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3. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97

Author

Pozner, Amir, Li, Li, Verma, Shiv Prakash, Wang, Shuxin, Barrott, Jared J., Nelson, Mary L., Yu, Jamie S. E., Negri, Gian Luca, Colborne, Shane, Hughes, Christopher S., Zhu, Ju-Fen, Lambert, Sydney L., Carroll, Lara S., Smith-Fry, Kyllie, Stewart, Michael G., Kannan, Sarmishta, Jensen, Bodrie, John, Cini M., Sikdar, Saif, Liu, Hongrui, Dang, Ngoc Ha, Bourdage, Jennifer, Li, Jinxiu, Vahrenkamp, Jeffery M., Mortenson, Katelyn L., Groundland, John S., Wustrack, Rosanna, Senger, Donna L., Zemp, Franz J., Mahoney, Douglas J., Gertz, Jason, Zhang, Xiaoyang, Lazar, Alexander J., Hirst, Martin, Morin, Gregg B., Nielsen, Torsten O., Shen, Peter S., and Jones, Kevin B.

Published
2024
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5. International Multicenter Retrospective Study From the Ultra-rare Sarcoma Working Group on Low-grade Fibromyxoid Sarcoma, Sclerosing Epithelioid Fibrosarcoma, and Hybrid Forms: Outcome of Primary Localized Disease

Author

Giani, Claudia, Salawu, Abdulazeez, Ljevar, Silva, Denu, Ryan A., Napolitano, Andrea, Palmerini, Emanuela, Connolly, Elizabeth A., Ogura, Koichi, Wong, Daniel D., Scanferla, Roberto, Rosenbaum, Evan, Bajpai, Jyoti, Li, Zola Chia-Chen, Bae, Susie, D’Ambrosio, Lorenzo, Bialick, Steve, Wagner, Andrew J., Lee, Alexander T.J., Koseła-Paterczyk, Hanna, Baldi, Giacomo G., Brunello, Antonella, Lee, Yeh Chen, Loong, Herbert H., Boikos, Sosipatros, Campos, Fernando, Cicala, Carlo M., Maki, Robert G., Hindi, Nadia, Figura, Costanza, Almohsen, Shahd S., Patel, Sheyaskumar, Jones, Robin L., Ibrahim, Toni, Karim, Rooshdiya, Kawai, Akira, Carey-Smith, Richard, Boyle, Richard, Taverna, Silvia M., Lazar, Alexander J., Demicco, Elizabeth G., Bovee, Judith V.M.G., Dei Tos, Angelo P., Fletcher, Christopher, Baumhoer, Daniel, Sbaraglia, Marta, Schaefer, Inga-Marie, Miceli, Rosalba, Gronchi, Alessandro, and Stacchiotti, Silvia

Published
2025
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6. A randomized, non-comparative phase 2 study of neoadjuvant immune-checkpoint blockade in retroperitoneal dedifferentiated liposarcoma and extremity/truncal undifferentiated pleomorphic sarcoma

Author

Roland, Christina L., Nassif Haddad, Elise F., Keung, Emily Z., Wang, Wei-Lien, Lazar, Alexander J., Lin, Heather, Chelvanambi, Manoj, Parra, Edwin R., Wani, Khalida, Guadagnolo, B. Ashleigh, Bishop, Andrew J., Burton, Elizabeth M., Hunt, Kelly K., Torres, Keila E., Feig, Barry W., Scally, Christopher P., Lewis, Valerae O., Bird, Justin E., Ratan, Ravin, Araujo, Dejka, Zarzour, M. Alexandra, Patel, Shreyaskumar, Benjamin, Robert, Conley, Anthony P., Livingston, J. Andrew, Ravi, Vinod, Tawbi, Hussein A., Lin, Patrick P., Moon, Bryan S., Satcher, Robert L., Mujtaba, Bilal, Witt, Russell G., Traweek, Raymond S., Cope, Brandon, Lazcano, Rossana, Wu, Chia-Chin, Zhou, Xiao, Mohammad, Mohammad M., Chu, Randy A., Zhang, Jianhua, Damania, Ashish, Sahasrabhojane, Pranoti, Tate, Taylor, Callahan, Kate, Nguyen, Sa, Ingram, Davis, Morey, Rohini, Crosby, Shadarra, Mathew, Grace, Duncan, Sheila, Lima, Cibelle F., Blay, Jean-Yves, Fridman, Wolf Herman, Shaw, Kenna, Wistuba, Ignacio, Futreal, Andrew, Ajami, Nadim, Wargo, Jennifer A., and Somaiah, Neeta

Published
2024
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7. ASO Visual Abstract: Clinical Variables Influencing Outcomes in Patients with Atypical Intradermal Smooth Muscle Neoplasms (Formerly Cutaneous Leiomyosarcomas)—Single-Institution Study of 95 Surgical Patients

Author

Gingrich, Alicia, Wangsiricharoen, Sintawat, Torres, Madeline B., Ravi, Vinod, Ratan, Ravin, Keung, Emily Z., Scally, Christopher P., Lazar, Alexander J., Wang, Wei-Lien, Roland, Christina L., Hunt, Kelly K., Yu, Wendong, and Torres, Keila E.

Published
2024
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8. Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets

Author

Ellrott, Kyle, Wong, Christopher K., Yau, Christina, Castro, Mauro A.A., Lee, Jordan A., Karlberg, Brian J., Grewal, Jasleen K., Lagani, Vincenzo, Tercan, Bahar, Friedl, Verena, Hinoue, Toshinori, Uzunangelov, Vladislav, Westlake, Lindsay, Loinaz, Xavier, Felau, Ina, Wang, Peggy I., Kemal, Anab, Caesar-Johnson, Samantha J., Shmulevich, Ilya, Lazar, Alexander J., Tsamardinos, Ioannis, Hoadley, Katherine A., Robertson, A. Gordon, Knijnenburg, Theo A., Benz, Christopher C., Stuart, Joshua M., Zenklusen, Jean C., Cherniack, Andrew D., and Laird, Peter W.

Published
2025
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9. Revision of the Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis Classification Schema for Melanocytic Lesions

Author

Barnhill, Raymond L, Elder, David E, Piepkorn, Michael W, Knezevich, Stevan R, Reisch, Lisa M, Eguchi, Megan M, Bastian, Boris C, Blokx, Willeke, Bosenberg, Marcus, Busam, Klaus J, Carr, Richard, Cochran, Alistair, Cook, Martin G, Duncan, Lyn M, Elenitsas, Rosalie, de la Fouchardière, Arnaud, Gerami, Pedram, Johansson, Iva, Ko, Jennifer, Landman, Gilles, Lazar, Alexander J, Lowe, Lori, Massi, Daniela, Messina, Jane, Mihic-Probst, Daniela, Parker, Douglas C, Schmidt, Birgitta, Shea, Christopher R, Scolyer, Richard A, Tetzlaff, Michael, Xu, Xiaowei, Yeh, Iwei, Zembowicz, Artur, and Elmore, Joann G

Subjects
Health Services and Systems, Biomedical and Clinical Sciences, Health Sciences, Clinical Research, Cancer, 7.3 Management and decision making, 4.2 Evaluation of markers and technologies, Humans, Skin Neoplasms, Melanoma, Pathologists, Consensus, Health Facilities, Biomedical and clinical sciences, Health sciences
Abstract

ImportanceA standardized pathology classification system for melanocytic lesions is needed to aid both pathologists and clinicians in cataloging currently existing diverse terminologies and in the diagnosis and treatment of patients. The Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis (MPATH-Dx) has been developed for this purpose.ObjectiveTo revise the MPATH-Dx version 1.0 classification tool, using feedback from dermatopathologists participating in the National Institutes of Health-funded Reducing Errors in Melanocytic Interpretations (REMI) Study and from members of the International Melanoma Pathology Study Group (IMPSG).Evidence reviewPracticing dermatopathologists recruited from 40 US states participated in the 2-year REMI study and provided feedback on the MPATH-Dx version 1.0 tool. Independently, member dermatopathologists participating in an IMPSG workshop dedicated to the MPATH-Dx schema provided additional input for refining the MPATH-Dx tool. A reference panel of 3 dermatopathologists, the original authors of the MPATH-Dx version 1.0 tool, integrated all feedback into an updated and refined MPATH-Dx version 2.0.FindingsThe new MPATH-Dx version 2.0 schema simplifies the original 5-class hierarchy into 4 classes to improve diagnostic concordance and to provide more explicit guidance in the treatment of patients. This new version also has clearly defined histopathological criteria for classification of classes I and II lesions; has specific provisions for the most frequently encountered low-cumulative sun damage pathway of melanoma progression, as well as other, less common World Health Organization pathways to melanoma; provides guidance for classifying intermediate class II tumors vs melanoma; and recognizes a subset of pT1a melanomas with very low risk and possible eventual reclassification as neoplasms lacking criteria for melanoma.Conclusions and relevanceThe implementation of the newly revised MPATH-Dx version 2.0 schema into clinical practice is anticipated to provide a robust tool and adjunct for standardized diagnostic reporting of melanocytic lesions and management of patients to the benefit of both health care practitioners and patients.

Published
2023

11. Analysis of germline-driven ancestry-associated gene expression in cancers

Author

Chambwe, Nyasha, Sayaman, Rosalyn W, Hu, Donglei, Huntsman, Scott, Network, The Cancer Genome Analysis, Carrot-Zhang, Jian, Berger, Ashton C, Han, Seunghun, Meyerson, Matthew, Damrauer, Jeffrey S, Hoadley, Katherine A, Felau, Ina, Demchok, John A, Mensah, Michael KA, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin Y, Frampton, Garrett M, Mashl, R Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Zhou, Wanding, Laird, Peter W, Shen, Hui, Wong, Christopher K, Stuart, Joshua M, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Kemal, Anab, Caesar-Johnson, Samantha, Zenklusen, Jean C, Ziv, Elad, Beroukhim, Rameen, and Cherniack, Andrew D

Subjects
Biological Sciences, Health Sciences, Genetics, Human Genome, Cancer Genomics, Precision Medicine, Cancer, 1.1 Normal biological development and functioning, Good Health and Well Being, Gene Expression, Germ Cells, Humans, Neoplasms, Quantitative Trait Loci, RNA, Messenger, Cancer Genome Analysis Network, Bioinformatics, Computer sciences, Genomics, RNAseq, Sequence analysis
Abstract

Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).

Published
2022

12. Epigenomic and Transcriptomic Profiling of Solitary Fibrous Tumors Identifies Site-Specific Patterns and Candidate Genes Regulated by DNA Methylation

Author

Beird, Hannah C., Cloutier, Jeffrey M., Gokgoz, Nalan, Eeles, Christopher, Griffin, Anthony M., Ingram, Davis R., Wani, Khalida M., Segura, Rossana Lazcano, Cohen, Luca, Ho, Carl, Wunder, Jay S., Andrulis, Irene L., Futreal, P. Andrew, Haibe-Kains, Benjamin, Lazar, Alexander J., Wang, Wei-Lien, Przybyl, Joanna, and Demicco, Elizabeth G.

Published
2024
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14. The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms

Author

Alaggio, Rita, Amador, Catalina, Anagnostopoulos, Ioannis, Attygalle, Ayoma D, Araujo, Iguaracyra Barreto de Oliveira, Berti, Emilio, Bhagat, Govind, Borges, Anita Maria, Boyer, Daniel, Calaminici, Mariarita, Chadburn, Amy, Chan, John KC, Cheuk, Wah, Chng, Wee-Joo, Choi, John K, Chuang, Shih-Sung, Coupland, Sarah E, Czader, Magdalena, Dave, Sandeep S, de Jong, Daphne, Du, Ming-Qing, Elenitoba-Johnson, Kojo S, Ferry, Judith, Geyer, Julia, Gratzinger, Dita, Guitart, Joan, Gujral, Sumeet, Harris, Marian, Harrison, Christine J, Hartmann, Sylvia, Hochhaus, Andreas, Jansen, Patty M, Karube, Kennosuke, Kempf, Werner, Khoury, Joseph, Kimura, Hiroshi, Klapper, Wolfram, Kovach, Alexandra E, Kumar, Shaji, Lazar, Alexander J, Lazzi, Stefano, Leoncini, Lorenzo, Leung, Nelson, Leventaki, Vasiliki, Li, Xiao-Qiu, Lim, Megan S, Liu, Wei-Ping, Louissaint, Abner, Marcogliese, Andrea, Medeiros, L Jeffrey, Michal, Michael, Miranda, Roberto N, Mitteldorf, Christina, Montes-Moreno, Santiago, Morice, William, Nardi, Valentina, Naresh, Kikkeri N, Natkunam, Yasodha, Ng, Siok-Bian, Oschlies, Ilske, Ott, German, Parrens, Marie, Pulitzer, Melissa, Rajkumar, S Vincent, Rawstron, Andrew C, Rech, Karen, Rosenwald, Andreas, Said, Jonathan, Sarkozy, Clémentine, Sayed, Shahin, Saygin, Caner, Schuh, Anna, Sewell, William, Siebert, Reiner, Sohani, Aliyah R, Tooze, Reuben, Traverse-Glehen, Alexandra, Vega, Francisco, Vergier, Beatrice, Wechalekar, Ashutosh D, Wood, Brent, Xerri, Luc, and Xiao, Wenbin

Subjects
Cancer, Hematologic Neoplasms, Humans, Lymphoma, World Health Organization, Clinical Sciences, Oncology and Carcinogenesis, Immunology
Abstract

We herein present an overview of the upcoming 5th edition of the World Health Organization Classification of Haematolymphoid Tumours focussing on lymphoid neoplasms. Myeloid and histiocytic neoplasms will be presented in a separate accompanying article. Besides listing the entities of the classification, we highlight and explain changes from the revised 4th edition. These include reorganization of entities by a hierarchical system as is adopted throughout the 5th edition of the WHO classification of tumours of all organ systems, modification of nomenclature for some entities, revision of diagnostic criteria or subtypes, deletion of certain entities, and introduction of new entities, as well as inclusion of tumour-like lesions, mesenchymal lesions specific to lymph node and spleen, and germline predisposition syndromes associated with the lymphoid neoplasms.

Published
2022

15. Correction: “The 5th edition of The World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms” Leukemia. 2022 Jul;36(7):1720–1748

Author

Alaggio, Rita, Amador, Catalina, Anagnostopoulos, Ioannis, Attygalle, Ayoma D., de Oliveira Araujo, Iguaracyra Barreto, Berti, Emilio, Bhagat, Govind, Borges, Anita Maria, Boyer, Daniel, Calaminici, Mariarita, Chadburn, Amy, Chan, John K. C., Cheuk, Wah, Chng, Wee-Joo, Choi, John K., Chuang, Shih-Sung, Coupland, Sarah E., Czader, Magdalena, Dave, Sandeep S., de Jong, Daphne, Di Napoli, Arianna, Du, Ming-Qing, Elenitoba-Johnson, Kojo S., Ferry, Judith, Geyer, Julia, Gratzinger, Dita, Guitart, Joan, Gujral, Sumeet, Harris, Marian, Harrison, Christine J., Hartmann, Sylvia, Hochhaus, Andreas, Jansen, Patty M., Karube, Kennosuke, Kempf, Werner, Khoury, Joseph, Kimura, Hiroshi, Klapper, Wolfram, Kovach, Alexandra E., Kumar, Shaji, Lazar, Alexander J., Lazzi, Stefano, Leoncini, Lorenzo, Leung, Nelson, Leventaki, Vasiliki, Li, Xiao-Qiu, Lim, Megan S., Liu, Wei-Ping, Louissaint, Jr, Abner, Marcogliese, Andrea, Medeiros, L. Jeffrey, Michal, Michael, Miranda, Roberto N., Mitteldorf, Christina, Montes-Moreno, Santiago, Morice, William, Nardi, Valentina, Naresh, Kikkeri N., Natkunam, Yasodha, Ng, Siok-Bian, Oschlies, Ilske, Ott, German, Parrens, Marie, Pulitzer, Melissa, Rajkumar, S. Vincent, Rawstron, Andrew C., Rech, Karen, Rosenwald, Andreas, Said, Jonathan, Sarkozy, Clémentine, Sayed, Shahin, Saygin, Caner, Schuh, Anna, Sewell, William, Siebert, Reiner, Sohani, Aliyah R., Suzuki, Ritsuro, Tooze, Reuben, Traverse-Glehen, Alexandra, Vega, Francisco, Vergier, Beatrice, Wechalekar, Ashutosh D., Wood, Brent, Xerri, Luc, and Xiao, Wenbin

Published
2023
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16. Appropriate use criteria for ancillary diagnostic testing in dermatopathology: New recommendations for 11 tests and 220 clinical scenarios from the American Society of Dermatopathology Appropriate Use Criteria Committee

Author

Members, AUC Committee, Fung, Maxwell A, Vidal, Claudia I, Armbrecht, Eric A, Andea, Aleodor A, Cassarino, David S, Comfere, Nneka I, Emanuel, Patrick O, Ferringer, Tammie, Hristov, Alexandra C, Kim, Jinah, Lauer, Scott R, Linos, Konstantinos, Missall, Tricia A, Motaparthi, Kiran, Novoa, Roberto A, Patel, Rajiv, Shalin, Sara C, Sundram, Uma, Panel, Rating, Calame, Antoanella, Bennett, Daniel D, Duncan, Lyn M, Elston, Dirk M, Hosler, Gregory A, Hurley, Yadira M, Lazar, Alexander J, Lowe, Lori, Messina, Jane, Myles, Jonathan, Plaza, Jose A, Prieto, Victor G, Reddy, Vijaya, Schaffer, András, and Subtil, Antonio

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Dermatology, Evidence-Based Medicine, Humans, Pathology, Clinical, Skin Diseases, Societies, Medical, United States, ancillary studies, angiosarcoma, appropriate use criteria, choosing wisely, cMYC, dermatitis, dermatology, dermatopathology, dermatophytosis, diagnosis, evidence-based medicine, expert rating, Gomori methenamine silver, Grocott-Gomori, immunohistochemistry, in situ hybridization, kappa, lambda, lymphoma, onychomycosis, pathology, periodic acid-Schiff, RAND, UCLA appropriateness method, TERT promoter, tinea, AUC Committee Members, Rating Panel, Grocott-Gömöri, Gömöri methenamine silver, RAND/UCLA appropriateness method, Clinical Sciences, Dermatology & Venereal Diseases, Clinical sciences
Abstract

BackgroundAppropriate use criteria (AUC) provide patient-centered physician guidance in test selection. An initial set of AUC was reported by the American Society of Dermatopathology (ASDP) in 2018. AUC reflect evidence collected at single timepoints and may be affected by evolving evidence and experience. The objective of this study was to update and expand AUC for selected tests.MethodsRAND/UCLA (RAND Corporation [Santa Monica, CA]/University of California Los Angeles) methodology used includes the following: (a) literature review; (b) review of previously rated tests and previously employed clinical scenarios; (c) selection of previously rated tests for new ratings; (d) development of new clinical scenarios; (e) selection of additional tests; (f) three rating rounds with feedback and group discussion after rounds 1 and 2.ResultsFor 220 clinical scenarios comprising lymphoproliferative (light chain clonality), melanocytic (comparative genomic hybridization, fluorescence in situ hybridization, reverse transcription polymerase chain reaction, telomerase reverse transcriptase promoter), vascular disorders (MYC), and inflammatory dermatoses (periodic acid-Schiff, Gömöri methenamine silver), consensus by panel raters was reached in 172 of 220 (78%) scenarios, with 103 of 148 (70%) rated "usually appropriate" or "rarely appropriate" and 45 of 148 (30%), "appropriateness uncertain."LimitationsThe study design only measures appropriateness. Cost, availability, test comparison, and additional clinical considerations are not measured. The possibility that the findings of this study may be influenced by the inherent biases of the dermatopathologists involved in the study cannot be excluded.ConclusionsAUC are reported for selected diagnostic tests in clinical scenarios that occur in dermatopathology practice. Adhering to AUC may reduce inappropriate test utilization and improve healthcare delivery.

Published
2022

17. The Impact of Next-generation Sequencing on Interobserver Agreement and Diagnostic Accuracy of Desmoplastic Melanocytic Neoplasms

Author

Chen, Alice, Sharma, Natasha, Patel, Pragi, Olivares, Shantel, Bahrami, Armita, Barnhill, Raymond L., Blokx, Willeke A.M., Bosenberg, Marcus, Busam, Klaus J., de La Fouchardière, Arnaud, Duncan, Lyn M., Elder, David E., Ko, Jennifer S., Landman, Gilles, Lazar, Alexander J., Lezcano, Cecilia, Lowe, Lori, Maher, Nigel, Massi, Daniela, Messina, Jane, Mihic-Probst, Daniela, Parker, Douglas C., Redpath, Margaret, Scolyer, Richard A., Shea, Christopher R., Spatz, Alan, Tron, Victor, Xu, Xiaowei, Yeh, Iwei, Jung Yun, Sook, Zembowicz, Artur, and Gerami, Pedram

Published
2024
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18. BRAF Mutated and Morphologically Spitzoid Tumors, a Subgroup of Melanocytic Neoplasms Difficult to Distinguish From True Spitz Neoplasms

Author

Gerami, Pedram, Chen, Alice, Sharma, Natasha, Patel, Pragi, Hagstrom, Michael, Kancherla, Pranav, Geraminejad, Tara, Olivares, Shantel, Biswas, Asok, Bosenberg, Marcus, Busam, Klaus J., de La Fouchardière, Arnaud, Duncan, Lyn M., Elder, David E., Ko, Jennifer, Landman, Gilles, Lazar, Alexander J., Lowe, Lori, Massi, Daniela, Mihic-Probst, Daniela, Parker, Douglas C., Scolyer, Richard A., Shea, Christopher R., Zembowicz, Artur, Yun, Sook Jung, Blokx, Willeke A.M., and Barnhill, Raymond L.

Published
2024
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19. Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma

Author

Gounder, Mrinal M, Agaram, Narasimhan P, Trabucco, Sally E, Robinson, Victoria, Ferraro, Richard A, Millis, Sherri Z, Krishnan, Anita, Lee, Jessica, Attia, Steven, Abida, Wassim, Drilon, Alexander, Chi, Ping, Angelo, Sandra P D’, Dickson, Mark A, Keohan, Mary Lou, Kelly, Ciara M, Agulnik, Mark, Chawla, Sant P, Choy, Edwin, Chugh, Rashmi, Meyer, Christian F, Myer, Parvathi A, Moore, Jessica L, Okimoto, Ross A, Pollock, Raphael E, Ravi, Vinod, Singh, Arun S, Somaiah, Neeta, Wagner, Andrew J, Healey, John H, Frampton, Garrett M, Venstrom, Jeffrey M, Ross, Jeffrey S, Ladanyi, Marc, Singer, Samuel, Brennan, Murray F, Schwartz, Gary K, Lazar, Alexander J, Thomas, David M, Maki, Robert G, Tap, William D, Ali, Siraj M, and Jin, Dexter X

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Oncology and Carcinogenesis, Cancer, Biotechnology, Clinical Research, Human Genome, Genetic Testing, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Biomarkers, Tumor, Bone Neoplasms, Genomics, Humans, Mutation, Osteosarcoma, Prospective Studies, Sarcoma
Abstract

There are more than 70 distinct sarcomas, and this diversity complicates the development of precision-based therapeutics for these cancers. Prospective comprehensive genomic profiling could overcome this challenge by providing insight into sarcomas' molecular drivers. Through targeted panel sequencing of 7494 sarcomas representing 44 histologies, we identify highly recurrent and type-specific alterations that aid in diagnosis and treatment decisions. Sequencing could lead to refinement or reassignment of 10.5% of diagnoses. Nearly one-third of patients (31.7%) harbor potentially actionable alterations, including a significant proportion (2.6%) with kinase gene rearrangements; 3.9% have a tumor mutational burden ≥10 mut/Mb. We describe low frequencies of microsatellite instability (

Published
2022

20. Analytical protocol to identify local ancestry-associated molecular features in cancer

Author

Carrot-Zhang, Jian, Han, Seunghun, Zhou, Wanding, Damrauer, Jeffrey S, Kemal, Anab, Network, Cancer Genome Atlas Analysis, Berger, Ashton C, Meyerson, Matthew, Hoadley, Katherine A, Felau, Ina, Caesar-Johnson, Samantha, Demchok, John A, Mensah, Michael KA, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Chambwe, Nyasha, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin, Frampton, Garret, Mashl, R Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Sayaman, Rosalyn W, Ziv, Elad, Laird, Peter W, Shen, Hui, Wong, Christopher K, Stuart, Joshua M, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Cherniack, Andrew D, and Beroukhim, Rameen

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Health Sciences, Oncology and Carcinogenesis, Human Genome, Cancer Genomics, Health Disparities, Cancer, Minority Health, 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, Genetics, Population, Genome, Human, Genomics, Genotyping Techniques, Humans, Neoplasms, Phenotype, Cancer Genome Atlas Analysis Network, Bioinformatics
Abstract

People of different ancestries vary in cancer risk and outcome, and their molecular differences may indicate sources of these variations. Determining the "local" ancestry composition at each genetic locus across ancestry-admixed populations can suggest causal associations. We present a protocol to identify local ancestry and detect the associated molecular changes, using data from the Cancer Genome Atlas. This workflow can be applied to cancer cohorts with matched tumor and normal data from admixed patients to examine germline contributions to cancer. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020).

Published
2021

21. Comprehensive proteogenomic characterization of rare kidney tumors

Author

Lazar, Alexander J., Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Ma’ayan, Avi, Pruetz, Barb, Zhang, Bing, Reva, Boris, Druker, Brian J., Goldthwaite, Charles A., Jr., Birger, Chet, Mani, D.R., Chesla, David, Fenyö, David, Schadt, Eric E., Wilson, George, Kołodziejczak, Iga, John, Ivy, Hafron, Jason, Vo, Josh, Zaalishvili, Kakhaber, Ketchum, Karen A., Rodland, Karin D., Nyce, Kristen, Wiznerowicz, Maciej, Domagalski, Marcin J., Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Edwards, Nathan J., Vatanian, Negin, VanderKolk, Pamela, McGarvey, Peter B., Dhir, Rajiv, Thangudu, Ratna R., Crispen, Reese, Smith, Richard D., Payne, Samuel H., Cottingham, Sandra, Cai, Shuang, Carr, Steven A., Liu, Tao, Le, Toan, Ma, Weiping, Zhang, Xu, Lu, Yin, Shutack, Yvonne, Zhang, Zhen, Li, Ginny Xiaohe, Chen, Lijun, Hsiao, Yi, Mannan, Rahul, Zhang, Yuping, Luo, Jie, Petralia, Francesca, Cho, Hanbyul, Hosseini, Noshad, Leprevost, Felipe da Veiga, Calinawan, Anna, Li, Yize, Anand, Shankara, Dagar, Aniket, Geffen, Yifat, Kumar-Sinha, Chandan, Chugh, Seema, Le, Anne, Ponce, Sean, Guo, Shenghao, Zhang, Cissy, Schnaubelt, Michael, Al Deen, Nataly Naser, Chen, Feng, Caravan, Wagma, Houston, Andrew, Hopkins, Alex, Newton, Chelsea J., Wang, Xiaoming, Polasky, Daniel A., Haynes, Sarah, Yu, Fengchao, Jing, Xiaojun, Chen, Siqi, Robles, Ana I., Mesri, Mehdi, Thiagarajan, Mathangi, An, Eunkyung, Getz, Gad A., Linehan, W. Marston, Hostetter, Galen, Jewell, Scott D., Chan, Daniel W., Wang, Pei, Omenn, Gilbert S., Mehra, Rohit, Ricketts, Christopher J., Ding, Li, Chinnaiyan, Arul M., Cieslik, Marcin P., Dhanasekaran, Saravana M., Zhang, Hui, and Nesvizhskii, Alexey I.

Published
2024
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24. Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells

Author

Goyal, Yogesh, Busch, Gianna T., Pillai, Maalavika, Li, Jingxin, Boe, Ryan H., Grody, Emanuelle I., Chelvanambi, Manoj, Dardani, Ian P., Emert, Benjamin, Bodkin, Nicholas, Braun, Jonas, Fingerman, Dylan, Kaur, Amanpreet, Jain, Naveen, Ravindran, Pavithran T., Mellis, Ian A., Kiani, Karun, Alicea, Gretchen M., Fane, Mitchell E., Ahmed, Syeda Subia, Li, Haiyin, Chen, Yeqing, Chai, Cedric, Kaster, Jessica, Witt, Russell G., Lazcano, Rossana, Ingram, Davis R., Johnson, Sarah B., Wani, Khalida, Dunagin, Margaret C., Lazar, Alexander J., Weeraratna, Ashani T., Wargo, Jennifer A., Herlyn, Meenhard, and Raj, Arjun

Published
2023
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25. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance

Author

Chu, Yanshuo, Dai, Enyu, Li, Yating, Han, Guangchun, Pei, Guangsheng, Ingram, Davis R., Thakkar, Krupa, Qin, Jiang-Jiang, Dang, Minghao, Le, Xiuning, Hu, Can, Deng, Qing, Sinjab, Ansam, Gupta, Pravesh, Wang, Ruiping, Hao, Dapeng, Peng, Fuduan, Yan, Xinmiao, Liu, Yunhe, Song, Shumei, Zhang, Shaojun, Heymach, John V., Reuben, Alexandre, Elamin, Yasir Y., Pizzi, Melissa P., Lu, Yang, Lazcano, Rossana, Hu, Jian, Li, Mingyao, Curran, Michael, Futreal, Andrew, Maitra, Anirban, Jazaeri, Amir A., Ajani, Jaffer A., Swanton, Charles, Cheng, Xiang-Dong, Abbas, Hussein A., Gillison, Maura, Bhat, Krishna, Lazar, Alexander J., Green, Michael, Litchfield, Kevin, Kadara, Humam, Yee, Cassian, and Wang, Linghua

Published
2023
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26. Pan-cancer proteogenomics characterization of tumor immunity

Author

Abelin, Jennifer, Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cao, Song, Carr, Steven A., Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Ding, Li, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Heiman, David I., Hong, Runyu, Hu, Yingwei, Huang, Chen, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, McDermott, Jason, McKerrow, Wilson, Mesri, Mehdi, Mumphrey, Michael Brodie, Newton, Chelsea J., Oldroyd, Robert, Payne, Samuel H., Pugliese, Pietro, Rodland, Karin D., Rodrigues, Fernanda Martins, Ruggles, Kelly V., Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Feng, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Li, Qing Kay, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Petralia, Francesca, Ma, Weiping, Yaron, Tomer M., Caruso, Francesca Pia, Tignor, Nicole, Wang, Joshua M., Charytonowicz, Daniel, Johnson, Jared L., Huntsman, Emily M., Marino, Giacomo B., Calinawan, Anna, Evangelista, John Erol, Selvan, Myvizhi Esai, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Song, Xiaoyu, Turhan, Berk, Christianson, Karen E., Lewis, David A., Deng, Eden Z., Clarke, Daniel J.B., Whiteaker, Jeffrey R., Kennedy, Jacob J., Zhao, Lei, Segura, Rossana Lazcano, Batra, Harsh, Raso, Maria Gabriela, Parra, Edwin Roger, Soundararajan, Rama, Tang, Ximing, Li, Yize, Yi, Xinpei, Satpathy, Shankha, Wang, Ying, Wiznerowicz, Maciej, González-Robles, Tania J., Iavarone, Antonio, Gosline, Sara J.C., Reva, Boris, Robles, Ana I., Nesvizhskii, Alexey I., Mani, D.R., Gillette, Michael A., Klein, Robert J., Cieslik, Marcin, Zhang, Bing, Paulovich, Amanda G., Sebra, Robert, Gümüş, Zeynep H., Hostetter, Galen, Fenyö, David, Omenn, Gilbert S., Cantley, Lewis C., Ma'ayan, Avi, Lazar, Alexander J., Ceccarelli, Michele, and Wang, Pei

Published
2024
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28. Complete loss of TP53 and RB1 is associated with complex genome and low immune infiltrate in pleomorphic rhabdomyosarcoma

Author

Beird, Hannah C., Wu, Chia-Chin, Nakazawa, Michael, Ingram, Davis, Daniele, Joseph R., Lazcano, Rossana, Little, Latasha, Davies, Christopher, Daw, Najat C., Wani, Khalida, Wang, Wei-Lien, Song, Xingzhi, Gumbs, Curtis, Zhang, Jianhua, Rubin, Brian, Conley, Anthony, Flanagan, Adrienne M., Lazar, Alexander J., and Futreal, P. Andrew

Published
2023
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29. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Author

Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Ozgun, Bavarva, Jasmin, Birger, Chet, Birrer, Michael, Calinawan, Anna, Cantley, Lewis C., Cao, Song, Carr, Steve, Ceccarelli, Michele, Chan, Daniel, Chinnaiyan, Arul, Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Mohan, Domagalski, Marcin, Dou, Yongchao, Druker, Brian, Edwards, Nathan, Ellis, Matthew, Selvan, Myvizhi Esai, Francis, Alicia, Getz, Gad, Gillette, Michael A., Robles, Tania Gonzalez, Gosline, Sara, Gümüş, Zeynep, Heiman, David, Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric, Jewel, Scott, Ji, Jiayi, Jiang, Wen, Lee Johnson, Jared, Katsnelson, Lizabeth, Ketchum, Karen, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan, Liao, Yuxing, Lindgren, Caleb, Liu, Tao, Liu, Wenke, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert, Paulovich, Amanda, Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Ruggles, Kelly, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara, Schadt, Eric, Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Dick, Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik, Tan, Jimin, Terekhanova, Nadezhda, Thangudu, Ratna, Thiagarajan, Mathangi, Tignor, Nicole, Wang, Joshua, Wang, Liang-Bo, Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wu, Yige, Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Chan, Daniel W., Dhanasekaran, Saravana M., Schürer, Stephan, Smith, Richard D., Wyczalkowski, Matthew A., Liang, Wen-Wei, Lu, Rita Jui-Hsien, Jayasinghe, Reyka G., Foltz, Steven M., Porta-Pardo, Eduard, Geffen, Yifat, Wendl, Michael C., Lazcano, Rossana, Kolodziejczak, Iga, Song, Yizhe, Govindan, Akshay, Demicco, Elizabeth G., Li, Xiang, Li, Yize, Sethuraman, Sunantha, Payne, Samuel H., Fenyö, David, Rodriguez, Henry, Wiznerowicz, Maciej, Shen, Hui, Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Robles, Ana I., and Ding, Li

Published
2023
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30. Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Author

Antczak, Andrzej, Anurag, Meenakshi, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Borucki, Melissa, Cai, Shuang, Calinawan, Anna, Carr, Steven A., Castro, Patricia, Cerda, Sandra, Chan, Daniel W., Chesla, David, Cieslik, Marcin P., Cottingham, Sandra, Dhir, Rajiv, Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Edwards, Nathan J., Edwards, Robert, Ellis, Matthew J., Eschbacher, Jennifer, Fam, Mina, Fevrier-Sullivan, Brenda, Francis, Jesse, Freymann, John, Gabriel, Stacey, Getz, Gad, Gillette, Michael A., Godwin, Andrew K., Goldthwaite, Charles A., Grady, Pamela, Hafron, Jason, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Ittmann, Michael M., Johnson, Ashlie, Jones, Corbin D., Ketchum, Karen A., Kirby, Justin, Le, Toan, Ma'ayan, Avi, Madan, Rashna, Mareedu, Sailaja, McGarvey, Peter B., Modugno, Francesmary, Montgomery, Rebecca, Nyce, Kristen, Paulovich, Amanda G., Pruetz, Barbara L., Qi, Liqun, Richey, Shannon, Schadt, Eric E., Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Tansil, Darlene, Thangudu, Ratna R., Tobin, Matt, Um, Ki Sung, Vatanian, Negin, Webster, Alex, Wilson, George D., Wright, Jason, Zaalishvili, Kakhaber, Zhang, Zhen, Zhao, Grace, Dou, Yongchao, Katsnelson, Lizabeth, Gritsenko, Marina A., Hu, Yingwei, Reva, Boris, Hong, Runyu, Wang, Yi-Ting, Kolodziejczak, Iga, Lu, Rita Jui-Hsien, Tsai, Chia-Feng, Bu, Wen, Liu, Wenke, Guo, Xiaofang, An, Eunkyung, Arend, Rebecca C., Bavarva, Jasmin, Chen, Lijun, Chu, Rosalie K., Czekański, Andrzej, Davoli, Teresa, Demicco, Elizabeth G., DeLair, Deborah, Devereaux, Kelly, Dhanasekaran, Saravana M., Dottino, Peter, Dover, Bailee, Fillmore, Thomas L., Foxall, McKenzie, Hermann, Catherine E., Hiltke, Tara, Hostetter, Galen, Jędryka, Marcin, Jewell, Scott D., Johnson, Isabelle, Kahn, Andrea G., Ku, Amy T., Kumar-Sinha, Chandan, Kurzawa, Paweł, Lazar, Alexander J., Lazcano, Rossana, Lei, Jonathan T., Li, Yi, Liao, Yuxing, Lih, Tung-Shing M., Lin, Tai-Tu, Martignetti, John A., Masand, Ramya P., Matkowski, Rafał, McKerrow, Wilson, Mesri, Mehdi, Monroe, Matthew E., Moon, Jamie, Moore, Ronald J., Nestor, Michael D., Newton, Chelsea, Omelchenko, Tatiana, Omenn, Gilbert S., Payne, Samuel H., Petyuk, Vladislav A., Robles, Ana I., Rodriguez, Henry, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schepmoes, Athena A., Shi, Tujin, Shi, Zhiao, Tan, Jimin, Taylor, Mason, Thiagarajan, Mathangi, Wang, Joshua M., Weitz, Karl K., Wen, Bo, Williams, C.M., Wu, Yige, Wyczalkowski, Matthew A., Yi, Xinpei, Zhang, Xu, Zhao, Rui, Mutch, David, Chinnaiyan, Arul M., Smith, Richard D., Nesvizhskii, Alexey I., Wang, Pei, Wiznerowicz, Maciej, Ding, Li, Mani, D.R., Zhang, Hui, Anderson, Matthew L., Rodland, Karin D., Zhang, Bing, Liu, Tao, and Fenyö, David

Published
2023
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31. Multiplatform Analysis of Intratumoral PTEN Heterogeneity in Melanoma

Author

Chagani, Sharmeen, De Macedo, Mariana P., Carapeto, Fernando, Wang, Feng, Marzese, Diego M., Wani, Khalida, Haydu, Lauren E., Peng, Weiyi, Ong, Giang T., Warren, Sarah E., Beechem, Joseph M., Hoon, Dave S.B., Mills, Gordon B., Tetzlaff, Michael T., Lazar, Alexander J., Kwong, Lawrence N., and Davies, Michael A.

Published
2023
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32. IGF-1R/mTOR Targeted Therapy for Ewing Sarcoma: A Meta-Analysis of Five IGF-1R-Related Trials Matched to Proteomic and Radiologic Predictive Biomarkers.

Author

Amin, Hesham M, Morani, Ajaykumar C, Daw, Najat C, Lamhamedi-Cherradi, Salah-Eddine, Subbiah, Vivek, Menegaz, Brian A, Vishwamitra, Deeksha, Eskandari, Ghazaleh, George, Bhawana, Benjamin, Robert S, Patel, Shreyaskumar, Song, Juhee, Lazar, Alexander J, Wang, Wei-Lien, Kurzrock, Razelle, Pappo, Alberto, Anderson, Peter M, Schwartz, Gary K, Araujo, Dejka, Cuglievan, Branko, Ratan, Ravin, McCall, David, Mohiuddin, Sana, Livingston, John A, Molina, Eric R, Naing, Aung, and Ludwig, Joseph A

Subjects
Ewing sarcoma, PET/CT, biological therapies, biomarker, drug response, pIGF-1R, PET, CT, Oncology and Carcinogenesis
Abstract

Background : Ten to fourteen percent of Ewing sarcoma (ES) study participants treated nationwide with IGF-1 receptor (IGF-1R)-targeted antibodies achieved tumor regression. Despite this success, low response rates and short response durations (approximately 7-weeks) have slowed the development of this therapy. Methods: We performed a meta-analysis of five phase-1b/2 ES-oriented trials that evaluated the anticancer activity of IGF-1R antibodies +/- mTOR inhibitors (mTORi). Our meta-analysis provided a head-to-head comparison of the clinical benefits of IGF-1R antibodies vs. the IGF-1R/mTOR-targeted combination. Available pretreatment clinical samples were semi-quantitatively scored using immunohistochemistry to detect proteins in the IGF-1R/PI3K/AKT/mTOR pathway linked to clinical response. Early PET/CT imaging, obtained within the first 2 weeks (median 10 days), were examined to determine if reduced FDG avidity was predictive of progression-free survival (PFS). Results: Among 56 ES patients treated at MD Anderson Cancer Center (MDACC) with IGF-1R antibodies, our analysis revealed a significant ~two-fold improvement in PFS that favored a combination of IGF-1R/mTORi therapy (1.6 vs. 3.3-months, p = 0.042). Low pIGF-1R in the pretreatment specimens was associated with treatment response. Reduced total-lesion glycolysis more accurately predicted the IGF-1R response than other previously reported radiological biomarkers. Conclusion: Synergistic drug combinations, and newly identified proteomic or radiological biomarkers of IGF-1R response, may be incorporated into future IGF-1R-related trials to improve the response rate in ES patients.

Published
2020

33. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

Author

Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C, Huang, Kuan-lin, Newberg, Justin Y, Mashl, R Jay, Romanel, Alessandro, Sayaman, Rosalyn W, Demichelis, Francesca, Felau, Ina, Frampton, Garrett M, Han, Seunghun, Hoadley, Katherine A, Kemal, Anab, Laird, Peter W, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K, Zenklusen, Jean C, Ziv, Elad, Network, Cancer Genome Atlas Analysis, Aguet, Francois, Ding, Li, Demchok, John A, Mensah, Michael KA, Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J, MacArthur, Daniel G, Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M, Cherniack, Andrew D, and Beroukhim, Rameen

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Cancer, Urologic Diseases, Human Genome, Cancer Genomics, Biotechnology, DNA Methylation, DNA-Binding Proteins, Ethnicity, F-Box-WD Repeat-Containing Protein 7, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Genetics, Population, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, MicroRNAs, Mutation, Neoplasm Proteins, Neoplasms, Transcription Factors, Von Hippel-Lindau Tumor Suppressor Protein, Cancer Genome Atlas Analysis Network, TCGA, admixture, ancestry, cancer, eQTL, genomics, mRNA, methylation, miRNA, mutation, Neurosciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer Genome Atlas. We demonstrated that cancer subtypes and ancestry-related technical artifacts are important confounders that have been insufficiently accounted for. Once accounted for, ancestry-associated differences spanned all molecular features and hundreds of genes. Biologically significant differences were usually tissue specific but not specific to cancer. However, admixture and pathway analyses suggested some of these differences are causally related to cancer. Specific findings included increased FBXW7 mutations in patients of African origin, decreased VHL and PBRM1 mutations in renal cancer patients of African origin, and decreased immune activity in bladder cancer patients of East Asian origin.

Published
2020

36. Pan-cancer proteogenomics connects oncogenic drivers to functional states

Author

An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Thangudu, Ratna R., Tignor, Nicole, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Li, Yize, Porta-Pardo, Eduard, Tokheim, Collin, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Liang, Wen-Wei, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Dhanasekaran, Saravana M., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Chheda, Milan G., Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Rodriguez, Henry, Robles, Ana I., Gillette, Michael A., Kumar-Sinha, Chandan, Lazar, Alexander J., Cantley, Lewis C., Getz, Gad, and Ding, Li

Published
2023
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37. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author

An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Babur, Özgün, Cao, Song, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Mani, D.R., Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik P., Schürer, Stephan, Selvan, Myvizhi Esai, Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Tignor, Nicole, Thiagarajan, Mathangi, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Zhou, Daniel Cui, Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Maruvka, Yosef E., Haradhvala, Nicholas J., Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Satpathy, Shankha, Payne, Samuel H., Gillette, Michael A., Dhanasekaran, Saravana M., Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Aguet, François, Cantley, Lewis C., Ding, Li, and Getz, Gad

Published
2023
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38. Proteogenomic data and resources for pan-cancer analysis

Author

Lazar, Alexander J., Paulovich, Amanda G., Colaprico, Antonio, Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Huang, Chen, Mani, D.R., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Hostetter, Galen, Omenn, Gilbert S., Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Rodland, Karin D., Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Ellis, Matthew J., Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Gosline, Sara J.C., Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Liu, Tao, Hiltke, Tara, Yaron, Tomer M., Stathias, Vasileios, Liu, Wenke, Zhang, Xu, Song, Yizhe, Zhang, Zhen, Chan, Daniel W., Li, Yize, Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Akiyama, Yo, Anand, Shankara, Birger, Chet, Cao, Song, Chaudhary, Rekha, Chilappagari, Padmini, Cieslik, Marcin, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Esai Selvan, Myvizhi, Fenyö, David, Foltz, Steven M., Francis, Alicia, Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Holck, Michael, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Klein, Robert J., Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, McKerrow, Wilson, Nguyen, Ngoc, Oldroyd, Robert, Pilozzi, Alexander, Reva, Boris, Rudnick, Paul, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Song, Xiaoyu, Storrs, Erik, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wang, Ying, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Yi, Xinpei, Zhang, Qing, Zuhl, Maya, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Wang, Pei, Robles, Ana I., Zhang, Bing, and Payne, Samuel H.

Published
2023
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39. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Author

Francis, Alicia, Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Colaprico, Antonio, Hakimi, Ari, Pruetz, Barb, Hindenach, Barbara, Yadav, Birendra Kumar, Reva, Boris, Fevrier-Sullivan, Brenda, Druker, Brian J., Szczylik, Cezary, Goldthwaite, Charles A., Jr., Birger, Chet, Jones, Corbin D., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Duffy, Elizabeth, Schadt, Eri E., Petralia, Francesca, Bromiński, Gabriel, Quiroga-Garza, Gabriela M., Wilson, George D., Li, Ginny Xiaohe, Zhao, Grace, Hsiao, Yi, Hsieh, James, Lubiński, Jan, Bavarva, Jasmin, Huang, Jasmine, Hafron, Jason, Eschbacher, Jennifer, Hon, Jennifer, Francis, Jesse, Freymann, John, Vo, Josh, Wang, Joshua, Kirby, Justin, Zaalishvili, Kakhaber, Ketchum, Karen A., Hoadley, Katherine A., Um, Ki Sung, Qi, Liqun, Domagalski, Marcin J., Tobin, Matt, Dyer, Maureen, Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Ittmann, Michael M., Roehrl, Michael H., Schnaubelt, Michael, Smith, Michael, Fam, Mina, Roche, Nancy, Vatanian, Negin, Maunganidze, Nicollette, Potapova, Olga, Paklina, Oxana V., VanderKolk, Pamela, Castro, Patricia, Kurzawa, Paweł, Hariharan, Pushpa, Li, Qin, Li, Qing Kay, Dhir, Rajiv, Thangudu, Ratna R., Montgomery, Rebecca, Smith, Richard D., Mareedu, Sailaja, Payne, Samuel H., Cerda, Sandra, Cottingham, Sandra, Haynes, Sarah, Satpathy, Shankha, Richey, Shannon, Singh, Shilpi, Tsang, Shirley X., Cai, Shuang, Cao, Song, Gabriel, Stacey, Carr, Steven A., Liu, Tao, Bauer, Thomas, Le, Toan, Chen, Xi S., Zhang, Xu, Shutack, Yvonne, Zhang, Zhen, Li, Yize, Lih, Tung-Shing M., Dhanasekaran, Saravana M., Mannan, Rahul, Chen, Lijun, Cieslik, Marcin, Wu, Yige, Lu, Rita Jiu-Hsien, Clark, David J., Kołodziejczak, Iga, Hong, Runyu, Chen, Siqi, Zhao, Yanyan, Chugh, Seema, Caravan, Wagma, Naser Al Deen, Nataly, Hosseini, Noshad, Newton, Chelsea J., Krug, Karsten, Xu, Yuanwei, Cho, Kyung-Cho, Hu, Yingwei, Zhang, Yuping, Kumar-Sinha, Chandan, Ma, Weiping, Calinawan, Anna, Wyczalkowski, Matthew A., Wendl, Michael C., Wang, Yuefan, Guo, Shenghao, Zhang, Cissy, Le, Anne, Dagar, Aniket, Hopkins, Alex, Cho, Hanbyul, Leprevost, Felipe da Veiga, Jing, Xiaojun, Teo, Guo Ci, Liu, Wenke, Reimers, Melissa A., Pachynski, Russell, Lazar, Alexander J., Chinnaiyan, Arul M., Van Tine, Brian A., Zhang, Bing, Rodland, Karin D., Getz, Gad, Mani, D.R., Wang, Pei, Chen, Feng, Hostetter, Galen, Thiagarajan, Mathangi, Linehan, W. Marston, Fenyö, David, Jewell, Scott D., Omenn, Gilbert S., Mehra, Rohit, Wiznerowicz, Maciej, Robles, Ana I., Mesri, Mehdi, Hiltke, Tara, An, Eunkyung, Rodriguez, Henry, Chan, Daniel W., Ricketts, Christopher J., Nesvizhskii, Alexey I., Zhang, Hui, and Ding, Li

Published
2023
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40. Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome

Author

Simpson, Rebecca C., Shanahan, Erin R., Batten, Marcel, Reijers, Irene L. M., Read, Mark, Silva, Ines P., Versluis, Judith M., Ribeiro, Rosilene, Angelatos, Alexandra S., Tan, Jian, Adhikari, Chandra, Menzies, Alexander M., Saw, Robyn P. M., Gonzalez, Maria, Shannon, Kerwin F., Spillane, Andrew J., Velickovic, Rebecca, Lazar, Alexander J., Damania, Ashish V., Mishra, Aditya K., Chelvanambi, Manoj, Banerjee, Anik, Ajami, Nadim J., Wargo, Jennifer A., Macia, Laurence, Holmes, Andrew J., Wilmott, James S., Blank, Christian U., Scolyer, Richard A., and Long, Georgina V.

Published
2022
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41. B cells and tertiary lymphoid structures promote immunotherapy response

Author

Helmink, Beth A, Reddy, Sangeetha M, Gao, Jianjun, Zhang, Shaojun, Basar, Rafet, Thakur, Rohit, Yizhak, Keren, Sade-Feldman, Moshe, Blando, Jorge, Han, Guangchun, Gopalakrishnan, Vancheswaran, Xi, Yuanxin, Zhao, Hao, Amaria, Rodabe N, Tawbi, Hussein A, Cogdill, Alex P, Liu, Wenbin, LeBleu, Valerie S, Kugeratski, Fernanda G, Patel, Sapna, Davies, Michael A, Hwu, Patrick, Lee, Jeffrey E, Gershenwald, Jeffrey E, Lucci, Anthony, Arora, Reetakshi, Woodman, Scott, Keung, Emily Z, Gaudreau, Pierre-Olivier, Reuben, Alexandre, Spencer, Christine N, Burton, Elizabeth M, Haydu, Lauren E, Lazar, Alexander J, Zapassodi, Roberta, Hudgens, Courtney W, Ledesma, Deborah A, Ong, SuFey, Bailey, Michael, Warren, Sarah, Rao, Disha, Krijgsman, Oscar, Rozeman, Elisa A, Peeper, Daniel, Blank, Christian U, Schumacher, Ton N, Butterfield, Lisa H, Zelazowska, Monika A, McBride, Kevin M, Kalluri, Raghu, Allison, James, Petitprez, Florent, Fridman, Wolf Herman, Sautès-Fridman, Catherine, Hacohen, Nir, Rezvani, Katayoun, Sharma, Padmanee, Tetzlaff, Michael T, Wang, Linghua, and Wargo, Jennifer A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Immunization, Cancer, Vaccine Related, Genetics, B-Lymphocytes, Biomarkers, Tumor, Carcinoma, Renal Cell, Cell Cycle Checkpoints, Clone Cells, Dendritic Cells, Follicular, Gene Expression Regulation, Neoplastic, Humans, Immunologic Memory, Immunotherapy, Mass Spectrometry, Melanoma, Neoplasm Metastasis, Phenotype, Prognosis, RNA-Seq, Receptors, Immunologic, Single-Cell Analysis, T-Lymphocytes, Tertiary Lymphoid Structures, Transcriptome, General Science & Technology
Abstract

Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers1-10 and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity11-15, although these have been less well-studied in ICB treatment16. A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling17 that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter18) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.

Published
2020

43. Durvalumab plus tremelimumab in advanced or metastatic soft tissue and bone sarcomas: a single-centre phase 2 trial

Author

Somaiah, Neeta, Conley, Anthony P, Parra, Edwin Roger, Lin, Heather, Amini, Behrang, Solis Soto, Luisa, Salazar, Ruth, Barreto, Carmelia, Chen, Honglei, Gite, Swati, Haymaker, Cara, Nassif, Elise F, Bernatchez, Chantale, Mitra, Akash, Livingston, John Andrew, Ravi, Vinod, Araujo, Dejka M, Benjamin, Robert, Patel, Shreyaskumar, Zarzour, Maria A, Sabir, Sharjeel, Lazar, Alexander J, Wang, Wei-Lien, Daw, Najat C, Zhou, Xiao, Roland, Christina L, Cooper, Zachary A, Rodriguez-Canales, Jaime, Futreal, Andrew, Soria, Jean-Charles, Wistuba, Ignacio I, and Hwu, Patrick

Published
2022
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44. Androgen receptor blockade promotes response to BRAF/MEK-targeted therapy

Author

Vellano, Christopher P., White, Michael G., Andrews, Miles C., Chelvanambi, Manoj, Witt, Russell G., Daniele, Joseph R., Titus, Mark, McQuade, Jennifer L., Conforti, Fabio, Burton, Elizabeth M., Lastrapes, Matthew J., Ologun, Gabriel, Cogdill, Alexandria P., Morad, Golnaz, Prieto, Peter, Lazar, Alexander J., Chu, Yanshuo, Han, Guangchun, Khan, M. A. Wadud, Helmink, Beth, Davies, Michael A., Amaria, Rodabe N., Kovacs, Jeffrey J., Woodman, Scott E., Patel, Sapna, Hwu, Patrick, Peoples, Michael, Lee, Jeffrey E., Cooper, Zachary A., Zhu, Haifeng, Gao, Guang, Banerjee, Hiya, Lau, Mike, Gershenwald, Jeffrey E., Lucci, Anthony, Keung, Emily Z., Ross, Merrick I., Pala, Laura, Pagan, Eleonora, Segura, Rossana Lazcano, Liu, Qian, Borthwick, Mikayla S., Lau, Eric, Yates, Melinda S., Westin, Shannon N., Wani, Khalida, Tetzlaff, Michael T., Haydu, Lauren E., Mahendra, Mikhila, Ma, XiaoYan, Logothetis, Christopher, Kulstad, Zachary, Johnson, Sarah, Hudgens, Courtney W., Feng, Ningping, Federico, Lorenzo, Long, Georgina V., Futreal, P. Andrew, Arur, Swathi, Tawbi, Hussein A., Moran, Amy E., Wang, Linghua, Heffernan, Timothy P., Marszalek, Joseph R., and Wargo, Jennifer A.

Published
2022
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45. Experimental models of undifferentiated pleomorphic sarcoma and malignant peripheral nerve sheath tumor

Author

Bhalla, Angela D., Landers, Sharon M., Singh, Anand K., Landry, Jace P., Yeagley, Michelle G., Myerson, Gabryella S. B., Delgado-Baez, Cristian B., Dunnand, Stephanie, Nguyen, Theresa, Ma, Xiaoyan, Bolshakov, Svetlana, Menegaz, Brian A., Lamhamedi-Cherradi, Salah-Eddine, Mao, Xizeng, Song, Xingzhi, Lazar, Alexander J., McCutcheon, Ian E., Slopis, John M., Ludwig, Joseph A., Lev, Dina C., Rai, Kunal, and Torres, Keila E.

Published
2022
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46. Plasma DNA Methylation‐Based Biomarkers for MPNST Detection in Patients With Neurofibromatosis Type 1.

Author

Tomczak, Katarzyna, Patel, Manishkumar S., Bhalla, Angela D., Peterson, Christine B., Landers, Sharon M., Callahan, S. Carson, Zhang, Di, Wong, Justin, Landry, Jace P., Lazar, Alexander J., Livingston, J. Andrew, Guadagnolo, B. Ashleigh, Lyu, Heather G., Lillemoe, Heather, Roland, Christina L., Keung, Emily Z., Scally, Christopher P., Hunt, Kelly K., McCutcheon, Ian E., and Slopis, John M.

Published
2025
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48. Approach to determining etiology of hypophosphatemia in a patient with coexisting phosphaturic mesenchymal tumor and fibrous dysplasia.

Author

Patil, Madhuri D, Wangsiricharoen, Sintawat, Lazar, Alexander J, Moon, Bryan, Madewell, John E, Collins, Michael T, and Guise, Theresa A

Subjects
FIBROBLAST growth factors, IN situ hybridization, OSTEOMALACIA, HYPOPHOSPHATEMIA, RICKETS, RIB cage
Abstract

Dysregulated FGF23 production is a demonstrated cause of hypophosphatemia and osteomalacia. Diseases associated with these conditions include phosphaturic mesenchymal tumor (PMT) causing tumor induced osteomalacia, various forms of rickets, and fibrous dysplasia (FD). Coexistence of 2 conditions that can increase FGF23 concentrations is rare. We report a case of a 79-yr-old man who presented with rib and right flank pain. Imaging revealed bone lesions in the right iliac wing, left supra-acetabular area, and L4 vertebral body. Biopsies showed a right iliac PMT and left supra-acetabular FD. Cryoablation of both lesions resolved the phosphaturia with normalization of phosphorus level. Coexistence of PMT and FD in this patient with hypophosphatemia raised questions about the source of the FGF23, meaning of coexistence of PMT and FD in the same patient and, about the nature of the third lesion in the L4 vertebral body. Using FGF23 mRNA chromogenic in situ hybridization, we identified the PMT, rather than the FD, as the source of FGF23. Lack of GNAS mutation in the PMT suggested it being independent of FD. Assessment by the intact FGF23: total FGF23 ratio as well as gallium-DOTATATE scan suggested that the vertebral body lesion could represent FD. Other than understanding difference in underlying molecular processing of FGF23 in PMT and FD, testing for mutations, imaging studies as well as in situ hybridization helped solve the questions arising from this unique case of coexistence of PMT and FD. [ABSTRACT FROM AUTHOR]

Published
2025
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49. Oncologic Outcomes in Patients with Localized, Primary Head and Neck Synovial Sarcoma.

Author

Patel, Riddhi R., Gopalakrishnan, Vancheswaran, Amini, Behrang, Lazar, Alexander J., Lin, Patrick P., Benjamin, Robert S., Bishop, Andrew J., Goepfert, Ryan P., and Araujo, Dejka M.

Subjects
HEAD & neck cancer treatment, STATISTICAL models, SARCOMA, HEAD & neck cancer, SYMPTOMS, CANCER patients, RETROSPECTIVE studies, DESCRIPTIVE statistics, KAPLAN-Meier estimator, LOG-rank test, ADJUVANT chemotherapy, METASTASIS, MEDICAL records, ACQUISITION of data, COMBINED modality therapy, SURVIVAL analysis (Biometry), CONFIDENCE intervals, DATA analysis software, OVERALL survival, PROPORTIONAL hazards models, PERIOPERATIVE care
Abstract

Simple Summary: Synovial sarcoma in the head and neck region is rare, making up just 2–3% of sarcomas in that area. This anatomic location is challenging to treat due to its proximity to vital structures like the airways and cranial nerves. Studying this rare malignant tumor at an early, localized stage is important, as multidisciplinary treatments might improve survival outcomes. Therefore, this study aims to explore the survival outcomes of patients with localized head and neck synovial sarcomas. We find that radiation therapy is associated with improved local control of the tumor. While the role of perioperative chemotherapy is still debatable in synovial sarcoma patients, we observe that undergoing chemotherapy in addition to surgery and radiation can promote metastasis-free survival in patients with localized head and neck synovial sarcomas, especially when the tumor is ≥4 cm. By providing updated information on this rare cancer type, such findings may help improve treatment approaches and outcomes, benefiting both patients and the medical community. Background: this study aims to evaluate the survival outcomes of patients suffering from head and neck synovial sarcoma (HNSS), especially in relation to patients with a localized disease at diagnosis. Methods: this retrospective chart review includes 57 patients diagnosed with primary HNSS between 1981 and 2020 who presented with a localized disease at diagnosis. Overall survival (OS) from diagnosis, local recurrence-free survival (LRFS), and metastasis-free survival (MFS) from the end of the primary tumor treatment are estimated. The Kaplan–Meier method, the log-rank test, and the Cox proportional hazards regression are used. Results: the 5-year OS, LRFS, and MFS are estimated at 80.4% (95% CI: 66.6%, 88.9%), 67.7% (95% CI: 50.0%, 80.4%), and 50.6% (95% CI: 34.4%, 64.8), respectively. Compared to patients undergoing surgical resection alone, those receiving radiation therapy (RT) with surgery have better LRFS (HR: 0.03, 95% CI: 0.001, 0.57), and those undergoing neo/adjuvant chemotherapy with surgery and RT have better MFS (HR: 0.10, 95% CI: 0.01, 0.95). Moreover, among the patients with tumors ≥ 4 cm, those subject to neo/adjuvant chemotherapy have significantly better MFS (5-year MFS: 53.2%, 95% CI: 29.0%, 72.5%) than those treated with surgery and RT alone (5-year MFS: 20.0%, 95% CI: 0.8%, 58.2%) (LR-p = 0.003). Conclusions: overall, the prognosis of HNSS patients looks favorable. Perioperative RT significantly improves local control, and perioperative chemotherapy plays a vital role in delaying metastasis formation in patients with primary HNSS when diagnosed with a localized disease. Importantly, we recommend that systemic therapy should be considered for HNSS patients with tumors ≥ 4 cm. [ABSTRACT FROM AUTHOR]

Published
2024
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50. Interleukin-6 blockade abrogates immunotherapy toxicity and promotes tumor immunity

Author

Hailemichael, Yared, Johnson, Daniel H., Abdel-Wahab, Noha, Foo, Wai Chin, Bentebibel, Salah-Eddine, Daher, May, Haymaker, Cara, Wani, Khalida, Saberian, Chantal, Ogata, Dai, Kim, Sang T., Nurieva, Roza, Lazar, Alexander J., Abu-Sbeih, Hamzah, Fa'ak, Faisal, Mathew, Antony, Wang, Yinghong, Falohun, Adewunmi, Trinh, Van, Zobniw, Chrystia, Spillson, Christine, Burks, Jared K., Awiwi, Muhammad, Elsayes, Khaled, Soto, Luisa Solis, Melendez, Brenda D., Davies, Michael A., Wargo, Jennifer, Curry, Jonathan, Yee, Cassian, Lizee, Gregory, Singh, Shalini, Sharma, Padmanee, Allison, James P., Hwu, Patrick, Ekmekcioglu, Suhendan, and Diab, Adi

Published
2022
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