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Background Immune checkpoint blockade (ICB) has transformed cancer therapy; however, response rates remain modest in head and neck cancer (HNCa) patients. 1–4 While many studies focus on manipulating immune cells to restore anti-tumor immunity, the tumor’s role in establishing and sustaining immune suppression is poorly understood.5 Thus, we sought to define how malignant cells shape the immune microenvironment to drive ICB resistance.Methods We first analyzed RNA-seq from HNCa patients (n=19) enrolled in a neoadjuvant pembrolizumab trial to identify pre-treatment markers of therapeutic resistance. 1 We modeled these findings in our HNCa murine models of anti-PD-1 response (MOC1sens) and resistance (MOC1res). Using scRNA-seq, functional perturbations, and flow cytometry, we uncovered the tumor-intrinsic activity shaping ICB outcomes (n≥7 mice/group). Finally, we extended our results to patient datasets across epithelial cancers.Results The epithelial-specific transcription factor Elf3 was enriched in pembrolizumab-refractory HNCa patients (p=.006), and Elf3 expression was inversely correlated with T cell infiltration signatures (p<.0001). In our MOC1res model of anti-PD-1 resistance, Elf3 drove a transcriptional program, ‘ICB-resistance,’ mimicking epithelial antimicrobial response (Muc4, Ltf, Pigr, myeloid-chemotaxis genes). In contrast, ICB-sensitive MOC1sens tumors exhibited a canonical interferon-response program (‘IFN-response,’ Cxcl9/10, MHCII, Ifit3).CRISPR knockout of Elf3 in MOC1res tumors restored therapeutic sensitivity (p<.001), while overexpression of Elf3 was sufficient to convert MOC1sens into resistant tumors (p<.001). Mechanistically, combination anti-PD-1 treatment + Elf3 knockout reduced MOC1res tumor-infiltrating neutrophils (p<.001) and increased intra-tumoral T cells (p<.01; p<.01).In vitro, Elf3 and the ICB-resistance program were induced under chronic—but not acute—IFN-γ exposure (p<.001), suggesting an adaptive response to sustained immune pressure. ICB-sensitive MOC1 cells conditioned with chronic IFN-γ acquired resistance to ICB in vivo, and this effect was Elf3-driven (p=.003). In these tumors, flow cytometry confirmed that Elf3 is required for chronic IFN-induced neutrophil chemotaxis (p<.001) and T cell exclusion (p<.001).Across many epithelial cancers in TCGA (n=8,711 tumors), Elf3 expression strongly correlated with neutrophil infiltration and ICB-resistance signatures. In NSCLC patients treated with immunotherapy (n=27 patients), pre-treatment Elf3 expression predicted poor survival (p=.01) and reduced cytotoxic T cell signatures (p=.023;p=.017).Conclusions In response to ICB, chronic IFN-γ signaling induces an Elf3-driven transcriptional program that suppresses anti-tumor immunity. This program potentially represents a conserved mechanism of resistance shared by epithelial cancers that may guide both therapeutic intervention and, importantly, identification of patients likely to benefit from ICB.References Uppaluri R, Campbell KM, Egloff AM, Zolkind P, Skidmore ZL, Nussenbaum B, Paniello RC, Rich JT, Jackson R, Pipkorn P, Michel LS, Ley J, Oppelt P, Dunn GP, Barnell EK, Spies NC, Lin T, Li T, Mulder DT, Hanna Y, Cirlan I, Pugh TJ, Mudianto T, Riley R, Zhou L, Jo VY, Stachler MD, Hanna GJ, Kass J, Haddad R, Schoenfeld JD, Gjini E, Lako A, Thorstad W, Gay HA, Daly M, Rodig SJ, Hagemann IS, Kallogjeri D, Piccirillo JF, Chernock RD, Griffith M, Griffith OL, Adkins DR. Neoadjuvant and adjuvant pembrolizumab in resectable locally advanced, human papillomavirus-unrelated head and neck cancer: a multicenter, phase II trial. Clin Cancer Res. 2020 Oct 1;26(19):5140–5152. doi: 10.1158/1078-0432.CCR-20-1695. Epub 2020 Jul 14. 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PMID: 37683037; PMCID: PMC10794154.Uppaluri R, Haddad RI, Tao Y, Le Tourneau C, Lee NY, Westra W, Chernock R, Tahara M, Harrington KJ, Klochikhin AL, Braña I, Vasconcelos Alves G, Hughes BGM, Oliva M, Pinto Figueiredo Lima I, Ueda T, Rutkowski T, Schroeder U, Mauz PS, Fuereder T, Laban S, Oridate N, Popovtzer A, Mach N, Korobko Y, Costa DA, Hooda-Nehra A, Rodriguez CP, Bell RB, Manschot C, Benjamin K, Gumuscu B, Adkins D; KEYNOTE-689 investigators. neoadjuvant and adjuvant pembrolizumab in locally advanced head and neck cancer. N Engl J Med. 2025 Jun 18. doi: 10.1056/NEJMoa2415434. Epub ahead of print. PMID: 40532178.Goswami S, Pauken KE, Wang L, Sharma P. Next-generation combination approaches for immune checkpoint therapy. Nat Immunol. 2024 Dec;25(12):2186-2199. doi: 10.1038/s41590-024-02015-4. Epub 2024 Nov 25. PMID: 39587347.Ethics Approval All animal procedures were approved by the Washington University Institutional Animal Care and Use Committee (IACUC), protocol #21-0220.