Search

Your search keyword '"Cieslik, Marcin P."' showing total 94 results
Start Over Author "Cieslik, Marcin P."
94 results on '"Cieslik, Marcin P."'

1. A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations

Author

Gondal, Mahnoor N., Shah, Saad Ur Rehman, Chinnaiyan, Arul M., and Cieslik, Marcin

Subjects
Quantitative Biology - Genomics
Abstract

Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Furthermore, we propose that bridging the gap between computational and wet lab scientists through user-friendly web-based platforms is needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field., Comment: 17 pages, 1 figure, 1 table

Published
2024

2. PIKfyve, expressed by CD11c-positive cells, controls tumor immunity

Author

Choi, Jae Eun, Qiao, Yuanyuan, Kryczek, Ilona, Yu, Jiali, Gurkan, Jonathan, Bao, Yi, Gondal, Mahnoor, Tien, Jean Ching-Yi, Maj, Tomasz, Yazdani, Sahr, Parolia, Abhijit, Xia, Houjun, Zhou, JiaJia, Wei, Shuang, Grove, Sara, Vatan, Linda, Lin, Heng, Li, Gaopeng, Zheng, Yang, Zhang, Yuping, Cao, Xuhong, Su, Fengyun, Wang, Rui, He, Tongchen, Cieslik, Marcin, Green, Michael D., Zou, Weiping, and Chinnaiyan, Arul M.

Published
2024
Full Text
View/download PDF

3. Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis

Author

Singhal, Udit, Nallandhighal, Srinivas, Tosoian, Jeffrey J., Hu, Kevin, Pham, Trinh M., Stangl-Kremser, Judith, Liu, Chia-Jen, Karim, Razeen, Plouffe, Komal R., Morgan, Todd M., Cieslik, Marcin, Lucianò, Roberta, Shariat, Shahrokh F., Finocchio, Nadia, Dambrosio, Lucia, Doglioni, Claudio, Chinnaiyan, Arul M., Tomlins, Scott A., Briganti, Alberto, Palapattu, Ganesh S., Udager, Aaron M., and Salami, Simpa S.

Published
2024
Full Text
View/download PDF

4. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

Author

Chowdhury, Shrabanti, Kennedy, Jacob, Ivey, Richard, Murillo, Oscar, Hosseini, Noshad, Song, Xiaoyu, Petralia, Francesca, Calinawan, Anna, Savage, Sara, Berry, Anna, Reva, Boris, Ozbek, Umut, Krek, Azra, Ma, Weiping, da Veiga Leprevost, Felipe, Ji, Jiayi, Yoo, Seungyeul, Lin, Chenwei, Voytovich, Uliana, Huang, Yajue, Lee, Sun-Hee, Bergan, Lindsay, Lorentzen, Travis, Mesri, Mehdi, Rodriguez, Henry, Hoofnagle, Andrew, Herbert, Zachary, Nesvizhskii, Alexey, Zhang, Bing, Whiteaker, Jeffrey, Fenyo, David, McKerrow, Wilson, Wang, Joshua, Schürer, Stephan, Stathias, Vasileios, Chen, X, Starr, Timothy, Winterhoff, Boris, Nelson, Andrew, Mok, Samuel, Kaufmann, Scott, Drescher, Charles, Cieslik, Marcin, Wang, Pei, Birrer, Michael, Paulovich, Amanda, and Barcellos-Hoff, Mary Helen

Subjects
chemorefractory, high-grade serous ovarian cancer, machine learning, mass spectrometry, multiple reaction monitoring, platinum, precision oncology, predictive biomarker, prognostic biomarker, proteogenomic, Female, Humans, Cystadenocarcinoma, Serous, Ovarian Neoplasms, Proteogenomics
Abstract

To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.

Published
2023

5. Loss of LCMT1 and biased protein phosphatase 2A heterotrimerization drive prostate cancer progression and therapy resistance

Author

Rasool, Reyaz ur, O’Connor, Caitlin M., Das, Chandan Kanta, Alhusayan, Mohammed, Verma, Brijesh Kumar, Islam, Sehbanul, Frohner, Ingrid E., Deng, Qu, Mitchell-Velasquez, Erick, Sangodkar, Jaya, Ahmed, Aqila, Linauer, Sarah, Mudrak, Ingrid, Rainey, Jessica, Zawacki, Kaitlin P., Suhan, Tahra K., Callahan, Catherine G., Rebernick, Ryan, Natesan, Ramakrishnan, Siddiqui, Javed, Sauter, Guido, Thomas, Dafydd, Wang, Shaomeng, Taylor, Derek J., Simon, Ronald, Cieslik, Marcin, Chinnaiyan, Arul M., Busino, Luca, Ogris, Egon, Narla, Goutham, and Asangani, Irfan A.

Published
2023
Full Text
View/download PDF

8. 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
Full Text
View/download PDF

10. Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas

Author

Panwalkar, Pooja, Tamrazi, Benita, Dang, Derek, Chung, Chan, Sweha, Stefan, Natarajan, Siva Kumar, Pun, Matthew, Bayliss, Jill, Ogrodzinski, Martin P, Pratt, Drew, Mullan, Brendan, Hawes, Debra, Yang, Fusheng, Lu, Chao, Sabari, Benjamin R, Achreja, Abhinav, Heon, Jin, Animasahun, Olamide, Cieslik, Marcin, Dunham, Christopher, Yip, Stephen, Hukin, Juliette, Phillips, Joanna J, Bornhorst, Miriam, Griesinger, Andrea M, Donson, Andrew M, Foreman, Nicholas K, Garton, Hugh JL, Heth, Jason, Muraszko, Karin, Nazarian, Javad, Koschmann, Carl, Jiang, Li, Filbin, Mariella G, Nagrath, Deepak, Kool, Marcel, Korshunov, Andrey, Pfister, Stefan M, Gilbertson, Richard J, Allis, C David, Chinnaiyan, Arul M, Lunt, Sophia Y, Blüml, Stefan, Judkins, Alexander R, and Venneti, Sriram

Subjects
Cancer, Biotechnology, Genetics, Rare Diseases, Orphan Drug, Neurosciences, Brain Disorders, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Animals, Child, Ependymoma, Epigenesis, Genetic, Epigenomics, Histones, Humans, Metabolic Networks and Pathways, Mice, Biological Sciences, Medical and Health Sciences
Abstract

Childhood posterior fossa group A ependymomas (PFAs) have limited treatment options and bear dismal prognoses compared to group B ependymomas (PFBs). PFAs overexpress the oncohistone-like protein EZHIP (enhancer of Zeste homologs inhibitory protein), causing global reduction of repressive histone H3 lysine 27 trimethylation (H3K27me3), similar to the oncohistone H3K27M. Integrated metabolic analyses in patient-derived cells and tumors, single-cell RNA sequencing of tumors, and noninvasive metabolic imaging in patients demonstrated enhanced glycolysis and tricarboxylic acid (TCA) cycle metabolism in PFAs. Furthermore, high glycolytic gene expression in PFAs was associated with a poor outcome. PFAs demonstrated high EZHIP expression associated with poor prognosis and elevated activating mark histone H3 lysine 27 acetylation (H3K27ac). Genomic H3K27ac was enriched in PFAs at key glycolytic and TCA cycle–related genes including hexokinase-2 and pyruvate dehydrogenase. Similarly, mouse neuronal stem cells (NSCs) expressing wild-type EZHIP (EZHIP-WT) versus catalytically attenuated EZHIP-M406K demonstrated H3K27ac enrichment at hexokinase-2 and pyruvate dehydrogenase, accompanied by enhanced glycolysis and TCA cycle metabolism. AMPKα-2, a key component of the metabolic regulator AMP-activated protein kinase (AMPK), also showed H3K27ac enrichment in PFAs and EZHIP-WT NSCs. The AMPK activator metformin lowered EZHIP protein concentrations, increased H3K27me3, suppressed TCA cycle metabolism, and showed therapeutic efficacy in vitro and in vivo in patient-derived PFA xenografts in mice. Our data indicate that PFAs and EZHIP-WT–expressing NSCs are characterized by enhanced glycolysis and TCA cycle metabolism. Repurposing the antidiabetic drug metformin lowered pathogenic EZHIP, increased H3K27me3, and suppressed tumor growth, suggesting that targeting integrated metabolic/epigenetic pathways is a potential therapeutic strategy for treating childhood ependymomas.

Published
2021

11. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author

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

Published
2023
Full Text
View/download PDF

12. 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
Full Text
View/download PDF

13. 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
Full Text
View/download PDF

14. 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
Full Text
View/download PDF

15. Clinical Outcomes in Cyclin-dependent Kinase 12 Mutant Advanced Prostate Cancer

Author

Reimers, Melissa A, Yip, Steven M, Zhang, Li, Cieslik, Marcin, Dhawan, Mallika, Montgomery, Bruce, Wyatt, Alexander W, Chi, Kim N, Small, Eric J, Chinnaiyan, Arul M, Alva, Ajjai S, Feng, Felix Y, and Chou, Jonathan

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Aging, Prostate Cancer, Urologic Diseases, Clinical Research, Genetics, Cancer, Detection, screening and diagnosis, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, Aetiology, Aged, Cyclin-Dependent Kinases, Humans, Male, Middle Aged, Mutation, Neoplasm Staging, Prostatic Neoplasms, Retrospective Studies, Treatment Outcome, Genomics, Next-generation sequencing, Prostate cancer, Cyclin-dependent kinase 12, Urology & Nephrology, Clinical sciences
Abstract

BackgroundCyclin-dependent kinase 12 (CDK12) loss occurs in 3-7% of metastatic prostate cancer patients and is characterized by a genomic instability signature, but the clinical implications of CDK12 loss are not well established.ObjectiveTo determine the clinical course of patients with CDK12 mutant advanced prostate cancer compared with other genomic subtypes.Design, setting, and participantsA retrospective analysis of data from three academic medical centers, including 317 patients with advanced prostate cancer and prior next-generation sequencing from tumor tissue (n = 172) or circulating tumor DNA (n = 145), was performed. Forty-six patients had CDK12 mutations; 34 had biallelic CDK12 loss (79%).Outcome measurements and statistical analysisPatients were stratified by mutation status (CDK12, homologous recombination deficiency [HRD; BRCA1/2 and ATM], TP53, and other cohort). The Kaplan-Meier method was used to evaluate time to event outcomes: time to development of metastatic disease, time to development of castration resistance, and time to prostate-specific antigen (PSA) progression after first-line androgen receptor pathway inhibitor (ARPI) therapy in a patient subset.Results and limitationsThe median follow-up was 66.6 mo. Patients with CDK12 mutant prostate cancer exhibited shorter time to metastasis (median = 34.9 mo, p =  0.004) and development of castration-resistant disease (median = 32.7 mo, p

Published
2020

16. PROMISE: a real-world clinical-genomic database to address knowledge gaps in prostate cancer

Author

Koshkin, Vadim S., Patel, Vaibhav G., Ali, Alicia, Bilen, Mehmet A., Ravindranathan, Deepak, Park, Joseph J., Kellezi, Olesia, Cieslik, Marcin, Shaya, Justin, Cabal, Angelo, Brown, Landon, Labriola, Matthew, Graham, Laura S., Pritchard, Colin, Tripathi, Abhishek, Nusrat, Sanober, Barata, Pedro, Jang, Albert, Chen, Shuang R., Garje, Rohan, Acharya, Luna, Hwang, Clara, Pilling, Amanda, Oh, William, Jun, Tomi, Natesan, Divya, Nguyen, Chris, Kilari, Deepak, Pierro, Michael, Thapa, Bicky, Cackowski, Frank, Mack, Alleda, Heath, Elisabeth, Marshall, Catherine H., Tagawa, Scott T., Halabi, Susan, Schweizer, Michael T., Armstrong, Andrew, Dorff, Tanya, Alva, Ajjai, and McKay, Rana

Published
2022
Full Text
View/download PDF

17. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Author

Quigley, David A, Dang, Ha X, Zhao, Shuang G, Lloyd, Paul, Aggarwal, Rahul, Alumkal, Joshi J, Foye, Adam, Kothari, Vishal, Perry, Marc D, Bailey, Adina M, Playdle, Denise, Barnard, Travis J, Zhang, Li, Zhang, Jin, Youngren, Jack F, Cieslik, Marcin P, Parolia, Abhijit, Beer, Tomasz M, Thomas, George, Chi, Kim N, Gleave, Martin, Lack, Nathan A, Zoubeidi, Amina, Reiter, Robert E, Rettig, Matthew B, Witte, Owen, Ryan, Charles J, Fong, Lawrence, Kim, Won, Friedlander, Terence, Chou, Jonathan, Li, Haolong, Das, Rajdeep, Li, Hui, Moussavi-Baygi, Ruhollah, Goodarzi, Hani, Gilbert, Luke A, Lara, Primo N, Evans, Christopher P, Goldstein, Theodore C, Stuart, Joshua M, Tomlins, Scott A, Spratt, Daniel E, Cheetham, R Keira, Cheng, Donavan T, Farh, Kyle, Gehring, Julian S, Hakenberg, Jörg, Liao, Arnold, Febbo, Philip G, Shon, John, Sickler, Brad, Batzoglou, Serafim, Knudsen, Karen E, He, Housheng H, Huang, Jiaoti, Wyatt, Alexander W, Dehm, Scott M, Ashworth, Alan, Chinnaiyan, Arul M, Maher, Christopher A, Small, Eric J, and Feng, Felix Y

Subjects
Humans, Prostatic Neoplasms, Neoplasm Metastasis, Cyclin-Dependent Kinases, Proto-Oncogene Proteins c-myc, BRCA2 Protein, Receptors, Androgen, Gene Expression Profiling, Genomics, Tandem Repeat Sequences, Mutation, Aged, Aged, 80 and over, Middle Aged, Male, Tumor Suppressor Protein p53, Genomic Structural Variation, DNA Copy Number Variations, Exome, Whole Genome Sequencing, BRCA2, androgen receptor, castration resistant prostate cancer, chromothripsis, gene fusion, genomics, metastases, structural variation, tandem duplication, whole-genome sequencing, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole-genome and -transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor/38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kb upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer.

Published
2018

18. Evaluating Immune Checkpoint Blockade in Metastatic Castration-Resistant Prostate Cancers with Deleterious CDK12 Alterations in the Phase 2 IMPACT Trial

Author

Nguyen, Charles B., primary, Reimers, Melissa A., additional, Perera, Chamila, additional, Abida, Wassim, additional, Chou, Jonathan, additional, Feng, Felix Y., additional, Antonarakis, Emmanuel S., additional, McKay, Rana R., additional, Pachynski, Russell K., additional, Zhang, Jingsong, additional, Reichert, Zachery R., additional, Palmbos, Phillip L., additional, Caram, Megan E.V., additional, Vaishampayan, Ulka N., additional, Heath, Elisabeth I., additional, Hopkins, Alexander C., additional, Cieslik, Marcin P., additional, Wu, Yi-Mi, additional, Robinson, Dan, additional, Baladandayuthapani, Veerabhadran, additional, Chinnaiyan, Arul M., additional, and Alva, Ajjai S., additional

Published
2024
Full Text
View/download PDF

20. Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas

Author

Bayliss, Jill, Mukherjee, Piali, Lu, Chao, Jain, Siddhant U, Chung, Chan, Martinez, Daniel, Sabari, Benjamin, Margol, Ashley S, Panwalkar, Pooja, Parolia, Abhijit, Pekmezci, Melike, McEachin, Richard C, Cieslik, Marcin, Tamrazi, Benita, Garcia, Benjamin A, La Rocca, Gaspare, Santi, Mariarita, Lewis, Peter W, Hawkins, Cynthia, Melnick, Ari, Allis, C David, Thompson, Craig B, Chinnaiyan, Arul M, Judkins, Alexander R, and Venneti, Sriram

Subjects
Medical Biotechnology, Biomedical and Clinical Sciences, Brain Disorders, Pediatric, Neurosciences, Human Genome, Rare Diseases, Cancer, Pediatric Cancer, Brain Cancer, Genetics, Brain Neoplasms, Central Nervous System, Child, CpG Islands, DNA Methylation, Ependymoma, Epigenesis, Genetic, Gene Expression Profiling, Genome, Human, Histones, Humans, Mutation, Prognosis, Treatment Outcome, Biological Sciences, Medical and Health Sciences, Medical biotechnology, Biomedical engineering
Abstract

Childhood posterior fossa (PF) ependymomas cause substantial morbidity and mortality. These tumors lack recurrent genetic mutations, but a subset of these ependymomas exhibits CpG island (CpGi) hypermethylation [PF group A (PFA)], implicating epigenetic alterations in their pathogenesis. Further, histological grade does not reliably predict prognosis, highlighting the importance of developing more robust prognostic markers. We discovered global H3K27me3 reduction in a subset of these tumors (PF-ve ependymomas) analogous to H3K27M mutant gliomas. PF-ve tumors exhibited many clinical and biological similarities with PFA ependymomas. Genomic H3K27me3 distribution showed an inverse relationship with CpGi methylation, suggesting that CpGi hypermethylation drives low H3K27me3 in PF-ve ependymomas. Despite CpGi hypermethylation and global H3K27me3 reduction, these tumors showed DNA hypomethylation in the rest of the genome and exhibited increased H3K27me3 genomic enrichment at limited genomic loci similar to H3K27M mutant gliomas. Combined integrative analysis of PF-ve ependymomas with H3K27M gliomas uncovered common epigenetic deregulation of select factors that control radial glial biology, and PF radial glia in early human development exhibited reduced H3K27me3. Finally, H3K27me3 immunostaining served as a biomarker of poor prognosis and delineated radiologically invasive tumors, suggesting that reduced H3K27me3 may be a prognostic indicator in PF ependymomas.

Published
2016

21. Liver metastasis restrains immunotherapy efficacy via macrophage-mediated T cell elimination

Author

Yu, Jiali, Green, Michael D., Li, Shasha, Sun, Yilun, Journey, Sara N., Choi, Jae Eun, Rizvi, Syed Monem, Qin, Angel, Waninger, Jessica J., Lang, Xueting, Chopra, Zoey, El Naqa, Issam, Zhou, Jiajia, Bian, Yingjie, Jiang, Long, Tezel, Alangoya, Skvarce, Jeremy, Achar, Rohan K., Sitto, Merna, Rosen, Benjamin S., Su, Fengyun, Narayanan, Sathiya P., Cao, Xuhong, Wei, Shuang, Szeliga, Wojciech, Vatan, Linda, Mayo, Charles, Morgan, Meredith A., Schonewolf, Caitlin A., Cuneo, Kyle, Kryczek, Ilona, Ma, Vincent T., Lao, Christopher D., Lawrence, Theodore S., Ramnath, Nithya, Wen, Fei, Chinnaiyan, Arul M., Cieslik, Marcin, Alva, Ajjai, and Zou, Weiping

Published
2021
Full Text
View/download PDF

22. Abstractions, Algorithms and Data Structures for Structural Bioinformatics in PyCogent

Author

Cieslik, Marcin, Derewenda, Zygmunt, and Mura, Cameron

Subjects
Quantitative Biology - Biomolecules, Computer Science - Data Structures and Algorithms, Computer Science - Software Engineering
Abstract

To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which provide object-oriented abstractions (based on a hierarchical representation of macromolecules), efficient data structures (e.g. kD-trees), fast implementations of common algorithms (e.g. surface-area calculations), read/write support for Protein Data Bank-related file formats and wrappers for external command-line applications (e.g. Stride). Integration of this code into PyCogent is symbiotic, allowing sequence-based work to benefit from structure-derived data and, reciprocally, enabling structural studies to leverage PyCogent's versatile tools for phylogenetic and evolutionary analyses., Comment: 36 pages, 4 figures (including supplemental information)

Published
2014
Full Text
View/download PDF

23. PaPy: Parallel and Distributed Data-processing Pipelines in Python

Author

Cieslik, Marcin and Mura, Cameron

Subjects
Computer Science - Programming Languages, Quantitative Biology - Quantitative Methods
Abstract

PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written Python functions (nodes) connected by 'pipes' (edges) into a directed acyclic graph. These functions are arbitrarily definable, and can make use of any Python modules or external binaries. Given a user-defined topology and collection of input data, functions are composed into nested higher-order maps, which are transparently and robustly evaluated in parallel on a single computer or on remote hosts. Local and remote computational resources can be flexibly pooled and assigned to functional nodes, thereby allowing facile load-balancing and pipeline optimization to maximize computational throughput. Input items are processed by nodes in parallel, and traverse the graph in batches of adjustable size -- a trade-off between lazy-evaluation, parallelism, and memory consumption. The processing of a single item can be parallelized in a scatter/gather scheme. The simplicity and flexibility of distributed workflows using PaPy bridges the gap between desktop -> grid, enabling this new computing paradigm to be leveraged in the processing of large scientific datasets., Comment: 7 pages, 5 figures, 2 tables, some use-cases; more at http://muralab.org/PaPy

Published
2014

24. Cancer SLC43A2 alters T cell methionine metabolism and histone methylation

Author

Bian, Yingjie, Li, Wei, Kremer, Daniel M., Sajjakulnukit, Peter, Li, Shasha, Crespo, Joel, Nwosu, Zeribe C., Zhang, Li, Czerwonka, Arkadiusz, Pawłowska, Anna, Xia, Houjun, Li, Jing, Liao, Peng, Yu, Jiali, Vatan, Linda, Szeliga, Wojciech, Wei, Shuang, Grove, Sara, Liu, J. Rebecca, McLean, Karen, Cieslik, Marcin, Chinnaiyan, Arul M., Zgodziński, Witold, Wallner, Grzegorz, Wertel, Iwona, Okła, Karolina, Kryczek, Ilona, Lyssiotis, Costas A., and Zou, Weiping

Published
2020
Full Text
View/download PDF

25. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author

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

Published
2023
Full Text
View/download PDF

26. Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Author

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

Published
2023
Full Text
View/download PDF

28. CD8+ T cells regulate tumour ferroptosis during cancer immunotherapy

Author

Wang, Weimin, Green, Michael, Choi, Jae Eun, Gijón, Miguel, Kennedy, Paul D., Johnson, Jeffrey K., Liao, Peng, Lang, Xueting, Kryczek, Ilona, Sell, Amanda, Xia, Houjun, Zhou, Jiajia, Li, Gaopeng, Li, Jing, Li, Wei, Wei, Shuang, Vatan, Linda, Zhang, Hongjuan, Szeliga, Wojciech, Gu, Wei, Liu, Rebecca, Lawrence, Theodore S., Lamb, Candice, Tanno, Yuri, Cieslik, Marcin, Stone, Everett, Georgiou, George, Chan, Timothy A., Chinnaiyan, Arul, and Zou, Weiping

Published
2019
Full Text
View/download PDF

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

Author

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

Published
2023
Full Text
View/download PDF

30. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author

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

Published
2023
Full Text
View/download PDF

32. Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma

Author

Iyer, Ashwin R., primary, Gurumurthy, Aishwarya, additional, Kodgule, Rohan, additional, Aguilar, Athalee R., additional, Saari, Travis, additional, Ramzan, Abdullah, additional, Rausch, Dylan, additional, Gupta, Juhi, additional, Hall, Cody N., additional, Runge, John S., additional, Weiss, Matthew B., additional, Rahmat, Mahshid, additional, Anyoha, Rockwell, additional, Fulco, Charles P., additional, Ghobrial, Irene M, additional, Engreitz, Jesse M., additional, Cieslik, Marcin P., additional, and Ryan, Russell JH, additional

Published
2023
Full Text
View/download PDF

33. Supplementary Information file from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

34. Supplementary Table 1 from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

35. Supplementary Table 2 from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

36. Supplementary Table 4 from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

37. Supplementary Table 3 from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

38. Supplementary Table 6 from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

39. Data from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

40. Supplementary Table 5 from ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., primary, Monovich, Alexander C., primary, Saari, Travis, primary, Aguilar, Athalee R., primary, Hall, Cody N., primary, Rajesh, Niharika, primary, Gupta, Juhi, primary, Chu, Shih-Chun A., primary, Ye, Li, primary, Gurumurthy, Aishwarya, primary, Iyer, Ashwin, primary, Brown, Noah A., primary, Chiang, Mark Y., primary, Cieslik, Marcin P., primary, and Ryan, Russell J.H., primary

Published
2023
Full Text
View/download PDF

43. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., additional, Monovich, Alexander C., additional, Saari, Travis, additional, Aguilar, Athalee R., additional, Hall, Cody N., additional, Rajesh, Niharika, additional, Gupta, Juhi, additional, Chu, Shih-Chun A., additional, Ye, Li, additional, Gurumurthy, Aishwarya, additional, Iyer, Ashwin, additional, Brown, Noah A., additional, Chiang, Mark Y., additional, Cieslik, Marcin P., additional, and Ryan, Russell J.H., additional

Published
2022
Full Text
View/download PDF

44. ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia

Author

Kodgule, Rohan, primary, Goldman, Joshua W., additional, Monovich, Alexander C., additional, Saari, Travis, additional, Hall, Cody N., additional, Rajesh, Niharika, additional, Gupta, Juhi, additional, Aguilar, Athalee, additional, Brown, Noah A., additional, Chiang, Mark Y., additional, Cieslik, Marcin P., additional, and Ryan, Russell J.H., additional

Published
2022
Full Text
View/download PDF

45. Abstract 1461: ETV6 deficiency and microsatellite enhancers drive transcriptional dysregulation in B-lymphoblastic leukemia

Author

Goldman, Joshua W., primary, Kodgule, Rohan, additional, Monovich, Alexander C., additional, Saari, Travis, additional, Hall, Cody N., additional, Rajesh, Niharika, additional, Gupta, Juhi, additional, Aguilar, Athalee, additional, Brown, Noah, additional, Chiang, Mark Y., additional, Cieslik, Marcin P., additional, and Ryan, Russell J., additional

Published
2022
Full Text
View/download PDF

46. CDK12 loss drives prostate cancer progression, transcription-replication conflicts, and synthetic lethality with paralog CDK13

Author

Tien, Jean Ching-Yi, Luo, Jie, Chang, Yu, Zhang, Yuping, Cheng, Yunhui, Wang, Xiaoju, Yang, Jianzhang, Mannan, Rahul, Mahapatra, Somnath, Shah, Palak, Wang, Xiao-Ming, Todd, Abigail J., Eyunni, Sanjana, Cheng, Caleb, Rebernick, Ryan J., Xiao, Lanbo, Bao, Yi, Neiswender, James, Brough, Rachel, Pettitt, Stephen J., Cao, Xuhong, Miner, Stephanie J., Zhou, Licheng, Wu, Yi-Mi, Labanca, Estefania, Wang, Yuzhuo, Parolia, Abhijit, Cieslik, Marcin, Robinson, Dan R., Wang, Zhen, Feng, Felix Y., Chou, Jonathan, Lord, Christopher J., Ding, Ke, and Chinnaiyan, Arul M.

Abstract

Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a metastatic castration-resistant prostate cancer (mCRPC) subtype. It remains unclear, however, whether CDK12loss drives prostate cancer (PCa) development or uncovers pharmacologic vulnerabilities. Here, we show Cdk12ablation in murine prostate epithelium is sufficient to induce preneoplastic lesions with lymphocytic infiltration. In allograft-based CRISPR screening, Cdk12loss associates positively with Trp53inactivation but negatively with Pteninactivation. Moreover, concurrent Cdk12/Trp53ablation promotes proliferation of prostate-derived organoids, while Cdk12knockout in Pten-null mice abrogates prostate tumor growth. In syngeneic systems, Cdk12/Trp53-null allografts exhibit luminal morphology and immune checkpoint blockade sensitivity. Mechanistically, Cdk12inactivation mediates genomic instability by inducing transcription-replication conflicts. Strikingly, CDK12-mutant organoids and patient-derived xenografts are sensitive to inhibition or degradation of the paralog kinase, CDK13. We therein establish CDK12as a bona fidetumor suppressor, mechanistically define how CDK12inactivation causes genomic instability, and advance a therapeutic strategy for CDK12-mutant mCRPC.

Published
2024
Full Text
View/download PDF

47. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Author

Gillette, Michael A., primary, Satpathy, Shankha, additional, Cao, Song, additional, Dhanasekaran, Saravana M., additional, Vasaikar, Suhas V., additional, Krug, Karsten, additional, Petralia, Francesca, additional, Li, Yize, additional, Liang, Wen-Wei, additional, Reva, Boris, additional, Krek, Azra, additional, Ji, Jiayi, additional, Song, Xiaoyu, additional, Liu, Wenke, additional, Hong, Runyu, additional, Yao, Lijun, additional, Blumenberg, Lili, additional, Savage, Sara R., additional, Wendl, Michael C., additional, Wen, Bo, additional, Li, Kai, additional, Tang, Lauren C., additional, MacMullan, Melanie A., additional, Avanessian, Shayan C., additional, Kane, M. Harry, additional, Newton, Chelsea J., additional, Cornwell, MacIntosh, additional, Kothadia, Ramani B., additional, Ma, Weiping, additional, Yoo, Seungyeul, additional, Mannan, Rahul, additional, Vats, Pankaj, additional, Kumar-Sinha, Chandan, additional, Kawaler, Emily A., additional, Omelchenko, Tatiana, additional, Colaprico, Antonio, additional, Geffen, Yifat, additional, Maruvka, Yosef E., additional, da Veiga Leprevost, Felipe, additional, Wiznerowicz, Maciej, additional, Gümüş, Zeynep H., additional, Veluswamy, Rajwanth R., additional, Hostetter, Galen, additional, Heiman, David I., additional, Wyczalkowski, Matthew A., additional, Hiltke, Tara, additional, Mesri, Mehdi, additional, Kinsinger, Christopher R., additional, Boja, Emily S., additional, Omenn, Gilbert S., additional, Chinnaiyan, Arul M., additional, Rodriguez, Henry, additional, Li, Qing Kay, additional, Jewell, Scott D., additional, Thiagarajan, Mathangi, additional, Getz, Gad, additional, Zhang, Bing, additional, Fenyö, David, additional, Ruggles, Kelly V., additional, Cieslik, Marcin P., additional, Robles, Ana I., additional, Clauser, Karl R., additional, Govindan, Ramaswamy, additional, Wang, Pei, additional, Nesvizhskii, Alexey I., additional, Ding, Li, additional, Mani, D.R., additional, Carr, Steven A., additional, Webster, Alex, additional, Francis, Alicia, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Godwin, Andrew K., additional, Karnuta, Andrii, additional, Marrero-Oliveras, Annette, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kubisa, Bartosz, additional, Druker, Brian J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel Cui, additional, Chan, Daniel W., additional, Chesla, David, additional, Clark, David J., additional, Rykunov, Dmitry, additional, Tan, Donghui, additional, Ponomareva, Elena V., additional, Duffy, Elizabeth, additional, Burks, Eric J., additional, Schadt, Eric E., additional, Bergstrom, Erik J., additional, Fedorov, Eugene S., additional, Malc, Ewa, additional, Wilson, George D., additional, Chen, Hai-Quan, additional, Krzystek, Halina M., additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhang, Hui, additional, Day, Jacob, additional, Suh, James, additional, Whiteaker, Jeffrey R., additional, Eschbacher, Jennifer, additional, McGee, John, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Robinson, Karna, additional, Hoadley, Katherine A., additional, Suzuki, Kei, additional, Um, Ki Sung, additional, Elburn, Kim, additional, Wang, Liang-Bo, additional, Chen, Lijun, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Wojtyś, Małgorzata, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Beasley, Mary B., additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Sun, Meng-Hong, additional, Roehrl, Michael H., additional, Birrer, Michael J., additional, Noble, Michael, additional, Schnaubelt, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Krotevich, Mikhail, additional, Khan, Munziba, additional, Selvan, Myvizhi Esai, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Potapova, Olga, additional, Grady, Pamela, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Madan, Rashna, additional, Thangudu, Ratna R., additional, Smith, Richard D., additional, Welsh, Robert J., additional, Zelt, Robert, additional, Mehra, Rohit, additional, Matteotti, Ronald, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Chugh, Seema, additional, Smith, Shaleigh, additional, Tsang, Shirley, additional, Cai, Shuang, additional, Boca, Simina M., additional, Carter, Sonya, additional, Gabriel, Stacey, additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Shankar, Sunita, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Bauer, Thomas, additional, Velvulou, Uma, additional, Ozbek, Umut, additional, Petyuk, Vladislav A., additional, Sovenko, Volodymyr, additional, Bocik, William E., additional, Maggio, William W., additional, Chen, Xi, additional, Shi, Yan, additional, Wu, Yige, additional, Hu, Yingwei, additional, Liao, Yuxing, additional, Zhang, Zhen, additional, and Shi, Zhiao, additional

Published
2020
Full Text
View/download PDF

48. Proteogenomic Characterization of Endometrial Carcinoma

Author

Dou, Yongchao, primary, Kawaler, Emily A., additional, Cui Zhou, Daniel, additional, Gritsenko, Marina A., additional, Huang, Chen, additional, Blumenberg, Lili, additional, Karpova, Alla, additional, Petyuk, Vladislav A., additional, Savage, Sara R., additional, Satpathy, Shankha, additional, Liu, Wenke, additional, Wu, Yige, additional, Tsai, Chia-Feng, additional, Wen, Bo, additional, Li, Zhi, additional, Cao, Song, additional, Moon, Jamie, additional, Shi, Zhiao, additional, Cornwell, MacIntosh, additional, Wyczalkowski, Matthew A., additional, Chu, Rosalie K., additional, Vasaikar, Suhas, additional, Zhou, Hua, additional, Gao, Qingsong, additional, Moore, Ronald J., additional, Li, Kai, additional, Sethuraman, Sunantha, additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Heiman, David, additional, Krug, Karsten, additional, Clauser, Karl, additional, Kothadia, Ramani, additional, Maruvka, Yosef, additional, Pico, Alexander R., additional, Oliphant, Amanda E., additional, Hoskins, Emily L., additional, Pugh, Samuel L., additional, Beecroft, Sean J.I., additional, Adams, David W., additional, Jarman, Jonathan C., additional, Kong, Andy, additional, Chang, Hui-Yin, additional, Reva, Boris, additional, Liao, Yuxing, additional, Rykunov, Dmitry, additional, Colaprico, Antonio, additional, Chen, Xi Steven, additional, Czekański, Andrzej, additional, Jędryka, Marcin, additional, Matkowski, Rafał, additional, Wiznerowicz, Maciej, additional, Hiltke, Tara, additional, Boja, Emily, additional, Kinsinger, Christopher R., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Mutch, David, additional, Fuh, Katherine, additional, Ellis, Matthew J., additional, DeLair, Deborah, additional, Thiagarajan, Mathangi, additional, Mani, D.R., additional, Getz, Gad, additional, Noble, Michael, additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Anderson, Matthew L., additional, Levine, Douglas A., additional, Smith, Richard D., additional, Payne, Samuel H., additional, Ruggles, Kelly V., additional, Rodland, Karin D., additional, Ding, Li, additional, Zhang, Bing, additional, Liu, Tao, additional, Fenyö, David, additional, Agarwal, Anupriya, additional, Anurag, Meenakshi, additional, Avtonomov, Dmitry, additional, Birger, Chet, additional, Birrer, Michael J., additional, Boca, Simina M., additional, Bocik, William E., additional, Borate, Uma, additional, Borucki, Melissa, additional, Burke, Meghan C., additional, Cai, Shuang, additional, Calinawan, Anna, additional, Carr, Steven A., additional, Carter, Sonya, additional, Castro, Patricia, additional, Cerda, Sandra, additional, Chaikin, Michelle, additional, Chan, Daniel W., additional, Chan, Doug, additional, Charamut, Alyssa, additional, Chen, Feng, additional, Chen, Jin, additional, Chen, Lijun, additional, Chen, Lin S., additional, Chesla, David, additional, Chheda, Milan G., additional, Chinnaiyan, Arul M., additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Clark, David J., additional, Cottingham, Sandra, additional, Culpepper, Houston, additional, Day, Jacob, additional, De Young, Stephanie, additional, Demir, Emek, additional, Dhanasekaran, Saravana Mohan, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Dottino, Peter, additional, Druker, Brian, additional, Duffy, Elizabeth, additional, Dyer, Maureen, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Elburn, Kim, additional, Field, Jayson B., additional, Francis, Alicia, additional, Gabriel, Stacey, additional, Geffen, Yifat, additional, Geiszler, Daniel, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Grady, Pamela, additional, Hannick, Linda, additional, Hariharan, Pushpa, additional, Hilsenbeck, Sue, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hsieh, James J., additional, Hu, Yingwei, additional, Ittmann, Michael M., additional, Jaehnig, Eric, additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jones, Corbin D., additional, Karabon, Renee, additional, Ketchum, Karen A., additional, Khan, Munziba, additional, Kim, Beom-Jun, additional, Krek, Azra, additional, Krubit, Tanya, additional, Kumar-Sinha, Chandan, additional, Leprevost, Felipe D., additional, Lewis, Michael, additional, Li, Qing Kay, additional, Li, Yize, additional, Liu, Hongwei, additional, Lubinski, Jan, additional, Ma, Weiping, additional, Madan, Rashna, additional, Malc, Ewa, additional, Malovannaya, Anna, additional, Mareedu, Sailaja, additional, Markey, Sanford P., additional, Marrero-Oliveras, Annette, additional, Martignetti, John, additional, McDermott, Jason, additional, McGarvey, Peter B., additional, McGee, John, additional, Mieczkowski, Piotr, additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Newton, Chelsea J., additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Petralia, Francesca, additional, Piehowski, Paul, additional, Polonskaya, Larisa, additional, Qi, Liqun, additional, Richey, Shannon, additional, Robinson, Karna, additional, Roche, Nancy, additional, Rohrer, Daniel C., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Shi, Yan, additional, Skelly, Tara, additional, Sokoll, Lori J., additional, Song, Xiaoyu, additional, Stein, Stephen E., additional, Suh, James, additional, Tan, Donghui, additional, Tansil, Darlene, additional, Teo, Guo Ci, additional, Thangudu, Ratna R., additional, Tognon, Cristina, additional, Traer, Elie, additional, Tyner, Jeffrey, additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vatanian, Negin, additional, Vats, Pankaj, additional, Velvulou, Uma, additional, Vernon, Michael, additional, Wang, Liang-Bo, additional, Wang, Ying, additional, Webster, Alex, additional, Westbrook, Thomas, additional, Wheeler, David, additional, Whiteaker, Jeffrey R., additional, Wilson, George D., additional, Zakhartsev, Yuriy, additional, Zelt, Robert, additional, Zhang, Hui, additional, Zhang, Yuping, additional, Zhang, Zhen, additional, and Zhao, Grace, additional

Published
2020
Full Text
View/download PDF

49. Comprehensive proteogenomic characterization of rare kidney tumors

Author

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, Nesvizhskii, Alexey I., 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., 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, and Zhang, Zhen

Abstract

Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.

Published
2024
Full Text
View/download PDF

50. Assessment of Clinical Benefit of Integrative Genomic Profiling in Advanced Solid Tumors

Author

Cobain, Erin F., Wu, Yi-Mi, Vats, Pankaj, Chugh, Rashmi, Worden, Francis, Smith, David C., Schuetze, Scott M., Zalupski, Mark M., Sahai, Vaibhav, Alva, Ajjai, Schott, Anne F., Caram, Megan E. V., Hayes, Daniel F., Stoffel, Elena M., Jacobs, Michelle F., Kumar-Sinha, Chandan, Cao, Xuhong, Wang, Rui, Lucas, David, Ning, Yu, Rabban, Erica, Bell, Janice, Camelo-Piragua, Sandra, Udager, Aaron M., Cieslik, Marcin, Lonigro, Robert J., Kunju, Lakshmi P., Robinson, Dan R., Talpaz, Moshe, and Chinnaiyan, Arul M.

Abstract

IMPORTANCE: Use of next-generation sequencing (NGS) to identify clinically actionable genomic targets has been incorporated into routine clinical practice in the management of advanced solid tumors; however, the clinical utility of this testing remains uncertain. OBJECTIVE: To determine which patients derived the greatest degree of clinical benefit from NGS profiling. DESIGN, SETTING, AND PARTICIPANTS: Patients in this cohort study underwent fresh tumor biopsy and blood sample collection for genomic profiling of paired tumor and normal DNA (whole-exome or targeted-exome capture with analysis of 1700 genes) and tumor transcriptome (RNA) sequencing. Somatic and germline genomic alterations were annotated and classified according to degree of clinical actionability. Results were returned to treating oncologists. Data were collected from May 1, 2011, to February 28, 2018, and analyzed from May 1, 2011, to April 30, 2020. MAIN OUTCOMES AND MEASURES: Patients’ subsequent therapy and treatment response were extracted from the medical record to determine clinical benefit rate from NGS-directed therapy at 6 months and exceptional responses lasting 12 months or longer. RESULTS: During the study period, NGS was attempted on tumors from 1138 patients and was successful in 1015 (89.2%) (MET1000 cohort) (538 men [53.0%]; mean [SD] age, 57.7 [13.3] years). Potentially clinically actionable genomic alterations were discovered in 817 patients (80.5%). Of these, 132 patients (16.2%) received sequencing-directed therapy, and 49 had clinical benefit (37.1%). Exceptional responses were observed in 26 patients (19.7% of treated patients). Pathogenic germline variants (PGVs) were identified in 160 patients (15.8% of cohort), including 49 PGVs (4.8% of cohort) with therapeutic relevance. For 55 patients with carcinoma of unknown primary origin, NGS identified the primary site in 28 (50.9%), and sequencing-directed therapy in 13 patients resulted in clinical benefit in 7 instances (53.8%), including 5 exceptional responses. CONCLUSIONS AND RELEVANCE: The high rate of therapeutically relevant PGVs identified across diverse cancer types supports a recommendation for directed germline testing in all patients with advanced cancer. The high frequency of therapeutically relevant somatic and germline findings in patients with carcinoma of unknown primary origin and other rare cancers supports the use of comprehensive NGS profiling as a component of standard of care for these disease entities.

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results