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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...