Analysis of variants induced by combined ex vivo irradiation and in vivo tumorigenesis suggests a role for the ZNF831 p.R1393Q mutation in cutaneous melanoma development

Dmitrii Usoltsev; Ching-Ni Njauw; Zhenyu Ji; Raj Kumar; Alexey Sergushichev; Selena Zhang; Eugene Shlyakhto; Mark J Daly; Mykyta Artomov; Hensin Tsao

doi:10.1016/j.jid.2024.08.042

Analysis of variants induced by combined ex vivo irradiation and in vivo tumorigenesis suggests a role for the ZNF831 p.R1393Q mutation in cutaneous melanoma development

J Invest Dermatol. 2024 Dec 13:S0022-202X(24)03015-X. doi: 10.1016/j.jid.2024.08.042. Online ahead of print.

Authors

Affiliations

¹ ITMO University, St. Petersburg, Russia, 197101; Almazov National Medical Research Center, St. Petersburg, Russia; Broad Institute, Cambridge, USA., 02140.
² Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA 02114; Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA 02114.
³ ITMO University, St. Petersburg, Russia, 197101.
⁴ Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA 02114.
⁵ Almazov National Medical Research Center, St. Petersburg, Russia.
⁶ Broad Institute, Cambridge, USA., 02140; Institute for Molecular Medicine, Helsinki, Finland, 00290; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA., 02114.
⁷ Broad Institute, Cambridge, USA., 02140; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA., 02114; The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA, 43205; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA, 43205. Electronic address: [email protected].
⁸ Broad Institute, Cambridge, USA., 02140; Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA 02114; Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA 02114. Electronic address: [email protected].

PMID: 39675662
DOI: 10.1016/j.jid.2024.08.042

Abstract

Ultraviolet (UV) radiation is known to be the most important environmental carcinogen for cutaneous melanoma. While genomic analyses of melanoma tumors implicate a high rate of UV damage, the experimental induction and recovery of bona fide UV-signature changes have not been directly observed. To replicate recurrent UV mutations from TCGA_SKCM specimens, we UV-irradiated cultured immortalized human melanocytes and subjected them to in vivo tumorigenesis assays. Exome sequencing of the xenografted tumors revealed an increase in UV-signature mutations within the tumors and identified 48 induced variants that overlap with TCGA skin cutaneous melanoma UV-hotspot mutations. A UV-induced mutation, ZNF831 p.R1393Q, was correlated with a decreased survival (HR: 5.44; 95% CI: 1.92-15.47, p=0.0015) and was preferentially observed in melanomas compared to all TCGA tumors (p=4.42x10^-7). Additionally, ZNF831 mRNA expression loss was strongly associated with decreased patient survival (HR=2.14, 95% CI: 1.62-2.83, p=7.91x10^-8), though the transcripts may arise from multiple cell types, including T cells. In multiple melanoma lines, overexpression of wildtype ZNF831 reduced spheroid growth, heightened apoptosis, and increased cell motility with the ZNF831 p.R1393Q variant partially or wholly abolishing these functional phenotypes. We thus experimentally recovered a "functional UV-hotspot mutation" in ZNF831 that is altered in human melanoma specimens.

Keywords: UV hotspot; ZNF831; melanoma; tumorigenesis.