New Hypoxia Response Genes Are Involved In Tibetan High-altitude Adaptation By A Genome-wide Allelic Differentiation Scanning

Objective:Native Tibetans have a very strong ability to adapt to high-altitude hypoxiaenvironment, which has been demonstrated to be high heritability. Genome-wide scanis a reliable method for finding genetic disease/trait susceptibility loci. Previousstudies have found several candidate genes of high-altitude adaptation. Although anumber of studies suggested that HIF (Hypoxia inducible factor) related genes (suchas: EPAS1, EGLN1) were involved in the Tibetan high-altitude adaptation, thehypoxia response related pathways for the evolutionary adaptation process still needto be systematically evaluated.Methods:(1) SNP-MaP (SNP microarrays and pooling) analysis:300high-altitude (>4,500m) Tibetans and300low-altitude (<2,500m) Han Chinese were collected andtheir genomic DNA was extracted, then the DNA was mixed with an equal amount ofeach test subgroup to construct Tibetan and Han DNA mixed pools, using SNP chip toconduct a high-density SNPs hybridization, and calculate SNPs allelic frequency ofthe two groups to determine whether they are significant differences.⑵Tibetan/Hanpopulation data set integration: the Tibetan data of Simonson and Yi were download,using the CHB of HapMap and1000Genomes as a control for conducting anassociation analysis.(3) Functional annotation: the positive loci were mapped to agene and the candidate genes that are involved in the Tibetan high-altitude adaptationwere annotated and the biological pathways and altitude adaptation characteristics(p<10-2) involved in the high-altitude adaptation were analyzed by GSEA. Finally, agene-pathway-gene interaction network was constructed by combining selectedpositive pathways and hypoxia response related pathways.Result:(1)Quality control: By using high-throughput chip hybridization, we got twoalleles hybridization signal intensity value of SNPs sites, and through a QC, we foundthat there were862,411qualified autosomal region SNPs, the correlation between any two of three parallel experimental of Tibetan (Han) groups is greater than0.97,suggesting that chip technology has a high repeatability.⑵Candidate genes: thesignals of the differences in SNPs of EPAS1region were the strongest across thegenome in Han and Tibetan; a total49candidate genes were significantly different bythe SNP-MaP analysis and were confirmed in Simonson or Yi’s Tibet data set,Furthermore five genes which have hypoxia functional annotation, are EPAS1(rs13003074, p=2.16E-42)、IL10(rs4579758, p=5.54E-23)、SLC8A1(rs2160777,p=3.54E-18)、 EGLN1(rs2244986, p=7.75E-17) and PIK3R1(rs13156223,p=2.58E-09), respectively. However, the candidate genes which have been found toinvolved in high-altitude illness in previous studies have not been verified in thisstudy.⑶Pathway analysis: there is a significant difference in the pathways which arerelated with HIF(GO:0097411), energy metabolism, hematopoietic, iron ion balance,cell growth, nervous and immune between Han and Tibetan groups.Conclusion:In the present study, we are not only confirmed that EPAS1and EGLN1areassociated with Tibetan high-altitude adaptation, but also found that the IL10,SLC8A1and PIK3R1may be the new potential candidate genes. Alternation of HIFsignaling pathway could be the basis of high-altitude hypoxia adaptation, in which itplays an important role in erythropoiesis, angiogenesis and systolic and diastolic,energy metabolism and so on, and, it may promote Tibetans to adapt to high-altitudehypoxia environment.