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249 results on '"Johannessen, Cory M."'

1. Author Correction: Comprehensive mutational scanning of EGFR reveals TKI sensitivities of extracellular domain mutants

Author

Hayes, Tikvah K., Aquilanti, Elisa, Persky, Nicole S., Yang, Xiaoping, Kim, Erica E., Brenan, Lisa, Goodale, Amy B., Alan, Douglas, Sharpe, Ted, Shue, Robert E., Westlake, Lindsay, Golomb, Lior, Silverman, Brianna R., Morris, Myshal D., Fisher, Ty Running, Beyene, Eden, Li, Yvonne Y., Cherniack, Andrew D., Piccioni, Federica, Hicks, J. Kevin, Chi, Andrew S., Cahill, Daniel P., Dietrich, Jorg, Batchelor, Tracy T., Root, David E., Johannessen, Cory M., and Meyerson, Matthew

Published
2024
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2. Comprehensive mutational scanning of EGFR reveals TKI sensitivities of extracellular domain mutants

Author

Hayes, Tikvah K., Aquilanti, Elisa, Persky, Nicole S., Yang, Xiaoping, Kim, Erica E., Brenan, Lisa, Goodale, Amy B., Alan, Douglas, Sharpe, Ted, Shue, Robert E., Westlake, Lindsay, Golomb, Lior, Silverman, Brianna R., Morris, Myshal D., Fisher, Ty Running, Beyene, Eden, Li, Yvonne Y., Cherniack, Andrew D., Piccioni, Federica, Hicks, J. Kevin, Chi, Andrew S., Cahill, Daniel P., Dietrich, Jorg, Batchelor, Tracy T., Root, David E., Johannessen, Cory M., and Meyerson, Matthew

Published
2024
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3. Next-generation characterization of the Cancer Cell Line Encyclopedia

Author

Ghandi, Mahmoud, Huang, Franklin W, Jané-Valbuena, Judit, Kryukov, Gregory V, Lo, Christopher C, McDonald, E Robert, Barretina, Jordi, Gelfand, Ellen T, Bielski, Craig M, Li, Haoxin, Hu, Kevin, Andreev-Drakhlin, Alexander Y, Kim, Jaegil, Hess, Julian M, Haas, Brian J, Aguet, François, Weir, Barbara A, Rothberg, Michael V, Paolella, Brenton R, Lawrence, Michael S, Akbani, Rehan, Lu, Yiling, Tiv, Hong L, Gokhale, Prafulla C, de Weck, Antoine, Mansour, Ali Amin, Oh, Coyin, Shih, Juliann, Hadi, Kevin, Rosen, Yanay, Bistline, Jonathan, Venkatesan, Kavitha, Reddy, Anupama, Sonkin, Dmitriy, Liu, Manway, Lehar, Joseph, Korn, Joshua M, Porter, Dale A, Jones, Michael D, Golji, Javad, Caponigro, Giordano, Taylor, Jordan E, Dunning, Caitlin M, Creech, Amanda L, Warren, Allison C, McFarland, James M, Zamanighomi, Mahdi, Kauffmann, Audrey, Stransky, Nicolas, Imielinski, Marcin, Maruvka, Yosef E, Cherniack, Andrew D, Tsherniak, Aviad, Vazquez, Francisca, Jaffe, Jacob D, Lane, Andrew A, Weinstock, David M, Johannessen, Cory M, Morrissey, Michael P, Stegmeier, Frank, Schlegel, Robert, Hahn, William C, Getz, Gad, Mills, Gordon B, Boehm, Jesse S, Golub, Todd R, Garraway, Levi A, and Sellers, William R

Subjects
Genetics, Human Genome, Lung, Cancer, Biotechnology, Lung Cancer, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Antineoplastic Agents, Biomarkers, Tumor, Cell Line, Tumor, DNA Methylation, Drug Resistance, Neoplasm, Ethnicity, Gene Editing, Histones, Humans, MicroRNAs, Molecular Targeted Therapy, Neoplasms, Protein Array Analysis, RNA Splicing, General Science & Technology
Abstract

Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.

Published
2019

5. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers

Author

Ito, Takahiro, Young, Michael J., Li, Ruitong, Jain, Sidharth, Wernitznig, Andreas, Krill-Burger, John M., Lemke, Christopher T., Monducci, Davide, Rodriguez, Diego J., Chang, Liang, Dutta, Sanjukta, Pal, Debjani, Paolella, Brenton R., Rothberg, Michael V., Root, David E., Johannessen, Cory M., Parida, Laxmi, Getz, Gad, Vazquez, Francisca, Doench, John G., Zamanighomi, Mahdi, and Sellers, William R.

Published
2021
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6. Characterizing genomic alterations in cancer by complementary functional associations

Author

Kim, Jong Wook, Botvinnik, Olga B, Abudayyeh, Omar, Birger, Chet, Rosenbluh, Joseph, Shrestha, Yashaswi, Abazeed, Mohamed E, Hammerman, Peter S, DiCara, Daniel, Konieczkowski, David J, Johannessen, Cory M, Liberzon, Arthur, Alizad-Rahvar, Amir Reza, Alexe, Gabriela, Aguirre, Andrew, Ghandi, Mahmoud, Greulich, Heidi, Vazquez, Francisca, Weir, Barbara A, Van Allen, Eliezer M, Tsherniak, Aviad, Shao, Diane D, Zack, Travis I, Noble, Michael, Getz, Gad, Beroukhim, Rameen, Garraway, Levi A, Ardakani, Masoud, Romualdi, Chiara, Sales, Gabriele, Barbie, David A, Boehm, Jesse S, Hahn, William C, Mesirov, Jill P, and Tamayo, Pablo

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Cancer, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Good Health and Well Being, Biomarkers, Tumor, Chromosome Mapping, Drug Resistance, Neoplasm, Genes, Neoplasm, Genetic Predisposition to Disease, Genome, Human, Genome-Wide Association Study, Humans, Mutation, Neoplasm Proteins, Neoplasms, Polymorphism, Single Nucleotide, Signal Transduction
Abstract

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes.

Published
2016

8. DNA methyltransferase inhibition overcomes diphthamide pathway deficiencies underlying CD123-targeted treatment resistance

Author

Togami, Katsuhiro, Pastika, Timothy, Stephansky, Jason, Ghandi, Mahmoud, Christie, Amanda L., Jones, Kristen L., Johnson, Carl A., Lindsay, Ross W., Brooks, Christopher L., Letai, Anthony, Craig, Jeffrey W., Pozdnyakova, Olga, Weinstock, David M., Montero, Joan, Aster, Jon C., Johannessen, Cory M., and Lane, Andrew A.

Subjects
Thermo Fisher Scientific Inc., Interleukins, Blinatumomab, Methylation, Transferases, DNA, Dendritic cells, Inotuzumab ozogamicin, Scientific equipment industry, Tagraxofusp, Acute myelocytic leukemia, Cancer, Myeloid leukemia, Tumors, Genomes, Enzymes, Diphtheria, Health care industry
Abstract

The interleukin-3 receptor [alpha] subunit, CD123, is expressed in many hematologic malignancies including acute myeloid leukemia (AML) and blastic plasmacytoid dendritic cell neoplasm (BPDCN). Tagraxofusp (SL-401) is a CD123-targeted therapy consisting of interleukin-3 fused to a truncated diphtheria toxin payload. Factors influencing response to tagraxofusp other than CD123 expression are largely unknown. We interrogated tagraxofusp resistance in patients and experimental models and found that it was not associated with CD123 loss. Rather, resistant AML and BPDCN cells frequently acquired deficiencies in the diphthamide synthesis pathway, impairing tagraxofusp's ability to ADP- ribosylate cellular targets. Expression of DPH1, encoding a diphthamide pathway enzyme, was reduced by DNA CpG methylation in resistant cells. Treatment with the DNA methyltransferase inhibitor azacitidine restored DPH1 expression and tagraxofusp sensitivity. We also developed a drug-dependent ADP-ribosylation assay in primary cells that correlated with tagraxofusp activity and may represent an additional novel biomarker. As predicted by these results and our observation that resistance also increased mitochondrial apoptotic priming, we found that the combination of tagraxofusp and azacitidine was effective in patient-derived xenografts treated in vivo. These data have important implications for clinical use of tagraxofusp and led to a phase 1 study combining tagraxofusp and azacitidine in myeloid malignancies., Introduction CD123, or the interleukin-3 (IL-3) receptor (IL-3R) [alpha] chain, is a cell-surface marker associated with a variety of hematologic malignancies and is often enriched on tumor cells compared with [...]

Published
2019
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12. Mutational processes shape the landscape of TP53 mutations in human cancer

Author

Giacomelli, Andrew O., Yang, Xiaoping, Lintner, Robert E., McFarland, James M., Duby, Marc, Kim, Jaegil, Howard, Thomas P., Takeda, David Y., Ly, Seav Huong, Kim, Eejung, Gannon, Hugh S., Hurhula, Brian, Sharpe, Ted, Goodale, Amy, Fritchman, Briana, Steelman, Scott, Vazquez, Francisca, Tsherniak, Aviad, Aguirre, Andrew J., Doench, John G., Piccioni, Federica, Roberts, Charles W. M., Meyerson, Matthew, Getz, Gad, Johannessen, Cory M., Root, David E., and Hahn, William C.

Published
2018
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13. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Author

Tirosh, Itay, Izar, Benjamin, Prakadan, Sanjay M., Wadsworth, Marc H., Treacy, Daniel, Trombetta, John J., Rotem, Asaf, Rodman, Christopher, Lian, Christine, Murphy, George, Fallahi-Sichani, Mohammad, Dutton-Regester, Ken, Lin, Jia-Ren, Cohen, Ofir, Shah, Parin, Lu, Diana, Genshaft, Alex S., Hughes, Travis K., Ziegler, Carly G. K., Kazer, Samuel W., Gaillard, Aleth, Kolb, Kellie E., Villani, Alexandra-Chloé, Johannessen, Cory M., Andreev, Aleksandr Y., Van Allen, Eliezer M., Bertagnolli, Monica, Sorger, Peter K., Sullivan, Ryan J., Flaherty, Keith T., Frederick, Dennie T., Jané-Valbuena, Judit, Yoon, Charles H., Rozenblatt-Rosen, Orit, Shalek, Alex K., Regev, Aviv, and Garraway, Levi A.

Published
2016

14. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma

Author

Bandopadhayay, Pratiti, Piccioni, Federica, O’Rourke, Ryan, Ho, Patricia, Gonzalez, Elizabeth M., Buchan, Graham, Qian, Kenin, Gionet, Gabrielle, Girard, Emily, Coxon, Margo, Rees, Matthew G., Brenan, Lisa, Dubois, Frank, Shapira, Ofer, Greenwald, Noah F., Pages, Melanie, Balboni Iniguez, Amanda, Paolella, Brenton R., Meng, Alice, Sinai, Claire, Roti, Giovanni, Dharia, Neekesh V., Creech, Amanda, Tanenbaum, Benjamin, Khadka, Prasidda, Tracy, Adam, Tiv, Hong L., Hong, Andrew L., Coy, Shannon, Rashid, Rumana, Lin, Jia-Ren, Cowley, Glenn S., Lam, Fred C., Goodale, Amy, Lee, Yenarae, Schoolcraft, Kathleen, Vazquez, Francisca, Hahn, William C., Tsherniak, Aviad, Bradner, James E., Yaffe, Michael B., Milde, Till, Pfister, Stefan M., Qi, Jun, Schenone, Monica, Carr, Steven A., Ligon, Keith L., Kieran, Mark W., Santagata, Sandro, Olson, James M., Gokhale, Prafulla C., Jaffe, Jacob D., Root, David E., Stegmaier, Kimberly, Johannessen, Cory M., and Beroukhim, Rameen

Published
2019
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15. Abstract 1706: A non-canonical MiT/TFE-dependent NRF2 program is a druggable vulnerability in multiple cancer types

Author

Luo, Xinbo, primary, Lutterbach, Bart, additional, Pancholi, Priya, additional, Choi, Yeon Sook, additional, Liu, Xiao, additional, Munson, Phillip, additional, Faisal, Saqib, additional, Whipple, David A., additional, Smith, Robert A., additional, Weiner, Warren S., additional, Johnson, David K., additional, Boukhali, Myriam, additional, Persky, Nicole S., additional, Rees, Matthew G., additional, Kitajima, Shunsuke, additional, Barbie, David, additional, Roy, Anuradha, additional, Baltezor, Michael, additional, Rajewski, Lian, additional, McGuinness, William, additional, Haslam, John, additional, Sadagopan, Ananthan, additional, Yoon, Charles H., additional, Johannessen, Cory M., additional, Lian, Christine G., additional, Hornick, Jason L., additional, Viswanathan, Srinivas R., additional, Liu, David, additional, Nienaber, Vicki, additional, Haas, Wilhelm, additional, Schoenen, Frank J., additional, Fisher, David E., additional, and Haq, Rizwan, additional

Published
2023
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16. Data from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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18. Supplementary Table S4 from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer

Author

Stover, Elizabeth H., primary, Baco, Maria B., primary, Cohen, Ofir, primary, Li, Yvonne Y., primary, Christie, Elizabeth L., primary, Bagul, Mukta, primary, Goodale, Amy, primary, Lee, Yenarae, primary, Pantel, Sasha, primary, Rees, Matthew G., primary, Wei, Guo, primary, Presser, Adam G., primary, Gelbard, Maya K., primary, Zhang, Weiqun, primary, Zervantonakis, Ioannis K., primary, Bhola, Patrick D., primary, Ryan, Jeremy, primary, Guerriero, Jennifer L., primary, Montero, Joan, primary, Liang, Felice J., primary, Cherniack, Andrew D., primary, Piccioni, Federica, primary, Matulonis, Ursula A., primary, Bowtell, David D.L., primary, Sarosiek, Kristopher A., primary, Letai, Anthony, primary, Garraway, Levi A., primary, Johannessen, Cory M., primary, and Meyerson, Matthew, primary

Published
2023
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19. Data from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer

Author

Stover, Elizabeth H., primary, Baco, Maria B., primary, Cohen, Ofir, primary, Li, Yvonne Y., primary, Christie, Elizabeth L., primary, Bagul, Mukta, primary, Goodale, Amy, primary, Lee, Yenarae, primary, Pantel, Sasha, primary, Rees, Matthew G., primary, Wei, Guo, primary, Presser, Adam G., primary, Gelbard, Maya K., primary, Zhang, Weiqun, primary, Zervantonakis, Ioannis K., primary, Bhola, Patrick D., primary, Ryan, Jeremy, primary, Guerriero, Jennifer L., primary, Montero, Joan, primary, Liang, Felice J., primary, Cherniack, Andrew D., primary, Piccioni, Federica, primary, Matulonis, Ursula A., primary, Bowtell, David D.L., primary, Sarosiek, Kristopher A., primary, Letai, Anthony, primary, Garraway, Levi A., primary, Johannessen, Cory M., primary, and Meyerson, Matthew, primary

Published
2023
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21. Supplementary Table 3 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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22. Supplementary Table 2 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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23. Data from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma

Author

Van Allen, Eliezer M., primary, Wagle, Nikhil, primary, Sucker, Antje, primary, Treacy, Daniel J., primary, Johannessen, Cory M., primary, Goetz, Eva M., primary, Place, Chelsea S., primary, Taylor-Weiner, Amaro, primary, Whittaker, Steven, primary, Kryukov, Gregory V., primary, Hodis, Eran, primary, Rosenberg, Mara, primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Farlow, Deborah, primary, Zimmer, Lisa, primary, Hillen, Uwe, primary, Gutzmer, Ralf, primary, Goldinger, Simone M., primary, Ugurel, Selma, primary, Gogas, Helen J., primary, Egberts, Friederike, primary, Berking, Carola, primary, Trefzer, Uwe, primary, Loquai, Carmen, primary, Weide, Benjamin, primary, Hassel, Jessica C., primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Getz, Gad, primary, Garraway, Levi A., primary, and Schadendorf, Dirk, primary

Published
2023
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24. Supplementary Table S2 from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma

Author

Van Allen, Eliezer M., primary, Wagle, Nikhil, primary, Sucker, Antje, primary, Treacy, Daniel J., primary, Johannessen, Cory M., primary, Goetz, Eva M., primary, Place, Chelsea S., primary, Taylor-Weiner, Amaro, primary, Whittaker, Steven, primary, Kryukov, Gregory V., primary, Hodis, Eran, primary, Rosenberg, Mara, primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Farlow, Deborah, primary, Zimmer, Lisa, primary, Hillen, Uwe, primary, Gutzmer, Ralf, primary, Goldinger, Simone M., primary, Ugurel, Selma, primary, Gogas, Helen J., primary, Egberts, Friederike, primary, Berking, Carola, primary, Trefzer, Uwe, primary, Loquai, Carmen, primary, Weide, Benjamin, primary, Hassel, Jessica C., primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Getz, Gad, primary, Garraway, Levi A., primary, and Schadendorf, Dirk, primary

Published
2023
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25. Supplementary Materials and Methods from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

Author

Konieczkowski, David J., primary, Johannessen, Cory M., primary, Abudayyeh, Omar, primary, Kim, Jong Wook, primary, Cooper, Zachary A., primary, Piris, Adriano, primary, Frederick, Dennie T., primary, Barzily-Rokni, Michal, primary, Straussman, Ravid, primary, Haq, Rizwan, primary, Fisher, David E., primary, Mesirov, Jill P., primary, Hahn, William C., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, Tamayo, Pablo, primary, and Garraway, Levi A., primary

Published
2023
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27. Supplementary Table 4 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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28. Supplementary Table 1 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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29. Supplementary Table 6 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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30. Supplementary Figures from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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32. Supplementary figures and supplementary table legends from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer

Author

Stover, Elizabeth H., primary, Baco, Maria B., primary, Cohen, Ofir, primary, Li, Yvonne Y., primary, Christie, Elizabeth L., primary, Bagul, Mukta, primary, Goodale, Amy, primary, Lee, Yenarae, primary, Pantel, Sasha, primary, Rees, Matthew G., primary, Wei, Guo, primary, Presser, Adam G., primary, Gelbard, Maya K., primary, Zhang, Weiqun, primary, Zervantonakis, Ioannis K., primary, Bhola, Patrick D., primary, Ryan, Jeremy, primary, Guerriero, Jennifer L., primary, Montero, Joan, primary, Liang, Felice J., primary, Cherniack, Andrew D., primary, Piccioni, Federica, primary, Matulonis, Ursula A., primary, Bowtell, David D.L., primary, Sarosiek, Kristopher A., primary, Letai, Anthony, primary, Garraway, Levi A., primary, Johannessen, Cory M., primary, and Meyerson, Matthew, primary

Published
2023
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33. Supplementary Figures S1-S19 from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

Author

Konieczkowski, David J., primary, Johannessen, Cory M., primary, Abudayyeh, Omar, primary, Kim, Jong Wook, primary, Cooper, Zachary A., primary, Piris, Adriano, primary, Frederick, Dennie T., primary, Barzily-Rokni, Michal, primary, Straussman, Ravid, primary, Haq, Rizwan, primary, Fisher, David E., primary, Mesirov, Jill P., primary, Hahn, William C., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, Tamayo, Pablo, primary, and Garraway, Levi A., primary

Published
2023
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34. Data from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

Author

Konieczkowski, David J., primary, Johannessen, Cory M., primary, Abudayyeh, Omar, primary, Kim, Jong Wook, primary, Cooper, Zachary A., primary, Piris, Adriano, primary, Frederick, Dennie T., primary, Barzily-Rokni, Michal, primary, Straussman, Ravid, primary, Haq, Rizwan, primary, Fisher, David E., primary, Mesirov, Jill P., primary, Hahn, William C., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, Tamayo, Pablo, primary, and Garraway, Levi A., primary

Published
2023
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35. Supplementary methods from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer

Author

Stover, Elizabeth H., primary, Baco, Maria B., primary, Cohen, Ofir, primary, Li, Yvonne Y., primary, Christie, Elizabeth L., primary, Bagul, Mukta, primary, Goodale, Amy, primary, Lee, Yenarae, primary, Pantel, Sasha, primary, Rees, Matthew G., primary, Wei, Guo, primary, Presser, Adam G., primary, Gelbard, Maya K., primary, Zhang, Weiqun, primary, Zervantonakis, Ioannis K., primary, Bhola, Patrick D., primary, Ryan, Jeremy, primary, Guerriero, Jennifer L., primary, Montero, Joan, primary, Liang, Felice J., primary, Cherniack, Andrew D., primary, Piccioni, Federica, primary, Matulonis, Ursula A., primary, Bowtell, David D.L., primary, Sarosiek, Kristopher A., primary, Letai, Anthony, primary, Garraway, Levi A., primary, Johannessen, Cory M., primary, and Meyerson, Matthew, primary

Published
2023
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36. Supplementary Table Legends from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma

Author

Van Allen, Eliezer M., primary, Wagle, Nikhil, primary, Sucker, Antje, primary, Treacy, Daniel J., primary, Johannessen, Cory M., primary, Goetz, Eva M., primary, Place, Chelsea S., primary, Taylor-Weiner, Amaro, primary, Whittaker, Steven, primary, Kryukov, Gregory V., primary, Hodis, Eran, primary, Rosenberg, Mara, primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Farlow, Deborah, primary, Zimmer, Lisa, primary, Hillen, Uwe, primary, Gutzmer, Ralf, primary, Goldinger, Simone M., primary, Ugurel, Selma, primary, Gogas, Helen J., primary, Egberts, Friederike, primary, Berking, Carola, primary, Trefzer, Uwe, primary, Loquai, Carmen, primary, Weide, Benjamin, primary, Hassel, Jessica C., primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Getz, Gad, primary, Garraway, Levi A., primary, and Schadendorf, Dirk, primary

Published
2023
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37. Data Supplement from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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38. Supplementary Table 5 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

Author

Wagle, Nikhil, primary, Van Allen, Eliezer M., primary, Treacy, Daniel J., primary, Frederick, Dennie T., primary, Cooper, Zachary A., primary, Taylor-Weiner, Amaro, primary, Rosenberg, Mara, primary, Goetz, Eva M., primary, Sullivan, Ryan J., primary, Farlow, Deborah N., primary, Friedrich, Dennis C., primary, Anderka, Kristin, primary, Perrin, Danielle, primary, Johannessen, Cory M., primary, McKenna, Aaron, primary, Cibulskis, Kristian, primary, Kryukov, Gregory, primary, Hodis, Eran, primary, Lawrence, Donald P., primary, Fisher, Sheila, primary, Getz, Gad, primary, Gabriel, Stacey B., primary, Carter, Scott L., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, and Garraway, Levi A., primary

Published
2023
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39. Supplementary Tables S1-S2 from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

Author

Konieczkowski, David J., primary, Johannessen, Cory M., primary, Abudayyeh, Omar, primary, Kim, Jong Wook, primary, Cooper, Zachary A., primary, Piris, Adriano, primary, Frederick, Dennie T., primary, Barzily-Rokni, Michal, primary, Straussman, Ravid, primary, Haq, Rizwan, primary, Fisher, David E., primary, Mesirov, Jill P., primary, Hahn, William C., primary, Flaherty, Keith T., primary, Wargo, Jennifer A., primary, Tamayo, Pablo, primary, and Garraway, Levi A., primary

Published
2023
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41. Table S1 from Rhabdoid Tumors Are Sensitive to the Protein-Translation Inhibitor Homoharringtonine

Author

Howard, Thomas P., primary, Oberlick, Elaine M., primary, Rees, Matthew G., primary, Arnoff, Taylor E., primary, Pham, Minh-Tam, primary, Brenan, Lisa, primary, DoCarmo, Mariana, primary, Hong, Andrew L., primary, Kugener, Guillaume, primary, Chou, Hsien-Chao, primary, Drosos, Yiannis, primary, Mathias, Kaeli M., primary, Ramos, Pilar, primary, Seashore-Ludlow, Brinton, primary, Giacomelli, Andrew O., primary, Wang, Xiaofeng, primary, Freeman, Burgess B., primary, Blankenship, Kaley, primary, Hoffmann, Lauren, primary, Tiv, Hong L., primary, Gokhale, Prafulla C., primary, Johannessen, Cory M., primary, Stewart, Elizabeth A., primary, Schreiber, Stuart L., primary, Hahn, William C., primary, and Roberts, Charles W.M., primary

Published
2023
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43. Figures S1-S6 from Rhabdoid Tumors Are Sensitive to the Protein-Translation Inhibitor Homoharringtonine

Author

Howard, Thomas P., primary, Oberlick, Elaine M., primary, Rees, Matthew G., primary, Arnoff, Taylor E., primary, Pham, Minh-Tam, primary, Brenan, Lisa, primary, DoCarmo, Mariana, primary, Hong, Andrew L., primary, Kugener, Guillaume, primary, Chou, Hsien-Chao, primary, Drosos, Yiannis, primary, Mathias, Kaeli M., primary, Ramos, Pilar, primary, Seashore-Ludlow, Brinton, primary, Giacomelli, Andrew O., primary, Wang, Xiaofeng, primary, Freeman, Burgess B., primary, Blankenship, Kaley, primary, Hoffmann, Lauren, primary, Tiv, Hong L., primary, Gokhale, Prafulla C., primary, Johannessen, Cory M., primary, Stewart, Elizabeth A., primary, Schreiber, Stuart L., primary, Hahn, William C., primary, and Roberts, Charles W.M., primary

Published
2023
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44. A Functional Landscape of Resistance to ALK Inhibition in Lung Cancer

Author

Wilson, Frederick H., Johannessen, Cory M., Piccioni, Federica, Tamayo, Pablo, Kim, Jong Wook, Van Allen, Eliezer M., Corsello, Steven M., Capelletti, Marzia, Calles, Antonio, Butaney, Mohit, Sharifnia, Tanaz, Gabriel, Stacey B., Mesirov, Jill P., Hahn, William C., Engelman, Jeffrey A., Meyerson, Matthew, Root, David E., Jänne, Pasi A., and Garraway, Levi A.

Published
2015
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46. CANCER GENOMICS: Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Author

Tirosh, Itay, Izar, Benjamin, Prakadan, Sanjay M., Wadsworth, Marc H., II, Treacy, Daniel, Trombetta, John J., Rotem, Asaf, Rodman, Christopher, Lian, Christine, Murphy, George, Fallahi-Sichani, Mohammad, Dutton-Regester, Ken, Lin, Jia-Ren, Cohen, Ofir, Shah, Parin, Lu, Diana, Genshaft, Alex S., Hughes, Travis K., Ziegler, Carly G. K., Kazer, Samuel W., Gaillard, Aleth, Kolb, Kellie E., Villani, Alexandra-Chloé, Johannessen, Cory M., Andreev, Aleksandr Y., Van Allen, Eliezer M., Bertagnolli, Monica, Sorger, Peter K., Sullivan, Ryan J., Flaherty, Keith T., Frederick, Dennie T., Jané-Valbuena, Judit, Yoon, Charles H., Rozenblatt-Rosen, Orit, Shalek, Alex K., Regev, Aviv, and Garraway, Levi A.

Published
2016
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47. A melanocyte lineage program confers resistance to MAP kinase pathway inhibition

Author

Johannessen, Cory M., Johnson, Laura A., Piccioni, Federica, Townes, Aisha, Frederick, Dennie T., Donahue, Melanie K., Narayan, Rajiv, Flaherty, Keith T., Wargo, Jennifer A., Root, David E., and Garraway, Levi A.

Subjects
Cancer -- Genetic aspects, Genetic transcription -- Research, Melanoma -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Malignant melanomas harbouring point mutations (Val600Glu) in the serine/threonine-protein kinase BRAF (BRAF(V600E)) depend on RAF-MEK-ERK signalling for tumour cell growth (1). RAF and MEK inhibitors show remarkable clinical efficacy in BRAF(V600E) melanoma (2,3); however, resistance to these agents remains a formidable challenge (2,4). Global characterization of resistance mechanisms may inform the development of more effective therapeutic combinations. Here we carried out systematic gain-of-function resistance studies by expressing more than 15,500 genes individually in a BRAF(V600E) melanoma cell line treated with RAF, MEK, ERK or combined RAF-MEK inhibitors. These studies revealed a cyclic-AMP-dependent melanocytic signalling network not previously associated with drug resistance, including G-protein-coupled receptors, adenyl cyclase, protein kinase A and cAMP response element binding protein (CREB). Preliminary analysis of biopsies from BRAF(V600E) melanoma patients revealed that phosphorylated (active) CREB was suppressed by RAF-MEK inhibition but restored in relapsing tumours. Expression of transcription factors activated downstream of MAP kinase and cAMP pathways also conferred resistance, including c-FOS, NR4A1, NR4A2 and MITF. Combined treatment with MAPK-pathway and histone-deacetylase inhibitors suppressed MITF expression and cAMP-mediated resistance. Collectively, these data suggest that oncogenic dysregulation of a melanocyte lineage dependency can cause resistance to RAF-MEK-ERK inhibition, which may be overcome by combining signalling- and chromatin-directed therapeutics., To identify genes whose upregulation confers resistance to MAPK pathway inhibition, we expressed 15,906 human open reading frames (ORFs) (5) (Extended Data Fig. 1) in a BRAF(V600E)-mutant, MAPK-pathway-dependent melanoma cell [...]

Published
2013

48. COT drives resistance to RAF inhibition through MAP kinase pathway reactivation

Author

Johannessen, Cory M., Boehm, Jesse S., Kim, So Young, Thomas, Sapana R., Wardwell, Leslie, Johnson, Laura A., Emery, Caroline M., Stransky, Nicolas, Cogdill, Alexandria P., Barretina, Jordi, Caponigro, Giordano, Hieronymus, Haley, Murray, Ryan R., Salehi-Ashtiani, Kourosh, Hill, David E., Vidal, Marc, Zhao, Jean J., Yang, Xiaoping, Alkan, Ozan, Kim, Sungjoon, Harris, Jennifer L., Wilson, Christopher J., Myer, Vic E., Finan, Peter M., Root, David E., Roberts, Thomas M., Golub, Todd, Flaherty, Keith T., Dummer, Reinhard, Weber, Barbara L., Sellers, William R., Wargo, Jennifer A., Hahn, William C., and Garraway, Levi A.

Subjects
Cell lines -- Research, Protein research -- Research, Protein kinases -- Properties -- Research, Cancer cells -- Properties -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Oncogenic mutations in the serine/threonine kinase B-RAF (also known as BRAF) are found in 50-70% of malignant melanomas (1). Pre-clinical studies have demonstrated that the B-RAF(V600E) mutation predicts a dependency on the mitogen-activated protein kinase (MAPK) signalling cascade in melanoma (2-6)--an observation that has been validated by the success of RAF and MEK inhibitors in clinical trials (7-9) However, clinical responses to targeted anticancer therapeutics are frequently confounded by de novo or acquired resistance (10-12). Identification of resistance mechanisms in a manner that elucidates alternative 'druggable' targets may inform effective long-term treatment strategies (13). Here we expressed ~600 kinase and kinase-related open reading frames (ORFs) in parallel to interrogate resistance to a selective RAF kinase inhibitor. We identified MAP3K8 (the gene encoding COT/Tpl2) as a MAPK pathway agonist that drives resistance to RAF inhibition in B-RAF(V600E) cell lines. COT activates ERK primarily through MEK-dependent mechanisms that do not require RAF signalling. Moreover, COT expression is associated with de novo resistance in B-RAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. We further identify combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting. Together, these results provide new insights into resistance mechanisms involving the MAPK pathway and articulate an integrative approach through which high-throughput functional screens may inform the development of novel therapeutic strategies., To identify kinases capable of circumventing RAF inhibition, we assembled and stably expressed 597 sequence-validated kinase ORF clones representing ~75% of annotated kinases (Center for Cancer Systems Biology (CCSB)/Broad Institute [...]

Published
2010
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49. Defining protein variant functions using high-complexity mutagenesis libraries and enhanced mutant detection software ASMv1.0

Author

Yang, Xiaoping, primary, Hong, Andrew L., additional, Sharpe, Ted, additional, Giacomelli, Andrew O., additional, Lintner, Robert E., additional, Alan, Douglas, additional, Green, Thomas, additional, Hayes, Tikvah K., additional, Piccioni, Federica, additional, Fritchman, Briana, additional, Kawabe, Hinako, additional, Sawyer, Edith, additional, Sprenkle, Luke, additional, Lee, Benjamin P., additional, Persky, Nicole S., additional, Brown, Adam, additional, Greulich, Heidi, additional, Aguirre, Andrew J., additional, Meyerson, Matthew, additional, Hahn, William C., additional, Johannessen, Cory M., additional, and Root, David E., additional

Published
2021
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50. CloneSifter: enrichment of rare clones from heterogeneous cell populations

Author

Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Feldman, David, Tsai, FuNien, Garrity, Anthony J, O’Rourke, Ryan, Brenan, Lisa, Ho, Patricia, Gonzalez, Elizabeth, Konermann, Silvana, Johannessen, Cory M, Beroukhim, Rameen, Bandopadhayay, Pratiti, Blainey, Paul C, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Feldman, David, Tsai, FuNien, Garrity, Anthony J, O’Rourke, Ryan, Brenan, Lisa, Ho, Patricia, Gonzalez, Elizabeth, Konermann, Silvana, Johannessen, Cory M, Beroukhim, Rameen, Bandopadhayay, Pratiti, and Blainey, Paul C

Abstract

Background Many biological processes, such as cancer metastasis, organismal development, and acquisition of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. While large-scale barcoding with NGS readout has facilitated cellular fitness assessment at the population level, this approach does not support characterization of clones prior to selection. Single-cell genomics methods provide high biological resolution, but are challenging to scale across large populations to probe rare clones and are destructive, limiting further functional analysis of important clones. Results Here, we develop CloneSifter, a methodology for tracking and enriching rare clones throughout their response to selection. CloneSifter utilizes a CRISPR sgRNA-barcode library that facilitates the isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrate that CloneSifter can measure clonal fitness of cancer cell models in vitro and retrieve targeted clones at abundance as low as 1 in 1883 in a heterogeneous cell population. Conclusions CloneSifter provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.

Published
2021

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