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1. Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing

Author

Craig, Amanda J., Silveira, Maruhen A. Datsch, Ma, Lichun, Revsine, Mahler, Wang, Limin, Heinrich, Sophia, Rae, Zachary, Ruchinskas, Allison, Dadkhah, Kimia, Do, Whitney, Behrens, Shay, Mehrabadi, Farid R., Dominguez, Dana A., Forgues, Marshonna, Budhu, Anuradha, Chaisaingmongkol, Jittiporn, Hernandez, Jonathan M., Davis, Jeremy L., Tran, Bao, Marquardt, Jens U., Ruchirawat, Mathuros, Kelly, Michael, Greten, Tim F., and Wang, Xin W.

Published
2023
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2. Supplementary Table 2 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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3. Supplementary Table 5 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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4. Oligos and Primers - related to Methods from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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5. Data from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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6. Supplementary Table 1 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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7. Supplementary Table 6 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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8. Supplementary Table 7 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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9. Supplementary Methods from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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10. Supplementary Figures and Legends from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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11. Supplementary Table 4 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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12. Supplementary Table 3 from Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., primary, Wang, James Q., primary, Huang, DaWei, primary, Wright, George W., primary, Kasbekar, Monica, primary, Choi, Jaewoo, primary, Young, Ryan M., primary, Webster, Daniel E., primary, Yang, Yandan, primary, Zhao, Hong, primary, Yu, Xin, primary, Xu, Weihong, primary, Roulland, Sandrine, primary, Ceribelli, Michele, primary, Zhang, Xiaohu, primary, Wilson, Kelli M., primary, Chen, Lu, primary, McKnight, Crystal, primary, Klumpp-Thomas, Carleen, primary, Thomas, Craig J., primary, Häupl, Björn, primary, Oellerich, Thomas, primary, Rae, Zachary, primary, Kelly, Michael C., primary, Ahn, Inhye E., primary, Sun, Clare, primary, Gaglione, Erika M., primary, Wilson, Wyndham H., primary, Wiestner, Adrian, primary, and Staudt, Louis M., primary

Published
2023
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13. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers

Author

Hanada, Ken-ichi, primary, Zhao, Chihao, additional, Gil-Hoyos, Raul, additional, Gartner, Jared J., additional, Chow-Parmer, Christopher, additional, Lowery, Frank J., additional, Krishna, Sri, additional, Prickett, Todd D., additional, Kivitz, Scott, additional, Parkhurst, Maria R., additional, Wong, Nathan, additional, Rae, Zachary, additional, Kelly, Michael C., additional, Goff, Stephanie L., additional, Robbins, Paul F., additional, Rosenberg, Steven A., additional, and Yang, James C., additional

Published
2022
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14. Overcoming Acquired Epigenetic Resistance to BTK Inhibitors

Author

Shaffer, Arthur L., primary, Phelan, James D., additional, Wang, James Q., additional, Huang, DaWei, additional, Wright, George W., additional, Kasbekar, Monica, additional, Choi, Jaewoo, additional, Young, Ryan M., additional, Webster, Daniel E., additional, Yang, Yandan, additional, Zhao, Hong, additional, Yu, Xin, additional, Xu, Weihong, additional, Roulland, Sandrine, additional, Ceribelli, Michele, additional, Zhang, Xiaohu, additional, Wilson, Kelli M., additional, Chen, Lu, additional, McKnight, Crystal, additional, Klumpp-Thomas, Carleen, additional, Thomas, Craig J., additional, Häupl, Björn, additional, Oellerich, Thomas, additional, Rae, Zachary, additional, Kelly, Michael C., additional, Ahn, Inhye E., additional, Sun, Clare, additional, Gaglione, Erika M., additional, Wilson, Wyndham H., additional, Wiestner, Adrian, additional, and Staudt, Louis M., additional

Published
2021
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15. Abstract 1509: A signature for tumor neoantigen-reactive T-cells in fresh human lung cancers allows rapid cloning of their receptors

Author

Hanada, Kenichi, primary, Zhao, Chihao, additional, Gil-Hoyos, Raul, additional, Gartner, Jared, additional, Chow-Parmer, Christopher, additional, Lowery, Frank, additional, Krishna, Sri, additional, Chatmon, Samuel, additional, Todd, Prickett D., additional, Kivitz, Scott, additional, Parkhurst, Maria, additional, Langhan, Michelle, additional, Shelton, Thomas, additional, Franco, Zulmarie, additional, Somerville, Robert, additional, Wunderlich, John, additional, Danforth, David, additional, Rae, Zachary, additional, Michael, Kelly, additional, Wong, Nathan, additional, Robbins, Paul, additional, Rosenberg, Steven, additional, and Yang, James, additional

Published
2021
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17. Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis

Author

Kaczanowska, Sabina, primary, Beury, Daniel W., additional, Gopalan, Vishaka, additional, Tycko, Arielle K., additional, Qin, Haiying, additional, Clements, Miranda E., additional, Drake, Justin, additional, Nwanze, Chiadika, additional, Murgai, Meera, additional, Rae, Zachary, additional, Ju, Wei, additional, Alexander, Katherine A., additional, Kline, Jessica, additional, Contreras, Cristina F., additional, Wessel, Kristin M., additional, Patel, Shil, additional, Hannenhalli, Sridhar, additional, Kelly, Michael C., additional, and Kaplan, Rosandra N., additional

Published
2021
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18. Case Report: Single-Cell Transcriptomic Analysis of an Anaplastic Oligodendroglioma Post Immunotherapy

Author

Yu, Guangyang, primary, Butler, Madison K., additional, Abdelmaksoud, Abdalla, additional, Pang, Ying, additional, Su, Yu-Ting, additional, Rae, Zachary, additional, Dadkhah, Kimia, additional, Kelly, Michael C., additional, Song, Young K., additional, Wei, Jun S., additional, Terabe, Masaki, additional, Atony, Ramya, additional, Mentges, Kelly, additional, Theeler, Brett J., additional, Penas-Prado, Marta, additional, Butman, John, additional, Camphausen, Kevin, additional, Zaghloul, Kareem A., additional, Nduom, Edjah, additional, Quezado, Martha, additional, Aldape, Kenneth, additional, Armstrong, Terri S., additional, Gilbert, Mark R., additional, Gulley, James L., additional, Khan, Javed, additional, and Wu, Jing, additional

Published
2021
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19. An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development

Author

Chopp, Laura B., primary, Gopalan, Vishaka, additional, Ciucci, Thomas, additional, Ruchinskas, Allison, additional, Rae, Zachary, additional, Lagarde, Manon, additional, Gao, Yayi, additional, Li, Caiyi, additional, Bosticardo, Marita, additional, Pala, Francesca, additional, Livak, Ferenc, additional, Kelly, Michael C., additional, Hannenhalli, Sridhar, additional, and Bosselut, Rémy, additional

Published
2020
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20. Abstract 1500: Understanding tumor cell community and its evolution by single cell analysis in liver cancer

Author

Ma, Lichun, primary, Hernandez, Maria O., additional, Zhao, Yongmei, additional, Mehta, Monika, additional, Tran, Bao, additional, Kelly, Michael, additional, Rae, Zachary, additional, Hernandez, Jonathan M., additional, Davis, Jeremy L., additional, Martin, Sean P., additional, Kleiner, David E., additional, Hewitt, Stephen M., additional, Ylaya, Kris, additional, Wood, Bradford J., additional, Greten, Tim F., additional, and Wang, Xin Wei, additional

Published
2020
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21. Abstract LB-141: Increased epigenetic plasticity and tumor heterogeneity predict resistance to CD19 CAR T cell therapy in pre-treatment pediatric acute lymphoblastic leukemia

Author

Masih, Katherine E., primary, Abdelmaksoud, Abdalla, additional, Milewski, David, additional, Gryder, Berkley E., additional, Gardner, Rebecca, additional, Wilson, Ashley L., additional, Stanton, Benjamin Z., additional, Song, Young K., additional, Wang, Chaoyu, additional, Wen, Xinyu, additional, Adebola, Serifat, additional, Rae, Zachary, additional, Cheuk, Adam, additional, Lack, Justin, additional, Altan-Bonnet, Gregoire, additional, Kelly, Michael, additional, Wei, Jun, additional, Jensen, Michael, additional, and Orentas, Rimas J., additional

Published
2020
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22. Abstract A11: A comprehensive and integrative omic analysis of multiply relapsed refractory pediatric pre-B cell acute lymphoblastic leukemia predicts response to CD19 CAR T-cell therapy

Author

Masih, Katherine E., primary, Gardner, Rebecca, additional, Gryder, Berkley E., additional, Abdelmaksoud, Abdalla, additional, Wilson, Ashley, additional, Adebola, Serifat, additional, Stanton, Benjamin Z., additional, Song, Young K., additional, Lack, Justin, additional, Wang, Chaoyu, additional, Wen, Xinyu, additional, Rae, Zachary, additional, Cheuk, Adam, additional, Altan-Bonnet, Gregoire, additional, Kelly, Michael, additional, Wei, Jun S., additional, Jensen, Michael C., additional, Orentas, Rimas J., additional, and Khan, Javed, additional

Published
2020
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23. Detailed Multi-Method Analysis of Bone Marrow from Pediatric Pre-B-ALL Patients Prior to CD19-CAR-T Therapy Subsequently Evidencing Overt CAR-T Resistance

Author

Masih, Katherine Elizabeth, primary, Gardner, Rebecca, additional, Gryder, Berkley, additional, Abdallah, Abdelmaksoud, additional, Lack, Justin, additional, Stanton, Benjamin, additional, Wilson, Ashley, additional, Sindiri, Sivasish, additional, Song, Young, additional, Rae, Zachary, additional, Kelly, Michael, additional, Chaoyu, Wang, additional, Wen, Xinyu, additional, Cheuk, Adam, additional, Wei, Jun, additional, Jensen, Michael C., additional, Khan, Javed, additional, and Orentas, Rimas, additional

Published
2019
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24. Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer

Author

Ma, Lichun, primary, Hernandez, Maria O., additional, Zhao, Yongmei, additional, Mehta, Monika, additional, Tran, Bao, additional, Kelly, Michael, additional, Rae, Zachary, additional, Hernandez, Jonathan M., additional, Davis, Jeremy L., additional, Martin, Sean P., additional, Kleiner, David E., additional, Hewitt, Stephen M., additional, Ylaya, Kris, additional, Wood, Bradford J., additional, Greten, Tim F., additional, and Wang, Xin Wei, additional

Published
2019
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25. Abstract LB-056: An integrated genomic, epigenetic, proteomic, and single cell analysis of pediatric B cell acute lymphoblastic leukemia to elucidate resistance mechanisms to CD19 CAR T cell therapy

Author

Masih, Katherine E., primary, Gardner, Rebecca, additional, Gryder, Berkley E., additional, Lack, Justin, additional, Stanton, Benjamin Z., additional, Wilson, Ashley, additional, Finney, Olivia, additional, Sindiri, Sivasish, additional, Song, Young, additional, Rae, Zachary, additional, Kelly, Michael, additional, Wang, Chaoyu, additional, Wen, Xinyu, additional, Cheuk, Adam, additional, Wei, Jun S., additional, Jensen, Michael, additional, Orentas, Rimas, additional, and Khan, Javed, additional

Published
2019
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26. Multi-tiered approach to detect autoimmune cross-reactivity of therapeutic T cell receptors.

Author

Ishii, Kazusa, Davies, John S., Sinkoe, Andrew L., Nguyen, Kilyna A., Norberg, Scott M., McIntosh, Crystal P., Kadakia, Tejas, Serna, Carylinda, Rae, Zachary, Kelly, Michael C., and Hinrichs, Christian S.

Subjects
*T cells, *T cell receptors, *B cells, *CROSS reactions (Immunology), *REVERSE transcriptase polymerase chain reaction
Abstract

The article focuses on a study that presents a practical framework to detect potentially harmful cross-reactivity of therapeutic T cell receptor (TCR) candidates, employing various assays, including p-MHC tetramer binding, cell line recognition, and reactivity against candidate peptide libraries. The layered approach effectively identifies unsafe cross-reactivity, offering essential insights for the safe development of TCR-based therapies.

Published
2023
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