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Start Over Author "Amin H" Publisher american association for cancer research (aacr)
80 results on '"Amin H"'

1. Abstract A029: Epigenomic profiling nominates master transcription factors (TFs) driving sarcomatoid differentiation of renal cell carcinoma (RCC)

Author

Semaan, Karl, primary, Zarif, Talal El, additional, Eid, Marc, additional, Shah, Valisha, additional, Fortunato, Brad, additional, Saliby, Renee Maria, additional, Nassar, Amin H., additional, Alaiwi, Sarah Abou, additional, Seo, Ji-Heui, additional, Labaki, Chris, additional, Bakouny, Ziad, additional, Matar, Sayed, additional, Ahmar, Nourhan El, additional, Laimon, Yasmin Nabil, additional, Lee, Gwo-Shu Mary, additional, Pomerantz, Mark, additional, Berchuck, Jacob, additional, Signoretti, Sabina, additional, Van Allen, Eliezer, additional, Choueiri, Toni, additional, Braun, David, additional, Freedman, Matthew, additional, and Baca, Sylvan, additional

Published
2023
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2. Data from Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors

Author

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

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

Author

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

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

Author

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

Published
2023
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5. Supplementary Data from Gene Expression Signature Correlates with Outcomes in Metastatic Renal Cell Carcinoma Patients Treated with Everolimus Alone or with a Vascular Disrupting Agent

Author

Yang, Eddy S., primary, Nassar, Amin H., primary, Adib, Elio, primary, Jegede, Opeyemi A., primary, Alaiwi, Sarah Abou, primary, Manna, Deborah L. Della, primary, Braun, David A., primary, Zarei, Mahsa, primary, Du, Heng, primary, Pal, Sumanta K., primary, Naik, Gurudatta, primary, and Sonpavde, Guru P., primary

Published
2023
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6. Supplementary Data from Mutations and Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma

Author

Nassar, Amin H., primary, Hamieh, Lana, primary, Gray, Kathryn P., primary, Thorner, Aaron R., primary, Fay, Andre P., primary, Lasseter, Kathryn D., primary, Abou Alaiwi, Sarah, primary, Nuzzo, Pier Vitale, primary, Flippot, Ronan, primary, Krajewski, Katherine M., primary, Signoretti, Sabina, primary, Choueiri, Toni K., primary, and Kwiatkowski, David J., primary

Published
2023
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7. Data from Gene Expression Signature Correlates with Outcomes in Metastatic Renal Cell Carcinoma Patients Treated with Everolimus Alone or with a Vascular Disrupting Agent

Author

Yang, Eddy S., primary, Nassar, Amin H., primary, Adib, Elio, primary, Jegede, Opeyemi A., primary, Alaiwi, Sarah Abou, primary, Manna, Deborah L. Della, primary, Braun, David A., primary, Zarei, Mahsa, primary, Du, Heng, primary, Pal, Sumanta K., primary, Naik, Gurudatta, primary, and Sonpavde, Guru P., primary

Published
2023
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8. Data from Mutations and Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma

Author

Nassar, Amin H., primary, Hamieh, Lana, primary, Gray, Kathryn P., primary, Thorner, Aaron R., primary, Fay, Andre P., primary, Lasseter, Kathryn D., primary, Abou Alaiwi, Sarah, primary, Nuzzo, Pier Vitale, primary, Flippot, Ronan, primary, Krajewski, Katherine M., primary, Signoretti, Sabina, primary, Choueiri, Toni K., primary, and Kwiatkowski, David J., primary

Published
2023
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9. Table S1 from Gene Expression Signature Correlates with Outcomes in Metastatic Renal Cell Carcinoma Patients Treated with Everolimus Alone or with a Vascular Disrupting Agent

Author

Yang, Eddy S., primary, Nassar, Amin H., primary, Adib, Elio, primary, Jegede, Opeyemi A., primary, Alaiwi, Sarah Abou, primary, Manna, Deborah L. Della, primary, Braun, David A., primary, Zarei, Mahsa, primary, Du, Heng, primary, Pal, Sumanta K., primary, Naik, Gurudatta, primary, and Sonpavde, Guru P., primary

Published
2023
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10. Supplementary Figure S1 from Gene Expression Signature Correlates with Outcomes in Metastatic Renal Cell Carcinoma Patients Treated with Everolimus Alone or with a Vascular Disrupting Agent

Author

Yang, Eddy S., primary, Nassar, Amin H., primary, Adib, Elio, primary, Jegede, Opeyemi A., primary, Alaiwi, Sarah Abou, primary, Manna, Deborah L. Della, primary, Braun, David A., primary, Zarei, Mahsa, primary, Du, Heng, primary, Pal, Sumanta K., primary, Naik, Gurudatta, primary, and Sonpavde, Guru P., primary

Published
2023
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11. Supplementary Table 2 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., primary, Li, Yixiang, primary, Durmaz, Yavuz T., primary, Gao, Wenhua, primary, Walton, Emily, primary, Vajdi, Amir, primary, Thai, Tran, primary, Sticco-Ivins, Maura, primary, Sabet, Amin H., primary, Jones, Kristen L., primary, Schinzel, Anna C., primary, Bronson, Rod T., primary, Nguyen, Quang-De, primary, Tolstorukov, Michael Y., primary, Vivero, Marina, primary, Signoretti, Sabina, primary, Barbie, David A., primary, and Oser, Matthew G., primary

Published
2023
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12. Supplementary Table 5 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., primary, Li, Yixiang, primary, Durmaz, Yavuz T., primary, Gao, Wenhua, primary, Walton, Emily, primary, Vajdi, Amir, primary, Thai, Tran, primary, Sticco-Ivins, Maura, primary, Sabet, Amin H., primary, Jones, Kristen L., primary, Schinzel, Anna C., primary, Bronson, Rod T., primary, Nguyen, Quang-De, primary, Tolstorukov, Michael Y., primary, Vivero, Marina, primary, Signoretti, Sabina, primary, Barbie, David A., primary, and Oser, Matthew G., primary

Published
2023
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13. Supplementary Data from Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites

Author

Nassar, Amin H., primary, Umeton, Renato, primary, Kim, Jaegil, primary, Lundgren, Kevin, primary, Harshman, Lauren, primary, Van Allen, Eliezer M., primary, Preston, Mark, primary, Dong, Fei, primary, Bellmunt, Joaquim, primary, Mouw, Kent W., primary, Choueiri, Toni K., primary, Sonpavde, Guru, primary, and Kwiatkowski, David J., primary

Published
2023
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14. Supplementary Data from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., primary, Li, Yixiang, primary, Durmaz, Yavuz T., primary, Gao, Wenhua, primary, Walton, Emily, primary, Vajdi, Amir, primary, Thai, Tran, primary, Sticco-Ivins, Maura, primary, Sabet, Amin H., primary, Jones, Kristen L., primary, Schinzel, Anna C., primary, Bronson, Rod T., primary, Nguyen, Quang-De, primary, Tolstorukov, Michael Y., primary, Vivero, Marina, primary, Signoretti, Sabina, primary, Barbie, David A., primary, and Oser, Matthew G., primary

Published
2023
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15. Supplementary Figure 4 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Flaifel, Abdallah, primary, Xie, Wanling, primary, Braun, David A., primary, Ficial, Miriam, primary, Bakouny, Ziad, primary, Nassar, Amin H., primary, Jennings, Rebecca B., primary, Escudier, Bernard, primary, George, Daniel J., primary, Motzer, Robert J., primary, Morris, Michael J., primary, Powles, Thomas, primary, Wang, Evelyn, primary, Huang, Ying, primary, Freeman, Gordon J., primary, Choueiri, Toni K., primary, and Signoretti, Sabina, primary

Published
2023
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16. Data from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., primary, Li, Yixiang, primary, Durmaz, Yavuz T., primary, Gao, Wenhua, primary, Walton, Emily, primary, Vajdi, Amir, primary, Thai, Tran, primary, Sticco-Ivins, Maura, primary, Sabet, Amin H., primary, Jones, Kristen L., primary, Schinzel, Anna C., primary, Bronson, Rod T., primary, Nguyen, Quang-De, primary, Tolstorukov, Michael Y., primary, Vivero, Marina, primary, Signoretti, Sabina, primary, Barbie, David A., primary, and Oser, Matthew G., primary

Published
2023
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17. Supplementary Table from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Flaifel, Abdallah, primary, Xie, Wanling, primary, Braun, David A., primary, Ficial, Miriam, primary, Bakouny, Ziad, primary, Nassar, Amin H., primary, Jennings, Rebecca B., primary, Escudier, Bernard, primary, George, Daniel J., primary, Motzer, Robert J., primary, Morris, Michael J., primary, Powles, Thomas, primary, Wang, Evelyn, primary, Huang, Ying, primary, Freeman, Gordon J., primary, Choueiri, Toni K., primary, and Signoretti, Sabina, primary

Published
2023
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18. Supplementary Figure 1 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Flaifel, Abdallah, primary, Xie, Wanling, primary, Braun, David A., primary, Ficial, Miriam, primary, Bakouny, Ziad, primary, Nassar, Amin H., primary, Jennings, Rebecca B., primary, Escudier, Bernard, primary, George, Daniel J., primary, Motzer, Robert J., primary, Morris, Michael J., primary, Powles, Thomas, primary, Wang, Evelyn, primary, Huang, Ying, primary, Freeman, Gordon J., primary, Choueiri, Toni K., primary, and Signoretti, Sabina, primary

Published
2023
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19. Supplementary Figure 2 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Flaifel, Abdallah, primary, Xie, Wanling, primary, Braun, David A., primary, Ficial, Miriam, primary, Bakouny, Ziad, primary, Nassar, Amin H., primary, Jennings, Rebecca B., primary, Escudier, Bernard, primary, George, Daniel J., primary, Motzer, Robert J., primary, Morris, Michael J., primary, Powles, Thomas, primary, Wang, Evelyn, primary, Huang, Ying, primary, Freeman, Gordon J., primary, Choueiri, Toni K., primary, and Signoretti, Sabina, primary

Published
2023
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20. Supplementary Table 1 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., primary, Li, Yixiang, primary, Durmaz, Yavuz T., primary, Gao, Wenhua, primary, Walton, Emily, primary, Vajdi, Amir, primary, Thai, Tran, primary, Sticco-Ivins, Maura, primary, Sabet, Amin H., primary, Jones, Kristen L., primary, Schinzel, Anna C., primary, Bronson, Rod T., primary, Nguyen, Quang-De, primary, Tolstorukov, Michael Y., primary, Vivero, Marina, primary, Signoretti, Sabina, primary, Barbie, David A., primary, and Oser, Matthew G., primary

Published
2023
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21. Supplementary Figure 3 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Flaifel, Abdallah, primary, Xie, Wanling, primary, Braun, David A., primary, Ficial, Miriam, primary, Bakouny, Ziad, primary, Nassar, Amin H., primary, Jennings, Rebecca B., primary, Escudier, Bernard, primary, George, Daniel J., primary, Motzer, Robert J., primary, Morris, Michael J., primary, Powles, Thomas, primary, Wang, Evelyn, primary, Huang, Ying, primary, Freeman, Gordon J., primary, Choueiri, Toni K., primary, and Signoretti, Sabina, primary

Published
2023
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22. Supplementary Table 3 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., primary, Li, Yixiang, primary, Durmaz, Yavuz T., primary, Gao, Wenhua, primary, Walton, Emily, primary, Vajdi, Amir, primary, Thai, Tran, primary, Sticco-Ivins, Maura, primary, Sabet, Amin H., primary, Jones, Kristen L., primary, Schinzel, Anna C., primary, Bronson, Rod T., primary, Nguyen, Quang-De, primary, Tolstorukov, Michael Y., primary, Vivero, Marina, primary, Signoretti, Sabina, primary, Barbie, David A., primary, and Oser, Matthew G., primary

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

Author

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

Abstract

Supplementary Figures and Legends for Supplementary Tables

Published
2023

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

Author

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

Abstract

Prior data have variably implicated the inactivation of the mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) complex with increased tumor sensitivity to immune checkpoint inhibitors (ICI). Herein, we examined the association between mSWI/SNF variants and clinical outcomes to ICIs. We correlated somatic loss-of-function (LOF) variants in a predefined set of mSWI/SNF genes (ARID1A, ARID1B, SMARCA4, SMARCB1, PBRM1, and ARID2) with clinical outcomes in patients with cancer treated with systemic ICIs. We identified 676 patients from Dana-Farber Cancer Institute (DFCI, Boston, MA) and 848 patients from a publicly available database from Memorial Sloan Kettering Cancer Center (MSKCC, New York, NY) who met the inclusion criteria. Multivariable analyses were conducted and adjusted for available baseline factors and tumor mutational burden. Median follow-up was 19.6 (17.6–22.0) months and 28.0 (25.0–29.0) months for the DFCI and MSKCC cohorts, respectively. Seven solid tumor subtypes were examined. In the DFCI cohort, LOF variants of mSWI/SNF did not predict improved overall survival (OS), time-to-treatment failure (TTF), or disease control rate. Only patients with renal cell carcinoma with mSWI/SNF LOF showed significantly improved OS and TTF with adjusted HRs (95% confidence interval) of 0.33 (0.16–0.7) and 0.49 (0.27–0.88), respectively, and this was mostly driven by PRBM1. In the MSKCC cohort, where only OS was captured, LOF mSWI/SNF did not correlate with improved outcomes across any tumor subtype. We did not find a consistent association between mSWI/SNF LOF variants and improved clinical outcomes to ICIs, suggesting that mSWI/SNF variants should not be considered as biomarkers of response to ICIs.

Published
2023

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

Author

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

Abstract

Supplementary Tables

Published
2023

26. Data from Mutations and Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma

Author

David J. Kwiatkowski, Toni K. Choueiri, Sabina Signoretti, Katherine M. Krajewski, Ronan Flippot, Pier Vitale Nuzzo, Sarah Abou Alaiwi, Kathryn D. Lasseter, Andre P. Fay, Aaron R. Thorner, Kathryn P. Gray, Lana Hamieh, and Amin H. Nassar

Abstract

We previously showed that alterations in mTOR pathway genes were correlated with response to rapalog therapy in metastatic renal cell carcinoma (mRCC), when the analysis focused on extremes of response. Herein, we expand on the prior cohort and examine genetic correlations with rapalog response in a dataset not selected for extremes of response. Tumors from 58 patients from the phase III trial of temsirolimus and 51 local patients with mRCC treated with rapalogs were studied. Somatic mutations were investigated using a targeted sequencing platform covering 27 genes. Clinical benefit (CB) was defined as patients with complete remission, partial response, or stable disease lasting at least 22 weeks. Mutational analyses focused on 5 mTOR pathway genes (TSC1, TSC2, MTOR, PTEN, PIK3CA) and 6 genes commonly mutated in RCC (BAP1, KDM5C, PBRM1 SETD2, TP53, and VHL). Among the 109 patients, 93 (85%) patients had clear cell histology, and 31 (28%) showed CB. Nine of 30 (30%) patients harboring mTOR pathway mutations in their tumor achieved CB versus 22 of 79 (28%) in the wild-type group. There was no distinct association between any individual or combination of mTOR pathway gene mutations and CB. Three of 7 patients with TSC1 mutations showed CB. In addition, none of the 6 genes commonly mutated in RCC showed a mutation pattern that correlated with CB. Overall, in this large and diverse population of patients with mRCC, there is no suggestion of a correlation between response to rapalog therapy and mutation status for mTOR pathway genes.

Published
2023

31. Supplementary Data from Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites

Author

David J. Kwiatkowski, Guru Sonpavde, Toni K. Choueiri, Kent W. Mouw, Joaquim Bellmunt, Fei Dong, Mark Preston, Eliezer M. Van Allen, Lauren Harshman, Kevin Lundgren, Jaegil Kim, Renato Umeton, and Amin H. Nassar

Abstract

Histogram showing the distribution of alterations in KDM6A in males and females for 4 subtypes of urothelial carcinoma. Red bars are scaled to show the frequency (%) of female samples with an alteration in KDM6A; Gray bars are scaled to show the frequency of bi-allelic mutation in KDM6A in female samples; and blue bars show the frequency of KDM6A mutation in males. The numbers above each bar indicate the number of samples with each category of alteration; the numbers below show the total number of samples for each sex and UC subtype.

Published
2023

32. Supplementary Table 5 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Matthew G. Oser, David A. Barbie, Sabina Signoretti, Marina Vivero, Michael Y. Tolstorukov, Quang-De Nguyen, Rod T. Bronson, Anna C. Schinzel, Kristen L. Jones, Amin H. Sabet, Maura Sticco-Ivins, Tran Thai, Amir Vajdi, Emily Walton, Wenhua Gao, Yavuz T. Durmaz, Yixiang Li, Erik H. Knelson, and Deli Hong

Abstract

LISA analysis of master regulators of differentially expressed genes

Published
2023

33. Supplementary Data from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Matthew G. Oser, David A. Barbie, Sabina Signoretti, Marina Vivero, Michael Y. Tolstorukov, Quang-De Nguyen, Rod T. Bronson, Anna C. Schinzel, Kristen L. Jones, Amin H. Sabet, Maura Sticco-Ivins, Tran Thai, Amir Vajdi, Emily Walton, Wenhua Gao, Yavuz T. Durmaz, Yixiang Li, Erik H. Knelson, and Deli Hong

Abstract

Supplementary Data including supplementary methods, supplementary figures, and supplementary figure legends.

Published
2023

34. Supplementary Table from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Ying Huang, Evelyn Wang, Thomas Powles, Michael J. Morris, Robert J. Motzer, Daniel J. George, Bernard Escudier, Rebecca B. Jennings, Amin H. Nassar, Ziad Bakouny, Miriam Ficial, David A. Braun, Wanling Xie, and Abdallah Flaifel

Abstract

Supplementary Table 1. Patient demographic and clinical characteristics Supplementary Table 2. Associations of PD-L1 expression with response to therapy Supplementary Table 3. Treatment comparison on ORR and DCR, subgroup analysis by PD-L1 expression status on tumor cells (TC) Supplementary Table 4. Treatment comparison on PFS and OS, subgroup analysis by PD-L1 expression status on tumor cells (TC), immune cells (IC) or TC/IC combined scores*. Supplementary Table 5. Associations of MET and/or PD-L1 expression on tumor cells with treatment outcomes Supplementary Table 6. Treatment comparison on PFS and OS, subgroup analysis by MET and PD-L1 ({greater than or equal to}1% cutoff) expression on tumor cells Supplementary Table 7. Association of immune cell density (ICD) tertile groups* with PFS, OS, ORR and DCR Supplementary Table 8. Association of immune cell density (ICD) continuous scores with PFS and OS Supplementary Table 9. Treatment comparison on PFS and OS, subgroup analysis by immune cell density (ICD) (dichotomized at the upper 33% tertile value from the joint distribution of two trials)

Published
2023

35. Supplementary Table 2 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Matthew G. Oser, David A. Barbie, Sabina Signoretti, Marina Vivero, Michael Y. Tolstorukov, Quang-De Nguyen, Rod T. Bronson, Anna C. Schinzel, Kristen L. Jones, Amin H. Sabet, Maura Sticco-Ivins, Tran Thai, Amir Vajdi, Emily Walton, Wenhua Gao, Yavuz T. Durmaz, Yixiang Li, Erik H. Knelson, and Deli Hong

Abstract

GSEA Hallmarks analysis of RNA-seq of bulk lung tumors

Published
2023

36. Supplementary Table 1 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Matthew G. Oser, David A. Barbie, Sabina Signoretti, Marina Vivero, Michael Y. Tolstorukov, Quang-De Nguyen, Rod T. Bronson, Anna C. Schinzel, Kristen L. Jones, Amin H. Sabet, Maura Sticco-Ivins, Tran Thai, Amir Vajdi, Emily Walton, Wenhua Gao, Yavuz T. Durmaz, Yixiang Li, Erik H. Knelson, and Deli Hong

Abstract

RNA-seq data of bulk lung tumors from sgControl RPP, sgNotch1 RPP, sgNotch2 RPP, and sgAscl1 RPP CRISPR-based SCLC GEMMs

Published
2023

37. Supplementary Figure 3 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Ying Huang, Evelyn Wang, Thomas Powles, Michael J. Morris, Robert J. Motzer, Daniel J. George, Bernard Escudier, Rebecca B. Jennings, Amin H. Nassar, Ziad Bakouny, Miriam Ficial, David A. Braun, Wanling Xie, and Abdallah Flaifel

Abstract

Consort Diagram

Published
2023

38. Supplementary Figure 2 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Ying Huang, Evelyn Wang, Thomas Powles, Michael J. Morris, Robert J. Motzer, Daniel J. George, Bernard Escudier, Rebecca B. Jennings, Amin H. Nassar, Ziad Bakouny, Miriam Ficial, David A. Braun, Wanling Xie, and Abdallah Flaifel

Abstract

Figure S2 shows IHC image analysis workflow

Published
2023

39. Supplementary Table 3 from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Matthew G. Oser, David A. Barbie, Sabina Signoretti, Marina Vivero, Michael Y. Tolstorukov, Quang-De Nguyen, Rod T. Bronson, Anna C. Schinzel, Kristen L. Jones, Amin H. Sabet, Maura Sticco-Ivins, Tran Thai, Amir Vajdi, Emily Walton, Wenhua Gao, Yavuz T. Durmaz, Yixiang Li, Erik H. Knelson, and Deli Hong

Abstract

RNA-seq data of the SCLC adherent cells that are either Notch-WT or Notch-Mutant

Published
2023

40. Data from Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites

Author

David J. Kwiatkowski, Guru Sonpavde, Toni K. Choueiri, Kent W. Mouw, Joaquim Bellmunt, Fei Dong, Mark Preston, Eliezer M. Van Allen, Lauren Harshman, Kevin Lundgren, Jaegil Kim, Renato Umeton, and Amin H. Nassar

Abstract

Purpose:The purpose of this study is to characterize the mutational landscape across the spectrum of urothelial carcinoma (UC) to identify mutational features and potential therapeutic targets.Experimental Design:Using targeted exome sequencing (n = 237 genes), we analyzed the mutation spectra of 82 low-grade nonmuscle-invasive bladder cancers (LG-NMIBC), 126 high-grade (HG) NMIBC, 199 muscle-invasive bladder cancers (MIBC), 10 LG-upper tract urothelial cancers (LG-UTUC), and 55 HG-UTUC.Results:FGFR3 and KDM6A mutations were significantly more common in LG-NMIBC (72% and 44%, respectively) versus other bladder subtypes. FGFR3 alterations were also enriched in LG-UTUC versus HG-UTUC tumors (80% vs. 16%). In contrast, TP53 and RB1 mutations were significantly more frequent in all 3 HG urothelial carcinoma subtypes than in LG-NIMBC (45%–58% vs. 4%; 9%–22% vs. 0; respectively). Among LG-NMIBC tumors, KDM6A mutations were more common in women than in men (71% vs. 38%). HG-NMIBC and MIBC had higher tumor mutational burden (TMB) than LG-NMIBC (P = 0.001 and P < 0.01, respectively). DNA-damage repair (DDR) alterations were associated with a higher TMB in HG-NMIBC and MIBC tumors, and these two tumor types were also enriched for an APOBEC mutational signature compared with LG-NMIBC and HG-UTUC. Alterations in FGFR3, PIK3CA, and EP300 correlated with worse overall survival in HG-UTUC and occurred concurrently.Conclusions:Our analysis suggests that a fraction of MIBCs likely arise from precursor lesions other than LG-NMIBC. KDM6A mutations are twice as common in women with LG-NIMBC than those in men. DDR gene mutations and APOBEC mutagenesis drive mutations in HG-NMIBC and MIBC. UTUC has a distinct mutation profile from bladder cancer.

Published
2023

41. Supplementary Figure 1 from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Ying Huang, Evelyn Wang, Thomas Powles, Michael J. Morris, Robert J. Motzer, Daniel J. George, Bernard Escudier, Rebecca B. Jennings, Amin H. Nassar, Ziad Bakouny, Miriam Ficial, David A. Braun, Wanling Xie, and Abdallah Flaifel

Abstract

Figure S1 shows PD-L1 positive and negative staining

Published
2023

42. Data from Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Matthew G. Oser, David A. Barbie, Sabina Signoretti, Marina Vivero, Michael Y. Tolstorukov, Quang-De Nguyen, Rod T. Bronson, Anna C. Schinzel, Kristen L. Jones, Amin H. Sabet, Maura Sticco-Ivins, Tran Thai, Amir Vajdi, Emily Walton, Wenhua Gao, Yavuz T. Durmaz, Yixiang Li, Erik H. Knelson, and Deli Hong

Abstract

Neuroendocrine to nonneuroendocrine plasticity supports small cell lung cancer (SCLC) tumorigenesis and promotes immunogenicity. Approximately 20% to 25% of SCLCs harbor loss-of-function (LOF) NOTCH mutations. Previous studies demonstrated that NOTCH functions as a SCLC tumor suppressor, but can also drive nonneuroendocrine plasticity to support SCLC growth. Given the dual functionality of NOTCH, it is not understood why SCLCs select for LOF NOTCH mutations and how these mutations affect SCLC tumorigenesis. In a CRISPR-based genetically engineered mouse model of SCLC, genetic loss of Notch1 or Notch2 modestly accelerated SCLC tumorigenesis. Interestingly, Notch-mutant SCLCs still formed nonneuroendocrine subpopulations, and these Notch-independent, nonneuroendocrine subpopulations were driven by Runx2-mediated regulation of Rest. Notch2-mutant nonneuroendocrine cells highly express innate immune signaling genes including stimulator of interferon genes (STING) and were sensitive to STING agonists. This work identifies a Notch-independent mechanism to promote nonneuroendocrine plasticity and suggests that therapeutic approaches to activate STING could be selectively beneficial for SCLCs with NOTCH2 mutations.Significance:A genetically engineered mouse model of NOTCH-mutant SCLC reveals that nonneuroendocrine plasticity persists in the absence of NOTCH, driven by a RUNX2-REST–dependent pathway and innate immune signaling.

Published
2023

43. Data from PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Ying Huang, Evelyn Wang, Thomas Powles, Michael J. Morris, Robert J. Motzer, Daniel J. George, Bernard Escudier, Rebecca B. Jennings, Amin H. Nassar, Ziad Bakouny, Miriam Ficial, David A. Braun, Wanling Xie, and Abdallah Flaifel

Abstract

Purpose:Programmed death-ligand 1 (PD-L1) status by IHC is prognostic in metastatic renal cell carcinoma (mRCC), and its role as a potential predictive biomarker is under investigation. Using tumor tissue from the METEOR (NCT01865747) and CABOSUN (NCT01835158) clinical trials, we explored whether PD-L1 expression and the extent of the immune cell infiltrate can serve as prognostic and/or predictive biomarkers for cabozantinib and other targeted agents.Experimental Design:IHC double staining for PD-L1 and CD45/CD163 (immune cell markers) was performed on tumor tissue from METEOR (n = 306) and CABOSUN (n = 110) clinical trials. Immune cell density and MET expression levels were also analyzed. Our primary aim was to correlate progression-free survival (PFS) by independent central review with PD-L1 status in patients treated with cabozantinib, everolimus (METEOR), or sunitinib (CABOSUN). Overall survival (OS) was also interrogated.Results:Tumor cell (TC) PD-L1 expression (≥1% cutoff) was detected in 29% and 23% of tumors from patients in the METEOR and CABOSUN trials, respectively. On univariate analysis, patients with PD-L1–positive TC had poorer PFS and OS than patients with PD-L1–negative TC on both trials, independent of therapy. On multivariable analysis and when combining the two trials, the association between TC PD-L1 expression and OS was statistically significant for all patients (P = 0.034) and for patients treated with cabozantinib only (P = 0.038). Cabozantinib was associated with improved PFS (HR < 0.70) and OS (HR < 0.85) compared with everolimus and sunitinib irrespective of PD-L1 expression.Conclusions:Higher PD-L1 expression results in worse clinical outcomes in mRCC treated with targeted therapy. Furthermore, PD-L1 expression is not predictive of response to cabozantinib therapy.

Published
2023

44. Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Yavuz T Durmaz, Amin H Sabet, Deli Hong, Anna C. Schinzel, Emily Walton, Kristen L Jones, Maura Sticco-Ivins, Yixiang Li, Quang-Dé Nguyen, Roderick T. Bronson, Sabina Signoretti, Tran C. Thai, Erik H. Knelson, David A. Barbie, Amir Vajdi, Matthew G. Oser, Wenhua Gao, Michael Y. Tolstorukov, and Marina Vivero

Subjects
Cancer Research, Lung Neoplasms, Carcinogenesis, Cell Plasticity, Core Binding Factor Alpha 1 Subunit, Biology, Transfection, medicine.disease_cause, Article, law.invention, Mice, Loss of Function Mutation, law, Cell Line, Tumor, medicine, Animals, Humans, CRISPR, Receptor, Notch2, Receptor, Notch1, Gene, Loss function, Innate immune system, Small Cell Lung Carcinoma, respiratory tract diseases, RUNX2, Disease Models, Animal, Sting, Oncology, Cancer research, Suppressor, CRISPR-Cas Systems, Signal Transduction
Abstract

Neuroendocrine to nonneuroendocrine plasticity supports small cell lung cancer (SCLC) tumorigenesis and promotes immunogenicity. Approximately 20% to 25% of SCLCs harbor loss-of-function (LOF) NOTCH mutations. Previous studies demonstrated that NOTCH functions as a SCLC tumor suppressor, but can also drive nonneuroendocrine plasticity to support SCLC growth. Given the dual functionality of NOTCH, it is not understood why SCLCs select for LOF NOTCH mutations and how these mutations affect SCLC tumorigenesis. In a CRISPR-based genetically engineered mouse model of SCLC, genetic loss of Notch1 or Notch2 modestly accelerated SCLC tumorigenesis. Interestingly, Notch-mutant SCLCs still formed nonneuroendocrine subpopulations, and these Notch-independent, nonneuroendocrine subpopulations were driven by Runx2-mediated regulation of Rest. Notch2-mutant nonneuroendocrine cells highly express innate immune signaling genes including stimulator of interferon genes (STING) and were sensitive to STING agonists. This work identifies a Notch-independent mechanism to promote nonneuroendocrine plasticity and suggests that therapeutic approaches to activate STING could be selectively beneficial for SCLCs with NOTCH2 mutations. Significance: A genetically engineered mouse model of NOTCH-mutant SCLC reveals that nonneuroendocrine plasticity persists in the absence of NOTCH, driven by a RUNX2-REST–dependent pathway and innate immune signaling.

Published
2022

45. Plasticity in the Absence of NOTCH Uncovers a RUNX2-Dependent Pathway in Small Cell Lung Cancer

Author

Hong, Deli, primary, Knelson, Erik H., additional, Li, Yixiang, additional, Durmaz, Yavuz T., additional, Gao, Wenhua, additional, Walton, Emily, additional, Vajdi, Amir, additional, Thai, Tran, additional, Sticco-Ivins, Maura, additional, Sabet, Amin H., additional, Jones, Kristen L., additional, Schinzel, Anna C., additional, Bronson, Rod T., additional, Nguyen, Quang-De, additional, Tolstorukov, Michael Y., additional, Vivero, Marina, additional, Signoretti, Sabina, additional, Barbie, David A., additional, and Oser, Matthew G., additional

Published
2022
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46. Gene Expression Signature Correlates with Outcomes in Metastatic Renal Cell Carcinoma Patients Treated with Everolimus Alone or with a Vascular Disrupting Agent

Author

Yang, Eddy S., primary, Nassar, Amin H., additional, Adib, Elio, additional, Jegede, Opeyemi A., additional, Alaiwi, Sarah Abou, additional, Manna, Deborah L. Della, additional, Braun, David A., additional, Zarei, Mahsa, additional, Du, Heng, additional, Pal, Sumanta K., additional, Naik, Gurudatta, additional, and Sonpavde, Guru P., additional

Published
2021
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47. CDKN2A Alterations and Response to Immunotherapy in Solid Tumors

Author

Adib, Elio, primary, Nassar, Amin H., additional, Akl, Elie W., additional, Abou Alaiwi, Sarah, additional, Nuzzo, Pier Vitale, additional, Mouhieddine, Tarek H., additional, Sonpavde, Guru, additional, Haddad, Robert I., additional, Mouw, Kent W., additional, Giannakis, Marios, additional, Hodi, F. Stephen, additional, Shukla, Sachet A., additional, Gusev, Alexander, additional, Braun, David A., additional, Choueiri, Toni K., additional, and Kwiatkowski, David J., additional

Published
2021
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48. Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors

Author

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

Published
2020
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49. Mutations and Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma

Author

Nassar, Amin H., primary, Hamieh, Lana, additional, Gray, Kathryn P., additional, Thorner, Aaron R., additional, Fay, Andre P., additional, Lasseter, Kathryn D., additional, Abou Alaiwi, Sarah, additional, Nuzzo, Pier Vitale, additional, Flippot, Ronan, additional, Krajewski, Katherine M., additional, Signoretti, Sabina, additional, Choueiri, Toni K., additional, and Kwiatkowski, David J., additional

Published
2020
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50. PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN

Author

Flaifel, Abdallah, primary, Xie, Wanling, additional, Braun, David A., additional, Ficial, Miriam, additional, Bakouny, Ziad, additional, Nassar, Amin H., additional, Jennings, Rebecca B., additional, Escudier, Bernard, additional, George, Daniel J., additional, Motzer, Robert J., additional, Morris, Michael J., additional, Powles, Thomas, additional, Wang, Evelyn, additional, Huang, Ying, additional, Freeman, Gordon J., additional, Choueiri, Toni K., additional, and Signoretti, Sabina, additional

Published
2019
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