{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T03:17:04Z","timestamp":1790997424384,"version":"4.1.0"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T00:00:00Z","timestamp":1581897600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T00:00:00Z","timestamp":1581897600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100000051","name":"U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U01HG007910"],"award-info":[{"award-number":["U01HG007910"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R37AI147868"],"award-info":[{"award-number":["R37AI147868"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI111809"],"award-info":[{"award-number":["R01AI111809"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21AI119885"],"award-info":[{"award-number":["R21AI119885"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["P30 AI027763"],"award-info":[{"award-number":["P30 AI027763"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R24 AI067039"],"award-info":[{"award-number":["R24 AI067039"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI096109"],"award-info":[{"award-number":["AI096109"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI127966"],"award-info":[{"award-number":["AI127966"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000026","name":"U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["DP1DA034990"],"award-info":[{"award-number":["DP1DA034990"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000052","name":"U.S. Department of Health & Human Services | NIH | NIH Office of the Director","doi-asserted-by":"publisher","award":["P51OD011092"],"award-info":[{"award-number":["P51OD011092"]}],"id":[{"id":"10.13039\/100000052","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Immunol"],"published-print":{"date-parts":[[2020,3]]},"DOI":"10.1038\/s41590-020-0593-9","type":"journal-article","created":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T17:16:07Z","timestamp":1581959767000},"page":"274-286","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":93,"title":["HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells"],"prefix":"10.1038","volume":"21","author":[{"given":"Yetao","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lawrence","family":"Lifshitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3500-2025","authenticated-orcid":false,"given":"Kyle","family":"Gellatly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carol L.","family":"Vinton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8549-0023","authenticated-orcid":false,"given":"Kathleen","family":"Busman-Sahay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"McCauley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pranitha","family":"Vangala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9217-673X","authenticated-orcid":false,"given":"Kyusik","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Derr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Smita","family":"Jaiswal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9983-394X","authenticated-orcid":false,"given":"Alper","family":"Kucukural","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"McDonel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter W.","family":"Hunt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Greenough","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"JeanMarie","family":"Houghton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ma","family":"Somsouk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob D.","family":"Estes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason M.","family":"Brenchley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8732-1293","authenticated-orcid":false,"given":"Manuel","family":"Garber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6371-747X","authenticated-orcid":false,"given":"Steven G.","family":"Deeks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5650-4054","authenticated-orcid":false,"given":"Jeremy","family":"Luban","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,2,17]]},"reference":[{"key":"593_CR1","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.immuni.2013.10.001","volume":"39","author":"SG Deeks","year":"2013","unstructured":"Deeks, S. G., Tracy, R. & Douek, D. C. Systemic effects of inflammation on health during chronic HIV infection. Immunity 39, 633\u2013645 (2013).","journal-title":"Immunity"},{"key":"593_CR2","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1038\/nm1511","volume":"12","author":"JM Brenchley","year":"2006","unstructured":"Brenchley, J. M. et al. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat. Med. 12, 1365\u20131371 (2006).","journal-title":"Nat. Med."},{"key":"593_CR3","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/j.cell.2018.07.017","volume":"174","author":"E Vivier","year":"2018","unstructured":"Vivier, E. et al. Innate lymphoid cells: 10 years on. Cell 174, 1054\u20131066 (2018).","journal-title":"Cell"},{"key":"593_CR4","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.immuni.2016.01.006","volume":"44","author":"HN Kl\u00f8verpris","year":"2016","unstructured":"Kl\u00f8verpris, H. N. et al. Innate lymphoid cells are depleted irreversibly during acute HIV-1 infection in the absence of viral suppression. Immunity 44, 391\u2013405 (2016).","journal-title":"Immunity"},{"key":"593_CR5","volume":"9","author":"JC Mudd","year":"2018","unstructured":"Mudd, J. C. et al. Hallmarks of primate lentiviral immunodeficiency infection recapitulate loss of innate lymphoid cells. Nat. Commun. 9, 3967 (2018).","journal-title":"Nat. Commun."},{"key":"593_CR6","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms10844","volume":"7","author":"T Bruel","year":"2016","unstructured":"Bruel, T. et al. Elimination of HIV-1-infected cells by broadly neutralizing antibodies. Nat. Commun. 7, 10844 (2016).","journal-title":"Nat. Commun."},{"key":"593_CR7","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/nature10237","volume":"476","author":"G Alter","year":"2011","unstructured":"Alter, G. et al. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature 476, 96\u2013100 (2011).","journal-title":"Nature"},{"key":"593_CR8","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/nri.2015.9","volume":"16","author":"A Cerwenka","year":"2016","unstructured":"Cerwenka, A. & Lanier, L. L. Natural killer cell memory in infection, inflammation and cancer. Nat. Rev. Immunol. 16, 112\u2013123 (2016).","journal-title":"Nat. Rev. Immunol."},{"key":"593_CR9","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1016\/j.cell.2017.02.021","volume":"168","author":"AI Lim","year":"2017","unstructured":"Lim, A. I. et al. Systemic human ILC precursors provide a substrate for tissue ILC differentiation. Cell 168, 1086\u20131100.e10 (2017).","journal-title":"Cell"},{"key":"593_CR10","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1016\/j.immuni.2018.05.013","volume":"48","author":"M Colonna","year":"2018","unstructured":"Colonna, M. Innate lymphoid cells: diversity, plasticity, and unique functions in immunity. Immunity 48, 1104\u20131117 (2018).","journal-title":"Immunity"},{"key":"593_CR11","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/nri2023","volume":"7","author":"R Mazzucchelli","year":"2007","unstructured":"Mazzucchelli, R. & Durum, S. K. Interleukin-7 receptor expression: intelligent design. Nat. Rev. Immunol. 7, 144\u2013154 (2007).","journal-title":"Nat. Rev. Immunol."},{"key":"593_CR12","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1146\/annurev.immunol.16.1.293","volume":"16","author":"WJ Leonard","year":"1998","unstructured":"Leonard, W. J. & O\u2019Shea, J. J. JAKS and STATs: biological implications. Annu. Rev. Immunol. 16, 293\u2013322 (1998).","journal-title":"Annu. Rev. Immunol."},{"key":"593_CR13","doi-asserted-by":"crossref","first-page":"2886","DOI":"10.1073\/pnas.0409872102","volume":"102","author":"D Mavilio","year":"2005","unstructured":"Mavilio, D. et al. Characterization of CD56\u2013\/CD16+ natural killer (NK) cells: a highly dysfunctional NK subset expanded in HIV-infected viremic individuals. Proc. Natl Acad. Sci. USA 102, 2886\u20132891 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"593_CR14","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.immuni.2011.02.015","volume":"34","author":"M Fang","year":"2011","unstructured":"Fang, M. et al. CD94 is essential for NK cell-mediated resistance to a lethal viral disease. Immunity 34, 579\u2013589 (2011).","journal-title":"Immunity"},{"key":"593_CR15","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/j.celrep.2017.06.071","volume":"20","author":"B Jeevan-Raj","year":"2017","unstructured":"Jeevan-Raj, B. et al. The transcription factor Tcf1 contributes to normal NK cell development and function by limiting the expression of granzymes. Cell Rep. 20, 613\u2013626 (2017).","journal-title":"Cell Rep."},{"key":"593_CR16","doi-asserted-by":"crossref","first-page":"8437","DOI":"10.1158\/0008-5472.CAN-08-1440","volume":"68","author":"M Wendel","year":"2008","unstructured":"Wendel, M., Galani, I. E., Suri-Payer, E. & Cerwenka, A. Natural killer cell accumulation in tumors is dependent on IFN-\u03b3 and CXCR3 ligands. Cancer Res. 68, 8437\u20138445 (2008).","journal-title":"Cancer Res."},{"key":"593_CR17","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1182\/blood.V90.2.716","volume":"90","author":"G Sconocchia","year":"1997","unstructured":"Sconocchia, G., Titus, J. A. & Segal, D. M. Signaling pathways regulating CD44-dependent cytolysis in natural killer cells. Blood 90, 716\u2013725 (1997).","journal-title":"Blood"},{"key":"593_CR18","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1016\/j.celrep.2016.04.005","volume":"15","author":"LL Liu","year":"2016","unstructured":"Liu, L. L. et al. Critical role of CD2 co-stimulation in adaptive natural killer cell responses revealed in NKG2C-deficient humans. Cell Rep. 15, 1088\u20131099 (2016).","journal-title":"Cell Rep."},{"key":"593_CR19","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1182\/blood-2009-11-253286","volume":"116","author":"K Juelke","year":"2010","unstructured":"Juelke, K. et al. CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells. Blood 116, 1299\u20131307 (2010).","journal-title":"Blood"},{"key":"593_CR20","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1182\/blood-2003-11-3796","volume":"103","author":"R Gazit","year":"2004","unstructured":"Gazit, R. et al. Expression of KIR2DL1 on the entire NK cell population: a possible novel immunodeficiency syndrome. Blood 103, 1965\u20131966 (2004).","journal-title":"Blood"},{"key":"593_CR21","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","volume":"161","author":"AM Klein","year":"2015","unstructured":"Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187\u20131201 (2015).","journal-title":"Cell"},{"key":"593_CR22","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1198\/106186005X59243","volume":"14","author":"R Tibshirani","year":"2005","unstructured":"Tibshirani, R. & Walther, G. Cluster validation by prediction strength. J. Comput. Graph. Stat. 14, 511\u2013528 (2005).","journal-title":"J. Comput. Graph. Stat."},{"key":"593_CR23","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","volume":"32","author":"C Trapnell","year":"2014","unstructured":"Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381\u2013386 (2014).","journal-title":"Nat. Biotechnol."},{"key":"593_CR24","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/j.immuni.2016.07.021","volume":"45","author":"DT Utzschneider","year":"2016","unstructured":"Utzschneider, D. T. et al. T cell factor 1-expressing memory-like CD8+ T cells sustain the immune response to chronic viral infections. Immunity 45, 415\u2013427 (2016).","journal-title":"Immunity"},{"key":"593_CR25","doi-asserted-by":"crossref","first-page":"9777","DOI":"10.1073\/pnas.0914127107","volume":"107","author":"G Jeannet","year":"2010","unstructured":"Jeannet, G. et al. Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory. Proc. Natl Acad. Sci. USA 107, 9777\u20139782 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"593_CR26","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1038\/ni.3248","volume":"16","author":"Q Yang","year":"2015","unstructured":"Yang, Q. et al. TCF-1 upregulation identifies early innate lymphoid progenitors in the bone marrow. Nat. Immunol. 16, 1044\u20131050 (2015).","journal-title":"Nat. Immunol."},{"key":"593_CR27","doi-asserted-by":"crossref","first-page":"2996","DOI":"10.1634\/stemcells.2007-0066","volume":"25","author":"I Aksoy","year":"2007","unstructured":"Aksoy, I. et al. Self-renewal of murine embryonic stem cells is supported by the serine\/threonine kinases Pim-1 and Pim-3. Stem Cells 25, 2996\u20133004 (2007).","journal-title":"Stem Cells"},{"key":"593_CR28","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.immuni.2009.10.011","volume":"32","author":"BJG Baaten","year":"2010","unstructured":"Baaten, B. J. G. et al. CD44 regulates survival and memory development in Th1 cells. Immunity 32, 104\u2013115 (2010).","journal-title":"Immunity"},{"key":"593_CR29","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/nri3173","volume":"12","author":"N-P Weng","year":"2012","unstructured":"Weng, N.-P., Araki, Y. & Subedi, K. The molecular basis of the memory T cell response: differential gene expression and its epigenetic regulation. Nat. Rev. Immunol. 12, 306\u2013315 (2012).","journal-title":"Nat. Rev. Immunol."},{"key":"593_CR30","doi-asserted-by":"crossref","first-page":"3689","DOI":"10.1182\/blood-2010-09-303057","volume":"116","author":"L Moretta","year":"2010","unstructured":"Moretta, L. Dissecting CD56dim human NK cells. Blood 116, 3689\u20133691 (2010).","journal-title":"Blood"},{"key":"593_CR31","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/ni.1953","volume":"11","author":"S Paust","year":"2010","unstructured":"Paust, S. et al. Critical role for the chemokine receptor CXCR6 in NK cell-mediated antigen-specific memory of haptens and viruses. Nat. Immunol. 11, 1127\u20131135 (2010).","journal-title":"Nat. Immunol."},{"key":"593_CR32","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/ni.3441","volume":"17","author":"R Roychoudhuri","year":"2016","unstructured":"Roychoudhuri, R. et al. BACH2 regulates CD8+ T cell differentiation by controlling access of AP-1 factors to enhancers. Nat. Immunol. 17, 851\u2013860 (2016).","journal-title":"Nat. Immunol."},{"key":"593_CR33","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.immuni.2013.08.032","volume":"39","author":"HM Shin","year":"2013","unstructured":"Shin, H. M. et al. Epigenetic modifications induced by Blimp-1 regulate CD8+ T cell memory progression during acute virus infection. Immunity 39, 661\u2013675 (2013).","journal-title":"Immunity"},{"key":"593_CR34","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1016\/j.celrep.2014.12.025","volume":"10","author":"Y Kamimura","year":"2015","unstructured":"Kamimura, Y. & Lanier, L. L. Homeostatic control of memory cell progenitors in the natural killer cell lineage. Cell Rep. 10, 280\u2013291 (2015).","journal-title":"Cell Rep."},{"key":"593_CR35","doi-asserted-by":"crossref","first-page":"2711","DOI":"10.1182\/blood-2002-07-2103","volume":"101","author":"JM Brenchley","year":"2003","unstructured":"Brenchley, J. M. et al. Expression of CD57 defines replicative senescence and antigen-induced apoptotic death of CD8+ T cells. Blood 101, 2711\u20132720 (2003).","journal-title":"Blood"},{"key":"593_CR36","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1016\/j.immuni.2007.09.006","volume":"27","author":"EJ Wherry","year":"2007","unstructured":"Wherry, E. J. et al. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity 27, 670\u2013684 (2007).","journal-title":"Immunity"},{"key":"593_CR37","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1016\/j.celrep.2016.10.032","volume":"17","author":"W-HW Lin","year":"2016","unstructured":"Lin, W.-H. W. et al. CD8+ T lymphocyte self-renewal during effector cell determination. Cell Rep. 17, 1773\u20131782 (2016).","journal-title":"Cell Rep."},{"key":"593_CR38","doi-asserted-by":"crossref","first-page":"5632","DOI":"10.1128\/JVI.77.10.5632-5638.2003","volume":"77","author":"S Vigneau","year":"2003","unstructured":"Vigneau, S., Rohrlich, P.-S., Brahic, M. & Bureau, J.-F. Tmevpg1, a candidate gene for the control of Theiler\u2019s virus persistence, could be implicated in the regulation of gamma interferon. J. Virol. 77, 5632\u20135638 (2003).","journal-title":"J. Virol."},{"key":"593_CR39","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1016\/j.cell.2013.01.015","volume":"152","author":"JA Gomez","year":"2013","unstructured":"Gomez, J. A. et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-\u03b3 locus. Cell 152, 743\u2013754 (2013).","journal-title":"Cell"},{"key":"593_CR40","doi-asserted-by":"crossref","first-page":"5894","DOI":"10.4049\/jimmunol.162.10.5894","volume":"162","author":"W Walker","year":"1999","unstructured":"Walker, W., Aste-Amezaga, M., Kastelein, R. A., Trinchieri, G. & Hunter, C. A. IL-18 and CD28 use distinct molecular mechanisms to enhance NK cell production of IL-12-induced IFN-\u03b3. J. Immunol. 162, 5894\u20135901 (1999).","journal-title":"J. Immunol."},{"key":"593_CR41","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/S0065-2776(07)96002-2","volume":"96","author":"JR Schoenborn","year":"2007","unstructured":"Schoenborn, J. R. & Wilson, C. B. Regulation of interferon\u2010\u03b3 during innate and adaptive immune responses. Adv. Immunol. 96, 41\u2013101 (2007).","journal-title":"Adv. Immunol."},{"key":"593_CR42","doi-asserted-by":"crossref","first-page":"3853","DOI":"10.1182\/blood-2010-04-281675","volume":"116","author":"NK Bj\u00f6rkstr\u00f6m","year":"2010","unstructured":"Bj\u00f6rkstr\u00f6m, N. K. et al. Expression patterns of NKG2A, KIR, and CD57 define a process of CD56dim NK-cell differentiation uncoupled from NK-cell education. Blood 116, 3853\u20133864 (2010).","journal-title":"Blood"},{"key":"593_CR43","doi-asserted-by":"crossref","first-page":"4751","DOI":"10.1182\/blood-2012-04-419283","volume":"120","author":"R Romee","year":"2012","unstructured":"Romee, R. et al. Cytokine activation induces human memory-like NK cells. Blood 120, 4751\u20134760 (2012).","journal-title":"Blood"},{"key":"593_CR44","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1073\/pnas.0813192106","volume":"106","author":"MA Cooper","year":"2009","unstructured":"Cooper, M. A. et al. Cytokine-induced memory-like natural killer cells. Proc. Natl Acad. Sci. USA 106, 1915\u20131919 (2009).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"593_CR45","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/nri.2017.146","volume":"18","author":"AN Henning","year":"2018","unstructured":"Henning, A. N., Roychoudhuri, R. & Restifo, N. P. Epigenetic control of CD8+ T cell differentiation. Nat. Rev. Immunol. 18, 340\u2013356 (2018).","journal-title":"Nat. Rev. Immunol."},{"key":"593_CR46","volume":"4","author":"G Hu","year":"2013","unstructured":"Hu, G. & Chen, J. A genome-wide regulatory network identifies key transcription factors for memory CD8+ T-cell development. Nat. Commun. 4, 2830 (2013).","journal-title":"Nat. Commun."},{"key":"593_CR47","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1016\/j.immuni.2015.09.013","volume":"43","author":"TE O\u2019Sullivan","year":"2015","unstructured":"O\u2019Sullivan, T. E., Sun, J. C. & Lanier, L. L. Natural killer cell memory. Immunity 43, 634\u2013645 (2015).","journal-title":"Immunity"},{"key":"593_CR48","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/ni.3456","volume":"17","author":"S Xing","year":"2016","unstructured":"Xing, S. et al. Tcf1 and Lef1 transcription factors establish CD8+ T cell identity through intrinsic HDAC activity. Nat. Immunol. 17, 695\u2013703 (2016).","journal-title":"Nat. Immunol."},{"key":"593_CR49","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1089\/aid.2011.0253","volume":"28","author":"R Thomas","year":"2012","unstructured":"Thomas, R. et al. NKG2C deletion is a risk factor of HIV infection. AIDS Res. Hum. Retroviruses 28, 844\u2013851 (2012).","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"593_CR50","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1743-422X-10-33","volume":"10","author":"G Fregni","year":"2013","unstructured":"Fregni, G. et al. High number of CD56bright NK-cells and persistently low CD4+ T-cells in a hemophiliac HIV\/HCV co-infected patient without opportunistic infections. Virol. J. 10, 33 (2013).","journal-title":"Virol. J."},{"key":"593_CR51","doi-asserted-by":"crossref","first-page":"e1005421","DOI":"10.1371\/journal.ppat.1005421","volume":"12","author":"ZB Davis","year":"2016","unstructured":"Davis, Z. B. et al. A conserved HIV-1-derived peptide presented by HLA-E renders infected T-cells highly susceptible to attack by NKG2A\/CD94-bearing natural killer cells. PLoS Pathog. 12, e1005421 (2016).","journal-title":"PLoS Pathog."},{"key":"593_CR52","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1128\/CDLI.8.6.1131-1135.2001","volume":"8","author":"S Neri","year":"2001","unstructured":"Neri, S., Mariani, E., Meneghetti, A., Cattini, L. & Facchini, A. Calcein-acetyoxymethyl cytotoxicity assay: standardization of a method allowing additional analyses on recovered effector cells and supernatants. Clin. Diagn. Lab. Immunol. 8, 1131\u20131135 (2001).","journal-title":"Clin. Diagn. Lab. Immunol."},{"key":"593_CR53","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/nature09976","volume":"472","author":"T Pertel","year":"2011","unstructured":"Pertel, T. et al. TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Nature 472, 361\u2013365 (2011).","journal-title":"Nature"},{"key":"593_CR54","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1111\/j.1365-2567.2008.03027.x","volume":"126","author":"A Poli","year":"2009","unstructured":"Poli, A. et al. CD56bright natural killer (NK) cells: an important NK cell subset. Immunology 126, 458\u2013465 (2009).","journal-title":"Immunology"},{"key":"593_CR55","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-016-0938-8","volume":"17","author":"T Hashimshony","year":"2016","unstructured":"Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol. 17, 77 (2016).","journal-title":"Genome Biol."},{"key":"593_CR56","doi-asserted-by":"crossref","first-page":"e21856","DOI":"10.7554\/eLife.21856","volume":"6","author":"PJ Skene","year":"2017","unstructured":"Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6, e21856 (2017).","journal-title":"Elife"},{"key":"593_CR57","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1016\/j.cell.2019.03.014","volume":"177","author":"SJ Hainer","year":"2019","unstructured":"Hainer, S. J., Boskovic, A., Rando, O. J. & Fazzio, T. G. Profiling of pluripotency factors in individual stem cells and early embryos. Cell 177, 1319\u20131329.e11 (2019).","journal-title":"Cell"},{"key":"593_CR58","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1038\/nprot.2018.015","volume":"13","author":"PJ Skene","year":"2018","unstructured":"Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006\u20131019 (2018).","journal-title":"Nat. Protoc."},{"key":"593_CR59","doi-asserted-by":"crossref","first-page":"21.29.1","DOI":"10.1002\/0471142727.mb2129s109","volume":"109","author":"JD Buenrostro","year":"2015","unstructured":"Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-Seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 109, 21.29.1\u201321.29.9 (2015).","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"593_CR60","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213\u20131218 (2013).","journal-title":"Nat. Methods"},{"key":"593_CR61","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).","journal-title":"Genome Biol."},{"key":"593_CR62","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1101\/gr.207902.116","volume":"26","author":"A Derr","year":"2016","unstructured":"Derr, A. et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-Seq data. Genome Res. 26, 1397\u20131410 (2016).","journal-title":"Genome Res."},{"key":"593_CR63","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"M Love","year":"2014","unstructured":"Love, M., Anders, S. & Huber, W. Differential analysis of count data\u2014the DESeq2 package. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"593_CR64","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","volume":"11","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).","journal-title":"Genome Biol."},{"key":"593_CR65","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/S0893-6080(00)00026-5","volume":"13","author":"A Hyv\u00e4rinen","year":"2000","unstructured":"Hyv\u00e4rinen, A. & Oja, E. Independent component analysis: algorithms and applications. Neural Netw. 13, 411\u2013430 (2000).","journal-title":"Neural Netw."},{"key":"593_CR66","unstructured":"Hechenbichler, K. & Schliep, K. Weighted k-Nearest-Neighbor Techniques and Ordinal Classification Discussion Paper 399 (Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen Collaborative Reseach Center 386, 2004)."},{"key":"593_CR67","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"593_CR68","first-page":"3221","volume":"15","author":"L Van Der Maaten","year":"2014","unstructured":"Van Der Maaten, L. Accelerating t-SNE using tree-based algorithms. J. Mach. Learn. Res. 15, 3221\u20133245 (2014).","journal-title":"J. Mach. Learn. Res."},{"key":"593_CR69","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"593_CR70","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."}],"container-title":["Nature Immunology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/s41590-020-0593-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41590-020-0593-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41590-020-0593-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,27]],"date-time":"2023-09-27T01:00:06Z","timestamp":1695776406000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41590-020-0593-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,2,17]]},"references-count":70,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2020,3]]}},"alternative-id":["593"],"URL":"https:\/\/doi.org\/10.1038\/s41590-020-0593-9","relation":{},"ISSN":["1529-2908","1529-2916"],"issn-type":[{"value":"1529-2908","type":"print"},{"value":"1529-2916","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,17]]},"assertion":[{"value":"11 January 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 December 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 February 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}