Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type-specific regulatory landscape of human melanocytes, which give rise to melanoma but account for <5% of typical human skin biopsies, we performed an eQTL analysis in primary melanocyte cultures from 106 newborn males. We identified 597,335 cis-eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05). Melanocyte eQTLs differed considerably from those identified in the 44 GTEx tissue types, including skin. Over a third of melanocyte eGenes, including key genes in melanin synthesis pathways, were unique to melanocytes compared to those of GTEx skin tissues or TCGA melanomas. The melanocyte data set also identified trans-eQTLs, including those connecting a pigmentation-associated functional SNP with four genes, likely through cis-regulation of IRF4. Melanocyte eQTLs are enriched in cis-regulatory signatures found in melanocytes as well as in melanoma-associated variants identified through genome-wide association studies. Melanocyte eQTLs also colocalized with melanoma GWAS variants in five known loci. Finally, a transcriptome-wide association study using melanocyte eQTLs uncovered four novel susceptibility loci, where imputed expression levels of five genes (ZFP90, HEBP1, MSC, CBWD1, and RP11-383H13.1) were associated with melanoma at genome-wide significant P-values. Our data highlight the utility of lineage-specific eQTL resources for annotating GWAS findings, and present a robust database for genomic research of melanoma risk and melanocyte biology.

16Prior genome-wide association studies have identified a melanoma-associated locus on 17 chr1q42.1 that encompasses a ~100 kb region spanning the PARP1 gene. eQTL analysis in 18 multiple cell types of melanocytic lineage consistently demonstrated that the 1q42.1 melanoma 19 risk allele (rs3219090, G) is correlated with higher PARP1 levels. In silico fine-mapping and 20 functional validation identified a common intronic indel, rs144361550 (-/GGGCCC, r 2 =0.947 21 with rs3219090) as displaying allele-specific transcriptional activity. A proteomic screen 22 identified RECQL as binding to rs144361550 in an allele-preferential manner. In human primary 23 melanocytes, PARP1 promotes cell proliferation and rescues BRAF V600E -induced senescence 24 phenotypes in a PARylation-independent manner. PARP1 also transforms TERT-immortalized 25 melanocytes expressing BRAF V600E . PARP1-mediated senescence rescue is accompanied by 26 transcriptional activation of melanocyte lineage survival oncogene, MITF, highlighting a new role 27 of PARP1 in melanomagenesis. 28 29To date, genome-wide association studies (GWAS) have identified twenty common, 30 genome-wide significant melanoma susceptibility loci [1][2][3][4][5][6][7][8][9] , most of which do not appear to be 31 explained by protein-coding variants. A subset of these loci harbor known pigmentation genes 32 that mediate melanoma-associated phenotypes such as eye, hair, and skin color. While several 33 loci harbor genes implicated in cancer, evidence directly linking common risk variants within 34 most of these loci to altered function of specific genes is lacking. 35MacGregor and colleagues initially identified a melanoma risk locus tagged by 36 rs3219090 on chromosome band 1q42.1 in an Australian case-control study at a near genome-37 wide level of significance (P = 9.3 x 10 -8 , OR = 0.87, protective allele A) 8 . The association has 38 since been replicated by multiple other studies 3,10 , including most recently by a meta-analysis of 39 12,874 melanoma cases (rs1858550, P = 1.7 x 10 -13 ) 7 . Notably, the locus at 1q42.1 has also 40 been associated with melanoma survival 11 , where the melanoma risk allele correlates with 41 increased survival, an association that has since been replicated 12 . The region of association 42 spans from 226.52 Mb to 226.63 Mb (hg19) of chromosome 1, encompassing the entirety of the 43 poly(ADP-ribose) (PAR) polymerase-1 (PARP1) (OMIM: 173870) gene, and fine-mapping 44 suggests that the association is best explained by a single-SNP model 3 . 45While a number of other genes are located in the vicinity of the association peak, PARP1 46 has the most well-established role in cancer. PARP1 is best known for its role as a DNA repair 47 enzyme and genotoxic sensor that functions in base excision repair (BER), single-strand break 48 repair, and double-strand break repair , and appear to play a role in oncogene-induced senescence (OIS) 20,21 . 56Aside from DNA repair, PARP1 functions in regulating gene expression by modif...

Genetic alterations associated with prostate cancer (PCa) may be identified by sequencing metastatic tumor genomes to identify molecular markers at this lethal stage of disease. Previously, we characterized somatic alterations in metastatic tumors in the methylcytosine dioxygenase ten-eleven translocation 2 (TET2), which is altered in 5–15% of myeloid, kidney, colon and prostate cancers. Genome-wide association studies previously identified non-coding risk variants associated with PCa and melanoma. We performed fine-mapping of PCa risk across TET2 using genotypes from the PEGASUS case-control cohort and identified six new risk variants in introns 1 and 2. Oligonucleotides containing two risk variants were bound by the transcription factor octamer-binding protein 1 (Oct1/POU2F1) and TET2 and Oct1 expression were positively correlated in prostate tumors. TET2 is expressed in normal prostate tissue and reduced in a subset of tumors from the Cancer Genome Atlas (TCGA). Small interfering RNA (siRNA)-mediated TET2 knockdown (KD) increases LNCaP cell proliferation, migration, and wound healing, verifying loss drives a cancer phenotype. Endogenous TET2 bound the androgen receptor (AR) and AR-coactivator proteins in LNCaP cell extracts, and TET2 KD increases prostate-specific antigen (KLK3/PSA) expression. Published data reveal TET2 binding sites and hydroxymethylcytosine (hmC) proximal to KLK3. A gene co-expression network identified using TCGA prostate tumor RNA-sequencing identifies co-regulated cancer genes associated with 2-oxoglutarate (2-OG) and succinate metabolism, including TET2, lysine demethylase (KDM) KDM6A, BRCA1-associated BAP1, and citric acid cycle enzymes IDH1/2, SDHA/B, and FH. The co-expression signature is conserved across 31 TCGA cancers suggesting a putative role for TET2 as an energy sensor (of 2-OG) that modifies aspects of androgen-AR signaling. Decreased TET2 mRNA expression in TCGA PCa tumors is strongly associated with reduced patient survival indicating reduced expression in tumors maybe an informative biomarker of disease progression and perhaps metastatic disease.