Silva Lab Research Summary

The interest of our group is focused on understanding the molecular mechanisms that promote breast carcinogenesis with the ultimate goal to identify novel targets from “personalized therapies”.

We have pioneered RNAi-based genetic approaches to facilitate genome-wide loss of function studies in mammalian systems. This strategy represents a unique opportunity to functionally interrogate the entire genome in an unbiased way. By applying this state-of-the-art technology in combination with genomics, biochemical as well as mouse models we are involved in three major projects. These projects aim to answer general questions such as identification and characterization of novel breast cancer relevant genes and also more focused studies to understand the effect of actin dynamics in epithelial tumorigenesis. 

-Identification of novel breast cancer tumor suppressor: We have recently completed and are currently expanding a series of genome-wide RNAi screens in-vitro to uncover genes that, upon silencing, induce tumor associated characteristics. From these screens, several hits are emerging as putative tumor suppressors. We have selected the most promising candidates and we are characterizing their function, studying the mechanisms that inactivate these genes in primary tumors and translating our findings to in-vivo models.    

-Uncovering Genetic Synthetic Lethal Interactions with Bona-Fide breast cancer genes: Cancer therapy is rapidly evolving toward personalized treatments. Novel therapies, based on the specific molecular alterations present in each individual tumor, are emerging as more efficient and less harmful approach than classical treatments. Genetic synthetic lethal interactions are defined as two alterations that are innocuous individually but in combination cause cell death or reduced fitness. Although this process has been widely applied in yeast to dissect cellular pathways, its use in mammals has been very limited, mainly because of the lack of the proper genetic tools. Recently, RNA interference (RNAi) technology has eliminated this handicap. In this project we are taking advantage of our RNAi technology to identify genes that, when silenced, exclusively reduce the viability of breast cancer cells that carry preexistent genetic alterations in ErbB2, c-Myc, Cyclin D1 or RB without affecting normal cells.

-Study the role of actin dynamics in epithelial tumorigenesis: Uncontrolled proliferation and resistance to stress stimuli are hallmarks of cancers; however, they are not the only ones. In epithelial cancers, tumor progression is also characterized by the acquisition of invasion and metastatic abilities. Recently we have identified Cyfip1, a subunit of the WAVE complex that regulates actin dynamics, as a putative suppressor of invasion. Through high-resolution genomic analysis we have found that Cyfip1 gene is commonly deleted in epithelial tumors. Suppression of Cyfip1 expression disturbed normal epithelial morphogenesis in vitro and cooperated with oncogenic stimuli to produce invasive carcinomas in vivo. Moreover, reduced expression of Cyfip1 is commonly observed during invasion of epithelial tumors. Currently, we are characterizing in detail the defects in cell adhesion induced by loss of Wave function, studying the effects on cell motility and exploring the function and regulation of the WAVE-complex during EMT-like processes.

Selected Publications

Research articles:

1.- Silva JM, Ezhkova E, Silva J, Bonilla F, Powers S, Fuchs E, Hannon GJ. Cell. 2009 Jun 12;137(6):1047-61. CYFIP1 is an invasion suppressor in epithelial cancers.

2.- Silva JM, Parker J, Marran K, Silva J, Chang K, Hannon GJ. Highly parallel RNAi identify proliferative and survival signals of genetically distinct cell lines. Science. 2008 Feb 1;319(5863):617-20.

3.- Silva JM, Li M, Chang K et al. Second-generation shRNA libraries to the mouse and human genome. Nat. Genet. 2005 Nov;37(11):1281-8.

4.- Paddison PJ, Cleary M, Silva JM, et al. ‘Cloning of short hairpin RNAs for gene knockdown in mammalian cells’. Nature Methods. 2004. 1:163-7.

5.- Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ. RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6548-52.

6.- Paddison PJ, Silva JM^*(*Coauthor), Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ. A resource for large-scale RNA-interference-based screens in mammals. Nature. 2004 Mar 25;428(6981):427-31.

7.- Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH. A micrococcal nuclease homologue in RNAi effector complexes. Nature. 2003 Sep 25;425(6956):411-4.

Review Articles:

1.- Silva J, Chang K, Hannon G, Rivas F. Oncogene. 2004. 23(51): 8401-9. ‘RNA-interference-based functional genomics in mammalian cells: Reverse genetics coming of age.

2.- Silva JM, Sachidanandam R, Hannon GJ. Nat Genet. 2003 Dec;35(4):303-5. Free energy lights the path toward more effective RNAi.

3.- Silva JM, Hammond SM, Hannon GJ. Trends Mol Med. 2002 Nov;8(11):505-8. RNA interference: a promising approach to antiviral therapy?