Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [TCR-seq]

Melanomas are generated from melanocytes, the neural crest derivatives sharing a neuroectodermal origin with the nervous system. In investigating whether immune privilege of the nervous system might be exploited by melanoma, we found that nerve growth factor (NGF) exerts both melanoma cell-intrinsic and -extrinsic immunosuppression. In melanoma cells, autocrine NGF engages TrkA receptor to desensitize IFN-gamma?signaling, leading to T and NK cell exclusion. In effector T cells, which upregulate surface TrkA expression upon T cell receptor (TCR) activation, paracrine NGF dampens TCR signaling and effector function. Targeting NGF genetically or pharmacologically with larotrectinib sensitizes melanoma responsiveness to immune checkpoint blockade (ICB) therapy for tumor eradication and induces durable protection by eliciting robust memory of low-affinity T cells. Together, these findings uncover a comprehensive mechanism through which the NGF-TrkA axis suppresses anti-tumor T cell immunity, thus providing a novel mode of action to repurpose larotrectinib for immune sensitization. Moreover, by enlisting low-affinity tumor-specific T cells, anti-NGF reduces acquired resistance to ICB therapy and prevents melanoma recurrence. Overall design: This data contains 4 TCR-seq datasets. 1. For B16OVA experiment, B16OVA cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues day 11 and analyzed by RNA-seq. 2. For YUMM experiment, YUMM1.7 cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues day 12 and analyzed by RNA-seq. 3. For dLN_KO experiment, C57BL/6J mice were subcutaneously injected with 50,000 Ctrl or NGF sgRNA B16-OVA cells. All mice in the Ctrl sgRNA group were sacrificed when tumor growth limits were exceeded. Tumor-free mice in the NGF sgRNA group were rechallenged with B16-OVA cells on day 78. 9 days later, OVA-tetramer+ CD8+ T cells were sorted from tumor draining lymph nodes and submitted for TCRb-seq. 4. For dLN_NT_aPD-1 and dLN_KO_aPD-1 experiment, C57BL/6J mice were subcutaneously injected with 50,000 Ctrl or NGF sgRNA B16-OVA cells. 250 ug/mouse anti-PD-1 antibody was given twice. Tumor-free mice in both groups were rechallenged with B16-OVA cells on day 78. 9 days later, OVA-tetramer+ CD8+ T cells were sorted from tumor draining lymph nodes and submitted for TCRb-seq. 5. For OVAtetramer_high and OVAtetramer_low experiment, C57BL/6 mice were vaccinated i.v. with 0.1 LD50 of attenuated recombinant Listeria-OVA strain. OVA-tetramer-high and –low CD8 T cells were FACS-sorted from spleen on day 7 after a single vaccination, and then submitted for TCRb-seq.