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Supplementary Figures and Supplementary Materials and Methods with References from Targeting ULK1 Decreases IFNγ-Mediated Resistance to Immune Checkpoint Inhibitors

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posted on 2023-04-03, 08:40 authored by Sarah E. Fenton, Markella Zannikou, Liliana Ilut, Mariafausta Fischietti, Chunni Ji, Chidera V. Oku, Curt M. Horvath, I. Caroline Le Poole, Marcus Bosenberg, Elizabeth T. Bartom, Masha Kocherginsky, Leonidas C. Platanias, Diana Saleiro

S1. Overexpression of ULK1 in melanoma cells has minor effects on transcription of IFNγ-induced immunostimulatory genes.S2. Effects of gene targeted inhibition of ULK1 in transcription of IFNγ-induced immunostimulatory genes in melanoma cells.S3. Effects of drug-targeted inhibition of ULK1 in transcription of IFNγ-induced immunostimulatory genes in melanoma cells.S4. Effects of siRNA-mediated knockdown of ULK1 on IFNγ-inducedSTAT1 phosphorylation.S5. Identification of putative cytoplasmic and nuclear ULK1 binding partners in melanoma cells upon IFNγ stimulation by mass spectrometry analysis.S6. Pharmacological inhibition of ULK1 enhances the anti-tumor effects of anti-PD-1 therapy in YUMMER1.7 mouse melanoma in vivo model.S7. Tumor infiltrating CD8+ T cells and TAMCs in vehicle-isotype-treated mice.S8. Tumor infiltrating CD8+ T cells and TAMCs in ULK inhibitor-treated mice.S9. Tumor infiltrating CD8+ T cells and TAMCs in anti-PD-1-treated mice.S10. Tumor infiltrating CD8+ T cells and TAMCs in ULKi plus anti-PD-1-treated mice.S11. Tumor infiltrating CD4+ T cells and Tregs in vehicle-isotype-treated mice.S12. Tumor infiltrating CD4+ T cells and Tregs in ULK inhibitor-treated mice.S13. Tumor infiltrating CD4+ T cells and Tregs in anti-PD-1treated mice.S14. Tumor infiltrating CD4+ T cells and Tregs in ULKi plus anti-PD-1-treated mice.S15. Tumor infiltrating CD8+ T cells and TAMCs in control, ULKi and/or anti-PD-1-treated mice.S16. Tumor infiltrating CD4+ T cells and Tregs in control, ULKi and/or anti-PD-1-treated mice.S17. Gating strategy for flow cytometric immunophenotyping of mouse melanoma tumors.

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National Cancer Institute (NCI)

United States Department of Health and Human Services

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American Society of Clinical Oncology (ASCO)

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ARTICLE ABSTRACT

Immune checkpoint inhibitors (ICI) have transformed the treatment of melanoma. However, the majority of patients have primary or acquired resistance to ICIs, limiting durable responses and patient survival. IFNγ signaling and the expression of IFNγ-stimulated genes correlate with either response or resistance to ICIs, in a context-dependent manner. While IFNγ-inducible immunostimulatory genes are required for response to ICIs, chronic IFNγ signaling induces the expression of immunosuppressive genes, promoting resistance to these therapies. Here, we show that high levels of Unc-51 like kinase 1 (ULK1) correlate with poor survival in patients with melanoma and overexpression of ULK1 in melanoma cells enhances IFNγ-induced expression of immunosuppressive genes, with minimal effects on the expression of immunostimulatory genes. In contrast, genetic or pharmacologic inhibition of ULK1 reduces expression of IFNγ-induced immunosuppressive genes. ULK1 binds IRF1 in the nuclear compartment of melanoma cells, controlling its binding to the programmed death-ligand 1 promoter region. In addition, pharmacologic inhibition of ULK1 in combination with anti-programmed cell death protein 1 therapy further reduces melanoma tumor growth in vivo. Our data suggest that targeting ULK1 represses IFNγ-dependent immunosuppression. These findings support the combination of ULK1 drug-targeted inhibition with ICIs for the treatment of patients with melanoma to improve response rates and patient outcomes. This study identifies ULK1, activated downstream of IFNγ signaling, as a druggable target to overcome resistance mechanisms to ICI therapy in metastatic melanoma.

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