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810 results on '"Nesvizhskii, Alexey I."'

4. Author Correction: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

Author

Xiao, Lanbo, Parolia, Abhijit, Qiao, Yuanyuan, Bawa, Pushpinder, Eyunni, Sanjana, Mannan, Rahul, Carson, Sandra E., Chang, Yu, Wang, Xiaoju, Zhang, Yuping, Vo, Josh N., Kregel, Steven, Simko, Stephanie A., Delekta, Andrew D., Jaber, Mustapha, Zheng, Heng, Apel, Ingrid J., McMurry, Lisa, Su, Fengyun, Wang, Rui, Zelenka-Wang, Sylvia, Sasmal, Sanjita, Khare, Leena, Mukherjee, Subhendu, Abbineni, Chandrasekhar, Aithal, Kiran, Bhakta, Mital S., Ghurye, Jay, Cao, Xuhong, Navone, Nora M., Nesvizhskii, Alexey I., Mehra, Rohit, Vaishampayan, Ulka, Blanchette, Marco, Wang, Yuzhuo, Samajdar, Susanta, Ramachandra, Murali, and Chinnaiyan, Arul M.

Published
2024
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7. 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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12. SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines

Author

Desai, Heta S, Yan, Tianyang, Yu, Fengchao, Sun, Alexander W, Villanueva, Miranda, Nesvizhskii, Alexey I, and Backus, Keriann M

Subjects
Analytical Chemistry, Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Cysteine, Mass Spectrometry, Oxidation-Reduction, Proteome, Proteomics, Biochemistry & Molecular Biology
Abstract

Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation.

Published
2022

13. Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation

Author

Yan, Tianyang, Palmer, Andrew B, Geiszler, Daniel J, Polasky, Daniel A, Boatner, Lisa M, Burton, Nikolas R, Armenta, Ernest, Nesvizhskii, Alexey I, and Backus, Keriann M

Subjects
Alkynes, Azides, Catalysis, Click Chemistry, Copper, Cycloaddition Reaction, Cysteine, Humans, Tandem Mass Spectrometry, Analytical Chemistry, Other Chemical Sciences
Abstract

Mass spectrometry-based chemoproteomics has enabled functional analysis and small molecule screening at thousands of cysteine residues in parallel. Widely adopted chemoproteomic sample preparation workflows rely on the use of pan cysteine-reactive probes such as iodoacetamide alkyne combined with biotinylation via copper-catalyzed azide-alkyne cycloaddition (CuAAC) or "click chemistry" for cysteine capture. Despite considerable advances in both sample preparation and analytical platforms, current techniques only sample a small fraction of all cysteines encoded in the human proteome. Extending the recently introduced labile mode of the MSFragger search engine, here we report an in-depth analysis of cysteine biotinylation via click chemistry (CBCC) reagent gas-phase fragmentation during MS/MS analysis. We find that CBCC conjugates produce both known and novel diagnostic fragments and peptide remainder ions. Among these species, we identified a candidate signature ion for CBCC peptides, the cyclic oxonium-biotin fragment ion that is generated upon fragmentation of the N(triazole)-C(alkyl) bond. Guided by our empirical comparison of fragmentation patterns of six CBCC reagent combinations, we achieved enhanced coverage of cysteine-labeled peptides. Implementation of labile searches afforded unique PSMs and provides a roadmap for the utility of such searches in enhancing chemoproteomic peptide coverage.

Published
2022

14. Integrated proteogenomic characterization of glioblastoma evolution

Author

Kim, Kyung-Hee, Migliozzi, Simona, Koo, Harim, Hong, Jun-Hee, Park, Seung Min, Kim, Sooheon, Kwon, Hyung Joon, Ha, Seokjun, Garofano, Luciano, Oh, Young Taek, D'Angelo, Fulvio, Kim, Chan Il, Kim, Seongsoo, Lee, Ji Yoon, Kim, Jiwon, Hong, Jisoo, Jang, Eun-Hae, Mathon, Bertrand, Di Stefano, Anna-Luisa, Bielle, Franck, Laurenge, Alice, Nesvizhskii, Alexey I., Hur, Eun-Mi, Yin, Jinlong, Shi, Bingyang, Kim, Youngwook, Moon, Kyung-Sub, Kwon, Jeong Taik, Lee, Shin Heon, Lee, Seung Hoon, Gwak, Ho Shin, Lasorella, Anna, Yoo, Heon, Sanson, Marc, Sa, Jason K., Park, Chul-Kee, Nam, Do-Hyun, Iavarone, Antonio, and Park, Jong Bae

Published
2024
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15. 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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16. Multiomic characterization of pancreatic cancer-associated macrophage polarization reveals deregulated metabolic programs driven by the GM-CSF–PI3K pathway

Author

Boyer, Seth, Lee, Ho-Joon, Steele, Nina, Zhang, Li, Sajjakulnukit, Peter, Andren, Anthony, Ward, Matthew H, Singh, Rima, Basrur, Venkatesha, Zhang, Yaqing, Nesvizhskii, Alexey I, di Magliano, Marina Pasca, Halbrook, Christopher J, and Lyssiotis, Costas A

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Immunology, Medical Biochemistry and Metabolomics, Oncology and Carcinogenesis, Digestive Diseases, Cancer, Biotechnology, Pancreatic Cancer, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Animals, Cell Line, Tumor, Cell Transformation, Neoplastic, Gene Expression Profiling, Granulocyte-Macrophage Colony-Stimulating Factor, Humans, Metabolic Networks and Pathways, Metabolomics, Mice, Mice, Inbred C57BL, Pancreatic Neoplasms, Proteomics, Signal Transduction, Transcription Factors, Tumor-Associated Macrophages, pancreatic cancer, tumor-associated macrophages, metabolomics, proteomics, Human, Mouse, cancer biology, human, immunology, inflammation, mouse, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The pancreatic ductal adenocarcinoma microenvironment is composed of a variety of cell types and marked by extensive fibrosis and inflammation. Tumor-associated macrophages (TAMs) are abundant, and they are important mediators of disease progression and invasion. TAMs are polarized in situ to a tumor promoting and immunosuppressive phenotype via cytokine signaling and metabolic crosstalk from malignant epithelial cells and other components of the tumor microenvironment. However, the specific distinguishing features and functions of TAMs remain poorly defined. Here, we generated tumor-educated macrophages (TEMs) in vitro and performed detailed, multiomic characterization (i.e., transcriptomics, proteomics, metabolomics). Our results reveal unique genetic and metabolic signatures of TEMs, the veracity of which were queried against our in-house single-cell RNA sequencing dataset of human pancreatic tumors. This analysis identified expression of novel, metabolic TEM markers in human pancreatic TAMs, including ARG1, ACLY, and TXNIP. We then utilized our TEM model system to study the role of mutant Kras signaling in cancer cells on TEM polarization. This revealed an important role for granulocyte-macrophage colony-stimulating factor (GM-CSF) and lactate on TEM polarization, molecules released from cancer cells in a mutant Kras-dependent manner. Lastly, we demonstrate that GM-CSF dysregulates TEM gene expression and metabolism through PI3K-AKT pathway signaling. Collectively, our results define new markers and programs to classify pancreatic TAMs, how these are engaged by cancer cells, and the precise signaling pathways mediating polarization.

Published
2022

18. 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
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19. 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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20. 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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21. 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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22. 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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23. 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, 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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24. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

Author

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

Published
2023
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26. LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes

Author

Li, Jin, primary, Zhu, Jie, additional, Deng, Yamei, additional, Reck, Emma C., additional, Walker, Emily M., additional, Sidarala, Vaibhav, additional, Hubers, Dre L., additional, Pasmooij, Mabelle B., additional, Shin, Chun-Shik, additional, Bandesh, Khushdeep, additional, Motakis, Eftyhmios, additional, Nargund, Siddhi, additional, Kursawe, Romy, additional, Basrur, Venkatesha, additional, Nesvizhskii, Alexey I., additional, Stitzel, Michael L., additional, Chan, David C., additional, and Soleimanpour, Scott A., additional

Published
2024
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27. Tumor‐Selective Altered Glycosylation and Functional Attenuation of CD73 in Human Hepatocellular Carcinoma

Author

Alcedo, Karel P, Guerrero, Andres, Basrur, Venkatesha, Fu, Dong, Richardson, Monea L, McLane, Joshua S, Tsou, Chih‐Chiang, Nesvizhskii, Alexey I, Welling, Theodore H, Lebrilla, Carlito B, Otey, Carol A, Kim, Hong Jin, Omary, M Bishr, and Snider, Natasha T

Subjects
Cancer, Liver Disease, Liver Cancer, Biotechnology, Digestive Diseases, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology
Abstract

CD73, a cell-surface N-linked glycoprotein that produces extracellular adenosine, is a novel target for cancer immunotherapy. Although anti-CD73 antibodies have entered clinical development, CD73 has both protumor and antitumor functions, depending on the target cell and tumor type. The aim of this study was to characterize CD73 regulation in human hepatocellular carcinoma (HCC). We examined CD73 expression, localization, and activity using molecular, biochemical, and cellular analyses on primary HCC surgical specimens, coupled with mechanistic studies in HCC cells. We analyzed CD73 glycan signatures and global alterations in transcripts encoding other N-linked glycoproteins by using mass spectrometry glycomics and RNA sequencing (RNAseq), respectively. CD73 was expressed on tumor hepatocytes where it exhibited abnormal N-linked glycosylation, independent of HCC etiology, tumor stage, or fibrosis presence. Aberrant glycosylation of tumor-associated CD73 resulted in a 3-fold decrease in 5'-nucleotidase activity (P

Published
2019

30. Glycoproteomics

Author

Bagdonaite, Ieva, Malaker, Stacy A., Polasky, Daniel A., Riley, Nicholas M., Schjoldager, Katrine, Vakhrushev, Sergey Y., Halim, Adnan, Aoki-Kinoshita, Kiyoko F., Nesvizhskii, Alexey I., Bertozzi, Carolyn R., Wandall, Hans H., Parker, Benjamin L., Thaysen-Andersen, Morten, and Scott, Nichollas E.

Published
2022
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32. Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

Author

Xiao, Lanbo, Parolia, Abhijit, Qiao, Yuanyuan, Bawa, Pushpinder, Eyunni, Sanjana, Mannan, Rahul, Carson, Sandra E., Chang, Yu, Wang, Xiaoju, Zhang, Yuping, Vo, Josh N., Kregel, Steven, Simko, Stephanie A., Delekta, Andrew D., Jaber, Mustapha, Zheng, Heng, Apel, Ingrid J., McMurry, Lisa, Su, Fengyun, Wang, Rui, Zelenka-Wang, Sylvia, Sasmal, Sanjita, Khare, Leena, Mukherjee, Subhendu, Abbineni, Chandrasekhar, Aithal, Kiran, Bhakta, Mital S., Ghurye, Jay, Cao, Xuhong, Navone, Nora M., Nesvizhskii, Alexey I., Mehra, Rohit, Vaishampayan, Ulka, Blanchette, Marco, Wang, Yuzhuo, Samajdar, Susanta, Ramachandra, Murali, and Chinnaiyan, Arul M.

Published
2022
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33. HSC70 is a chaperone for wild-type and mutant cardiac myosin binding protein C

Author

Glazier, Amelia A, Hafeez, Neha, Mellacheruvu, Dattatreya, Basrur, Venkatesha, Nesvizhskii, Alexey I, Lee, Lap Man, Shao, Hao, Tang, Vi, Yob, Jaime M, Gestwicki, Jason E, Helms, Adam S, and Day, Sharlene M

Subjects
Heart Disease, Cardiovascular, Genetics, 2.1 Biological and endogenous factors, Aetiology, Acetylcysteine, Animals, Animals, Newborn, Cardiomyopathy, Hypertrophic, Carrier Proteins, Cell Nucleus, Gene Knockdown Techniques, HEK293 Cells, HSC70 Heat-Shock Proteins, Haploinsufficiency, Humans, Myocardium, Proteasome Endopeptidase Complex, Proteasome Inhibitors, Proteolysis, Proteostasis, Rats, Sarcomeres, Ventricular Septum, Cardiology, Cardiovascular disease, Chaperones, Muscle Biology, Protein misfolding
Abstract

Cardiac myosin binding protein C (MYBPC3) is the most commonly mutated gene associated with hypertrophic cardiomyopathy (HCM). Haploinsufficiency of full-length MYBPC3 and disruption of proteostasis have both been proposed as central to HCM disease pathogenesis. Discriminating the relative contributions of these 2 mechanisms requires fundamental knowledge of how turnover of WT and mutant MYBPC3 proteins is regulated. We expressed several disease-causing mutations in MYBPC3 in primary neonatal rat ventricular cardiomyocytes. In contrast to WT MYBPC3, mutant proteins showed reduced expression and failed to localize to the sarcomere. In an unbiased coimmunoprecipitation/mass spectrometry screen, we identified HSP70-family chaperones as interactors of both WT and mutant MYBPC3. Heat shock cognate 70 kDa (HSC70) was the most abundant chaperone interactor. Knockdown of HSC70 significantly slowed degradation of both WT and mutant MYBPC3, while pharmacologic activation of HSC70 and HSP70 accelerated degradation. HSC70 was expressed in discrete striations in the sarcomere. Expression of mutant MYBPC3 did not affect HSC70 localization, nor did it induce a protein folding stress response or ubiquitin proteasome dysfunction. Together these data suggest that WT and mutant MYBPC3 proteins are clients for HSC70, and that the HSC70 chaperone system plays a major role in regulating MYBPC3 protein turnover.

Published
2018

34. Nuclear lamina genetic variants, including a truncated LAP2, in twins and siblings with nonalcoholic fatty liver disease

Author

Brady, Graham F, Kwan, Raymond, Ulintz, Peter J, Nguyen, Phirum, Bassirian, Shirin, Basrur, Venkatesha, Nesvizhskii, Alexey I, Loomba, Rohit, and Omary, M Bishr

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Immunology, Chronic Liver Disease and Cirrhosis, Rare Diseases, Genetics, Digestive Diseases, Liver Disease, 2.1 Biological and endogenous factors, Aetiology, Adult, DNA-Binding Proteins, Female, Fluorescent Antibody Technique, Genetic Predisposition to Disease, Genetic Variation, Genotyping Techniques, Heterozygote, High-Throughput Nucleotide Sequencing, Humans, Immunoblotting, Immunoprecipitation, Liver, Male, Membrane Proteins, Middle Aged, Mutation, Non-alcoholic Fatty Liver Disease, Nuclear Lamina, Prospective Studies, Siblings, Tandem Mass Spectrometry, Twins, Medical Biochemistry and Metabolomics, Gastroenterology & Hepatology, Clinical sciences
Abstract

Nonalcoholic fatty liver disease (NAFLD) is becoming the major chronic liver disease in many countries. Its pathogenesis is multifactorial, but twin and familial studies indicate significant heritability, which is not fully explained by currently known genetic susceptibility loci. Notably, mutations in genes encoding nuclear lamina proteins, including lamins, cause lipodystrophy syndromes that include NAFLD. We hypothesized that variants in lamina-associated proteins predispose to NAFLD and used a candidate gene-sequencing approach to test for variants in 10 nuclear lamina-related genes in a cohort of 37 twin and sibling pairs: 21 individuals with and 53 without NAFLD. Twelve heterozygous sequence variants were identified in four lamina-related genes (ZMPSTE24, TMPO, SREBF1, SREBF2). The majority of NAFLD patients (>90%) had at least one variant compared to 80% versus

Published
2018

35. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows

Author

Kwon, Yumi, primary, Woo, Jongmin, additional, Yu, Fengchao, additional, Williams, Sarah M., additional, Markillie, Lye Meng, additional, Moore, Ronald J., additional, Nakayasu, Ernesto S., additional, Chen, Jing, additional, Campbell-Thompson, Martha, additional, Mathews, Clayton E., additional, Nesvizhskii, Alexey I., additional, Qian, Wei-Jun, additional, and Zhu, Ying, additional

Published
2024
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36. Pan-cancer proteogenomics characterization of tumor immunity

Author

Petralia, Francesca, primary, Ma, Weiping, additional, Yaron, Tomer M., additional, Caruso, Francesca Pia, additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Charytonowicz, Daniel, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Marino, Giacomo B., additional, Calinawan, Anna, additional, Evangelista, John Erol, additional, Selvan, Myvizhi Esai, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Song, Xiaoyu, additional, Turhan, Berk, additional, Christianson, Karen E., additional, Lewis, David A., additional, Deng, Eden Z., additional, Clarke, Daniel J.B., additional, Whiteaker, Jeffrey R., additional, Kennedy, Jacob J., additional, Zhao, Lei, additional, Segura, Rossana Lazcano, additional, Batra, Harsh, additional, Raso, Maria Gabriela, additional, Parra, Edwin Roger, additional, Soundararajan, Rama, additional, Tang, Ximing, additional, Li, Yize, additional, Yi, Xinpei, additional, Satpathy, Shankha, additional, Wang, Ying, additional, Wiznerowicz, Maciej, additional, González-Robles, Tania J., additional, Iavarone, Antonio, additional, Gosline, Sara J.C., additional, Reva, Boris, additional, Robles, Ana I., additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Gillette, Michael A., additional, Klein, Robert J., additional, Cieslik, Marcin, additional, Zhang, Bing, additional, Paulovich, Amanda G., additional, Sebra, Robert, additional, Gümüş, Zeynep H., additional, Hostetter, Galen, additional, Fenyö, David, additional, Omenn, Gilbert S., additional, Cantley, Lewis C., additional, Ma'ayan, Avi, additional, Lazar, Alexander J., additional, Ceccarelli, Michele, additional, Wang, Pei, additional, Abelin, Jennifer, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cao, Song, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Heiman, David I., additional, Hong, Runyu, additional, Hu, Yingwei, additional, Huang, Chen, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, 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, Liu, Wenke, additional, McDermott, Jason, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Mumphrey, Michael Brodie, additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Payne, Samuel H., additional, Pugliese, Pietro, additional, Rodland, Karin D., additional, Rodrigues, Fernanda Martins, additional, Ruggles, Kelly V., additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Feng, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Li, Qing Kay, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2024
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37. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

Author

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

Published
2024
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38. High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response.

Author

Mi, Yuxin, Burnham, Katie L., Charles, Philip D., Heilig, Raphael, Vendrell, Iolanda, Whalley, Justin, Torrance, Hew D., Antcliffe, David B., May, Shaun M., Neville, Matt J., Berridge, Georgina, Hutton, Paula, Geoghegan, Cyndi G., Radhakrishnan, Jayachandran, Nesvizhskii, Alexey I., Yu, Fengchao, Davenport, Emma E., McKechnie, Stuart, Davies, Roger, and O'Callaghan, David J. P.

Subjects
SEPSIS, MASS spectrometry, INDUCTIVELY coupled plasma mass spectrometry, LIQUID chromatography-mass spectrometry, TANDEM mass spectrometry
Abstract

Sepsis, the dysregulated host response to infection causing life-threatening organ dysfunction, is a global health challenge requiring better understanding of pathophysiology and new therapeutic approaches. Here, we applied high-throughput tandem mass spectrometry to delineate the plasma proteome for sepsis and comparator groups (noninfected critical illness, postoperative inflammation, and healthy volunteers) involving 2612 samples (from 1611 patients) and 4553 liquid chromatography–mass spectrometry analyses acquired through a single batch of continuous measurements, with a throughput of 100 samples per day. We show how this scale of data can delineate proteins, pathways, and coexpression modules in sepsis and be integrated with paired leukocyte transcriptomic data (837 samples from n = 649 patients). We mapped the plasma proteomic landscape of the host response in sepsis, including changes over time, and identified features relating to etiology, clinical phenotypes (including organ failures), and severity. This work reveals subphenotypes informative for sepsis response state, disease processes, and outcome; identifies potential biomarkers; and advances opportunities for a precision medicine approach to sepsis. Editor's summary: Sepsis is caused by an extreme immune response to infection and can damage organs and potentially lead to death. To better understand what happens to the body during sepsis, Mi et al. comprehensively profiled the plasma proteomes of ICU patients with sepsis. The longitudinal nature of their sampling allowed the authors to assess changes in the plasma proteome over time and to assess heterogeneity in patient responses. The group also profiled relevant comparator groups, including noninfected ICU patients, individuals with postoperative inflammation, and healthy individuals, allowing for the detection of sepsis-specific responses. This study offers insights into sepsis biology and a valuable resource for further research. —Catherine Charneski [ABSTRACT FROM AUTHOR]

Published
2024
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42. FIT: Tag based method for fusion proteins identification

Author

Ning, Kang and Nesvizhskii, Alexey I.

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Genomics
Abstract

There is increased interest in the identification and analysis of gene fusions and chimeric RNA transcripts. While most recent efforts focused on the analysis of genomic and transcriptomic data, identi-fication of novel peptides corresponding to such events in mass spectrometry-based proteomic datasets would provide complemen-tary, protein-level evidence. The process of identifying fusion pro-teins from mass spectrometry data is inherently difficult because such events are rare. It is also complicated due to large amount of spectra collected and the explosion in the number of candidate peptide sequences that need to be considered, which makes ex-haustive search for all possible fusion partner proteins impractical. In this work, we present a sequence tag based fusion protein identi-fication algorithm, FIT, that combines the virtue of both de novo sequence tag retrieval and peptide-spectrum matching for identifi-cation of fusion proteins. Results on simulated datasets show high sensitivity and low false positive rates for fusion protein identifica-tion by the FIT algorithm.

Published
2014

43. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation

Author

Hoang, Song My, Kaminski, Nicole, Bhargava, Ragini, Barroso-González, Jonathan, Lynskey, Michelle L., García-Expósito, Laura, Roncaioli, Justin L., Wondisford, Anne R., Wallace, Callen T., Watkins, Simon C., James, Dominic I., Waddell, Ian D., Ogilvie, Donald, Smith, Kate M., da Veiga Leprevost, Felipe, Mellacharevu, Dattatreya, Nesvizhskii, Alexey I., Li, Jianfeng, Ray-Gallet, Dominique, Sobol, Robert W., Almouzni, Genevieve, and O’Sullivan, Roderick J.

Published
2020
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49. Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Author

Müller, Maik, Gräbnitz, Fabienne, Barandun, Niculò, Shen, Yang, Wendt, Fabian, Steiner, Sebastian N., Severin, Yannik, Vetterli, Stefan U., Mondal, Milon, Prudent, James R., Hofmann, Raphael, van Oostrum, Marc, Sarott, Roman C., Nesvizhskii, Alexey I., Carreira, Erick M., Bode, Jeffrey W., Snijder, Berend, Robinson, John A., Loessner, Martin J., Oxenius, Annette, and Wollscheid, Bernd

Published
2021
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50. MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

Author

Choi, Meena, Carver, Jeremy, Chiva, Cristina, Tzouros, Manuel, Huang, Ting, Tsai, Tsung-Heng, Pullman, Benjamin, Bernhardt, Oliver M., Hüttenhain, Ruth, Teo, Guo Ci, Perez-Riverol, Yasset, Muntel, Jan, Müller, Maik, Goetze, Sandra, Pavlou, Maria, Verschueren, Erik, Wollscheid, Bernd, Nesvizhskii, Alexey I., Reiter, Lukas, Dunkley, Tom, Sabidó, Eduard, Bandeira, Nuno, and Vitek, Olga

Published
2020
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