Year: 2026
Type: conference-abstract
Abstract: Background Neoantigen-rich tumors are expected to promote immune recognition, yet many hypermutated cancers remain T-cell poor and resistant to immune-checkpoint blockade. This paradox is particularly evident in APOBEC3-driven cancers, where mutagenesis generates abundant neoantigens but does not uniformly translate into immune infiltration or treatment responsiveness. The tumor-intrinsic genomic and signaling mechanisms that allow neoantigen-rich tumors to remain immunologically silent remain poorly understood.Methods We integrated large multi-cohort datasets spanning bulk tumor genomics and transcriptomics, neoantigen prediction, mutational signatures, single-cell and spatial profiling, and immunotherapy-treated clinical cohorts across bladder and other cancer types. Candidate mechanisms were functionally evaluated using tumor-cell models, molecular and proteomic assays, imaging-based immune profiling, antibody-mediated perturbation, and immunogenic syngeneic bladder cancer models, including PD-1 blockade studies.Results We identified a recurrent neoantigen-high/CD8-low tumor state characterized by chromosome 1q23.3 amplification and enrichment for APOBEC3 mutational signatures. Despite high tumor mutational burden and predicted neoantigen load, this tumor subset exhibited coordinated suppression of cytokine and chemokine programs, HLA-mediated antigen-presentation machinery, and tumor-cell-expressed checkpoint-associated immune-engagement genes. Within the amplified 1q23.3 locus, NECTIN4 emerged as the dominant predictor of immune–neoantigen discordance and reduced T-cell infiltration. Across multiple cancer types, higher NECTIN4 expression was associated with poorer outcomes following immune-checkpoint blockade, supporting its broader relevance as a potential marker of immunotherapy resistance. Functionally, enforced NECTIN4 expression was sufficient to impose a T-cell-poor tumor microenvironment and confer resistance to PD-1 blockade in immunogenic bladder cancer models. Mechanistically, NECTIN4 engaged a DDR1–SHP2 signaling axis that restrained STAT1 phosphorylation, thereby suppressing interferon-responsive cytokine production, antigen presentation, and immune-engagement programs. Conversely, antibody-mediated NECTIN4 blockade restored STAT1 activity in tumor-cell models and reduced tumor growth in vivo, demonstrating that this suppressive state is therapeutically reversible. Finally, mutational-signature, breakpoint, genomic-timing, and germline genetic analyses linked APOBEC3-mediated mutagenesis to recurrent 1q23.3 amplification events encompassing NECTIN4, connecting neoantigen-generating mutational processes with structural genome evolution and immune escape.Conclusions These findings identify NECTIN4-driven STAT1 suppression as a copy-number–encoded mechanism by which APOBEC3-driven, neoantigen-rich bladder tumors evade immune engagement. We define this state as tumor-intrinsic immune cloaking and propose NECTIN4-targeted therapy as a strategy to restore cytokine-mediated immune recruitment, antigen presentation, and responsiveness to immune-checkpoint blockade.Acknowledgements This work was supported by the Intramural Research Program of the NIH/NCI Center for Cancer Research, including awards 1ZIABC012091, 1ZIABC011351, and 1ZIABC012104. Contributions by NIH authors were made as part of their official duties as federal employees, and the findings do not necessarily reflect the views of the NIH or the U.S. Department of Health and Human Services. We thank the CCR Microscopy Core, CCR Frederick Sequencing and Genomics Core, and CCR/LGI Flow Cytometry Core for imaging, sequencing, and flow cytometry support.Ethics Approval Human subject research and tissue procurement were conducted under NCI/NIH IRB protocols NCT02379429 and NCT04923178. Recombinant DNA experiments were approved under NIH IBC protocol RD-24-II-28, and animal studies were performed under NIH IACUC protocols GMB-012 and GMB-014, in accordance with institutional and federal guidelines.
Authors: Dhanusha Yesudhas, Bilal Lone, Ecem Unal, Arup Chakraborty, Ayse G Keskus, Jaimie Ryou, Kelly Butler, Tania Colon Aquino, Abbas Yousefi-rad, Weiming Yang, Lisa Jenkins, Elias Chandran, Raju Chelluri, Vladimir Valera Romero, Salah Boudjadi, Sandeep Gurram, Mikhail Kolmogorov, Andrea B Apolo, A Rouf Banday
Institutions: National Institutes of Health, National Cancer Institute
Language: English
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,490
OpenAlex ID: W7225137255