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1. 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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2. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Author

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

Published
2023
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3. Abstract 3127: Comprehensive proteogenomic characterization of rare kidney tumors

Author

Li, Ginny Xiaohe, primary, Hsiao, Yi, additional, Chen, Lijun, additional, Mannan, Rahul, additional, Zhang, Yuping, additional, Petralia, Francesca, additional, Cho, Hanbyul, additional, Hosseini, Noshad, additional, Calinawan, Anna, additional, Li, Yize, additional, Anand, Shankara, additional, Dagar, Aniket, additional, Geffen, Yifat, additional, Leprevost, Felipe V., additional, Le, Anne, additional, Ponce, Sean, additional, Schnaubelt, Michael, additional, Deen, Nataly Naser Al, additional, Caravan, Wagma, additional, Houston, Andrew, additional, Kumar-Sinha, Chandan, additional, Wang, Xiaoming, additional, Chugh, Seema, additional, Omenn, Gilbert S., additional, Chan, Daniel W., additional, Ricketts, Christopher, additional, Mehra, Rohit, additional, Chinnaiyan, Arul, additional, Ding, Li, additional, Cieslik, Marcin, additional, Zhang, Hui, additional, Dhanasekaran, Saravana M., additional, and Nesvizhskii, Alexey I., additional

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

Author

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

Published
2023
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6. Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms

Author

Mannan, Rahul, primary, Wang, Xiaoming, additional, Bawa, Pushpinder S., additional, Zhang, Yuping, additional, Skala, Stephanie L., additional, Chinnaiyan, Anya K., additional, Dagar, Aniket, additional, Wang, Lisha, additional, Zelenka-Wang, Sylvia B., additional, McMurry, Lisa M., additional, Daniel, Nikita, additional, Cao, Xuhong, additional, Sangoi, Ankur R., additional, Gupta, Sounak, additional, Vaishampayan, Ulka N., additional, Hafez, Khaled S., additional, Morgan, Todd M., additional, Spratt, Daniel E., additional, Tretiakova, Maria S., additional, Argani, Pedram, additional, Chinnaiyan, Arul M., additional, Dhanasekaran, Saravana M., additional, and Mehra, Rohit, additional

Published
2022
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7. Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms.

Author

Mannan, Rahul, Wang, Xiaoming, Bawa, Pushpinder S., Zhang, Yuping, Skala, Stephanie L., Chinnaiyan, Anya K., Dagar, Aniket, Wang, Lisha, Zelenka-Wang, Sylvia B., McMurry, Lisa M., Daniel, Nikita, Cao, Xuhong, Sangoi, Ankur R., Gupta, Sounak, Vaishampayan, Ulka N., Hafez, Khaled S., Morgan, Todd M., Spratt, Daniel E., Tretiakova, Maria S., and Argani, Pedram

Subjects
RENAL cell carcinoma, KIDNEY tumors, NUCLEIC acid hybridization, GENE expression, IN situ hybridization, MOLECULAR pathology
Abstract

Introduction. Chromophobe renal cell carcinoma (chromophobe RCC) is the third major subcategory of renal tumors after clear cell RCC and papillary RCC, accounting for approximately 5% of all RCC subtypes. Other oncocytic neoplasms seen commonly in surgical pathology practice include the eosinophilic variant of chromophobe RCC, renal oncocytoma, and low-grade oncocytic unclassified RCC. Methods. In our recent next-generation sequencing based study, we nominated a lineage-specific novel biomarker LINC01187 (long intergenic non-protein coding RNA 1187) which was found to be enriched in chromophobe RCC. Like KIT (cluster of differentiation 117; CD117), a clinically utilized chromophobe RCC related biomarker, LINC01187 is expressed in intercalated cells of the nephron. In this follow-up study, we performed KIT immunohistochemistry and LINC01187 RNA in situ hybridization (RNA-ISH) on a cohort of chromophobe RCC and other renal neoplasms, characterized the expression patterns, and quantified the expression signals of the two biomarkers in both primary and metastatic settings. Results. LINC01187, in comparison to KIT, exhibits stronger and more uniform expression within tumors while maintaining temporal and spatial consistency. LINC01187 also is devoid of intra-tumoral heterogeneous expression pattern, a phenomenon commonly noted with KIT. Conclusions. LINC01187 expression can augment the currently utilized KIT assay and help facilitate easy microscopic analyses in routine surgical pathology practice. [ABSTRACT FROM AUTHOR]

Published
2023
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8. sj-docx-8-ijs-10.1177_10668969221125793 - Supplemental material for Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms

Author

Mannan, Rahul, Wang, Xiaoming, Bawa, Pushpinder S., Zhang, Yuping, Skala, Stephanie L., Chinnaiyan, Anya K., Dagar, Aniket, Wang, Lisha, Zelenka-Wang, Sylvia B., McMurry, Lisa M., Daniel, Nikita, Cao, Xuhong, Sangoi, Ankur R., Gupta, Sounak, Vaishampayan, Ulka N., Hafez, Khaled S., Morgan, Todd M., Spratt, Daniel E., Tretiakova, Maria S., Argani, Pedram, Chinnaiyan, Arul M., Dhanasekaran, Saravana M., and Mehra, Rohit

Subjects
FOS: Clinical medicine, 110323 Surgery, 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
Abstract

Supplemental material, sj-docx-8-ijs-10.1177_10668969221125793 for Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms by Rahul Mannan, Xiaoming Wang, Pushpinder S. Bawa, Yuping Zhang, Stephanie L. Skala, Anya K. Chinnaiyan, Aniket Dagar, Lisha Wang, Sylvia B. Zelenka-Wang, Lisa M. McMurry, Nikita Daniel, Xuhong Cao, Ankur R. Sangoi, Sounak Gupta, Ulka N. Vaishampayan, Khaled S. Hafez, Todd M. Morgan, Daniel E. Spratt, Maria S. Tretiakova, Pedram Argani, Arul M. Chinnaiyan, Saravana M. Dhanasekaran and Rohit Mehra in International Journal of Surgical Pathology

Published
2022
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10. 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
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