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1. Early Circulating Tumor DNA Shedding Kinetics for Prediction of Platinum Sensitivity in Patients With Small Cell Lung Cancer

Author

Murciano-Goroff, Yonina R., Hui, Angela B.-Y., Araujo Filho, Jose A., Hamilton, Emily G., Chabon, Jacob J., Moding, Everett J., Bonilla, Rene F., Lebow, Emily S., Gomez, Daniel, Rimner, Andreas, Ginsberg, Michelle S., Offin, Michael, Kundra, Ritika, Allaj, Viola, Norton, Larry, Reis-Filho, Jorge S., Razavi, Pedram, Drilon, Alexander, Jones, David R., Isbell, James M., Lai, W. Victoria, Rudin, Charles M., Alizadeh, Ash A., Li, Bob T., and Diehn, Maximilian

Published
2024
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2. Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade

Author

Pai, Joy A., Hellmann, Matthew D., Sauter, Jennifer L., Mattar, Marissa, Rizvi, Hira, Woo, Hyung Jun, Shah, Nisargbhai, Nguyen, Evelyn M., Uddin, Fathema Z., Quintanal-Villalonga, Alvaro, Chan, Joseph M., Manoj, Parvathy, Allaj, Viola, Baine, Marina K., Bhanot, Umesh K., Jain, Mala, Linkov, Irina, Meng, Fanli, Brown, David, Chaft, Jamie E., Plodkowski, Andrew J., Gigoux, Mathieu, Won, Helen H., Sen, Triparna, Wells, Daniel K., Donoghue, Mark T.A., de Stanchina, Elisa, Wolchok, Jedd D., Loomis, Brian, Merghoub, Taha, Rudin, Charles M., Chow, Andrew, and Satpathy, Ansuman T.

Published
2023
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3. Genomic and transcriptomic analysis of a library of small cell lung cancer patient-derived xenografts

Author

Caeser, Rebecca, Egger, Jacklynn V., Chavan, Shweta, Socci, Nicholas D., Jones, Caitlin Byrne, Kombak, Faruk Erdem, Asher, Marina, Roehrl, Michael H., Shah, Nisargbhai S., Allaj, Viola, Manoj, Parvathy, Tischfield, Sam E., Kulick, Amanda, Meneses, Maximiliano, Iacobuzio-Donahue, Christine A., Lai, W. Victoria, Bhanot, Umeshkumar, Baine, Marina K., Rekhtman, Natasha, Hollmann, Travis J., de Stanchina, Elisa, Poirier, John T., Rudin, Charles M., and Sen, Triparna

Published
2022
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4. Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Published
2022
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5. Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation

Author

Quintanal-Villalonga, Alvaro, Taniguchi, Hirokazu, Zhan, Yingqian A., Hasan, Maysun M., Chavan, Shweta S., Meng, Fanli, Uddin, Fathema, Allaj, Viola, Manoj, Parvathy, Shah, Nisargbhai S., Chan, Joseph M., Ciampricotti, Metamia, Chow, Andrew, Offin, Michael, Ray-Kirton, Jordana, Egger, Jacklynn D., Bhanot, Umesh K., Linkov, Irina, Asher, Marina, Roehrl, Michael H., Ventura, Katia, Qiu, Juan, de Stanchina, Elisa, Chang, Jason C., Rekhtman, Natasha, Houck-Loomis, Brian, Koche, Richard P., Yu, Helena A., Sen, Triparna, and Rudin, Charles M.

Published
2021
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6. Regenerative lineages and immune-mediated pruning in lung cancer metastasis

Author

Laughney, Ashley M., Hu, Jing, Campbell, Nathaniel R., Bakhoum, Samuel F., Setty, Manu, Lavallée, Vincent-Philippe, Xie, Yubin, Masilionis, Ignas, Carr, Ambrose J., Kottapalli, Sanjay, Allaj, Viola, Mattar, Marissa, Rekhtman, Natasha, Xavier, Joao B., Mazutis, Linas, Poirier, John T., Rudin, Charles M., Pe’er, Dana, and Massagué, Joan

Published
2020
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7. Peptide-based PET quantifies target engagement of PD-L1 therapeutics

Author

Kumar, Dhiraj, Lisok, Ala, Dahmane, Elyes, McCoy, Matthew, Shelake, Sagar, Chatterjee, Samit, Allaj, Viola, Sysa-Shah, Polina, Wharram, Bryan, Lesniak, Wojciech G., Tully, Ellen, Gabrielson, Edward, Jaffee, Elizabeth M., Poirier, John T., Rudin, Charles M., Gobburu, Jogarao V.S., Pomper, Martin G., and Nimmagadda, Sridhar

Subjects
Cancer treatment -- Usage, Mass spectrometry -- Usage, Positron emission tomography -- Usage, Death, Diagnostic imaging, Monoclonal antibodies, Cancer, Peptides, Occupancy, Tumors, Tomography, Antibodies, Therapeutics, Health care industry
Abstract

Immune checkpoint therapies have shown tremendous promise in cancer therapy. However, tools to assess their target engagement, and hence the ability to predict their efficacy, have been lacking. Here, we show that target engagement and tumor-residence kinetics of antibody therapeutics targeting programmed death ligand-1 (PD-L1) can be quantified noninvasively. In computational docking studies, we observed that PD-L1-targeted monoclonal antibodies (atezolizumab, avelumab, and durvalumab) and a high-affinity PD-L1-binding peptide, WL12, have common interaction sites on PD-L1. Using the peptide radiotracer [[sup.64]Cu]WL12 in vivo, we employed positron emission tomography (PET) imaging and biodistribution studies in multiple xenograft models and demonstrated that variable PD-L1 expression and its saturation by atezolizumab, avelumab, and durvalumab can be quantified independently of biophysical properties and pharmacokinetics of antibodies. Next, we used [[sup.64]Cu]WL12 to evaluate the impact of time and dose on the unoccupied fraction of tumor PD-L1 during treatment. These quantitative measures enabled, by mathematical modeling, prediction of antibody doses needed to achieve therapeutically effective occupancy (defined as >90%). Thus, we show that peptide-based PET is a promising tool for optimizing dose and therapeutic regimens employing PD-L1 checkpoint antibodies, and can be used for improving therapeutic efficacy., Introduction The success of cancer drug therapy depends on a number of factors within the tumor including drug access, completeness of drug-target engagement, and targeting cancer cell heterogeneity. Target engagement [...]

Published
2019
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8. Data from Rlf–Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer

Author

Ciampricotti, Metamia, primary, Karakousi, Triantafyllia, primary, Richards, Allison L., primary, Quintanal-Villalonga, Àlvaro, primary, Karatza, Angeliki, primary, Caeser, Rebecca, primary, Costa, Emily A., primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Spainhower, Kyle B., primary, Kombak, Faruk E., primary, Sanchez-Rivera, Francisco J., primary, Jaspers, Janneke E., primary, Zavitsanou, Anastasia-Maria, primary, Maddalo, Danilo, primary, Ventura, Andrea, primary, Rideout, William M., primary, Akama-Garren, Elliot H., primary, Jacks, Tyler, primary, Donoghue, Mark T.A., primary, Sen, Triparna, primary, Oliver, Trudy G., primary, Poirier, John T., primary, Papagiannakopoulos, Thales, primary, and Rudin, Charles M., primary

Published
2023
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9. Supplementary Figures S1 - S5 from Rlf–Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer

Author

Ciampricotti, Metamia, primary, Karakousi, Triantafyllia, primary, Richards, Allison L., primary, Quintanal-Villalonga, Àlvaro, primary, Karatza, Angeliki, primary, Caeser, Rebecca, primary, Costa, Emily A., primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Spainhower, Kyle B., primary, Kombak, Faruk E., primary, Sanchez-Rivera, Francisco J., primary, Jaspers, Janneke E., primary, Zavitsanou, Anastasia-Maria, primary, Maddalo, Danilo, primary, Ventura, Andrea, primary, Rideout, William M., primary, Akama-Garren, Elliot H., primary, Jacks, Tyler, primary, Donoghue, Mark T.A., primary, Sen, Triparna, primary, Oliver, Trudy G., primary, Poirier, John T., primary, Papagiannakopoulos, Thales, primary, and Rudin, Charles M., primary

Published
2023
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10. Supplementary Tables from Rlf–Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer

Author

Ciampricotti, Metamia, primary, Karakousi, Triantafyllia, primary, Richards, Allison L., primary, Quintanal-Villalonga, Àlvaro, primary, Karatza, Angeliki, primary, Caeser, Rebecca, primary, Costa, Emily A., primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Spainhower, Kyle B., primary, Kombak, Faruk E., primary, Sanchez-Rivera, Francisco J., primary, Jaspers, Janneke E., primary, Zavitsanou, Anastasia-Maria, primary, Maddalo, Danilo, primary, Ventura, Andrea, primary, Rideout, William M., primary, Akama-Garren, Elliot H., primary, Jacks, Tyler, primary, Donoghue, Mark T.A., primary, Sen, Triparna, primary, Oliver, Trudy G., primary, Poirier, John T., primary, Papagiannakopoulos, Thales, primary, and Rudin, Charles M., primary

Published
2023
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11. Table S2 from Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Hao, Yuan, primary, Chow, Andrew, primary, Zhan, Yingqian A., primary, Chavan, Shweta S., primary, Uddin, Fathema, primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Shah, Nisargbhai S., primary, Chan, Joseph M., primary, Offin, Michael, primary, Ciampricotti, Metamia, primary, Ray-Kirton, Jordana, primary, Egger, Jacklynn, primary, Bhanot, Umesh, primary, Linkov, Irina, primary, Asher, Marina, primary, Roehrl, Michael H., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Hollmann, Travis J., primary, Koche, Richard P., primary, Sen, Triparna, primary, Poirier, John T., primary, and Rudin, Charles M., primary

Published
2023
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12. Data from Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Hao, Yuan, primary, Chow, Andrew, primary, Zhan, Yingqian A., primary, Chavan, Shweta S., primary, Uddin, Fathema, primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Shah, Nisargbhai S., primary, Chan, Joseph M., primary, Offin, Michael, primary, Ciampricotti, Metamia, primary, Ray-Kirton, Jordana, primary, Egger, Jacklynn, primary, Bhanot, Umesh, primary, Linkov, Irina, primary, Asher, Marina, primary, Roehrl, Michael H., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Hollmann, Travis J., primary, Koche, Richard P., primary, Sen, Triparna, primary, Poirier, John T., primary, and Rudin, Charles M., primary

Published
2023
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13. Data from Noninvasive Interrogation of DLL3 Expression in Metastatic Small Cell Lung Cancer

Author

Sharma, Sai Kiran, primary, Pourat, Jacob, primary, Abdel-Atti, Dalya, primary, Carlin, Sean D., primary, Piersigilli, Alessandra, primary, Bankovich, Alexander J., primary, Gardner, Eric E., primary, Hamdy, Omar, primary, Isse, Kumiko, primary, Bheddah, Sheila, primary, Sandoval, Joseph, primary, Cunanan, Kristen M., primary, Johansen, Eric B., primary, Allaj, Viola, primary, Sisodiya, Vikram, primary, Liu, David, primary, Zeglis, Brian M., primary, Rudin, Charles M., primary, Dylla, Scott J., primary, Poirier, John T., primary, and Lewis, Jason S., primary

Published
2023
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14. Figures S1 - S5 from Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Hao, Yuan, primary, Chow, Andrew, primary, Zhan, Yingqian A., primary, Chavan, Shweta S., primary, Uddin, Fathema, primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Shah, Nisargbhai S., primary, Chan, Joseph M., primary, Offin, Michael, primary, Ciampricotti, Metamia, primary, Ray-Kirton, Jordana, primary, Egger, Jacklynn, primary, Bhanot, Umesh, primary, Linkov, Irina, primary, Asher, Marina, primary, Roehrl, Michael H., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Hollmann, Travis J., primary, Koche, Richard P., primary, Sen, Triparna, primary, Poirier, John T., primary, and Rudin, Charles M., primary

Published
2023
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15. Supplementary Data from Noninvasive Interrogation of DLL3 Expression in Metastatic Small Cell Lung Cancer

Author

Sharma, Sai Kiran, primary, Pourat, Jacob, primary, Abdel-Atti, Dalya, primary, Carlin, Sean D., primary, Piersigilli, Alessandra, primary, Bankovich, Alexander J., primary, Gardner, Eric E., primary, Hamdy, Omar, primary, Isse, Kumiko, primary, Bheddah, Sheila, primary, Sandoval, Joseph, primary, Cunanan, Kristen M., primary, Johansen, Eric B., primary, Allaj, Viola, primary, Sisodiya, Vikram, primary, Liu, David, primary, Zeglis, Brian M., primary, Rudin, Charles M., primary, Dylla, Scott J., primary, Poirier, John T., primary, and Lewis, Jason S., primary

Published
2023
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16. The ectonucleotidase CD39 identifies tumor-reactive CD8+ T cells predictive of immune checkpoint blockade efficacy in human lung cancer

Author

Chow, Andrew, primary, Uddin, Fathema Z., additional, Liu, Michael, additional, Dobrin, Anton, additional, Nabet, Barzin Y., additional, Mangarin, Levi, additional, Lavin, Yonit, additional, Rizvi, Hira, additional, Tischfield, Sam E., additional, Quintanal-Villalonga, Alvaro, additional, Chan, Joseph M., additional, Shah, Nisargbhai, additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Mattar, Marissa, additional, Meneses, Maximiliano, additional, Landau, Rebecca, additional, Ward, Mariana, additional, Kulick, Amanda, additional, Kwong, Charlene, additional, Wierzbicki, Matthew, additional, Yavner, Jessica, additional, Egger, Jacklynn, additional, Chavan, Shweta S., additional, Farillas, Abigail, additional, Holland, Aliya, additional, Sridhar, Harsha, additional, Ciampricotti, Metamia, additional, Hirschhorn, Daniel, additional, Guan, Xiangnan, additional, Richards, Allison L., additional, Heller, Glenn, additional, Mansilla-Soto, Jorge, additional, Sadelain, Michel, additional, Klebanoff, Christopher A., additional, Hellmann, Matthew D., additional, Sen, Triparna, additional, de Stanchina, Elisa, additional, Wolchok, Jedd D., additional, Merghoub, Taha, additional, and Rudin, Charles M., additional

Published
2023
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17. Keap1 loss promotes Kras-driven lung cancer and results in dependence on glutaminolysis

Author

Romero, Rodrigo, Sayin, Volkan I, Davidson, Shawn M, Bauer, Matthew R, Singh, Simranjit X, LeBoeuf, Sarah E, Karakousi, Triantafyllia R, Ellis, Donald C, Bhutkar, Arjun, Sánchez-Rivera, Francisco J, Subbaraj, Lakshmipriya, Martinez, Britney, Bronson, Roderick T, Prigge, Justin R, Schmidt, Edward E, Thomas, Craig J, Goparaju, Chandra, Davies, Angela, Dolgalev, Igor, Heguy, Adriana, Allaj, Viola, Poirier, John T, Moreira, Andre L, Rudin, Charles M, Pass, Harvey I, Vander Heiden, Matthew G, Jacks, Tyler, and Papagiannakopoulos, Thales

Subjects
Gene mutations -- Research -- Usage, Cell proliferation -- Research -- Usage, Cancer -- Diagnosis, Lung cancer -- Care and treatment -- Diagnosis -- Research, CT imaging -- Usage -- Research, Biological sciences, Health
Abstract

Author(s): Rodrigo Romero [1, 2]; Volkan I Sayin [3]; Shawn M Davidson [1, 2]; Matthew R Bauer [1]; Simranjit X Singh [3]; Sarah E LeBoeuf [3]; Triantafyllia R Karakousi [3]; [...]

Published
2017
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19. Targeting Lysine-Specific Demethylase 1 Rescues Major Histocompatibility Complex Class I Antigen Presentation and Overcomes Programmed Death-Ligand 1 Blockade Resistance in SCLC

Author

Nguyen, Evelyn M., primary, Taniguchi, Hirokazu, additional, Chan, Joseph M., additional, Zhan, Yingqian A., additional, Chen, Xiaoping, additional, Qiu, Juan, additional, de Stanchina, Elisa, additional, Allaj, Viola, additional, Shah, Nisargbhai S., additional, Uddin, Fathema, additional, Manoj, Parvathy, additional, Liu, Michael, additional, Cai, Sheng F., additional, Levine, Ross, additional, Quintanal-Villalonga, Álvaro, additional, Sen, Triparna, additional, Chow, Andrew, additional, and Rudin, Charles M., additional

Published
2022
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20. Abstract 3594: Exportin 1 inhibition as a therapeutic strategy for small cell lung cancer

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, additional, Hao, Yuan, additional, Chow, Andrew, additional, Zhan, Yingqian A., additional, Uddin, Fathema, additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Shah, Nisargbhai S., additional, Bhanot, Umesh K., additional, Qiu, Juan, additional, de Stanchina, Elisa, additional, Koche, Richard P., additional, Sen, Triparna, additional, Poirier, John T., additional, and Rudin, Charles M., additional

Published
2022
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21. Abstract 658: AKT pathway as a therapeutic target to constrain lineage plasticity leading to histological transdifferentiation

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, additional, Zhan, Yingqian A., additional, Uddin, Fathema, additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Shah, Nisargbhai S., additional, Bhanot, Umesh K., additional, Egger, Jacklynn, additional, Qiu, Juan, additional, de Stanchina, Elisa, additional, Rekhtman, Natasha, additional, Houck-Loomis, Brian, additional, Koche, Richard P., additional, Yu, Helena A., additional, Sen, Triparna, additional, and Rudin, Charles M., additional

Published
2022
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22. Rlf–Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer

Author

Massachusetts Institute of Technology. Department of Biology, Ciampricotti, Metamia, Karakousi, Triantafyllia, Richards, Allison L, Quintanal-Villalonga, Àlvaro, Karatza, Angeliki, Caeser, Rebecca, Costa, Emily A, Allaj, Viola, Manoj, Parvathy, Spainhower, Kyle B, Kombak, Faruk E, Sanchez-Rivera, Francisco J, Jaspers, Janneke E, Zavitsanou, Anastasia-Maria, Maddalo, Danilo, Ventura, Andrea, Rideout, William M, Akama-Garren, Elliot H, Jacks, Tyler, Donoghue, Mark TA, Sen, Triparna, Oliver, Trudy G, Poirier, John T, Papagiannakopoulos, Thales, Rudin, Charles M, Massachusetts Institute of Technology. Department of Biology, Ciampricotti, Metamia, Karakousi, Triantafyllia, Richards, Allison L, Quintanal-Villalonga, Àlvaro, Karatza, Angeliki, Caeser, Rebecca, Costa, Emily A, Allaj, Viola, Manoj, Parvathy, Spainhower, Kyle B, Kombak, Faruk E, Sanchez-Rivera, Francisco J, Jaspers, Janneke E, Zavitsanou, Anastasia-Maria, Maddalo, Danilo, Ventura, Andrea, Rideout, William M, Akama-Garren, Elliot H, Jacks, Tyler, Donoghue, Mark TA, Sen, Triparna, Oliver, Trudy G, Poirier, John T, Papagiannakopoulos, Thales, and Rudin, Charles M

Abstract

Abstract Small cell lung cancer (SCLC) has limited therapeutic options and an exceptionally poor prognosis. Understanding the oncogenic drivers of SCLC may help define novel therapeutic targets. Recurrent genomic rearrangements have been identified in SCLC, most notably an in-frame gene fusion between RLF and MYCL found in up to 7% of the predominant ASCL1-expressing subtype. To explore the role of this fusion in oncogenesis and tumor progression, we used CRISPR/Cas9 somatic editing to generate a Rlf–Mycl-driven mouse model of SCLC. RLF–MYCL fusion accelerated transformation and proliferation of murine SCLC and increased metastatic dissemination and the diversity of metastatic sites. Tumors from the RLF–MYCL genetically engineered mouse model displayed gene expression similarities with human RLF–MYCL SCLC. Together, our studies support RLF–MYCL as the first demonstrated fusion oncogenic driver in SCLC and provide a new preclinical mouse model for the study of this subtype of SCLC. Significance: The biological and therapeutic implications of gene fusions in SCLC, an aggressive metastatic lung cancer, are unknown. Our study investigates the functional significance of the in-frame RLF–MYCL gene fusion by developing a Rlf–Mycl-driven genetically engineered mouse model and defining the impact on tumor growth and metastasis. This article is highlighted in the In This Issue feature, p. 2945

Published
2022

23. WEE1 inhibition enhances the antitumor immune response to PD-L1 blockade by the concomitant activation of STING and STAT1 pathways in SCLC

Author

Taniguchi, Hirokazu, primary, Caeser, Rebecca, additional, Chavan, Shweta S., additional, Zhan, Yingqian A., additional, Chow, Andrew, additional, Manoj, Parvathy, additional, Uddin, Fathema, additional, Kitai, Hidenori, additional, Qu, Rui, additional, Hayatt, Omar, additional, Shah, Nisargbhai S., additional, Quintanal Villalonga, Álvaro, additional, Allaj, Viola, additional, Nguyen, Evelyn M., additional, Chan, Joseph, additional, Michel, Adam O., additional, Mukae, Hiroshi, additional, de Stanchina, Elisa, additional, Rudin, Charles M., additional, and Sen, Triparna, additional

Published
2022
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24. Additional file 4 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 4: Figure S6. Overall survival of patients based on OncoCast-MPM risk group

Published
2022
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25. Additional file 8 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 8: Figure S9. Gene expression changes in TCGA mesothelioma tumors as a function of overall survival.

Published
2022
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26. Additional file 2 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 2: Figure S1. Clinical outcomes of patients based on histology

Published
2022
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27. Additional file 5 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 5: Table S2. Mapping statistics for RNA-Seq dataset

Published
2022
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28. Additional file 1 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 1: Table S1. Patient demographics at the time of PDX collection by histology.

Published
2022
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29. Additional file 7 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 7: Figure S8. Patient outcomes based on clinical benefit of platinum-based chemotherapy.

Published
2022
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30. Additional file 3 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 3: Figure S2-S5. Detailed annotation of comparative histology of available patient samples and PDX models.

Published
2022
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31. Additional file 6 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Author

Offin, Michael, Sauter, Jennifer L., Tischfield, Sam E., Egger, Jacklynn V., Chavan, Shweta, Shah, Nisargbhai S., Manoj, Parvathy, Ventura, Katia, Allaj, Viola, de Stanchina, Elisa, Travis, William, Ladanyi, Marc, Rimner, Andreas, Rusch, Valerie W., Adusumilli, Prasad S., Poirier, John T., Zauderer, Marjorie G., Rudin, Charles M., and Sen, Triparna

Abstract

Additional file 6: Figure S7. Gene expression changes in TCGA mesothelioma tumors as a function of consensus histology.

Published
2022
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32. Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, additional, Hao, Yuan, additional, Chow, Andrew, additional, Zhan, Yingqian A., additional, Chavan, Shweta S., additional, Uddin, Fathema, additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Shah, Nisargbhai S., additional, Chan, Joseph M., additional, Offin, Michael, additional, Ciampricotti, Metamia, additional, Ray-Kirton, Jordana, additional, Egger, Jacklynn, additional, Bhanot, Umesh, additional, Linkov, Irina, additional, Asher, Marina, additional, Roehrl, Michael H., additional, Qiu, Juan, additional, de Stanchina, Elisa, additional, Hollmann, Travis J., additional, Koche, Richard P., additional, Sen, Triparna, additional, Poirier, John T., additional, and Rudin, Charles M., additional

Published
2022
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33. CD39 Identifies Tumor-Reactive CD8 T cells in Patients With Lung Cancer

Author

Chow, Andrew, primary, Uddin, Fathema Z., additional, Mangarin, Levi, additional, Rizvi, Hira, additional, Dobrin, Anton, additional, Tischfield, Sam, additional, Quintanal-Villalonga, Alvaro, additional, Chan, Joseph M., additional, Shah, Nisargbhai, additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Mattar, Marissa, additional, Meneses, Maximiliano, additional, Liu, Michael, additional, Landau, Rebecca, additional, Ward, Mariana, additional, Kulick, Amanda, additional, Kwong, Charlene, additional, Wierzbicki, Matthew, additional, Yavner, Jessica, additional, Chavan, Shweta S., additional, Farillas, Abigail, additional, Holland, Aliya, additional, Sridhar, Harsha, additional, Ciampricotti, Metamia, additional, Hirschhorn, Daniel, additional, Richards, Allison L, additional, Donoghue, Mark T.A., additional, Heller, Glenn, additional, Klebanoff, Christopher A., additional, Hellmann, Matthew D., additional, de Stanchina, Elisa, additional, Sen, Triparna, additional, Wolchok, Jedd D., additional, Merghoub, Taha, additional, and Rudin, Charles M., additional

Published
2022
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34. Rlf–Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer

Author

Ciampricotti, Metamia, primary, Karakousi, Triantafyllia, additional, Richards, Allison L., additional, Quintanal-Villalonga, Àlvaro, additional, Karatza, Angeliki, additional, Caeser, Rebecca, additional, Costa, Emily A., additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Spainhower, Kyle B., additional, Kombak, Faruk E., additional, Sanchez-Rivera, Francisco J., additional, Jaspers, Janneke E., additional, Zavitsanou, Anastasia-Maria, additional, Maddalo, Danilo, additional, Ventura, Andrea, additional, Rideout, William M., additional, Akama-Garren, Elliot H., additional, Jacks, Tyler, additional, Donoghue, Mark T.A., additional, Sen, Triparna, additional, Oliver, Trudy G., additional, Poirier, John T., additional, Papagiannakopoulos, Thales, additional, and Rudin, Charles M., additional

Published
2021
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35. Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer

Author

Chan, Joseph M., primary, Quintanal-Villalonga, Álvaro, additional, Gao, Vianne Ran, additional, Xie, Yubin, additional, Allaj, Viola, additional, Chaudhary, Ojasvi, additional, Masilionis, Ignas, additional, Egger, Jacklynn, additional, Chow, Andrew, additional, Walle, Thomas, additional, Mattar, Marissa, additional, Yarlagadda, Dig V.K., additional, Wang, James L., additional, Uddin, Fathema, additional, Offin, Michael, additional, Ciampricotti, Metamia, additional, Qeriqi, Besnik, additional, Bahr, Amber, additional, de Stanchina, Elisa, additional, Bhanot, Umesh K., additional, Lai, W. Victoria, additional, Bott, Matthew J., additional, Jones, David R., additional, Ruiz, Arvin, additional, Baine, Marina K., additional, Li, Yanyun, additional, Rekhtman, Natasha, additional, Poirier, John T., additional, Nawy, Tal, additional, Sen, Triparna, additional, Mazutis, Linas, additional, Hollmann, Travis J., additional, Pe'er, Dana, additional, and Rudin, Charles M., additional

Published
2021
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36. Regional and clonal T cell dynamics at single cell resolution in immune checkpoint blockade

Author

Pai, Joy A., primary, Chow, Andrew, additional, Sauter, Jennifer L., additional, Mattar, Marissa, additional, Rizvi, Hira, additional, Woo, Hyung Jun, additional, Shah, Nisargbhai, additional, Uddin, Fathema, additional, Quintanal-Villalonga, Alvaro, additional, Chan, Joseph M., additional, Manoj, Parvathy, additional, Allaj, Viola, additional, Baine, Marina, additional, Chaft, Jamie, additional, Plodkowski, Andrew J., additional, Won, Helen, additional, Wells, Daniel, additional, Donoghue, Mark T.A., additional, de Stanchina, Elisa, additional, Sen, Triparna, additional, Wolchok, Jedd D., additional, Houck-Loomis, Brian, additional, Merghoub, Taha, additional, Rudin, Charles M., additional, Satpathy, Ansuman T., additional, and Hellmann, Matthew D., additional

Published
2021
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37. Tim-4+ cavity-resident macrophages impair anti-tumor CD8+ T cell immunity

Author

Chow, Andrew, primary, Schad, Sara, additional, Green, Michael D., additional, Hellmann, Matthew D., additional, Allaj, Viola, additional, Ceglia, Nicholas, additional, Zago, Giulia, additional, Shah, Nisargbhai S., additional, Sharma, Sai Kiran, additional, Mattar, Marissa, additional, Chan, Joseph, additional, Rizvi, Hira, additional, Zhong, Hong, additional, Liu, Cailian, additional, Bykov, Yonina, additional, Zamarin, Dmitriy, additional, Shi, Hongyu, additional, Budhu, Sadna, additional, Wohlhieter, Corrin, additional, Uddin, Fathema, additional, Gupta, Aditi, additional, Khodos, Inna, additional, Waninger, Jessica J., additional, Qin, Angel, additional, Markowitz, Geoffrey J., additional, Mittal, Vivek, additional, Balachandran, Vinod, additional, Durham, Jennifer N., additional, Le, Dung T., additional, Zou, Weiping, additional, Shah, Sohrab P., additional, McPherson, Andrew, additional, Panageas, Katherine, additional, Lewis, Jason S., additional, Perry, Justin S.A., additional, de Stanchina, Elisa, additional, Sen, Triparna, additional, Poirier, John T., additional, Wolchok, Jedd D., additional, Rudin, Charles M., additional, and Merghoub, Taha, additional

Published
2021
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38. Additional file 2 of Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation

Author

Quintanal-Villalonga, Alvaro, Taniguchi, Hirokazu, Zhan, Yingqian A., Hasan, Maysun M., Chavan, Shweta S., Meng, Fanli, Uddin, Fathema, Allaj, Viola, Manoj, Parvathy, Shah, Nisargbhai S., Chan, Joseph M., Ciampricotti, Metamia, Chow, Andrew, Offin, Michael, Ray-Kirton, Jordana, Egger, Jacklynn D., Bhanot, Umesh K., Linkov, Irina, Asher, Marina, Roehrl, Michael H., Ventura, Katia, Qiu, Juan, de Stanchina, Elisa, Chang, Jason C., Rekhtman, Natasha, Houck-Loomis, Brian, Koche, Richard P., Yu, Helena A., Sen, Triparna, and Rudin, Charles M.

Abstract

Additional file 2: Supporting supplementary figures.

Published
2021
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39. Signatures of plasticity and immunosuppression in a single-cell atlas of human small cell lung cancer.

Author

Chan, Joseph Minhow, primary, Quintanal-Villalonga, Alvaro, additional, Gao, Vianne, additional, Allaj, Viola, additional, Masilionis, Ignas, additional, Chaudhary, Ojasvi, additional, Egger, Jacklynn V., additional, Chow, Andrew, additional, Walle, Thomas, additional, Mattar, Marissa, additional, Offin, Michael, additional, Lai, W. Victoria Victoria, additional, Bott, Matthew, additional, Hollman, Travis, additional, Nawy, Tal, additional, Mazutis, Linas, additional, Sen, Triparna, additional, Pe'er, Dana, additional, and Rudin, Charles M., additional

Published
2021
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40. Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancer

Author

Chan, Joseph M, primary, Quintanal-Villalonga, Álvaro, additional, Gao, Vianne, additional, Xie, Yubin, additional, Allaj, Viola, additional, Chaudhary, Ojasvi, additional, Masilionis, Ignas, additional, Egger, Jacklynn, additional, Chow, Andrew, additional, Walle, Thomas, additional, Mattar, Marissa, additional, Yarlagadda, Dig VK, additional, Wang, James L., additional, Uddin, Fathema, additional, Offin, Michael, additional, Ciampricotti, Metamia, additional, Bhanot, Umesh K, additional, Lai, W Victoria, additional, Bott, Matthew J, additional, Jones, David R, additional, Ruiz, Arvin, additional, Hollmann, Travis, additional, Poirier, John T, additional, Nawy, Tal, additional, Mazutis, Linas, additional, Sen, Triparna, additional, Pe’er, Dana, additional, and Rudin, Charles M, additional

Published
2020
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41. 524 Tim-4+ resident macrophages impair anti-tumor immunity in the serous body cavities By sequestering viable and cytotoxic CD8+ T cells expressing high levels of phosphatidylserine

Author

Chow, Andrew, primary, Schad, Sara, additional, Green, Michael, additional, Hellmann, Matthew, additional, Ceglia, Nicholas, additional, Allaj, Viola, additional, Zago, Giulia, additional, Shah, Nisarg, additional, Sharma, Sai, additional, Mattar, Marissa, additional, Chan, Joseph, additional, Rizvi, Hira, additional, Zhong, Hong, additional, Liu, Cailian, additional, Bykov, Yonina, additional, Zamarin, Dmitriy, additional, Shi, Hongyu, additional, Budhu, Sadna, additional, Wohlhieter, Corrin, additional, Uddin, Fathema, additional, Gupta, Aditi, additional, Khodos, Inna, additional, Waninger, Jessica, additional, Qin, Angel, additional, Balachandran, Vinod, additional, Zou, Weiping, additional, Shah, Sohrab, additional, McPherson, Andrew, additional, Panageas, Katherine, additional, Lewis, Jason, additional, Perry, Justin, additional, Stanchina, Elisa de, additional, Sen, Triparna, additional, Poirier, John, additional, Wolchok, Jedd, additional, Rudin, Charles, additional, and Merghoub, Taha, additional

Published
2020
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43. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Author

Rozenblatt-Rosen, Orit, primary, Regev, Aviv, additional, Oberdoerffer, Philipp, additional, Nawy, Tal, additional, Hupalowska, Anna, additional, Rood, Jennifer E., additional, Ashenberg, Orr, additional, Cerami, Ethan, additional, Coffey, Robert J., additional, Demir, Emek, additional, Ding, Li, additional, Esplin, Edward D., additional, Ford, James M., additional, Goecks, Jeremy, additional, Ghosh, Sharmistha, additional, Gray, Joe W., additional, Guinney, Justin, additional, Hanlon, Sean E., additional, Hughes, Shannon K., additional, Hwang, E. Shelley, additional, Iacobuzio-Donahue, Christine A., additional, Jané-Valbuena, Judit, additional, Johnson, Bruce E., additional, Lau, Ken S., additional, Lively, Tracy, additional, Mazzilli, Sarah A., additional, Pe’er, Dana, additional, Santagata, Sandro, additional, Shalek, Alex K., additional, Schapiro, Denis, additional, Snyder, Michael P., additional, Sorger, Peter K., additional, Spira, Avrum E., additional, Srivastava, Sudhir, additional, Tan, Kai, additional, West, Robert B., additional, Williams, Elizabeth H., additional, Aberle, Denise, additional, Achilefu, Samuel I., additional, Ademuyiwa, Foluso O., additional, Adey, Andrew C., additional, Aft, Rebecca L., additional, Agarwal, Rachana, additional, Aguilar, Ruben A., additional, Alikarami, Fatemeh, additional, Allaj, Viola, additional, Amos, Christopher, additional, Anders, Robert A., additional, Angelo, Michael R., additional, Anton, Kristen, additional, Aster, Jon C., additional, Babur, Ozgun, additional, Bahmani, Amir, additional, Balsubramani, Akshay, additional, Barrett, David, additional, Beane, Jennifer, additional, Bender, Diane E., additional, Bernt, Kathrin, additional, Berry, Lynne, additional, Betts, Courtney B., additional, Bletz, Julie, additional, Blise, Katie, additional, Boire, Adrienne, additional, Boland, Genevieve, additional, Borowsky, Alexander, additional, Bosse, Kristopher, additional, Bott, Matthew, additional, Boyden, Ed, additional, Brooks, James, additional, Bueno, Raphael, additional, Burlingame, Erik A., additional, Cai, Qiuyin, additional, Campbell, Joshua, additional, Caravan, Wagma, additional, Chaib, Hassan, additional, Chan, Joseph M., additional, Chang, Young Hwan, additional, Chatterjee, Deyali, additional, Chaudhary, Ojasvi, additional, Chen, Alyce A., additional, Chen, Bob, additional, Chen, Changya, additional, Chen, Chia-hui, additional, Chen, Feng, additional, Chen, Yu-An, additional, Chheda, Milan G., additional, Chin, Koei, additional, Chiu, Roxanne, additional, Chu, Shih-Kai, additional, Chuaqui, Rodrigo, additional, Chun, Jaeyoung, additional, Cisneros, Luis, additional, Colditz, Graham A., additional, Cole, Kristina, additional, Collins, Natalie, additional, Contrepois, Kevin, additional, Coussens, Lisa M., additional, Creason, Allison L., additional, Crichton, Daniel, additional, Curtis, Christina, additional, Davidsen, Tanja, additional, Davies, Sherri R., additional, de Bruijn, Ino, additional, Dellostritto, Laura, additional, De Marzo, Angelo, additional, DeNardo, David G., additional, Diep, Dinh, additional, Diskin, Sharon, additional, Doan, Xengie, additional, Drewes, Julia, additional, Dubinett, Stephen, additional, Dyer, Michael, additional, Egger, Jacklynn, additional, Eng, Jennifer, additional, Engelhardt, Barbara, additional, Erwin, Graham, additional, Esserman, Laura, additional, Felmeister, Alex, additional, Feiler, Heidi S., additional, Fields, Ryan C., additional, Fisher, Stephen, additional, Flaherty, Keith, additional, Flournoy, Jennifer, additional, Fortunato, Angelo, additional, Frangieh, Allison, additional, Frye, Jennifer L., additional, Fulton, Robert S., additional, Galipeau, Danielle, additional, Gan, Siting, additional, Gao, Jianjiong, additional, Gao, Long, additional, Gao, Peng, additional, Gao, Vianne R., additional, Geiger, Tim, additional, George, Ajit, additional, Getz, Gad, additional, Giannakis, Marios, additional, Gibbs, David L., additional, Gillanders, William E., additional, Goedegebuure, Simon P., additional, Gould, Alanna, additional, Gowers, Kate, additional, Greenleaf, William, additional, Gresham, Jeremy, additional, Guerriero, Jennifer L., additional, Guha, Tuhin K., additional, Guimaraes, Alexander R., additional, Gutman, David, additional, Hacohen, Nir, additional, Hanlon, Sean, additional, Hansen, Casey R., additional, Harismendy, Olivier, additional, Harris, Kathleen A., additional, Hata, Aaron, additional, Hayashi, Akimasa, additional, Heiser, Cody, additional, Helvie, Karla, additional, Herndon, John M., additional, Hirst, Gilliam, additional, Hodi, Frank, additional, Hollmann, Travis, additional, Horning, Aaron, additional, Hsieh, James J., additional, Hughes, Shannon, additional, Huh, Won Jae, additional, Hunger, Stephen, additional, Hwang, Shelley E., additional, Ijaz, Heba, additional, Izar, Benjamin, additional, Jacobson, Connor A., additional, Janes, Samuel, additional, Jayasinghe, Reyka G., additional, Jiang, Lihua, additional, Johnson, Brett E., additional, Johnson, Bruce, additional, Ju, Tao, additional, Kadara, Humam, additional, Kaestner, Klaus, additional, Kagan, Jacob, additional, Kalinke, Lukas, additional, Keith, Robert, additional, Khan, Aziz, additional, Kibbe, Warren, additional, Kim, Albert H., additional, Kim, Erika, additional, Kim, Junhyong, additional, Kolodzie, Annette, additional, Kopytra, Mateusz, additional, Kotler, Eran, additional, Krueger, Robert, additional, Krysan, Kostyantyn, additional, Kundaje, Anshul, additional, Ladabaum, Uri, additional, Lake, Blue B., additional, Lam, Huy, additional, Laquindanum, Rozelle, additional, Laughney, Ashley M., additional, Lee, Hayan, additional, Lenburg, Marc, additional, Leonard, Carina, additional, Leshchiner, Ignaty, additional, Levy, Rochelle, additional, Li, Jerry, additional, Lian, Christine G., additional, Lim, Kian-Huat, additional, Lin, Jia-Ren, additional, Lin, Yiyun, additional, Liu, Qi, additional, Liu, Ruiyang, additional, Longabaugh, William J.R., additional, Longacre, Teri, additional, Ma, Cynthia X., additional, Macedonia, Mary Catherine, additional, Madison, Tyler, additional, Maher, Christopher A., additional, Maitra, Anirban, additional, Makinen, Netta, additional, Makowski, Danika, additional, Maley, Carlo, additional, Maliga, Zoltan, additional, Mallo, Diego, additional, Maris, John, additional, Markham, Nick, additional, Marks, Jeffrey, additional, Martinez, Daniel, additional, Mashl, Robert J., additional, Masilionais, Ignas, additional, Mason, Jennifer, additional, Massagué, Joan, additional, Massion, Pierre, additional, Mattar, Marissa, additional, Mazurchuk, Richard, additional, Mazutis, Linas, additional, McKinley, Eliot T., additional, McMichael, Joshua F., additional, Merrick, Daniel, additional, Meyerson, Matthew, additional, Miessner, Julia R., additional, Mills, Gordon B., additional, Mills, Meredith, additional, Mondal, Suman B., additional, Mori, Motomi, additional, Mori, Yuriko, additional, Moses, Elizabeth, additional, Mosse, Yael, additional, Muhlich, Jeremy L., additional, Murphy, George F., additional, Navin, Nicholas E., additional, Nederlof, Michel, additional, Ness, Reid, additional, Nevins, Stephanie, additional, Nikolov, Milen, additional, Nirmal, Ajit Johnson, additional, Nolan, Garry, additional, Novikov, Edward, additional, O’Connell, Brendan, additional, Offin, Michael, additional, Oh, Stephen T., additional, Olson, Anastasiya, additional, Ooms, Alex, additional, Ossandon, Miguel, additional, Owzar, Kouros, additional, Parmar, Swapnil, additional, Patel, Tasleema, additional, Patti, Gary J., additional, Pe'er, Itsik, additional, Peng, Tao, additional, Persson, Daniel, additional, Petty, Marvin, additional, Pfister, Hanspeter, additional, Polyak, Kornelia, additional, Pourfarhangi, Kamyar, additional, Puram, Sidharth V., additional, Qiu, Qi, additional, Quintanal-Villalonga, Álvaro, additional, Raj, Arjun, additional, Ramirez-Solano, Marisol, additional, Rashid, Rumana, additional, Reeb, Ashley N., additional, Reid, Mary, additional, Resnick, Adam, additional, Reynolds, Sheila M., additional, Riesterer, Jessica L., additional, Rodig, Scott, additional, Roland, Joseph T., additional, Rosenfield, Sonia, additional, Rotem, Asaf, additional, Roy, Sudipta, additional, Rozenblatt-Rosen, Orit, additional, Rudin, Charles M., additional, Ryser, Marc D., additional, Santi-Vicini, Maria, additional, Sato, Kazuhito, additional, Schrag, Deborah, additional, Schultz, Nikolaus, additional, Sears, Cynthia L., additional, Sears, Rosalie C., additional, Sen, Subrata, additional, Sen, Triparna, additional, Shalek, Alex, additional, Sheng, Jeff, additional, Sheng, Quanhu, additional, Shoghi, Kooresh I., additional, Shrubsole, Martha J., additional, Shyr, Yu, additional, Sibley, Alexander B., additional, Siex, Kiara, additional, Simmons, Alan J., additional, Singer, Dinah S., additional, Sivagnanam, Shamilene, additional, Slyper, Michal, additional, Sokolov, Artem, additional, Song, Sheng-Kwei, additional, Southard-Smith, Austin, additional, Spira, Avrum, additional, Stein, Janet, additional, Storm, Phillip, additional, Stover, Elizabeth, additional, Strand, Siri H., additional, Su, Timothy, additional, Sudar, Damir, additional, Sullivan, Ryan, additional, Surrey, Lea, additional, Suvà, Mario, additional, Terekhanova, Nadezhda V., additional, Ternes, Luke, additional, Thammavong, Lisa, additional, Thibault, Guillaume, additional, Thomas, George V., additional, Thorsson, Vésteinn, additional, Todres, Ellen, additional, Tran, Linh, additional, Tyler, Madison, additional, Uzun, Yasin, additional, Vachani, Anil, additional, Van Allen, Eliezer, additional, Vandekar, Simon, additional, Veis, Deborah J., additional, Vigneau, Sébastien, additional, Vossough, Arastoo, additional, Waanders, Angela, additional, Wagle, Nikhil, additional, Wang, Liang-Bo, additional, Wendl, Michael C., additional, West, Robert, additional, Wu, Chi-yun, additional, Wu, Hao, additional, Wu, Hung-Yi, additional, Wyczalkowski, Matthew A., additional, Xie, Yubin, additional, Yang, Xiaolu, additional, Yapp, Clarence, additional, Yu, Wenbao, additional, Yuan, Yinyin, additional, Zhang, Dadong, additional, Zhang, Kun, additional, Zhang, Mianlei, additional, Zhang, Nancy, additional, Zhang, Yantian, additional, Zhao, Yanyan, additional, Zhou, Daniel Cui, additional, Zhou, Zilu, additional, Zhu, Houxiang, additional, Zhu, Qin, additional, Zhu, Xiangzhu, additional, Zhu, Yuankun, additional, and Zhuang, Xiaowei, additional

Published
2020
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44. Keap1 loss promotes Kras-driven lung cancer and results in dependence on glutaminolysis

Author

Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Romero, Rodrigo, Davidson, Shawn M., Bauer, Matthew R., Ellis, Donald Christian, Bhutkar, Arjun, Sanchez-Rivera, Francisco Javier, Subbaraj, Lakshmipriya, Vander Heiden, Matthew G., Jacks, Tyler E., Sayin, Volkan I., Singh, Simranjit X., LeBoeuf, Sarah E., Karakousi, Triantafyllia R., Martinez, Britney, Bronson, Roderick T., Prigge, Justin R., Schmidt, Edward E., Thomas, Craig J., Goparaju, Chandra, Davies, Angela, Dolgalev, Igor, Heguy, Adriana, Allaj, Viola, Poirier, John T., Moreira, Andre L., Rudin, Charles M., Pass, Harvey I., Papagiannakopoulos, Thales, Romero, Rodrigo,Ph. D.Massachusetts Institute of Technology., Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Romero, Rodrigo, Davidson, Shawn M., Bauer, Matthew R., Ellis, Donald Christian, Bhutkar, Arjun, Sanchez-Rivera, Francisco Javier, Subbaraj, Lakshmipriya, Vander Heiden, Matthew G., Jacks, Tyler E., Sayin, Volkan I., Singh, Simranjit X., LeBoeuf, Sarah E., Karakousi, Triantafyllia R., Martinez, Britney, Bronson, Roderick T., Prigge, Justin R., Schmidt, Edward E., Thomas, Craig J., Goparaju, Chandra, Davies, Angela, Dolgalev, Igor, Heguy, Adriana, Allaj, Viola, Poirier, John T., Moreira, Andre L., Rudin, Charles M., Pass, Harvey I., Papagiannakopoulos, Thales, and Romero, Rodrigo,Ph. D.Massachusetts Institute of Technology.

Abstract

Treating KRAS-mutant lung adenocarcinoma (LUAD) remains a major challenge in cancer treatment given the difficulties associated with directly inhibiting the KRAS oncoprotein. One approach to addressing this challenge is to define mutations that frequently co-occur with those in KRAS, which themselves may lead to therapeutic vulnerabilities in tumors. Approximately 20% of KRAS-mutant LUAD tumors carry loss-of-function mutations in the KEAP1 gene encoding Kelch-like ECH-associated protein 1 (refs. 2, 3, 4), a negative regulator of nuclear factor erythroid 2-like 2 (NFE2L2; hereafter NRF2), which is the master transcriptional regulator of the endogenous antioxidant response. The high frequency of mutations in KEAP1 suggests an important role for the oxidative stress response in lung tumorigenesis. Using a CRISPR-Cas9-based approach in a mouse model of KRAS-driven LUAD, we examined the effects of Keap1 loss in lung cancer progression. We show that loss of Keap1 hyperactivates NRF2 and promotes KRAS-driven LUAD in mice. Through a combination of CRISPR-Cas9-based genetic screening and metabolomic analyses, we show that Keap1- or Nrf2-mutant cancers are dependent on increased glutaminolysis, and this property can be therapeutically exploited through the pharmacological inhibition of glutaminase. Finally, we provide a rationale for stratification of human patients with lung cancer harboring KRAS/KEAP1- or KRAS/NRF2-mutant lung tumors as likely to respond to glutaminase inhibition.

Published
2018

45. Abstract A43: Loss of Keap1 promotes KRAS-driven lung cancer and results in genotype-specific vulnerabilities

Author

Romero, Rodrigo, primary, Sayin, Volkan I., additional, Shawn, Davidson M., additional, Bauer, Matthew, additional, Singh, Simranjit X., additional, LeBoeuf, Sarah, additional, Karakousi, Triantafyllia R., additional, Ellis, Donald C., additional, Bhutkar, Arjun, additional, Sanchez-Rivera, Francisco, additional, Subbaraj, Lakshmipriya, additional, Martinez, Britney, additional, Bronson, Roderick T., additional, Prigge, Justin R., additional, Schmidt, Edward E., additional, Thomas, Craig J., additional, Davies, Angela, additional, Dolgalev, Igor, additional, Heguy, Adriana, additional, Allaj, Viola, additional, Piorier, John T., additional, Moreira, Andre L., additional, Rudin, Charles M., additional, Pass, Harvey I., additional, Heiden, Matthew G. Vander, additional, Jacks, Tyler, additional, and Papagiannakopoulos, Thales, additional

Published
2018
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47. Noninvasive Interrogation of DLL3 Expression in Metastatic Small Cell Lung Cancer

Author

Sharma, Sai Kiran, primary, Pourat, Jacob, additional, Abdel-Atti, Dalya, additional, Carlin, Sean D., additional, Piersigilli, Alessandra, additional, Bankovich, Alexander J., additional, Gardner, Eric E., additional, Hamdy, Omar, additional, Isse, Kumiko, additional, Bheddah, Sheila, additional, Sandoval, Joseph, additional, Cunanan, Kristen M., additional, Johansen, Eric B., additional, Allaj, Viola, additional, Sisodiya, Vikram, additional, Liu, David, additional, Zeglis, Brian M., additional, Rudin, Charles M., additional, Dylla, Scott J., additional, Poirier, John T., additional, and Lewis, Jason S., additional

Published
2017
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49. The ectonucleotidase CD39 identifies tumor-reactive CD8 + T cells predictive of immune checkpoint blockade efficacy in human lung cancer.

Author

Chow A, Uddin FZ, Liu M, Dobrin A, Nabet BY, Mangarin L, Lavin Y, Rizvi H, Tischfield SE, Quintanal-Villalonga A, Chan JM, Shah N, Allaj V, Manoj P, Mattar M, Meneses M, Landau R, Ward M, Kulick A, Kwong C, Wierzbicki M, Yavner J, Egger J, Chavan SS, Farillas A, Holland A, Sridhar H, Ciampricotti M, Hirschhorn D, Guan X, Richards AL, Heller G, Mansilla-Soto J, Sadelain M, Klebanoff CA, Hellmann MD, Sen T, de Stanchina E, Wolchok JD, Merghoub T, and Rudin CM

Subjects
Humans, Immune Checkpoint Inhibitors therapeutic use, CD8-Positive T-Lymphocytes, Immunotherapy, Lung Neoplasms genetics, Carcinoma, Non-Small-Cell Lung genetics
Abstract

Improved identification of anti-tumor T cells is needed to advance cancer immunotherapies. CD39 expression is a promising surrogate of tumor-reactive CD8 + T cells. Here, we comprehensively profiled CD39 expression in human lung cancer. CD39 expression enriched for CD8 + T cells with features of exhaustion, tumor reactivity, and clonal expansion. Flow cytometry of 440 lung cancer biospecimens revealed weak association between CD39 + CD8 + T cells and tumoral features, such as programmed death-ligand 1 (PD-L1), tumor mutation burden, and driver mutations. Immune checkpoint blockade (ICB), but not cytotoxic chemotherapy, increased intratumoral CD39 + CD8 + T cells. Higher baseline frequency of CD39 + CD8 + T cells conferred improved clinical outcomes from ICB therapy. Furthermore, a gene signature of CD39 + CD8 + T cells predicted benefit from ICB, but not chemotherapy, in a phase III clinical trial of non-small cell lung cancer. These findings highlight CD39 as a proxy of tumor-reactive CD8 + T cells in human lung cancer., Competing Interests: Declaration of interests C.A.K. received research funding support from Kite/Gilead and Intima Bioscience; is on the Scientific and/or Clinical Advisory Boards of Achilles Therapeutics, Aleta BioTherapeutics, Bellicum Pharmaceuticals, Catamaran Bio, Obsidian Therapeutics, and T-knife; and has performed consulting services for Bristol Myers Squibb, PACT Pharma, and Roche/Genentech. C.A.K. is a co-inventor on patent applications related to TCRs targeting public neoantigens unrelated to the current work. M.D.H. received a research grant from BMS; personal fees from Achilles, Arcus, AstraZeneca, Blueprint, BMS, Genentech/Roche, Genzyme, Immunai, Instil Bio, Janssen, Merck, Mirati, Natera, Nektar, Pact Pharma, Regeneron, Shattuck Labs, and Syndax; and equity options from Arcus, Factorial, Immunai, and Shattuck Labs. A patent filed by MSKCC related to the use of tumor mutational burden to predict response to immunotherapy (PCT/US2015/062208) is pending and licensed by PGDx. J.D.W. is a consultant for Amgen, Apricity, Ascentage Pharma, Astellas, AstraZeneca, Bicara Therapeutics, Boehringer Ingelheim, Bristol Myers Squibb, CellCarta, Chugai, Daiichi Sankyo, Dragonfly, Georgiamune, Idera, Imvaq, Larkspur, Maverick Therapeutics, Merck, Psioxus, Recepta, Tizona, Trishula, Sellas, Surface Oncology, and Werewolf Therapeutics. J.D.W. receives grant/research support from Bristol Myers Squibb and Sephora. J.D.W. has equity in Apricity, Arsenal IO, Ascentage, Beigene, Imvaq, Linneaus, Georgiamune, Maverick, Tizona Pharmaceuticals, and Trieza. J.D.W. is a co-inventor on the following patent application: xenogeneic (canine) DNA vaccines, myeloid-derived suppressor cell (MDSC) assay, anti-PD1 antibody, anti-CTLA4 antibodies, anti-GITR antibodies and methods of use thereof, Newcastle disease viruses for cancer therapy, and prediction of responsiveness to treatment with immunomodulatory therapeutics and method of monitoring abscopal effects during such treatment. J.D.W. and T.M. are co-inventors on patent applications related to CD40 and in situ vaccination (PCT/US2016/045970). T.M. is a consultant for Immunos Therapeutics and Pfizer. T.M. is a cofounder of and equity holder in IMVAQ Therapeutics. T.M. receives research funding from Bristol Myers Squibb, Surface Oncology, Kyn Therapeutics, Infinity Pharmaceuticals, Peregrine Pharmaceuticals, Adaptive Biotechnologies, Leap Therapeutics, and Aprea Therapeutics. T.M. is an inventor on patent applications related to work on oncolytic viral therapy, alpha virus-based vaccine, neoantigen modeling, CD40, GITR, OX40, PD-1, and CTLA-4. C.M.R. has consulted regarding oncology drug development with AbbVie, Amgen, Ascentage, AstraZeneca, BMS, Celgene, Daiichi Sankyo, Genentech/Roche, Ipsen, Loxo, and PharmaMar and is on the scientific advisory boards of Elucida, Bridge, and Harpoon. B.Y.N. and X.G. are employees and stockholders of Genentech/Roche., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Published
2023
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50. Tim-4 + cavity-resident macrophages impair anti-tumor CD8 + T cell immunity.

Author

Chow A, Schad S, Green MD, Hellmann MD, Allaj V, Ceglia N, Zago G, Shah NS, Sharma SK, Mattar M, Chan J, Rizvi H, Zhong H, Liu C, Bykov Y, Zamarin D, Shi H, Budhu S, Wohlhieter C, Uddin F, Gupta A, Khodos I, Waninger JJ, Qin A, Markowitz GJ, Mittal V, Balachandran V, Durham JN, Le DT, Zou W, Shah SP, McPherson A, Panageas K, Lewis JS, Perry JSA, de Stanchina E, Sen T, Poirier JT, Wolchok JD, Rudin CM, and Merghoub T

Subjects
Animals, Apoptosis, Cell Proliferation, Colonic Neoplasms metabolism, Colonic Neoplasms pathology, Female, Humans, Membrane Proteins genetics, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Prognosis, Retrospective Studies, Tumor Cells, Cultured, Xenograft Model Antitumor Assays, CD8-Positive T-Lymphocytes immunology, Colonic Neoplasms immunology, Gene Expression Regulation, Neoplastic, Macrophages immunology, Membrane Proteins metabolism, Tumor Microenvironment
Abstract

Immune checkpoint blockade (ICB) has been a remarkable clinical advance for cancer; however, the majority of patients do not respond to ICB therapy. We show that metastatic disease in the pleural and peritoneal cavities is associated with poor clinical outcomes after ICB therapy. Cavity-resident macrophages express high levels of Tim-4, a receptor for phosphatidylserine (PS), and this is associated with reduced numbers of CD8 + T cells with tumor-reactive features in pleural effusions and peritoneal ascites from patients with cancer. We mechanistically demonstrate that viable and cytotoxic anti-tumor CD8 + T cells upregulate PS and this renders them susceptible to sequestration away from tumor targets and proliferation suppression by Tim-4 + macrophages. Tim-4 blockade abrogates this sequestration and proliferation suppression and enhances anti-tumor efficacy in models of anti-PD-1 therapy and adoptive T cell therapy in mice. Thus, Tim-4 + cavity-resident macrophages limit the efficacy of immunotherapies in these microenvironments., Competing Interests: Declaration of interests JDW is a consultant for Adaptive Biotech, Amgen, Apricity, Ascentage Pharma, Arsenal IO, Astellas, AstraZeneca, Bayer, Beigene, Boehringer Ingelheim, Bristol Myers Squibb, Celgene, Chugai, Daiichi Sankyo, Dragonfly, Eli Lilly, Elucida, F Star, Georgiamune, Idera, Imvaq, Kyowa Hakko Kirin, Linneaus, Maverick Therapeutics, Merck, Neon Therapeutics, Polynoma, Psioxus, Recepta, Takara Bio, Trieza, Truvax, Trishula, Sellas, Serametrix, Surface Oncology, Syndax, Syntalogic, and Werewolf Therapeutics. JDW has received grant/research support from Bristol Myers Squibb; Sephora. JDW has equity in Tizona Pharmaceuticals, Adaptive Biotechnologies, Imvaq, Beigene, Linneaus, Apricity, Arsenal IO, and Georgiamune. JDW is a co-inventor on patent applications related to heteroclitic cancer vaccines and recombinant poxviruses for cancer immunotherapy. JDW and TM are co-inventors on patent applications related to CD40 and in situ vaccination (PCT/US2016/045970). TM is a consultant for Immunos Therapeutics and Pfizer. TM is a cofounder of and equity holder in IMVAQ Therapeutics. TM receives research funding from Bristol-Myers Squibb, Surface Oncology, Kyn Therapeutics, Infinity Pharmaceuticals, Peregrine Pharmaceuticals, Adaptive Biotechnologies, Leap Therapeutics, and Aprea Therapeutics. TM is an inventor on patent applications related to work on oncolytic viral therapy, alpha virus–based vaccine, neoantigen modeling, CD40, GITR, OX40, PD-1, and CTLA-4. C.M.R. has consulted regarding oncology drug development with AbbVie, Amgen, Ascentage, AstraZeneca, BMS, Celgene, Daiichi Sankyo, Genentech/Roche, Ipsen, Loxo and PharmaMar and is on the scientific advisory boards of Elucida, Bridge and Harpoon. Unrelated to this work, D.Z. reports clinical research support to his institution from Astra Zeneca, Plexxikon, and Genentech; and personal/consultancy fees from Merck, Synlogic Therapeutics, GSK, Genentech, Xencor, Memgen, Immunos, CrownBio, and Agenus. D.Z. is an inventor on patents related to the use of Newcastle Disease Virus that has been licensed to Merck. MDH received research grant from BMS; personal fees from Achilles, Arcus, AstraZeneca, Blueprint, BMS, Genentech/Roche, Genzyme, Immunai, Instil Bio, Janssen, Merck, Mirati, Natera, Nektar, Pact Pharma, Regeneron, Shattuck Labs, Syndax, as well as equity options from Arcus, Factorial, Immunai, and Shattuck Labs. A patent filed by MSKCC related to the use of tumor mutational burden to predict response to immunotherapy (PCT/US2015/062208) is pending and licensed by PGDx. DTL serves on advisory boards for Merck, Bristol Myers Squibb, and Janssen and has received research funding from Merck, Bristol Myers Squibb, Aduro Biotech, Curegenix, Medivir, and Nouscom. She has received speaking honoraria from Merck and is an inventor of licensed intellectual property related to technology for mismatch repair deficiency for diagnosis and therapy (WO2016077553A1) from Johns Hopkins University. SS is a shareholder of Canexia Health Inc., (Copyright © 2021. Published by Elsevier Inc.)

Published
2021
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