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1. 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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2. A tissue injury sensing and repair pathway distinct from host pathogen defense

Author

Liu, Siqi, Hur, Yun Ha, Cai, Xin, Cong, Qian, Yang, Yihao, Xu, Chiwei, Bilate, Angelina M., Gonzales, Kevin Andrew Uy, Parigi, S. Martina, Cowley, Christopher J., Hurwitz, Brian, Luo, Ji-Dung, Tseng, Tiffany, Gur-Cohen, Shiri, Sribour, Megan, Omelchenko, Tatiana, Levorse, John, Pasolli, Hilda Amalia, Thompson, Craig B., Mucida, Daniel, and Fuchs, Elaine

Published
2023
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4. Optimization of Technical Information Protection System’s Composition

Author

Nikishova, Arina, Umnitsyn, Yuriy, Umnitsyn, Mikhail, Omelchenko, Tatiana, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Yuan, Junsong, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Kravets, Alla G., editor, Groumpos, Peter P., editor, Shcherbakov, Maxim, editor, and Kultsova, Marina, editor

Published
2019
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5. Cryptographic Protection of Data Transmission Channel

Author

Nikishova, Arina, Vitenburg, Ekaterina, Umnitsyn, Mikhail, Omelchenko, Tatiana, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Yuan, Junsong, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Kravets, Alla G., editor, Groumpos, Peter P., editor, Shcherbakov, Maxim, editor, and Kultsova, Marina, editor

Published
2019
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6. 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
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8. Supplementary Data from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion

Author

Deborde, Sylvie, primary, Gusain, Laxmi, primary, Powers, Ann, primary, Marcadis, Andrea, primary, Yu, Yasong, primary, Chen, Chun-Hao, primary, Frants, Anna, primary, Kao, Elizabeth, primary, Tang, Laura H., primary, Vakiani, Efsevia, primary, Amisaki, Masataka, primary, Balachandran, Vinod P., primary, Calo, Annalisa, primary, Omelchenko, Tatiana, primary, Jessen, Kristjan R., primary, Reva, Boris, primary, and Wong, Richard J., primary

Published
2023
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9. Supplementary Video from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion

Author

Deborde, Sylvie, primary, Gusain, Laxmi, primary, Powers, Ann, primary, Marcadis, Andrea, primary, Yu, Yasong, primary, Chen, Chun-Hao, primary, Frants, Anna, primary, Kao, Elizabeth, primary, Tang, Laura H., primary, Vakiani, Efsevia, primary, Amisaki, Masataka, primary, Balachandran, Vinod P., primary, Calo, Annalisa, primary, Omelchenko, Tatiana, primary, Jessen, Kristjan R., primary, Reva, Boris, primary, and Wong, Richard J., primary

Published
2023
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10. Data from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion

Author

Deborde, Sylvie, primary, Gusain, Laxmi, primary, Powers, Ann, primary, Marcadis, Andrea, primary, Yu, Yasong, primary, Chen, Chun-Hao, primary, Frants, Anna, primary, Kao, Elizabeth, primary, Tang, Laura H., primary, Vakiani, Efsevia, primary, Amisaki, Masataka, primary, Balachandran, Vinod P., primary, Calo, Annalisa, primary, Omelchenko, Tatiana, primary, Jessen, Kristjan R., primary, Reva, Boris, primary, and Wong, Richard J., primary

Published
2023
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11. Supplementary Figure from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion

Author

Deborde, Sylvie, primary, Gusain, Laxmi, primary, Powers, Ann, primary, Marcadis, Andrea, primary, Yu, Yasong, primary, Chen, Chun-Hao, primary, Frants, Anna, primary, Kao, Elizabeth, primary, Tang, Laura H., primary, Vakiani, Efsevia, primary, Amisaki, Masataka, primary, Balachandran, Vinod P., primary, Calo, Annalisa, primary, Omelchenko, Tatiana, primary, Jessen, Kristjan R., primary, Reva, Boris, primary, and Wong, Richard J., primary

Published
2023
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16. The most likely but largely ignored triggering factor for breast (or all) cancer invasion

Author

Man, Yan-gao, primary, Mannion, Ciaran, additional, Stojadinovic, Alexander, additional, Peoples, George E, additional, Cho, William CS, additional, Fu, Sidney W., additional, Tan, Xiaohui, additional, Hsiao, Yi-Hsuan, additional, Liu, Aijun, additional, Semczuk, Andrzej, additional, Zarogoulidis, Paul, additional, Gapeev, Andrei B., additional, Deng, Xiyun, additional, Peng, Xiaoning, additional, Reva, Boris A., additional, Omelchenko, Tatiana, additional, Wang, Jialian, additional, Song, Guohong, additional, and Chen, Tingtao, additional

Published
2023
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17. A tissue injury repair pathway distinct but parallel to host pathogen defense

Author

Liu, Siqi, primary, Hur, Yun Ha, additional, Cai, Xin, additional, Cong, Qian, additional, Yang, Yihao, additional, Xu, Chiwei, additional, Bilate, Angelina M., additional, Uy Gonzales, Kevin Andrew, additional, Cowley, Christopher J., additional, Hurwitz, Brian, additional, Luo, Ji-Dung, additional, Tseng, Tiffany, additional, Gur-Cohen, Shiri, additional, Sribour, Megan, additional, Omelchenko, Tatiana, additional, Levorse, John, additional, Pasolli, Hilda Amalia, additional, Thompson, Craig B., additional, Mucida, Daniel, additional, and Fuchs, Elaine, additional

Published
2022
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19. Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion

Author

Deborde, Sylvie, primary, Gusain, Laxmi, additional, Powers, Ann, additional, Marcadis, Andrea, additional, Yu, Yasong, additional, Chen, Chun-Hao, additional, Frants, Anna, additional, Kao, Elizabeth, additional, Tang, Laura H., additional, Vakiani, Efsevia, additional, Amisaki, Masataka, additional, Balachandran, Vinod P., additional, Calo, Annalisa, additional, Omelchenko, Tatiana, additional, Jessen, Kristjan R., additional, Reva, Boris, additional, and Wong, Richard J., additional

Published
2022
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20. Schwann cells induce cancer cell dispersion and invasion

Author

Deborde, Sylvie, Omelchenko, Tatiana, Lyubchik, Anna, Zhou, Yi, He, Shizhi, McNamara, William F., Chernichenko, Natalya, Lee, Sei-Young, Barajas, Fernando, Chen, Chun-Hao, Bakst, Richard L., Vakiani, Efsevia, He, Shuangba, Hall, Alan, and Wong, Richard J.

Subjects
Schwann cells -- Usage, Cell proliferation -- Health aspects, Cancer cells -- Growth, Company growth, Health care industry
Abstract

Nerves enable cancer progression, as cancers have been shown to extend along nerves through the process of perineural invasion, which carries a poor prognosis. Furthermore, the innervation of some cancers promotes growth and metastases. It remains unclear, however, how nerves mechanistically contribute to cancer progression. Here, we demonstrated that Schwann cells promote cancer invasion through direct cancer cell contact. Histological evaluation of murine and human cancer specimens with perineural invasion uncovered a subpopulation of Schwann cells that associates with cancer cells. Coculture of cancer cells with dorsal root ganglion extracts revealed that Schwann cells direct cancer cells to migrate toward nerves and promote invasion in a contact-dependent manner. Upon contact, Schwann cells induced the formation of cancer cell protrusions in their direction and intercalated between the cancer cells, leading to cancer cell dispersion. The formation of these processes was dependent on Schwann cell expression of neural cell adhesion molecule 1 (NCAM1) and ultimately promoted perineural invasion. Moreover, NCAM1-deficient mice showed decreased neural invasion and less paralysis. Such Schwann cell behavior reflects normal Schwann cell programs that are typically activated in nerve repair but are instead exploited by cancer cells to promote perineural invasion and cancer progression., Introduction Nerves play an important role in cancer invasion. The innervation of prostate and gastric cancers promotes tumor growth and spread (1, 2), and perineural invasion is an aggressive form [...]

Published
2016
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21. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Author

Petralia, Francesca, primary, Tignor, Nicole, additional, Reva, Boris, additional, Koptyra, Mateusz, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Ma, Weiping, additional, Zhu, Yuankun, additional, Ji, Jiayi, additional, Calinawan, Anna, additional, Whiteaker, Jeffrey R., additional, Colaprico, Antonio, additional, Stathias, Vasileios, additional, Omelchenko, Tatiana, additional, Song, Xiaoyu, additional, Raman, Pichai, additional, Guo, Yiran, additional, Brown, Miguel A., additional, Ivey, Richard G., additional, Szpyt, John, additional, Guha Thakurta, Sanjukta, additional, Gritsenko, Marina A., additional, Weitz, Karl K., additional, Lopez, Gonzalo, additional, Kalayci, Selim, additional, Gümüş, Zeynep H., additional, Yoo, Seungyeul, additional, da Veiga Leprevost, Felipe, additional, Chang, Hui-Yin, additional, Krug, Karsten, additional, Katsnelson, Lizabeth, additional, Wang, Ying, additional, Kennedy, Jacob J., additional, Voytovich, Uliana J., additional, Zhao, Lei, additional, Gaonkar, Krutika S., additional, Ennis, Brian M., additional, Zhang, Bo, additional, Baubet, Valerie, additional, Tauhid, Lamiya, additional, Lilly, Jena V., additional, Mason, Jennifer L., additional, Farrow, Bailey, additional, Young, Nathan, additional, Leary, Sarah, additional, Moon, Jamie, additional, Petyuk, Vladislav A., additional, Nazarian, Javad, additional, Adappa, Nithin D., additional, Palmer, James N., additional, Lober, Robert M., additional, Rivero-Hinojosa, Samuel, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Broberg, Matilda, additional, Chu, Rosalie K., additional, Moore, Ronald J., additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Smith, Richard D., additional, Zhu, Jun, additional, Robles, Ana I., additional, Mesri, Mehdi, additional, Boja, Emily, additional, Hiltke, Tara, additional, Rodriguez, Henry, additional, Zhang, Bing, additional, Schadt, Eric E., additional, Mani, D.R., additional, Ding, Li, additional, Iavarone, Antonio, additional, Wiznerowicz, Maciej, additional, Schürer, Stephan, additional, Chen, Xi S., additional, Heath, Allison P., additional, Rokita, Jo Lynne, additional, Nesvizhskii, Alexey I., additional, Fenyö, David, additional, Rodland, Karin D., additional, Liu, Tao, additional, Gygi, Steven P., additional, Paulovich, Amanda G., additional, Resnick, Adam C., additional, Storm, Phillip B., additional, Rood, Brian R., additional, Wang, Pei, additional, Francis, Alicia, additional, Morgan, Allison M., additional, Waanders, Angela J., additional, Viaene, Angela N., additional, Buccoliero, Anna Maria, additional, Chinnaiyan, Arul M., additional, Leonard, Carina A., additional, Kline, Cassie N., additional, Caporalini, Chiara, additional, Kinsinger, Christopher R., additional, Li, Chunde, additional, Kram, David E., additional, Hanson, Derek, additional, Appert, Elizabeth, additional, Kawaler, Emily A., additional, Raabe, Eric H., additional, Jackson, Eric M., additional, Greenfield, Jeffrey P., additional, Stone, Gabrielle S., additional, Getz, Gad, additional, Grant, Gerald, additional, Teo, Guo Ci, additional, Pollack, Ian F., additional, Cain, Jason E., additional, Foster, Jessica B., additional, Phillips, Joanna J., additional, Palma, July E., additional, Ketchum, Karen A., additional, Ruggles, Kelly V., additional, Blumenberg, Lili, additional, Cornwell, Macintosh, additional, Sarmady, Mahdi, additional, Domagalski, Marcin J., additional, Cieślik, Marcin P., additional, Santi, Mariarita, additional, Li, Marilyn M., additional, Ellis, Matthew J., additional, Wyczalkowski, Matthew A., additional, Connors, Meghan, additional, Scagnet, Mirko, additional, Gupta, Nalin, additional, Edwards, Nathan J., additional, Vitanza, Nicholas A., additional, Vaske, Olena M., additional, Becher, Oren, additional, McGarvey, Peter B., additional, Firestein, Ron, additional, Mueller, Sabine, additional, Winebrake, Samuel G., additional, Dhanasekaran, Saravana Mohan, additional, Cai, Shuang, additional, Partap, Sonia, additional, Patton, Tatiana, additional, Le, Toan, additional, Lorentzen, Travis D., additional, Liu, Wenke, additional, and Bocik, William E., additional

Published
2020
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24. 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
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25. Cdc42 Mediates Cancer Cell Chemotaxis in Perineural Invasion

Author

Chernichenko, Natalya, primary, Omelchenko, Tatiana, additional, Deborde, Sylvie, additional, Bakst, Richard L., additional, He, Shizhi, additional, Chen, Chun-Hao, additional, Gusain, Laxmi, additional, Vakiani, Efsevia, additional, Katabi, Nora, additional, Hall, Alan, additional, and Wong, Richard J., additional

Published
2020
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26. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author

Clark, David J., primary, Dhanasekaran, Saravana M., additional, Petralia, Francesca, additional, Pan, Jianbo, additional, Song, Xiaoyu, additional, Hu, Yingwei, additional, da Veiga Leprevost, Felipe, additional, Reva, Boris, additional, Lih, Tung-Shing M., additional, Chang, Hui-Yin, additional, Ma, Weiping, additional, Huang, Chen, additional, Ricketts, Christopher J., additional, Chen, Lijun, additional, Krek, Azra, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Li, Qing Kay, additional, Chen, Lin S., additional, Ozbek, Umut, additional, Vasaikar, Suhas, additional, Wu, Yige, additional, Yoo, Seungyeul, additional, Chowdhury, Shrabanti, additional, Wyczalkowski, Matthew A., additional, Ji, Jiayi, additional, Schnaubelt, Michael, additional, Kong, Andy, additional, Sethuraman, Sunantha, additional, Avtonomov, Dmitry M., additional, Ao, Minghui, additional, Colaprico, Antonio, additional, Cao, Song, additional, Cho, Kyung-Cho, additional, Kalayci, Selim, additional, Ma, Shiyong, additional, Liu, Wenke, additional, Ruggles, Kelly, additional, Calinawan, Anna, additional, Gümüş, Zeynep H., additional, Geiszler, Daniel, additional, Kawaler, Emily, additional, Teo, Guo Ci, additional, Wen, Bo, additional, Zhang, Yuping, additional, Keegan, Sarah, additional, Li, Kai, additional, Chen, Feng, additional, Edwards, Nathan, additional, Pierorazio, Phillip M., additional, Chen, Xi Steven, additional, Pavlovich, Christian P., additional, Hakimi, A. Ari, additional, Brominski, Gabriel, additional, Hsieh, James J., additional, Antczak, Andrzej, additional, Omelchenko, Tatiana, additional, Lubinski, Jan, additional, Wiznerowicz, Maciej, additional, Linehan, W. Marston, additional, Kinsinger, Christopher R., additional, Thiagarajan, Mathangi, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Qian, Jiang, additional, Fenyö, David, additional, Zhang, Bing, additional, Ding, Li, additional, Schadt, Eric, additional, Chinnaiyan, Arul M., additional, Zhang, Zhen, additional, Omenn, Gilbert S., additional, Cieslik, Marcin, additional, Chan, Daniel W., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Zhang, Hui, additional, Hashimi, Abdul Samad, additional, Pico, Alexander R., additional, Karpova, Alla, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Malovannaya, Anna, additional, Marrero-Oliveras, Annette, additional, Agarwal, Anupriya, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kim, Beom-Jun, additional, Druker, Brian J., additional, Newton, Chelsea J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Tognon, Cristina, additional, Mani, D.R., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Wheeler, David, additional, Tan, Donghui, additional, Chan, Doug, additional, Demir, Emek, additional, Malc, Ewa, additional, Modugno, Francesmary, additional, Getz, Gaddy, additional, Hostetter, Galen, additional, Wilson, George D., additional, Hart, Gerald W., additional, Zhu, Heng, additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhou, Hua, additional, Day, Jacob, additional, Suh, James, additional, Huang, Jasmine, additional, McDermott, Jason, additional, Whiteaker, Jeffrey R., additional, Tyner, Jeffrey W., additional, Eschbacher, Jennifer, additional, Chen, Jin, additional, McGee, John, additional, Zhu, Jun, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Clauser, Karl, additional, Robinson, Karna, additional, Krug, Karsten, additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Elburn, Kim, additional, Holloway, Kimberly, additional, Wang, Liang-Bo, additional, Blumenberg, Lili, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Cornwell, MacIntosh, additional, Loriaux, Marc, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Anderson, Matthew, additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Lewis, Michael, additional, Ittmann, Michael M., additional, Smith, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Chheda, Milan G., additional, Khan, Munziba, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Tignor, Nicole, additional, Beckmann, Noam, additional, Grady, Pamela, additional, Castro, Patricia, additional, Piehowski, Paul, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Gao, Qingsong, additional, Dhir, Rajiv, additional, Kothadia, Ramani Bhupendra, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Jayasinghe, Reyka G., additional, Smith, Richard D., additional, Edwards, Robert, additional, Zelt, Robert, additional, Bremner, Ross, additional, Liu, Ruiyang, additional, Hong, Runyu, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Jewell, Scott D., additional, Patel, Shalin, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Davies, Sherri R., additional, Cai, Shuang, additional, Boca, Simina M., additional, Patil, Snehal, additional, Sengupta, Sohini, additional, Carter, Sonya, additional, Gabriel, Stacey, additional, Thomas, Stefani N., additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Foltz, Steven M., additional, Hilsenbeck, Sue, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Westbrook, Thomas, additional, Borate, Uma, additional, Velvulou, Uma, additional, Petyuk, Vladislav A., additional, Bocik, William E., additional, Chen, Xi, additional, Shi, Yan, additional, Geffen, Yifat, additional, Lu, Yihao, additional, Wang, Ying, additional, Maruvka, Yosef, additional, Li, Zhi, additional, Shi, Zhiao, additional, and Tu, Zhidong, additional

Published
2020
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27. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author

Clark, David J., primary, Dhanasekaran, Saravana M., additional, Petralia, Francesca, additional, Pan, Jianbo, additional, Song, Xiaoyu, additional, Hu, Yingwei, additional, da Veiga Leprevost, Felipe, additional, Reva, Boris, additional, Lih, Tung-Shing M., additional, Chang, Hui-Yin, additional, Ma, Weiping, additional, Huang, Chen, additional, Ricketts, Christopher J., additional, Chen, Lijun, additional, Krek, Azra, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Li, Qing Kay, additional, Chen, Lin S., additional, Ozbek, Umut, additional, Vasaikar, Suhas, additional, Wu, Yige, additional, Yoo, Seungyeul, additional, Chowdhury, Shrabanti, additional, Wyczalkowski, Matthew A., additional, Ji, Jiayi, additional, Schnaubelt, Michael, additional, Kong, Andy, additional, Sethuraman, Sunantha, additional, Avtonomov, Dmitry M., additional, Ao, Minghui, additional, Colaprico, Antonio, additional, Cao, Song, additional, Cho, Kyung-Cho, additional, Kalayci, Selim, additional, Ma, Shiyong, additional, Liu, Wenke, additional, Ruggles, Kelly, additional, Calinawan, Anna, additional, Gümüş, Zeynep H., additional, Geiszler, Daniel, additional, Kawaler, Emily, additional, Teo, Guo Ci, additional, Wen, Bo, additional, Zhang, Yuping, additional, Keegan, Sarah, additional, Li, Kai, additional, Chen, Feng, additional, Edwards, Nathan, additional, Pierorazio, Phillip M., additional, Chen, Xi Steven, additional, Pavlovich, Christian P., additional, Hakimi, A. Ari, additional, Brominski, Gabriel, additional, Hsieh, James J., additional, Antczak, Andrzej, additional, Omelchenko, Tatiana, additional, Lubinski, Jan, additional, Wiznerowicz, Maciej, additional, Linehan, W. Marston, additional, Kinsinger, Christopher R., additional, Thiagarajan, Mathangi, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Qian, Jiang, additional, Fenyö, David, additional, Zhang, Bing, additional, Ding, Li, additional, Schadt, Eric, additional, Chinnaiyan, Arul M., additional, Zhang, Zhen, additional, Omenn, Gilbert S., additional, Cieslik, Marcin, additional, Chan, Daniel W., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Zhang, Hui, additional, Hashimi, Abdul Samad, additional, Pico, Alexander R., additional, Karpova, Alla, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Malovannaya, Anna, additional, Marrero-Oliveras, Annette, additional, Agarwal, Anupriya, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kim, Beom-Jun, additional, Druker, Brian J., additional, Newton, Chelsea J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Tognon, Cristina, additional, Mani, D.R., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Wheeler, David, additional, Tan, Donghui, additional, Chan, Doug, additional, Demir, Emek, additional, Malc, Ewa, additional, Modugno, Francesmary, additional, Getz, Gaddy, additional, Hostetter, Galen, additional, Wilson, George D., additional, Hart, Gerald W., additional, Zhu, Heng, additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhou, Hua, additional, Day, Jacob, additional, Suh, James, additional, Huang, Jasmine, additional, McDermott, Jason, additional, Whiteaker, Jeffrey R., additional, Tyner, Jeffrey W., additional, Eschbacher, Jennifer, additional, Chen, Jin, additional, McGee, John, additional, Zhu, Jun, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Clauser, Karl, additional, Robinson, Karna, additional, Krug, Karsten, additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Elburn, Kim, additional, Holloway, Kimberly, additional, Wang, Liang-Bo, additional, Blumenberg, Lili, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Cornwell, MacIntosh, additional, Loriaux, Marc, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Anderson, Matthew, additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Lewis, Michael, additional, Ittmann, Michael M., additional, Smith, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Chheda, Milan G., additional, Khan, Munziba, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Tignor, Nicole, additional, Beckmann, Noam, additional, Grady, Pamela, additional, Castro, Patricia, additional, Piehowski, Paul, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Gao, Qingsong, additional, Dhir, Rajiv, additional, Kothadia, Ramani Bhupendra, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Jayasinghe, Reyka G., additional, Smith, Richard D., additional, Edwards, Robert, additional, Zelt, Robert, additional, Bremner, Ross, additional, Liu, Ruiyang, additional, Hong, Runyu, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Jewell, Scott D., additional, Patel, Shalin, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Davies, Sherri R., additional, Cai, Shuang, additional, Boca, Simina M., additional, Patil, Snehal, additional, Sengupta, Sohini, additional, Carter, Sonya, additional, Gabriel, Stacey, additional, Thomas, Stefani N., additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Foltz, Steven M., additional, Hilsenbeck, Sue, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Westbrook, Thomas, additional, Borate, Uma, additional, Velvulou, Uma, additional, Petyuk, Vladislav A., additional, Bocik, William E., additional, Chen, Xi, additional, Shi, Yan, additional, Geffen, Yifat, additional, Lu, Yihao, additional, Wang, Ying, additional, Maruvka, Yosef, additional, Li, Zhi, additional, Shi, Zhiao, additional, and Tu, Zhidong, additional

Published
2019
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37. A proteogenomic portrait of lung squamous cell carcinoma.

Author

Satpathy, Shankha, Krug, Karsten, Jean Beltran, Pierre M., Savage, Sara R., Petralia, Francesca, Kumar-Sinha, Chandan, Dou, Yongchao, Reva, Boris, Kane, M. Harry, Avanessian, Shayan C., Vasaikar, Suhas V., Krek, Azra, Lei, Jonathan T., Jaehnig, Eric J., Omelchenko, Tatiana, Geffen, Yifat, Bergstrom, Erik J., Stathias, Vasileios, Christianson, Karen E., and Heiman, David I.

Subjects
*SQUAMOUS cell carcinoma, *DRUG target, *BIOMARKERS, *METABOLIC regulation, *SURVIVIN (Protein), *POST-translational modification, *LUNG cancer treatment
Abstract

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC. [Display omitted] • Unsupervised clustering revealed subtype with EMT and phosphoprotein signatures • Potential therapeutic vulnerabilities included survivin, NSD3, LSD1, and EZH2 • Rb phosphorylation nominated as a biomarker for trials with CDK4/6 inhibitors • Detailed immune landscape analysis highlighted targetable points of immuneregulation Comprehensive proteogenomic characterization of lung squamous cell carcinomas and paired normal adjacent tissues identifies taxonomic subclasses, alternative driver events, and insights into immune modulation, as well as putative biomarkers and potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Published
2021
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