Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor

Anne-Céline Derrien; Alexandre Houy; Olivier Ganier; Florent Dingli; Massih Ningarhari; Lenha Mobuchon; María Isabel Espejo Díaz; Damarys Loew; Nathalie Cassoux; Olivier Cussenot; Géraldine Cancel-Tassin; Raphael Margueron; Josselin Noirel; Jessica Zucman-Rossi; Manuel Rodrigues; Marc-Henri Stern

doi:10.1016/j.ajhg.2022.11.004

Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor

Am J Hum Genet. 2022 Dec 1;109(12):2196-2209. doi: 10.1016/j.ajhg.2022.11.004.

Authors

Anne-Céline Derrien¹, Alexandre Houy¹, Olivier Ganier¹, Florent Dingli², Massih Ningarhari³, Lenha Mobuchon¹, María Isabel Espejo Díaz¹, Damarys Loew², Nathalie Cassoux⁴, Olivier Cussenot⁵, Géraldine Cancel-Tassin⁶, Raphael Margueron⁷, Josselin Noirel⁸, Jessica Zucman-Rossi⁹, Manuel Rodrigues¹⁰, Marc-Henri Stern¹¹

Affiliations

¹ Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris 75005, France.
² Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France.
³ Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, 75006 Paris, France; Functional Genomics of Solid Tumors laboratory, Équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, 75006 Paris, France.
⁴ Department of Ocular Oncology, Institut Curie, Paris 75005, France; Factulty of Medicine, University of Paris Descartes, Paris 75005, France.
⁵ CeRePP, Tenon Hospital, Paris 75020, France; Sorbonne University, GRC n°5 Predictive Onco-Urology, AP-HP, Tenon Hospital, Paris 75020, France; University of Oxford, Nuffield Department of Surgical Sciences, Oxford, UK.
⁶ CeRePP, Tenon Hospital, Paris 75020, France; Sorbonne University, GRC n°5 Predictive Onco-Urology, AP-HP, Tenon Hospital, Paris 75020, France.
⁷ Institut Curie, PSL Research University, Sorbonne University, Inserm U934/ CNRS UMR3215, 26, rue d'Ulm, 75005 Paris, France.
⁸ Laboratoire GBCM (EA7528), CNAM, HESAM Université, Paris, France.
⁹ Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, 75006 Paris, France; Functional Genomics of Solid Tumors laboratory, Équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, 75006 Paris, France; Hôpital Européen Georges Pompidou, APHP, 75015, Paris, France.
¹⁰ Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris 75005, France; Institut Curie, PSL Research University, Department of Medical Oncology, Paris 75005, France.
¹¹ Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris 75005, France. Electronic address: [email protected].

Abstract

The TERT/CLPTM1L risk locus on chromosome 5p15.33 is a pleiotropic cancer risk locus in which multiple independent risk alleles have been identified, across well over ten cancer types. We previously conducted a genome-wide association study in uveal melanoma (UM), which uncovered a role for the TERT/CLPTM1L risk locus in this intraocular tumor and identified multiple highly correlated risk alleles. Aiming to unravel the biological mechanisms in UM of this locus, which contains a domain enriched in active chromatin marks and enhancer elements, we demonstrated the allele-specific enhancer activity of this risk region using reporter assays. In UM, we identified the functional variant rs452384, of which the C risk allele is associated with higher gene expression, increased CLPTM1L expression in UM tumors, and a longer telomere length in peripheral blood mononuclear cells. Electrophoretic mobility shift assays and quantitative mass spectrometry identified NKX2.4 as an rs452384-T-specific binding protein, whereas GATA4 preferentially interacted with rs452384-C. Knockdown of NKX2.4 but not GATA4 resulted in increased TERT and CLPTM1L expression. In summary, the UM risk conferred by the 5p locus is at least partly due to rs452384, for which NKX2.4 presents strong differential binding activity and regulates CLPTM1L and TERT expression. Altogether, our work unraveled some of the complex regulatory mechanisms at the 5p15.33 susceptibility region in UM, and this might also shed light on shared mechanisms with other tumor types affected by this susceptibility region.

Keywords: TERT/CLPTM1L; cancer genetics; functional genomics; uveal melanoma.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Genome-Wide Association Study*
Humans
Leukocytes, Mononuclear
Melanoma
Uveal Neoplasms* / genetics

Supplementary concepts

Uveal melanoma