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Molecular profiling of driver events in metastatic uveal melanoma

Journal article
Authors Joakim Karlsson
Lisa M Nilsson
Suman Mitra
Samuel Alsén
Ganesh V Shelke
Vasu R. Sah
Elin Forsberg
Ulrika Stierner
C. All-Eriksson
Berglind Osk Einarsdottir
Henrik Jespersen
Lars Ny
Per Lindnér
Erik Larsson
Roger Olofsson Bagge
Jonas A Nilsson
Published in Nature Communications
Volume 11
Issue 1
ISSN 2041-1723
Publication year 2020
Published at Institute of Clinical Sciences, Department of Oncology
Sahlgrenska Cancer Center
Institute of Biomedicine
Institute of Clinical Sciences
Language en
Links dx.doi.org/10.1038/s41467-020-15606...
Keywords BRCA1 associated ring domain protein 1, CD39 antigen, cyclin dependent kinase inhibitor 2A, hepatitis A virus cellular receptor 2, programmed death 1 receptor, allele, cell, gene expression, genetic analysis, genome, mutation, skin, tumor, animal cell, animal experiment, animal model, animal tissue, Article, controlled study, cryopreservation, DNA sequencing, down regulation, female, flow cytometry, gene dosage, gene knockdown, gene mutation, genotyping technique, HLA typing, human, human tissue, immunohistochemistry, liquid chromatography-mass spectrometry, metastasis, metastatic uvea melanoma, molecular fingerprinting, mouse, nonhuman, protein expression, protein protein interaction, proteomics, real time reverse transcription polymerase chain reaction, single cell RNA seq, transcriptomics, tumor associated leukocyte, tumor biopsy, upregulation, whole genome sequencing
Subject categories Cancer and Oncology

Abstract

Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease. © 2020, The Author(s).

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