About

John K. Lee is an Associate Professor in the Department of Pharmacology at the University of California, Los Angeles. He holds a PhD from UCLA, obtained in 2016, and an MD from the Geisel School of Medicine at Dartmouth, earned in 2006. His current roles include Associate Professor-in-residence in Medicine, Urology, and Molecular and Medical Pharmacology. His research focuses on pharmacology, and he is involved in the academic and research activities within UCLA's Department of Pharmacology. He is accessible via phone at 310-206-2450 and email at jklee@mednet.ucla.edu.

Research topics

• Genetics
• Biology
• Chemistry
• Biochemistry
• Cell biology
• Cancer research

Selected publications

• Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering

  Science · 2026-03-19 · 1 citations

  articleOpen access

  T cells are often weakly responsive to tumor self-antigens because of central tolerance, constraining their ability to eliminate tumors. We exploited mechanical force to engineer a weakly reactive T cell receptor (TCR) specific for a nonmutated tumor-associated antigen (TAA), prostatic acid phosphatase (PAP). We identified a catch-bonding "hotspot" whose mutation enhanced T cell activity by increasing TCR-pMHC (peptide-major histocompatibility complex) bond lifetime while preserving physiological affinities and antigen fine specificities. T cells expressing these engineered TCRs showed vastly superior expansion in the tumor, effector phenotypes, and tumor elimination. Crystal structures and molecular dynamics simulations revealed a single amino acid mutation at the catch-bond hotspot primes the TCR for peptide interaction through water reorganization at the TCR-pMHC interface. Catch-bond engineering is a viable biophysically based strategy for transforming tolerized antitumor T cells into potent TCR-T cell therapy killers.

  PublisherOA PDFDOI

• Abstract 1524: Collagen-binding IL-12-armored STEAP1 CAR-T cells for advanced prostate cancer

  Cancer Research · 2026-04-03

  article

  Abstract Metastatic castration-resistant prostate cancer (mCRPC) remains an incurable and immunologically cold solid malignancy. Six-transmembrane epithelial antigen of the prostate 1 (STEAP1) is highly expressed in over 85% of mCRPC tumors and represents an attractive therapeutic target. Although chimeric antigen receptor (CAR)-T cell therapy has revolutionized the treatment of hematologic cancers, its efficacy in solid tumors, including prostate cancer, has been limited by the immunosuppressive tumor microenvironment (TME) and heterogeneous antigen expression. Interleukin-12 (IL-12) has the potential to overcome these barriers by activating and recruiting immune cells into tumors and promoting epitope spreading to counter antigen heterogeneity. While armored CAR-T cells engineered to produce IL-12 have been developed, further refinement is needed to optimize both potency and safety. Autologous IL-12-producing T cell therapy has previously shown clinical activity in melanoma, but systemic toxicity constrained its use, indicating that IL-12 secreted by CAR-T cells, though locally produced, can still diffuse into circulation. Here, we present STEAP1-directed CAR-T cells engineered to conditionally secrete a collagen-binding domain-IL-12 fusion protein (CBD-IL-12) upon antigen engagement. We demonstrate that fusing IL-12 to a CBD markedly enhances its retention within prostate tumors while limiting systemic spread in mice. As a result, intra-tumoral levels of IFN-γ, CXCL9, and GM-CSF remained comparably high to those induced by IL-12, yet without associated elevations in serum alanine aminotransferase (ALT) or off-target T cell infiltration in healthy organs. Flow cytometry revealed increased infiltration of T cells, NK cells, and cross-presenting dendritic cells, together with reduced monocytic myeloid-derived suppressor cells, following treatment with CBD-IL-12-expressing STEAP1 CAR-T cells. Immunohistochemistry and spatial transcriptomic analysis confirmed increased immune infiltrates and activation of IL-12 pathway and antigen processing and presentation by major histocompatibility complex-I in the CBD-IL-12 CAR-T treated tumor. Further, tertiary lymphoid structure-related chemokine and chemokine receptors including cxcr4, cxcr5, cxcl12 and cxcl13 as well as co-stimulatory molecules such as cd80, cd86, cd40 and tnfsf4 were upregulated in the tumor. When combined with anti-PD-1 and anti-CTLA-4 antibodies, CBD-IL-12 armored CAR-T cells eradicated established prostate tumors in mice without preconditioning. The CAR-T therapy generated durable anti-tumor immune memory to STEAP1 and other antigens. Our findings suggest that CBD fusion can localize potent but toxic immunomodulators such as IL-12 to the tumor site, offering a promising strategy to improve the safety and effectiveness of CAR-T therapies for solid tumors. Citation Format: Koichi Sasaki, Vipul Bhatia, Yuta Asano, Jakob Bakhtiari, Pooja Kaur, Chuyi Wang, Takumi Matsuo, Olivier Dubois, Po-Chuan Chiu, Donny Gun, Charanjit Singh, Ioanna Panagi, Laurine Noblecourt, Maria Nikolaidi, Truman Chong, Gerardo Javier, Saul J. Priceman, Aude G. Chapuis, John K. Lee, Jun Ishihara. Collagen-binding IL-12-armored STEAP1 CAR-T cells for advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1524.

  PublisherDOI

• Abstract 324: ASCL1-mediated transcriptional regulation of RET in neuroendocrine prostate cancer.

  Cancer Research · 2026-04-03

  article

  Abstract Resistance to second-generation anti-androgen therapies can cause neuroendocrine prostate cancer (NEPC), an aggressive disease variant, in castration-resistant prostate cancer (CRPC) patients. With low survival outcomes and limited therapies, it is imperative to study the molecular basis of NEPC. We show that the receptor tyrosine kinase RET has elevated activity in aggressive variant prostate cancer cell lines. We also show that RET kinase is crucial for the growth and survival of NEPC cells. We aim to unravel the mechanism of RET activation in NEPC to develop novel approaches to target RET and identify additional drug targets. NEPC can be categorized into two subtypes based on the expression of ASCL1 or NEUROD1, two pro-neuronal transcription factors. We show that RET gene expression strongly correlates to ASCL1 gene expression, but not NEUROD1 gene expression in NEPC patient samples. This data is corroborated by single cell-RNA-sequencing data in NEPC patient samples. Informatics modeling of whole transcriptome sequencing data from patient samples shows that RET and ASCL1 have substantially similar gene network signatures in NEPC, implying that these genes share a gene ecosystem in NEPC. To investigate the relationship between RET and ASCL1, we analyzed publicly available ChIP-sequencing data from LuCaP NEPC PDX models and small cell lung cancer (SCLC) cell lines. NEPC and SCLC are known to have similarities, including disease aggressiveness, expression of neuroendocrine markers, and the presence of ASCL1-positive and NEUROD1-positive subtypes. Our analysis showed that ASCL1 directly regulates RET by binding to RET promoter regions. Hence, we note a similar relationship between RET and ASCL1 in SCLC where ASCL1 regulates RET expression. Using knockdown models, we show that the RET-ASCL1 axis is unidirectional with RET having no impact on ASCL1 expression. To drug this pathway, we aim to focus on cell surface targets such as RET. RET inhibitors are approved for non-small cell lung cancers or thyroid cancers with RET fusions, however, they may induce resistance via mutations. Additionally, they may be less effective in tumors with wild-type RET expression, which is typically seen in NEPC. PROTACs can bypass these drawbacks by degrading the entire protein instead of enzymatically inhibiting it, thus overcoming drug resistance. Additionally, PROTACs have a catalytic mechanism that can cause degradation of several target molecules with one PROTAC molecule, leading to longer elimination of target protein with lower doses. We are using RD-23, a published RET PROTAC based on the RET inhibitor selpercatinib, to investigate its effects on NEPC and SCLC cells. While further studies are needed to stratify patients and develop novel pharmacological interventions, these results highlight the crucial role of ASCL1 in mediating RET signaling in NEPC and SCLC. Citation Format: Sachi B. Tengse, Song Yi Bae, Hannah E. Bergom, Ella Boytim, Halena R. VanDeusen, Quynh Chau Dinh, Abderrahman Day, Rayhan Biswas, Farzana Kabir, Laura E. Hirsch, Yingtian Xie, Daniel A. Harki, Sylvan C. Baca, Henry Long, John K. Lee, Leigh Ellis, Justin Hwang, Justin M. Drake. ASCL1-mediated transcriptional regulation of RET in neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 324.

  PublisherDOI

• Systematic Analysis of Hippo Pathway Signaling Identifies TEAD1 as a Transcriptional Regulator of Neuroendocrine Prostate Cancer

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Abstract LB-A013: Tuning TCR immunotherapy targeting prostatic acid phosphatase via catch bond modifications for advanced prostate cancer

  Cancer Immunology Research · 2026-03-05

  article

  Abstract Late-stage prostate cancer is an incurable disease with no effective therapy currently available. 20-30% of patients receiving local therapy will experience disease relapse. The rise in serum prostate-specific antigen (PSA) level in these patients is often described as biochemical recurrence. This stage of prostate cancer, when micro-metastasis has occurred and overall tumor burden is low, can be a critical time window for cell-mediated immunotherapy. We aim to develop T cell receptor (TCR) immunotherapy targeting prostatic acid phosphatase (PAP) to treat patients with chemically recurrent prostate cancer. Elevated expression of PAP is commonly observed in early and late stages of prostate cancer. PAP was previously used to develop the first FDA-approved cancer vaccine, Provenge, but the specific epitopes and cognate TCRs were not clearly defined. Our group has profiled the immunopeptidome of PAP on HLA-A*02:01 using a secreted MHC-based platform (ARTEMIS), and successfully isolated multiple TCRs reactive with PAP. Recent results have also demonstrated that further engineering with “catch bonds” on these candidate TCRs lead to dramatically improved cytotoxicity both in vitro and in vivo. This work demonstrated the feasibility of developing and enhancing TCRs targeting PAP for potential therapeutic usage. Citation Format: Zhiyuan Mao, Xiaojing Chen, Jami McLaughlin, Caitlin Gee, John K. Lee, K. Christopher. Garcia, Owen Witte. Tuning TCR immunotherapy targeting prostatic acid phosphatase via catch bond modifications for advanced prostate cancer [abstract]. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr LB-A013.

  PublisherDOI

• Solid tumour CAR-T cells engineered with fusion proteins targeting PD-L1 for localized IL-12 delivery

  Nature Biomedical Engineering · 2025-10-01 · 25 citations

  articleOpen access

  Chimeric antigen receptor (CAR)-T cell efficacy in solid tumours is limited due in part to the immunosuppressive tumour microenvironment (TME). To improve antitumour responses, we hypothesized that enabling CAR-T cells to secrete bifunctional fusion proteins consisting of a cytokine modifier such as TGFβtrap, IL-15 or IL-12, combined with an immune checkpoint inhibitor such as αPD-L1, would provide tumour-localized immunomodulation to improve CAR-T cell functionality. Here we engineer CAR-T cells to secrete TGFβtrap, IL-15 or IL-12 molecules fused to αPD-L1 scFv and assess in vitro functionality and in vivo safety and efficacy in prostate and ovarian cancer models. CAR-T cells engineered with αPD-L1–IL-12 are superior in safety and efficacy compared with CAR-T cells alone and those engineered with αPD-L1 fused with TGFβtrap or IL-15. Further, αPD-L1–IL-12 engineered CAR-T cells improve T cell trafficking and tumour infiltration, and localize IFNγ production, TME modulation and antitumour responses, with reduced systemic inflammation-associated toxicities. We believe our αPD-L1–IL-12 engineering strategy presents an opportunity to improve CAR-T cell clinical efficacy and safety across multiple solid tumour types. CAR-T cells engineered with αPD-L1–IL-12 fusion proteins show antitumour activity in mouse models of prostate and ovarian cancer.

  PublisherOA PDFDOI

• PROX1 is an early driver of lineage plasticity in prostate cancer

  Journal of Clinical Investigation · 2025-06-01 · 8 citations

  articleOpen access

  Lineage plasticity is recognized as a critical determinant of lethality and resistance to AR pathway inhibitors in prostate cancer. Lineage plasticity is a continuum, ranging from AR activity-low tumors, AR-null tumors that do not express a neuroendocrine prostate cancer (NEPC) program (i.e., double-negative prostate cancer [DNPC]), and AR-null NEPC tumors. Factors upregulated early in lineage plasticity are not well-characterized. The clarification of such factors is essential to identify tumors undergoing lineage plasticity or at risk of this occurring. Our integrative analysis of metastatic prostate cancer patient tumors, patient-derived xenografts, and cell models determined that PROX1 is upregulated early in the lineage plasticity continuum and progressively increases as tumors lose AR activity. We determined DNA methylation is a key regulator of PROX1 expression. PROX1 suppression in DNPC and NEPC reduces cell survival and impacts apoptosis and differentiation, demonstrating PROX1's functional importance. PROX1 is not directly targetable with standard drug development approaches. However, affinity immunopurification demonstrated histone deacetylases (HDACs) are among the top PROX1-interacting proteins; HDAC inhibition depletes PROX1 and recapitulates PROX1 suppression in DNPC and NEPC. Altogether, our results suggest PROX1 promotes the emergence of lineage plasticity, and HDAC inhibition is a promising approach to treat tumors across the lineage plasticity continuum.

  PublisherDOI

• Abstract 1241: Deciphering heterogeneity and tumor evolution in bladder cancer using multi-omics and liquid biopsies from rapid autopsies

  Cancer Research · 2025-04-21

  article

  Abstract Introduction: Metastatic bladder cancer (mBLCA) exhibits significant heterogeneity at the genomic, transcriptomic, molecular, and epigenetic levels, contributing to challenges in diagnosis, prognosis, and treatment. While 75% of mBLCA cases are urothelial carcinomas, 25% show divergent differentiation with variant histological features. This work characterizes intra-patient and inter-patient heterogeneity through comprehensive genomic and transcriptomic analyses of a rapid autopsy cohort of 20 patients with multiple tumors, matched normal tissue, and cell-free DNA (cfDNA). Our findings provide critical insights into tumor heterogeneity, clonal evolution, metastatic seeding, and the tumor microenvironment. Approach: Using bioinformatics tools, we reconstructed clonal evolution trees from whole-genome sequencing (WGS) analysis of tumors and inferred migration patterns to determine metastatic seeding. COSMIC mutational signatures were examined to correlate histological subtypes with clinical history. Single-nucleus RNA sequencing (snRNA-seq) revealed cell types and transcriptional heterogeneity using the human protein atlas and known marker annotations. To investigate alterations and clonality in tumors and their matched cfDNA, we used custom methodologies to evaluate mutations, CNAs, SVs, and rearrangements. Results: The clonal evolution trees and bulk RNA-seq highlight cisplatin resistance in the plasmacytoid urothelial carcinoma subtype, driven by upregulation of the DNA damage response pathway. Significant mutational heterogeneity (∼20-30% subclonal) emerges in later stages of tumor evolution, potentially contributing to therapy resistance. Additionally, a substantial proportion (60-70%) of structural variants arise later in tumor progression, particularly in driver genes. snRNA-seq revealed distinct clusters of epithelial cells, macrophages, fibroblasts, and other cell types. cfDNA analysis captured over 80% of subclonal deleterious tumor mutations in BLCA driver genes. Nucleosome profiling of cfDNA helps distinguish mBLCA from healthy samples and identify key transcription factors to differentiate between variants. Conclusion: This comprehensive study of mBLCA, leveraging a rapid autopsy dataset, uncovers critical insights into variant histologies across multiple omics layers. Integrating cfDNA analysis captures intra-patient and inter-patient tumor heterogeneity, providing a holistic view of clonal dynamics. By elucidating the patterns of clonal evolution, this work advances our understanding of tumor progression and establishes a foundation for precision therapies targeting adaptive and evolving clones. Citation Format: Pushpa Itagi, Samantha Schuster, Sonali Arora, Patricia Galipeau, Thomas Persse, Funda Vakar-Lopez, John K. Lee, Petros Grivas, Robert Montgomery, Jonathan Wright, Hung-Ming Lam, Andrew Hsieh, Gavin Ha. Deciphering heterogeneity and tumor evolution in bladder cancer using multi-omics and liquid biopsies from rapid autopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1241.

  PublisherDOI

• Abstract 4359043: NVC-001 – An AAV Gene Therapy Functional Cure for LMNA Dilated Cardiomyopathy

  Circulation · 2025-11-03

  article

  Background: LMNA-related Dilated Cardiomyopathy (LMNA-related DCM) is an aggressive type of DCM caused by pathogenic mutations in the LMNA gene that comprises 5-6% of genetic DCM cases. NVC-001 is an adeno-associated virus (serotype 9) gene-therapy vector encoding a truncated form of the naturally occurring human SUN1 protein (dnSUN1) that is being developed as a new treatment for LMNA-related DCM patients. Here we report the results of preclinical pharmacology, safety and biodistribution studies of NVC-001 that support a first-in-human clinical trial of NVC-001, which is a multicenter, non-randomized, open-label, ascending-dose Phase 1/2 study to assess the safety, tolerability and preliminary efficacy of NVC-001 in LMNA-related DCM patients. Methods: In vitro proof-of-concept studies were performed in human induced pluripotent stem cell (iPSC)-derived cardiomyocytes harboring the N195K pathogenic LMNA mutation. In vivo proof of concept studies were performed in a high-fidelity Lmna conditional deletion mouse model of LMNA DCM. Nonclinical biodistribution and safety of NVC-001 were assessed in both diseased and healthy mice, as well as in non-human primates. Results: NVC-001 successfully targeted the LINC complex in iPSC-derived human cardiomyocytes and rescued the arrhythmia phenotype of the N195K mutation. In the Lmna -deletion mouse model of LMNA DCM, NVC-001 treatment led to 8-fold longer survival in treated LMNA DCM mice (>300 days) compared to untreated mice (< 40 days), accompanied by halting of disease progression as indicated by stabilization of left ventricular function, rescue of conduction-system disease, and reduction in myocardial fibrosis. In biodistribution and safety studies in diseased and healthy mice and in cynomolgus monkeys, dnSUN1 transgene expression was restricted to the myocardium as intended with minimal to no expression in other tissues. No NVC-001-related clinical or histopathological adverse findings were observed at any dose level tested in diseased and healthy mice, or in cynomolgus monkeys. Conclusion: Collectively, these studies confirmed the transduction, target engagement and potential disease-modifying efficacy of NVC-001 in human target cells and in a LMNA DCM disease model. These data, together with the absence of adverse findings in multiple species, support investigation of NVC-001 in human LMNA-related DCM patients in a first-in-human adaptive-design Phase 1/2 clinical trial to be conducted in the US and in Europe.

  PublisherDOI

• Solid tumor CAR T cells engineered with fusion proteins targeting PDL1 for localized IL-12 delivery

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-09

  preprintOpen access

  CAR T cell efficacy in solid tumors is limited due in part to the immunosuppressive TME. To improve anti-tumor responses, we hypothesized that enabling CAR T cells to secrete bifunctional fusion proteins consisting of a cytokine modifier (e.g., TGFβtrap, IL15, or IL12) combined with an immune checkpoint inhibitor (e.g., αPDL1) will provide tumor localized immunomodulation to improve CAR T cell functionality. To that end, we engineered CAR T cells to secrete TGFβtrap, IL15, or IL12 molecules fused to αPDL1 scFv, and assessed in vitro functionality and in vivo safety and efficacy in prostate and ovarian cancer models. CAR T cells engineered with αPDL1-IL12 were superior in safety and efficacy compared to CAR T cells alone and to those engineered with αPDL1 fused with TGFβtrap or IL15. Further, αPDL1-IL12 engineered CAR T cells improved T cell trafficking and tumor infiltration, localized IFNγ production, TME modulation, and anti-tumor responses, with reduced systemic inflammation-associated toxicities. We believe our αPDL1-IL12 engineering strategy presents an opportunity to improve CAR T cell clinical efficacy and safety across multiple solid tumor types.

  PublisherOA PDFDOI

Recent grants

• Core A: Leadership and Administrative

  NIH · $53.6M · 2002–2028

Frequent coauthors

• Peter S. Nelson

  University of Washington

  158 shared

• Ilsa M. Coleman

  113 shared

• Lawrence D. True

  University of Washington

  105 shared

• Colm Morrissey

  University of Washington

  104 shared

• Eva Corey

  99 shared

• Daniel W. Lin

  Zhongshan Hospital

  95 shared

• Lisha G. Brown

  University of Washington

  74 shared

• Michael T. Schweizer

  Fred Hutch Cancer Center

  73 shared

Labs

• John K. Lee LaboratoryPI

Education

• Ph.D., Molecular Biology Institute

  University of California, Los Angeles

  2016

• M.D.

  Dartmouth College Geisel School of Medicine

  2006

• A.B.

  Harvard University

  2001