematology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | | | - Frédéric Lambert
- Center for Human Genetics, Pathology Institute, UniLab-Lg, Molecular Haemato-Oncology Unit, CHU of Liege, Liege, Belgium
| | | | - Christopher J Schofield
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Frank S Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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23
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Luo Y, Wang Y, Lu H, Gao Y. ‘Ome’ on the range: update on high-altitude acclimatization/adaptation and disease. ACTA ACUST UNITED AC 2014; 10:2748-55. [DOI: 10.1039/c4mb00119b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The main physiological challenge in high-altitude plateau environments is hypoxia.
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Affiliation(s)
- Yongjun Luo
- Department of Military Medical Geography
- Third Military Medical University
- Chongqing 400038, China
- Key Laboratory of High Altitude Medicine (Ministry of Education)
- Third Military Medical University
| | - Yuxiao Wang
- Department of Military Medical Geography
- Third Military Medical University
- Chongqing 400038, China
- Key Laboratory of High Altitude Medicine (Ministry of Education)
- Third Military Medical University
| | - Hongxiang Lu
- Department of Military Medical Geography
- Third Military Medical University
- Chongqing 400038, China
- Key Laboratory of High Altitude Medicine (Ministry of Education)
- Third Military Medical University
| | - Yuqi Gao
- Key Laboratory of High Altitude Medicine (Ministry of Education)
- Third Military Medical University
- Chongqing 400038, China
- Key Laboratory of High Altitude medicine (People's Liberation Army)
- Third Military Medical University
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24
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Khurana P, Sugadev R, Jain J, Singh SB. HypoxiaDB: a database of hypoxia-regulated proteins. Database (Oxford) 2013; 2013:bat074. [PMID: 24178989 PMCID: PMC3813937 DOI: 10.1093/database/bat074] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 08/04/2013] [Accepted: 09/27/2013] [Indexed: 01/29/2023]
Abstract
There has been intense interest in the cellular response to hypoxia, and a large number of differentially expressed proteins have been identified through various high-throughput experiments. These valuable data are scattered, and there have been no systematic attempts to document the various proteins regulated by hypoxia. Compilation, curation and annotation of these data are important in deciphering their role in hypoxia and hypoxia-related disorders. Therefore, we have compiled HypoxiaDB, a database of hypoxia-regulated proteins. It is a comprehensive, manually-curated, non-redundant catalog of proteins whose expressions are shown experimentally to be altered at different levels and durations of hypoxia. The database currently contains 72 000 manually curated entries taken on 3500 proteins extracted from 73 peer-reviewed publications selected from PubMed. HypoxiaDB is distinctive from other generalized databases: (i) it compiles tissue-specific protein expression changes under different levels and duration of hypoxia. Also, it provides manually curated literature references to support the inclusion of the protein in the database and establish its association with hypoxia. (ii) For each protein, HypoxiaDB integrates data on gene ontology, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, protein-protein interactions, protein family (Pfam), OMIM (Online Mendelian Inheritance in Man), PDB (Protein Data Bank) structures and homology to other sequenced genomes. (iii) It also provides pre-compiled information on hypoxia-proteins, which otherwise requires tedious computational analysis. This includes information like chromosomal location, identifiers like Entrez, HGNC, Unigene, Uniprot, Ensembl, Vega, GI numbers and Genbank accession numbers associated with the protein. These are further cross-linked to respective public databases augmenting HypoxiaDB to the external repositories. (iv) In addition, HypoxiaDB provides an online sequence-similarity search tool for users to compare their protein sequences with HypoxiaDB protein database. We hope that HypoxiaDB will enrich our knowledge about hypoxia-related biology and eventually will lead to the development of novel hypothesis and advancements in diagnostic and therapeutic activities. HypoxiaDB is freely accessible for academic and non-profit users via http://www.hypoxiadb.com.
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Affiliation(s)
- Pankaj Khurana
- Bioinformatics Group, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization, Lucknow Road, Timarpur, New Delhi-110054, India
| | - Ragumani Sugadev
- Bioinformatics Group, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization, Lucknow Road, Timarpur, New Delhi-110054, India
| | - Jaspreet Jain
- Bioinformatics Group, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization, Lucknow Road, Timarpur, New Delhi-110054, India
| | - Shashi Bala Singh
- Bioinformatics Group, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization, Lucknow Road, Timarpur, New Delhi-110054, India
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25
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Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet 2013; 93:452-62. [PMID: 23954164 DOI: 10.1016/j.ajhg.2013.07.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/09/2013] [Accepted: 07/01/2013] [Indexed: 11/16/2022] Open
Abstract
The hypoxic conditions at high altitudes present a challenge for survival, causing pressure for adaptation. Interestingly, many high-altitude denizens (particularly in the Andes) are maladapted, with a condition known as chronic mountain sickness (CMS) or Monge disease. To decode the genetic basis of this disease, we sequenced and compared the whole genomes of 20 Andean subjects (10 with CMS and 10 without). We discovered 11 regions genome-wide with significant differences in haplotype frequencies consistent with selective sweeps. In these regions, two genes (an erythropoiesis regulator, SENP1, and an oncogene, ANP32D) had a higher transcriptional response to hypoxia in individuals with CMS relative to those without. We further found that downregulating the orthologs of these genes in flies dramatically enhanced survival rates under hypoxia, demonstrating that suppression of SENP1 and ANP32D plays an essential role in hypoxia tolerance. Our study provides an unbiased framework to identify and validate the genetic basis of adaptation to high altitudes and identifies potentially targetable mechanisms for CMS treatment.
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Affiliation(s)
- Dan Zhou
- Division of Respiratory Medicine, Department of Pediatrics, University of California-San Diego, La Jolla, CA 92093, USA
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26
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Liu C, Zhang L, Li N. The specific expression pattern of globin mRNAs in Tibetan chicken during late embryonic stage under hypoxia. Comp Biochem Physiol A Mol Integr Physiol 2013; 164:638-44. [DOI: 10.1016/j.cbpa.2012.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/02/2012] [Accepted: 09/04/2012] [Indexed: 11/16/2022]
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EGLN1 variants influence expression and SaO2 levels to associate with high-altitude pulmonary oedema and adaptation. Clin Sci (Lond) 2013; 124:479-89. [PMID: 23130672 DOI: 10.1042/cs20120371] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
EGLN1 [encoding HIF (hypoxia-inducible factor)-prolyl hydroxylase 2] plays a pivotal role in the HIF pathway and has emerged as one of the most intriguing genes with respect to physiology at HA (high altitude). EGLN1, being an actual oxygen sensor, appears to have a potential role in the functional adaptation to the hypobaric hypoxic environment. In the present study, we screened 30 polymorphisms of EGLN1, evaluated its gene expression and performed association analyses. In addition, the role of allelic variants in altering TF (transcription factor)-binding sites and consequently the replacement of TFs at these loci was also investigated. The study was performed in 250 HAPE-p [HAPE (HA pulmonary oedema)-patients], 210 HAPE-f (HAPE-free controls) and 430 HLs (healthy Ladakhi highland natives). The genotypes of seven polymorphisms, rs1538664, rs479200, rs2486729, rs2790879, rs480902, rs2486736 and rs973252, differed significantly between HAPE-p and HAPE-f (P<0.008). The genotypes AA, TT, AA, GG, CC, AA and GG of rs1538664, rs479200, rs2486729, rs2790879, rs480902, rs2486736 and rs973252, prevalent in HAPE-p, were identified as risk genotypes and their counterpart homozygotes, prevalent in HLs, were identified as protective. EGLN1 expression was up-regulated 4.56-fold in HAPE-p (P=0.0084). The risk genotypes, their haplotypes and interacting genotypes were associated with up-regulated EGLN1 expression (P<0.05). Similarly, regression analysis showed that the risk alleles and susceptible haplotypes were associated with decreased SaO2 (arterial oxygen saturation) levels in the three groups. The significant inverse correlation of SaO2 levels with PASP (pulmonary artery systolic pressure) and EGLN1 expression and the association of these polymorphisms with SaO2 levels and EGLN1 expression contributed to uncovering the molecular mechanism underlying hypobaric hypoxic adaptation and maladaptation.
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