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1. 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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2. Autoimmunity in Down’s syndrome via cytokines, CD4 T cells and CD11c+ B cells

Author

Malle, Louise, Patel, Roosheel S., Martin-Fernandez, Marta, Stewart, O Jay, Philippot, Quentin, Buta, Sofija, Richardson, Ashley, Barcessat, Vanessa, Taft, Justin, Bastard, Paul, Samuels, Julie, Mircher, Clotilde, Rebillat, Anne-Sophie, Maillebouis, Louise, Vilaire-Meunier, Marie, Tuballes, Kevin, Rosenberg, Brad R., Trachtman, Rebecca, Casanova, Jean-Laurent, Notarangelo, Luigi D., Gnjatic, Sacha, Bush, Douglas, and Bogunovic, Dusan

Published
2023
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3. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

Author

Thompson, Ryan C., Simons, Nicole W., Wilkins, Lillian, Cheng, Esther, Del Valle, Diane Marie, Hoffman, Gabriel E., Cervia, Carlo, Fennessy, Brian, Mouskas, Konstantinos, Francoeur, Nancy J., Johnson, Jessica S., Lepow, Lauren, Le Berichel, Jessica, Chang, Christie, Beckmann, Aviva G., Wang, Ying-chih, Nie, Kai, Zaki, Nicholas, Tuballes, Kevin, Barcessat, Vanessa, Cedillo, Mario A., Yuan, Dan, Huckins, Laura, Roussos, Panos, Marron, Thomas U., Glicksberg, Benjamin S., Nadkarni, Girish, Heath, James R., Gonzalez-Kozlova, Edgar, Boyman, Onur, Kim-Schulze, Seunghee, Sebra, Robert, Merad, Miriam, Gnjatic, Sacha, Schadt, Eric E., Charney, Alexander W., and Beckmann, Noam D.

Published
2023
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4. Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR

Author

Schwarz, Megan, Torre, Denis, Lozano-Ojalvo, Daniel, Tan, Anthony T., Tabaglio, Tommaso, Mzoughi, Slim, Sanchez-Tarjuelo, Rodrigo, Le Bert, Nina, Lim, Joey Ming Er, Hatem, Sandra, Tuballes, Kevin, Camara, Carmen, Lopez-Granados, Eduardo, Paz-Artal, Estela, Correa-Rocha, Rafael, Ortiz, Alberto, Lopez-Hoyos, Marcos, Portoles, Jose, Cervera, Isabel, Gonzalez-Perez, Maria, Bodega-Mayor, Irene, Conde, Patricia, Oteo-Iglesias, Jesús, Borobia, Alberto M., Carcas, Antonio J., Frías, Jesús, Belda-Iniesta, Cristóbal, Ho, Jessica S. Y., Nunez, Kemuel, Hekmaty, Saboor, Mohammed, Kevin, Marsiglia, William M., Carreño, Juan Manuel, Dar, Arvin C., Berin, Cecilia, Nicoletti, Giuseppe, Della Noce, Isabella, Colombo, Lorenzo, Lapucci, Cristina, Santoro, Graziano, Ferrari, Maurizio, Nie, Kai, Patel, Manishkumar, Barcessat, Vanessa, Gnjatic, Sacha, Harris, Jocelyn, Sebra, Robert, Merad, Miriam, Krammer, Florian, Kim-schulze, Seunghee, Marazzi, Ivan, Bertoletti, Antonio, Ochando, Jordi, and Guccione, Ernesto

Published
2022
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5. Evaluation of immunological responses to third COVID-19 vaccine among people treated with sphingosine receptor-1 modulators and anti-CD20 therapy

Author

Katz Sand, Ilana, Gnjatic, Sacha, Krammer, Florian, Tuballes, Kevin, Carreño, Juan Manuel, Satyanarayan, Sammita, Filomena, Susan, Staker, Erin, Tcheou, Johnstone, Miller, Aaron, Fabian, Michelle, Safi, Neha, Nichols, Jamie, Patel, Jasmin, Krieger, Stephen, Tankou, Stephanie, Horng, Sam, Klineova, Sylvia, Beck, Erin, Merad, Miriam, and Lublin, Fred

Published
2023
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6. 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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7. 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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8. 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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9. 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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10. An inflammatory cytokine signature predicts COVID-19 severity and survival

Author

Del Valle, Diane Marie, Kim-Schulze, Seunghee, Huang, Hsin-Hui, Beckmann, Noam D., Nirenberg, Sharon, Wang, Bo, Lavin, Yonit, Swartz, Talia H., Madduri, Deepu, Stock, Aryeh, Marron, Thomas U., Xie, Hui, Patel, Manishkumar, Tuballes, Kevin, Van Oekelen, Oliver, Rahman, Adeeb, Kovatch, Patricia, Aberg, Judith A., Schadt, Eric, Jagannath, Sundar, Mazumdar, Madhu, Charney, Alexander W., Firpo-Betancourt, Adolfo, Mendu, Damodara Rao, Jhang, Jeffrey, Reich, David, Sigel, Keith, Cordon-Cardo, Carlos, Feldmann, Marc, Parekh, Samir, Merad, Miriam, and Gnjatic, Sacha

Published
2020
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11. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)

Author

Gruber, Conor N., primary, Patel, Roosheel S., additional, Trachtman, Rebecca, additional, Lepow, Lauren, additional, Amanat, Fatima, additional, Krammer, Florian, additional, Wilson, Karen M., additional, Onel, Kenan, additional, Geanon, Daniel, additional, Tuballes, Kevin, additional, Patel, Manishkumar, additional, Mouskas, Konstantinos, additional, O’Donnell, Timothy, additional, Merritt, Elliot, additional, Simons, Nicole W., additional, Barcessat, Vanessa, additional, Del Valle, Diane M., additional, Udondem, Samantha, additional, Kang, Gurpawan, additional, Agashe, Charuta, additional, Karekar, Neha, additional, Grabowska, Joanna, additional, Nie, Kai, additional, Le Berichel, Jessica, additional, Xie, Hui, additional, Beckmann, Noam, additional, Gangadharan, Sandeep, additional, Ofori-Amanfo, George, additional, Laserson, Uri, additional, Rahman, Adeeb, additional, Kim-Schulze, Seunghee, additional, Charney, Alexander W., additional, Gnjatic, Sacha, additional, Gelb, Bruce D., additional, Merad, Miriam, additional, and Bogunovic, Dusan, additional

Published
2023
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12. Supplementary Table 2 from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, primary, Ferran, Luis, primary, Ritter, Erika, primary, Sedrak, Christine, primary, Tuballes, Kevin, primary, Jungbluth, Achim A., primary, Ritter, Gerd, primary, Aghajanian, Carol, primary, Bell-McGuinn, Katherine, primary, Hensley, Martee L., primary, Konner, Jason, primary, Tew, William, primary, Spriggs, David R., primary, Hoffman, Eric W., primary, Venhaus, Ralph, primary, Pan, Linda, primary, Salazar, Andres M., primary, Diefenbach, Catherine Magid, primary, Old, Lloyd J., primary, and Gnjatic, Sacha, primary

Published
2023
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13. Supplementary Figure 2 from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, primary, Ferran, Luis, primary, Ritter, Erika, primary, Sedrak, Christine, primary, Tuballes, Kevin, primary, Jungbluth, Achim A., primary, Ritter, Gerd, primary, Aghajanian, Carol, primary, Bell-McGuinn, Katherine, primary, Hensley, Martee L., primary, Konner, Jason, primary, Tew, William, primary, Spriggs, David R., primary, Hoffman, Eric W., primary, Venhaus, Ralph, primary, Pan, Linda, primary, Salazar, Andres M., primary, Diefenbach, Catherine Magid, primary, Old, Lloyd J., primary, and Gnjatic, Sacha, primary

Published
2023
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14. Supplementary Figure Legend from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, primary, Ferran, Luis, primary, Ritter, Erika, primary, Sedrak, Christine, primary, Tuballes, Kevin, primary, Jungbluth, Achim A., primary, Ritter, Gerd, primary, Aghajanian, Carol, primary, Bell-McGuinn, Katherine, primary, Hensley, Martee L., primary, Konner, Jason, primary, Tew, William, primary, Spriggs, David R., primary, Hoffman, Eric W., primary, Venhaus, Ralph, primary, Pan, Linda, primary, Salazar, Andres M., primary, Diefenbach, Catherine Magid, primary, Old, Lloyd J., primary, and Gnjatic, Sacha, primary

Published
2023
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15. Supplementary Table 1 from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, primary, Ferran, Luis, primary, Ritter, Erika, primary, Sedrak, Christine, primary, Tuballes, Kevin, primary, Jungbluth, Achim A., primary, Ritter, Gerd, primary, Aghajanian, Carol, primary, Bell-McGuinn, Katherine, primary, Hensley, Martee L., primary, Konner, Jason, primary, Tew, William, primary, Spriggs, David R., primary, Hoffman, Eric W., primary, Venhaus, Ralph, primary, Pan, Linda, primary, Salazar, Andres M., primary, Diefenbach, Catherine Magid, primary, Old, Lloyd J., primary, and Gnjatic, Sacha, primary

Published
2023
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16. Supplementary Figure 3 from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, primary, Ferran, Luis, primary, Ritter, Erika, primary, Sedrak, Christine, primary, Tuballes, Kevin, primary, Jungbluth, Achim A., primary, Ritter, Gerd, primary, Aghajanian, Carol, primary, Bell-McGuinn, Katherine, primary, Hensley, Martee L., primary, Konner, Jason, primary, Tew, William, primary, Spriggs, David R., primary, Hoffman, Eric W., primary, Venhaus, Ralph, primary, Pan, Linda, primary, Salazar, Andres M., primary, Diefenbach, Catherine Magid, primary, Old, Lloyd J., primary, and Gnjatic, Sacha, primary

Published
2023
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17. Supplementary Figure 1 from Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, primary, Ferran, Luis, primary, Ritter, Erika, primary, Sedrak, Christine, primary, Tuballes, Kevin, primary, Jungbluth, Achim A., primary, Ritter, Gerd, primary, Aghajanian, Carol, primary, Bell-McGuinn, Katherine, primary, Hensley, Martee L., primary, Konner, Jason, primary, Tew, William, primary, Spriggs, David R., primary, Hoffman, Eric W., primary, Venhaus, Ralph, primary, Pan, Linda, primary, Salazar, Andres M., primary, Diefenbach, Catherine Magid, primary, Old, Lloyd J., primary, and Gnjatic, Sacha, primary

Published
2023
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18. Neutralizing Anti-Granulocyte Macrophage-Colony Stimulating Factor Autoantibodies Recognize Post-Translational Glycosylations on Granulocyte Macrophage-Colony Stimulating Factor Years Before Diagnosis and Predict Complicated Crohn’s Disease

Author

Mortha, Arthur, primary, Remark, Romain, additional, Del Valle, Diane Marie, additional, Chuang, Ling-Shiang, additional, Chai, Zhi, additional, Alves, Inês, additional, Azevedo, Catarina, additional, Gaifem, Joana, additional, Martin, Jerome, additional, Petralia, Francesca, additional, Tuballes, Kevin, additional, Barcessat, Vanessa, additional, Tai, Siu Ling, additional, Huang, Hsin-Hui, additional, Laface, Ilaria, additional, Jerez, Yeray Arteaga, additional, Boschetti, Gilles, additional, Villaverde, Nicole, additional, Wang, Mona D., additional, Korie, Ujunwa M., additional, Murray, Joseph, additional, Choung, Rok-Seon, additional, Sato, Takahiro, additional, Laird, Renee M., additional, Plevy, Scott, additional, Rahman, Adeeb, additional, Torres, Joana, additional, Porter, Chad, additional, Riddle, Mark S., additional, Kenigsberg, Ephraim, additional, Pinho, Salomé S., additional, Cho, Judy H., additional, Merad, Miriam, additional, Colombel, Jean-Frederic, additional, and Gnjatic, Sacha, additional

Published
2022
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19. Evaluation of immunological responses to third COVID-19 vaccine among people treated with sphingosine receptor-1 modulators and anti-CD20 therapy

Author

Katz Sand, Ilana, primary, Gnjatic, Sacha, additional, Krammer, Florian, additional, Tuballes, Kevin, additional, Carreno Quiroz, Juan Manuel, additional, Satyanarayan, Sammita, additional, Filomena, Susan, additional, Staker, Erin, additional, Tcheou, Johnstone, additional, Miller, Aaron, additional, Fabian, Michelle, additional, Safi, Neha, additional, Nichols, Jamie, additional, Patel, Jasmin, additional, Krieger, Stephen, additional, Tankou, Stephanie, additional, Horng, Sam, additional, Klineova, Sylvia, additional, Beck, Erin, additional, Merad, Miriam, additional, and Lublin, Fred, additional

Published
2022
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20. Autoimmunity in Down’s syndrome via cytokines, CD4 T cells and CD11c+ B cells.

Author

Malle, Louise, Patel, Roosheel S., Martin-Fernandez, Marta, Stewart, O Jay, Philippot, Quentin, Buta, Sofija, Richardson, Ashley, Barcessat, Vanessa, Taft, Justin, Bastard, Paul, Samuels, Julie, Mircher, Clotilde, Rebillat, Anne-Sophie, Maillebouis, Louise, Vilaire-Meunier, Marie, Tuballes, Kevin, Rosenberg, Brad R., Trachtman, Rebecca, Casanova, Jean-Laurent, and Notarangelo, Luigi D.

Abstract

Down’s syndrome (DS) presents with a constellation of cardiac, neurocognitive and growth impairments. Individuals with DS are also prone to severe infections and autoimmunity including thyroiditis, type 1 diabetes, coeliac disease and alopecia areata1,2. Here, to investigate the mechanisms underlying autoimmune susceptibility, we mapped the soluble and cellular immune landscape of individuals with DS. We found a persistent elevation of up to 22 cytokines at steady state (at levels often exceeding those in patients with acute infection) and detected basal cellular activation: chronic IL-6 signalling in CD4 T cells and a high proportion of plasmablasts and CD11c+TbethighCD21low B cells (Tbet is also known as TBX21). This subset is known to be autoimmune-prone and displayed even greater autoreactive features in DS including receptors with fewer non-reference nucleotides and higher IGHV4-34 utilization. In vitro, incubation of naive B cells in the plasma of individuals with DS or with IL-6-activated T cells resulted in increased plasmablast differentiation compared with control plasma or unstimulated T cells, respectively. Finally, we detected 365 auto-antibodies in the plasma of individuals with DS, which targeted the gastrointestinal tract, the pancreas, the thyroid, the central nervous system, and the immune system itself. Together, these data point to an autoimmunity-prone state in DS, in which a steady-state cytokinopathy, hyperactivated CD4 T cells and ongoing B cell activation all contribute to a breach in immune tolerance. Our findings also open therapeutic paths, as we demonstrate that T cell activation is resolved not only with broad immunosuppressants such as Jak inhibitors, but also with the more tailored approach of IL-6 inhibition.An autoimmune-prone state of steady-state cytokinopathy, hyperactivated CD4 T cells and ongoing B cell activation contributes to a breach in immune tolerance in individuals with Down’s syndrome. [ABSTRACT FROM AUTHOR]

Published
2023
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21. 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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22. 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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23. 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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24. 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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25. 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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26. Tu1897 ASSOCIATION OF ANTI-GRANULOCYTE-MACROPHAGE COLONYSTIMULATING FACTOR ANTIBODIES WITH THE RISK OF CROHN'S DISEASE ONSET AND INTERACTION WITH GUT MICROBIOTA

Author

Xue, Mingyue, Lee, Sun-Ho, Turpin, Williams, Griffiths, Anne M., Steinhart, A. Hillary, Panaccione, Remo, Dieleman, Levinus A., Huynh, Hien Q., Turner, Dan, Jacobson, Kevan, Aumais, Guy L., Mack, David R., Tuballes, Kevin, Barcessat, Vanessa, Ungaro, Ryan C., Mortha, Arthur, Colombel, Jean Frederic, Korzenik, Joshua, Gnjatic, Sacha, and Croitoru, Kenneth

Published
2024
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30. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

Author

Leader, Andrew M., primary, Grout, John A., additional, Maier, Barbara B., additional, Nabet, Barzin Y., additional, Park, Matthew D., additional, Tabachnikova, Alexandra, additional, Chang, Christie, additional, Walker, Laura, additional, Lansky, Alona, additional, Le Berichel, Jessica, additional, Troncoso, Leanna, additional, Malissen, Nausicaa, additional, Davila, Melanie, additional, Martin, Jerome C., additional, Magri, Giuliana, additional, Tuballes, Kevin, additional, Zhao, Zhen, additional, Petralia, Francesca, additional, Samstein, Robert, additional, D’Amore, Natalie Roy, additional, Thurston, Gavin, additional, Kamphorst, Alice O., additional, Wolf, Andrea, additional, Flores, Raja, additional, Wang, Pei, additional, Müller, Sören, additional, Mellman, Ira, additional, Beasley, Mary Beth, additional, Salmon, Hélène, additional, Rahman, Adeeb H., additional, Marron, Thomas U., additional, Kenigsberg, Ephraim, additional, and Merad, Miriam, additional

Published
2021
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31. 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

32. Suboptimal Humoral and Cellular Immune Response to SARS-CoV-2 RNA Vaccination in Myeloma Patients Is Associated with Anti-CD38 and BCMA-Targeted Treatment

Author

Van Oekelen, Oliver, primary, Agte, Sarita, additional, Aleman, Adolfo, additional, Upadhyaya, Bhaskar, additional, Gleason, Charles R., additional, Srivastava, Komal, additional, Beach, Katherine F., additional, Tuballes, Kevin, additional, Kappes, Katerina, additional, Mouhieddine, Tarek H., additional, Wang, Bo, additional, Kim-Schulze, Seunghee, additional, Chari, Ajai, additional, Gnjatic, Sacha, additional, Bhardwaj, Nina, additional, Brown, Brian D., additional, Merad, Miriam, additional, Cordon-Cardo, Carlos, additional, Krammer, Florian, additional, Jagannath, Sundar, additional, Simon, Viviana, additional, Wajnberg, Ania, additional, and Parekh, Samir, additional

Published
2021
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33. Variable cellular responses to SARS-CoV-2 in fully vaccinated patients with multiple myeloma

Author

Aleman, Adolfo, primary, Upadhyaya, Bhaskar, additional, Tuballes, Kevin, additional, Kappes, Katerina, additional, Gleason, Charles.R., additional, Beach, Katherine, additional, Agte, Sarita, additional, Srivastava, Komal, additional, Van Oekelen, Oliver, additional, Barcessat, Vanessa, additional, Bhardwaj, Nina, additional, Kim-Schulze, Seunghee, additional, Gnjatic, Sacha, additional, Brown, Brian, additional, Cordon-Cardo, Carlos, additional, Krammer, Florian, additional, Merad, Miriam, additional, Jagannath, Sundar, additional, Wajnberg, Ania, additional, Simon, Viviana, additional, Parekh, Samir, additional, Andre, D., additional, Azad, A., additional, Banu, R., additional, Bermúdez-González, M.C., additional, Cai, G., additional, Cognigni, C., additional, David, K., additional, Floda, D., additional, Firpo, A., additional, Kleiner, G., additional, Lyttle, N., additional, Mendez, W., additional, Mulder, L.C.F., additional, Mendu, R., additional, Oostenink, A., additional, Rooker, A., additional, Russo, K., additional, Salimbangon, A., additional, Saksena, M., additional, Shin, A., additional, and Sominsky, L., additional

Published
2021
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34. Autoimmunity in Down’s syndrome via cytokines, CD4 T cells and CD11c+B cells

Author

Malle, Louise, Patel, Roosheel S., Martin-Fernandez, Marta, Stewart, O Jay, Philippot, Quentin, Buta, Sofija, Richardson, Ashley, Barcessat, Vanessa, Taft, Justin, Bastard, Paul, Samuels, Julie, Mircher, Clotilde, Rebillat, Anne-Sophie, Maillebouis, Louise, Vilaire-Meunier, Marie, Tuballes, Kevin, Rosenberg, Brad R., Trachtman, Rebecca, Casanova, Jean-Laurent, Notarangelo, Luigi D., Gnjatic, Sacha, Bush, Douglas, and Bogunovic, Dusan

Abstract

Down’s syndrome (DS) presents with a constellation of cardiac, neurocognitive and growth impairments. Individuals with DS are also prone to severe infections and autoimmunity including thyroiditis, type 1 diabetes, coeliac disease and alopecia areata1,2. Here, to investigate the mechanisms underlying autoimmune susceptibility, we mapped the soluble and cellular immune landscape of individuals with DS. We found a persistent elevation of up to 22 cytokines at steady state (at levels often exceeding those in patients with acute infection) and detected basal cellular activation: chronic IL-6 signalling in CD4 T cells and a high proportion of plasmablasts and CD11c+TbethighCD21lowB cells (Tbet is also known as TBX21). This subset is known to be autoimmune-prone and displayed even greater autoreactive features in DS including receptors with fewer non-reference nucleotides and higher IGHV4-34utilization. In vitro, incubation of naive B cells in the plasma of individuals with DS or with IL-6-activated T cells resulted in increased plasmablast differentiation compared with control plasma or unstimulated T cells, respectively. Finally, we detected 365 auto-antibodies in the plasma of individuals with DS, which targeted the gastrointestinal tract, the pancreas, the thyroid, the central nervous system, and the immune system itself. Together, these data point to an autoimmunity-prone state in DS, in which a steady-state cytokinopathy, hyperactivated CD4 T cells and ongoing B cell activation all contribute to a breach in immune tolerance. Our findings also open therapeutic paths, as we demonstrate that T cell activation is resolved not only with broad immunosuppressants such as Jak inhibitors, but also with the more tailored approach of IL-6 inhibition.

Published
2023
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35. Anti–GM-CSF autoantibodies promote a “pre-diseased” state in Crohn’s Disease

Author

Mortha, Arthur, primary, Remark, Romain, additional, Del Valle, Diane Marie, additional, Chuang, Ling-Shiang, additional, Chai, Zhi, additional, Alves, Inês, additional, Azevedo, Catarina, additional, Gaifem, Joana, additional, Martin, Jerome, additional, Tuballes, Kevin, additional, Barcessat, Vanessa, additional, Tai, Siu Ling, additional, Huang, Hsin-Hui, additional, Laface, Ilaria, additional, Jerez, Yeray Arteaga, additional, Boschetti, Gilles, additional, Villaverde, Nicole, additional, Wang, Mona D., additional, Korie, Ujunwa M., additional, Murray, Joseph, additional, Choung, Rok-Seon, additional, Sato, Takahiro, additional, Laird, Renee M., additional, Plevy, Scot, additional, Rahman, Adeeb, additional, Torres, Joana, additional, Porter, Chad, additional, Riddle, Mark S., additional, Kenigsberg, Ephraim, additional, Pinho, Salomé S., additional, Cho, Judy H., additional, Merad, Miriam, additional, Colombel, Jean-Frederic, additional, and Gnjatic, Sacha, additional

Published
2021
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36. Serologic Response to Messenger RNA Coronavirus Disease 2019 Vaccines in Inflammatory Bowel Disease Patients Receiving Biologic Therapies

Author

Wong, Serre-Yu, primary, Dixon, Rebekah, additional, Martinez Pazos, Vicky, additional, Gnjatic, Sacha, additional, Colombel, Jean-Frederic, additional, Cadwell, Ken, additional, Gold, Stephanie, additional, Helmus, Drew, additional, Neil, Jessica Anne, additional, Sota, Stela, additional, Jang, Kyung Ku, additional, Ching, Krystal, additional, Venzon, Mericien, additional, Yao, Xiaomin, additional, Bernard, Lucie, additional, Chen, Xin, additional, Navalurkar, Reema, additional, Mendiolaza, Michelle, additional, Reyes-Mercedes, Pamela, additional, Nunez, Sara, additional, Stanley, Stephanie, additional, Jimenez, Darwin, additional, Tankelevich, Michael, additional, Phillipe, Brianne, additional, Ramos, Julio, additional, Tuballes, Kevin, additional, Barcessat, Vanessa, additional, Herrera, Natalia, additional, Satsangi, Jack, additional, Watanabe, Kenji, additional, Vermeire, Séverine, additional, Steinwurz, Flavio, additional, Silverberg, Mark, additional, Rubin, David T., additional, Roda, Giulia, additional, Reinisch, Walter, additional, Ng, Siew Chien, additional, Lindsay, James, additional, Halfvarson, Jonas, additional, Allez, Matthieu, additional, Ahuja, Vineet, additional, and Abreu, Maria, additional

Published
2021
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37. 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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39. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)

Author

Gruber, Conor N., primary, Patel, Roosheel S., additional, Trachtman, Rebecca, additional, Lepow, Lauren, additional, Amanat, Fatima, additional, Krammer, Florian, additional, Wilson, Karen M., additional, Onel, Kenan, additional, Geanon, Daniel, additional, Tuballes, Kevin, additional, Patel, Manishkumar, additional, Mouskas, Konstantinos, additional, O’Donnell, Timothy, additional, Merritt, Elliot, additional, Simons, Nicole W., additional, Barcessat, Vanessa, additional, Del Valle, Diane M., additional, Udondem, Samantha, additional, Kang, Gurpawan, additional, Gangadharan, Sandeep, additional, Ofori-Amanfo, George, additional, Laserson, Uri, additional, Rahman, Adeeb, additional, Kim-Schulze, Seunghee, additional, Charney, Alexander W., additional, Gnjatic, Sacha, additional, Gelb, Bruce D., additional, Merad, Miriam, additional, and Bogunovic, Dusan, additional

Published
2020
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40. CITEseq analysis of non-small-cell lung cancer lesions reveals an axis of immune cell activation associated with tumor antigen load and TP53 mutations

Author

Leader, Andrew M., primary, Grout, John A., additional, Chang, Christie, additional, Maier, Barbara, additional, Tabachnikova, Alexandra, additional, Walker, Laura, additional, Lansky, Alona, additional, LeBerichel, Jessica, additional, Malissen, Naussica, additional, Davila, Melanie, additional, Martin, Jerome, additional, Magri, Giuliana, additional, Tuballes, Kevin, additional, Zhao, Zhen, additional, Petralia, Francesca, additional, Samstein, Robert, additional, D’Amore, Natalie Roy, additional, Thurston, Gavin, additional, Kamphorst, Alice, additional, Wolf, Andrea, additional, Flores, Raja, additional, Wang, Pei, additional, Beasley, Mary Beth, additional, Salmon, Helene, additional, Rahman, Adeeb H., additional, Marron, Thomas U., additional, Kenigsberg, Ephraim, additional, and Merad, Miriam, additional

Published
2020
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41. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)

Author

Gruber, Conor, primary, Patel, Roosheel, additional, Trachman, Rebecca, additional, Lepow, Lauren, additional, Amanat, Fatima, additional, Krammer, Florian, additional, Wilson, Karen M., additional, Onel, Kenan, additional, Geanon, Daniel, additional, Tuballes, Kevin, additional, Patel, Manishkumar, additional, Mouskas, Konstantinos, additional, Simons, Nicole, additional, Barcessat, Vanessa, additional, Del Valle, Diane, additional, Udondem, Samantha, additional, Kang, Gurpawan, additional, Gangadharan, Sandeep, additional, Ofori-Amanfo, George, additional, Rahman, Adeeb, additional, Kim-Schulze, Seunghee, additional, Charney, Alexander, additional, Gnjatic, Sacha, additional, Gelb, Bruce D., additional, Merad, Miriam, additional, and Bogunovic, Dusan, additional

Published
2020
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42. A Phase 1b Study Evaluating the Safety, Tolerability, and Immunogenicity of CMB305, a Lentiviral-Based Prime-Boost Vaccine Regimen, in Patients with Locally Advanced, Relapsed, or Metastatic Cancer Expressing NY-ESO-1

Author

Somaiah, Neeta, primary, Chawla, Sant P., additional, Block, Matthew S., additional, Morris, John C., additional, Do, Khanh, additional, Kim, Joseph W., additional, Druta, Mihaela, additional, Sankhala, Kamalesh K., additional, Hwu, Patrick, additional, Jones, Robin L., additional, Gnjatic, Sacha, additional, Kim-Schulze, Seunghee, additional, Tuballes, Kevin, additional, Yishak, Mahlet, additional, Lu, Hailing, additional, Yakovich, Adam, additional, Ter Meulen, Jan, additional, Chen, Michael, additional, Kenney, Richard T., additional, Bohac, Chet, additional, and Pollack, Seth M., additional

Published
2020
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43. 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

44. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

Author

Thompson, Ryan C., Simons, Nicole W., Wilkins, Lillian, Cheng, Esther, Del Valle, Diane Marie, Hoffman, Gabriel E., Cervia, Carlo, Fennessy, Brian, Mouskas, Konstantinos, Francoeur, Nancy J., Johnson, Jessica S., Lepow, Lauren, Le Berichel, Jessica, Chang, Christie, Beckmann, Aviva G., Wang, Ying-chih, Nie, Kai, Zaki, Nicholas, Tuballes, Kevin, Barcessat, Vanessa, Cedillo, Mario A., Yuan, Dan, Huckins, Laura, Roussos, Panos, Marron, Thomas U., Glicksberg, Benjamin S., Nadkarni, Girish, Heath, James R., Gonzalez-Kozlova, Edgar, Boyman, Onur, Kim-Schulze, Seunghee, Sebra, Robert, Merad, Miriam, Gnjatic, Sacha, Schadt, Eric E., Charney, Alexander W., and Beckmann, Noam D.

Abstract

Post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are debilitating, clinically heterogeneous and of unknown molecular etiology. A transcriptome-wide investigation was performed in 165 acutely infected hospitalized individuals who were followed clinically into the post-acute period. Distinct gene expression signatures of post-acute sequelae were already present in whole blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell-associated gene expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in individuals with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.

Published
2022
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46. Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients

Author

Sabbatini, Paul, primary, Tsuji, Takemasa, additional, Ferran, Luis, additional, Ritter, Erika, additional, Sedrak, Christine, additional, Tuballes, Kevin, additional, Jungbluth, Achim A., additional, Ritter, Gerd, additional, Aghajanian, Carol, additional, Bell-McGuinn, Katherine, additional, Hensley, Martee L., additional, Konner, Jason, additional, Tew, William, additional, Spriggs, David R., additional, Hoffman, Eric W., additional, Venhaus, Ralph, additional, Pan, Linda, additional, Salazar, Andres M., additional, Diefenbach, Catherine Magid, additional, Old, Lloyd J., additional, and Gnjatic, Sacha, additional

Published
2012
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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. Evaluation of immunological responses to third COVID-19 vaccine among people treated with sphingosine receptor-1 modulators and anti-CD20 therapy.

Author

Sand IK, Gnjatic S, Krammer F, Tuballes K, Carreño JM, Satyanarayan S, Filomena S, Staker E, Tcheou J, Miller A, Fabian M, Safi N, Nichols J, Patel J, Krieger S, Tankou S, Horng S, Klineova S, Beck E, Merad M, and Lublin F

Abstract

Importance: People living with multiple sclerosis (MS) and other disorders treated with immunomodulatory therapies remain concerned about suboptimal responses to coronavirus disease 2019 (COVID-19) vaccines. Important questions persist regarding immunological response to third vaccines, particularly with respect to newer virus variants., Objective: Evaluate humoral and cellular immune responses to third COVID-19 vaccine dose in people on anti-CD20 therapy and sphingosine 1-phosphate receptor (S1PR) modulators, including Omicron-specific assays., Design: Observational study evaluating immunological response to third COVID-19 vaccine dose in volunteers treated with anti-CD20 agents, S1PR modulators, and healthy controls. Neutralizing antibodies against USA-WA1/2020 (WA1) and B.1.1.529 (BA.1) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were measured before and after third vaccine. Cellular responses to spike peptide pools generated from WA1 and BA.1 were evaluated., Setting: Mount Sinai Hospital., Participants: People treated with anti-CD20 therapy or S1PR modulators and healthy volunteers., Exposure: Treatment with anti-CD20 therapy, S1PR modulator, or neither., Main Outcomes and Measures: Serum neutralizing antibodies and ex vivo T cell responses against SARS-CoV-2 antigens., Results: This cohort includes 25 participants on anti-CD20 therapy, 12 on S1PR modulators, and 14 healthy controls. Among those on anti-CD20 therapy, neutralizing antibodies to WA1 were significantly reduced compared to healthy controls (ID50% GM post-vaccination of 8.1 ± 2.8 in anti-CD20 therapy group vs 452.6 ± 8.442 healthy controls, P<0.0001) and neutralizing antibodies to BA.1 were below the threshold of detection nearly universally. However, cellular responses, including to Omicron-specific peptides, were not significantly different from controls. Among those on S1PR modulators, neutralizing antibodies to WA1 were detected in a minority, and only 3/12 had neutralizing antibodies just at the limit of detection to BA.1. Cellular responses to Spike antigen in those on S1PR modulators were reduced by a factor of 100 compared to controls (median 0.0008% vs. 0.08%, p<0.001) and were not significantly "boosted" by a third injection., Conclusions and Relevance: Participants on immunomodulators had impaired antibody neutralization capacity, particularly to BA.1, even after a third vaccine. T cell responses were not affected by anti-CD20 therapies, but were nearly abrogated by S1PR modulators. These results have clinical implications warranting further study.

Published
2022
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