Jiyeon Choi, Tongwu Zhang, Andrew Vu, Julien Ablain, Matthew M. Makowski et al.
Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes. Among these, we further characterize the locus encompassing the HIV-1 restriction gene, MX2 (Chr21q22.3), and validate a functional intronic variant, rs398206. rs398206 mediates the binding of the transcription factor, YY1, to increase MX2 levels, consistent with the cis-eQTL of MX2 in primary human melanocytes. Melanocyte-specific expression of human MX2 in a zebrafish model demonstrates accelerated melanoma formation in a BRAFV600E background. Our integrative approach streamlines GWAS follow-up studies and highlights a pleiotropic function of MX2 in melanoma susceptibility.
Jiyeon Choi, Tongwu Zhang, Andrew Vu, Julien Ablain, Matthew M. Makowski, Leandro M. Colli, Mai Xu, Rebecca C. Hennessey, Jinhu Yin, Harriet Rothschild, Cathrin Gräwe, Michael A. Kovacs, Karen M. Funderburk, Myriam Brossard, John Taylor, Bogdan Pasaniuc, Raj Chari, Stephen J. Chanock, Clive J. Hoggart, Florence Demenais, Jennifer H. Barrett, Matthew H. Law, Mark M. Iles, Kai Yu, Michiel Vermeulen, Leonard I. Zon, Kevin M. Brown. Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. 2020-06-01. https://doi.org/10.1038/s41467-020-16590-1
A two-library luciferase MPRA tested 145-bp reference, alternative, and scrambled sequences from 840 melanoma-associated variants in HEK293FT cells. Enhancer and promoter configurations were transfected in two biological replicates per library/configuration, with four enhancer replicates for Library1, and barcode RNA/DNA activity was quantified.
A two-library luciferase MPRA tested 145-bp reference, alternative, and scrambled sequences from 840 melanoma-associated variants in the UACC903 melanoma cell line. Enhancer and promoter configurations were transfected in two biological replicates per library/configuration, and barcode RNA/DNA activity was quantified.
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