Now showing items 1-14 of 14

    • Activation of the NOTCH Pathway in Head and Neck Cancer 

      Ochs, Michael F.; Gaykalova, Daria A.; Sun, Wenyue; Mambo, Elizabeth; Arnaoutakis, Demetri; Liu, Yan; Loyo, Myriam; Agrawal, Nishant; Howard, Jason D.; Li, Ryan; Ahn, Sun Mi; Fertig, Elana J.; Sidransky, David; Houghton, Jeffery; Buddavarapu, Kalyan; Sanford, Tiffany; Choudhary, Ashish; Darden, Will; Adai, Alex; Latham, Gary; Bishop, Justin A.; Sharma, Rajni; Westra, William H.; Hennessey, Patrick T.; Chung, Christine H.; Califano, Joseph A. (American Association for Cancer Research, 2014)
      NOTCH1 mutations have been reported to occur in 10% to 15% of head and neck squamous cell carcinomas (HNSCC). To determine the significance of these mutations, we embarked upon a comprehensive study of NOTCH signaling in ...
    • Coordinated Activation of Candidate Proto-Oncogenes and Cancer Testes Antigens via Promoter Demethylation in Head and Neck Cancer and Lung Cancer 

      Ochs, Michael F.; Smith, Ian M.; Glazer, Chad A.; Mithani, Suhail; Sun, Wenyue; Bhan, Sheetal; Vostrov, Alexander; Abdullaev, Ziedulla; Lobanenkov, Victor; Gray, Andrew; Liu, Chunyan; Chang, Steven S.; Ostrow, Kimberly L.; Westra, William H.; Begum, Shahnaz; Dhara, Mousumi; Califano, Joseph A. (Public Library of Science, 2009)
      Background Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to ...
    • Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma 

      Ochs, Michael F.; Li, Ryan; Ahn, Sun Mi; Hennessey, Patrick T.; Tan, Marietta; Soudry, Ethan; Gaykalova, Daria A.; Uemura, Mamoru; Brait, Mariana; Shao, Chunbo; Westra, William H.; Bishop, Justin A.; Fertig, Elana J.; Califano, Joseph A. (Public Library of Science, 2014)
      Purpose Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma ...
    • Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC 

      Ochs, Michael F.; Gaykalova, Daria A.; Zizkova, Veronika; Guo, Theresa; Tiscareno, Ilse; Wei, Yingying; Vatapalli, Rajita; Hennessey, Patrick T.; Ahn, Julie; Danilova, Ludmila V.; Khan, Zubair; Bishop, Justin A.; Gutkind, J. Silvio; Koch, Wayne M.; Westra, William H.; Fertig, Elana J.; Califano, Joseph A. (Impact Journals, 2017)
      Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have ...
    • Integrative Discovery of Epigenetically Derepressed Cancer Testis Antigens in NSCLC 

      Glazer, Chad A.; Smith, Ian M.; Ochs, Michael F.; Begum, Shahnaz; Westra, William H.; Chang, Steven S.; Sun, Wenyue; Bhan, Sheetal; Khan, Zubair; Ahrendt, Steven A.; Califano, Joseph A. (Public Library of Science, 2009)
      Background Cancer/testis antigens (CTAs) were first discovered as immunogenic targets normally expressed in germline cells, but differentially expressed in a variety of human cancers. In this study, we used an integrative ...
    • MAGEB2 is Activated by Promoter Demethylation in Head and Neck Squamous Cell Carcinoma 

      Ochs, Michael F.; Soudry, Ethan; Glazer, Chad A.; Wang, Hao; Schussel, Juliana; Sun, Wenyue; Hennessey, Patrick T.; Mydlarz, Wojchiech; Loyo, Myriam; Demokan, Semra; Smith, Ian M.; Califano, Joseph A. (Public Library of Science, 2012)
      Purpose Although promoter hypermethylation has been an accepted means of tumor suppressor gene inactivation, activation of otherwise normally repressed proto-oncogenes by promoter demethylation has been infrequently ...
    • NF‐κB and stat3 transcription factor signatures differentiate HPV‐positive and HPV‐negative head and neck squamous cell carcinoma 

      Gaykalova, Daria A.; Manola, Judith B.; Ozawa, Hiroyuki; Zizkova, Veronika; Morton, Kathryn; Bishop, Justin A.; Sharma, Rajni; Zhang, Chi; Michailidi, Christina; Considine, Michael; Tan, Marietta; Fertig, Elana J.; Hennessey, Patrick T.; Ahn, Julie; Koch, Wayne M.; Westra, William H.; Khan, Zubair; Chung, Christine H.; Ochs, Michael F.; Califano, Joseph A. (Wiley, 2015)
      Using high-throughput analyses and the TRANSFAC database, we characterized TF signatures of head and neck squamous cell carcinoma (HNSCC) subgroups by inferential analysis of target gene expression, correcting for the ...
    • Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma 

      Ochs, Michael F.; Gaykalova, Daria A.; Mambo, Elizabeth; Choudhary, Ashish; Houghton, Jeffery; Buddavarapu, Kalyan; Sanford, Tiffany; Darden, Will; Adai, Alex; Hadd, Andrew; Latham, Gary; Danilova, Ludmila V.; Bishop, Justin A.; Li, Ryan; Westra, William H.; Hennessey, Patrick T.; Koch, Wayne M.; Califano, Joseph A.; Sun, Wenyue (Public Library of Science, 2014)
      Development of head and neck squamous cell carcinoma (HNSCC) is characterized by accumulation of mutations in several oncogenes and tumor suppressor genes. We have formerly described the mutation pattern of HNSCC and ...
    • Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients 

      Gaykalova, Daria A.; Vatapalli, Rajita; Wei, Yingying; Tsai, Hua-Ling; Wang, Hao; Zhang, Chi; Hennessey, Patrick T.; Guo, Theresa; Tan, Marietta; Li, Ryan; Ahn, Julie; Khan, Zubair; Westra, William H.; Bishop, Justin A.; Zaboli, David; Koch, Wayne M.; Khan, Tanbir; Ochs, Michael F.; Califano, Joseph A. (Public Library of Science, 2015)
      Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance ...
    • Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis 

      Ochs, Michael F.; Fertig, Elana J.; Markovic, Ana; Danilova, Ludmila V.; Gaykalova, Daria A.; Cope, Leslie; Chung, Christine H.; Califano, Joseph A. (Public Library of Science, 2013)
      Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and –negative. Global DNA methylation changes are known to drive oncogene and ...
    • Promoter Methylation in Head and Neck Squamous Cell Carcinoma Cell Lines Is Significantly Different than Methylation in Primary Tumors and Xenografts 

      Ochs, Michael F.; Hennessey, Patrick T.; Mydlarz, Wojchiech; Hsueh, Wayne; Cope, Leslie; Yu, Wayne; Califano, Joseph A. (Public Library of Science, 2011)
      Studies designed to identify novel methylation events related to cancer often employ cancer cell lines in the discovery phase of the experiments and have a relatively low rate of discovery of cancer-related methylation ...
    • Serum microRNA Biomarkers for Detection of Non-Small Cell Lung Cancer 

      Ochs, Michael F.; Hennessey, Patrick T.; Sanford, Tiffany; Choudhary, Ashish; Mydlarz, Wojchiech; Ahrendt, Steven A.; Califano, Joseph A.; Brown, David; Adai, Alex (Public Library of Science, 2012)
      Non small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality world-wide and the majority of cases are diagnosed at late stages of disease. There is currently no cost-effective screening test for ...
    • Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer 

      Ochs, Michael F.; Bahman, Asfari; Guo, Theresa; Considine, Michael; Florea, Liliana; Kagohara, Luciane T.; Stein-O'Brien, Genevieve L.; Kelley, Dylan; Flam, Emily; Zambo, Kristina; Ha, Patrick K.; German, Donald; Califano, Joseph A.; Gaykalova, Daria A.; Favorov, Alexander V.; Fertig, Elana J. (Oxford University Press, 2018)
      Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in ...
    • Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination 

      Ochs, Michael F.; Stansfield, John C.; Rusay, Matthew; Shan, Roger; Kelton, Conor; Gaykalova, Daria A.; Fertig, Elana J.; Califano, Joseph A. (Libertas Academica, 2016)
      The goal of this study was to discover a minimally invasive pathway-specific biomarker that is immune to normal cell mRNA contamination for diagnosing head and neck squamous cell carcinoma (HNSCC). Using Elsevier's MedScan ...