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Mapping of cis-acting expression quantitative trait loci in human scalp hair follicles.

ABSTRACT: BACKGROUND:The association of molecular phenotypes, such as gene transcript levels, with human common genetic variation can help to improve our understanding of interindividual variability of tissue-specific gene regulation and its implications for disease. METHODS:With the aim to capture the spectrum of biological processes affected by regulatory common genetic variants (minor allele frequency ? 1%) in healthy hair follicles (HFs) from scalp tissue, we performed a genome-wide mapping of cis-acting expression quantitative trait loci (eQTLs) in plucked HFs, and applied these eQTLs to help further explain genomic findings for hair-related traits. RESULTS:We report 374 high-confidence eQTLs found in occipital scalp tissue, whose associated genes (eGenes) showed enrichments for metabolic, mitotic and immune processes, as well as responses to steroid hormones. We were able to replicate 68 of these associations in a smaller, independent dataset, in either frontal and/or occipital scalp tissue. Furthermore, we found three genomic regions overlapping reported genetic loci for hair shape and hair color. We found evidence to confirm the contributions of PADI3 to human variation in hair traits and suggest a novel potential candidate gene within known loci for androgenetic alopecia. CONCLUSIONS:Our study shows that an array of basic cellular functions relevant for hair growth are genetically regulated within the HF, and can be applied to aid the interpretation of interindividual variability on hair traits, as well as genetic findings for common hair disorders.

SUBMITTER: Herrera-Rivero M

PROVIDER: S-EPMC7653834 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Mapping of cis-acting expression quantitative trait loci in human scalp hair follicles.

Herrera-Rivero Marisol M Hochfeld Lara M LM Sivalingam Sugirthan S Nöthen Markus M MM Heilmann-Heimbach Stefanie S

BMC dermatology 20201110 1

<h4>Background</h4>The association of molecular phenotypes, such as gene transcript levels, with human common genetic variation can help to improve our understanding of interindividual variability of tissue-specific gene regulation and its implications for disease.<h4>Methods</h4>With the aim to capture the spectrum of biological processes affected by regulatory common genetic variants (minor allele frequency ≥ 1%) in healthy hair follicles (HFs) from scalp tissue, we performed a genome-wide map ...[more]

PMID: 33167971

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Project description:BackgroundExpression quantitative trait loci (eQTL) have been identified using tissue or cell samples from diverse human populations, thus enhancing our understanding of regulation of gene expression. However, few studies have attempted to identify eQTL in racially admixed populations such as Hispanics.MethodsWe performed a systematic eQTL study to identify regulatory variants of gene expression in whole blood from 121 Puerto Rican children with (n = 63) and without (n = 58) asthma. Genome-wide genotyping was conducted using the Illumina Omni2.5M Bead Chip, and gene expression was assessed using the Illumina HT-12 microarray. After completing quality control, we performed a pair-wise genome analysis of ~15 K transcripts and ~1.3 M SNPs for both local and distal effects. This analysis was conducted under a regression framework adjusting for age, gender and principal components derived from both genotypic and mRNA data. We used a false discovery rate (FDR) approach to identify significant eQTL signals, which were next compared to top eQTL signals from existing eQTL databases. We then performed a pathway analysis for our top genes.ResultsWe identified 36,720 local pairs in 3,391 unique genes and 1,851 distal pairs in 446 unique genes at FDR <0.05, corresponding to unadjusted P values lower than 1.5x10-4 and 4.5x10-9, respectively. A significant proportion of genes identified in our study overlapped with those identified in previous studies. We also found an enrichment of disease-related genes in our eQTL list.ConclusionsWe present results from the first eQTL study in Puerto Rican children, who are members of a unique Hispanic cohort disproportionately affected with asthma, prematurity, obesity and other common diseases. Our study confirmed eQTL signals identified in other ethnic groups, while also detecting additional eQTLs unique to our study population. The identified eQTLs will help prioritize findings from future genome-wide association studies in Puerto Ricans.

Dataset Information

Mapping of cis-acting expression quantitative trait loci in human scalp hair follicles.

Publications

Mapping of cis-acting expression quantitative trait loci in human scalp hair follicles.

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