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401 results on '"Shukla, Sachet A."'

1. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma

Author

Nassar, Amin H., Abou Alaiwi, Sarah, Baca, Sylvan C., Adib, Elio, Corona, Rosario I., Seo, Ji-Heui, Fonseca, Marcos A. S., Spisak, Sandor, El Zarif, Talal, Tisza, Viktoria, Braun, David A., Du, Heng, He, Monica, Flaifel, Abdallah, Alchoueiry, Michel, Denize, Thomas, Matar, Sayed G., Acosta, Andres, Shukla, Sachet, Hou, Yue, Steinharter, John, Bouchard, Gabrielle, Berchuck, Jacob E., O’Connor, Edward, Bell, Connor, Nuzzo, Pier Vitale, Mary Lee, Gwo-Shu, Signoretti, Sabina, Hirsch, Michelle S., Pomerantz, Mark, Henske, Elizabeth, Gusev, Alexander, Lawrenson, Kate, Choueiri, Toni K., Kwiatkowski, David J., and Freedman, Matthew L.

Published
2023
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2. Germline variants associated with toxicity to immune checkpoint blockade

Author

Groha, Stefan, Alaiwi, Sarah Abou, Xu, Wenxin, Naranbhai, Vivek, Nassar, Amin H., Bakouny, Ziad, El Zarif, Talal, Saliby, Renee Maria, Wan, Guihong, Rajeh, Ahmad, Adib, Elio, Nuzzo, Pier V., Schmidt, Andrew L., Labaki, Chris, Ricciuti, Biagio, Alessi, Joao Victor, Braun, David A., Shukla, Sachet A., Keenan, Tanya E., Van Allen, Eliezer, Awad, Mark M., Manos, Michael, Rahma, Osama, Zubiri, Leyre, Villani, Alexandra-Chloe, Fairfax, Benjamin, Hammer, Christian, Khan, Zia, Reynolds, Kerry, Semenov, Yevgeniy, Schrag, Deborah, Kehl, Kenneth L., Freedman, Matthew L., Choueiri, Toni K., and Gusev, Alexander

Published
2022
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3. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect

Author

Bachireddy, Pavan, Ennis, Christina, Nguyen, Vinhkhang N, Gohil, Satyen H, Clement, Kendell, Shukla, Sachet A, Forman, Juliet, Barkas, Nikolaos, Freeman, Samuel, Bavli, Natalie, Elagina, Liudmila, Leshchiner, Ignaty, Mohammad, Arman W, Mathewson, Nathan D, Keskin, Derin B, Rassenti, Laura Z, Kipps, Thomas J, Brown, Jennifer R, Getz, Gad, Ho, Vincent T, Gnirke, Andreas, Neuberg, Donna, Soiffer, Robert J, Ritz, Jerome, Alyea, Edwin P, Kharchenko, Peter V, and Wu, Catherine J

Subjects
Stem Cell Research, Hematology, Rare Diseases, Cancer, Stem Cell Research - Nonembryonic - Human, Lymphoma, Transplantation, Genetics, Stem Cell Research - Nonembryonic - Non-Human, Graft vs Host Disease, Graft vs Leukemia Effect, HLA Antigens, Hematopoietic Stem Cell Transplantation, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Transplantation, Homologous, Biological Sciences, Medical and Health Sciences
Abstract

Leukemic relapse remains a major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis for relapse of advanced lymphoid malignancies remains incompletely understood and may involve escape from the graft-versus-leukemia (GvL) effect. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features influence transplant outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic, and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post-HSCT relapse are shaped by distinct molecular dynamics. Early relapses after allo-HSCT exhibited notable genetic stability; single CLL cell transcriptional analysis demonstrated a cellular heterogeneity that was static over time. In contrast, CLL cells relapsing late after allo-HSCT displayed notable genetic evolution and evidence of neoantigen depletion, consistent with marked single-cell transcriptional shifts that were unique to each patient. We observed a greater rate of epigenetic change for late relapses not seen in early relapses or relapses after chemotherapy alone, suggesting that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for human leukocyte antigen (HLA) loss was observed, even when present in pretransplant subpopulations. Gain of stem cell modules was a common signature associated with leukemia relapse regardless of posttransplant relapse kinetics. These data elucidate the biological pathways that underlie GvL resistance and posttransplant relapse.

Published
2020

4. ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome

Author

Parry, Erin M., Lemvigh, Camilla K., Deng, Stephanie, Dangle, Nathan, Ruthen, Neil, Knisbacher, Binyamin A., Broséus, Julien, Hergalant, Sébastien, Guièze, Romain, Li, Shuqiang, Zhang, Wandi, Johnson, Connor, Long, Jaclyn M., Yin, Shanye, Werner, Lillian, Anandappa, Annabelle, Purroy, Noelia, Gohil, Satyen, Oliveira, Giacomo, Bachireddy, Pavan, Shukla, Sachet A., Huang, Teddy, Khoury, Joseph D., Thakral, Beenu, Dickinson, Michael, Tam, Constantine, Livak, Kenneth J., Getz, Gad, Neuberg, Donna, Feugier, Pierre, Kharchenko, Peter, Wierda, William, Olsen, Lars Rønn, Jain, Nitin, and Wu, Catherine J.

Published
2023
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7. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

Author

Ouspenskaia, Tamara, Law, Travis, Clauser, Karl R., Klaeger, Susan, Sarkizova, Siranush, Aguet, François, Li, Bo, Christian, Elena, Knisbacher, Binyamin A., Le, Phuong M., Hartigan, Christina R., Keshishian, Hasmik, Apffel, Annie, Oliveira, Giacomo, Zhang, Wandi, Chen, Sarah, Chow, Yuen Ting, Ji, Zhe, Jungreis, Irwin, Shukla, Sachet A., Justesen, Sune, Bachireddy, Pavan, Kellis, Manolis, Getz, Gad, Hacohen, Nir, Keskin, Derin B., Carr, Steven A., Wu, Catherine J., and Regev, Aviv

Published
2022
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8. Genetic mechanisms of immune evasion in colorectal cancer

Author

Grasso, Catherine S, Giannakis, Marios, Wells, Daniel K, Hamada, Tsuyoshi, Mu, Xinmeng Jasmine, Quist, Michael, Nowak, Jonathan A, Nishihara, Reiko, Qian, Zhi Rong, Inamura, Kentaro, Morikawa, Teppei, Nosho, Katsuhiko, Abril-Rodriguez, Gabriel, Connolly, Charles, Escuin-Ordinas, Helena, Geybels, Milan S, Grady, William M, Hsu, Li, Hu-Lieskovan, Siwen, Huyghe, Jeroen R, Kim, Yeon Joo, Krystofinski, Paige, Leiserson, Mark DM, Montoya, Dennis J, Nadel, Brian B, Pellegrini, Matteo, Pritchard, Colin C, Puig-Saus, Cristina, Quist, Elleanor H, Raphael, Ben J, Salipante, Stephen J, Shin, Daniel Sanghoon, Shinbrot, Eve, Shirts, Brian, Shukla, Sachet, Stanford, Janet L, Sun, Wei, Tsoi, Jennifer, Upfill-Brown, Alexander, Wheeler, David A, Wu, Catherine J, Yu, Ming, Zaidi, Syed H, Zaretsky, Jesse M, Gabriel, Stacey B, Lander, Eric S, Garraway, Levi A, Hudson, Thomas J, Fuchs, Charles S, Ribas, Antoni, Ogino, Shuji, and Peters, Ulrike

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Genetic Testing, Digestive Diseases, Cancer, Colo-Rectal Cancer, Genetics, Aetiology, 2.1 Biological and endogenous factors, Colorectal Neoplasms, DNA Copy Number Variations, DNA Methylation, Germ-Line Mutation, HLA Antigens, Humans, Loss of Heterozygosity, Microsatellite Instability, Tumor Escape, Wnt Signaling Pathway, beta 2-Microglobulin, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

To understand the genetic drivers of immune recognition and evasion in colorectal cancer, we analyzed 1,211 colorectal cancer primary tumor samples, including 179 classified as microsatellite instability-high (MSI-high). This set includes The Cancer Genome Atlas colorectal cancer cohort of 592 samples, completed and analyzed here. MSI-high, a hypermutated, immunogenic subtype of colorectal cancer, had a high rate of significantly mutated genes in important immune-modulating pathways and in the antigen presentation machinery, including biallelic losses of B2M and HLA genes due to copy-number alterations and copy-neutral loss of heterozygosity. WNT/β-catenin signaling genes were significantly mutated in all colorectal cancer subtypes, and activated WNT/β-catenin signaling was correlated with the absence of T-cell infiltration. This large-scale genomic analysis of colorectal cancer demonstrates that MSI-high cases frequently undergo an immunoediting process that provides them with genetic events allowing immune escape despite high mutational load and frequent lymphocytic infiltration and, furthermore, that colorectal cancer tumors have genetic and methylation events associated with activated WNT signaling and T-cell exclusion.Significance: This multi-omic analysis of 1,211 colorectal cancer primary tumors reveals that it should be possible to better monitor resistance in the 15% of cases that respond to immune blockade therapy and also to use WNT signaling inhibitors to reverse immune exclusion in the 85% of cases that currently do not. Cancer Discov; 8(6); 730-49. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 663.

Published
2018

9. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

Author

Robertson, A Gordon, Kim, Jaegil, Al-Ahmadie, Hikmat, Bellmunt, Joaquim, Guo, Guangwu, Cherniack, Andrew D, Hinoue, Toshinori, Laird, Peter W, Hoadley, Katherine A, Akbani, Rehan, Castro, Mauro AA, Gibb, Ewan A, Kanchi, Rupa S, Gordenin, Dmitry A, Shukla, Sachet A, Sanchez-Vega, Francisco, Hansel, Donna E, Czerniak, Bogdan A, Reuter, Victor E, Su, Xiaoping, Carvalho, Benilton de Sa, Chagas, Vinicius S, Mungall, Karen L, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Lu, Yiling, Klimczak, Leszek J, Zhang, Jiexin, Choo, Caleb, Ojesina, Akinyemi I, Bullman, Susan, Leraas, Kristen M, Lichtenberg, Tara M, Wu, Catherine J, Schultz, Nicholaus, Getz, Gad, Meyerson, Matthew, Mills, Gordon B, McConkey, David J, Network, TCGA Research, Albert, Monique, Alexopoulou, Iakovina, Ally, Adrian, Antic, Tatjana, Aron, Manju, Balasundaram, Miruna, Bartlett, John, Baylin, Stephen B, Beaver, Allison, Birol, Inanc, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Broom, Bradley M, Bshara, Wiam, Burks, Eric, Cárcano, Flavio M, Carlsen, Rebecca, Carvalho, Benilton S, Carvalho, Andre L, Castle, Eric P, Castro, Patricia, Catto, James W, Chesla, David W, Chuah, Eric, Chudamani, Sudha, Cortessis, Victoria K, Cottingham, Sandra L, Crain, Daniel, Curley, Erin, Daneshmand, Siamak, Demchok, John A, Dhalla, Noreen, Djaladat, Hooman, Eckman, John, Egea, Sophie C, Engel, Jay, Felau, Ina, Ferguson, Martin L, Gardner, Johanna, Gastier-Foster, Julie M, Gerken, Mark, Gomez-Fernandez, Carmen R, and Harr, Jodi

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Genetics, Cancer Genomics, Urologic Diseases, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Aged, Cluster Analysis, DNA Methylation, Humans, MicroRNAs, Middle Aged, Muscle, Smooth, RNA, Long Noncoding, Survival Analysis, Urinary Bladder, Urinary Bladder Neoplasms, TCGA Research Network, APOBEC mutation, DNA methylation, basal mRNA subtype, lncRNA transcriptome, luminal mRNA subtype, microRNA, muscle-invasive bladder cancer, neoantigen, neuronal subtype, regulon, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.

Published
2017

10. Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

Author

Oliveira, Giacomo, Stromhaug, Kari, Klaeger, Susan, Kula, Tomasz, Frederick, Dennie T., Le, Phuong M., Forman, Juliet, Huang, Teddy, Li, Shuqiang, Zhang, Wandi, Xu, Qikai, Cieri, Nicoletta, Clauser, Karl R., Shukla, Sachet A., Neuberg, Donna, Justesen, Sune, MacBeath, Gavin, Carr, Steven A., Fritsch, Edward F., Hacohen, Nir, Sade-Feldman, Moshe, Livak, Kenneth J., Boland, Genevieve M., Ott, Patrick A., Keskin, Derin B., and Wu, Catherine J.

Published
2021
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11. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

Author

Hu, Zhuting, Leet, Donna E., Allesøe, Rosa L., Oliveira, Giacomo, Li, Shuqiang, Luoma, Adrienne M., Liu, Jinyan, Forman, Juliet, Huang, Teddy, Iorgulescu, J. Bryan, Holden, Rebecca, Sarkizova, Siranush, Gohil, Satyen H., Redd, Robert A., Sun, Jing, Elagina, Liudmila, Giobbie-Hurder, Anita, Zhang, Wandi, Peter, Lauren, Ciantra, Zoe, Rodig, Scott, Olive, Oriol, Shetty, Keerthi, Pyrdol, Jason, Uduman, Mohamed, Lee, Patrick C., Bachireddy, Pavan, Buchbinder, Elizabeth I., Yoon, Charles H., Neuberg, Donna, Pentelute, Bradley L., Hacohen, Nir, Livak, Kenneth J., Shukla, Sachet A., Olsen, Lars Rønn, Barouch, Dan H., Wucherpfennig, Kai W., Fritsch, Edward F., Keskin, Derin B., Wu, Catherine J., and Ott, Patrick A.

Published
2021
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12. Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit

Author

Barroso-Sousa, Romualdo, Forman, Juliet, Collier, Katharine, Weber, Zachary T., Jammihal, Tejas R., Kao, Katrina Z., Richardson, Edward T., III, Keenan, Tanya, Cohen, Ofir, Manos, Michael P., Brennick, Ryan C., Ott, Patrick A., Hodi, F. Stephen, Dillon, Deborah A., Attaya, Victoria, OʼMeara, Tess, Lin, Nancy U., Van Allen, Eliezer M., Rodig, Scott, Winer, Eric P., Mittendorf, Elizabeth A., Wu, Catherine J., Wagle, Nikhil, Stover, Daniel G., Shukla, Sachet A., and Tolaney, Sara M.

Published
2022
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13. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia

Author

Wang, Lili, Brooks, Angela N, Fan, Jean, Wan, Youzhong, Gambe, Rutendo, Li, Shuqiang, Hergert, Sarah, Yin, Shanye, Freeman, Samuel S, Levin, Joshua Z, Fan, Lin, Seiler, Michael, Buonamici, Silvia, Smith, Peter G, Chau, Kevin F, Cibulskis, Carrie L, Zhang, Wandi, Rassenti, Laura Z, Ghia, Emanuela M, Kipps, Thomas J, Fernandes, Stacey, Bloch, Donald B, Kotliar, Dylan, Landau, Dan A, Shukla, Sachet A, Aster, Jon C, Reed, Robin, DeLuca, David S, Brown, Jennifer R, Neuberg, Donna, Getz, Gad, Livak, Kenneth J, Meyerson, Matthew M, Kharchenko, Peter V, and Wu, Catherine J

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Lymphoma, Genetics, Clinical Research, Cancer, Rare Diseases, Hematology, 2.1 Biological and endogenous factors, Aetiology, Alternative Splicing, Cell Line, Tumor, Dishevelled Proteins, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Mutation, Phosphoproteins, RNA Splicing Factors, Receptors, Notch, Signal Transduction, CLL, Notch signaling, RNA sequencing, SF3B1, alternative splicing, Neurosciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to CLL progression remains poorly understood. We undertook a transcriptomic characterization of primary human CLL cells to identify transcripts and pathways affected by SF3B1 mutation. Splicing alterations, identified in the analysis of bulk cells, were confirmed in single SF3B1-mutated CLL cells and also found in cell lines ectopically expressing mutant SF3B1. SF3B1 mutation was found to dysregulate multiple cellular functions including DNA damage response, telomere maintenance, and Notch signaling (mediated through KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively). SF3B1 mutation leads to diverse changes in CLL-related pathways.

Published
2016

14. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer

Author

Weber, Zachary T., Collier, Katharine A., Tallman, David, Forman, Juliet, Shukla, Sachet, Asad, Sarah, Rhoades, Justin, Freeman, Samuel, Parsons, Heather A., Williams, Nicole O., Barroso-Sousa, Romualdo, Stover, Elizabeth H., Mahdi, Haider, Cibulskis, Carrie, Lennon, Niall J., Ha, Gavin, Adalsteinsson, Viktor A., Tolaney, Sara M., and Stover, Daniel G.

Published
2021
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15. Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma

Author

Bakouny, Ziad, Braun, David A., Shukla, Sachet A., Pan, Wenting, Gao, Xin, Hou, Yue, Flaifel, Abdallah, Tang, Stephen, Bosma-Moody, Alice, He, Meng Xiao, Vokes, Natalie, Nyman, Jackson, Xie, Wanling, Nassar, Amin H., Abou Alaiwi, Sarah, Flippot, Ronan, Bouchard, Gabrielle, Steinharter, John A., Nuzzo, Pier Vitale, Ficial, Miriam, Sant’Angelo, Miriam, Forman, Juliet, Berchuck, Jacob E., Dudani, Shaan, Bi, Kevin, Park, Jihye, Camp, Sabrina, Sticco-Ivins, Maura, Hirsch, Laure, Baca, Sylvan C., Wind-Rotolo, Megan, Ross-Macdonald, Petra, Sun, Maxine, Lee, Gwo-Shu Mary, Chang, Steven L., Wei, Xiao X., McGregor, Bradley A., Harshman, Lauren C., Genovese, Giannicola, Ellis, Leigh, Pomerantz, Mark, Hirsch, Michelle S., Freedman, Matthew L., Atkins, Michael B., Wu, Catherine J., Ho, Thai H., Linehan, W. Marston, McDermott, David F., Heng, Daniel Y. C., Viswanathan, Srinivas R., Signoretti, Sabina, Van Allen, Eliezer M., and Choueiri, Toni K.

Published
2021
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16. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma

Author

Braun, David A., Hou, Yue, Bakouny, Ziad, Ficial, Miriam, Sant’ Angelo, Miriam, Forman, Juliet, Ross-Macdonald, Petra, Berger, Ashton C., Jegede, Opeyemi A., Elagina, Liudmilla, Steinharter, John, Sun, Maxine, Wind-Rotolo, Megan, Pignon, Jean-Christophe, Cherniack, Andrew D., Lichtenstein, Lee, Neuberg, Donna, Catalano, Paul, Freeman, Gordon J., Sharpe, Arlene H., McDermott, David F., Van Allen, Eliezer M., Signoretti, Sabina, Wu, Catherine J., Shukla, Sachet A., and Choueiri, Toni K.

Published
2020
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17. Enriched Signalling Pathways in Venetoclax-Relapsed Chronic Lymphocytic Leukemia (CLL) Cells and Targeting Using a Protac-Based Bcl-2/Bcl-Xl Degrader

Author

Diaz Rohena, Daisy, primary, Peris Cuesta, Arnau, additional, Slawin, Bailey, additional, Ravikrishnan, Janani, additional, Liu, Chaomei, additional, Williams, Charmelle, additional, Hu, Wanyi, additional, Zhang, Peiyi, additional, Thompson, Philip, additional, Wierda, William G., additional, Jain, Nitin, additional, Shukla, Sachet, additional, Zheng, Guangrong, additional, Zhou, Daohong, additional, Woyach, Jennifer A., additional, and Sampath, Deepa, additional

Published
2023
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18. A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens

Author

Hu, Zhuting, Anandappa, Annabelle J., Sun, Jing, Kim, Jintaek, Leet, Donna E., Bozym, David J., Chen, Christina, Williams, Louise, Shukla, Sachet A., Zhang, Wandi, Tabbaa, Diana, Steelman, Scott, Olive, Oriol, Livak, Kenneth J., Kishi, Hiroyuki, Muraguchi, Atsushi, Guleria, Indira, Stevens, Jonathan, Lane, William J., Burkhardt, Ute E., Fritsch, Edward F., Neuberg, Donna, Ott, Patrick A., Keskin, Derin B., Hacohen, Nir, and Wu, Catherine J.

Published
2018
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19. The Somatic Genomic Landscape of Glioblastoma

Author

Brennan, Cameron W, Verhaak, Roel GW, McKenna, Aaron, Campos, Benito, Noushmehr, Houtan, Salama, Sofie R, Zheng, Siyuan, Chakravarty, Debyani, Sanborn, J Zachary, Berman, Samuel H, Beroukhim, Rameen, Bernard, Brady, Wu, Chang-Jiun, Genovese, Giannicola, Shmulevich, Ilya, Barnholtz-Sloan, Jill, Zou, Lihua, Vegesna, Rahulsimham, Shukla, Sachet A, Ciriello, Giovanni, Yung, WK, Zhang, Wei, Sougnez, Carrie, Mikkelsen, Tom, Aldape, Kenneth, Bigner, Darell D, Van Meir, Erwin G, Prados, Michael, Sloan, Andrew, Black, Keith L, Eschbacher, Jennifer, Finocchiaro, Gaetano, Friedman, William, Andrews, David W, Guha, Abhijit, Iacocca, Mary, O’Neill, Brian P, Foltz, Greg, Myers, Jerome, Weisenberger, Daniel J, Penny, Robert, Kucherlapati, Raju, Perou, Charles M, Hayes, D Neil, Gibbs, Richard, Marra, Marco, Mills, Gordon B, Lander, Eric, Spellman, Paul, Wilson, Richard, Sander, Chris, Weinstein, John, Meyerson, Matthew, Gabriel, Stacey, Laird, Peter W, Haussler, David, Getz, Gad, Chin, Lynda, Network, TCGA Research, Benz, Christopher, Barrett, Wendi, Ostrom, Quinn, Wolinsky, Yingli, Bose, Bikash, Boulos, Paul T, Boulos, Madgy, Brown, Jenn, Czerinski, Christine, Eppley, Matthew, Kempista, Thelma, Kitko, Teresa, Koyfman, Yakov, Rabeno, Brenda, Rastogi, Pawan, Sugarman, Michael, Swanson, Patricia, Yalamanchii, Kennedy, Otey, Ilana P, Liu, Yingchun Spring, Xiao, Yonghong, Auman, J Todd, Chen, Peng-Chieh, Hadjipanayis, Angela, Lee, Eunjung, Lee, Semin, Park, Peter J, Seidman, Jonathan, Yang, Lixing, Kalkanis, Steven, Poisson, Laila M, Raghunathan, Aditya, Scarpace, Lisa, Bressler, Ryan, and Eakin, Andrea

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Brain Cancer, Precision Medicine, Orphan Drug, Biotechnology, Rare Diseases, Brain Disorders, Cancer, Neurosciences, Cancer Genomics, Human Genome, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, 5.1 Pharmaceuticals, 4.2 Evaluation of markers and technologies, Brain Neoplasms, Female, Gene Expression Profiling, Gene Regulatory Networks, Glioblastoma, Humans, Male, Mutation, Proteome, Signal Transduction, TCGA Research Network, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.

Published
2013

22. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

Author

Keskin, Derin B., Anandappa, Annabelle J., Sun, Jing, Tirosh, Itay, Mathewson, Nathan D., Li, Shuqiang, Oliveira, Giacomo, Giobbie-Hurder, Anita, Felt, Kristen, Gjini, Evisa, Shukla, Sachet A., Hu, Zhuting, Li, Letitia, Le, Phuong M., Allesøe, Rosa L., Richman, Alyssa R., Kowalczyk, Monika S., Abdelrahman, Sara, Geduldig, Jack E., Charbonneau, Sarah, Pelton, Kristine, Iorgulescu, J. Bryan, Elagina, Liudmila, Zhang, Wandi, Olive, Oriol, McCluskey, Christine, Olsen, Lars R., Stevens, Jonathan, Lane, William J., Salazar, Andres M., Daley, Heather, Wen, Patrick Y., Chiocca, E. Antonio, Harden, Maegan, Lennon, Niall J., Gabriel, Stacey, Getz, Gad, Lander, Eric S., Regev, Aviv, Ritz, Jerome, Neuberg, Donna, Rodig, Scott J., Ligon, Keith L., Suvà, Mario L., Wucherpfennig, Kai W., Hacohen, Nir, Fritsch, Edward F., Livak, Kenneth J., Ott, Patrick A., Wu, Catherine J., and Reardon, David A.

Published
2019
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23. Comprehensive genomic characterization of squamous cell lung cancers

Author

Hammerman, Peter S, Lawrence, Michael S, Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S, Gabriel, Stacey, Getz, Gad, Sougnez, Carrie, Imielinski, Marcin, Helman, Elena, Hernandez, Bryan, Pho, Nam H, Meyerson, Matthew, Chu, Andy, Chun, Hye-Jung E, Mungall, Andrew J, Pleasance, Erin, Gordon Robertson, A, Sipahimalani, Payal, Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Chuah, Eric, Coope, Robin JN, Corbett, Richard, Dhalla, Noreen, Guin, Ranabir, He, An, Hirst, Carrie, Hirst, Martin, Holt, Robert A, Lee, Darlene, Li, Haiyan I, Mayo, Michael, Moore, Richard A, Mungall, Karen, Ming Nip, Ka, Olshen, Adam, Schein, Jacqueline E, Slobodan, Jared R, Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven JM, Marra, Marco A, Saksena, Gordon, Cherniack, Andrew D, Schumacher, Stephen E, Tabak, Barbara, Carter, Scott L, Nguyen, Huy, Onofrio, Robert C, Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Protopopov, Alexei, Zhang, Jianhua, Hadjipanayis, Angela, Lee, Semin, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Lee, Eunjung, Chin, Lynda, Park, Peter J, Kucherlapati, Raju, Socci, Nicholas D, Liang, Yupu, Schultz, Nikolaus, Borsu, Laetitia, Lash, Alex E, Viale, Agnes, Sander, Chris, Ladanyi, Marc, Todd Auman, J, Hoadley, Katherine A, Wilkerson, Matthew D, Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J, Topal, Michael D, and Tan, Donghui

Subjects
Human Genome, Biotechnology, Genetics, Rare Diseases, Cancer, Lung Cancer, Lung, Aetiology, 2.1 Biological and endogenous factors, Adenocarcinoma, Adenocarcinoma of Lung, Carcinoma, Squamous Cell, DNA Mutational Analysis, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genes, p16, Genes, p53, Genome, Human, Genomics, Humans, Lung Neoplasms, Molecular Targeted Therapy, Mutation, Mutation Rate, Phosphatidylinositol 3-Kinases, Signal Transduction, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.

Published
2012

24. Impact of renal cell carcinoma molecular subtypes on immunotherapy and targeted therapy outcomes

Author

Saliby, Renée Maria, Labaki, Chris, Jammihal, Tejas R., Xie, Wanling, Sun, Maxine, Shah, Valisha, Saad, Eddy, Kane, M. Harry, Kashima, Soki, Sadak, Katherine, El Zarif, Talal, Poduval, Deepak, Motzer, Robert J., Powles, Thomas, Rini, Brian I., Albiges, Laurence, Pal, Sumanta K., McGregor, Bradley A., McKay, Rana R., Signoretti, Sabina, Van Allen, Eliezer M., Shukla, Sachet A., Choueiri, Toni K., and Braun, David A.

Published
2024
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25. Characterization of the Cellular Origin and Oncogenic Mechanisms of Chromophobe Renal Cell Carcinoma (ChRCC) and Renal Oncocytic Neoplasms

Author

Labaki, Chris, primary, Al-Choueiry, Michel, additional, Nyman, Jackson, additional, Hou, Yue, additional, Bi, Kevin, additional, Zhang, Long, additional, Hobeika, Charbel, additional, Bakouny, Ziad, additional, Priolo, Carmen, additional, Khabibullin, Damir, additional, Schindler, Nicholas, additional, Fu, Jingxin, additional, Camp, Sabrina, additional, Maria Saliby, Renee, additional, Saad, Eddy, additional, Van Allen, Eliezer M, additional, Shukla, Sachet, additional, Henske, Elizabeth P, additional, Choueiri, Toni, additional, and Braun, David, additional

Published
2023
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26. Abstract PR015: Tumor-specific immunity generated by a personalized neoantigen vaccination incorporating locally delivered ipilimumab in renal cell carcinoma

Author

Braun, David A., primary, Keskin, Derin B., additional, Shukla, Sachet A., additional, McGregor, Bradley A., additional, Schindler, Nicholas R., additional, Blass, Eryn, additional, Klaeger, Susan, additional, Pomerance, Lucas, additional, Sarkizova, Siranush, additional, Li, Shuqiang, additional, Southard, Jackson, additional, Moranzoni, Giorgia, additional, Pedersen, Christina B., additional, Liu, Yiwen, additional, Chang, Steven L., additional, Hirsch, Michelle S., additional, LeBoeuf, Nicole R., additional, Mossanen, Matthew, additional, Chea, Vipheaviny, additional, Carulli, Isabel, additional, Olive, Oriol, additional, Mehndiratta, Ambica, additional, Greenslade, Haley, additional, Oliveira, Giacomo, additional, Iorgulescu, J. Bryan, additional, Signoretti, Sabina, additional, Aster, Jon C., additional, Elagina, Liudmila, additional, Leshchiner, Ignaty, additional, Getz, Gad, additional, Harden, Maegan, additional, Gabriel, Stacey, additional, Olsen, Lars R., additional, Neuberg, Donna S., additional, Fritsch, Edward F., additional, Hacohen, Nir, additional, Livak, Kenneth J., additional, Carr, Steven, additional, Ott, Patrick A., additional, Wu, Catherine J., additional, and Choueiri, Toni K., additional

Published
2023
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27. Abstract A013: Tumor-specific immunity generated by a personalized neoantigen vaccination incorporating locally delivered ipilimumab in renal cell carcinoma

Author

Braun, David A., primary, Keskin, Derin B., additional, Shukla, Sachet A., additional, McGregor, Bradley A., additional, Schindler, Nicholas R., additional, Blass, Eryn, additional, Klaeger, Susan, additional, Pomerance, Lucas, additional, Sarkizova, Siranush, additional, Li, Shuqiang, additional, Southard, Jackson, additional, Moranzoni, Giorgia, additional, Pedersen, Christina B., additional, Liu, Yiwen, additional, Chang, Steven L., additional, Hirsch, Michelle S., additional, LeBoeuf, Nicole R., additional, Mossanen, Matthew, additional, Chea, Vipheaviny, additional, Carulli, Isabel, additional, Olive, Oriol, additional, Mehndiratta, Ambica, additional, Greenslade, Haley, additional, Oliveira, Giacomo, additional, Iorgulescu, J. Bryan, additional, Signoretti, Sabina, additional, Aster, Jon C., additional, Elagina, Liudmila, additional, Leshchiner, Ignaty, additional, Getz, Gad, additional, Harden, Maegan, additional, Gabriel, Stacey, additional, Olsen, Lars R., additional, Neuberg, Donna S., additional, Fritsch, Edward F., additional, Hacohen, Nir, additional, Livak, Kenneth J., additional, Carr, Steven, additional, Ott, Patrick A., additional, Wu, Catherine J., additional, and Choueiri, Toni K., additional

Published
2023
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28. Abstract B019: Clinical and molecular characterization of chromophobe renal cell carcinoma: A focus on immunotherapy based regimens and the tumor immune microenvironment

Author

Alchoueiry, Michel, primary, Labaki, Chris, additional, Zhang, Long, additional, Hou, Yue, additional, Bi, Kevin, additional, Hobeika, Charbel, additional, Wells, J. Connor, additional, Takemura, Kosuke, additional, Bakouny, Ziad, additional, Camp, Sabrina, additional, Priolo, Carmen, additional, Khabibullin, Damir, additional, Schindler, Nicholas, additional, Saliby, Renee Maria, additional, Saad, Eddy, additional, Salem, Samer, additional, Daou, Melissa, additional, McKay, Rana, additional, Pal, Sumanta, additional, Heng, Daniel, additional, Van Allen, Eliezer, additional, Shukla, Sachet, additional, Choueiri, Toni, additional, Braun, David, additional, and Henske, Elizabeth, additional

Published
2023
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29. Immunogenomic determinants of exceptional response to immune checkpoint inhibition in renal cell carcinoma

Author

Shukla, Sachet, primary, Jammihal, Tejas, additional, Saliby, Renée-Maria, additional, Labaki, Chris, additional, Soulati, Hanna, additional, Gallegos, Juan, additional, Cuesta, Arnau Peris, additional, McCurry, Dustin, additional, Yu, Chunlei, additional, Shah, Valisha, additional, Poduval, Deepak, additional, Zarif, Talal El, additional, Ahmar, Nourhan El, additional, Laimon, Yasmin, additional, Eid, Marc, additional, Heng, Daniel, additional, Casellas, Rafael, additional, Rai, Kunal, additional, Millward, Niki Zacharias, additional, Msaouel, Pavlos, additional, Karam, Jose, additional, Signoretti, Sabina, additional, Allen, Eliezer Van, additional, Choueiri, Toni, additional, and Braun, David, additional

Published
2023
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30. Cellular and molecular determinants of limited anti-tumor immunity in chromophobe renal carcinoma (ChRCC).

Author

Labaki, Chris, Alchoueiry, Michel, Bi, Kevin, Zhang, Long, Hobeika, Charbel, Bakouny, Ziad, El Ahmar, Nourhan, Matar, Sayed, Priolo, Carmen, Khabibullin, Damir, Schindler, Nicholas R., Camp, Sabrina Yvonne, Saliby, Renee Maria, Saad, Eddy, Signoretti, Sabina, Van Allen, Eliezer Mendel, Shukla, Sachet A, Henske, Elizabeth, Choueiri, Toni K., and Braun, David A.

Published
2024
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31. Data from Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors

Author

Abou Alaiwi, Sarah, primary, Nassar, Amin H., primary, Xie, Wanling, primary, Bakouny, Ziad, primary, Berchuck, Jacob E., primary, Braun, David A., primary, Baca, Sylvan C., primary, Nuzzo, Pier Vitale, primary, Flippot, Ronan, primary, Mouhieddine, Tarek H., primary, Spurr, Liam F., primary, Li, Yvonne Y., primary, Li, Taiwen, primary, Flaifel, Abdallah, primary, Steinharter, John A., primary, Margolis, Claire A., primary, Vokes, Natalie I., primary, Du, Heng, primary, Shukla, Sachet A., primary, Cherniack, Andrew D., primary, Sonpavde, Guru, primary, Haddad, Robert I., primary, Awad, Mark M., primary, Giannakis, Marios, primary, Hodi, F. Stephen, primary, Liu, X. Shirley, primary, Signoretti, Sabina, primary, Kadoch, Cigall, primary, Freedman, Matthew L., primary, Kwiatkowski, David J., primary, Van Allen, Eliezer M., primary, and Choueiri, Toni K., primary

Published
2023
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32. Supplementary Figures Legends from Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors

Author

Abou Alaiwi, Sarah, primary, Nassar, Amin H., primary, Xie, Wanling, primary, Bakouny, Ziad, primary, Berchuck, Jacob E., primary, Braun, David A., primary, Baca, Sylvan C., primary, Nuzzo, Pier Vitale, primary, Flippot, Ronan, primary, Mouhieddine, Tarek H., primary, Spurr, Liam F., primary, Li, Yvonne Y., primary, Li, Taiwen, primary, Flaifel, Abdallah, primary, Steinharter, John A., primary, Margolis, Claire A., primary, Vokes, Natalie I., primary, Du, Heng, primary, Shukla, Sachet A., primary, Cherniack, Andrew D., primary, Sonpavde, Guru, primary, Haddad, Robert I., primary, Awad, Mark M., primary, Giannakis, Marios, primary, Hodi, F. Stephen, primary, Liu, X. Shirley, primary, Signoretti, Sabina, primary, Kadoch, Cigall, primary, Freedman, Matthew L., primary, Kwiatkowski, David J., primary, Van Allen, Eliezer M., primary, and Choueiri, Toni K., primary

Published
2023
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33. Supplementary Tables from Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors

Author

Abou Alaiwi, Sarah, primary, Nassar, Amin H., primary, Xie, Wanling, primary, Bakouny, Ziad, primary, Berchuck, Jacob E., primary, Braun, David A., primary, Baca, Sylvan C., primary, Nuzzo, Pier Vitale, primary, Flippot, Ronan, primary, Mouhieddine, Tarek H., primary, Spurr, Liam F., primary, Li, Yvonne Y., primary, Li, Taiwen, primary, Flaifel, Abdallah, primary, Steinharter, John A., primary, Margolis, Claire A., primary, Vokes, Natalie I., primary, Du, Heng, primary, Shukla, Sachet A., primary, Cherniack, Andrew D., primary, Sonpavde, Guru, primary, Haddad, Robert I., primary, Awad, Mark M., primary, Giannakis, Marios, primary, Hodi, F. Stephen, primary, Liu, X. Shirley, primary, Signoretti, Sabina, primary, Kadoch, Cigall, primary, Freedman, Matthew L., primary, Kwiatkowski, David J., primary, Van Allen, Eliezer M., primary, and Choueiri, Toni K., primary

Published
2023
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35. Supplementary Tables 1-7 from Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System

Author

Trinh, Anne, primary, Gil Del Alcazar, Carlos R., primary, Shukla, Sachet A., primary, Chin, Koei, primary, Chang, Young Hwan, primary, Thibault, Guillaume, primary, Eng, Jennifer, primary, Jovanović, Bojana, primary, Aldaz, C. Marcelo, primary, Park, So Yeon, primary, Jeong, Joon, primary, Wu, Catherine, primary, Gray, Joe, primary, and Polyak, Kornelia, primary

Published
2023
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36. Supplementary Methods and Figures 1-5 from Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System

Author

Trinh, Anne, primary, Gil Del Alcazar, Carlos R., primary, Shukla, Sachet A., primary, Chin, Koei, primary, Chang, Young Hwan, primary, Thibault, Guillaume, primary, Eng, Jennifer, primary, Jovanović, Bojana, primary, Aldaz, C. Marcelo, primary, Park, So Yeon, primary, Jeong, Joon, primary, Wu, Catherine, primary, Gray, Joe, primary, and Polyak, Kornelia, primary

Published
2023
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37. Supplementary Table S7 from The Genomic Landscape of Pediatric Ewing Sarcoma

Author

Crompton, Brian D., primary, Stewart, Chip, primary, Taylor-Weiner, Amaro, primary, Alexe, Gabriela, primary, Kurek, Kyle C., primary, Calicchio, Monica L., primary, Kiezun, Adam, primary, Carter, Scott L., primary, Shukla, Sachet A., primary, Mehta, Swapnil S., primary, Thorner, Aaron R., primary, de Torres, Carmen, primary, Lavarino, Cinzia, primary, Suñol, Mariona, primary, McKenna, Aaron, primary, Sivachenko, Andrey, primary, Cibulskis, Kristian, primary, Lawrence, Michael S., primary, Stojanov, Petar, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Seepo, Sara, primary, Blumenstiel, Brendan, primary, DeFelice, Matthew, primary, Imaz-Rosshandler, Ivan, primary, Schwarz-Cruz y Celis, Angela, primary, Rivera, Miguel N., primary, Rodriguez-Galindo, Carlos, primary, Fleming, Mark D., primary, Golub, Todd R., primary, Getz, Gad, primary, Mora, Jaume, primary, and Stegmaier, Kimberly, primary

Published
2023
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38. Data from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma

Author

Genovese, Giannicola, primary, Ergun, Ayla, primary, Shukla, Sachet A., primary, Campos, Benito, primary, Hanna, Jason, primary, Ghosh, Papia, primary, Quayle, Steven N., primary, Rai, Kunal, primary, Colla, Simona, primary, Ying, Haoqiang, primary, Wu, Chang-Jiun, primary, Sarkar, Sharmistha, primary, Xiao, Yonghong, primary, Zhang, Jianhua, primary, Zhang, Hailei, primary, Kwong, Lawrence, primary, Dunn, Katherine, primary, Wiedemeyer, Wolf Ruprecht, primary, Brennan, Cameron, primary, Zheng, Hongwu, primary, Rimm, David L., primary, Collins, James J., primary, and Chin, Lynda, primary

Published
2023
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39. Supplementary Tables 1-10 from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma

Author

Genovese, Giannicola, primary, Ergun, Ayla, primary, Shukla, Sachet A., primary, Campos, Benito, primary, Hanna, Jason, primary, Ghosh, Papia, primary, Quayle, Steven N., primary, Rai, Kunal, primary, Colla, Simona, primary, Ying, Haoqiang, primary, Wu, Chang-Jiun, primary, Sarkar, Sharmistha, primary, Xiao, Yonghong, primary, Zhang, Jianhua, primary, Zhang, Hailei, primary, Kwong, Lawrence, primary, Dunn, Katherine, primary, Wiedemeyer, Wolf Ruprecht, primary, Brennan, Cameron, primary, Zheng, Hongwu, primary, Rimm, David L., primary, Collins, James J., primary, and Chin, Lynda, primary

Published
2023
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40. Supp. Table S22 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author

Grasso, Catherine S., primary, Giannakis, Marios, primary, Wells, Daniel K., primary, Hamada, Tsuyoshi, primary, Mu, Xinmeng Jasmine, primary, Quist, Michael, primary, Nowak, Jonathan A., primary, Nishihara, Reiko, primary, Qian, Zhi Rong, primary, Inamura, Kentaro, primary, Morikawa, Teppei, primary, Nosho, Katsuhiko, primary, Abril-Rodriguez, Gabriel, primary, Connolly, Charles, primary, Escuin-Ordinas, Helena, primary, Geybels, Milan S., primary, Grady, William M., primary, Hsu, Li, primary, Hu-Lieskovan, Siwen, primary, Huyghe, Jeroen R., primary, Kim, Yeon Joo, primary, Krystofinski, Paige, primary, Leiserson, Mark D.M., primary, Montoya, Dennis J., primary, Nadel, Brian B., primary, Pellegrini, Matteo, primary, Pritchard, Colin C., primary, Puig-Saus, Cristina, primary, Quist, Elleanor H., primary, Raphael, Ben J., primary, Salipante, Stephen J., primary, Shin, Daniel Sanghoon, primary, Shinbrot, Eve, primary, Shirts, Brian, primary, Shukla, Sachet, primary, Stanford, Janet L., primary, Sun, Wei, primary, Tsoi, Jennifer, primary, Upfill-Brown, Alexander, primary, Wheeler, David A., primary, Wu, Catherine J., primary, Yu, Ming, primary, Zaidi, Syed H., primary, Zaretsky, Jesse M., primary, Gabriel, Stacey B., primary, Lander, Eric S., primary, Garraway, Levi A., primary, Hudson, Thomas J., primary, Fuchs, Charles S., primary, Ribas, Antoni, primary, Ogino, Shuji, primary, and Peters, Ulrike, primary

Published
2023
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41. Supplementary Methods, Figure Legends, Figures S1 - S6, Tables S1, S3 - S6, S8 - S15, S17 from The Genomic Landscape of Pediatric Ewing Sarcoma

Author

Crompton, Brian D., primary, Stewart, Chip, primary, Taylor-Weiner, Amaro, primary, Alexe, Gabriela, primary, Kurek, Kyle C., primary, Calicchio, Monica L., primary, Kiezun, Adam, primary, Carter, Scott L., primary, Shukla, Sachet A., primary, Mehta, Swapnil S., primary, Thorner, Aaron R., primary, de Torres, Carmen, primary, Lavarino, Cinzia, primary, Suñol, Mariona, primary, McKenna, Aaron, primary, Sivachenko, Andrey, primary, Cibulskis, Kristian, primary, Lawrence, Michael S., primary, Stojanov, Petar, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Seepo, Sara, primary, Blumenstiel, Brendan, primary, DeFelice, Matthew, primary, Imaz-Rosshandler, Ivan, primary, Schwarz-Cruz y Celis, Angela, primary, Rivera, Miguel N., primary, Rodriguez-Galindo, Carlos, primary, Fleming, Mark D., primary, Golub, Todd R., primary, Getz, Gad, primary, Mora, Jaume, primary, and Stegmaier, Kimberly, primary

Published
2023
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42. Data from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author

Grasso, Catherine S., primary, Giannakis, Marios, primary, Wells, Daniel K., primary, Hamada, Tsuyoshi, primary, Mu, Xinmeng Jasmine, primary, Quist, Michael, primary, Nowak, Jonathan A., primary, Nishihara, Reiko, primary, Qian, Zhi Rong, primary, Inamura, Kentaro, primary, Morikawa, Teppei, primary, Nosho, Katsuhiko, primary, Abril-Rodriguez, Gabriel, primary, Connolly, Charles, primary, Escuin-Ordinas, Helena, primary, Geybels, Milan S., primary, Grady, William M., primary, Hsu, Li, primary, Hu-Lieskovan, Siwen, primary, Huyghe, Jeroen R., primary, Kim, Yeon Joo, primary, Krystofinski, Paige, primary, Leiserson, Mark D.M., primary, Montoya, Dennis J., primary, Nadel, Brian B., primary, Pellegrini, Matteo, primary, Pritchard, Colin C., primary, Puig-Saus, Cristina, primary, Quist, Elleanor H., primary, Raphael, Ben J., primary, Salipante, Stephen J., primary, Shin, Daniel Sanghoon, primary, Shinbrot, Eve, primary, Shirts, Brian, primary, Shukla, Sachet, primary, Stanford, Janet L., primary, Sun, Wei, primary, Tsoi, Jennifer, primary, Upfill-Brown, Alexander, primary, Wheeler, David A., primary, Wu, Catherine J., primary, Yu, Ming, primary, Zaidi, Syed H., primary, Zaretsky, Jesse M., primary, Gabriel, Stacey B., primary, Lander, Eric S., primary, Garraway, Levi A., primary, Hudson, Thomas J., primary, Fuchs, Charles S., primary, Ribas, Antoni, primary, Ogino, Shuji, primary, and Peters, Ulrike, primary

Published
2023
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43. Supplementary Figures 1-13 from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma

Author

Genovese, Giannicola, primary, Ergun, Ayla, primary, Shukla, Sachet A., primary, Campos, Benito, primary, Hanna, Jason, primary, Ghosh, Papia, primary, Quayle, Steven N., primary, Rai, Kunal, primary, Colla, Simona, primary, Ying, Haoqiang, primary, Wu, Chang-Jiun, primary, Sarkar, Sharmistha, primary, Xiao, Yonghong, primary, Zhang, Jianhua, primary, Zhang, Hailei, primary, Kwong, Lawrence, primary, Dunn, Katherine, primary, Wiedemeyer, Wolf Ruprecht, primary, Brennan, Cameron, primary, Zheng, Hongwu, primary, Rimm, David L., primary, Collins, James J., primary, and Chin, Lynda, primary

Published
2023
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45. Supp. Tables S1, S3-S15, S20, and S23 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author

Grasso, Catherine S., primary, Giannakis, Marios, primary, Wells, Daniel K., primary, Hamada, Tsuyoshi, primary, Mu, Xinmeng Jasmine, primary, Quist, Michael, primary, Nowak, Jonathan A., primary, Nishihara, Reiko, primary, Qian, Zhi Rong, primary, Inamura, Kentaro, primary, Morikawa, Teppei, primary, Nosho, Katsuhiko, primary, Abril-Rodriguez, Gabriel, primary, Connolly, Charles, primary, Escuin-Ordinas, Helena, primary, Geybels, Milan S., primary, Grady, William M., primary, Hsu, Li, primary, Hu-Lieskovan, Siwen, primary, Huyghe, Jeroen R., primary, Kim, Yeon Joo, primary, Krystofinski, Paige, primary, Leiserson, Mark D.M., primary, Montoya, Dennis J., primary, Nadel, Brian B., primary, Pellegrini, Matteo, primary, Pritchard, Colin C., primary, Puig-Saus, Cristina, primary, Quist, Elleanor H., primary, Raphael, Ben J., primary, Salipante, Stephen J., primary, Shin, Daniel Sanghoon, primary, Shinbrot, Eve, primary, Shirts, Brian, primary, Shukla, Sachet, primary, Stanford, Janet L., primary, Sun, Wei, primary, Tsoi, Jennifer, primary, Upfill-Brown, Alexander, primary, Wheeler, David A., primary, Wu, Catherine J., primary, Yu, Ming, primary, Zaidi, Syed H., primary, Zaretsky, Jesse M., primary, Gabriel, Stacey B., primary, Lander, Eric S., primary, Garraway, Levi A., primary, Hudson, Thomas J., primary, Fuchs, Charles S., primary, Ribas, Antoni, primary, Ogino, Shuji, primary, and Peters, Ulrike, primary

Published
2023
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46. Supplementary Methods, Figure Legends 1-13, Table Legends 1-10 from microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma

Author

Genovese, Giannicola, primary, Ergun, Ayla, primary, Shukla, Sachet A., primary, Campos, Benito, primary, Hanna, Jason, primary, Ghosh, Papia, primary, Quayle, Steven N., primary, Rai, Kunal, primary, Colla, Simona, primary, Ying, Haoqiang, primary, Wu, Chang-Jiun, primary, Sarkar, Sharmistha, primary, Xiao, Yonghong, primary, Zhang, Jianhua, primary, Zhang, Hailei, primary, Kwong, Lawrence, primary, Dunn, Katherine, primary, Wiedemeyer, Wolf Ruprecht, primary, Brennan, Cameron, primary, Zheng, Hongwu, primary, Rimm, David L., primary, Collins, James J., primary, and Chin, Lynda, primary

Published
2023
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47. Supp. Tables S16-S19 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author

Grasso, Catherine S., primary, Giannakis, Marios, primary, Wells, Daniel K., primary, Hamada, Tsuyoshi, primary, Mu, Xinmeng Jasmine, primary, Quist, Michael, primary, Nowak, Jonathan A., primary, Nishihara, Reiko, primary, Qian, Zhi Rong, primary, Inamura, Kentaro, primary, Morikawa, Teppei, primary, Nosho, Katsuhiko, primary, Abril-Rodriguez, Gabriel, primary, Connolly, Charles, primary, Escuin-Ordinas, Helena, primary, Geybels, Milan S., primary, Grady, William M., primary, Hsu, Li, primary, Hu-Lieskovan, Siwen, primary, Huyghe, Jeroen R., primary, Kim, Yeon Joo, primary, Krystofinski, Paige, primary, Leiserson, Mark D.M., primary, Montoya, Dennis J., primary, Nadel, Brian B., primary, Pellegrini, Matteo, primary, Pritchard, Colin C., primary, Puig-Saus, Cristina, primary, Quist, Elleanor H., primary, Raphael, Ben J., primary, Salipante, Stephen J., primary, Shin, Daniel Sanghoon, primary, Shinbrot, Eve, primary, Shirts, Brian, primary, Shukla, Sachet, primary, Stanford, Janet L., primary, Sun, Wei, primary, Tsoi, Jennifer, primary, Upfill-Brown, Alexander, primary, Wheeler, David A., primary, Wu, Catherine J., primary, Yu, Ming, primary, Zaidi, Syed H., primary, Zaretsky, Jesse M., primary, Gabriel, Stacey B., primary, Lander, Eric S., primary, Garraway, Levi A., primary, Hudson, Thomas J., primary, Fuchs, Charles S., primary, Ribas, Antoni, primary, Ogino, Shuji, primary, and Peters, Ulrike, primary

Published
2023
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48. Data from Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System

Author

Trinh, Anne, primary, Gil Del Alcazar, Carlos R., primary, Shukla, Sachet A., primary, Chin, Koei, primary, Chang, Young Hwan, primary, Thibault, Guillaume, primary, Eng, Jennifer, primary, Jovanović, Bojana, primary, Aldaz, C. Marcelo, primary, Park, So Yeon, primary, Jeong, Joon, primary, Wu, Catherine, primary, Gray, Joe, primary, and Polyak, Kornelia, primary

Published
2023
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49. Supp. Figures and Legends from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author

Grasso, Catherine S., primary, Giannakis, Marios, primary, Wells, Daniel K., primary, Hamada, Tsuyoshi, primary, Mu, Xinmeng Jasmine, primary, Quist, Michael, primary, Nowak, Jonathan A., primary, Nishihara, Reiko, primary, Qian, Zhi Rong, primary, Inamura, Kentaro, primary, Morikawa, Teppei, primary, Nosho, Katsuhiko, primary, Abril-Rodriguez, Gabriel, primary, Connolly, Charles, primary, Escuin-Ordinas, Helena, primary, Geybels, Milan S., primary, Grady, William M., primary, Hsu, Li, primary, Hu-Lieskovan, Siwen, primary, Huyghe, Jeroen R., primary, Kim, Yeon Joo, primary, Krystofinski, Paige, primary, Leiserson, Mark D.M., primary, Montoya, Dennis J., primary, Nadel, Brian B., primary, Pellegrini, Matteo, primary, Pritchard, Colin C., primary, Puig-Saus, Cristina, primary, Quist, Elleanor H., primary, Raphael, Ben J., primary, Salipante, Stephen J., primary, Shin, Daniel Sanghoon, primary, Shinbrot, Eve, primary, Shirts, Brian, primary, Shukla, Sachet, primary, Stanford, Janet L., primary, Sun, Wei, primary, Tsoi, Jennifer, primary, Upfill-Brown, Alexander, primary, Wheeler, David A., primary, Wu, Catherine J., primary, Yu, Ming, primary, Zaidi, Syed H., primary, Zaretsky, Jesse M., primary, Gabriel, Stacey B., primary, Lander, Eric S., primary, Garraway, Levi A., primary, Hudson, Thomas J., primary, Fuchs, Charles S., primary, Ribas, Antoni, primary, Ogino, Shuji, primary, and Peters, Ulrike, primary

Published
2023
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50. Supplementary Figure from Transcriptomic Correlates of Tumor Cell PD-L1 Expression and Response to Nivolumab Monotherapy in Metastatic Clear Cell Renal Cell Carcinoma

Author

Denize, Thomas, primary, Hou, Yue, primary, Pignon, Jean-Christophe, primary, Walton, Emily, primary, West, Destiny J., primary, Freeman, Gordon J., primary, Braun, David A., primary, Wu, Catherine J., primary, Gupta, Saurabh, primary, Motzer, Robert J., primary, Atkins, Michael B., primary, McDermott, David, primary, Choueiri, Toni K., primary, Shukla, Sachet A., primary, and Signoretti, Sabina, primary

Published
2023
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