EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda

Abstract

It is being realized that identification of subgroups within normal controls corresponding to contrasting disease susceptibility is likely to lead to more effective predictive marker discovery. We have previously used the Ayurvedic concept of Prakriti, which relates to phenotypic differences in normal individuals, including response to external environment as well as susceptibility to diseases, to explore molecular differences between three contrasting Prakriti types: Vata, Pitta, and Kapha. EGLN1 was one among 251 differentially expressed genes between the Prakriti types. In the present study, we report a link between high-altitude adaptation and common variations rs479200 (C/T) and rs480902 (T/C) in the EGLN1 gene. Furthermore, the TT genotype of rs479200, which was more frequent in Kapha types and correlated with higher expression of EGLN1, was associated with patients suffering from high-altitude pulmonary edema, whereas it was present at a significantly lower frequency in Pitta and nearly absent in natives of high altitude. Analysis of Human Genome Diversity Panel-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) and Indian Genome Variation Consortium panels showed that disparate genetic lineages at high altitudes share the same ancestral allele (T) of rs480902 that is overrepresented in Pitta and positively correlated with altitude globally (P < 0.001), including in India. Thus, EGLN1 polymorphisms are associated with high-altitude adaptation, and a genotype rare in highlanders but overrepresented in a subgroup of normal lowlanders discernable by Ayurveda may confer increased risk for high-altitude pulmonary edema.

Fig. 1.

Representation of allele frequencies of common variations among extreme constitution types. A representative set of SNPs that shows significant difference between the constitution types Kapha (K), Pitta (P), Vata (V), and differences from the V, P, and K/IE pool are depicted. The gene and SNP with the alleles are given in each panel. IE represents individuals with heterogeneous phenotypes from Indo-European populations, and V, P, and K represent individuals of different constitution types pooled into a single group.

Fig. 2.

Distribution of T allele frequency of rs480902 in diverse IGVC and HGDP-CEPH populations from different altitudes. (A) Frequency in the 24 IGV populations and their altitude. (B) Spatial frequency map of rs480902 in IGV populations. The color gradient below the map depicts the range of observed frequency of the T allele from minimum to maximum. (C) Frequency distribution in the HGDP-CEPH panel of 52 populations along with their altitudes. Diverse continental populations residing at high altitudes selectively retain the ancestral T allele.

Fig. 3.

Allele frequency distribution of rs480902 in HGDP-CEPH populations. (A) Correlation of T allele frequency of rs480902 with increasing altitude (R² = 0.1056) in HGDP-CEPH populations. (B) Spatial frequency map of rs480902 in the HGDP-CEPH populations retrieved from the HGDP selection browser. Frequencies of the ancestral T allele that is predominantly present in populations residing at high altitude and the derived C allele are represented by dark and light shades, respectively.

Fig. 4.

Correlation between EGLN1 genotypes of rs479200 and expression and the association of TT genotype and the T allele with HAPE. (A) Box plot representing ΔCT values of gene expression of EGLN1 by RT-PCR in TT, TC, and CC genotypes of rs479200 in Ayurveda samples. (B) Frequency of TT genotype of rs479200 in different constitution types (K, P, and V), VPK, IE, natives of high altitude, and patients of HAPE. (C) Frequency of T allele of rs479200 in different constitution types (K, P, and V), VPK, IE, natives of high altitude, and patients of HAPE. Fisher's exact test was performed for association analysis of EGLN1 SNP rs479200 between different controls and HAPE. The numbers over each of the bars represent the P values of comparison of each group with HAPE.