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651 results on '"Koch, Wayne M."'

1. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers

Author

Ren, Shuling, Gaykalova, Daria A, Guo, Theresa, Favorov, Alexander V, Fertig, Elana J, Tamayo, Pablo, Callejas-Valera, Juan Luis, Allevato, Mike, Gilardi, Mara, Santos, Jessica, Fukusumi, Takahito, Sakai, Akihiro, Ando, Mizuo, Sadat, Sayed, Liu, Chao, Xu, Guorong, Fisch, Kathleen M, Wang, Zhiyong, Molinolo, Alfredo A, Gutkind, J Silvio, Ideker, Trey, Koch, Wayne M, and Califano, Joseph A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Digestive Diseases, Cancer, Biotechnology, Human Genome, HIV/AIDS, Women's Health, Cervical Cancer, Sexually Transmitted Infections, Infectious Diseases, Genetics, 2.1 Biological and endogenous factors, Animals, Antineoplastic Combined Chemotherapy Protocols, Carcinogenesis, Cell Line, Tumor, Cell Proliferation, Datasets as Topic, Disease Models, Animal, Disease-Free Survival, Female, Gene Expression Regulation, Neoplastic, Gene Expression Regulation, Viral, Host-Pathogen Interactions, Human papillomavirus 16, Humans, Mice, Mice, Transgenic, Oncogene Proteins, Viral, Papillomavirus Infections, Pharyngeal Neoplasms, Primary Cell Culture, Receptors, Fibroblast Growth Factor, Signal Transduction, Squamous Cell Carcinoma of Head and Neck, TOR Serine-Threonine Kinases, Tumor Suppressor Protein p53, Uterine Cervical Neoplasms, Clinical Sciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

The dominant paradigm for HPV carcinogenesis includes integration into the host genome followed by expression of E6 and E7 (E6/E7). We explored an alternative carcinogenic pathway characterized by episomal E2, E4, and E5 (E2/E4/E5) expression. Half of HPV positive cervical and pharyngeal cancers comprised a subtype with increase in expression of E2/E4/E5, as well as association with lack of integration into the host genome. Models of the E2/E4/E5 carcinogenesis show p53 dependent enhanced proliferation in vitro, as well as increased susceptibility to induction of cancer in vivo. Whole genomic expression analysis of the E2/E4/E5 pharyngeal cancer subtype is defined by activation of the fibroblast growth factor receptor (FGFR) pathway and this subtype is susceptible to combination FGFR and mTOR inhibition, with implications for targeted therapy.

Published
2020

2. Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

Author

Kelley, Dylan Z, Flam, Emily L, Guo, Theresa, Danilova, Ludmila V, Zamuner, Fernando T, Bohrson, Craig, Considine, Michael, Windsor, Eric J, Bishop, Justin A, Zhang, Chi, Koch, Wayne M, Sidransky, David, Westra, William H, Chung, Christine H, Califano, Joseph A, Wheelan, Sarah, Favorov, Alexander V, Florea, Liliana, Fertig, Elana J, and Gaykalova, Daria A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Dental/Oral and Craniofacial Disease, Genetics, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Alternative Splicing, Cell Line, Tumor, Cell Movement, Cell Proliferation, Cell Survival, Gelsolin, Gene Expression Regulation, Neoplastic, Humans, Models, Biological, Neoplasm Invasiveness, Neoplasm Metastasis, Squamous Cell Carcinoma of Head and Neck, Clinical Sciences, General Clinical Medicine, Biochemistry and cell biology, Clinical sciences
Abstract

We have recently performed the characterization of alternative splicing events (ASEs) in head and neck squamous cell carcinoma, which allows dysregulation of protein expression common for cancer cells. Such analysis demonstrated a high ASE prevalence among tumor samples, including tumor-specific alternative splicing in the GSN gene.In vitro studies confirmed that overall expression of either ASE-GSN or wild-type GSN (WT-GSN) isoform inversely correlated with cell proliferation, whereas the high ratio of ASE-GSN to WT-GSN correlated with increased cellular invasion. Additionally, a change in expression of either isoform caused compensatory changes in expression of the other isoform. Our results suggest that the overall expression and the balance between GSN isoforms are mediating factors in proliferation, while increased overall expression of ASE-GSN is specific to cancer tissues. As a result, we propose ASE-GSN can serve not only as a biomarker of disease and disease progression, but also as a neoantigen for head and neck squamous cell carcinoma treatment, for which only a limited number of disease-specific targeted therapies currently exist.

Published
2018

3. Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks

Author

Kelley, Dylan Z, Flam, Emily L, Izumchenko, Evgeny, Danilova, Ludmila V, Wulf, Hildegard A, Guo, Theresa, Singman, Dzov A, Afsari, Bahman, Skaist, Alyza M, Considine, Michael, Welch, Jane A, Stavrovskaya, Elena, Bishop, Justin A, Westra, William H, Khan, Zubair, Koch, Wayne M, Sidransky, David, Wheelan, Sarah J, Califano, Joseph A, Favorov, Alexander V, Fertig, Elana J, and Gaykalova, Daria A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Infectious Diseases, Dental/Oral and Craniofacial Disease, HIV/AIDS, Biotechnology, Human Genome, Sexually Transmitted Infections, Cancer, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Base Sequence, Cell Line, Tumor, Chromatin, Chromatin Immunoprecipitation, Gene Expression Regulation, Neoplastic, Genome, Human, Head and Neck Neoplasms, Humans, Papillomaviridae, Sequence Analysis, DNA, Virus Integration, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis. Cancer Res; 77(23); 6538-50. ©2017 AACR.

Published
2017

4. A novel surgeon credentialing and quality assurance process using transoral surgery for oropharyngeal cancer in ECOG-ACRIN Cancer Research Group Trial E3311

Author

Ferris, Robert L., Flamand, Yael, Holsinger, F. Christopher, Weinstein, Gregory S., Quon, Harry, Mehra, Ranee, Garcia, Joaquin J., Hinni, Michael L., Gross, Neil D., Sturgis, Erich M., Duvvuri, Umamaheswar, Méndez, Eduardo, Ridge, John A., Magnuson, J. Scott, Higgins, Kerry A., Patel, Mihir R., Smith, Russel B., Karakla, Daniel W., Kupferman, Michael E., Malone, James P., Judson, Benjamin L., Richmon, Jeremy, Boyle, Jay O., Bayon, Rodrigo, O'Malley, Bert W., Jr, Ozer, Enver, Thomas, Giovana R., Koch, Wayne M., Bell, R. Bryan, Saba, Nabil F., Li, Shuli, Sigurdson, Elin R., and Burtness, Barbara

Published
2020
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5. Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC.

Author

Gaykalova, Daria A, Zizkova, Veronika, Guo, Theresa, Tiscareno, Ilse, Wei, Yingying, Vatapalli, Rajita, Hennessey, Patrick T, Ahn, Julie, Danilova, Ludmila, Khan, Zubair, Bishop, Justin A, Gutkind, J Silvio, Koch, Wayne M, Westra, William H, Fertig, Elana J, Ochs, Michael F, and Califano, Joseph A

Subjects
Cell Line, Tumor, Humans, Carcinoma, Squamous Cell, Head and Neck Neoplasms, Ubiquitin-Protein Ligases, Cluster Analysis, Cohort Studies, Gene Expression Profiling, Reverse Transcriptase Polymerase Chain Reaction, Computational Biology, Signal Transduction, Cell Movement, DNA Methylation, Gene Expression Regulation, Neoplastic, RNA Interference, Genes, Tumor Suppressor, Adult, Aged, Aged, 80 and over, Middle Aged, Female, Male, Receptors, Notch, Epigenomics, DTX1, HNSCC, expression, integration, methylation, Rare Diseases, Cancer, Dental/Oral and Craniofacial Disease, Genetics, Clinical Research, Biotechnology, Genetic Testing, Human Genome, Oncology and Carcinogenesis
Abstract

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 accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates (BANK1, BIN2, and DTX1) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1, which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.

Published
2017

6. Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke

Author

Li, Ryan, Faden, Daniel L, Fakhry, Carole, Langelier, Chaz, Jiao, Yuchen, Wang, Yuxuan, Wilkerson, Matthew D, Pedamallu, Chandra Sekhar, Old, Matthew, Lang, James, Loyo, Myriam, Ahn, Sun Mi, Tan, Marietta, Gooi, Zhen, Chan, Jason, Richmon, Jeremy, Wood, Laura D, Hruban, Ralph H, Bishop, Justin, Westra, William H, Chung, Christine H, Califano, Joseph, Gourin, Christine G, Bettegowda, Chetan, Meyerson, Matthew, Papadopoulos, Nickolas, Kinzler, Kenneth W, Vogelstein, Bert, DeRisi, Joseph L, Koch, Wayne M, and Agrawal, Nishant

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Tobacco, Cancer, Digestive Diseases, Genetics, Dental/Oral and Craniofacial Disease, Rare Diseases, Human Genome, Cancer Genomics, Tobacco Smoke and Health, 2.1 Biological and endogenous factors, 2.2 Factors relating to the physical environment, Good Health and Well Being, Adult, Age Distribution, Carcinoma, Squamous Cell, Cohort Studies, DNA, Neoplasm, Databases, Factual, Female, Genetic Predisposition to Disease, Genomics, Humans, Incidence, Male, Metagenome, Middle Aged, Mutation, Neoplasm Invasiveness, Neoplasm Staging, Prognosis, RNA, Messenger, Retrospective Studies, Risk Assessment, Sex Distribution, Smoking, Tongue Neoplasms, Tumor Suppressor Protein p53, head and neck cancer, oral tongue, squamous cell carcinoma, next-generation sequencing, nonsmokers, Dentistry, Otorhinolaryngology, Clinical sciences
Abstract

BackgroundEvidence suggests the incidence of oral tongue squamous cell carcinoma is increasing in young patients, many who have no history of tobacco use.MethodsWe clinically reviewed 89 patients with oral tongue cancer. Exomic sequencing of tumor DNA from 6 nonsmokers was performed and compared to previously sequenced cases. RNA from 20 tumors was evaluated by massively parallel sequencing to search for potentially oncogenic viruses.ResultsNon-smokers (53 of 89) were younger than smokers (36 of 89; mean, 50.4 vs 61.9 years; p

Published
2015

7. Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas

Author

Wang, Yuxuan, Springer, Simeon, Mulvey, Carolyn L, Silliman, Natalie, Schaefer, Joy, Sausen, Mark, James, Nathan, Rettig, Eleni M, Guo, Theresa, Pickering, Curtis R, Bishop, Justin A, Chung, Christine H, Califano, Joseph A, Eisele, David W, Fakhry, Carole, Gourin, Christine G, Ha, Patrick K, Kang, Hyunseok, Kiess, Ana, Koch, Wayne M, Myers, Jeffrey N, Quon, Harry, Richmon, Jeremy D, Sidransky, David, Tufano, Ralph P, Westra, William H, Bettegowda, Chetan, Diaz, Luis A, Papadopoulos, Nickolas, Kinzler, Kenneth W, Vogelstein, Bert, and Agrawal, Nishant

Subjects
Genetics, Clinical Research, Rare Diseases, Dental/Oral and Craniofacial Disease, Genetic Testing, Cancer, Carcinoma, Squamous Cell, DNA, Neoplasm, Female, Head and Neck Neoplasms, Humans, Male, Middle Aged, Mutation, Neoplasm Staging, Papillomaviridae, Saliva, Biological Sciences, Medical and Health Sciences
Abstract

To explore the potential of tumor-specific DNA as a biomarker for head and neck squamous cell carcinomas (HNSCC), we queried DNA from saliva or plasma of 93 HNSCC patients. We searched for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n = 10) and 95% (n = 37), respectively. When segregated by site, tumor DNA was detected in 100% (n = 15), 91% (n = 22), 100% (n = 7), and 100% (n = 3) of patients with tumors of the oral cavity, oropharynx, larynx, and hypopharynx, respectively. In saliva, tumor DNA was found in 100% of patients with oral cavity cancers and in 47 to 70% of patients with cancers of the other sites. In plasma, tumor DNA was found in 80% of patients with oral cavity cancers, and in 86 to 100% of patients with cancers of the other sites. Thus, saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in saliva was found postsurgically in three patients before clinical diagnosis of recurrence, but in none of the five patients without recurrence. Tumor DNA in the saliva and plasma appears to be a potentially valuable biomarker for detection of HNSCC.

Published
2015

8. Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients.

Author

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, and Califano, Joseph A

Subjects
Saliva, Papillomaviridae, Head and Neck Neoplasms, DNA-Binding Proteins, Repressor Proteins, Sensitivity and Specificity, DNA Methylation, Gene Expression Regulation, Neoplastic, Zinc Fingers, Apoptosis Regulatory Proteins, Genome-Wide Association Study, Biomarkers, Tumor, Gene Expression Regulation, Neoplastic, Biomarkers, Tumor, General Science & Technology
Abstract

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 of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.

Published
2015

11. Data from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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14. Supplementary Table 3 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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15. Supplementary Table 4 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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16. Supplementary Figure 3 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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17. Supplemental Experimental Procedures from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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18. Supplementary Figure 2 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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19. Supplementary Table 2 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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20. Supplementary Figure 1 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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21. Supplementary Table 1 from JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients

Author

Guerrero-Preston, Rafael, primary, Lawson, Fahcina, primary, Rodriguez-Torres, Sebastian, primary, Noordhuis, Maartje G., primary, Pirini, Francesca, primary, Manuel, Laura, primary, Valle, Blanca L., primary, Hadar, Tal, primary, Rivera, Bianca, primary, Folawiyo, Oluwasina, primary, Baez, Adriana, primary, Marchionni, Luigi, primary, Koch, Wayne M., primary, Westra, William H., primary, Kim, Young J., primary, Eshleman, James R., primary, and Sidransky, David, primary

Published
2023
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24. Data from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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25. Supplementary Materials and Methods from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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26. Supplemental Tables S1-S11 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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28. Supplemental File 1 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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31. Supplemental File 2 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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32. Supplementary Methods, Tables 1 - 4, Figures 1 - 10 from Tadalafil Augments Tumor Specific Immunity in Patients with Head and Neck Squamous Cell Carcinoma

Author

Califano, Joseph A., primary, Khan, Zubair, primary, Noonan, Kimberly A., primary, Rudraraju, Lakshmi, primary, Zhang, Zhe, primary, Wang, Hao, primary, Goodman, Steven, primary, Gourin, Christine G., primary, Ha, Patrick K., primary, Fakhry, Carole, primary, Saunders, John, primary, Levine, Marshall, primary, Tang, Mei, primary, Neuner, Geoffrey, primary, Richmon, Jeremy D., primary, Blanco, Ray, primary, Agrawal, Nishant, primary, Koch, Wayne M., primary, Marur, Shanthi, primary, Weed, Donald T., primary, Serafini, Paolo, primary, and Borrello, Ivan, primary

Published
2023
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33. Legends for supplemental figures and table from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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36. Supplemental Figures S1-S15 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Author

Kelley, Dylan Z., primary, Flam, Emily L., primary, Izumchenko, Evgeny, primary, Danilova, Ludmila V., primary, Wulf, Hildegard A., primary, Guo, Theresa, primary, Singman, Dzov A., primary, Afsari, Bahman, primary, Skaist, Alyza M., primary, Considine, Michael, primary, Welch, Jane A., primary, Stavrovskaya, Elena, primary, Bishop, Justin A., primary, Westra, William H., primary, Khan, Zubair, primary, Koch, Wayne M., primary, Sidransky, David, primary, Wheelan, Sarah J., primary, Califano, Joseph A., primary, Favorov, Alexander V., primary, Fertig, Elana J., primary, and Gaykalova, Daria A., primary

Published
2023
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37. Supplementary Figure 1 from ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer

Author

Wu, Guojun, primary, Osada, Motonobu, primary, Guo, Zhongmin, primary, Fomenkov, Alexey, primary, Begum, Shahnaz, primary, Zhao, Ming, primary, Upadhyay, Sunil, primary, Xing, Mingzhao, primary, Wu, Feng, primary, Moon, Chulso, primary, Westra, William H., primary, Koch, Wayne M., primary, Mantovani, Roberto, primary, Califano, Joseph A., primary, Ratovitski, Edward, primary, Sidransky, David, primary, and Trink, Barry, primary

Published
2023
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38. Supplementary Figure 1 Legend from ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer

Author

Wu, Guojun, primary, Osada, Motonobu, primary, Guo, Zhongmin, primary, Fomenkov, Alexey, primary, Begum, Shahnaz, primary, Zhao, Ming, primary, Upadhyay, Sunil, primary, Xing, Mingzhao, primary, Wu, Feng, primary, Moon, Chulso, primary, Westra, William H., primary, Koch, Wayne M., primary, Mantovani, Roberto, primary, Califano, Joseph A., primary, Ratovitski, Edward, primary, Sidransky, David, primary, and Trink, Barry, primary

Published
2023
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45. Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

Author

Agrawal, Nishant, Frederick, Mitchell J., Pickering, Curtis R., Bettegowda, Chetan, Chang, Kyle, Li, Ryan J., Fakhry, Carole, Xie, Tong-Xin, Zhang, Jiexin, Wang, Jing, Zhang, Nianxiang, El-Naggar, Adel K., Jasser, Samar A., Weinstein, John N., Treviño, Lisa, Drummond, Jennifer A., Muzny, Donna M., Wu, Yuanqing, Wood, Laura D., Hruban, Ralph H., Westra, William H., Koch, Wayne M., Califano, Joseph A., Gibbs, Richard A., Sidransky, David, Vogelstein, Bert, Velculescu, Victor E., Papadopoulos, Nickolas, Wheeler, David A., Kinzler, Kenneth W., and Myers, Jeffrey N.

Published
2011
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47. Surgeon Volume and Laryngectomy Outcomes

Author

Saraswathula, Anirudh, primary, Austin, J. Matthew, additional, Fakhry, Carole, additional, Vosler, Peter S., additional, Mandal, Rajarsi, additional, Koch, Wayne M., additional, Tan, Marietta, additional, Eisele, David W., additional, Frick, Kevin D., additional, and Gourin, Christine G., additional

Published
2022
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49. Surgeon Volume and Laryngectomy Outcomes.

Author

Saraswathula, Anirudh, Austin, J. Matthew, Fakhry, Carole, Vosler, Peter S., Mandal, Rajarsi, Koch, Wayne M., Tan, Marietta, Eisele, David W., Frick, Kevin D., and Gourin, Christine G.

Abstract

Objective: To examine the relationship between surgeon volume and operative morbidity and mortality for laryngectomy. Data Sources: The Nationwide Inpatient Sample was used to identify 45,156 patients who underwent laryngectomy procedures for laryngeal or hypopharyngeal cancer between 2001 and 2011. Hospital and surgeon laryngectomy volume were modeled as categorical variables. Methods: Relationships between hospital and surgeon volume and mortality, surgical complications, and acute medical complications were examined using multivariable regression. Results: Higher‐volume surgeons were more likely to operate at large, teaching, nonprofit hospitals and were more likely to treat patients who were white, had private insurance, hypopharyngeal cancer, low comorbidity, admitted electively, and to perform partial laryngectomy, concurrent neck dissection, and flap reconstruction. Surgeons treating more than 5 cases per year were associated with lower odds of medical and surgical complications, with a greater reduction in the odds of complications with increasing surgical volume. Surgeons in the top volume quintile (>9 cases/year) were associated with a decreased odds of in‐hospital mortality (OR = 0.09 [0.01–0.74]), postoperative surgical complications (OR = 0.58 [0.45–0.74]), and acute medical complications (OR = 0.49 [0.37–0.64]). Surgeon volume accounted for 95% of the effect of hospital volume on mortality and 16%–47% of the effect of hospital volume on postoperative morbidity. Conclusion: There is a strong volume‐outcome relationship for laryngectomy, with reduced mortality and morbidity associated with higher surgeon and higher hospital volumes. Observed associations between hospital volume and operative morbidity and mortality are mediated by surgeon volume, suggesting that surgeon volume is an important component of the favorable outcomes of high‐volume hospital care. Laryngoscope, 133:834–840, 2023 [ABSTRACT FROM AUTHOR]

Published
2023
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50. Evidence-Based Clinical Recommendations Regarding Screening for Oral Squamous Cell Carcinomas

Author

Rethman, Michael P., Carpenter, William, Cohen, Ezra E.W., Epstein, Joel, Evans, Caswell A., Flaitz, Catherine M., Graham, Frank J., Hujoel, Philippe P., Kalmar, John R., Koch, Wayne M., Lambert, Paul M., Lingen, Mark W., Oettmeier, Bert W., Jr., Patton, Lauren L., Perkins, David, Reid, Britt C., Sciubba, James J., Tomar, Scott L., Wyatt, Alfred D., Jr., Aravamudhan, Krishna, Frantsve-Hawley, Julie, Cleveland, Jennifer L., and Meyer, Daniel M.

Published
2010
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