Cytotoxic CD4+ T cells eliminate senescent cells by targeting cytomegalovirus antigen

Authors: Hasegawa, Tatsuya, Oka, Tomonori, Son, Heehwa G., Oliver-García, Valeria S., Azin, Marjan, Eisenhaure, Thomas M., Lieb, David J., Hacohen, Nir, Demehri, Shadmehr

Source: In Cell 30 March 2023 186(7):1417-1431

Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease

Authors: Dahlqvist, Johanna, Fulco, Charles P, Ray, John P, Liechti, Thomas, de Boer, Carl G, Lieb, David J, Eisenhaure, Thomas M, Engreitz, Jesse M, Roederer, Mario, Hacohen, Nir

Source: Human molecular genetics. 31(12):1946-1961

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Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue.

Authors: Bell, Richard D., Brendel, Matthew, Konnaris, Maxwell A., Xiang, Justin, Otero, Miguel, Fontana, Mark A., Bai, Zilong, Albrecht, Jennifer, Apruzzese, William, Boyce, Brendan F., Boyle, David L., Brenner, Michael B., Bridges Jr., S. Louis, Buckley, Christopher D., Buckner, Jane H., Bykerk, Vivian P., Dolan, James, Eisenhaure, Thomas M., Filer, Andrew, Firestein, Gary S.

Source: Nature Communications; 8/29/2024, Vol. 15 Issue 1, p1-17, 17p

Subject Terms: RHEUMATOID arthritis, MEDICAL research, PHENOTYPES, HISTOPATHOLOGY, ARTHRITIS

The immune cell landscape in kidneys of patients with lupus nephritis

Authors: Arazi, Arnon, Rao, Deepak, Berthier, Celine, Davidson, Anne, Liu, Yanyan, Hoover, Paul, Chicoine, Adam, Eisenhaure, Thomas, Jonsson, A., Li, Shuqiang, Lieb, David, Zhang, Fan, Slowikowski, Kamil, Browne, Edward, Noma, Akiko, Sutherby, Danielle, Steelman, Scott, Smilek, Dawn, Tosta, Patti, Apruzzese, William, Massarotti, Elena, Dall'Era, Maria, Park, Meyeon, Kamen, Diane, Furie, Richard, Payan-Schober, Fernanda, Pendergraft, William, McInnis, Elizabeth, Buyon, Jill, Petri, Michelle, Putterman, Chaim, Kalunian, Kenneth, Woodle, E., Lederer, James, Hildeman, David, Nusbaum, Chad, Raychaudhuri, Soumya, Kretzler, Matthias, Anolik, Jennifer, Brenner, Michael, Wofsy, David, Hacohen, Nir, Diamond, Betty

Source: Nature immunology. 20(7):902-914

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100189903013.0x000001&indx=1&recIds=ETOCvdc_100189903013.0x000001

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

Authors: Zhang, Fan, Wei, Kevin, Slowikowski, Kamil, Fonseka, Chamith, Rao, Deepak, Kelly, Stephen, Goodman, Susan, Tabechian, Darren, Hughes, Laura, Salomon-Escoto, Karen, Watts, Gerald, Jonsson, A., Rangel-Moreno, Javier, Meednu, Nida, Rozo, Cristina, Apruzzese, William, Eisenhaure, Thomas, Lieb, David, Boyle, David, Mandelin, Arthur, Boyce, Brendan, DiCarlo, Edward, Gravallese, Ellen, Gregersen, Peter, Moreland, Larry, Firestein, Gary, Hacohen, Nir, Nusbaum, Chad, Lederer, James, Perlman, Harris, Pitzalis, Costantino, Filer, Andrew, Holers, V., Bykerk, Vivian, Donlin, Laura, Anolik, Jennifer, Brenner, Michael, Raychaudhuri, Soumya

Source: Nature immunology. 20(7):928-942

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181195337.0x000001&indx=1&recIds=ETOCvdc_100181195337.0x000001

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling

Authors: Mertins, Philipp, Przybylski, Dariusz, Yosef, Nir, Qiao, Jana, Clauser, Karl, Raychowdhury, Raktima, Eisenhaure, Thomas M., Maritzen, Tanja, Haucke, Volker, Satoh, Takashi, Akira, Shizuo, Carr, Steven A., Regev, Aviv, Hacohen, Nir, Chevrier, Nicolas

Source: In Cell Reports 27 June 2017 19(13):2853-2866

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

Authors: Abelin, Jennifer G., Keskin, Derin B., Sarkizova, Siranush, Hartigan, Christina R., Zhang, Wandi, Sidney, John, Stevens, Jonathan, Lane, William, Zhang, Guang Lan, Eisenhaure, Thomas M., Clauser, Karl R., Hacohen, Nir, Rooney, Michael S., Carr, Steven A., Wu, Catherine J.

Source: In Immunity 21 February 2017 46(2):315-326

Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue

Authors: Donlin, Laura, Rao, Deepak, Wei, Kevin, Slowikowski, Kamil, McGeachy, Mandy, Turner, Jason, Meednu, Nida, Mizoguchi, Fumitaka, Gutierrez-Arcelus, Maria, Lieb, David, Keegan, Joshua, Muskat, Kaylin, Hillman, Joshua, Rozo, Cristina, Ricker, Edd, Eisenhaure, Thomas, Li, Shuqiang, Browne, Edward, Chicoine, Adam, Sutherby, Danielle, Noma, Akiko, Nusbaum, Chad, Kelly, Stephen, Pernis, Alessandra, Ivashkiv, Lionel, Goodman, Susan, Robinson, William, Utz, Paul, Lederer, James, Gravallese, Ellen, Boyce, Brendan, Hacohen, Nir, Pitzalis, Costantino, Gregersen, Peter, Firestein, Gary, Raychaudhuri, Soumya, Moreland, Larry, Holers, V. Michael, Bykerk, Vivian, Filer, Andrew, Boyle, David, Brenner, Michael, Anolik, Jennifer

Source: Arthritis research & therapy. 20(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174866048.0x000001&indx=1&recIds=ETOCvdc_100174866048.0x000001

A secreted PD-L1 splice variant that covalently dimerizes and mediates immunosuppression

Authors: Mahoney, Kathleen M., Shukla, Sachet A., Patsoukis, Nikolaos, Chaudhri, Apoorvi, Browne, Edward P., Arazi, Arnon, Eisenhaure, Thomas M., Pendergraft, William F., Hua, Ping, Pham, Hung C., Bu, Xia, Zhu, Baogong, Hacohen, Nir, Fritsch, Edward F., Boussiotis, Vassiliki A., Wu, Catherine J., Freeman, Gordon J.

Source: Cancer immunology, immunotherapy. 68(3):421-432

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125514997.0x000001&indx=1&recIds=ETOCvdc_100125514997.0x000001

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Authors: Parnas, Oren, Jovanovic, Marko, Eisenhaure, Thomas M., Herbst, Rebecca H., Dixit, Atray, Ye, Chun Jimmie, Przybylski, Dariusz, Platt, Randall J., Tirosh, Itay, Sanjana, Neville E., Shalem, Ophir, Satija, Rahul, Raychowdhury, Raktima, Mertins, Philipp, Carr, Steven A., Zhang, Feng, Hacohen, Nir, Regev, Aviv

Source: In Cell 30 July 2015 162(3):675-686

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

Authors: Platt, Randall J., Chen, Sidi, Zhou, Yang, Yim, Michael J., Swiech, Lukasz, Kempton, Hannah R., Dahlman, James E., Parnas, Oren, Eisenhaure, Thomas M., Jovanovic, Marko, Graham, Daniel B., Jhunjhunwala, Siddharth, Heidenreich, Matthias, Xavier, Ramnik J., Langer, Robert, Anderson, Daniel G., Hacohen, Nir, Regev, Aviv, Feng, Guoping, Sharp, Phillip A., Zhang, Feng

Source: In Cell 9 October 2014 159(2):440-455

Dynamic profiling of the protein life cycle in response to pathogens

Authors: Jovanovic, Marko, Rooney, Michael S., Mertins, Philipp, Przybylski, Dariusz, Chevrier, Nicolas, Satija, Rahul, Rodriguez, Edwin H., Fields, Alexander P., Schwartz, Schraga, Raychowdhury, Raktima, Mumbach, Maxwell R., Eisenhaure, Thomas, Rabani, Michal, Gennert, Dave, Lu, Diana, Delorey, Toni, Weissman, Jonathan S., Carr, Steven A., Hacohen, Nir, Regev, Aviv

Source: Science, 2015 Mar 01. 347(6226), 1112-1112.

Access URL: http://www.jstor.org/stable/24746514

Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis

Authors: Thomas, Molly Fisher, Slowikowski, Kamil, Manakongtreecheep, Kasidet, Sen, Pritha, Samanta, Nandini, Tantivit, Jessica, Nasrallah, Mazen, Zubiri, Leyre, Smith, Neal P., Tirard, Alice, Ramesh, Swetha, Arnold, Benjamin Y., Nieman, Linda T., Chen, Jonathan H., Eisenhaure, Thomas, Pelka, Karin, Song, Yuhui, Xu, Katherine H., Jorgji, Vjola, Pinto, Christopher J., Sharova, Tatyana, Glasser, Rachel, Chan, PuiYee, Sullivan, Ryan J., Khalili, Hamed, Juric, Dejan, Boland, Genevieve M., Dougan, Michael, Hacohen, Nir, Li, Bo, Reynolds, Kerry L., Villani, Alexandra-Chloé

Source: Nature Medicine; 20240101, Issue: Preprints p1-14, 14p

Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection

Authors: Li, Bo, Clohisey, Sara M., Chia, Bing Shao, Wang, Bo, Cui, Ang, Eisenhaure, Thomas, Schweitzer, Lawrence D., Hoover, Paul, Parkinson, Nicholas J., Nachshon, Aharon, Smith, Nikki, Regan, Tim, Farr, David, Gutmann, Michael U., Bukhari, Syed Irfan, Law, Andrew, Sangesland, Maya, Gat-Viks, Irit, Digard, Paul, Vasudevan, Shobha, Lingwood, Daniel, Dockrell, David H., Doench, John G., Baillie, J. Kenneth, Hacohen, Nir

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131056965.0x000001&indx=1&recIds=ETOCvdc_100131056965.0x000001

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Authors: Lee, Mark N., Ye, Chun, Villani, Alexandra-Chloé, Raj, Towfique, Li, Weibo, Eisenhaure, Thomas M., Imboywa, Selina H., Chipendo, Portia I., Ran, F. Ann, Slowikowski, Kamil, Ward, Lucas D., Raddassi, Khadir, McCabe, Cristin, Lee, Michelle H., Frohlich, Irene Y., Hafler, David A., Kellis, Manolis, Raychaudhuri, Soumya, Zhang, Feng, Stranger, Barbara E., Benoist, Christophe O., De Jager, Philip L., Regev, Aviv, Hacohen, Nir

Source: Science, 2014 Mar 01. 343(6175), 1119-1119.

Access URL: http://www.jstor.org/stable/24743322

Methods for Quantification of in vivo Changes in Protein Ubiquitination following Proteasome and Deubiquitinase Inhibition

Alternate Title: Methods for Analyzing Global Effects on Ubiquitination (English)

Authors: Udeshi, Namrata D. ^‡, Mani, D.R. ^‡, Eisenhaure, Thomas ^{‡, §}, Mertins, Philipp ^‡, Jaffe, Jacob D. ^‡, Clauser, Karl R. ^‡, Hacohen, Nir ^{‡, §}, Carr, Steven A. ^{‡, ¶}

Source: In Molecular & Cellular Proteomics May 2012 11(5):148-159

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Authors: Amit, Ido, Garber, Manuel, Chevrier, Nicolas, Leite, Ana Paula, Donner, Yoni, Eisenhaure, Thomas, Guttman, Mitchell, Grenier, Jennifer K., Li, Weibo, Zuk, Or, Schubert, Lisa A., Birditt, Brian, Shay, Tal, Goren, Alon, Zhang, Xiaolan, Smith, Zachary, Deering, Raquel, McDonald, Rebecca C., Cabili, Moran, Bernstein, Bradley E., Rinn, John L., Meissner, Alex, Root, David E., Hacohen, Nir, Regev, Aviv

Source: Science, 2009 Oct 01. 326(5950), 257-263.

Access URL: https://www.jstor.org/stable/40328840

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

Authors: Chevrier, Nicolas, Mertins, Philipp, Artyomov, Maxim N., Shalek, Alex K., Iannacone, Matteo, Ciaccio, Mark F., Gat-Viks, Irit, Tonti, Elena, DeGrace, Marciela M., Clauser, Karl R., Garber, Manuel, Eisenhaure, Thomas M., Yosef, Nir, Robinson, Jacob, Sutton, Amy, Andersen, Mette S., Root, David E., von Andrian, Ulrich, Jones, Richard B., Park, Hongkun, Carr, Steven A., Regev, Aviv, Amit, Ido, Hacohen, Nir

Source: In Cell 2011 147(4):853-867

Extranuclear DNA accumulates in aged cells and contributes to senescence and inflammation

Authors: Lan, Yuk Yuen, Heather, James M., Eisenhaure, Thomas, Garris, Christopher Stuart, Lieb, David, Raychowdhury, Raktima, Hacohen, Nir

Source: Aging cell. 18(2)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100083894279.0x000001&indx=1&recIds=ETOCvdc_100083894279.0x000001

Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease.

Authors: Dahlqvist, Johanna, Fulco, Charles P, Ray, John P, Liechti, Thomas, Boer, Carl G de, Lieb, David J, Eisenhaure, Thomas M, Engreitz, Jesse M, Roederer, Mario, Hacohen, Nir

Source: Human Molecular Genetics; 6/15/2022, Vol. 31 Issue 12, p1946-1961, 16p