Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations.

Abstract

PURPOSE:

Uveal melanomas (UM) are genetically simple tumors carrying few copy number alterations (CNA) and a low mutation burden, except in rare MBD4-deficient, hypermutated cases. The genomics of uveal melanoma metastatic progression has not been described. We assessed the genetic heterogeneity of primary and metastatic MBD4-proficient and -deficient uveal melanomas.Experimental Design: We prospectively collected 75 metastatic and 16 primary samples from 25 consecutive uveal melanoma patients, and performed whole-exome sequencing.

RESULTS:

MBD4-proficient uveal melanomas contained stable genomes at the nucleotide level, acquiring few new single nucleotide variants (SNVs; 16 vs. 13 in metastases and primary tumors, respectively), and no new driver mutation. Five CNAs were recurrently acquired in metastases (losses of 1p, 6q, gains of 1q, 8q, and isodisomy 3). In contrast, MBD4-deficient uveal melanomas carried more than 266 SNVs per sample, with high genetic heterogeneity and TP53, SMARCA4, and GNAS new driver mutations. SNVs in MBD4-deficient contexts were exploited to unveil the timeline of oncogenic events, revealing that metastatic clones arose early after tumor onset. Surprisingly, metastases were not enriched in monosomy 3, a previously defined metastatic risk genomic feature. Monosomy 3 was associated with shorter metastatic-free interval compared with disomy 3 rather than higher rate of relapse.

CONCLUSIONS:

MBD4-proficient uveal melanomas are stable at the nucleotide level, without new actionable alterations when metastatic. In contrast, MBD4 deficiency is associated with high genetic heterogeneity and acquisition of new driver mutations. Monosomy 3 is associated with time to relapse rather than rate of relapse, thus opening avenues for a new genetic prognostic classification of uveal melanomas.

• Authors: Manuel Rodrigues, Lenha Mobuchon, Alexandre Houy, Samar Alsafadi, Sylvain Baulande, Odette Mariani, Benjamin Marande, Khadija Ait Rais, Monique K Van der Kooij, Ellen Kapiteijn, Sieta Gassama, Sophie Gardrat, Raymond L Barnhill, Vincent Servois, Rémi Dendale, Marc Putterman, Sarah Tick, Sophie Piperno-Neumann, Nathalie Cassoux, Gaëlle Pierron, Joshua J Waterfall, Sergio Roman-Roman, Pascale Mariani, Marc-Henri Stern
• Journal: Clinical cancer research : an official journal of the American Association for Cancer Research (Clin Cancer Res) Vol. 25 Issue 18 Pg. 5513-5524 (09 15 2019) ISSN: 1557-3265 [Electronic] United States
• PMID: 31227496 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: ©2019 American Association for Cancer Research.

Chemical References

• Endodeoxyribonucleases
• MBD4 protein, human

Topics

• Adult
• Aged
• Alleles
• Combined Modality Therapy
• DNA Copy Number Variations
• Disease Progression
• Endodeoxyribonucleases (genetics)
• Female
• Genetic Association Studies
• Genetic Heterogeneity
• Genetic Variation
• Genotype
• Humans
• Kaplan-Meier Estimate
• Male
• Melanoma (genetics, mortality, pathology, therapy)
• Middle Aged
• Models, Biological
• Monosomy
• Mutation
• Neoplasm Metastasis
• Neoplasm Staging
• Prognosis
• Uveal Neoplasms (genetics, mortality, pathology, therapy)