I completed by undergraduate studies at Stanford (BA-Anthropology, BS-Biology)., followed by medical school and pediatric residency at UCSF. I then completed clinical training in pediatric oncology at the Dana Farber Cancer Institute and Boston Children's Hospital, followed by a research post-doctoral fellowship under the mentorship of Tyler Jacks at MIT. I have been on the Stanford faculty since 2005. I run a research lab focused on cancer biology with disease interests in pediatric sarcomas and lung cancer. I am a physician-scientist and I attend on the oncology service at Packard Children's Hospital.

Clinical Focus

  • Pediatric Hematology-Oncology
  • clinical genomics
  • pediatric sarcomas

Academic Appointments

Honors & Awards

  • Sidney Kimmel Scholar, Sidney Kimmel Foundation (2006-2008)
  • Clinical Scientist Development Award, Doris Duke Foundation (2007-2010)
  • Scholar Award, Rita Allen Foundation (2008-2011)
  • member, American Society for Clinical Investigation (2010)
  • Innovative Research Award, SU2C (6/2011-6/2014)

Boards, Advisory Committees, Professional Organizations

  • Member, American Association for Cancer Research (2006 - Present)
  • member, American Society for Clinical Investigation (2011 - Present)

Professional Education

  • Fellowship:Dana Farber Cancer Institute Hematology Oncology Fellowship (2002) MA
  • Board Certification: Pediatric Hematology-Oncology, American Board of Pediatrics (2002)
  • Residency:Univ of California San Francisco (1998) CA
  • Internship:Univ of California San Francisco (1996) CA
  • Medical Education:UCSF School of Medicine (1995) CA
  • B.A., Stanford University, Anthropology (1989)
  • B.S., Stanford University, Biology (1989)
  • MD, UC San Francisco, Medicine (1995)
  • Residency, UC San Francisco, Pediatrics (1998)
  • Fellowship, Boston Children's/Dana Farber, Hematology and Oncology (2002)

Current Research and Scholarly Interests

The long-term goal of our laboratory is to identify novel targets for cancer therapy in order to improve the lives of cancer patients. We use genome-wide analysis tools (RNAseq, WGS, microarrays etc) to understand the consequences of oncogenic mutations at a system-wide level. We have found that comparing genome-wide changes in mouse models of cancer with those seen in primary human tumors is a fruitful approach for the discovery of novel genes and pathways important in oncogenesis. We continue to exploit such cross species comparisons as a tool for understanding cancer pathways and networks. We also use shRNA technology both in vitro and in vivo to perform functional studies of genes identified in our genomic screens. Our laboratory has a genome-wide lentiviral shRNA library available which greatly facilitates these studies.

Specific Projects Include:

Kras signaling.

Kras is one of the most frequently mutated genes in human cancer. Many signaling pathways have been described as being necessary for Kras induced oncogenic transformation. However, the specific pathways required are strongly dependent on the tissue origin (fibroblast vs epithelial cell) and the species of the model system used. Using cross-species microarray analysis, we have uncovered a gene expression profile associated with Kras mutation across species and in different tissues (Sweet-Cordero, Nature Genetics 2005). We have used shRNA- based screens to study the functional significance of this signature. For example, we identified Wt1 as a key regulator of the Kras signature and also a gene whose loss leads to “synthetic senescence” in the context of oncogenic Kras activation (Vicent et al, JCI, 2010). Current studies are focused on identifying novel critical regulators of Kras function, primarily in lung cancer.

Chemotherapy response in vivo

Despite decades of clinical use, much is still unknown about the molecular and cellular determinants of chemotherapy response in cancer. We rely on mouse models that closely recapitulate important aspects of human oncogenesis to study chemotherapy response (Oliver et al Genes and Development, 2010). We are particularly interested in uncovering why tumor-propagating cells (TPCs, also called cancer stem cells) are chemoresistant. Recently, we described and characterized a tumor-propagating population of cells that is dependent on Notch3 signaling (Zheng et al Cancer Cell 2013). Other work is focused on determining how the tumor microenvironment contributes to tumor growth (Vicent et al, Cancer Research 2012) and understanding the kinetics of TPCs in vivo (Zheng et al, Cancer Research 2013).

Modeling solid tumor translocations in vivo and in vitro

Translocations are genetic events present in many cancer types. They are particularly frequent in tumors common in pediatric patients. We use gene targeting to produce mouse models in which translocation events can be activated temporally or in specific tissues. We are using gene targeting approaches in the mouse to study the oncogenesis mediated by fusion of the gene EWS with ets family transcription factors such as Fli-1 and Erg. Such translocations are seen in Ewing’s Sarcoma, a bone tumor found mostly in children. Using human mesenchymal stem cells, we are also exploring what genetic events other than oncogenic translocation are required for tumor initiation and progression. Recently we described a role for a long non-coding RNA (lncRNA) in the pathogenesis of Ewing sarcoma (Howarth et al Journal of Clinical Investigation, 2014).

Personalized Approaches to Pediatric Oncology

Our lab is leading an effort in the division of pediatric oncology at Packard Children’s hospital to develop more focused, genomics-based approaches to the care of patients with solid tumors. This effort focuses on using WGS, RNAseq and other genomic technologies to identify novel theapies for patients with metastatic or relapsed cancer.

Clinical Trials

  • Genomic Analysis of Pediatric Bone Tumors Recruiting

    To determine whether gene expression analysis of primary tumor samples before and after chemotherapy are predictive of long-term survival in pediatric patients with bone sarcomas (Ewings sarcoma (ES) and Osteosarcoma(OS)).

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2016-17 Courses

Stanford Advisees

Graduate and Fellowship Programs

All Publications

  • Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis JOURNAL OF CLINICAL INVESTIGATION Howarth, M. M., Simpson, D., Ngok, S. P., Nieves, B., Chen, R., Siprashvili, Z., Vaka, D., Breese, M. R., Crompton, B. D., Alexe, G., Hawkins, D. S., Jacobson, D., Brunner, A. L., West, R., Mora, J., Stegmaier, K., Khavari, P., Sweet-Cordero, E. A. 2014; 124 (12): 5275-5290


    Chromosomal translocation that results in fusion of the genes encoding RNA-binding protein EWS and transcription factor FLI1 (EWS-FLI1) is pathognomonic for Ewing sarcoma. EWS-FLI1 alters gene expression through mechanisms that are not completely understood. We performed RNA sequencing (RNAseq) analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify gene targets of this oncoprotein. We determined that long noncoding RNA-277 (Ewing sarcoma-associated transcript 1 [EWSAT1]) is upregulated by EWS-FLI1 in pMPCs. Inhibition of EWSAT1 expression diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar, whereas EWSAT1 inhibition had no effect on other cell types tested. Expression of EWS-FLI1 and EWSAT1 repressed gene expression, and a substantial fraction of targets that were repressed by EWS-FLI1 were also repressed by EWSAT1. Analysis of RNAseq data from primary human Ewing sarcoma further supported a role for EWSAT1 in mediating gene repression. We identified heterogeneous nuclear ribonucleoprotein (HNRNPK) as an RNA-binding protein that interacts with EWSAT1 and found a marked overlap in HNRNPK-repressed genes and those repressed by EWS-FLI1 and EWSAT1, suggesting that HNRNPK participates in EWSAT1-mediated gene repression. Together, our data reveal that EWSAT1 is a downstream target of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes.

    View details for DOI 10.1172/JC172124

    View details for Web of Science ID 000345677200020

  • A Meta-analysis of Lung Cancer Gene Expression Identifies PTK7 as a Survival Gene in Lung Adenocarcinoma CANCER RESEARCH Chen, R., Khatri, P., Mazur, P. K., Polin, M., Zheng, Y., Vaka, D., Hoang, C. D., Shrager, J., Xu, Y., Vicent, S., Butte, A. J., Sweet-Cordero, E. A. 2014; 74 (10): 2892-2902


    Lung cancer remains the most common cause of cancer-related death worldwide and it continues to lack effective treatment. The increasingly large and diverse public databases of lung cancer gene expression constitute a rich source of candidate oncogenic drivers and therapeutic targets. To define novel targets for lung adenocarcinoma, we conducted a large-scale meta-analysis of genes specifically overexpressed in adenocarcinoma. We identified an 11-gene signature that was overexpressed consistently in adenocarcinoma specimens relative to normal lung tissue. Six genes in this signature were specifically overexpressed in adenocarcinoma relative to other subtypes of non-small cell lung cancer (NSCLC). Among these genes was the little studied protein tyrosine kinase PTK7. Immunohistochemical analysis confirmed that PTK7 is highly expressed in primary adenocarcinoma patient samples. RNA interference-mediated attenuation of PTK7 decreased cell viability and increased apoptosis in a subset of adenocarcinoma cell lines. Further, loss of PTK7 activated the MKK7-JNK stress response pathway and impaired tumor growth in xenotransplantation assays. Our work defines PTK7 as a highly and specifically expressed gene in adenocarcinoma and a potential therapeutic target in this subset of NSCLC. Cancer Res; 74(10); 2892-902. ©2014 AACR.

    View details for DOI 10.1158/0008-5472.CAN-13-2775

    View details for Web of Science ID 000336720700024

    View details for PubMedID 24654231

  • A Rare Population of CD24(+)ITGB4(+)Notch(hi) Cells Drives Tumor Propagation in NSCLC and Requires Notch3 for Self-Renewal CANCER CELL Zheng, Y., de la Cruz, C. C., Sayles, L. C., Alleyne-Chin, C., Vaka, D., Knaak, T. D., Bigos, M., Xu, Y., Hoang, C. D., Shrager, J. B., Fehling, H. J., French, D., Forrest, W., Jiang, Z., Carano, R. A., Barck, K. H., Jackson, E. L., Sweet-Cordero, E. A. 2013; 24 (1): 59-74


    Sustained tumor progression has been attributed to a distinct population of tumor-propagating cells (TPCs). To identify TPCs relevant to lung cancer pathogenesis, we investigated functional heterogeneity in tumor cells isolated from Kras-driven mouse models of non-small-cell lung cancer (NSCLC). CD24(+)ITGB4(+)Notch(hi) cells are capable of propagating tumor growth in both a clonogenic and an orthotopic serial transplantation assay. While all four Notch receptors mark TPCs, Notch3 plays a nonredundant role in tumor cell propagation in two mouse models and in human NSCLC. The TPC population is enriched after chemotherapy, and the gene signature of mouse TPCs correlates with poor prognosis in human NSCLC. The role of Notch3 in tumor propagation may provide a therapeutic target for NSCLC.

    View details for DOI 10.1016/j.ccr.2013.05.021

    View details for Web of Science ID 000321604000010

  • Cross-Species Functional Analysis of Cancer-Associated Fibroblasts Identifies a Critical Role for CLCF1 and IL-6 in Non-Small Cell Lung Cancer In Vivo CANCER RESEARCH Vicent, S., Sayles, L. C., Vaka, D., Khatri, P., Gevaert, O., Chen, R., Zheng, Y., Gillespie, A. K., Clarke, N., Xu, Y., Shrager, J., Hoang, C. D., Plevritis, S., Butte, A. J., Sweet-Cordero, E. A. 2012; 72 (22): 5744-5756


    Cancer-associated fibroblasts (CAF) have been reported to support tumor progression by a variety of mechanisms. However, their role in the progression of non-small cell lung cancer (NSCLC) remains poorly defined. In addition, the extent to which specific proteins secreted by CAFs contribute directly to tumor growth is unclear. To study the role of CAFs in NSCLCs, a cross-species functional characterization of mouse and human lung CAFs was conducted. CAFs supported the growth of lung cancer cells in vivo by secretion of soluble factors that directly stimulate the growth of tumor cells. Gene expression analysis comparing normal mouse lung fibroblasts and mouse lung CAFs identified multiple genes that correlate with the CAF phenotype. A gene signature of secreted genes upregulated in CAFs was an independent marker of poor survival in patients with NSCLC. This secreted gene signature was upregulated in normal lung fibroblasts after long-term exposure to tumor cells, showing that lung fibroblasts are "educated" by tumor cells to acquire a CAF-like phenotype. Functional studies identified important roles for CLCF1-CNTFR and interleukin (IL)-6-IL-6R signaling in promoting growth of NSCLCs. This study identifies novel soluble factors contributing to the CAF protumorigenic phenotype in NSCLCs and suggests new avenues for the development of therapeutic strategies.

    View details for DOI 10.1158/0008-5472.CAN-12-1097

    View details for Web of Science ID 000311141300012

    View details for PubMedID 22962265

  • Wilms tumor 1 (WT1) regulates KRAS-driven oncogenesis and senescence in mouse and human models JOURNAL OF CLINICAL INVESTIGATION Vicent, S., Chen, R., Sayles, L. C., Lin, C., Walker, R. G., Gillespie, A. K., Subramanian, A., Hinkle, G., Yang, X., Saif, S., Root, D. E., Huff, V., Hahn, W. C., Sweet-Cordero, E. A. 2010; 120 (11): 3940-3952


    KRAS is one of the most frequently mutated human oncogenes. In some settings, oncogenic KRAS can trigger cellular senescence, whereas in others it produces hyperproliferation. Elucidating the mechanisms regulating these 2 drastically distinct outcomes would help identify novel therapeutic approaches in RAS-driven cancers. Using a combination of functional genomics and mouse genetics, we identified a role for the transcription factor Wilms tumor 1 (WT1) as a critical regulator of senescence and proliferation downstream of oncogenic KRAS signaling. Deletion or suppression of Wt1 led to senescence of mouse primary cells expressing physiological levels of oncogenic Kras but had no effect on wild-type cells, and Wt1 loss decreased tumor burden in a mouse model of Kras-driven lung cancer. In human lung cancer cell lines dependent on oncogenic KRAS, WT1 loss decreased proliferation and induced senescence. Furthermore, WT1 inactivation defined a gene expression signature that was prognostic of survival only in lung cancer patients exhibiting evidence of oncogenic KRAS activation. These findings reveal an unexpected role for WT1 as a key regulator of the genetic network of oncogenic KRAS and provide important insight into the mechanisms that regulate proliferation or senescence in response to oncogenic signals.

    View details for DOI 10.1172/JCI44165

    View details for Web of Science ID 000283621800028

    View details for PubMedID 20972333

  • Chronic cisplatin treatment promotes enhanced damage repair and tumor progression in a mouse model of lung cancer GENES & DEVELOPMENT Oliver, T. G., Mercer, K. L., Sayles, L. C., Burke, J. R., Mendus, D., Lovejoy, K. S., Cheng, M., Subramanian, A., Mu, D., Powers, S., Crowley, D., Bronson, R. T., Whittaker, C. A., Bhutkar, A., Lippard, S. J., Golub, T., Thomale, J., Jacks, T., Sweet-Cordero, E. A. 2010; 24 (8): 837-852


    Chemotherapy resistance is a major obstacle in cancer treatment, yet the mechanisms of response to specific therapies have been largely unexplored in vivo. Employing genetic, genomic, and imaging approaches, we examined the dynamics of response to a mainstay chemotherapeutic, cisplatin, in multiple mouse models of human non-small-cell lung cancer (NSCLC). We show that lung tumors initially respond to cisplatin by sensing DNA damage, undergoing cell cycle arrest, and inducing apoptosis-leading to a significant reduction in tumor burden. Importantly, we demonstrate that this response does not depend on the tumor suppressor p53 or its transcriptional target, p21. Prolonged cisplatin treatment promotes the emergence of resistant tumors with enhanced repair capacity that are cross-resistant to platinum analogs, exhibit advanced histopathology, and possess an increased frequency of genomic alterations. Cisplatin-resistant tumors express elevated levels of multiple DNA damage repair and cell cycle arrest-related genes, including p53-inducible protein with a death domain (Pidd). We demonstrate a novel role for PIDD as a regulator of chemotherapy response in human lung tumor cells.

    View details for DOI 10.1101/gad.1897010

    View details for Web of Science ID 000276730300011

    View details for PubMedID 20395368

  • Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma NATURE MEDICINE Mazur, P. K., Herner, A., Mello, S. S., Wirth, M., Hausmann, S., Sanchez-Rivera, F. J., Lofgren, S. M., Kuschma, T., Hahn, S. A., Vangala, D., Trajkovic-Arsic, M., Gupta, A., Heid, I., Noel, P. B., Braren, R., Erkan, M., Kleeff, J., Sipos, B., Sayles, L. C., Heikenwalder, M., Hessmann, E., Ellenrieder, V., Esposito, I., Jacks, T., Bradner, J. E., Khatri, P., Sweet-Cordero, E. A., Attardi, L. D., Schmid, R. M., Schneider, G., Sage, J., Siveke, J. T. 2015; 21 (10): 1163-?

    View details for DOI 10.1038/nm.3952

    View details for Web of Science ID 000362355400018

  • Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Nature medicine Mazur, P. K., Herner, A., Mello, S. S., Wirth, M., Hausmann, S., Sánchez-Rivera, F. J., Lofgren, S. M., Kuschma, T., Hahn, S. A., Vangala, D., Trajkovic-Arsic, M., Gupta, A., Heid, I., Noël, P. B., Braren, R., Erkan, M., Kleeff, J., Sipos, B., Sayles, L. C., Heikenwalder, M., Heßmann, E., Ellenrieder, V., Esposito, I., Jacks, T., Bradner, J. E., Khatri, P., Sweet-Cordero, E. A., Attardi, L. D., Schmid, R. M., Schneider, G., Sage, J., Siveke, J. T. 2015; 21 (10): 1163-1171


    Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human cancers and shows resistance to any therapeutic strategy used. Here we tested small-molecule inhibitors targeting chromatin regulators as possible therapeutic agents in PDAC. We show that JQ1, an inhibitor of the bromodomain and extraterminal (BET) family of proteins, suppresses PDAC development in mice by inhibiting both MYC activity and inflammatory signals. The histone deacetylase (HDAC) inhibitor SAHA synergizes with JQ1 to augment cell death and more potently suppress advanced PDAC. Finally, using a CRISPR-Cas9-based method for gene editing directly in the mouse adult pancreas, we show that de-repression of p57 (also known as KIP2 or CDKN1C) upon combined BET and HDAC inhibition is required for the induction of combination therapy-induced cell death in PDAC. SAHA is approved for human use, and molecules similar to JQ1 are being tested in clinical trials. Thus, these studies identify a promising epigenetic-based therapeutic strategy that may be rapidly implemented in fatal human tumors.

    View details for DOI 10.1038/nm.3952

    View details for PubMedID 26390243

  • Upregulation of the microRNA cluster at the Dlkl-Dio3 locus in lung adenocarcinoma ONCOGENE Valdmanis, P. N., Roy-Chaudhuri, B., Kim, H. K., Sayles, L. C., Zheng, Y., Chuang, C., Caswell, D. R., Chu, K., Zhang, Y., Winslow, M. M., Sweet-Cordero, E. A., Kay, M. A. 2015; 34 (1): 94-103


    Mice in which lung epithelial cells can be induced to express an oncogenic Kras(G12D) develop lung adenocarcinomas in a manner analogous to humans. A myriad of genetic changes accompany lung adenocarcinomas, many of which are poorly understood. To get a comprehensive understanding of both the transcriptional and post-transcriptional changes that accompany lung adenocarcinomas, we took an omics approach in profiling both the coding genes and the non-coding small RNAs in an induced mouse model of lung adenocarcinoma. RNAseq transcriptome analysis of Kras(G12D) tumors from F1 hybrid mice revealed features specific to tumor samples. This includes the repression of a network of GTPase-related genes (Prkg1, Gnao1 and Rgs9) in tumor samples and an enrichment of Apobec1-mediated cytosine to uridine RNA editing. Furthermore, analysis of known single-nucleotide polymorphisms revealed not only a change in expression of Cd22 but also that its expression became allele specific in tumors. The most salient finding, however, came from small RNA sequencing of the tumor samples, which revealed that a cluster of ∼53 microRNAs and mRNAs at the Dlk1-Dio3 locus on mouse chromosome 12qF1 was markedly and consistently increased in tumors. Activation of this locus occurred specifically in sorted tumor-originating cancer cells. Interestingly, the 12qF1 RNAs were repressed in cultured Kras(G12D) tumor cells but reactivated when transplanted in vivo. These microRNAs have been implicated in stem cell pleuripotency and proteins targeted by these microRNAs are involved in key pathways in cancer as well as embryogenesis. Taken together, our results strongly imply that these microRNAs represent key targets in unraveling the mechanism of lung oncogenesis.Oncogene advance online publication, 9 December 2013; doi:10.1038/onc.2013.523.

    View details for DOI 10.1038/onc.2013.523

    View details for Web of Science ID 000349740100009

    View details for PubMedID 24317514

  • Mathematical Modeling of Tumor Cell Proliferation Kinetics and Label Retention in a Mouse Model of Lung Cancer CANCER RESEARCH Zheng, Y., Moore, H., Piryatinska, A., Solis, T., Sweet-Cordero, E. A. 2013; 73 (12): 3525-3533


    Slowly cycling tumor cells that may be present in human tumors may evade cytotoxic therapies, which tend to be more efficient at destroying cells with faster growth rates. However, the proportion and growth rate of slowly cycling tumor cells is often unknown in preclinical model systems used for drug discovery. Here, we report a quantitative approach to quantitate slowly cycling malignant cells in solid tumors, using a well-established mouse model of Kras-induced lung cancer (Kras(G12D/+)). 5-Bromo-2-deoxyuridine (BrdUrd) was administered to tumor-bearing mice, and samples were collected at defined times during pulse and chase phases. Mathematical and statistical modeling of the label-retention data during the chase phase supported the existence of a slowly cycling label-retaining population in this tumor model and permitted the estimation of its proportion and proliferation rate within a tumor. The doubling time of the slowly cycling population was estimated at approximately 5.7 weeks, and this population represented approximately 31% of the total tumor cells in this model system. The mathematical modeling techniques implemented here may be useful in other tumor models where direct observation of cell-cycle kinetics is difficult and may help evaluate tumor cell subpopulations with distinct cell-cycling rates. Cancer Res; 73(12); 3525-33. ©2013 AACR.

    View details for DOI 10.1158/0008-5472.CAN-12-4244

    View details for Web of Science ID 000320380300006

    View details for PubMedID 23576555

  • Two is better than one: combining IGF1R and MEK blockade as a promising novel treatment strategy against KRAS-mutant lung cancer. Cancer discovery Chen, R., Sweet-Cordero, E. A. 2013; 3 (5): 491-493


    Summary: A small-molecule inhibitor screen on a panel of human lung cancer cell lines has uncovered an unexpected sensitivity of cells expressing oncogenic KRAS toward insulin-like growth factor 1 receptor (IGF1R) inhibition. Combining IGF1R and MAP-ERK kinase blockade led to significant effects on viability in human non-small cell lung cancer (NSCLC) cell lines and in 2 mouse models of oncogenic KRAS-driven lung cancer. The mechanistic basis for this effect seems to be an increased baseline activation of IGF1R-mediated activation of AKT in cells that express oncogenic KRAS. The studies thus point to a novel approach for treatment of KRAS-driven NSCLC, a particularly difficult subset of patients to treat with existing approaches. Cancer Discov; 3(5); 491-3. ©2013 AACR.

    View details for DOI 10.1158/2159-8290.CD-13-0128

    View details for PubMedID 23658296

  • The phosphatase PP2A links glutamine to the tumor suppressor p53. Molecular cell Gwinn, D., Sweet-Cordero, E. A. 2013; 50 (2): 157-158


    In this issue of Molecular Cell, Reid et al. (2013) show that glutamine withdrawal causes PP2A-mediated activation of p53 through its regulator EDD, linking levels of a critical metabolite to an important regulator of cell survival and proliferation.

    View details for DOI 10.1016/j.molcel.2013.04.010

    View details for PubMedID 23622513

  • Blocking NRG1 and Other Ligand-Mediated Her4 Signaling Enhances the Magnitude and Duration of the Chemotherapeutic Response of Non-Small Cell Lung Cancer SCIENCE TRANSLATIONAL MEDICINE Hegde, G. V., de la Cruz, C. C., Chiu, C., Alag, N., Schaefer, G., Crocker, L., Ross, S., Goldenberg, D., Merchant, M., Tien, J., Shao, L., Roth, L., Tsai, S., Stawicki, S., Jin, Z., Wyatt, S. K., Carano, R. A., Zheng, Y., Sweet-Cordero, E. A., Wu, Y., Jackson, E. L. 2013; 5 (171)
  • Residual Tumor Cells That Drive Disease Relapse after Chemotherapy Do Not Have Enhanced Tumor Initiating Capacity PLOS ONE Hegde, G. V., de la Cruz, C., Eastham-Anderson, J., Zheng, Y., Sweet-Cordero, E. A., Jackson, E. L. 2012; 7 (10)


    Although chemotherapy is used to treat most advanced solid tumors, recurrent disease is still the major cause of cancer-related mortality. Cancer stem cells (CSCs) have been the focus of intense research in recent years because they provide a possible explanation for disease relapse. However, the precise role of CSCs in recurrent disease remains poorly understood and surprisingly little attention has been focused on studying the cells responsible for re-initiating tumor growth within the original host after chemotherapy treatment. We utilized both xenograft and genetically engineered mouse models of non-small cell lung cancer (NSCLC) to characterize the residual tumor cells that survive chemotherapy treatment and go on to cause tumor regrowth, which we refer to as tumor re-initiating cells (TRICs). We set out to determine whether TRICs display characteristics of CSCs, and whether assays used to define CSCs also provide an accurate readout of a cell's ability to cause tumor recurrence. We did not find consistent enrichment of CSC marker positive cells or enhanced tumor initiating potential in TRICs. However, TRICs from all models do appear to be in EMT, a state that has been linked to chemoresistance in numerous types of cancer. Thus, the standard CSC assays may not accurately reflect a cell's ability to drive disease recurrence.

    View details for DOI 10.1371/journal.pone.0045647

    View details for Web of Science ID 000310310200010

    View details for PubMedID 23115623

  • Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data SCIENCE TRANSLATIONAL MEDICINE Sirota, M., Dudley, J. T., Kim, J., Chiang, A. P., Morgan, A. A., Sweet-Cordero, A., Sage, J., Butte, A. J. 2011; 3 (96)


    The application of established drug compounds to new therapeutic indications, known as drug repositioning, offers several advantages over traditional drug development, including reduced development costs and shorter paths to approval. Recent approaches to drug repositioning use high-throughput experimental approaches to assess a compound's potential therapeutic qualities. Here, we present a systematic computational approach to predict novel therapeutic indications on the basis of comprehensive testing of molecular signatures in drug-disease pairs. We integrated gene expression measurements from 100 diseases and gene expression measurements on 164 drug compounds, yielding predicted therapeutic potentials for these drugs. We recovered many known drug and disease relationships using computationally derived therapeutic potentials and also predict many new indications for these 164 drugs. We experimentally validated a prediction for the antiulcer drug cimetidine as a candidate therapeutic in the treatment of lung adenocarcinoma, and demonstrate its efficacy both in vitro and in vivo using mouse xenograft models. This computational method provides a systematic approach for repositioning established drugs to treat a wide range of human diseases.

    View details for DOI 10.1126/scitranslmed.3001318

    View details for Web of Science ID 000293953100005

    View details for PubMedID 21849665

  • Expression and Silencing of the Microtubule-Associated Protein Tau in Breast Cancer Cells MOLECULAR CANCER THERAPEUTICS Spicakova, T., O'Brien, M. M., Duran, G. E., Sweet-Cordero, A., Sikic, B. I. 2010; 9 (11): 2970-2981


    The microtubule-associated protein Tau has been reported to be a predictive factor for clinical response to taxanes in metastatic breast cancer. We generated a panel of eight taxane-resistant variants from four human breast cancer cell lines (MCF-7, T-47D, MDA-MB-231, and BT-549). Four variants had higher levels of Tau compared with their T-47D and MDA-MB-231 parental cells. Using isoform-specific primers, we found that Tau 0N, 1N, 2N, 3R, and 4R isoforms are overexpressed in the resistant variants, as is Tau exon 6 but not exons 4A or 8. To determine whether Tau overexpression produces resistance to taxanes, we derived three independent T-47D clones stably overexpressing Tau 3R and 4R isoforms. Tau overexpression did not result in taxane resistance compared with parental cells transfected with vector alone. We then knocked down Tau expression in three cell lines that expressed Tau constitutively (MCF-7 and ZR-75-1 breast cancer cells, and OVCAR-3 ovarian cancer cells). Lentivirus-mediated silencing of Tau expression in MCF-7 and OVCAR-3 cells did not result in increased taxane sensitivity compared with luciferase short hairpin RNA-infected cells and uninfected parental cells. Transient silencing using Tau-specific small interfering RNAs also did not alter taxane sensitivity relative to nontargeting controls in both MCF-7 and ZR-75-1 cells. These results show that neither overexpression nor depletion of Tau modulates cellular sensitivity to taxanes. Although Tau overexpression has been reported to be a predictive marker of taxane resistance, it is not likely to be a direct mechanism of taxane resistance in breast cancer.

    View details for DOI 10.1158/1535-7163.MCT-10-0780

    View details for Web of Science ID 000283998200012

    View details for PubMedID 21062914

  • Hypoxia in Models of Lung Cancer: Implications for Targeted Therapeutics CLINICAL CANCER RESEARCH Graves, E. E., Vilalta, M., Cecic, I. K., Erler, J. T., Tran, P. T., Felsher, D., Sayles, L., Sweet-Cordero, A., Le, Q., Giaccia, A. J. 2010; 16 (19): 4843-4852


    To efficiently translate experimental methods from bench to bedside, it is imperative that laboratory models of cancer mimic human disease as closely as possible. In this study, we sought to compare patterns of hypoxia in several standard and emerging mouse models of lung cancer to establish the appropriateness of each for evaluating the role of oxygen in lung cancer progression and therapeutic response.Subcutaneous and orthotopic human A549 lung carcinomas growing in nude mice as well as spontaneous K-ras or Myc-induced lung tumors grown in situ or subcutaneously were studied using fluorodeoxyglucose and fluoroazomycin arabinoside positron emission tomography, and postmortem by immunohistochemical observation of the hypoxia marker pimonidazole. The response of these models to the hypoxia-activated cytotoxin PR-104 was also quantified by the formation of ?H2AX foci in vitro and in vivo. Finally, our findings were compared with oxygen electrode measurements of human lung cancers.Minimal fluoroazomycin arabinoside and pimonidazole accumulation was seen in tumors growing within the lungs, whereas subcutaneous tumors showed substantial trapping of both hypoxia probes. These observations correlated with the response of these tumors to PR-104, and with the reduced incidence of hypoxia in human lung cancers relative to other solid tumor types.These findings suggest that in situ models of lung cancer in mice may be more reflective of the human disease, and encourage judicious selection of preclinical tumor models for the study of hypoxia imaging and antihypoxic cell therapies.

    View details for DOI 10.1158/1078-0432.CCR-10-1206

    View details for Web of Science ID 000282647900017

    View details for PubMedID 20858837

  • HIF-2 alpha deletion promotes Kras-driven lung tumor development PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mazumdar, J., Hickey, M. M., Pant, D. K., Durham, A. C., Sweet-Cordero, A., Vachani, A., Jacks, T., Chodosh, L. A., Kissil, J. L., Simon, M. C., Keith, B. 2010; 107 (32): 14182-14187


    Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. The oxygen-sensitive hypoxia inducible factor (HIF) transcriptional regulators HIF-1alpha and HIF-2alpha are overexpressed in many human NSCLCs, and constitutive HIF-2alpha activity can promote murine lung tumor progression, suggesting that HIF proteins may be effective NSCLC therapeutic targets. To investigate the consequences of inhibiting HIF activity in lung cancers, we deleted Hif-1alpha or Hif-2alpha in an established Kras(G12D)-driven murine NSCLC model. Deletion of Hif-1alpha had no obvious effect on tumor growth, whereas Hif-2alpha deletion resulted in an unexpected increase in tumor burden that correlated with reduced expression of the candidate tumor suppressor gene Scgb3a1 (HIN-1). Here, we identify Scgb3a1 as a direct HIF-2alpha target gene and demonstrate that HIF-2alpha regulates Scgb3a1 expression and tumor formation in human Kras(G12D)-driven NSCLC cells. AKT pathway activity, reported to be repressed by Scgb3a1, was enhanced in HIF-2alpha-deficient human NSCLC cells and xenografts. Finally, a direct correlation between HIF-2alpha and SCGB3a1 expression was observed in approximately 70% of human NSCLC samples analyzed. These data suggest that, whereas HIF-2alpha overexpression can contribute to NSCLC progression, therapeutic inhibition of HIF-2alpha below a critical threshold may paradoxically promote tumor growth by reducing expression of tumor suppressor genes, including Scgb3a1.

    View details for DOI 10.1073/pnas.1001296107

    View details for Web of Science ID 000280767700039

    View details for PubMedID 20660313

  • Loss of p130 Accelerates Tumor Development in a Mouse Model for Human Small-Cell Lung Carcinoma CANCER RESEARCH Schaffer, B. E., Park, K., Yiu, G., Conklin, J. F., Lin, C., Burkhart, D. L., Karnezis, A. N., Sweet-Cordero, E. A., Sage, J. 2010; 70 (10): 3877-3883


    Small-cell lung carcinoma (SCLC) is a neuroendocrine subtype of lung cancer. Although SCLC patients often initially respond to therapy, tumors nearly always recur, resulting in a 5-year survival rate of less than 10%. A mouse model has been developed based on the fact that the RB and p53 tumor suppressor genes are mutated in more than 90% of human SCLCs. Emerging evidence in patients and mouse models suggests that p130, a gene related to RB, may act as a tumor suppressor in SCLC cells. To test this idea, we used conditional mutant mice to delete p130 in combination with Rb and p53 in adult lung epithelial cells. We found that loss of p130 resulted in increased proliferation and significant acceleration of SCLC development in this triple-knockout mouse model. The histopathologic features of the triple-mutant mouse tumors closely resembled that of human SCLC. Genome-wide expression profiling experiments further showed that Rb/p53/p130-mutant mouse tumors were similar to human SCLC. These findings indicate that p130 plays a key tumor suppressor role in SCLC. Rb/p53/p130-mutant mice provide a novel preclinical mouse model to identify novel therapeutic targets against SCLC.

    View details for DOI 10.1158/0008-5472.CAN-09-4228

    View details for Web of Science ID 000278486300004

    View details for PubMedID 20406986

  • Differential effects of oncogenic K-Ras and N-Ras on proliferation, differentiation and tumor progression in the colon NATURE GENETICS Haigis, K. M., Kendall, K. R., Wang, Y., Cheung, A., Haigis, M. C., Glickman, J. N., Niwa-Kawakita, M., Sweet-Cordero, A., Sebolt-leopold, J., Shannon, K. M., Settleman, J., Giovannini, M., Jacks, T. 2008; 40 (5): 600-608


    Kras is commonly mutated in colon cancers, but mutations in Nras are rare. We have used genetically engineered mice to determine whether and how these related oncogenes regulate homeostasis and tumorigenesis in the colon. Expression of K-Ras(G12D) in the colonic epithelium stimulated hyperproliferation in a Mek-dependent manner. N-Ras(G12D) did not alter the growth properties of the epithelium, but was able to confer resistance to apoptosis. In the context of an Apc-mutant colonic tumor, activation of K-Ras led to defects in terminal differentiation and expansion of putative stem cells within the tumor epithelium. This K-Ras tumor phenotype was associated with attenuated signaling through the MAPK pathway, and human colon cancer cells expressing mutant K-Ras were hypersensitive to inhibition of Raf, but not Mek. These studies demonstrate clear phenotypic differences between mutant Kras and Nras, and suggest that the oncogenic phenotype of mutant K-Ras might be mediated by noncanonical signaling through Ras effector pathways.

    View details for DOI 10.1038/ng.115

    View details for Web of Science ID 000255366700028

    View details for PubMedID 18372904

  • Requirement for Rac1 in a K-ras-induced lung cancer in the mouse CANCER RESEARCH Kissil, J. L., Walmsley, M. J., Hanlon, L., Haigis, K. M., Kim, C. F., Sweet-Cordero, A., Eckman, M. S., Tuveson, D. A., Capobianco, A. J., Tybulewicz, V. L., Jacks, T. 2007; 67 (17): 8089-8094


    Given the prevalence of Ras mutations in human cancer, it is critical to understand the effector pathways downstream of oncogenic Ras leading to transformation. To directly assess the requirement for Rac1 in K-ras-induced tumorigenesis, we employed a model of lung cancer in which an oncogenic allele of K-ras could be activated by Cre-mediated recombination in the presence or absence of conditional deletion of Rac1. We show that Rac1 function is required for tumorigenesis in this model. Furthermore, although Rac1 deletion alone was compatible with cell viability and proliferation, when combined with K-ras activation in primary epithelial cells, loss of Rac1 caused a profound reduction in proliferation. These data show a specific requirement for Rac1 function in cells expressing oncogenic K-ras.

    View details for DOI 10.1158/0008-5472.CAN-07-2300

    View details for Web of Science ID 000249406700024

    View details for PubMedID 17804720

  • Comparison of gene expression and DNA copy number changes in a murine model of lung cancer GENES CHROMOSOMES & CANCER Sweet-Cordero, A., Tseng, G. C., You, H., Douglass, M., Huey, B., Albertson, D., Jacks, T. 2006; 45 (4): 338-348


    Activation of oncogenic Kras in murine lung leads to the development of numerous small adenomas, only some of which progress over time to overt adenocarcinoma. Thus, although Kras is the initiating oncogene, it is likely that secondary genetic events are required for progression from adenoma to adenocarcinoma. Some of these secondary events may also be important in human lung adenocarcinoma. By comparing gene expression profiles with DNA copy number changes, we sought to identify genes that play key roles in tumor progression in this model. Gene expression profiling revealed significant heterogeneity among the tumor samples. In 27% of the tumors analyzed, whole- or sub-chromosome duplications or deletions in one or more chromosomes were seen. Recurrent duplications were seen on chromosomes 6, 8, 16, and 19, whereas chromosomes 4, 11, and 17 were frequently lost. Notably, focal amplifications or deletions were not seen. Despite the lack of focal amplification, we showed that chromosome duplication has a measurable effect on gene expression that is not uniform across the genome. We identified a group of genes whose gene expression was highly correlated with changes in DNA copy number. These highly correlated genes were enriched for gene ontology categories involved in the DNA damage response and telomere maintenance.

    View details for DOI 10.1002/gcc.20296

    View details for Web of Science ID 000235743400003

    View details for PubMedID 16323170

  • MicroRNA expression profiles classify human cancers NATURE Lu, J., Getz, G., Miska, E. A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebet, B. L., Mak, R. H., Ferrando, A. A., Downing, J. R., Jacks, T., Horvitz, H. R., Golub, T. R. 2005; 435 (7043): 834-838


    Recent work has revealed the existence of a class of small non-coding RNA species, known as microRNAs (miRNAs), which have critical functions across various biological processes. Here we use a new, bead-based flow cytometric miRNA expression profiling method to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers. The miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours. We observe a general downregulation of miRNAs in tumours compared with normal tissues. Furthermore, we were able to successfully classify poorly differentiated tumours using miRNA expression profiles, whereas messenger RNA profiles were highly inaccurate when applied to the same samples. These findings highlight the potential of miRNA profiling in cancer diagnosis.

    View details for DOI 10.1038/nature03702

    View details for Web of Science ID 000229638700054

    View details for PubMedID 15944708

  • An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis NATURE GENETICS Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., Jacks, T. 2005; 37 (1): 48-55


    Using advanced gene targeting methods, generating mouse models of cancer that accurately reproduce the genetic alterations present in human tumors is now relatively straightforward. The challenge is to determine to what extent such models faithfully mimic human disease with respect to the underlying molecular mechanisms that accompany tumor progression. Here we describe a method for comparing mouse models of cancer with human tumors using gene-expression profiling. We applied this method to the analysis of a model of Kras2-mediated lung cancer and found a good relationship to human lung adenocarcinoma, thereby validating the model. Furthermore, we found that whereas a gene-expression signature of KRAS2 activation was not identifiable when analyzing human tumors with known KRAS2 mutation status alone, integrating mouse and human data uncovered a gene-expression signature of KRAS2 mutation in human lung cancer. We confirmed the importance of this signature by gene-expression analysis of short hairpin RNA-mediated inhibition of oncogenic Kras2. These experiments identified both a pattern of gene expression indicative of KRAS2 mutation and potential effectors of oncogenic KRAS2 activity in human cancer. This approach provides a strategy for using genomic analysis of animal models to probe human disease.

    View details for DOI 10.1038/ng1490

    View details for Web of Science ID 000225997500020

    View details for PubMedID 15608639