Publications
Highlighted Publications
Plotkin AL, Mullins GN, Green WD, Shi H, Chung HK, Stanley N, Milner JJ. Optimal transport fate mapping resolves T cell differentiation dynamics across tissues. bioRxiv. 2026. Preprint. doi:10.64898/2026.02.24.707057.
Pratt BM, Mullins GN, Brown N, Green WD, Modliszewski J, Xie F, van Rooyen L, Zhabotynsky V, Jambor AN, Cannon G, Green JM, Kennedy A, Alicea Paunto CDM, Shi H, Merritt E, Egawa T, Somasundaram A, Wang W, Thaxton JE, Dotti G, Chung HK, Milner JJ. Latent Regulatory Programs Generate Synthetic T Cell States with Enhanced Therapeutic Potential. bioRxiv [Preprint]. 2026 Jan 8:2026.01.07.698190.
Green WD, Gomez A, Plotkin AL, Pratt BM, Merritt EF, Mullins GN, Kren NP, Modliszewski JL, Zhabotynsky V, Woodcock MG, Green JM, Cannon G, Pipkin ME, Dotti G, Thaxton JE, Pylayeva-Gupta Y, Baldwin AS, Morris JP 4th, Stanley N, Milner JJ. Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. Immunity. 2025. Epub ahead of print.
Pratt B.M., Milner J.J. Cancer immunosurveillance by gut T cells. Science. 380(6649):1011-1012. Perspective.
Milner J.J., Toma C., Quon S., Omilusik K., Scharping N.E., Dey A., Reina-Campos M., Nguyen H., Getzler A.J., Diao H., Yu B., Deploux A., Yoshida T., Li D., Qi J., Vincek A., Hedrick S.M., Egawa T., Zhou M., Crotty S., Ozato K., Pipkin M.E., Goldrath A.W. Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection. J Exp Med. 2021; 218(8):e20202512.
Milner J.J.*,#, Nguyen H.*, Omilusik K., Reina-Campos M., Toma C., Delpoux A., Boland B.S., Hedrick S.M., Chang J.T., Goldrath A.W.# Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population. PNAS. 2020; 117(41):25667-25678 . *Co-first authors; #Co-corresponding authors.
Milner J.J., Toma C., He Z., Kurd N.S., Nguyen Q.P., McDonald B., Quezada L., Widjaja C.E., Witherden D.A., Crowl J.T., Shaw L., Yeo G.W., Chang J.T., Omilusik K.D.*, Goldrath A.W.* Heterogenous populations of tissue-resident CD8 T cells are generated in response to infection and malignancy. Immunity. 2020; 52(5):808-824.
Milner J.J., Goldrath A.W. Transcriptional programming of tissue-resident memory CD8+ T cells. Curr Opin Immunol. 2018; 51:162-169. Review
Milner J.J., Toma C., Yu B., Zhang K., Omilusik K., Phan A.T., Wang D., Getzler A.J., Ngyuen T., Crotty S., Wang W., Pipkin M.E., Goldrath A.W. Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours. Nature. 2017; 552(7684):253-257.
Additional Publications
9) Chung KH, Liu C., Jambor A.N., Riesenberg B.P., Sun M., Casillas E., Chick B., LaPorte M., Mann T.H., Chen D., Hoffmann F., Tripple V., Hargreaves D.C., Thaxton J.E., Milner J.J., Kaech S.M.*, Wang W.* Multi-omics atlas-assisted discovery of transcription factors for selective T cell state reprogramming. Nature. 2025 In press.
10) Stanland LJ, Huggins HP, Sahoo SS, Porrello A, Chareddy Y, Azam SH, Perry JL, Pallan PS, Whately K, Edatt L, Green WD, Fleming MC, Im J, Gutierrez-Ford C, Simmons I, Dawoud A, Zhou KI, Jayaprakash V, Sellers RS, Cruz G, Wielgus A, Milner JJ, Egli M, Bowers AA, Pecot CV. A first-in-class EGFR-directed KRAS G12V selective inhibitor. Cancer Cell. 2025 Jun 16:S1535-6108(25)00225-9. Epub ahead of print.
11) Alicea Pauneto, C. D. M., Riesenberg, B. P., Gandy, E., Kennedy, A. S., Hunt, E. G., Hurst, K. E., Clutton, G., Modliszewski, J. L., Guerriero, J. L., Miller, B. C., Esther, R. J., Moschos, S. J., Milner, J. J., Luke Wiseman, R., & Thaxton, J. The tumor microenvironment enforces ATF4 in CD8 TILs to obstruct immune checkpoint blockade efficacy. Immunity. 2025. Epub ahead of print.
12) Sengottuvel N, Whately KM, Modliszewski JL, Sellers RS, Green WD, Gong W, Woods AT, Livingston EW, Fagan-Solis KD, Cannon G, Edatt L, Yuan H, Chack AC, Sanchez Y, Zhou K, Dawoud A, Green JM, Godfrey V, Milner JJ, Gupta GP, Pecot CV. Tumor suppressors in Sox2-mediated lung cancers promote distinct cell intrinsic and immunologic remodeling. JCI Insight. 2025 May 6:e171364. doi: 10.1172/jci.insight.171364. Epub ahead of print.
13) Green WD, Gomez AG, Plotkin AL, Pratt B.M., Mullins G.N., Modliszewski J.L., Zhabotynsky V., Woodcock M.G., Green J.M., Cannon G., Kren N.P., Beckabir W., Whately K., Bang S., Tsahouridis R., Cui X., Fecci P.E., Thaxton J.E., Pipkin M.E., Dotti G., Morris J.P., Baldwin A.S., Stanley N., Milner J.J. Enhancer-driven gene regulatory networks reveal transcription factors governing CD8 T cell adaptation and differentiation in the tumor microenvironment. Immunity. 2025. 58(7):1725-1741.
14) Song F., Tsahouridis O., Stucchi S., Walhart T., Mendell S., Hardy B., Gilbert T.S.K., Graves L.M., Herring L.E., Savoldo B., Ma X., Woodcock M.G., Milner J.J., Ivanova A., Hugh K.H., Pearce H., Xu Y., Dotti G. A multi-kinase inhibitor screen identifies inhibitors reserving stem-cell like chimeric antigen receptor T cells. Nature Immunology 2025; 26(2):279-293.
15) Ulibarri M.R., L. Ying, Ramprashad J.R., Han G., Hasan M.H., Mithila F.J., Ma C., Gopinath S., Zhang N., Milner J.J., Beura L.K. Epithelial organoid supports resident memory CD8 T cell differentiation. Cell Reports. 2024; 43(8):114621.
16) Cheng M., Ka A., Chu Y., Zhijun L., Yang S., Smith M., Zhang Q., Brown N., Marzluff W., Bardeesy N., Milner J.J., Welch J., Xiong Y., Baldwin A. TET2 promotes tumor antigen presentation and T cell IFNg, which is enhanced by vitamin C treatment. JCI Insight. 2024; 9(22):e175098.
17) Zhou X., Wang Y., Dou Z., Delfanti G., Tsahouridis O., Pellegry M.M., Atassi G., Woodcock M., Casorati G., Dellabona P., Kim W., Savoldo B., Guo L., Tsagaratou A., Milner J.J., Metelitsa L., Dotti G. CAR-redirected natural killer T cells demonstrate superior antitumor activity to CAR-T cells through multimodal CD1d-dependent mechanisms. Nature Cancer. 2024. 5(11):1607-1621.
18) Ranek J.S, Stallaert W., Milner J.J., Stanley N., Purvis J.E. Feature selection for preserving biological trajectories in single-cell data. bioRxiv. 2023; 540043
https://www.biorxiv.org/content/10.1101/2023.05.09.540043v1
19) Nguyen Q., Takehara K., Deng T., O’Shea S., Heeg M., Omilusik K., Milner J.J., Quon S., Pipkin M.P., Choi J., Crotty S., Goldrath A.W. Transcriptional programming of CD4+ TRM differentiation following viral infection balances TH1 effector- and memory-associated gene expression. 2023. Science Immunology. In press.
https://pubmed.ncbi.nlm.nih.gov/37172104/
20) Quon S., Yu, B., Russ B.E., Tsyganov K., Nguyen H., Toma C., Heeg M., Hocker J.D., Milner J.J., Crotty S., Pipkin M.E., Turner S.J., Goldrath A.W. DNA architectural protein CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8 T cells. Immunity. 2023; 56, 1-20.
https://pubmed.ncbi.nlm.nih.gov/37040762/
21) Getzler A.J., Frederick M.A., Diao H., Milner J.J., Belanger S., Tsuda S.M., Albao D., Kim J., Crotty S., Goldrath A.W., Pipkin M.E. Mixed lineage leukemia (MLL1) establishes global histone H3K4 trimethylation and stem like memory CD8 T cell formation. bioRxiv. 2023; 524461.
https://www.biorxiv.org/content/10.1101/2023.01.18.524461v2
22) Crowl J.T., Heeg M., Ferry A., Milner J.J., Omilusik K., Toma C., He Z., Chang J.T., Goldrath A.G. Tissue-resident memory CD8 T cells possess unique transcriptional, epigenetic, and functional adaptions to different tissue environments. Nature Immunology. 2022; 23(7):1121-1131.
https://pubmed.ncbi.nlm.nih.gov/35761084/
23) Diao H., Chen R., Tsuda S.M., Wang D., Frderick M.A., Kim J., Karunadharma P.P., Martinez G., Getzler A.J., Toma C., Milner J.J., Venables C.T., Martin D.M., Goldrath A.W., Crotty S., Pipkin M.E. Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny. bioRxiv. 2021; 456014
https://www.biorxiv.org/content/10.1101/2021.08.11.456014v3
24) Clark M., Kroger C.J., Ke Q., Zhang R., Statum K., Milner J.J., Martin A., Wang B., Tisch R. Coreceptor therapy has distinct short- and long-term tolerogenic effects intrinsic to autoreactive effector T cells. Journal of Clinical Investigation Insight. 2021; 6(17):149130.
https://pubmed.ncbi.nlm.nih.gov/34314385/
25) Liu C., Qi T., Milner J.J., Lu Y., Cao Y. Speed and location both matter: antigen stimulus dynamics controls CAR-T cell response. Frontiers in Immunology. 2021; 748768.
https://pubmed.ncbi.nlm.nih.gov/34691062/
26) Green W., Al-Shaer A., Shi Q., Gowdy K., MacIver N., Milner J.J., Beck M.A., Shaikh S.R. Metabolic and functional impairment of CD8 T cells from the lungs of influenza-infected obese mice. Journal of Leukocyte Biology. 2021; 111(1):147-159.
https://pubmed.ncbi.nlm.nih.gov/33847405/
27) Aguilar S.V. et al.. ImmGen at 15. Nature Immunology. 2020; 21(7):700-703.
https://pubmed.ncbi.nlm.nih.gov/32577013/
28) Kurd N.S., He Z., Louis T.L., Milner J.J., Omilusik K.D., Tsai M.S., Widjaja C.E., Kanbar J.N., Olvera J.G., Tysl T., Quezada L.K., Boland B.S., Goldrath A.W., Yeo G.W., Chang J.T. Early precursors and molecular determinants tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA-sequencing. Science Immunology. 2020; 5(47):eaa6894.
https://pubmed.ncbi.nlm.nih.gov/32414833/
29) Boland B.S., He Z., Tsai M.S., Olvera J.G., Omilusik K.O., Duong H.G. Kim E.S., Limary A.E., Jin W., Milner J.J., Yu B., Patel S.A., Louis T.L., Tysl T., Kurd N.S., Bortnick A., Quezada L.K., Kanbar J.N., Miralles A., Huylebroeck D., Valasek M.A., Dulai P.S., Singh S., Lu L., Bui J.D., Murre C., Sandborn W.J., Goldrath A.W., Yeo G.Y., Chang J.T. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses. Science Immunology. 2020; 5(50): eabb4432.
https://pubmed.ncbi.nlm.nih.gov/32826341/
30) Freemerman AJ., Zhao L., Pingili A.K., Teng B., Cozzo A.J., Fuller A.M., Johnson A.R., Milner J.J., Lim M.F., Galanko J.A., Beck M.A., Bear J.E., Rotty J.D. Brezavada L., Smallwood H.S., Puchowicz M.A., Liu J., Locasale J., Lee D.P., Bennet B.J., Abel E.D. Rathmell J.C., Makowski L. Myeloid Slc2a1-Deficient Murine Model Revealed Macrophage Activation and Metabolic Phenotype Are Fueled by GLUT1. The Journal of Immunology. 2019; 202(4):1265-1286.
https://pubmed.ncbi.nlm.nih.gov/30659108/
31) Karlsson E.A., Milner J.J., Green W.D., Rebeles J., Schultz-Cherry S., Beck M.A. Chapter 10: Influence of obesity on the response to influenza infection and vaccination. Editors: Johnston R.A., Suratt B.T. Mechanisms and manifestations of obesity in lung disease. Academic Press. 2019: p. 227-259.
Influence of obesity on the response to influenza infection and vaccination – ScienceDirect
32) Wang D., Diao, H., Getzler A.J., Rogal W., Frederick M.A., Milner J.J., Yu B., Crotty S., Goldrath A.W., Pipkin M.E. The transcription factor Runx3 establishes chromatin accessibility of cis-regulatory landscapes that drive memory cytotoxic T lymphocyte formation. Immunity. 2018; 48(4):659-674.
https://pubmed.ncbi.nlm.nih.gov/29669249/
33) Omilusik K., Nadjsombati M., Shaw L., Yu, B., Milner, J.J., Goldrath A.W. Sustained Id2 regulation of E proteins is required for terminal differentiation of effector CD8+ T cells. The Journal of Experimental Medicine. 2018; 215(3):773-783.
https://pubmed.ncbi.nlm.nih.gov/29440362/
34) Yu B., Zhang K., Milner J.J., Toma C., Chen R., Scott-Browne J.P., Pereira R.M, Crotty S., Chang J.T., Pipkin M.E., Wang W., Goldrath A.W. Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation. Nature Immunology. 2017; 18(5):573-582.
https://pubmed.ncbi.nlm.nih.gov/28288100/
35) Kasaraju R., Guesdon W., Crouch M.J., Teague H.L., Sullivan E.M., Karlsson E.A., Schultz-Cherry S., Gowdy K., Bridges L.C., Reese L.R., Neufer P.D., Armstrong M., Reisdorph M., Milner J.J., Beck M.A., Shaikh S.R. B cell activity is impaired in human and mouse obesity and is responsive to an essential fatty acid upon murine influenza infection. The Journal of Immunology. 2017; 198:4738-4752.
https://pubmed.ncbi.nlm.nih.gov/28500069/
36) Johnson A.R., Qin Y., Freemerman A.J., Huang M.J., Cozzo A.J., Zhao L., Sampey B.P. Milner J.J., Beck M.A., Damania B.A., Galanko J.A., Edin M.L., Zeldin D.C., Fueger P.T., Bvins B., Stahl A., Wu Y., Mohlke K.L., Makowski L. Metabolic reprograming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammation. Molecular Metabolism. 2016; 5:506-526.
https://pubmed.ncbi.nlm.nih.gov/27408776/
37) Antoniak S., Tatsumi K., Hisada Y., Milner J.J., Neidich N., Shaver C.M., Pawlinski R., Beck M.A., Bastarache J., Mackman N. Tissue factor deficiency increases alveolar hemorrhage and death in influenza A infected mice. Journal of Thrombosis and Haemostasis. 2016; 14:1238-1248.
https://pubmed.ncbi.nlm.nih.gov/27408776/
38) Milner J.J., Rebeles J., Dhungana S., Stewart D.A., Sumner S.C. Meyers M.H., Mancuso P., Beck M.A. Obesity increases mortality and modulates the lung metabolome during pandemic H1N1 influenza virus infection in mice. The Journal of Immunology. 2015; 198: 4846-4859.
https://pubmed.ncbi.nlm.nih.gov/25862817/
39) Milner J.J., Wang J., Sheridan P.A., Ebbels T., Beck M.A., Saric, J. 1H NMR-based profiling reveals differential immune-metabolic networks during influenza infection in obese mice. PLoS One. 2014; 9:e97238.
https://pubmed.ncbi.nlm.nih.gov/24844920/
40) Milner J.J., Beck M.A. Obesity and influenza infection severity. Future Virology. 2014; 9:223-225. Editorial
https://www.futuremedicine.com/doi/10.2217/fvl.14.2
41) Freemerman A.J., Johnson A.R., Sacks G.N., Milner J.J., Kirk E.L., Troester M.A., Macintrye A.N., Goraksha-Hicks P., Rathmell J.C., Makowski L. Metabolic reprogramming of macrophages: GLUT1-mediated glucose metabolism drives a pro-inflammatory phenotype. The Journal of Biological Chemistry. 2014; 289:7884-7896.
https://pubmed.ncbi.nlm.nih.gov/24492615/
42) Milner J.J., Sheridan P.A., Karlsson E.A., Schultz-Cherry S., Shi Q., Beck M.A. Diet-induced obese mice exhibit altered heterologous immunity during a secondary 2009 pandemic H1N1 infection. The Journal of Immunology. 2013; 191: 2474-2485.
https://pubmed.ncbi.nlm.nih.gov/23904168/
43) Sundaram S., Freemerman A.J., Johnson A.R., Milner J.J., McNaughton K.K., Galanko J.A., Bendt K.M., Darr D.B., Perou C.M., Troester M.A., Makowski L. Role of HGF in obesity-associated tumorigenesis: C3(1)-TAg mice as a model for human basal-like breast cancer. Breast Cancer Research and Treatment. 2013; 142: 489-503.
https://pubmed.ncbi.nlm.nih.gov/24218051/
44) Johnson A.R., Milner J.J., Makowski L. The inflammation highway: metabolism accelerates inflammatory traffic in obesity. Immunological Reviews. 2012; 249: 218-238. Review
https://pubmed.ncbi.nlm.nih.gov/22889225/
45) Milner J.J., Beck M.A. The impact of obesity on the immune response to infection. Proceedings of the Nutrition Society. 2012; 71: 298-306. Review