Shared and distinct biological circuits in effector, memory and exhausted CD8+ T cells revealed by temporal single-cell transcriptomics and epigenetics

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

Im, S. J., Hashimoto, M., Gerner, M. Y., Lee, J., Kissick, H. T., Burger, M. C., Shan, Q., Hale, J. S., Lee, J., Nasti, T. H., et al. (2016) · Nature · doi:10.1038/nature19330 · Cited by 2,070

CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer

McLane, L. M., Abdel-Hakeem, M. S., & Wherry, E. J. (2019) · Annual Review of Immunology · doi:10.1146/annurev-immunol-041015-055318 · Cited by 2,054

Lineage relationship and protective immunity of memory CD8 T cell subsets

Wherry, E. J., Teichgräber, V., Becker, T. C., Masopust, D., Kaech, S. M., Antia, R., von Andrian, U. H., & Ahmed, R. (2003) · Nature Immunology · doi:10.1038/ni889 · Cited by 1,864

Inflammation Directs Memory Precursor and Short-Lived Effector CD8+ T Cell Fates via the Graded Expression of T-bet Transcription Factor

Joshi, N. S., Cui, W., Chandele, A., Lee, H. K., Urso, D. R., Hagman, J., Gapin, L., & Kaech, S. M. (2007) · Immunity · doi:10.1016/j.immuni.2007.07.010 · Cited by 1,861

Selective expression of the interleukin 7 receptor identifies effector CD8 T cells that give rise to long-lived memory cells

Kaech, S. M., Tan, J. T., Wherry, E. J., Konieczny, B. T., Surh, C. D., & Ahmed, R. (2003) · Nature Immunology · doi:10.1038/ni1009 · Cited by 1,830

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

Khan, O., Giles, J. R., McDonald, S., Manne, S., Ngiow, S. F., Patel, K. P., Werner, M. T., Huang, A. C., Alexander, K. A., Wu, J. E., et al. (2019) · Nature · doi:10.1038/s41586-019-1325-x · Cited by 1,646

Pan-cancer single-cell landscape of tumor-infiltrating T cells

Zheng, L., Qin, S., Si, W., Wang, A., Xing, B., Gao, R., Ren, X., Wang, L., Wu, X., Zhang, J., et al. (2021) · Science · doi:10.1126/science.abe6474 · Cited by 1,402

Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade

Pauken, K. E., Sammons, M. A., Odorizzi, P. M., Manne, S., Godec, J., Khan, O., Drake, A. M., Chen, Z., Sen, D. R., Kurachi, M., et al. (2016) · Science · doi:10.1126/science.aaf2807 · Cited by 1,348

The energetics of genome complexity.

Lane, N., & Martin, W. (2010) · Nature · doi:10.1038/nature09486 · Cited by 1,289

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3646 · Cited by 1,151

Single-cell RNA sequencing reveals the dynamics and heterogeneity of lymph node immune cells during acute and chronic viral infections

Jin, Y.-B., He, Y., Liu, B., Zhang, X., Song, C., Wu, Y., Hu, W., Yan, Y., Chen, N., Ding, Y., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1341985 · Cited by 13

Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level

Li, Y.-Q., Li, J., Li, W., Liang, S., Wei, W., Chu, J., Lai, J., Lin, Y., Chen, H., Su, J., et al. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae039 · Cited by 13

BCOR and ZC3H12A suppress a core stemness program in exhausted CD8+ T cells

Xu, J., Jia, Z., Zhao, X., Wang, L., Jin, G., Li, Z., Yin, N., Li, Y., & Peng, M. (2025) · The Journal of Experimental Medicine · doi:10.1084/jem.20241133 · Cited by 14

Clonal Spreading of Tumor-Infiltrating T Cells Underlies the Robust Antitumor Immune Responses

Aoki, H., Tsunoda, M., Ogiwara, H., Shimizu, H., Abe, H., Ogawa, T., Abe, T., Shichino, S., Matsushima, K., & Ueha, S. (2023) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-22-0517 · Cited by 12

LRP11 promotes stem-like T cells via MAPK13-mediated TCF1 phosphorylation, enhancing anti-PD1 immunotherapy

Sun, L., Ma, Z., Zhao, X., Tan, X., Tu, Y., Wang, J., Chen, L., Chen, Z., Chen, G., & Lan, P. (2024) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2023-008367 · Cited by 13

HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection

Rîca, R., Waldherr, M., Miyakoda, E., Kutschat, A. P., Schülein, M., Zhang, J., Orbegozo-Medina, R. A., Sandner, L., Stolz, V., Waltenberger, D., et al. (2025) · The Journal of Experimental Medicine · doi:10.1084/jem.20240829 · Cited by 13

Xylulose 5-phosphate fosters sustained antitumor activity of progenitor-like exhausted SLC35E2+ CD8+ T effector cells

Shi, T., Shao, J., Ding, Y., Tang, H., Tan, X., Zhou, S., Yu, S., Wang, X., Yu, G., Feng, N., et al. (2025) · Cell Metabolism · doi:10.1016/j.cmet.2025.06.011 · Cited by 13

T‐cell heterogeneity, progenitor–progeny relationships, and function during latent and chronic viral infections

Sandu, I., & Oxenius, A. (2023) · Immunological Reviews · doi:10.1111/imr.13203 · Cited by 14

Myeloid cells mediate interferon-driven resistance to immunotherapy in advanced renal cell carcinoma

Bi, K., Kashima, S., Camp, S. Y., Meli, K., Saad, E., Titchen, B. M., Labaki, C., Bakouny, Z., Pimenta, E. M., Park, J., et al. (2025) · Immunity · doi:10.1016/j.immuni.2025.10.013 · Cited by 11

Integrative systems biology reveals NKG2A-biased immune responses correlate with protection in infectious disease, autoimmune disease, and cancer

Chen, D. G., Xie, J., Choi, J., Ng, R. H., Zhang, R., Li, S., Edmark, R., Zheng, H., Solomon, B. D., Campbell, K. M., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113872 · Cited by 11

Epigenetic scars in regulatory T cells are retained after successful treatment of chronic hepatitis C with direct-acting antivirals

Kim, S. Y., Koh, J., Lee, D. H., Kim, H., Choi, S. J., Ko, Y. Y., Lee, H. S., Lee, J. S., Choi, I. A., Lee, E. Y., et al. (2024) · Journal of Hepatology · doi:10.1016/j.jhep.2024.06.011 · Cited by 11

Long-lived central memory γδ T cells confer protection against murine cytomegalovirus reinfection

Yared, N., Papadopoulou, M., Barennes, P., Pham, H., Quiniou, V., Netzer, S., Kaminski, H., Burguet, L., Demeste, A., Colas, P., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1010785 · Cited by 11

Coupling of response biomarkers between tumor and peripheral blood in patients undergoing chemoimmunotherapy

Chin, W. L., Cook, A., Chee, J., Principe, N., Hoang, T. S., Kidman, J., Hmon, K. P. W., Yeow, Y. L., Jones, M. E., Hou, R., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101882 · Cited by 14

T‐cell exhaustion from a multiomics perspective: Differentiation mechanisms and regulatory networks in the journey from progenitor‐Exhausted T cells to terminally exhausted T cells

Zhu, T., Teng, X., Jiao, Q., Ren, Y., Wang, Y., & Feng, M. (2026) · Clinical and Translational Medicine · doi:10.1002/ctm2.70609 · Cited by 12

Functional Impairment of 'Helpless' CD8 Memory T Cells is Transient and Driven by Prolonged But Finite Cognate Antigen Presentation

van der Heide, V., Laghlali, G., Davenport, B., Cubitt, B., Roudko, V., Choo, D. K., Jhun, K., Humblin, É., Vaidya, A. B., Angeliadis, K., et al. (2024) · Immunity · doi:10.1016/j.immuni.2025.05.025 · Cited by 9

Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer

Soto, M., Filbert, E. L., Yang, H. L., Starzinski, S., Starzinski, A., Gin, M., Chen, B. K., Le, P. L., Li, T., Bol, B., et al. (2024) · Cancer Research Communications · doi:10.1158/2767-9764.crc-23-0550 · Cited by 10

Triple checkpoint blockade of PD-1, Tim-3, and Lag-3 enhances adoptive T cell immunotherapy in a mouse model of ovarian cancer

Alencar, G. F., Mohamed, A. O., Burnett, M. G., Jean, S. C. S., Nelson, A. R., Su, Y., Voillet, V., Bates, B. M., Suarez, M. L. R., Ruskin, S. L., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2419888122 · Cited by 9

Immune Niches in Cancer

Slingerland, N., Runderkamp, E., & Thommen, D. S. (2026) · Annual Review of Immunology · doi:10.1146/annurev-immunol-082724-123843 · Cited by 10

Regulation and Immunotherapeutic Targeting of the Epigenome in Exhausted CD8 T Cell Responses

Ford, B. R., & Poholek, A. C. (2023) · The Journal of Immunology · doi:10.4049/jimmunol.2200681 · Cited by 9

Pregnancy dedifferentiates memory CD8+ T cells into hypofunctional cells with exhaustion-enriched programs

Pollard, J. M., Hynes, G. E., Yin, D., Mandal, M., Gounari, F., Alegre, M., & Chong, A. S. (2024) · JCI Insight · doi:10.1172/jci.insight.176381 · Cited by 9

Unravelling the modified T cell receptor through Gen-Next CAR T cell therapy in Glioblastoma: Current status and future challenges

Bhutani, B., Sharma, V., Ganguly, N. K., & Rana, R. (2025) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2025.117987 · Cited by 9

Constructing heterogeneous single-cell landscape and identifying microenvironment molecular characteristics of primary and lymphatic metastatic head and neck squamous cell carcinoma

Zhang, J., Liu, Y., Xia, L., Jia, Z., Gao, J., & Tomokiyo, A. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.107459 · Cited by 8

Enhancing the potency of CAR-T cells against solid tumors through transcription factor engineering

Chen, R., Chen, L., Tang, Y. R., Xiaolin, S., Wang, Y., Tang, P., Shentu, X., & Sun, J. (2025) · JCI Insight · doi:10.1172/jci.insight.193048 · Cited by 9

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Xie, J., Chen, D. G., Chour, W., Ng, R. H., Zhang, R., Yuan, D., Choi, J., McKasson, M., Troisch, P., Smith, B., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56659-3 · Cited by 8

Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T-cell differentiation

Liu, Q., Dong, W., Liu, R., Xu, L., Ran, L., Xie, Z., Lei, S., Su, X., Yue, Z., Xiong, D., et al. (2025) · Protein & Cell · doi:10.1093/procel/pwaf003 · Cited by 7

Gfi1 controls the formation of effector-like CD8+ T cells during chronic infection and cancer

Ojo, O. A., Shen, H., Ingram, J. T., Bonner, J. A., Welner, R. S., Lacaud, G., Zajac, A. J., & Shi, L. Z. (2025) · Nature Communications · doi:10.1038/s41467-025-59784-1 · Cited by 9

T cell exhaustion in bi- and trispecific T cell engager therapy in hematologic malignancies: Mechanisms and implications

Muth, A., Holzem, A. M. E., Neumann, A.-S., Bücklein, V., Subklewe, M. S., & Philipp, N. (2026) · Med · doi:10.1016/j.medj.2026.101031 · Cited by 9

Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data

Wang, X., Lian, Q., Dong, H., Xu, S., Su, Y., & Wu, X. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae014 · Cited by 7

CD7 regulates the persistence of terminally exhausted CD8+ T cells during chronic infection

Hyslop, S., Hofferek, C. J., Stegantseva, M. V., Kan, E., McCord, K. A., Alvarez, V. M., Xia, A. Y., Conarty, J. P., Wieland, A., & Hudson, W. H. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116316 · Cited by 8

Durable Response and Improved CD8 T Cell Plasticity in Lung Cancer Patients After PD1 Blockade and JAK InhibitionPreprint

Mathew, D., Marmarelis, M. E., Foley, C., Bauml, J. M., Ye, D., Ghinnagow, R., Ngiow, S. F., Klapholz, M., Jun, S., Zhang, Z., et al. (2022) · medRxiv · doi:10.1101/2022.11.05.22281973 · Cited by 7

Dysfunctional KLRB1+CD8+ T-cell responses are generated in chronically inflamed systemic sclerosis skin

Gaydosik, A. M., Tabib, T., Das, J., Larregina, A. T., Lafyatis, R., & Fuschiotti, P. (2025) · Annals of the Rheumatic Diseases · doi:10.1016/j.ard.2025.01.022 · Cited by 6

Identification of anti-TIM-3 based checkpoint inhibitor combinations with activity in immunotherapy refractory melanoma models

Phadke, M. S., Li, J., Sriramareddy, S. N., Rodrı́guez, P. C., Ruffell, B., Luca, V. C., Tran, T. T. T., Chen, Y. A., & Smalley, K. S. M. (2025) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2025-012011 · Cited by 6

Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application

Zhang, H., Liu, Y., Liu, W., Lin, A., Fang, Y., Qu, L., Zhang, X., Luo, P., Wang, L., & Jiang, A. (2025) · Biomarker Research · doi:10.1186/s40364-025-00811-0 · Cited by 8

High efficiency CRISPR knock-in demonstrates that TCF1 is insufficient to reverse T cell exhaustion

de Menezes, M. N., Chen, A. X. Y., Kulkarni, N., Sampurno, S., Saw, N. Y. L., Yap, K. M., Pérez-Núñez, I., Roth, S., Deguit, C., Haugen, B., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69671-y · Cited by 7

Immune checkpoint inhibition as a therapeutic strategy for HIV eradication: current insights and future directions

Lee, J., & Whitney, J. B. (2024) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000863 · Cited by 7

Interconnected lineage trajectories link conventional and natural killer (NK)-like exhausted CD8+ T cells beneficial in type 1 diabetes

Witkop, E. M., Diggins, K. E., WIEDEMAN, A. E., Serti, E., Nepom, G. T., Gersuk, V. H., Fuchs, B., Long, S. A., & Linsley, P. S. (2024) · Communications Biology · doi:10.1038/s42003-024-06456-3 · Cited by 5

Metabolomic profiling reveals the potential of fatty acids as regulators of exhausted CD8 T cells during chronic viral infection

Kazane, K. R., Labarta-Bajo, L., Zangwill, D., Liimatta, K., Vargas, F., Weldon, K. C., Dorrestein, P., & Zúñiga, E. I. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2419820122 · Cited by 9

New insights into progenitor exhausted T cell populations

Ahmed, R., Hofmann, M., Kallies, A., Oxenius, A., Philip, M., Wherry, E. J., Ye, L., & Zehn, D. (2026) · Nature reviews. Immunology · doi:10.1038/s41577-026-01328-9 · Cited by 7

Systems immunology approaches to study T cells in health and disease

Yang, A., & Poholek, A. C. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00446-1 · Cited by 5

Neonatal CD8+ T Cells Resist Exhaustion during Chronic Infection

Maymí, V. I., Zhu, H., Jager, M. C., Johnson, S., Getchell, R. G., Casey, J. W., Grenier, J. K., Wherry, E. J., Smith, N. L., Grimson, A., et al. (2024) · The Journal of Immunology · doi:10.4049/jimmunol.2300396 · Cited by 7

NRF2-dependent regulation of the prostacyclin receptor PTGIR drives CD8 T cell exhaustionPreprint

Dahabieh, M. S., DeCamp, L. M., Oswald, B. M., Kitchen-Goosen, S. M., Fu, Z. F., Vos, M., Compton, S. E., Longo, J., Williams, K. S., Ellis, A. E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.23.600279 · Cited by 5

Mapping heterogeneity in the tumor microenvironment of renal cell carcinoma through single-cell omics

Yavuz, B. G., Khanmammadova, N., Majeed, Z., Ali, M., Hasanov, M., Bilen, M. A., Singer, E. A., & Hasanov, E. (2025) · Trends in cancer · doi:10.1016/j.trecan.2025.11.001 · Cited by 6

Integrated temporal transcriptional and epigenetic single-cell analysis reveals the intrarenal immune characteristics in an early-stage model of IgA nephropathy during its acute injury

Chen, X., Zhang, Y., Zhou, J., Zhang, J., Dong, H., Chen, X., Tian, Y., & Wu, Y. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1405748 · Cited by 4

One-carbon metabolism is distinct metabolic signature for proliferative intermediate exhausted T cells of ICB-resistant cancer patients

Park, Y.-C., Hwang, Y., Jeong, J. W., Lee, C. M., Kim, M., Jo, S., Joo, S., Hwang, N., & Fang, S. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02332-z · Cited by 4

A Dual Role for NKG7 in T-cell Cytotoxicity and Longevity

Dong, H., Ham, H., Barham, W. J., Wen, T., Hirdler, J. B., Mao, Z., Ashton, D. S., Zhang, W., Lucien, F., da Silva, H. B., et al. (2025) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-25-0384 · Cited by 4

Deciphering the MYCN-driven metabolic microenvironment of neuroblastoma

Wolf, A. B., Leardini, D., Li, L., Masetti, R., Lyssiotis, C. A., & Barbieri, E. (2025) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2025.08.005 · Cited by 5

PRMT6 Promotes the Immune Evasion of Gastric Cancer by Upregulating ANXA1

Xu, L., Zhang, F., Yu, B., Jia, S., & Fan, S. (2024) · Critical Reviews in Eukaryotic Gene Expression · doi:10.1615/critreveukaryotgeneexpr.2024052979 · Cited by 4

DNA methylation profiling identifies TBKBP1 as potent amplifier of cytotoxic activity in CMV-specific human CD8+ T cells

Zheng, Y., Sasidharan-Nair, V., Buchta, T., Bonifacius, A., Khan, F., Pietzsch, B., Ahmadi, H., Beckstette, M., Niemz, J., Hilgendorf, P., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012581 · Cited by 4

Circulating T cells fuel anti-PD-1 and lenvatinib efficacy

Matulich, P. J., & Burger, M. L. (2025) · Cancer Cell · doi:10.1016/j.ccell.2024.12.003 · Cited by 4

Metabolomic Profiling Reveals Potential of Fatty Acids as Regulators of Stem-like Exhausted CD8 T Cells During Chronic Viral InfectionPreprint

Kazane, K. R., Labarta-Bajo, L., Zangwill, D., Liimatta, K., Vargas, F., Weldon, K. C., Dorrestein, P. C., & Zúñiga, E. I. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.07.617124 · Cited by 4

IL-2 immunotherapy rescues irradiation-induced T cell exhaustion in mouse colon cancer

Yong, C. S. M., Telarović, I., Gregor, L., Raeber, M. E., Pruschy, M. N., & Boyman, O. (2025) · iScience · doi:10.1016/j.isci.2025.112639 · Cited by 3

Interferon Regulatory Factor 4 dose-dependently controls peripheral Treg cell differentiation and homeostasis by modulating chromatin accessibility in mice

Voß, L. C., Schmidt, C., Harberts, A., Spohn, M., Bradtke, P., Borchers, A., Fertig, S., Schmid, J., Koch‐Nolte, F., Krebs, C. F., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1604888 · Cited by 3

TOX-induced lnc-SUMF2-8 compromises antitumor function and anti-PD-1 response of CD8+ T cells via lysosome-dependent degradation of TCF-1

Jiang, P., Chen, D., Chen, J., Wu, J., Zhong, Y., Huang, S., Mu, X., Lu, X., & Wang, X. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.09.006 · Cited by 3

Stem-like T cells: molecular regulation, functional diversity, and therapeutic implications across diseases

Wang, Z., Lai, L., Ran, S., Li, Y., Zhao, J., Wu, J., Guo, C., Cui, J., & Xia, J. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-07383-5 · Cited by 4

Stem-like T cells in cancer immunotherapy: biology, regulation and therapeutic targeting

Wang, H., Yao, Z., Luo, R., Kang, K., Na, F., & Lu, Y. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1764549 · Cited by 4

Constitutive STAT3 Signaling, in Comparison with STAT5, Enhances CAR T-cell Efficacy and Lowers Systemic Toxicity

Zhang, H., Ito, Y., Kasuya, H., Hayakawa, T., Li, Y., Inoue, S., Ouchida, T., & Kagoya, Y. (2026) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-25-0611 · Cited by 3

Oncolytic virotherapy potentiates chemo-PD-1 immunotherapy by engaging chemo-resistant bystander CD8 + T cells

Yang, Y., He, J., Liang, T., Li, K., Lin, Y., Wang, H., Xi, W., Ye, S., Qiu, D., Xie, C., et al. (2026) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2026-014897 · Cited by 3

Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted CD8+ T cell fate

Hu, W., Chen, Q., Zhu, S., Hu, S. S., Yu, H., Patel, V., Wang, Y., Badovinac, V. P., Zhang, Y., Zang, C., et al. (2026) · Nature Immunology · doi:10.1038/s41590-026-02578-4 · Cited by 3

PD-1⁺ CD8⁺ T cells: roles of PD-1 beyond an exhaustion marker

Chen, J., Chen, Z., Xu, L., Jia, J., Rui, K., & Tian, J. (2026) · Seminars in Immunopathology · doi:10.1007/s00281-026-01078-9 · Cited by 4

Mapping the gene space at single-cell resolution with gene signal pattern analysis

Venkat, A., Leone, S., Youlten, S. E., Fagerberg, E., Attanasio, J., Joshi, N. S., Perlmutter, M., & Krishnaswamy, S. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00734-0 · Cited by 5

CD226 identifies effector CD8+ T cells during tuberculosis and costimulates recognition of Mycobacterium tuberculosis-infected macrophages

Shinkawa, T., Chang, E., Rakib, T., Cavallo, K., Lai, R., & Behar, S. M. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116184 · Cited by 3

Quantitating CD8+ T cell memory development

Nizharadze, T., Becker, N. B., & Höfer, T. (2023) · Trends in Immunology · doi:10.1016/j.it.2023.05.004 · Cited by 5

Degradation of IKAROS prevents epigenetic progression of T cell exhaustion in a novel antigen-specific assayPreprint

Tay, T., Bommakanti, G., Jaensch, E. S., Gorthi, A., Reddy, I. K., Hu, Y., Zhang, R., Doshi, A. S., Tan, S. L., Brucklacher-Waldert, V., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.22.581548 · Cited by 3

Altered Purinergic Signaling and CD8+ T Cell Dysregulation in STAT3 GOF SyndromePreprint

Campos, J. S., Sayed, S. U., Dalalo, M. C., Mauracher, A. A., Knight, M., Conrey, P. E., Schultz, A. B., Hay, C. A., Lindell, R. B., Howard, C. A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.12.626682 · Cited by 3

Biosynthetic plasticity enables CD8+ T cell functional resilience under nutrient stressPreprint

Scaglione, M., Knight, M., Trihemasava, K., Rome, K., Archambault, A., Oh, J., Tanaka, E., Hall, E., Le, T. N. V., Lines, C. L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.22.632829 · Cited by 3

Type I interferon–driven lung pathology restricts T cell accumulation and motility during tuberculosisPreprint

Caouaille, M., Fromont, L., Shinkawa, T., Faucher, M., Hamid, A. I. A., Béhar, A., Mazères, S., Duvergé, Y., Decarpentrie, E., Lorreyte, Y., et al. (2025) · bioRxiv · doi:10.64898/2025.12.05.692491 · Cited by 1

Flt3L enhances clonal diversification and selective expansion of intratumoral CD8+ T cells while differentiating into effector-like cells

Chun, D., Park, J., Lee, S., Kim, H. J., Park, J.-E., & Kang, S. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.115023 · Cited by 2

Chromatin repression by PRC2 results in reduced gene expression driving key features of CD8 T cell exhaustion

Samareh, P., Agudelo-Garcia, P. A., Zhang, Z., Gilbert, M. B., Mendoza, M. R., Huang, H., Wu, J. E., Baxter, A. E., Chen, Z., Alexander, K., et al. (2025) · The Journal of Immunology · doi:10.1093/jimmun/vkaf188 · Cited by 2

A Dapl1 + subpopulation of naïve CD8 T cells is enriched for memory-lineage precursors

Lynch, A. C., Hioki, K. A., Liang, X., Thesmar, I., Cernjul, J., He, X. D., Mager, J., Cui, W., Alfandari, D., Pobezinskaya, E. L., et al. (2025) · Science Advances · doi:10.1126/sciadv.adx5687 · Cited by 2

Lpar5 regulates the CD8 T-cell response to persistent virus infection by altering exhaustion programming, survival, and NK receptor expression

D’Antonio, M. A., Ware, B. C., DiLisio, J. E., Michaels, M. J., Turner, J. A., Habenicht, L. M., Davenport, B., Morrison, T. E., Pelanda, R., Gapin, L., et al. (2025) · The Journal of Immunology · doi:10.1093/jimmun/vkaf210 · Cited by 2

Single-cell RNA-sequencing of myasthenia gravis reveals transcriptional heterogeneity and dysfunction of immune cell populations

Qx, W., Guo, Y., Zhou, L., Tian, Y., Yu, H., Zhou, T., Yin, S., & Zou, L. R. (2026) · International Immunology · doi:10.1093/intimm/dxag010 · Cited by 2

T cell–intrinsic VISTA expression promotes resistance to CTLA-4 blockade by restricting CD8+ T cell responses

Gilmour, C., Delaney, E., Parthasarathy, P. B., Roy, D., Ta, H. M., Zakeri, A., Grandez, P. E., Patnaik, S., Zhang, K., Juric, I., et al. (2026) · Journal of Clinical Investigation · doi:10.1172/jci195668 · Cited by 3

From cellular heterogeneity to precision medicine: single-cell multi-omics in CNS disease research

Liu, T., Zhang, Y., Hou, W., Hao, H., Geng, A., Zhao, G., & Zhang, Y. (2026) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2026.1848558 · Cited by 3

The transcription factor IRF8 drives tumor-specific exhaustion in CD8+ T cells

Ongaro, M., Thouenon, R., Crespo, I., Dumez, A., Charmoy, M., Camacho, E. R., Morel, V. J., Cropp, D., Desponds, E., Zanette, G., et al. (2026) · The Journal of Experimental Medicine · doi:10.1084/jem.20252115 · Cited by 3

The transcription factor Eomes drives a stemness program in CD4+ T cells that promotes anti-tumor immunity in response to immunotherapy

Agesta, A., Ferrand, C., Dorze, A.-L. L., Peillex, C., Carrié, N., Barascud, R., Palak, A., Esteban, L., Bernal, T., Joulia, E., et al. (2026) · Immunity · doi:10.1016/j.immuni.2026.05.018 · Cited by 3

Tumor-specific CXCR6 positive precursor CD8+ T cells mediate tumor control in metastatic melanoma

Song, Y., Chen, J., Zhang, Y., Wu, N., Zhu, Y., Chen, G., Miao, F., Chen, Z., & Wang, Y. (2025) · Cellular Oncology · doi:10.1007/s13402-025-01040-1 · Cited by 3

TIM3 and TIGIT-expressing CD4 T cells are impacted by kidney transplantation and associated with risk of infection

Pickering, H. C., Sen, S., Cappelletti, M., Lum, E. L., Bunnapradist, S., Reed, E. F., & Schaenman, J. M. D. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1550154 · Cited by 2

CCR2+ monocytes promote memory CD8+ T-cell differentiation via membrane-bound TGF-β

Sun, L., Zhang, C., Jiao, A., Su, Y., Zhang, T., Wang, Q., Ge, Y., Chen, Y., Yuan, N., Zhang, L., et al. (2025) · Cellular and Molecular Immunology · doi:10.1038/s41423-025-01299-2 · Cited by 2

GITR and TIGIT immunotherapy provokes divergent multi-cellular responses in the tumor microenvironment of gastrointestinal cancersPreprint

Sathe, A., Ayala, C., Bai, X.-Q., Grimes, S., Lee, B., Kin, C., Shelton, A., Poultsides, G., & Ji, H. P. (2023) · bioRxiv · doi:10.1101/2023.03.13.532299 · Cited by 2

Boosting Single-Cell RNA Sequencing Analysis with Simple Neural AttentionPreprint

Davalos, O. A., Heydari, A. A., Fertig, E. J., Sindi, S., & Hoyer, K. K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.29.542760 · Cited by 2

Engineered NKG2C + NK-like T cells exhibit superior antitumor efficacy while mitigating cytokine release syndromePreprint

Lupo, K. B., Panjwani, M. K., Shahid, S., Sottile, R., Lawry, C., Kolk, G., Kontopolous, T., Daniyan, A. F., Chandran, S. S., Klebanoff, C. A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.16.603785 · Cited by 2

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumoursPreprint

Burn, T. N., Schröder, J., Gandolfo, L. C., Osman, M., Wainwright, E. N., Lam, E. Y. N., McDonald, K. M., Evans, R. B., Li, S., Rawlinson, D., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.23.666465 · Cited by 2

Dual-inactivation of Regnase-1 and SOCS1 rewires exhausted CD8 + T cell fate to enhance anti-tumor functionalityPreprint

Mercier, I. L., Monteiro, D., Halpin-Veszeleiova, K., Wong, K. K. W., Dodson, A. E., Martinez, G. J., Matos, D. A., Hamza, B. M., Yeri, A., McKenney, S., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.21.700812 · Cited by 2

PD-1 blockade drug holiday improves exhausted progenitor CD8 T cell (Tpex) reinvigoration by avoiding Tpex adaptive resistancePreprint

Ngiow, S. F., O’Connell, R. P., Manne, S., Huang, Y. J., Giles, J. R., Alcalde, V., Mathew, D., Klapholz, M., Nzingha, K., Chen, Z., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.14.725199 · Cited by 3

Delving Into the Dialogue between Epigenetic Modifications and Immunometabolism in Cancer

Xie, X., Liu, W. L., Zhang, Z., Luo, P., Tang, B., & Mao, W. (2025) · Advanced Genetics · doi:10.1002/ggn2.202500034 · Cited by 1

Single-Cell Clonal Lineage Tracing Identifies the Transcriptional Program Controlling the Cell-Fate Decisions by Neoantigen-Specific CD8+ T Cells

Luo, Y., Hu, T., Yao, C., & Wu, T. (2025) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-25-0203 · Cited by 2

Progenitor effects and unique transcriptomic signatures linked to differentiation phenotype in clonally expanded antigen-specific CD8 T memory stem cells

Zhao, Y., Samir, J., Keoshkerian, E., Li, H., An, H., Bull, R. A., Luciani, F., & Lloyd, A. R. (2025) · The Journal of Immunology · doi:10.1093/jimmun/vkaf299 · Cited by 1

CARM1-mediated hypoxanthine-enriched exosomes rewire inosine metabolism and impair CD8+ T cell antitumor function

Yin, J., Su, Z., Hu, X., Sun, H., Sun, Z., Zhou, S., Xu, W., Xi, Y., Liu, L., Zhang, J., et al. (2026) · Cell Death and Differentiation · doi:10.1038/s41418-026-01673-1 · Cited by 1

Genetic disruption of Pdcd-1 upstream enhancer boosts T cell function and antitumor responses

Jerin, C., Seo, W., & Nishikawa, H. (2026) · Immunology Letters · doi:10.1016/j.imlet.2026.107171 · Cited by 2

Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity

Geng, S., Li, Z., Li, W., Liang, H., Xu, F., Zhang, L., Zhang, W., Tao, S., Wang, Y., Zhou, Y., et al. (2026) · Immunity · doi:10.1016/j.immuni.2026.03.029 · Cited by 2

CKS1B is a tumor-intrinsic factor driving CD8 + T cell exhaustion via maintaining persistent tumor-antigen stimulation

Yu, S., Wu, P., Xie, X., Zhu, L. C., Chen, L., Yu, Y., Tan, W., Zhang, S., Wu, C. H., & Lin, D. X. (2026) · Science Advances · doi:10.1126/sciadv.aec9179 · Cited by 1

Hypoxia Impairs CD8+ T Cell Fitness and Is Associated with a Dysfunctional CD8+ T Cell State in Pancreatic Cancer

Mello, A. M., di Magliano, M. P., & Lee, K. P. (2026) · Cancers · doi:10.3390/cancers18101508 · Cited by 1

Early sex-related transcriptional differences in CD8+ T cells responding to chronic viral infection reveal a sex bias in exhaustion

Arsenio, J., Kahia, N., Robertson, S., Rodriguez, M., Layug, P. J., Vats, H., Kannan, K., Spicer, V., Ozturk-Aptekmann, A., & Wilkins, O. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1783098 · Cited by 2

Targeting tumor-specific T cells with LAG3-directed interleukin-2 prevents T-cell exhaustion and reinvigorates antitumor immunity

Yu, X., Liao, H., Lv, J., Sun, Y., Zhang, R., Chen, Y., Lin, Y., Liu, L., Li, S., Tang, H., et al. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-026-02667-8 · Cited by 2

Tumor-draining lymph nodes shape the tumor microenvironment through enrichment of tumor-reactive effector-exhausted CD8+ T cells

Kong, D., Feng, L., Sun, Y. X., Zhang, H., Fan, J., An, Y., Zhu, Y., Zhu, Y., Zhang, Q., Xiang, R., et al. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-026-02858-3 · Cited by 1

Single-cell RNA-seq of myasthenia gravis reveals transcriptional heterogenity and dysfunction of immune cell populationsPreprint

Zou, L., Wu, Q., Guo, Y., Tian, Y., Yu, H., Zhou, T., & Yin, S. (2024) · Research Square · doi:10.21203/rs.3.rs-4918125/v1 · Cited by 1

Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockadePreprint

Raposo, C. J., Yan, P., Chen, A. Y., Majidi, S., Hiam-Galvez, K. J., & Satpathy, A. T. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.10.637523 · Cited by 3

Divergent ontogeny of Tissue Resident Memory and Tissue Resident Exhausted CD8 + T cells underlies distinct functional potentialPreprint

Park, S. L., Painter, M. M., Manne, S., Alcalde, V., McLaughlin, M., Sullivan, M. A., Mathew, D., Torres, L., Huang, Y., Reeg, D. B., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.08.669213 · Cited by 1

Single-cell multi-omics reveals archetypal regulatory programs shared across T cell subsets

Walker, S. K., van der Veeken, J., Rudensky, A. Y., & Pritykin, Y. (2026) · Cell Reports · doi:10.1101/2025.09.08.675014 · Cited by 1

CD8 T cells mediate immunosurveillance for neoantigen+ epithelial stem cells in the colonPreprint

Buck, J. N., Iyer, N. R., Fagerberg, E., Micevic, G., He, J., Denis, K. S., Shah, V., Blackburn, H. N., Venkatesan, S., Attanasio, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.19.683142 · Cited by 1

Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fatesPreprint

Giles, J. R., Ngiow, S. F., Manne, S., Baxter, A. E., Khan, O., Wang, P., Staupe, R. P., Abdel-Hakeem, M. S., Huang, H., Mathew, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.27.485974 · Cited by 6

Giant bulla or pneumothorax

Chang, C., & Ko, H. (2020) · Postgraduate Medical Journal · doi:10.1136/postgradmedj-2020-139077 · Cited by 1

Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection

Quezada, L. K., Jin, W., Liu, Y. C., Kim, E. S., He, Z., Indralingam, C. S., Tysl, T., Labarta-Bajo, L., Wehrens, E. J., Jo, Y., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3001983 · Cited by 24

Developmental relationships of four exhausted CD8 T cell subsets reveals underlying transcriptional and epigenetic control mechanisms

Beltra, J., Manne, S., Abdel-Hakeem, M. S., Kurachi, M., Giles, J. R., Chen, Z., Casella, V., Ngiow, S. F., Khan, O., Huang, Y., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.204.supp.77.16 · Cited by 4

Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade

Jadhav, R. R., Im, S. J., Hu, B., Hashimoto, M., Li, P., Lin, J., Leonard, W. J., Greenleaf, W. J., Ahmed, R., & Goronzy, J. J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1903520116 · Cited by 224