| Literature DB >> 31417607 |
Steven Gazal1,2,3,4, Jose R Espinoza5, Frédéric Austerlitz6, Dominique Marchant7, Jose Luis Macarlupu8, Jorge Rodriguez5, Hugo Ju-Preciado8, Maria Rivera-Chira8, Olivier Hermine9,10, Fabiola Leon-Velarde8, Francisco C Villafuerte8, Jean-Paul Richalet7,10, Laurent Gouya10,11.
Abstract
Chronic mountain sickness (CMS) is a pathological condition resulting from chronic exposure to high-altitude hypoxia. While its prevalence is high in native Andeans (>10%), little is known about the genetic architecture of this disease. Here, we performed the largest genome-wide association study (GWAS) of CMS (166 CMS patients and 146 controls living at 4,380 m in Peru) to detect genetic variants associated with CMS. We highlighted four new candidate loci, including the first CMS-associated variant reaching GWAS statistical significance (rs7304081; P = 4.58 × 10-9). By looking at differentially expressed genes between CMS patients and controls around these four loci, we suggested AEBP2, CAST, and MCTP2 as candidate CMS causal genes. None of the candidate loci were under strong natural selection, consistent with the observation that CMS affects fitness mainly after the reproductive years. Overall, our results reveal new insights on the genetic architecture of CMS and do not provide evidence that CMS-associated variants are linked to a strong ongoing adaptation to high altitude.Entities:
Keywords: GWAS—genome-wide association study; Monge’s disease; chronic mountain sickness (CMS); high altitude adaptation; natural selection
Year: 2019 PMID: 31417607 PMCID: PMC6682665 DOI: 10.3389/fgene.2019.00690
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Clinical and physiological variables in chronic mountain sickness patients (CMS) and controls (CTRL).
| Variable |
| CMS | CTRL |
|
|---|---|---|---|---|
| Age (years) | 166/146 | 46.8 ± 13.4 | 43.0 ± 13.1 | NS |
| Body weight (kg) | 166/146 | 68.8 ± 9.2 | 64.9 ± 8.7 | 0.001 |
| Height (cm) | 166/146 | 162.6 ± 5.9 | 163.0 ± 5.9 | NS |
| Body mass index (kg/m2) | 166/146 | 26.1 ± 3.3 | 24.4 ± 2.7 | <0.001 |
| Hematocrit (%) | 166/146 | 67.2 ± 3.8 | 52.0 ± 3.2 | <0.001 |
| SpO2 (%) | 166/146 | 85.3 ± 5.2 | 89.7 ± 4.8 | <0.001 |
| Heart rate (b/min) | 165/144 | 72.1 ± 11.3 | 67.6 ± 9.2 | <0.001 |
| Systolic BP (mmHg) | 164/144 | 116.3 ± 15.2 | 115.4 ± 13.6 | NS |
| Diastolic BP (mmHg) | 164/144 | 76.9 ± 10.3 | 76.0 ± 10.1 | NS |
| CMS clinical score | 164/144 | 6.8 ± 3.6 | 2.2 ± 2.1 | <0.001 |
| RVH | 166/146 | 120 (72%) | 61 (42%) | <0.001 |
| Smoking habit (0–4 cig./day) | 141/100 | 26 (18%) | 21 (21%) | NS |
| Alcohol use | 141/101 | 64 (45%) | 52 (51%) | NS |
| Birth at high altitude | 165/146 | 157 (95%) | 136 (93%) | NS |
| Parents from high altitude | 166/146 | 159 (96%) | 138 (95%) | NS |
| Frequent trips to sea level | 140/101 | 77 (55%) | 72 (71%) | 0.009 |
| Past history of work in mine | 166/146 | 23 (14%) | 12 (8%) | NS |
| Physical well being | 94/56 | 6.2 ± 1.9 | 6.7 ± 2.0 | NS |
| Psychological/emotional well being | 94/55 | 6.6 ± 2.0 | 7.1 ± 1.8 | NS |
| Overall Quality of Life score | 94/55 | 68.8 ± 15.1 | 70.5 ± 12.7 | NS |
SpO2, arterial oxygen saturation; BP, blood pressure; RVH, right ventricular hypertrophy. Results presented are mean ± standard deviation or n (%). P values were computed using logistic regressions on 267 unrelated individuals (143 CMS and 124 controls), adjusting for batch effect for quantitative and qualitative variables. NS, non-significant.
Figure 1Genome-wide structure of Cerro de Pasco population. (A,B) Projection of the 312 individuals (small black points) on Human Genome Diversity (HGDP-CEPH) (color open points) and 1000G (color close points) panels. Peruvian from Lima (PEL) of the 1000G panel are represented with pink points. (C) Admixture proportions of European and Native American ancestries for the 312 individuals. These proportions were estimated from 21 Native American of HGDP-CEPH panel and 21 European from 1000G panel. Each vertical line represents an individual. (D) Mean European admixture proportions (and quantiles) in unrelated CMS patients and controls.
Figure 2Genome-wide association results. Dashed red line represents the discovery threshold for selection of candidate SNPs (P < 10−5).
Characteristics of main loci associated to chronic mountain sickness (CMS) disease.
| Variant | Chr | Position (hg19) | Alleles1 | OR [95% CI] |
| Nearest genes2 | Candidate gene3 |
|
|
|
|
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs75810402 | 5 | 96,747,224 |
| 3.57 [2.00; 7.69] | 7.37 × 10−6 |
| CAST | 0.96 | 0.87 | 0.96 | 0.33 | 0.29 |
| rs7832232 | 8 | 38,469,303 |
| 2.16 [1.56; 3.04] | 2.63 × 10−6 |
| – | 0.42 | 0.24 | 0.34 | 0.96 | 0.85 |
| rs7304081 | 12 | 19,561,543 |
| 2.52 [1.85; 3.48] | 4.58 × 10−9 |
|
| 0.57 | 0.34 | 0.44 | 0.99 | 0.94 |
| rs7168430 | 15 | 94,349,452 | G/ | 2.23 [1.57; 3.24] | 6.48 × 10−6 |
|
| 0.38 | 0.22 | 0.32 | 0.91 | 0.75 |
Chr, chromosome; OR, odd ratio of the minor allele; CI, confidence interval; P, P value; f, allele frequency of the risk allele; CMS, chronic mountain sickness patients; CTRL, controls; PEL, Peruvian from Lima; RIOK2, serine/threonine-protein kinase 2; LINC01340, long intergenic non-protein coding RNA 1340; CAST, calpastatin; RNF5P1, ring finger protein 5 pseudogene 1; TACC1, transforming acidic coiled-coil containing protein 1; PLEKHA5, pleckstrin homology domain containing A5; AEBP2, adipocyte enhancer-binding protein; RGMA, repulsive guidance molecule BMP co-receptor A; MCTP2, multiple C2 and transmembrane domain containing 2.
1risk/protective allele in our sample, ancestral allele in bold. 2the previous and following genes around the variant (none of the variants fall inside a gene); 3 candidate gene based on expression analyses.
Figure 3Gene expression in peripheral blood under hypoxia condition in CMS cases and controls around candidate loci. P values indicate the difference of level of expression in CMS cases (red) and controls (blue). Expression values were clustered into genotypes for representation purposes; note that for rs7304081, heterozygous genotypes AC were clustered with CC in controls and AA in cases.
Figure 4Cross-results of association signals with selection scans and admixture mapping. We compared GWAS signals with the iHS (A) and nSL (B) tests of recent positive selection and European admixture mapping (C).