Search

Your search keyword '"Stuart, Josh M."' showing total 12 results
Start Over Author "Stuart, Josh M."
12 results on '"Stuart, Josh M."'

1. Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.

Author

Westbrook, Thomas C, Guan, Xiangnan, Rodansky, Eva, Flores, Diana, Liu, Chia Jen, Udager, Aaron M, Patel, Radhika A, Haffner, Michael C, Hu, Ya-Mei, Sun, Duanchen, Beer, Tomasz M, Foye, Adam, Aggarwal, Rahul, Quigley, David A, Youngren, Jack F, Ryan, Charles J, Gleave, Martin, Wang, Yuzhuo, Huang, Jiaoti, Coleman, Ilsa, Morrissey, Colm, Nelson, Peter S, Evans, Christopher P, Lara, Primo, Reiter, Robert E, Witte, Owen, Rettig, Matthew, Wong, Christopher K, Weinstein, Alana S, Uzunangelov, Vlado, Stuart, Josh M, Thomas, George V, Feng, Felix Y, Small, Eric J, Yates, Joel A, Xia, Zheng, and Alumkal, Joshi J

Subjects
Cell Line, Tumor, Humans, Benzamides, Nitriles, Phenylthiohydantoin, Receptors, Androgen, RNA, Biopsy, Drug Resistance, Neoplasm, Male, E2F1 Transcription Factor, Androgen Receptor Antagonists, Prostatic Neoplasms, Castration-Resistant, Prostate Cancer, Genetics, Urologic Diseases, Cancer, Clinical Research, 2.1 Biological and endogenous factors, Aetiology
Abstract

The androgen receptor (AR) signaling inhibitor enzalutamide (enza) is one of the principal treatments for metastatic castration-resistant prostate cancer (CRPC). Several emergent enza clinical resistance mechanisms have been described, including lineage plasticity in which the tumors manifest reduced dependency on the AR. To improve our understanding of enza resistance, herein we analyze the transcriptomes of matched biopsies from men with metastatic CRPC obtained prior to treatment and at progression (n = 21). RNA-sequencing analysis demonstrates that enza does not induce marked, sustained changes in the tumor transcriptome in most patients. However, three patients' progression biopsies show evidence of lineage plasticity. The transcription factor E2F1 and pathways linked to tumor stemness are highly activated in baseline biopsies from patients whose tumors undergo lineage plasticity. We find a gene signature enriched in these baseline biopsies that is strongly associated with poor survival in independent patient cohorts and with risk of castration-induced lineage plasticity in patient-derived xenograft models, suggesting that tumors harboring this gene expression program may be at particular risk for resistance mediated by lineage plasticity and poor outcomes.

Published
2022

2. Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment

Author

Liu, Tiffany T, Achrol, Achal S, Mitchell, Lex A, Rodriguez, Scott A, Feroze, Abdullah, Iv, Michael, Kim, Christine, Chaudhary, Navjot, Gevaert, Olivier, Stuart, Josh M, Harsh, Griffith R, Chang, Steven D, and Rubin, Daniel L

Subjects
Biomedical Imaging, Clinical Trials and Supportive Activities, Neurosciences, Rare Diseases, Cancer, Brain Cancer, Biotechnology, Brain Disorders, Clinical Research, Adult, Aged, Aged, 80 and over, Angiogenesis Inhibitors, Brain Neoplasms, Cluster Analysis, Cohort Studies, Female, Genotype, Glioblastoma, Humans, Kaplan-Meier Estimate, Magnetic Resonance Angiography, Male, Middle Aged, Neovascularization, Pathologic, Treatment Outcome, Young Adult, angiogenesis, antiangiogenic therapy, patient stratification, quantitative perfusion-weighted imaging, radiogenomic analysis, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

BackgroundIn previous clinical trials, antiangiogenic therapies such as bevacizumab did not show efficacy in patients with newly diagnosed glioblastoma (GBM). This may be a result of the heterogeneity of GBM, which has a variety of imaging-based phenotypes and gene expression patterns. In this study, we sought to identify a phenotypic subtype of GBM patients who have distinct tumor-image features and molecular activities and who may benefit from antiangiogenic therapies.MethodsQuantitative image features characterizing subregions of tumors and the whole tumor were extracted from preoperative and pretherapy perfusion magnetic resonance (MR) images of 117 GBM patients in 2 independent cohorts. Unsupervised consensus clustering was performed to identify robust clusters of GBM in each cohort. Cox survival and gene set enrichment analyses were conducted to characterize the clinical significance and molecular pathway activities of the clusters. The differential treatment efficacy of antiangiogenic therapy between the clusters was evaluated.ResultsA subgroup of patients with elevated perfusion features was identified and was significantly associated with poor patient survival after accounting for other clinical covariates (P values 3) consistently found in both cohorts. Angiogenesis and hypoxia pathways were enriched in this subgroup of patients, suggesting the potential efficacy of antiangiogenic therapy. Patients of the angiogenic subgroups pooled from both cohorts, who had chemotherapy information available, had significantly longer survival when treated with antiangiogenic therapy (log-rank P=.022).ConclusionsOur findings suggest that an angiogenic subtype of GBM patients may benefit from antiangiogenic therapy with improved overall survival.

Published
2017

3. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A Gordon, Hinoue, Toshinori, Hoadley, Katherine A, Gibb, Ewan A, Roszik, Jason, Covington, Kyle R, Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Hess, Julian M, Auman, J Todd, Rhie, Suhn K, Bowlby, Reanne, Borad, Mitesh J, Cancer Genome Atlas Network, Zhu, Andrew X, Stuart, Josh M, Sander, Chris, Akbani, Rehan, Cherniack, Andrew D, Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael S, Kleiner, David E, Laird, Peter W, Wheeler, David A, McRee, Autumn J, Bathe, Oliver F, Andersen, Jesper B, Bardeesy, Nabeel, Roberts, Lewis R, and Kwong, Lawrence N

Subjects
Cancer Genome Atlas Network, Liver, Chromatin, Mitochondria, Humans, Cholangiocarcinoma, Bile Duct Neoplasms, Liver Neoplasms, Pancreatic Neoplasms, Isocitrate Dehydrogenase, Nuclear Proteins, Transcription Factors, RNA, Messenger, Genomics, DNA Methylation, Gene Expression Regulation, Neoplastic, Mutation, Adult, Aged, Aged, 80 and over, Middle Aged, Female, Male, Promoter Regions, Genetic, RNA, Long Noncoding, ARID1A, DNA methylation, IDH, RNA sequencing, TCGA, cholangiocarcinoma, integrative genomics, lncRNAs, multi-omics, whole exome, RNA, Messenger, Gene Expression Regulation, Neoplastic, and over, Promoter Regions, Genetic, Long Noncoding, Biochemistry and Cell Biology, Medical Physiology
Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Published
2017

4. Assessing the clinical utility of cancer genomic and proteomic data across tumor types

Author

Yuan, Yuan, Van Allen, Eliezer M, Omberg, Larsson, Wagle, Nikhil, Amin-Mansour, Ali, Sokolov, Artem, Byers, Lauren A, Xu, Yanxun, Hess, Kenneth R, Diao, Lixia, Han, Leng, Huang, Xuelin, Lawrence, Michael S, Weinstein, John N, Stuart, Josh M, Mills, Gordon B, Garraway, Levi A, Margolin, Adam A, Getz, Gad, and Liang, Han

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Clinical Research, Human Genome, Biotechnology, Rare Diseases, Cancer, Biomarkers, Tumor, DNA, Neoplasm, Databases, Genetic, Genetic Markers, Genetic Predisposition to Disease, Humans, Neoplasms, Prevalence, Proteome, Risk Assessment, Survival Analysis
Abstract

Molecular profiling of tumors promises to advance the clinical management of cancer, but the benefits of integrating molecular data with traditional clinical variables have not been systematically studied. Here we retrospectively predict patient survival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, microRNA and protein expression) from 953 samples of four cancer types from The Cancer Genome Atlas project. We find that incorporating molecular data with clinical variables yields statistically significantly improved predictions (FDR < 0.05) for three cancers but those quantitative gains were limited (2.2-23.9%). Additional analyses revealed little predictive power across tumor types except for one case. In clinically relevant genes, we identified 10,281 somatic alterations across 12 cancer types in 2,928 of 3,277 patients (89.4%), many of which would not be revealed in single-tumor analyses. Our study provides a starting point and resources, including an open-access model evaluation platform, for building reliable prognostic and therapeutic strategies that incorporate molecular data.

Published
2014

5. Computational approaches to identify functional genetic variants in cancer genomes

Author

Gonzalez-Perez, Abel, Mustonen, Ville, Reva, Boris, Ritchie, Graham RS, Creixell, Pau, Karchin, Rachel, Vazquez, Miguel, Fink, J Lynn, Kassahn, Karin S, Pearson, John V, Bader, Gary D, Boutros, Paul C, Muthuswamy, Lakshmi, Ouellette, BF Francis, Reimand, Jueri, Linding, Rune, Shibata, Tatsuhiro, Valencia, Alfonso, Butler, Adam, Dronov, Serge, Flicek, Paul, Shannon, Nick B, Carter, Hannah, Ding, Li, Sander, Chris, Stuart, Josh M, Stein, Lincoln D, and Lopez-Bigas, Nuria

Subjects
Cancer, Computational Biology, Genetic Variation, Genome, Human, Humans, Mutation, Neoplasms, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

The International Cancer Genome Consortium (ICGC) aims to catalog genomic abnormalities in tumors from 50 different cancer types. Genome sequencing reveals hundreds to thousands of somatic mutations in each tumor but only a minority of these drive tumor progression. We present the result of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy, and recommend computational techniques to annotate somatic variants and predict their impact on cancer phenotype.

Published
2013

7. Comprehensive molecular characterization of gastric adenocarcinoma

Author

Bass, Adam J., Thorsson, Vesteinn, Shmulevich, Ilya, Reynolds, Sheila M., Miller, Michael, Bernard, Brady, Hinoue, Toshinori, Laird, Peter W., Curtis, Christina, Shen, Hui, Weisenberger, Daniel J., Schultz, Nikolaus, Shen, Ronglai, Weinhold, Nils, Kelsen, David P., Bowlby, Reanne, Chu, Andy, Kasaian, Katayoon, Mungall, Andrew J., Robertson, Gordon A., Sipahimalani, Payal, Cherniack, Andrew, Getz, Gad, Liu, Yingchun, Noble, Michael S., Pedamallu, Chandra, Sougnez, Carrie, Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B., Yang, Da, Zhang, Wei, Pantazi, Angeliki, Gulley, Margaret, Piazuelo, Blanca M., Schneider, Barbara G., Kim, Jihun, Boussioutas, Alex, Sheth, Margi, Demchok, John A., Rabkin, Charles S., Willis, Joseph E., Ng, Sam, Garman, Katherine, Beer, David G., Pennathur, Arjun, Raphael, Benjamin J., Wu, Hsin-Ta, Odze, Robert, Kim, Hark K., Bowen, Jay, Leraas, Kristen M., Lichtenberg, Tara M., Weaver, Stephanie, McLellan, Michael, Wiznerowicz, Maciej, Sakai, Ryo, Lawrence, Michael S., Cibulskis, Kristian, Lichtenstein, Lee, Fisher, Sheila, Gabriel, Stacey B., Lander, Eric S., Ding, Li, Niu, Beifang, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Brooks, Denise, Butterfield, Yaron S. N., Carlsen, Rebecca, Chu, Justin, Chuah, Eric, Chun, Hye-Jung E., Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan A., Lim, Emilia, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Karen L., Nip, Ka Ming, Schein, Jacqueline E., Tam, Angela, Thiessen, Nina, Beroukhim, Rameen, Carter, Scott L., Cherniack, Andrew D., Cho, Juok, DiCara, Daniel, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Jung, Joonil, Kim, Jaegil, Lin, Pei, Meyerson, Matthew, Ojesina, Akinyemi I., Pedamallu, Chandra Sekhar, Saksena, Gordon, Schumacher, Steven E., Stojanov, Petar, Tabak, Barbara, Voet, Doug, Rosenberg, Mara, Zack, Travis I., Zhang, Hailei, Zou, Lihua, Protopopov, Alexei, Santoso, Netty, Parfenov, Michael, Lee, Semin, Zhang, Jianhua, Mahadeshwar, Harshad S., Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Yang, Lixing, Xu, Andrew W., Song, Xingzhi, Xi, Ruibin, Bristow, Christopher A., Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Ling, Shiyun, Rao, Arvind, Weinstein, John N., Kim, Sang-Bae, Lu, Yiling, Mills, Gordon, Bootwalla, Moiz S., Lai, Phillip H., Triche, Timothy, Jr, Van Den Berg, David J., Baylin, Stephen B., Herman, James G., Murray, Bradley A., Askoy, Arman B., Ciriello, Giovanni, Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Lee, William, Ramirez, Ricardo, Sander, Chris, Senbabaoglu, Yasin, Sinha, Rileen, Sumer, Onur S., Sun, Yichao, Thorsson, Vésteinn, Iype, Lisa, Kramer, Roger W., Kreisberg, Richard, Rovira, Hector, Tasman, Natalie, Haussler, David, Stuart, Josh M., Verhaak, Roeland G. W., Leiserson, Mark D. M., Taylor, Barry S., Black, Aaron D., Carney, Julie Ann, Gastier-Foster, Julie M., Helsel, Carmen, McAllister, Cynthia, Ramirez, Nilsa C., Tabler, Teresa R., Wise, Lisa, Zmuda, Erik, Penny, Robert, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Curely, Erin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Shelton, Troy, Shelton, Candace, Sherman, Mark, Benz, Christopher, Lee, Jae-Hyuk, Fedosenko, Konstantin, Manikhas, Georgy, Potapova, Olga, Voronina, Olga, Belyaev, Dmitry, Dolzhansky, Oleg, Rathmell, Kimryn W., Brzezinski, Jakub, Ibbs, Matthew, Korski, Konstanty, Kycler, Witold, Łaźniak, Radoslaw, Leporowska, Ewa, Mackiewicz, Andrzej, Murawa, Dawid, Murawa, Pawel, Spychała, Arkadiusz, Suchorska, Wiktoria M., Tatka, Honorata, Teresiak, Marek, Abdel-Misih, Raafat, Bennett, Joseph, Brown, Jennifer, Iacocca, Mary, Rabeno, Brenda, Kwon, Sun-Young, Kemkes, Ariane, Curley, Erin, Alexopoulou, Iakovina, Engel, Jay, Bartlett, John, Albert, Monique, Park, Do-Youn, Dhir, Rajiv, Luketich, James, Landreneau, Rodney, Janjigian, Yelena Y., Cho, Eunjung, Ladanyi, Marc, Tang, Laura, McCall, Shannon J., Park, Young S., Cheong, Jae-Ho, Ajani, Jaffer, Camargo, Constanza M., Alonso, Shelley, Ayala, Brenda, Jensen, Mark A., Pihl, Todd, Raman, Rohini, Walton, Jessica, Wan, Yunhu, Eley, Greg, Mills Shaw, Kenna R., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Davidsen, Tanja, Hutter, Carolyn M., Sofia, Heidi J., Burton, Robert, Chudamani, Sudha, and Liu, Jia

Published
2014
Full Text
View/download PDF

8. Erratum: Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles (Cell Reports (2017) 18(11) (2780–2794) (S2211124717302140) (10.1016/j.celrep.2017.02.033))

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J. M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, McLellan, Michael D., McRee, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., O'Brien, Daniel R., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Roberts, Lewis R., Saksena, Gordon, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G. W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wu, Ye, Xi, Liu, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zmuda, Erik, Zhu, Andrew X., Stuart, Josh M., Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Chia-Chin, Wu, Shinbrot, Eve, Stransky, Nicola, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Guido, Carpino, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nil, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J. M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Yiling, Lu, Yussanne, Ma, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, Mclellan, Michael D., Mcree, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., O'Brien, Daniel R., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Roberts, Lewis R., Saksena, Gordon, Sander, Chri, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G. W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Ye, Wu, Liu, Xi, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zmuda, Erik, Zhu, Andrew X., and Stuart, Josh M.

Subjects
Genetics and Molecular Biology (all), Biochemistry, Genetics and Molecular Biology (all), Biochemistry
Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Published
2017

9. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author

Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Borad, Mitesh J., Bowen, Jay, Bowlby, Reanne, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Covington, Kyle R., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Farshidfar, Farshad, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Gingras, Marie-Claude, Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Hess, Julian M., Hinoue, Toshinori, Hoadley, Katherine A., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, McLellan, Michael D., McRee, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Newton, Yulia, Noble, Michael S., O’Brien, Daniel R., Ojesina, Akinyemi I., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Pedamallu, Chandra Sekhar, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Reznik, Ed, Rhie, Suhn K., Roach, Jeffrey, Roberts, Lewis R., Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shih, Juliann, Shinbrot, Eve, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stransky, Nicolas, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wu, Chia-Chin, Wu, Ye, Xi, Liu, Yang, Ju Dong, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zheng, Siyuan, Zmuda, Erik, Gibb, Ewan A., Roszik, Jason, Hegde, Apurva, Zhu, Andrew X., and Stuart, Josh M.

Published
2017
Full Text
View/download PDF

10. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles - correction

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A Gordon, Hinoue, Toshinori, Hoadley, Katherine A, Gibb, Ewan A, Roszik, Jason, Covington, Kyle R, Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Hess, Julian M, Auman, J Todd, Rhie, Suhn Kyong, Bowlby, Reanne, Borad, Mitesh J, Zhu, Andrew X, Stuart, Josh M, Sander, Chris, Akbani, Rehan, Cherniack, Andrew D, Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael S, Kleiner, David E, Laird, Peter W, Wheeler, David A, McRee, Autumn J, Bathe, Oliver F, Andersen, Jesper B, Bardeesy, Nabeel, Roberts, Lewis R, Kwong, Lawrence N, Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A Gordon, Hinoue, Toshinori, Hoadley, Katherine A, Gibb, Ewan A, Roszik, Jason, Covington, Kyle R, Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Hess, Julian M, Auman, J Todd, Rhie, Suhn Kyong, Bowlby, Reanne, Borad, Mitesh J, Zhu, Andrew X, Stuart, Josh M, Sander, Chris, Akbani, Rehan, Cherniack, Andrew D, Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael S, Kleiner, David E, Laird, Peter W, Wheeler, David A, McRee, Autumn J, Bathe, Oliver F, Andersen, Jesper B, Bardeesy, Nabeel, Roberts, Lewis R, and Kwong, Lawrence N

Published
2017

Catalog

Books, media, physical & digital resources
See catalog results