Now showing items 1-20 of 28

    • Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis 

      Chanock, Stephen J.; Schafer, Eric J.; Tabernero, Josep; Baselga, José; Oh, William K.; Pomerantz, Mark M; Shrestha, Yashaswi; Flavin, Richard John; Regan, Meredith Margaret; Penney, Kathryn Lee; Mucci, Lorelei Ann; Stampfer, Meir Jonathan; Hunter, David J.; Chan, Jennifer Ang; Richardson, Andrea Lynn; Loda, Massimo; Kantoff, Philip Wayne; Hahn, William C.; Freedman, Matthew Lawrence (Public Library of Science, 2010)
      Genome-wide association studies (GWAS) have established a variant, rs10993994, on chromosome 10q11 as being associated with prostate cancer risk. Since the variant is located outside of a protein-coding region, the target ...
    • The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis 

      Pomerantz, Mark M.; Li, Fugen; Takeda, David; Lenci, Romina; Chonkar, Apurva; Chabot, Matthew; Cejas, Paloma; Vazquez, Francisca; Cook, Jennifer; Shivdasani, Ramesh A.; Bowden, Michaela; Lis, Rosina; Hahn, William C.; Kantoff, Philip W.; Brown, Myles; Loda, Massimo; Long, Henry W.; Freedman, Matthew L. (2015)
      Master transcription factors interact with DNA to establish cell-type identity and to regulate gene expression in mammalian cells1,2. The genome-wide map of these transcription factor binding sites has been termed the ...
    • BRAF Activation Initiates but Does Not Maintain Invasive Prostate Adenocarcinoma 

      Jeong, Joseph H.; Wang, Zhenxiong; Ouyang, Xuesong; Jiang, Shan; Guney, Isil; Kang, Gyeong Hoon; Abate-Shen, Cory; Guimaraes, Alexander Savio Ramos; Figueiredo, Jose L.; Ding, Zhihu; Shin, Eyoung; Hahn, William C.; Loda, Massimo; Weissleder, Ralph; Chin, Lynda (Public Library of Science, 2008)
      Prostate cancer is the second leading cause of cancer-related deaths in men. Activation of MAP kinase signaling pathway has been implicated in advanced and androgen-independent prostate cancers, although formal genetic ...
    • BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers 

      Abo, Ryan P.; Ducar, Matthew; Garcia, Elizabeth P.; Thorner, Aaron R.; Rojas-Rudilla, Vanesa; Lin, Ling; Sholl, Lynette M.; Hahn, William C.; Meyerson, Matthew; Lindeman, Neal I.; Van Hummelen, Paul; MacConaill, Laura E. (Oxford University Press, 2015)
      Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially ...
    • CK1\(\varepsilon\) is Required for Breast Cancers Dependent on \(\beta\)-Catenin Activity 

      Firestein, Ron; Gupta, Piyush; Repich, Kara; Silver, Serena J.; Boehm, Jesse S.; Kim, So Young; Dunn, Ian Frederick; Wardwell, Leslie; Schinzel, Anna; Wittner, Ben; Root, David E.; Ramaswamy, Sridhar; Lander, Eric Steven; Hahn, William C. (Public Library of Science, 2010)
      Background: Aberrant \(\beta\)-catenin signaling plays a key role in several cancer types, notably colon, liver and breast cancer. However approaches to modulate \(\beta\)-catenin activity for therapeutic purposes have ...
    • Colorectal Cancers from Distinct Ancestral Populations Show Variations in BRAF Mutation Frequency 

      Hanna, Megan C.; Go, Christina; Roden, Christine; Jones, Robert T.; Pochanard, Panisa; Javed, Ahmed Yasir; Javed, Awais; Mondal, Chandrani; Palescandolo, Emanuele; Van Hummelen, Paul; Hatton, Charles; Bass, Adam J.; Chun, Sung Min; Na, Deuk Chae; Kim, Tae-Im; Jang, Se Jin; Osarogiagbon, Raymond U.; Hahn, William C.; Meyerson, Matthew; Garraway, Levi A.; MacConaill, Laura E. (Public Library of Science, 2013)
      It has been demonstrated for some cancers that the frequency of somatic oncogenic mutations may vary in ancestral populations. To determine whether key driver alterations might occur at different frequencies in colorectal ...
    • Elucidating the Regulation and Effectors of the Breast Cancer Oncogene, IKKepsilon 

      Zhou, Alicia (2012-12-19)
      The IkappaB kinase epsilon (IKKepsilon, IKKi, IKBKE) is both a regulator of innate immunity and a breast cancer oncogene that is amplified and overexpressed in ~30% of breast cancers. IKKepsilon promotes malignant ...
    • Feedback Circuit among INK4 Tumor Suppressors Constrains Human Glioblastoma Development 

      Wiedemeyer, Ruprecht; Brennan, Cameron; Heffernan, Timothy P.; Xiao, Yonghong; Mahoney, John T.; Protopopov, Alexei; Zheng, Hongwu; Bignell, Graham; Furnari, Frank; Cavenee, Webster K.; Hahn, William C.; Ichimura, Koichi; Collins, Peter V.; Chu, Gerald C.; Stratton, Michael R.; Ligon, Keith Lloyd; Futreal, Andrew P.; Chin, Lynda (Cell Press, 2008)
      We have developed a nonheuristic genome topography scan (GTS) algorithm to characterize the patterns of genomic alterations in human glioblastoma (GBM), identifying frequent p18^{INK4C} and p16^{INK4A} codeletion. Functional ...
    • Functional genomic screening reveals asparagine dependence as a metabolic vulnerability in sarcoma 

      Hettmer, Simone; Schinzel, Anna C; Tchessalova, Daria; Schneider, Michaela; Parker, Christina L; Bronson, Roderick T; Richards, Nigel GJ; Hahn, William C; Wagers, Amy J (eLife Sciences Publications, Ltd, 2015)
      Current therapies for sarcomas are often inadequate. This study sought to identify actionable gene targets by selective targeting of the molecular networks that support sarcoma cell proliferation. Silencing of asparagine ...
    • Functional Genomics Approaches to Identify and Characterize Oncogenic Signaling 

      Shao, Diane Donghui (2013-10-15)
      Oncogenes drive cancer by hijacking normal cellular functions involved in proliferation and survival. Suppression of the driving oncogene is highly effective for promoting tumor regression, a phenomenon termed "oncogenic ...
    • Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations 

      Brastianos, Priscilla K.; Horowitz, Peleg M.; Santagata, Sandro; Jones, Robert T.; McKenna, Aaron; Getz, Gad; Ligon, Keith L.; Palescandolo, Emanuele; Van Hummelen, Paul; Ducar, Matthew D.; Raza, Alina; Sunkavalli, Ashwini; MacConaill, Laura E.; Stemmer-Rachamimov, Anat O.; Louis, David N.; Hahn, William C.; Dunn, Ian F.; Beroukhim, Rameen (2013)
      Meningiomas are the most common primary nervous system tumor. The tumor suppressor NF2 is disrupted in approximately half of meningiomas1 but the complete spectrum of genetic changes remains undefined. We performed ...
    • Integrated genetic and pharmacologic interrogation of rare cancers 

      Hong, Andrew L.; Tseng, Yuen-Yi; Cowley, Glenn S.; Jonas, Oliver; Cheah, Jaime H.; Kynnap, Bryan D.; Doshi, Mihir B.; Oh, Coyin; Meyer, Stephanie C.; Church, Alanna J.; Gill, Shubhroz; Bielski, Craig M.; Keskula, Paula; Imamovic, Alma; Howell, Sara; Kryukov, Gregory V.; Clemons, Paul A.; Tsherniak, Aviad; Vazquez, Francisca; Crompton, Brian D.; Shamji, Alykhan F.; Rodriguez-Galindo, Carlos; Janeway, Katherine A.; Roberts, Charles W. M.; Stegmaier, Kimberly; van Hummelen, Paul; Cima, Michael J.; Langer, Robert S.; Garraway, Levi A.; Schreiber, Stuart L.; Root, David E.; Hahn, William C.; Boehm, Jesse S. (Nature Publishing Group, 2016)
      Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, ...
    • An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer 

      Sulahian, R; Casey, F; Shen, J; Qian, Zhirong; Shin, H; Ogino, Shuji; Weir, Barbara Ann; Vazquez, F; Liu, Xiaole (Shirley) Shirley; Hahn, William Chun; Bass, Adam Joel; Chan, Vivian; Shivdasani, Ramesh Arjun (Springer Nature, 2013)
      Lineage-restricted transcription factors (TFs) are frequently mutated or overexpressed in cancer and contribute toward malignant behaviors, but the molecular bases of their oncogenic properties are largely unknown. Because ...
    • Integrative functional genomics identifies RINT1 as a novel GBM oncogene 

      Quayle, Steven N.; Chheda, Milan G.; Shukla, Sachet A.; Wiedemeyer, Ruprecht; Tamayo, Pablo; Dewan, Robert W.; Zhuang, Li; Huang-Hobbs, Emmet; Haidar, Sam; Xiao, Yonghong; Ligon, Keith L.; Hahn, William C.; Chin, Lynda (Oxford University Press, 2012)
      Large-scale cancer genomics efforts are identifying hundreds of somatic genomic alterations in glioblastoma (GBM). Distinguishing between active driver and neutral passenger alterations requires functional assessment of ...
    • Oncogenic Transformation by Inhibitor-Sensitive and -Resistant EGFR Mutants 

      Chen, Tzu-Hsiu; Feng, Whei; Jänne, Pasi A; Alvarez, James V; Zappaterra, Mauro; Bulmer, Sara E; Sellers, William R; Greulich, Heidi E.; Frank, David Alan; Hahn, William C.; Meyerson, Matthew Langer (Public Library of Science, 2005)
      Background: Somatic mutations in the kinase domain of the epidermal growth factor receptor tyrosine kinase gene EGFR are common in lung adenocarcinoma. The presence of mutations correlates with tumor sensitivity to the ...
    • PAK1 is a Breast Cancer Oncogene that Coordinately Activates MAPK and MET Signaling 

      Shrestha, Yashaswi; Schafer, Eric J.; Boehm, Jesse S.; He, Frank; Wang, Shumei; Barretina, Jordi; Thomas, Sapana Rachael; Du, Jinyan; Weir, Barbara Ann; Zhao, Jean J.; Golub, Todd R.; Beroukhim, Rameen; Hahn, William C.; Polyak, Kornelia (Nature Publishing Group, 2012)
      Activating mutations in the RAS family or BRAF frequently occur in many types of human cancers but are rarely detected in breast tumors. However, activation of the RAS-RAF-MEK-ERK Mitogen-Activated Protein Kinase (MAPK) ...
    • Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies 

      Cowley, Glenn S; Weir, Barbara A; Vazquez, Francisca; Tamayo, Pablo; Scott, Justine A; Rusin, Scott; East-Seletsky, Alexandra; Ali, Levi D; Gerath, William FJ; Pantel, Sarah E; Lizotte, Patrick H; Jiang, Guozhi; Hsiao, Jessica; Tsherniak, Aviad; Dwinell, Elizabeth; Aoyama, Simon; Okamoto, Michael; Harrington, William; Gelfand, Ellen; Green, Thomas M; Tomko, Mark J; Gopal, Shuba; Wong, Terence C; Li, Hubo; Howell, Sara; Stransky, Nicolas; Liefeld, Ted; Jang, Dongkeun; Bistline, Jonathan; Hill Meyers, Barbara; Armstrong, Scott A; Anderson, Ken C; Stegmaier, Kimberly; Reich, Michael; Pellman, David; Boehm, Jesse S; Mesirov, Jill P; Golub, Todd R; Root, David E; Hahn, William C (Nature Publishing Group, 2014)
      Using a genome-scale, lentivirally delivered shRNA library, we performed massively parallel pooled shRNA screens in 216 cancer cell lines to identify genes that are required for cell proliferation and/or viability. Cell ...
    • PRKACA Mediates Resistance to HER2-Targeted Therapy in Breast Cancer Cells and Restores Anti-Apoptotic Signaling 

      Moody, Susan E.; Schinzel, Anna C.; Singh, Shambhavi; Izzo, Francesca; Strickland, Matthew R.; Luo, Leo; Thomas, Sapana R.; Boehm, Jesse S.; Kim, So Young; Wang, Zhigang C.; Hahn, William C. (2014)
      Targeting HER2 with antibodies or small molecule inhibitors in HER2-positive breast cancer leads to improved survival, but resistance is a common clinical problem. To uncover novel mechanisms of resistance to anti-HER2 ...
    • Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples 

      Campbell, Catarina D.; Kehoe, Sarah M.; Hatton, Charles; Niu, Lili; Yao, Keluo; Hanna, Megan; Mondal, Chandrani; Luongo, Lauren; Baker, Alissa C.; Philips, Juliet; Goff, Deborah J.; Rubin, Mark A.; Corso, Gianni; Roviello, Franco; MacConaill, Laura Eleanor; Bass, Adam Joel; Davis, Matthew J; Emery, Caroline Margaret; Fiorentino, Michelangelo; Polyak, Kornelia; Chan, Jennifer Ang; Wang, Yufang; Fletcher, Jonathan A.; Santagata, Sandro; Shivdasani, Ramesh Arjun; Kieran, Mark W.; Ligon, Keith Lloyd; Stiles, Charles Dean; Hahn, William C.; Meyerson, Matthew Langer; Garraway, Levi Alexander; Jones, Chris (Public Library of Science, 2009)
      Background: Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic ...
    • PTK6 Regulates IGF-1-Induced Anchorage-Independent Survival 

      Iida, Naoko; Zou, Lihua; Yao, Jun; Lu, Yiling; Epstein, Charles B.; Natesan, Sridaran; Mills, Gordon B.; Irie, Hanna Yoko; Shrestha, Yashaswi; Selfors, Laura Marie; Frye, Fabianne; Wang, Zhigang C.; Richardson, Andrea Lynn; Polyak, Kornelia; Hahn, William C.; Brugge, Joan S. (Public Library of Science, 2010)
      Background: Proteins that are required for anchorage-independent survival of tumor cells represent attractive targets for therapeutic intervention since this property is believed to be critical for survival of tumor cells ...