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NR4A Transcription Factors Limit CAR T Cell Function in Solid Tumors

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NR4A Transcription Factors Limit CAR T Cell Function in Solid Tumors LETTER https://doi.org/10.1038/s41586-019-0985-x NR4A transcription factors limit CAR T cell function in solid tumours Joyce Chen1,2,3,4*, Isaac F. López-Moyado1,4,5, Hyungseok Seo1, Chan-Wang J. Lio1, Laura J. Hempleman1, Takashi Sekiya6, Akihiko Yoshimura7, James P. Scott-Browne1,4,9,10* & Anjana Rao1,3,4,8,10* T cells expressing chimeric antigen receptors (CAR T cells) targeting CD8+CD45.1+ OT-I cells (specific for chicken ovalbumin (OVA) human CD19 (hCD19) have shown clinical efficacy against B cell SIINFEKL peptide presented by H-2Kb; Extended Data Fig. 2a, b) malignancies1,2. CAR T cells have been less effective against solid showed similar tumour growth rates (Extended Data Fig. 2c); low tumours3–5, in part because they enter a hyporesponsive (‘exhausted’ numbers of CAR T cells were transferred to minimize tumour rejec- or ‘dysfunctional’) state6–9 triggered by chronic antigen stimulation tion (Extended Data Fig. 2d). Eight days after adoptive transfer, CAR and characterized by upregulation of inhibitory receptors and loss of and OT-I tumour-infiltrating lymphocytes (TILs) (Fig. 1b, Extended effector function. To investigate the function of CAR T cells in solid Data Fig. 2b, e, f) comprised around 18% and 9%, respectively, of CD8+ tumours, we transferred hCD19-reactive CAR T cells into hCD19+ TILs (Fig. 1c) and exhibited similar proportions of PD-1hiTIM3hi cells tumour-bearing mice. CD8+CAR+ tumour-infiltrating lymphocytes compared to endogenous TILs (Fig. 1b, Extended Data Fig. 2b). All and CD8+ endogenous tumour-infiltrating lymphocytes expressing TILs produced low levels of TNF and IFNγ upon re-stimulation with the inhibitory receptors PD-1 and TIM3 exhibited similar profiles PMA and ionomycin (Fig. 1d, e), confirming their decreased function. of gene expression and chromatin accessibility, associated with The transcriptional profiles of ‘highly exhausted’ PD-1hiTIM3hi secondary activation of nuclear receptor transcription factors CAR TILs (population A, Fig. 1b) were similar to those of endoge- NR4A1 (also known as NUR77), NR4A2 (NURR1) and NR4A3 nous PD-1hiTIM3hi TILs (population C, Fig. 1b), but distinct from (NOR1) by the initiating transcription factor NFAT (nuclear factor those of CAR and endogenous ‘antigen-specific memory precursor’ of activated T cells)10–12. CD8+ T cells from humans with cancer PD-1hiTIM3lo TILs18 (populations B and D) and naive-like endog- or chronic viral infections13–15 expressed high levels of NR4A enous PD-1loTIM3lo TILs (population E) (Fig. 2a, Extended Data transcription factors and displayed enrichment of NR4A-binding Fig. 2g, Supplementary Table 1). The chromatin accessibility profiles motifs in accessible chromatin regions. CAR T cells lacking all of endogenous, OT-I and CAR PD-1hiTIM3hi and PD-1hiTIM3lo TIL three NR4A transcription factors (Nr4a triple knockout) promoted subsets (A–D, F) were similar to one another, but distinct from those tumour regression and prolonged the survival of tumour-bearing of PD-1loTIM3lo endogenous TILs (E), which resembled naive CD8+ mice. Nr4a triple knockout CAR tumour-infiltrating lymphocytes T cells (Fig. 2b, Extended Data Fig. 3). PD-1hiTIM3lo TILs (B, D) resem- displayed phenotypes and gene expression profiles characteristic of bled memory-precursor CD8+ T cells7,11,12, with accessible regions CD8+ effector T cells, and chromatin regions uniquely accessible showing substantial enrichment for consensus TCF1 motifs (Fig. 2b, in Nr4a triple knockout CAR tumour-infiltrating lymphocytes cluster 6). Regions that were selectively accessible in PD-1hi populations compared to wild type were enriched for binding motifs for NF-κB (A–D, F) were enriched for consensus NR4A (nuclear receptor, NR) and AP-1, transcription factors involved in activation of T cells. We as well as NFAT, NFκB, bZIP and IRF:bZIP motifs (Fig. 2b, clusters identify NR4A transcription factors as having an important role in 8, 9). NR4A protein expression was higher in PD-1hiTIM3hi than in the cell-intrinsic program of T cell hyporesponsiveness and point to PD-1hiTIM3lo TILs (Fig. 2c, Extended Data Fig. 4a–d). NR4A inhibition as a promising strategy for cancer immunotherapy. Single-cell RNA-sequencing (RNA-seq) data from human CD8+ Mouse B16-OVA melanoma, EL4 thymoma and MC38 colon adeno- TILs provided further justification for studies of NR4A. In CD8+ TILs carcinoma cell lines were engineered to express hCD19 (Extended Data infiltrating a human melanoma14, NR4A1 and NR4A2 expression Fig. 1a). B16-OVA-hCD19 cells stably maintained hCD19 expression showed a strong positive correlation with PDCD1 (PD-1) and HAVCR2 after growth in syngeneic C57BL/6J mice for 18 days and subsequent (TIM3) expression, and NR4A3 showed a moderate positive correlation culture for 7 days ex vivo (Extended Data Fig. 1a, right). B16-OVA and (Fig. 2d). PDCD1 and HAVCR2 expression correlated positively with B16-OVA-hCD19 cells grew at the same rate in vivo, indicating that TIGIT, CD38, CTLA4, JUN, TOX, TOX2 and IRF4 and negatively with the hCD19 antigen did not cause tumour rejection (Extended Data TCF7 (Extended Data Fig. 4e–g, Supplementary Table 2). Additionally, Fig. 1b, left). On the basis of tumour growth rate, we inoculated mice NR4A, NFAT, bZIP and IRF:bZIP motifs were enriched in regions with 500,000 B16-OVA-hCD19 tumour cells (Extended Data Fig. 1b, uniquely accessible in CD8+PD-1hi TILs from human melanoma and right). Mouse CD8+ T cells retrovirally transduced with a second- non-small cell lung cancer13 and in HIV-antigen-specific CD8+ T cells generation CAR against hCD1916,17 exhibited a transduction efficiency of from infected humans15 (Fig. 2e, cluster 9). The upregulation of NR4A 95.5 ± 4.0% (mean ± s.d.) (Extended Data Fig. 1c, d), produced TNF and family members and enrichment of NR4A binding motifs in differen- IFNγ upon re-stimulation with EL4-hCD19 cells, and exhibited dose-de- tially accessible regions of chronically stimulated human and mouse pendent lysis of B16-OVA-hCD19 cells (Extended Data Fig. 1e–g). CAR CD8+PD-1hi T cells11,12,15,19 led us to focus on NR4A family members T cells did not express higher surface levels of PD-1, TIM3 or LAG3 than as potential transcriptional effectors of CD8+ T cell exhaustion. mock-transduced cells under resting conditions (Extended Data Fig. 1h). The three NR4A proteins are essential for regulatory T cell develop- C57BL/6J mice bearing B16-OVA-hCD19 tumours and adoptively ment20, indicating redundant function. We compared NR4A-sufficient transferred with CD8+CD45.1+Thy1.1+ CAR T cells (Fig. 1a, b) or (wild type) CAR TILs with NR4A triple knockout (Nr4a TKO) CAR 1Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA. 2Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA. 3Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA. 4Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA. 5Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA. 6Department of Immune Regulation, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan. 7Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan. 8Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA. 9Present address: Department of 10 Biomedical Research, National Jewish Health, Denver, CO, USA. These authors contributed equally: James P. Scott-Browne, Anjana Rao. *e-mail: [email protected]; [email protected]; [email protected] NATURE| www.nature.com/nature RESEARCH LETTER IFN TNF TNF and IFN a d γ P = 0.1723 γ CAR ** ** Inoculate adoptive *** ** tumour transfer Day 21: 50 * *** 50 ** isolate TILs 60 ** C57BL/6J 40 40 30 40 30 mice Day 13 20 20 20 b Day 8 after adoptive transfer: CAR CD8+ T cells 10 10 0 0 0 + + Percentage of cells CAR CAR CAR All CD8 T cells CAR CD8 producing cytokines CAR Endo.OT-I CAR Endo.OT-I CAREndo.OT-I 5 in vitro in vitro in vitro 2.14 25.4 10 105 No stimulation PMA + ionomycin 104 A + 103 B 68.4 Tumour-inltrating CD8 T cells 104 e 0 CAR Endogenous OT-I In vitro CAR CD8+ TILs CD8+ TILs CD8+ TILs CD8+ T cells + 5 No stimulation CAR CD8 Endogenous CD8+ 10 0.31 0.26 0.35 0.17 0.24 0.25 0.068 0.051 103 105 104 D 3 0 104 10 Endogenous PD-1: BV421 C + CD8 3 10 70.2 0 90.8 8.63 93.8 5.70 92.7 6.80 99.3 0.61 72.3 0.077 PMA + ionomcyin 0 105 1.60 4.89 1.20 1.56 0.99 1.75 15.7 39.4 CD45.1:PeCy7 0103 104 105 E 15.2 104 Thy1.1: PerCP–Cy5.5 0 103 104 105 103 TIM3: PE CAR Endogenous c 0 OT-I Endogenous 60.4 33.1 76.5 20.8 73.3 24.0 37.2 7.76 3 4 5 3 4 5 3 4 5 3 4 5 TNF: BV421 0 10 10 10 010 10 10 0 10 10 10 0 10 10 10 020406080 100 IFN : APC Percentage of all CD8+ T cells γ Fig. 1 | CAR, OT-I and endogenous CD8+ TILs isolated from B16-OVA- show mean values with data points for 6, 5 and 11 independent experiments hCD19 tumours exhibit similar phenotypes. a, Experimental design to for CAR, OT-I and endogenous TILs, respectively. d, Quantification assess CAR and endogenous TILs; 1.5 × 106 CAR T cells were adoptively of cytokine production after re-stimulation of CAR, OT-I and transferred into C57BL/6J mice 13 days after tumour inoculation. b, Left, endogenous (endo.) CD8+ TILs, compared to cultured CD8+ CAR T cells representative flow cytometry plot identifying CD8+CD45.2+ endogenous re-stimulated with PMA and ionomycin or left unstimulated.
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