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1. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial.

Author

Parra, Edwin, Zhang, Jiexin, Duose, Dzifa, Gonzalez-Kozlova, Edgar, Redman, Mary, Chen, Hong, Manyam, Ganiraju, Kumar, Gayatri, Zhang, Jianhua, Song, Xingzhi, Lazcano, Rossana, Marques-Piubelli, Mario, Laberiano-Fernandez, Caddie, Rojas, Frank, Zhang, Baili, Taing, Len, Jhaveri, Aashna, Geisberg, Jacob, Altreuter, Jennifer, Michor, Franziska, Provencher, James, Yu, Joyce, Cerami, Ethan, Moravec, Radim, Kannan, Kasthuri, Luthra, Rajyalakshmi, Alatrash, Gheath, Huang, Hsin-Hui, Xie, Hui, Patel, Manishkumar, Nie, Kai, Harris, Jocelyn, Argueta, Kimberly, Lindsay, James, Biswas, Roshni, Van Nostrand, Stephen, Kim-Schulze, Seunghee, Gray, Jhanelle, Herbst, Roy, Wistuba, Ignacio, Gettinger, Scott, Kelly, Karen, Bazhenova, Lyudmila, Gnjatic, Sacha, Lee, J, Zhang, Jianjun, and Haymaker, Cara

Subjects
Humans, Nivolumab, Lung Neoplasms, Multiomics, Antineoplastic Combined Chemotherapy Protocols, Carcinoma, Non-Small-Cell Lung, Carcinoma, Squamous Cell, Immunotherapy, Lung, Epithelial Cells, Ipilimumab, Tumor Microenvironment
Abstract

PURPOSE: Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. EXPERIMENTAL DESIGN: Tissue and longitudinal blood specimens from phase III trial S1400I in patients with metastatic squamous non-small cell carcinoma (SqNSCLC) treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink. RESULTS: Higher immune scores from immune gene expression profiling or immune cell infiltration by mIF were associated with response to ICIs and improved survival, except regulatory T cells, which were associated with worse overall survival (OS) for patients receiving nivo+ipi. Immune cell density and closer proximity of CD8+GZB+ T cells to malignant cells were associated with superior progression-free survival and OS. The cold immune landscape of NSCLC was associated with a higher level of chromosomal copy-number variation (CNV) burden. Patients with LRP1B-mutant tumors had a shorter survival than patients with LRP1B-wild-type tumors. Olink assays revealed soluble proteins such as LAMP3 increased in responders while IL6 and CXCL13 increased in nonresponders. Upregulation of serum CXCL13, MMP12, CSF-1, and IL8 were associated with worse survival before radiologic progression. CONCLUSIONS: The frequency, distribution, and clustering of immune cells relative to malignant ones can impact ICI efficacy in patients with SqNSCLC. High CNV burden may contribute to the cold immune microenvironment. Soluble inflammation/immune-related proteins in the blood have the potential to monitor therapeutic benefit from ICI treatment in patients with SqNSCLC.

Published
2024

2. Proteomic characterization of acute kidney injury in patients hospitalized with SARS-CoV2 infection

Author

Paranjpe, Ishan, Jayaraman, Pushkala, Su, Chen-Yang, Zhou, Sirui, Chen, Steven, Thompson, Ryan, Del Valle, Diane Marie, Kenigsberg, Ephraim, Zhao, Shan, Jaladanki, Suraj, Chaudhary, Kumardeep, Ascolillo, Steven, Vaid, Akhil, Gonzalez-Kozlova, Edgar, Kauffman, Justin, Kumar, Arvind, Paranjpe, Manish, Hagan, Ross O., Kamat, Samir, Gulamali, Faris F., Xie, Hui, Harris, Joceyln, Patel, Manishkumar, Argueta, Kimberly, Batchelor, Craig, Nie, Kai, Dellepiane, Sergio, Scott, Leisha, Levin, Matthew A., He, John Cijiang, Suarez-Farinas, Mayte, Coca, Steven G., Chan, Lili, Azeloglu, Evren U., Schadt, Eric, Beckmann, Noam, Gnjatic, Sacha, Merad, Miram, Kim-Schulze, Seunghee, Richards, Brent, Glicksberg, Benjamin S., Charney, Alexander W., and Nadkarni, Girish N.

Published
2023
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3. Circulating proteins to predict COVID-19 severity

Author

Su, Chen-Yang, Zhou, Sirui, Gonzalez-Kozlova, Edgar, Butler-Laporte, Guillaume, Brunet-Ratnasingham, Elsa, Nakanishi, Tomoko, Jeon, Wonseok, Morrison, David R., Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael A., Langenberg, Claudia, Forgetta, Vincenzo, Pineau, Joelle, Mooser, Vincent, Marron, Thomas, Beckmann, Noam D., Kim-schulze, Seunghee, Charney, Alexander W., Gnjatic, Sacha, Kaufmann, Daniel E., Merad, Miriam, and Richards, J. Brent

Published
2023
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4. A methylation clock model of mild SARS‐CoV‐2 infection provides insight into immune dysregulation

Author

Mao, Weiguang, Miller, Clare M, Nair, Venugopalan D, Ge, Yongchao, Amper, Mary Anne S, Cappuccio, Antonio, George, Mary‐Catherine, Goforth, Carl W, Guevara, Kristy, Marjanovic, Nada, Nudelman, German, Pincas, Hanna, Ramos, Irene, Sealfon, Rachel S G, Soares‐Schanoski, Alessandra, Vangeti, Sindhu, Vasoya, Mital, Weir, Dawn L, Zaslavsky, Elena, Barcessat, Vanessa, Tuballes, Kevin, Del Valle, Diane Marie, Nie, Kai, Xie, Hui, Chung, Grace, Patel, Manishkumar, Harris, Jocelyn, Argueta, Kimberly, Fehr, Jacques, Gruberg, Barr, Zaki, Nicholas, Kim‐Schulze, Seunghee, Gnjatic, Sacha, Merad, Miriam, Letizia, Andrew G, Troyanskaya, Olga G, Sealfon, Stuart C, and Chikina, Maria

Published
2023
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5. Correction: The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Aflalo, Jonathan, Aflalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam D., Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J. Brent

Published
2022
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6. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Published
2022
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7. Supplementary Table 6 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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8. Supplementary Figure 6 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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9. Supplementary Figure 8 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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10. Supplementary Table 3 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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11. Supplementary Figure 1 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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12. Supplementary Table 1 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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13. Supplementary Figure 7 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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14. Data from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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15. Supplementary Figure 2 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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16. Supplementary Table 7 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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17. Supplementary Table 4 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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18. Supplementary Figure 5 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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19. Supplementary Table 2 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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20. Supplementary Figure 3 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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21. Supplementary Figure 4 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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22. Supplementary Table 5 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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23. Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children

Author

Beckmann, Noam D., Comella, Phillip H., Cheng, Esther, Lepow, Lauren, Beckmann, Aviva G., Tyler, Scott R., Mouskas, Konstantinos, Simons, Nicole W., Hoffman, Gabriel E., Francoeur, Nancy J., Del Valle, Diane Marie, Kang, Gurpawan, Do, Anh, Moya, Emily, Wilkins, Lillian, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Yi, Nancy, Yu, Alex, Chung, Jonathan, Hartnett, Matthew, Eaton, Melody, Hatem, Sandra, Jamal, Hajra, Akyatan, Alara, Tabachnikova, Alexandra, Liharska, Lora E., Cotter, Liam, Fennessy, Brian, Vaid, Akhil, Barturen, Guillermo, Shah, Hardik, Wang, Ying-chih, Sridhar, Shwetha Hara, Soto, Juan, Bose, Swaroop, Madrid, Kent, Ellis, Ethan, Merzier, Elyze, Vlachos, Konstantinos, Fishman, Nataly, Tin, Manying, Smith, Melissa, Xie, Hui, Patel, Manishkumar, Nie, Kai, Argueta, Kimberly, Harris, Jocelyn, Karekar, Neha, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Tuballes, Kevin, Scott, Ieisha, Kumar, Arvind, Jaladanki, Suraj, Agashe, Charuta, Thompson, Ryan, Clark, Evan, Losic, Bojan, Peters, Lauren, Roussos, Panagiotis, Zhu, Jun, Wang, Wenhui, Kasarskis, Andrew, Glicksberg, Benjamin S., Nadkarni, Girish, Bogunovic, Dusan, Elaiho, Cordelia, Gangadharan, Sandeep, Ofori-Amanfo, George, Alesso-Carra, Kasey, Onel, Kenan, Wilson, Karen M., Argmann, Carmen, Bunyavanich, Supinda, Alarcón-Riquelme, Marta E., Marron, Thomas U., Rahman, Adeeb, Kim-Schulze, Seunghee, Gnjatic, Sacha, Gelb, Bruce D., Merad, Miriam, Sebra, Robert, Schadt, Eric E., and Charney, Alexander W.

Published
2021
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24. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

Author

Nadkarni, Girish, primary, Paranjpe, Ishan, additional, Jayaraman, Pushkala, additional, Su, Chen-Yang, additional, Zhou, Sirui, additional, Chen, Steven, additional, Valle, Diane Del, additional, Thompson, Ryan, additional, Kenigsberg, Ephraim, additional, Zhao, Shan, additional, Jaladanki, Suraj, additional, Chaudhary, Kumardeep, additional, Ascolillo, Steven, additional, Vaid, Akhil, additional, Gonzalez-Kozlova, Edgar, additional, Kumar, Arvind, additional, Paranjpe, Manish, additional, O'Hagan, Ross, additional, Kamat, Samir, additional, Gulamali, Faris, additional, Kauffman, Justin, additional, Xie, Hui, additional, Harris, Joceyln, additional, Patel, Manishkumar, additional, Argueta, Kimberly, additional, Batchelor, Craig, additional, Nie, Kai, additional, Dellepiane, Sergio, additional, Scott, Leisha, additional, Levin, Matthew, additional, He, John, additional, Suárez-Fariñas, Mayte, additional, Coca, Steven, additional, Chan, Lili, additional, Azeloglu, Evren, additional, Schadt, Eric, additional, Beckmann, Noam, additional, Gnjatic, Sacha, additional, Merad, Miriam, additional, Kim-Schulze, Seunghee, additional, Richards, J. Brent, additional, Glicksberg, Benjamin, additional, and Charney, Alexander, additional

Published
2023
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25. 1477 First efficacy and multi-omic analysis data from phase 1 clinical trial of oncolytic viral immunotherapy with CAN-2409 + valacyclovir in combination with nivolumab and standard of care in newly diagnosed high-grade glioma

Author

Wen, Patrick, primary, Duault, Caroline, additional, Gonzalez-Kozlova, Edgar, additional, Brennan, Kevin, additional, Holmes, Tyson, additional, Kim-Schulze, Seunghee, additional, Nie, Kai, additional, Argueta, Kimberly, additional, Fehr, Jacques, additional, Pichavant, Mina, additional, Valle, Diane Del, additional, Gentles, Andrew, additional, Gnjatic, Sacha, additional, Maecker, Holden, additional, Ye, Xiaobu, additional, Reardon, David, additional, Bi, Wenya Linda, additional, Peruzzi, Pierpaolo, additional, Patel, Nirav, additional, Strowd, Roy, additional, Tatter, Stephen, additional, Lee, Ian, additional, Walbert, Tobias, additional, Snyder, James, additional, Brem, Steven, additional, Desai, Arati, additional, Bagley, Stephen, additional, Amankulor, Nduka, additional, Lieberman, Frank, additional, Mantica, Megan, additional, Lopez, Lenika, additional, Bell, Susan, additional, Manzanera, Andrea, additional, Lawler, Sean, additional, Jin, Lixian, additional, Danda, Neeraja, additional, Desideri, Serena, additional, Burt Nabors, L, additional, Grossman, Stuart, additional, Chiocca, E, additional, Tak, Paul, additional, and Barone, Francesca, additional

Published
2022
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26. Abstract 5026: Dynamic changes in circulating protein levels reveal an association between ipilimumab and nivolumab combination treatment (SWOG Lung-MAP S1400I trial) with outcomes in squamous cell lung cancer

Author

Gonzalez-Kozlova, Edgar, primary, Huang, Hsin-Hui, additional, Redman, Mary, additional, Herbst, Roy, additional, Gettinger, Scott, additional, Bazhenova, Luda, additional, Xie, Hui, additional, Patel, Manishkumar, additional, Nie, Kai, additional, Harris, Jocelyn, additional, Argueta, Kimberly, additional, Kelly, Karen, additional, Cerami, Ethan, additional, Lindsay, James, additional, Yu, Joyce, additional, Biswas, Roshni, additional, Van Nostrand, Stephen, additional, Moravec, Radim, additional, Valle, Diane Marie Del, additional, Kim-schulze, Seunghee, additional, and Gnjatic, Sacha, additional

Published
2022
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27. Dynamic changes in serum analyte levels associated with clinical outcome in squamous cell lung cancer trial SWOG Lung-MAP S1400I of nivolumab ± ipilimumab.

Author

Gonzalez-Kozlova, Edgar, primary, Huang, Hsin-Hui, additional, Redman, Mary Weber, additional, Herbst, Roy S., additional, Gettinger, Scott N., additional, Bazhenova, Lyudmila, additional, Xie, Hui, additional, Patel, Manishkumar, additional, Nie, Kai, additional, Harris, Jocelyn, additional, Argueta, Kimberly, additional, Cerami, Ethan, additional, Hong, Joyce, additional, Biswas, Roshni, additional, Van Nostrand, Stephen, additional, Kelly, Karen, additional, Moravec, Radim, additional, Del Valle, Diane, additional, Kim-Schulze, Seunghee, additional, and Gnjatic, Sacha, additional

Published
2022
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28. Additional file 3 of The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Abstract

Additional file 3: Protein correlation heatmaps.

Published
2022
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29. Additional file 6 of The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Abstract

Additional file 6: Mount Sinai investigators.

Published
2022
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30. Additional file 1 of The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Abstract

Additional file 1: List of immunity-related proteins measured.

Published
2022
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31. Additional file 2 of The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Abstract

Additional file 2: Sample code for the generalized additive models.

Published
2022
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32. Additional file 5 of The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Abstract

Additional file 5: Inferred protein levels over time.

Published
2022
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33. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A, Schadt, Eric, Nie, Kai, Simons, Nicole W, Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M T, Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W, Kim-Schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E, Gnjatic, Sacha, Richards, J Brent, Rezk, Nardin [0000-0001-5358-7704], Richards, J Brent [0000-0002-3746-9086], and Apollo - University of Cambridge Repository

Subjects
Proteomics, Somascan, Immunity, Covid-19
Abstract

IntroductionSevere COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions.MethodsWe measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support.Results580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p -4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex.ConclusionsSevere COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.

Published
2021

34. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

Author

Paranjpe, Ishan, primary, Jayaraman, Pushkala, additional, Su, Chen-Yang, additional, Zhou, Sirui, additional, Chen, Steven, additional, Thompson, Ryan, additional, Del Valle, Diane Marie, additional, Kenigsberg, Ephraim, additional, Zhao, Shan, additional, Jaladanki, Suraj, additional, Chaudhary, Kumardeep, additional, Ascolillo, Steven, additional, Vaid, Akhil, additional, Kumar, Arvind, additional, Kozlova, Edgar, additional, Paranjpe, Manish, additional, O’Hagan, Ross, additional, Kamat, Samir, additional, Gulamali, Faris F., additional, Kauffman, Justin, additional, Xie, Hui, additional, Harris, Joceyln, additional, Patel, Manishkumar, additional, Argueta, Kimberly, additional, Batchelor, Craig, additional, Nie, Kai, additional, Dellepiane, Sergio, additional, Scott, Leisha, additional, Levin, Matthew A, additional, He, John Cijiang, additional, Suarez-Farinas, Mayte, additional, Coca, Steven G, additional, Chan, Lili, additional, Azeloglu, Evren U, additional, Schadt, Eric, additional, Beckmann, Noam, additional, Gnjatic, Sacha, additional, Merad, Miram, additional, Kim-Schulze, Seunghee, additional, Richards, Brent, additional, Glicksberg, Benjamin S, additional, Charney, Alexander W, additional, and Nadkarni, Girish N, additional

Published
2021
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35. Immune Landscape Associated with Response to Brentuximab Vedotin with Ipilimumab and/or Nivolumab in Relapsed/Refractory Hodgkin Lymphoma (E4412 Phase 1)

Author

Diefenbach, Catherine S, Gonzalez-Kozlova, Edgar, Del Valle, Diane Marie, Huang, Hsin-Hui, Jegede, Opeyemi, Barcessat, Vanessa, Tuballes, Kevin, Kelly, Geoffrey, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Argueta, Kimberly, Nie, Kai, Moravec, Radim, Altreuter, Jennifer, Duose, Dzifa Yawa, Kahl, Brad S., Ansell, Stephen M, Yu, Joyce, Cerami, Ethan, Lindsay, James, Wistuba, Ignacio, Kim-Schulze, Seunghee, and Gnjatic, Sacha

Published
2023
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36. Climate change is the enemy of mankind

Author

Argueta, Kimberly

Subjects
Global temperature changes -- Environmental aspects, Weather -- Environmental aspects, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta April 21, 2021 File photo Climate change occurs when the typical weather of a region that has been experienced for a long time begins [...]

Published
2021

37. How to choose the best way of online learning

Author

Argueta, Kimberly

Subjects
Online education, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta February 3, 2021 As the pandemic continues, college students are stuck wondering what type of classes they should take. Since normal in-person classes are [...]

Published
2021

38. The spread of COVID-19 in Houston should be addressed

Author

Argueta, Kimberly

Subjects
News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta January 28, 2021 Courtesy of the Centers for Disease Control and Prevention/The Cougar With the passing of the holiday season, it isn't surprising that [...]

Published
2021

40. Sampling the host response to SARS-CoV-2 in hospitals under siege

Author

Charney, Alexander W., Simons, Nicole W., Mouskas, Konstantinos, Lepow, Lauren, Cheng, Esther, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Del Valle, Diane Marie, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Patel, Manishkumar, Xie, Hui, Yi, Nancy, Yu, Alex, Kang, Gurpawan, Mendoza, Anthony, Liharska, Lora E., Moya, Emily, Hartnett, Matthew, Hatem, Sandra, Wilkins, Lillian, Eaton, Melody, Jamal, Hajra, Tuballes, Kevin, Chen, Steven T., Tabachnikova, Alexandra, Chung, Jonathan, Harris, Jocelyn, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Argueta, Kimberly, Karekar, Neha, Lee, Brian, Kelly, Geoffrey, Geanon, Daniel, Handler, Diana, Leech, John, Stefanos, Hiyab, Dawson, Travis, Scott, Ieisha, Francoeur, Nancy, Johnson, Jessica S., Vaid, Akhil, Glicksberg, Benjamin S., Nadkarni, Girish N., Schadt, Eric E., Gelb, Bruce D., Rahman, Adeeb, Sebra, Robert, Martin, Glenn, Agashe, Charuta, Agrawal, Priyal, Akyatan, Alara, Alesso-Carra, Kasey, Alibo, Eziwoma, Alvarez, Kelvin, Amabile, Angelo, Ascolillo, Steven, Bailey, Rasheed, Begani, Priya, Correra, Paloma Bravo, Brown, Stacey-Ann, Buckup, Mark, Burka, Larissa, Cambron, Lena, Carrara, Gina, Chang, Serena, Chien, Jonathan, Chowdhury, Mashkura, Bozkus, Cansu Cimen, Comella, Phillip, Cosgrove, Dana, Cossarini, Francesca, Cotter, Liam, Dave, Arpit, Dayal, Bheesham, Dhainaut, Maxime, Dornfeld, Rebecca, Dul, Katie, Eber, Nissan, Elaiho, Cordelia, Fabris, Frank, Faith, Jeremiah, Falci, Dominique, Feng, Susie, Fennessy, Brian, Fernandes, Marie, Gangadharan, Sandeep, Grabowska, Joanna, Gyimesi, Gavin, Hamdani, Maha, Herbinet, Manon, Herrera, Elva, Hochman, Arielle, Hoffman, Gabriel E., Hook, Jaime, Horta, Laila, Humblin, Etienne, Karim, Subha, Kim, Jessica, Lebovitch, Dannielle, Lee, Grace, Lee, Gyu Ho, Lee, Jacky, Leventhal, Mike, Lindblad, Katherine, Livanos, Alexandra, Machado, Rosalie, Mahmood, Zafar, Mar, Kelcey, Maskey, Shrisha, Matthews, Paul, Meckel, Katherine, Mehandru, Saurabh, Mercedes, Cynthia, Meyer, Dara, Mollaoglu, Gurkan, Morris, Sarah, Nie, Kai, Nisenholtz, Marjorie, Ofori-Amanfo, George, Onel, Kenan, Ounadjela, Merouane, Patel, Vishwendra, Pruitt, Cassandra, Rathi, Shivani, Redes, Jamie, Reyes-Torres, Ivan, Rodrigues, Alcina, Rodriguez, Alfonso, Roudko, Vladimir, Ruiz, Evelyn, Scalzo, Pearl, Silva, Pedro, Schanoski, Alessandra Soares, Straw, Meghan, Tabachnikova, Sasha, Teague, Collin, Upadhyaya, Bhaskar, Van Der Heide, Verena, Vaninov, Natalie, Wacker, Daniel, Walsh, Hadley, Wilk, C. Matthias, Wilson, Jessica, Wilson, Karen M., Xue, Li, Yeboah, Naa-akomaah, Young, Sabina, Zaks, Nina, Zha, Renyuan, Marron, Thomas, Beckmann, Noam, Kim-Schulze, Seunghee, Gnjatic, Sacha, and Merad, Miriam

Subjects
Siege, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), biology, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Host response, Sampling (statistics), General Medicine, biology.organism_classification, Virology, General Biochemistry, Genetics and Molecular Biology, Pandemic, Medicine, business, Betacoronavirus
Published
2020
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41. The benefits of volunteering go beyond helping your community

Author

Argueta, Kimberly

Subjects
Volunteerism, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta October 7, 2020 Gerald Sastra/The Cougar The world is an extremely complicated place and humans largely contribute to its list of troubles. One large [...]

Published
2020

42. Don't forget to reach out to your loved ones, socialize

Author

Argueta, Kimberly

Subjects
Social distancing (Public health), Mental health, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta September 23, 2020 Juana Garcia/The Cougar While in quarantine and practicing social distancing, it can be difficult to both make new friends and keep [...]

Published
2020

43. Decreasing your screen time might be the best thing for your health

Author

Argueta, Kimberly

Subjects
Online education, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta September 21, 2020 Juana Garcia/The Cougar As we stay inside for a longer period of time, many of us have to utilize technology and [...]

Published
2020

44. Voter education is more important than ever before

Author

Argueta, Kimberly

Subjects
Presidential elections, Voting, Voting rights, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta September 15, 2020 Gerald Sastra/The Cougar The 2020 presidential election is coming up and as voters, our voices have a right to be heard. [...]

Published
2020

45. Universities should lower tuition in light of the pandemic

Author

Argueta, Kimberly

Subjects
Universities and colleges, Family, Epidemics, Higher education costs, Online education, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta September 7, 2020 Juana Garcia/The Cougar As universities begin the fall semester, their prices and tuition remain the same. This lack of change in [...]

Published
2020

46. We're all in the same boat: there is no shame in seeking counseling

Author

Argueta, Kimberly

Subjects
Mental health, Mental health services, Boats, News, opinion and commentary, Sports and fitness
Abstract

Byline: Kimberly Argueta By Kimberly Argueta September 1, 2020 As students face an unprecedented semester, it is important for them to prioritize their mental health and to remember that UH [...]

Published
2020

47. Author Correction: Sampling the host response to SARS-CoV-2 in hospitals under siege

Author

Charney, Alexander W., Simons, Nicole W., Mouskas, Konstantinos, Lepow, Lauren, Cheng, Esther, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Del Valle, Diane Marie, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Patel, Manishkumar, Xie, Hui, Yi, Nancy, Yu, Alex, Kang, Gurpawan, Mendoza, Anthony, Liharska, Lora E., Moya, Emily, Hartnett, Matthew, Hatem, Sandra, Wilkins, Lillian, Eaton, Melody, Jamal, Hajra, Tuballes, Kevin, Chen, Steven T., Tabachnikova, Alexandra, Chung, Jonathan, Harris, Jocelyn, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Argueta, Kimberly, Karekar, Neha, Lee, Brian, Kelly, Geoffrey, Geanon, Daniel, Handler, Diana, Leech, John, Stefanos, Hiyab, Dawson, Travis, Scott, Ieisha, Francoeur, Nancy, Johnson, Jessica S., Vaid, Akhil, Glicksberg, Benjamin S., Nadkarni, Girish N., Schadt, Eric E., Gelb, Bruce D., Rahman, Adeeb, Sebra, Robert, Martin, Glenn, Marron, Thomas, Beckmann, Noam, Kim-Schulze, Seunghee, Gnjatic, Sacha, and Merad, Miriam

Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41591-021-01247-3.

Published
2021
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48. Author Correction: Sampling the host response to SARS-CoV-2 in hospitals under siege

Author

Charney, Alexander W., Simons, Nicole W., Mouskas, Konstantinos, Lepow, Lauren, Cheng, Esther, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Del Valle, Diane Marie, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Patel, Manishkumar, Xie, Hui, Yi, Nancy, Yu, Alex, Kang, Gurpawan, Liharska, Lora E., Moya, Emily, Hartnett, Matthew, Hatem, Sandra, Wilkins, Lillian, Eaton, Melody, Jamal, Hajra, Tuballes, Kevin, Chen, Steven T., Chung, Jonathan, Harris, Jocelyn, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Argueta, Kimberly, Karekar, Neha, Lee, Brian, Kelly, Geoffrey, Geanon, Daniel, Handler, Diana, Leech, John, Stefanos, Hiyab, Dawson, Travis, Scott, Ieisha, Francoeur, Nancy, Johnson, Jessica S., Vaid, Akhil, Glicksberg, Benjamin S., Nadkarni, Girish N., Schadt, Eric E., Gelb, Bruce D., Rahman, Adeeb, Sebra, Robert, Martin, Glenn, Marron, Thomas, Beckmann, Noam, Kim-Schulze, Seunghee, Gnjatic, Sacha, and Merad, Miriam

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020
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49. Tumor-Immune Signatures of Treatment Resistance to Brentuximab Vedotin with Ipilimumab and/or Nivolumab in Hodgkin Lymphoma.

Author

Gonzalez-Kozlova E, Huang HH, Jagede OA, Tuballes K, Del Valle DM, Kelly G, Patel M, Xie H, Harris J, Argueta K, Nie K, Barcessat V, Moravec R, Altreuter J, Duose DY, Kahl BS, Ansell SM, Yu J, Cerami E, Lindsay JR, Wistuba II, Kim-Schulze S, Diefenbach CS, and Gnjatic S

Subjects
Humans, Female, Male, Adult, Middle Aged, Aged, Young Adult, Brentuximab Vedotin therapeutic use, Hodgkin Disease drug therapy, Hodgkin Disease immunology, Hodgkin Disease blood, Nivolumab therapeutic use, Nivolumab administration & dosage, Ipilimumab therapeutic use, Ipilimumab administration & dosage, Ipilimumab pharmacology, Drug Resistance, Neoplasm, Antineoplastic Combined Chemotherapy Protocols therapeutic use
Abstract

To investigate the cellular and molecular mechanisms associated with targeting CD30-expressing Hodgkin lymphoma (HL) and immune checkpoint modulation induced by combination therapies of CTLA4 and PD1, we leveraged Phase 1/2 multicenter open-label trial NCT01896999 that enrolled patients with refractory or relapsed HL (R/R HL). Using peripheral blood, we assessed soluble proteins, cell composition, T-cell clonality, and tumor antigen-specific antibodies in 54 patients enrolled in the phase 1 component of the trial. NCT01896999 reported high (>75%) overall objective response rates with brentuximab vedotin (BV) in combination with ipilimumab (I) and/or nivolumab (N) in patients with R/R HL. We observed a durable increase in soluble PD1 and plasmacytoid dendritic cells as well as decreases in plasma CCL17, ANGPT2, MMP12, IL13, and CXCL13 in N-containing regimens (BV + N and BV + I + N) compared with BV + I (P < 0.05). Nonresponders and patients with short progression-free survival showed elevated CXCL9, CXCL13, CD5, CCL17, adenosine-deaminase, and MUC16 at baseline or after one treatment cycle and a higher prevalence of NY-ESO-1-specific autoantibodies (P < 0.05). The results suggest a circulating tumor-immune-derived signature of BV ± I ± N treatment resistance that may be useful for patient stratification in combination checkpoint therapy., Significance: Identification of multi-omic immune markers from peripheral blood may help elucidate resistance mechanisms to checkpoint inhibitor and antibody-drug conjugate combinations with potential implications for treatment decisions in relapsed HL., (©2024 The Authors; Published by the American Association for Cancer Research.)

Published
2024
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50. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection.

Author

Nadkami G, Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Valle DD, Thompson R, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Gonzalez-Kozlova E, Kumar A, Paranjpe M, O'Hagan R, Kamat S, Gulamali F, Kauffman J, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin M, He J, Suárez-Fariñas M, Coca S, Chan L, Azeloglu E, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards JB, Glicksberg B, and Charney A

Abstract

Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). Results We demonstrate that COVID-AKI is associated with increased markers of tubular injury ( NGAL ) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2 , trefoil factor 3 , transmembrane emp24 domain-containing protein 10 , and cystatin-C indicating tubular dysfunction and injury. Conclusions Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.

Published
2023
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