{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T21:10:11Z","timestamp":1792098611019,"version":"4.4.0"},"reference-count":63,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T00:00:00Z","timestamp":1667952000000},"content-version":"vor","delay-in-days":8,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000884","name":"Cancer Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019660","name":"Alliance for a Healthier World, Johns Hopkins University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019660","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI125741"],"award-info":[{"award-number":["AI125741"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI153537"],"award-info":[{"award-number":["AI153537"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA246920"],"award-info":[{"award-number":["CA246920"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK127526"],"award-info":[{"award-number":["DK127526"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["AI148403"],"award-info":[{"award-number":["AI148403"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["T32-GM080202"],"award-info":[{"award-number":["T32-GM080202"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2022,11]]},"DOI":"10.1016\/j.celrep.2022.111736","type":"journal-article","created":{"date-parts":[[2022,11,29]],"date-time":"2022-11-29T10:34:01Z","timestamp":1669718041000},"page":"111736","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":20,"title":["Spatial transcriptomics demonstrates the role of CD4 T\u00a0cells in effector CD8 T\u00a0cell differentiation during chronic viral infection"],"prefix":"10.1016","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3902-7652","authenticated-orcid":false,"given":"Paytsar","family":"Topchyan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Zander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moujtaba Y.","family":"Kasmani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siying","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Burns","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1562-9218","authenticated-orcid":false,"given":"Weiguo","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2022.111736_bib1","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1146\/annurev.immunol.23.021704.115825","article-title":"Cooperation between CD4+ and CD8+ T\u00a0cells: when, where, and how","volume":"24","author":"Castellino","year":"2006","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib2","doi-asserted-by":"crossref","first-page":"8056","DOI":"10.1128\/jvi.68.12.8056-8063.1994","article-title":"CD4+ T\u00a0cells are required to sustain CD8+ cytotoxic T-cell responses during chronic viral infection","volume":"68","author":"Matloubian","year":"1994","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.celrep.2022.111736_bib3","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1016\/j.immuni.2019.10.009","article-title":"CD4(+) T\u00a0cell help is required for the formation of a cytolytic CD8(+) T\u00a0cell subset that Protects against chronic infection and cancer","volume":"51","author":"Zander","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib4","doi-asserted-by":"crossref","first-page":"20070","DOI":"10.1073\/pnas.1902701116","article-title":"Proliferation-competent Tcf1+ CD8 T\u00a0cells in dysfunctional populations are CD4 T\u00a0cell help independent","volume":"116","author":"Kanev","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2022.111736_bib5","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/j.immuni.2016.07.021","article-title":"T cell factor 1-expressing memory-like CD8(+) T\u00a0cells sustain the immune response to chronic viral infections","volume":"45","author":"Utzschneider","year":"2016","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib6","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nature19330","article-title":"Defining CD8+ T\u00a0cells that provide the proliferative burst after PD-1 therapy","volume":"537","author":"Im","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2022.111736_bib7","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1038\/nature19317","article-title":"Follicular CXCR5- expressing CD8(+) T\u00a0cells curtail chronic viral infection","volume":"537","author":"He","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2022.111736_bib8","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1038\/ni.3543","article-title":"CXCR5(+) follicular cytotoxic T\u00a0cells control viral infection in B cell follicles","volume":"17","author":"Leong","year":"2016","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib9","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/j.immuni.2019.11.002","article-title":"Proliferating transitory T\u00a0cells with an effector-like transcriptional signature emerge from PD-1(+) stem-like CD8(+) T\u00a0cells during chronic infection","volume":"51","author":"Hudson","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib10","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1016\/j.immuni.2019.09.013","article-title":"TCF-1-Centered transcriptional network drives an effector versus exhausted CD8 T\u00a0cell-fate decision","volume":"51","author":"Chen","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib11","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/s41590-019-0312-6","article-title":"Subsets of exhausted CD8(+) T\u00a0cells differentially mediate tumor control and respond to checkpoint blockade","volume":"20","author":"Miller","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib12","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/j.immuni.2020.04.014","article-title":"Developmental relationships of four exhausted CD8(+) T\u00a0cell subsets reveals underlying transcriptional and epigenetic landscape control mechanisms","volume":"52","author":"Beltra","year":"2020","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib13","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1016\/j.immuni.2018.08.002","article-title":"CD8(+) T\u00a0cell priming in established chronic viral infection Preferentially directs differentiation of memory-like cells for sustained immunity","volume":"49","author":"Snell","year":"2018","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib14","doi-asserted-by":"crossref","first-page":"4700","DOI":"10.1128\/jvi.68.7.4700-4704.1994","article-title":"Enhanced establishment of a virus carrier state in adult CD4+ T-cell-deficient mice","volume":"68","author":"Battegay","year":"1994","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.celrep.2022.111736_bib15","doi-asserted-by":"crossref","first-page":"2205","DOI":"10.1084\/jem.188.12.2205","article-title":"Viral immune evasion due to persistence of activated T\u00a0cells without effector function","volume":"188","author":"Zajac","year":"1998","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib16","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1016\/j.celrep.2015.09.069","article-title":"A critical role of IL-21-induced BATF in sustaining CD8-T-cell-mediated chronic viral control","volume":"13","author":"Xin","year":"2015","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2022.111736_bib17","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1126\/science.1174182","article-title":"IL-21 is required to control chronic viral infection","volume":"324","author":"Elsaesser","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.celrep.2022.111736_bib18","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1126\/science.1172815","article-title":"IL-21R on T\u00a0cells is critical for sustained functionality and control of chronic viral infection","volume":"324","author":"Fr\u00f6hlich","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.celrep.2022.111736_bib19","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1126\/science.1175194","article-title":"A vital role for interleukin-21 in the control of a chronic viral infection","volume":"324","author":"Yi","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.celrep.2022.111736_bib20","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/s41590-021-00965-7","article-title":"BATF regulates progenitor to cytolytic effector CD8(+) T\u00a0cell transition during chronic viral infection","volume":"22","author":"Chen","year":"2021","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib21","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/j.immuni.2022.01.018","article-title":"Tfh-cell-derived interleukin 21 sustains effector CD8(+) T\u00a0cell responses during chronic viral infection","volume":"55","author":"Zander","year":"2022","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib22","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1084\/jem.20091738","article-title":"IL-21 acts directly on B cells to regulate Bcl-6 expression and germinal center responses","volume":"207","author":"Linterman","year":"2010","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib23","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1084\/jem.20091777","article-title":"IL-21 regulates germinal center B cell differentiation and proliferation through a B cell-intrinsic mechanism","volume":"207","author":"Zotos","year":"2010","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib24","doi-asserted-by":"crossref","first-page":"7737","DOI":"10.1128\/JVI.00063-13","article-title":"Interleukin-21 is a critical cytokine for the generation of virus-specific long-lived plasma cells","volume":"87","author":"Rasheed","year":"2013","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.celrep.2022.111736_bib25","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1128\/jvi.69.2.1059-1070.1995","article-title":"Virus-induced immunosuppression: immune system-mediated destruction of virus-infected dendritic cells results in generalized immune suppression","volume":"69","author":"Borrow","year":"1995","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.celrep.2022.111736_bib26","doi-asserted-by":"crossref","first-page":"15430","DOI":"10.1073\/pnas.0702579104","article-title":"Viral targeting of fibroblastic reticular cells contributes to immunosuppression and persistence during chronic infection","volume":"104","author":"Mueller","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2022.111736_bib27","doi-asserted-by":"crossref","first-page":"8252","DOI":"10.1073\/pnas.88.18.8252","article-title":"Virus-triggered acquired immunodeficiency by cytotoxic T-cell-dependent destruction of antigen-presenting cells and lymph follicle structure","volume":"88","author":"Odermatt","year":"1991","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2022.111736_bib28","doi-asserted-by":"crossref","first-page":"5420","DOI":"10.1073\/pnas.1913776117","article-title":"Chronic virus infection drives CD8 T\u00a0cell-mediated thymic destruction and impaired negative selection","volume":"117","author":"Elsaesser","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2022.111736_bib29","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1146\/annurev.immunol.021908.132723","article-title":"Regulatory T\u00a0cells in the control of host-microorganism interactions (\u2217)","volume":"27","author":"Belkaid","year":"2009","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib30","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1084\/jem.20132577","article-title":"Interplay between regulatory T\u00a0cells and PD-1 in modulating T\u00a0cell exhaustion and viral control during chronic LCMV infection","volume":"211","author":"Penaloza-MacMaster","year":"2014","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib31","doi-asserted-by":"crossref","first-page":"4278","DOI":"10.1128\/JVI.00039-16","article-title":"Transient CD4+ T\u00a0cell depletion results in delayed development of functional vaccine-elicited antibody responses","volume":"90","author":"Provine","year":"2016","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.celrep.2022.111736_bib32","article-title":"Delineating the transcriptional landscape and clonal diversity of virus-specific CD4+ T\u00a0cells during chronic viral infection","author":"Zander","year":"2022","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2022.111736_bib33","doi-asserted-by":"crossref","first-page":"6682","DOI":"10.4049\/jimmunol.0900080","article-title":"PD-1-mediated suppression of IL-2 production induces CD8+ T\u00a0cell anergy in\u00a0vivo","volume":"182","author":"Chikuma","year":"2009","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib34","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.immuni.2011.06.015","article-title":"Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8(+) T\u00a0cells","volume":"35","author":"Youngblood","year":"2011","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib35","doi-asserted-by":"crossref","first-page":"540","DOI":"10.4049\/jimmunol.1203161","article-title":"Cutting edge: prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T\u00a0cells","volume":"191","author":"Youngblood","year":"2013","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib36","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1182\/blood-2008-12-195792","article-title":"Tumor antigen-specific CD8 T\u00a0cells infiltrating the tumor express high levels of PD-1 and are functionally impaired","volume":"114","author":"Ahmadzadeh","year":"2009","journal-title":"Blood"},{"key":"10.1016\/j.celrep.2022.111736_bib37","article-title":"PD-1 expression on tumor-specific T\u00a0cells: friend or foe for immunotherapy?","volume":"7","author":"Simon","year":"2017","journal-title":"OncoImmunology"},{"key":"10.1016\/j.celrep.2022.111736_bib38","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1126\/science.272.5270.1947","article-title":"Induction of bystander T\u00a0cell proliferation by viruses and type I interferon in\u00a0vivo","volume":"272","author":"Tough","year":"1996","journal-title":"Science"},{"key":"10.1016\/j.celrep.2022.111736_bib39","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.immuni.2014.10.004","article-title":"T follicular helper cell differentiation, function, and roles in disease","volume":"41","author":"Crotty","year":"2014","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib40","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1146\/annurev-immunol-031210-101400","article-title":"Follicular helper CD4 T\u00a0cells (TFH)","volume":"29","author":"Crotty","year":"2011","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib41","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1038\/ni.3554","article-title":"TFH cells progressively differentiate to regulate the germinal center response","volume":"17","author":"Weinstein","year":"2016","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib42","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1084\/jem.20101773","article-title":"Viral persistence redirects CD4 T\u00a0cell differentiation toward T follicular helper cells","volume":"208","author":"Fahey","year":"2011","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib43","doi-asserted-by":"crossref","first-page":"e50","DOI":"10.1093\/nar\/gkab043","article-title":"SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes","volume":"49","author":"Elosua-Bayes","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2022.111736_bib44","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1084\/jem.192.11.1545","article-title":"Follicular B helper T\u00a0cells express CXC chemokine receptor 5, localize to B cell follicles, and support immunoglobulin production","volume":"192","author":"Breitfeld","year":"2000","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib45","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1084\/jem.192.11.1553","article-title":"CXC chemokine receptor 5 expression defines follicular homing T\u00a0cells with B cell helper function","volume":"192","author":"Schaerli","year":"2000","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib46","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.4049\/jimmunol.1403237","article-title":"CD4 T\u00a0cell depletion substantially augments the rescue potential of PD-L1 blockade for deeply exhausted CD8 T\u00a0cells","volume":"195","author":"Penaloza-MacMaster","year":"2015","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib47","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/nature04444","article-title":"Restoring function in exhausted CD8 T\u00a0cells during chronic viral infection","volume":"439","author":"Barber","year":"2006","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2022.111736_bib48","doi-asserted-by":"crossref","first-page":"4292","DOI":"10.1073\/pnas.1917298117","article-title":"PD-1+ stemlike CD8 T\u00a0cells are resident in lymphoid tissues during persistent LCMV infection","volume":"117","author":"Im","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2022.111736_bib49","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/79724","article-title":"T cell depletion in HIV-1 infection: how CD4+ T\u00a0cells go out of stock","volume":"1","author":"Hazenberg","year":"2000","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib50","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1146\/annurev-immunol-041015-055318","article-title":"CD8 T\u00a0cell exhaustion during chronic viral infection and cancer","volume":"37","author":"McLane","year":"2019","journal-title":"Annu. Rev. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib51","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1016\/j.immuni.2012.11.020","article-title":"Persistent antigen and germinal center B cells sustain T follicular helper cell responses and phenotype","volume":"38","author":"Baumjohann","year":"2013","journal-title":"Immunity"},{"key":"10.1016\/j.celrep.2022.111736_bib52","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.4049\/jimmunol.1100853","article-title":"Cutting edge: dendritic cell-restricted antigen presentation initiates the follicular helper T\u00a0cell program but cannot complete ultimate effector differentiation","volume":"187","author":"Goenka","year":"2011","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib53","doi-asserted-by":"crossref","first-page":"6101","DOI":"10.1016\/j.cell.2021.11.007","article-title":"Neoantigen-driven B cell and CD4\u00a0T follicular helper cell collaboration promotes anti-tumor CD8 T\u00a0cell responses","volume":"184","author":"Cui","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2022.111736_bib54","doi-asserted-by":"crossref","first-page":"3677","DOI":"10.1073\/pnas.1100213108","article-title":"Regulatory T-cell expansion during chronic viral infection is dependent on endogenous retroviral superantigens","volume":"108","author":"Punkosdy","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2022.111736_bib55","doi-asserted-by":"crossref","first-page":"eaao3125","DOI":"10.1126\/sciimmunol.aao3125","article-title":"Enhancing FcgammaR-mediated antibody effector function during persistent viral infection","volume":"3","author":"Wieland","year":"2018","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.celrep.2022.111736_bib56","article-title":"A comprehensive comparison on cell type composition inference for spatial transcriptomics data","author":"Chen","year":"2022","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2022.111736_bib57","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1093\/nar\/gkac084","article-title":"CellDART: cell type inference by domain adaptation of single-cell and spatial transcriptomic data","volume":"50","author":"Bae","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2022.111736_bib58","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/s41587-021-01139-4","article-title":"Cell2location maps fine-grained cell types in spatial transcriptomics","volume":"40","author":"Kleshchevnikov","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2022.111736_bib59","doi-asserted-by":"crossref","first-page":"e20220679","DOI":"10.1084\/jem.20220679","article-title":"Clonal lineage tracing reveals mechanisms skewing CD8+ T\u00a0cell fate decisions in chronic infection","volume":"220","author":"Kasmani","year":"2022","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2022.111736_bib60","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/s41586-018-0590-4","article-title":"Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris","volume":"562","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2022.111736_bib61","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109160","article-title":"Suppressive neutrophils require PIM1 for metabolic fitness and survival during chronic viral infection","volume":"35","author":"Volberding","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2022.111736_bib62","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2022.111736_bib63","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S221112472201614X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S221112472201614X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T11:52:13Z","timestamp":1761911533000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S221112472201614X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11]]},"references-count":63,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2022,11]]}},"alternative-id":["S221112472201614X"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2022.111736","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2022,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Spatial transcriptomics demonstrates the role of CD4 T\u00a0cells in effector CD8 T\u00a0cell differentiation during chronic viral infection","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2022.111736","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Authors.","name":"copyright","label":"Copyright"}],"article-number":"111736"}}