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Zhao B, Liu C, Qi Y, Zhang T, Wang Y, He X, Wang L, Jin T. Preliminary study of identified novel susceptibility loci for HAPE risk in a Chinese male Han population. Per Med 2024; 21:227-241. [PMID: 38940394 DOI: 10.1080/17410541.2024.2365617] [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: 02/02/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024]
Abstract
High altitude pulmonary edema (HAPE) is a life-threatening form of non-cardiogenic pulmonary edema. In recent years, association studies have become the main method for identifying HAPE genetic loci. A genome-wide association study (GWAS) of HAPE risk-associated loci was performed in Chinese male Han individuals (164 HAPE cases and 189 healthy controls) by the Precision Medicine Diversity Array Chip with 2,771,835 loci (Applied Biosystems Axiom™). Eight overlapping candidate loci in CCNG2, RP11-445O3.2, NUPL1 and WWOX were finally selected. In silico functional analyses displayed the PPI network, functional enrichment and signal pathways related to CCNG2, NUPL1, WWOX and NRXN1. This study provides data supplements for HAPE susceptibility gene loci and new insights into HAPE susceptibility.
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Affiliation(s)
- Beibei Zhao
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Changchun Liu
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Yijin Qi
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Tianyi Zhang
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Yuhe Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Xue He
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Li Wang
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Tianbo Jin
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
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Chen M, Yi F, Qi Y, Zhao B, Zhang Z, He X, Yuan D, Jin T. Whole-exome sequencing in searching for novel variants associated with the development of high altitude pulmonary edema. Gene 2023; 870:147384. [PMID: 37001572 DOI: 10.1016/j.gene.2023.147384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND High altitude pulmonary edema (HAPE) is a high-altitude idiopathic disease with serious consequences due to hypoxia at high altitude, and there is individual genetic susceptibility. Whole-exome sequencing (WES) is an effective tool for studying the genetic etiology of HAPE and can identify potentially novel mutations that may cause protein instability and may contribute to the development of HAPE. MATERIALS AND METHODS A total of 50 unrelated HAPE patients were examined using WES, and the available bioinformatics tools were used to perform an analysis of exonic regions. Using the Phenolyzer program, disease candidate gene analysis was carried out. SIFT, PolyPhen-2, Mutation Taster, CADD, DANN, and I-Mutant software were used to assess the effects of genetic variations on protein function. RESULTS The results showed that rs368502694 (p. R1022Q) located in NOS3, rs1595850639 (p. G61S) located in MYBPC3, and rs1367895529 (p. R333H) located in ITGAV were correlated with a high risk of HAPE, and thus could be regarded as potential genetic variations associated with HAPE. CONCLUSION WES was used in this study for the first time to directly screen genetic variations related to HAPE. Notably, our study offers fresh information for the subsequent investigation into the etiology of HAPE.
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Affiliation(s)
- Mingyue Chen
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Faling Yi
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Yijin Qi
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Beibei Zhao
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Zhanhao Zhang
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Xue He
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China
| | - Dongya Yuan
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Tianbo Jin
- Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, Shaanxi 710069, China; Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi 710069, China.
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Genetics of High-Altitude Pulmonary Edema. Heart Fail Clin 2023; 19:89-96. [DOI: 10.1016/j.hfc.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Yee J, Park T, Park M. Identification of the associations between genes and quantitative traits using entropy-based kernel density estimation. Genomics Inform 2022; 20:e17. [PMID: 35794697 PMCID: PMC9299569 DOI: 10.5808/gi.22033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/15/2022] [Indexed: 11/20/2022] Open
Abstract
Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.
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Affiliation(s)
- Jaeyong Yee
- Department of Physiology and Biophysics, Eulji University, Daejeon 34824, Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul 08826, Korea
| | - Mira Park
- Department of Preventive Medicine, Eulji University, Daejeon 34824, Korea
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Childebayeva A, Goodrich JM, Leon-Velarde F, Rivera-Chira M, Kiyamu M, Brutsaert TD, Dolinoy DC, Bigham AW. Genome-Wide Epigenetic Signatures of Adaptive Developmental Plasticity in the Andes. Genome Biol Evol 2020; 13:5981114. [PMID: 33185669 PMCID: PMC7859850 DOI: 10.1093/gbe/evaa239] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 01/03/2023] Open
Abstract
High-altitude adaptation is a classic example of natural selection operating on the human genome. Physiological and genetic adaptations have been documented in populations with a history of living at high altitude. However, the role of epigenetic gene regulation, including DNA methylation, in high-altitude adaptation is not well understood. We performed an epigenome-wide DNA methylation association study based on whole blood from 113 Peruvian Quechua with differential lifetime exposures to high altitude (>2,500) and recruited based on a migrant study design. We identified two significant differentially methylated positions (DMPs) and 62 differentially methylated regions (DMRs) associated with high-altitude developmental and lifelong exposure statuses. DMPs and DMRs were found in genes associated with hypoxia-inducible factor pathway, red blood cell production, blood pressure, and others. DMPs and DMRs associated with fractional exhaled nitric oxide also were identified. We found a significant association between EPAS1 methylation and EPAS1 SNP genotypes, suggesting that local genetic variation influences patterns of methylation. Our findings demonstrate that DNA methylation is associated with early developmental and lifelong high-altitude exposures among Peruvian Quechua as well as altitude-adaptive phenotypes. Together these findings suggest that epigenetic mechanisms might be involved in adaptive developmental plasticity to high altitude. Moreover, we show that local genetic variation is associated with DNA methylation levels, suggesting that methylation associated SNPs could be a potential avenue for research on genetic adaptation to hypoxia in Andeans.
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Affiliation(s)
- Ainash Childebayeva
- Department of Anthropology, University of Michigan.,Department of Environmental Health Sciences, School of Public Health, University of Michigan.,Department of Archaeogenetics, Max Planck Institute for the Study of Human History, Jena, Germany
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan
| | - Fabiola Leon-Velarde
- Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Rivera-Chira
- Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melisa Kiyamu
- Departamento de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan.,Department of Nutritional Sciences, School of Public Health, University of Michigan
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles
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Chang Y, He J, Tang J, Chen K, Wang Z, Xia Q, Li H. Investigation of the gene co-expression network and hub genes associated with acute mountain sickness. Hereditas 2020; 157:13. [PMID: 32299499 PMCID: PMC7164164 DOI: 10.1186/s41065-020-00127-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/24/2020] [Indexed: 12/21/2022] Open
Abstract
Background Acute mountain sickness has become a heavily researched topic in recent years. However, the genetic mechanism and effects have not been elucidated. Our goal is to construct a gene co-expression network to identify the key modules and hub genes associated with high altitude hypoxia. Results The GSE46480 dataset of rapidly transported healthy adults with acute mountain sickness was selected and analyzed by weighted gene co-expression network analysis (WGCNA) to construct a co-expression network. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the data set were carried out using Database for Annotation Visualization and Integrated Discovery (DAVID), and the hub genes were selected. We found that the turquoise module was most significantly correlated with acute mountain sickness. The functional enrichment analysis showed that the turquoise module was related to the apoptotic process, protein transport, and translation processes. The metabolic pathway analysis identified hsa03010:ribosome and hsa04144:endocytosis as the most important pathways in the turquoise module. Ten top 10 hub genes (MRPL3, PSMC6, AIMP1, HAT1, DPY30, ATP5L, COX7B, UQCRB, DPM1, and COMMD6) for acute mountain sickness were identified. Conclusion One module and 10 hub genes were identified, which were related to acute mountain sickness. The reference provided by this module may help to elucidate the mechanism of acute mountain sickness. In addition, the hub genes may be used in the future as a biomarker and therapeutic target for accurate diagnosis and treatment.
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Affiliation(s)
- Yue Chang
- Department of Hepatopancreatobiliary and Splenic Medicine, Characteristic Medical Center of People's Armed Police Force, Tianjin, 300162, China.,Tianjin Key Laboratory of Hepatopancreatic Fibrosis and Molecular Diagnosis and Treatment, Tianjin, 300162, China
| | - Jiange He
- Institute of Special War Trauma Emergency Technology, Characteristic Medical Center of People's Armed Police Force, 220 Chenglin Road, Hedong District, Tianjin, 300162, China
| | - Jiqiang Tang
- Department of Orthopaedics, Characteristic Medical Center of People's Armed Police Force, Tianjin, 300162, China
| | - Kai Chen
- Department of Hepatopancreatobiliary and Splenic Medicine, Characteristic Medical Center of People's Armed Police Force, Tianjin, 300162, China.,Tianjin Key Laboratory of Hepatopancreatic Fibrosis and Molecular Diagnosis and Treatment, Tianjin, 300162, China
| | - Zhenguo Wang
- Department of Hepatopancreatobiliary and Splenic Medicine, Characteristic Medical Center of People's Armed Police Force, Tianjin, 300162, China
| | - Qun Xia
- Institute of Special War Trauma Emergency Technology, Characteristic Medical Center of People's Armed Police Force, 220 Chenglin Road, Hedong District, Tianjin, 300162, China.
| | - Hai Li
- Tianjin Key Laboratory of Hepatopancreatic Fibrosis and Molecular Diagnosis and Treatment, Tianjin, 300162, China. .,Division of Gastroenterology and Hepatology, Tianjin Xiqing Hospital, No.403 Xiqing Road, Xiqing District, Tianjin, 300380, China.
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Cai W, Liu Z, Li G, Xiao P, Lv Q, Gong Y, Fan H, Hou S, Ding H. The effects of a graded increase in chronic hypoxia exposure duration on healthy rats at high-altitude. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1975-1991. [PMID: 31934020 PMCID: PMC6949644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 03/27/2019] [Indexed: 06/10/2023]
Abstract
To investigate the effects of chronic hypoxia exposure at high altitude on the formation of pulmonary edema in rats, we randomized rats into normoxic control groups and hypoxic 24, 48, and 72-hour exposure groups. In the hypoxic exposure group, the arterial blood gas, wet-dry weight ratio (W/D), lung tissue permeability index (LPI), bronchoalveolar lavage fluid (BALF) and plasma levels of the inflammatory factors were measured after continuous, chronic hypoxic exposure for a corresponding time, and the pathological changes in the lung tissue and the expression of tight junction-associated protein occludin were observed. We found that the contents of arterial blood gas, W/D, LPI, BALF and plasma IL-6, TNF-α, and IL-10 in the hypoxic exposure group were significantly different from the contents of arterial blood gas in the normoxic control group. H&E staining showed tissue effusion, a marked thickening of the pulmonary septum, interstitial inflammatory cells, and erythrocytic infiltration. Compared with the normoxic control group, the pulmonary edema score was significantly increased in the hypoxic 48-hour group. Toluidine blue staining showed that the mast cell count and degranulation rate were significantly increased in the hypoxic 48-hour and 72-hour groups, but massone staining showed no significant pulmonary interstitial fibrosis in the 4 groups. Occludin expression was significantly higher in the normoxic control group than it was in the hypoxic exposure group. These results indicated that different chronic hypoxic exposure durations at the plateau all caused high-altitude pulmonary edema in rats, but there was no significant difference in some indicators among the groups.
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Affiliation(s)
- Wei Cai
- Logistics University of Chinese People’s Armed Police ForcesTianjin, China
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
- Chinese People’s Armed Police Force (PAP) Medical CenterTianjin, China
| | - Ziquan Liu
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
| | - Guangzong Li
- Chinese People’s Armed Police Force (PAP) Medical CenterTianjin, China
| | - Peixin Xiao
- Hubei Provincial Corps Hospital, Chinese People’s Armed Police ForcesWuhan, China
| | - Qi Lv
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
| | - Yanhua Gong
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
| | - Haojun Fan
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
| | - Shike Hou
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
| | - Hui Ding
- School of Disaster Medical Research, Tianjin UniversityTianjin, China
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Luan F, Li M, Han K, Ma Q, Wang J, Qiu Y, Yu L, He X, Liu D, Lv H. Phenylethanoid glycosides of Phlomis younghusbandii Mukerjee ameliorate acute hypobaric hypoxia-induced brain impairment in rats. Mol Immunol 2019; 108:81-88. [DOI: 10.1016/j.molimm.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/25/2019] [Accepted: 02/03/2019] [Indexed: 12/29/2022]
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