Research Faculty

Irving Cancer Research Center
Room 403
1130 St. Nicholas Ave
New York, NY 10032

Phone: 212-851-4752
Jose M. Silva, Ph.D.
Assistant Professor of Pathology & Cell Biology
Research Summary

The overall interest of my group is focused on understanding the molecular mechanisms that regulate mammary development and tumor progression in breast cancers with the ultimate goal to identify novel targets for “Patient oriented therapies”.

During the past years, we have concentrated our efforts in three specific research areas related with our primary interest and with collaborations:

• Primary Research
-MiRNAs that regulates the development of the mammary gland epithelium and their contribution to tumorigenesis.
-Identify and characterize the genetic fingerprint of breast cancers (tumor suppressors and oncogenes).
-Genome-wide synthetic lethality studies to identify novel breast cancer targets (oncogene and non-oncogene addiction hubs).

• Collaborations
-Unveiling the regulatory networks that control tumor inciting/cancer stem cell fate and how it relates to normal development

The mammary gland is a very dynamic organ that undergoes continuous remodeling. The critical regulators of this process are not fully understood. We have identified the microRNA cluster miR-424(322)/503 as an important regulator of epithelial involution after pregnancy. Through the generation of a knock-out mouse model, we found that regression of the secretory acini of the mammary gland was compromised in the absence of miR-424(322)/503. Remarkably, we have found that this miRNA cluster is deleted in breast cancers and that its deletion induces tumor formation in mice. This data suggest the miR-424((322)/503 as a novel breast cancer miRNA with a tumor suppressor role. Mechanistically, we show that miR-424(322)/503 orchestrates cell life and death decisions by targeting CDC25A, BCL-2 and IGF1R. Furthermore, we demonstrate that the expression of this miR-cluster is regulated by TGF-β, a well characterized regulator of mammary involution. Overall, our data unveil a previously unknown, multilayered-regulation of epithelial tissue remodeling coordinated by the microRNA cluster miR-424(322)/503 (Dev.Cell, under final review.

-Identify and characterize the genetic fingerprint of breast cancers (tumor suppressors and oncogenes).

We have recently identified and characterized one novel breast cancer tumor suppressor (Bin3) and a novel oncogene (RSF1).
- A genome wide shRNA screen designed to find genes that promote hallmarks of epithelial cancers combined with a novel algorithm to analyze copy number alterations identified Bin3 as the top tumor suppressor candidate in the chromosomal region 8p21, which is deleted in almost half of all breast cancers. We demonstrate that loss of expression of Bin3 enhances primary tumor growth and promotes metastasis. In contrast, restoration of Bin3 reduces primary tumor burden and reduces metastatic potential of breast cancer cells. Mechanistically we linked its tumor suppression function to its ability to relocate to the membrane and to activate the stress sensor protein P38-α during anoikis. Furthermore, we identified CDC42 as a critical factor to transduce the loss-of-attachment signal from BIN3 to P38-α. Our results present, for the first time, Bin3 as a novel breast cancer tumors suppressor and provides novel clues about how breast cancer cells escape anoikis. (Nature, submitted).

- RSF1 was identified through an integrative approach that combines genome-wide RNAi screens as well as CNV and mutational genomic analysis with the ultimate goal to identify oncogene addiction hubs. RSF1 was found to be amplified and overexpressed in half of the highly aggressive luminal-B subtype of breast cancer. Importantly, attenuation of RSF1 compromised tumor cell growth and inhibited metastasis formation. Mechanistically, we have found that RSF1modulate a stem cell transcriptional program that is necessary for tumor progression. Furthermore, we have found out that RSF1 is genetically linked to the Bona-Fide oncogene and cell cycle regulator CCND1and that the co-amplification of RSF1 and CCND1 defines a group of breast cancer patients (about ¼) with poor clinicopathological characteristics and reduced survival. (submitted Cell).

-Genome-wide functional genomics studies to identify novel tumor targets (oncogene and non-oncogene addiction hubs).
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 approaches than classical treatments.
Recently, by combining genome-wide RNAi loss-of-function screens with system biology interactome models we have found that the JAK/STAT3 pathway is activated in ERBB2+ breast tumors. Activation of STAT3 was found to be essential to maintain the homeostasis of tumor cells. Mechanistically, we discovered that cancer cells transformed by ERBB2 produce high levels of IL-6 and upregulate its bona-fide receptor IL6R. Secretion of this interleukin generates an autocrine loop that induces the phosphorylation of STAT3 (activation) through the canonical Jak/Stat pathway. Activated STAT3 initiates a transcriptional program that upregulates the S100A8/9 complex (calprotectin). Notably, this complex is secreted and activates a second autocrine loop that involves the Toll-like receptor 4 (TLR-4) and leads to higher activation levels of the proliferation and pro-survival signaling proteins ERK1/2 and AKT.
Importantly, small molecule inhibitors of JAK (ruxolutinib, FDA approved for Myelofibrosis) and S100A9 (tasquinimod in phase II clinical trials for prostate cancer), as well as antibodies against IL-6 (tocilizumab, FDA approved for rheumatic diseases), are already available for testing. We have recently completed preclinical animal studies using ruxolutinib, in which we observed a strong anti-tumor effect in ERBB2+ tumors. Furthermore, we also revealed a significant additive effect when trastuzumab and ruxolutinib were used in combination. Currently, we are translating our findings to the clinic and we have started a phase-II clinical trial to test the efficacy of Ruxolutinib in metastatic ERBB2+ breast cancer patients that have become refractory to standard therapy (manuscript in preparation for Cancer Cell).

• Research Collaborations

Despite breast cancer biology being the main interest of my laboratory we have pioneered the development of RNAi technologies that allow us the functional study of the entire genome at the same time (Cell. 2009 Jun 12;137(6):1047-6; Science. 2008 Feb 1;319(5863):617-20). This technology has fostered a large number of collaborations with other laboratories in multiple institutions.

Below I am describing one of the most productive research areas of collaboration.

-Unveil the regulatory networks that control tumor inciting/cancer stem cell fate and how it relates to normal development.

Modern cancer biology has made evident the tight connections that exist between key developmental processes and cancer. We are collaborating with several groups to understand at a molecular level the relationship between cancer and normal stem cells by using a diverse array of in vitro and in vivo models (adult epidermal stem cells, prostate cancers, germ cell tumors, glioblastoma and breast cancers).
These studies have uncover the essential role that the polycomb-complex has on the fate of adult epidermal stem cells (Genes Dev. 2011 Mar 1;25(5):485-98) and how the absence of H3-K27 trimethylation at a specific loci affects Merkel cell lineage commitment and impact Merkel cell cancer development (EMBO J. 2013 Jul 17;32(14):1990-2000).
In prostate cancers, our studies have uncovered that resistance to standard chemotherapy is mediated by a small population of cells with tumor initiating characteristics. Importantly, these cells depend on the activation of Notch and Hedgehog signaling to maintain the resistant phenotype. This finding has open new possibilities for treating prostate tumors that have become refractory to standard chemotherapy with a combination of chemotherapy plus Notch and Hedgehog inhibitors (Cancer Cell. 2012 Sep 11;22(3):373-88).
Finally, by combining the state-of-the-art computational interactome models with RNA-interference screening we have completed a comprehensive study of functionally-validated novel regulatory modules controlling pluripotency. Our data challenges the original assumption that the pluripotent cell state may be determined by a handful of on/off genetic switches and instead supports the view that pluripotency control is distributed across many distinct regulators, with shared functional programs (Cell, under review).
Selected Publications

Andrew Varble, Asiel A. Benitez, Sonja Schmid, Ruth Roriguez-Barrueco, Marshall Crumiller, Jose M. Silva, Ravi Sachidanandam, Benjamin R. tenOever. Cell Host & Microbe. 2013;14(3):346-56). In vivo RNAi screen identifies general transcriptional enhancers as critical components to the antiviral response.

Josep Domingo-Domenech, Mireia Castillo-Martin, Veronica Rodriguez-Bravo, Samuel J. Vidal, S.Aidan Quinn, Ruth Rodriguez-Barrueco, Dennis M. Bonal, Daniel P. Petrylak, Barry H. Smith, Mitchell C. Benson, Jose M. Silva and Carlos Cordon-Cardo. Cancer Cell. 2012 Sep 11;22(3):373-88.Identification of Docetaxel Resistant, Notch and Hedgehog Signaling Dependent Prostate Tumor Initiating Cells

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.

Silva JM, Parker J, Marran K, Silva JM, 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

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.

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.

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.

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.

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.

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