Cancer Discov. 2016 Jul;6(7):714-26. doi: 10.1158/2159-8290.CD-16-0160. Epub 2016 May 4.

Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles.

Kim E¹, Ilic N¹, Shrestha Y², Zou L³, Kamburov A³, Zhu C², Yang X², Lubonja R², Tran N², Nguyen C², Lawrence MS², Piccioni F², Bagul M², Doench JG², Chouinard CR², Wu X², Hogstrom L², Natoli T², Tamayo P⁴, Horn H⁵, Corsello SM¹, Lage K⁵, Root DE², Subramanian A², Golub TR⁶, Getz G³, Boehm JS², Hahn WC⁷.

Author information

1: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
2: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
3: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
4: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medicine, University of California, San Diego, La Jolla, California.
5: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts.
6: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
7: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. william_hahn@dfci.harvard.edu.

Abstract

Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies.

SIGNIFICANCE:

Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.