In Vivo Genetic Screens of Patient-Derived Tumors Revealed Unexpected Frailty of the Transformed Phenotype.

Abstract

UNLABELLED:

The identification of genes maintaining cancer growth is critical to our understanding of tumorigenesis. We report the first in vivo genetic screen of patient-derived tumors, using metastatic melanomas and targeting 236 chromatin genes by expression of specific shRNA libraries. Our screens revealed unprecedented numerosity of genes indispensable for tumor growth (∼50% of tested genes) and unexpected functional heterogeneity among patients (<15% in common). Notably, these genes were not activated by somatic mutations in the same patients and are therefore distinguished from mutated cancer driver genes. We analyzed underlying molecular mechanisms of one of the identified genes, the Histone-lysine N-methyltransferase KMT2D, and showed that it promotes tumorigenesis by dysregulating a subset of transcriptional enhancers and target genes involved in cell migration. The assembly of enhancer genomic patterns by activated KMT2D was highly patient-specific, regardless of the identity of transcriptional targets, suggesting that KMT2D might be activated by distinct upstream signaling pathways.

SIGNIFICANCE:

Drug targeting of biologically relevant cancer-associated mutations is considered a critical strategy to control cancer growth. Our functional in vivo genetic screens of patient-derived tumors showed unprecedented numerosity and interpatient heterogeneity of genes that are essential for tumor growth, but not mutated, suggesting that multiple, patient-specific signaling pathways are activated in tumors. Cancer Discov; 6(6); 650-63. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 561.

• Authors: Daniela Bossi, Angelo Cicalese, Gaetano I Dellino, Lucilla Luzi, Laura Riva, Carolina D'Alesio, Giuseppe R Diaferia, Alessandro Carugo, Elena Cavallaro, Rossana Piccioni, Massimo Barberis, Giovanni Mazzarol, Alessandro Testori, Simona Punzi, Isabella Pallavicini, Giulio Tosti, Luciano Giacó, Giorgio Melloni, Timothy P Heffernan, Gioacchino Natoli, Giulio F Draetta, Saverio Minucci, PierGiuseppe Pelicci, Luisa Lanfrancone
• Journal: Cancer discovery (Cancer Discov) Vol. 6 Issue 6 Pg. 650-63 (06 2016) ISSN: 2159-8290 [Electronic] United States
• PMID: 27179036 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: ©2016 American Association for Cancer Research.

Chemical References

• DNA-Binding Proteins
• KMT2D protein, human
• Membrane Proteins
• Neoplasm Proteins
• RNA, Small Interfering
• GTP Phosphohydrolases
• NRAS protein, human

Topics

• Animals
• Cell Line, Tumor
• Cell Transformation, Neoplastic (genetics)
• Chromatin Immunoprecipitation
• Computational Biology (methods)
• DNA-Binding Proteins (metabolism)
• Disease Models, Animal
• Enhancer Elements, Genetic
• Epigenesis, Genetic
• Epigenomics (methods)
• GTP Phosphohydrolases (genetics, metabolism)
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Genetic Association Studies
• Genetic Predisposition to Disease
• Genetic Testing
• Heterografts
• High-Throughput Nucleotide Sequencing
• Humans
• Male
• Membrane Proteins (genetics, metabolism)
• Mice
• Neoplasm Metastasis
• Neoplasm Proteins (metabolism)
• Neoplasms (diagnosis, genetics)
• Phenotype
• Protein Binding
• RNA, Small Interfering (genetics)
• Reproducibility of Results