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A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF

Abstract

Previous genome-wide association studies have identified a melanoma-associated locus at 1q42.1 that encompasses a 100-kb region spanning the PARP1 gene. Expression quantitative trait locus (eQTL) analysis in multiple cell types of the melanocytic lineage consistently demonstrated that the 1q42.1 melanoma risk allele (rs3219090[G]) is correlated with higher PARP1 levels. In silico fine-mapping and functional validation identified a common intronic indel, rs144361550 (−/GGGCCC; r2 = 0.947 with rs3219090), as displaying allele-specific transcriptional activity. A proteomic screen identified RECQL as binding to rs144361550 in an allele-preferential manner. In human primary melanocytes, PARP1 promoted cell proliferation and rescued BRAFV600E-induced senescence phenotypes in a PARylation-independent manner. PARP1 also transformed TERT-immortalized melanocytes expressing BRAFV600E. PARP1-mediated senescence rescue was accompanied by transcriptional activation of the melanocyte-lineage survival oncogene MITF, highlighting a new role for PARP1 in melanomagenesis.

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Figure 1: The melanoma risk-associated G allele at rs3219090 is correlated with increased PARP1 expression.
Figure 2: Functional annotation of a 3-kb region encompassing rs144361550 in primary melanocytes.
Figure 3: The melanoma-associated indel rs144361550 drives allelic transcriptional activity and protein binding.
Figure 4: RECQL binds to the insertion allele and mediates allelic expression.
Figure 5: Cell growth and H3K9me3 focus formation in primary human melanocytes expressing PARP1 and BRAFV600E.
Figure 6: MITF expression is restored in primary human melanocytes coexpressing PARP1 and BRAFV600E in a PARylation-independent manner, concurrent with partial reversal of senescence phenotypes.
Figure 7: PARP1 binds to the MITF-M promoter.

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Acknowledgements

The results appearing here are in part based on data generated by the TCGA Research Network (http://cancergenome.nih.gov/). Data were also obtained from the GTEx Portal on 2 December 2015 or dbGaP accession phs000424.v6.p1 on 17 December 2015. We would like to thank H. Widlund (Brigham and Women's Hospital, Harvard Medical School) for providing p'mel cells and technical assistance, D. Fisher (Dana-Farber/Harvard Cancer Center) for providing luciferase construct pMITF-382 and experimental advice, W. Pavan (National Human Genome Research Institute, National Institutes of Health) for providing luciferase construct pMITF-2256, M. Herlyn (Wistar Institute) for providing pLU-TCMV-FMCS-pPURO vector, G. Jönsson (Lund University) for assistance with assessment of MITF methylation, the Arizona State University DNA Laboratory, C. Hautman, C. Dagnall, K. Jones, and C. Chung at the National Cancer Institute Cancer Genomics Research Laboratory (CGR), D. Peeper (Netherlands Cancer Institute) for providing the lentiviral expression vector for BRAFV600E constructs, M. Webster and A. Weeraratna at the Wistar Institute Melanoma Research Center, S. Chanock, M. Dean, L. Amundadottir, J. Hoskins, L. Colli, A. Vu, and C. Lee from the National Cancer Institute, Laboratory of Translational Genomics, and D. Youngkin (Translational Genomics Research Institute). This work has been supported by the Intramural Research Program (IRP) of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US government. S.M. was supported by an Australian Research Council Future Fellowship, and N.K.H. was supported by a fellowship from the National Health and Medical Research Council of Australia. M.V. was supported by the Netherlands Organization for Scientific Research (NWO Gravitation Program Cancer Genomics Netherlands). M.M.M. was supported by a grant from the Marie Curie Initial Training Network (ITN) DevCom (FP7, grant 607142). M.M.I., J.A.N.-B., and D.T.B. were supported by the CRUK programme (c588/A19167) and the National Cancer Institute, National Institutes of Health (R01 CA083115). We would like to thank the GenoMEL consortium for its contributions.

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J.C., M.X., and K.M.B. designed the study. J.C., M.M.M., M.A.K., and W.J.K. conducted experiments for molecular characterization of PARP1 risk variants. M.X. performed phenotypic analyses of PARP1 in primary and immortalized melanocytes. Proteomics analysis was conducted by M.M.M. and M.V. In vitro biophysical analysis of DNA structures was performed by A.G. and M.-P.T.-F. Data were analyzed by T.Z., M.H.L., H.P., and M.M.I. Fine-mapping of GWAS data was performed by M.M.I., D.T.B., J.A.N.-B., S.M., and M.H.L. Melanoma cell line eQTL and ASE experiments were performed by K.M.B., N.K.H., J.M.T., M.G., and J.C. The manuscript was written by J.C., M.X., and K.M.B.

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Correspondence to Kevin M Brown.

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Supplementary Figures 1–26, Supplementary Tables 1–7 and 9–14, and Supplementary Note. (PDF 23584 kb)

Supplementary Table 8

rs144361550 genotype of HapMap CEU individuals by fragment analysis. (XLSX 29 kb)

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Choi, J., Xu, M., Makowski, M. et al. A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF. Nat Genet 49, 1326–1335 (2017). https://doi.org/10.1038/ng.3927

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