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A genetic mechanism for Tibetan high-altitude adaptation


Tibetans do not exhibit increased hemoglobin concentration at high altitude. We describe a high-frequency missense mutation in the EGLN1 gene, which encodes prolyl hydroxylase 2 (PHD2), that contributes to this adaptive response. We show that a variant in EGLN1, c.[12C>G; 380G>C], contributes functionally to the Tibetan high-altitude phenotype. PHD2 triggers the degradation of hypoxia-inducible factors (HIFs), which mediate many physiological responses to hypoxia, including erythropoiesis. The PHD2 p.[Asp4Glu; Cys127Ser] variant exhibits a lower Km value for oxygen, suggesting that it promotes increased HIF degradation under hypoxic conditions. Whereas hypoxia stimulates the proliferation of wild-type erythroid progenitors, the proliferation of progenitors with the c.[12C>G; 380G>C] mutation in EGLN1 is significantly impaired under hypoxic culture conditions. We show that the c.[12C>G; 380G>C] mutation originated 8,000 years ago on the same haplotype previously associated with adaptation to high altitude. The c.[12C>G; 380G>C] mutation abrogates hypoxia-induced and HIF-mediated augmentation of erythropoiesis, which provides a molecular mechanism for the observed protection of Tibetans from polycythemia at high altitude.

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Figure 1: Genome-wide allele frequency differentiation between Tibetans, Mongolians and Europeans.
Figure 2: The p.[Asp4Glu; Cys127Ser] PHD2 mutant shows gain of function under hypoxia.
Figure 3: Erythroid colony (BFU-E) assays.
Figure 4: Hypoxia increases the proliferation of control BFU-E colonies but decreases that of colonies with the c.[12C>G; 380G>C] mutation in EGLN1.

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P.K. is supported by Academy of Finland grants 120156, 140765 and 218129, the S. Juselius Foundation, the Finnish Cultural Foundation and the Finnish Cancer Organizations. B.O. is supported by US National Institutes of Health (NIH) Mentored Career Development Award HL119355-01. J.X. is supported by the National Human Genome Research Institute (HG005846). G.R.-L. is supported by the National Basic Research Program of China (grant 2012CB518200) and by the Program of International Science and Technology Cooperation of China (grant 2011DFA32720). S.S. is supported by US NIH grant P01CA108671. T.S.S. is supported by the US NIH T32 Postdoctoral Fellowship HL098062. L.B.J. is supported by the University of Utah Seed Grant Program for studies of hypoxic adaptation. G.L.S. is supported by the Johns Hopkins Institute for Cell Engineering. J.T.P. is supported by US NIH grant P01CA108671, a Veterans Affairs Merit Review Award and the University of Utah Seed Grant Program for studies of hypoxic adaptation.

Author information




F.R.L. screened and discovered the PHD2 alteration, designed the experiment, performed expression studies and data analysis, and drafted and edited the manuscript. M.M. and P.K. performed the kinetic studies and wrote and edited the manuscript. C.H., J.X., T.S.S. and L.B.J. analyzed array data, characterized and estimated the origin of the variants and edited the manuscript. P.A.K. and G.R.-L. hosted F.R.L., T.T. and J.T.P. in their countries, assisted with the recruitment of subjects in India and China, and obtained necessary local regulatory and institutional review board documents. T.W. helped organize and assisted with the collection and phenotyping of samples from the Tibetan plateau. P.G. helped organize collection and assisted in the preparation and extraction of DNA in India. S.S. performed the erythroid colony assays, interpreted their results and edited the manuscript. M.E.S. performed the quantification of mean size and hemoglobinization of BFU-Es. A.W. designed and performed the statistical analysis of changes in BFU-E hypersensitivity to EPO. V.G. and D.A.M. critically revised the concept, contributed to the intellectual content and design, and gave final approval of the manuscript. G.L.S. critically revised the concept, contributed to the intellectual content and wrote the manuscript. B.O., W.G.K., E.L. and T.M.K. performed the knockdown study and edited the manuscript. J.T.P. conceived and designed the study, analyzed the data, and wrote and edited the manuscript.

Corresponding author

Correspondence to Josef T Prchal.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Genetic relationship between local Tibetans and other East Asian populations.

(A) Principal-components analysis. The first two principal components (PCs) are shown. Each individual is represented by one dot, and color corresponds to the population. The percentage of variance explained by each PC is shown on the axis. (b) Individual grouping inferred by ADMIXTURE. Results from k = 4 are shown. Each individual’s genome is represented by a vertical bar composed of colored sections, where each section represents the proportion of an individual’s ancestry derived from one of the k ancestral populations. Individuals are arrayed horizontally and grouped by population as indicated. JPT, Japanese; CHB, Chinese; Local Tibetan, Tibetans collected in this study. The two Local Tibetans who have the wild-type D4E variant (TU09 and TU12) are indicated in the plots.

Supplementary Figure 2 Analysis of purified wild-type PHD2 enzyme, the D4E and C127S single mutants, and the D4E and C127S double mutant.

Recombinant enzymes were expressed in insect cells and were affinity purified exploiting their C-terminal Flag tags in anti-Flag affinity gel columns. The near-to-homogeneity purified enzymes were analyzed by 10% SDS-PAGE followed by Coomassie Blue staining. Molecular weight markers (kDa) are shown on the left.

Supplementary Figure 3 Expression study of hypoxia and several HIF target genes.

(a) Expression of hypoxia-regulated genes in granulocytes from Tibetan (n = 4) versus control (n = 6) subjects. (b) BFU-E expression of selected HIF target genes in Tibetan (n = 1) versus control (n = 2) erythroid progenitors grown at optimal EPO levels (3,000 mU). Two independent experiments (technical replicates) from BFU-Es were pooled together and utilized the statistical randomization test using the Relative Expression Software Tool (REST, Qiagen). Error bars represent s.d.

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Supplementary Figures 1–3, Supplementary Tables 1–5 and Supplementary Note. (PDF 1555 kb)

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Lorenzo, F., Huff, C., Myllymäki, M. et al. A genetic mechanism for Tibetan high-altitude adaptation. Nat Genet 46, 951–956 (2014).

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