Alternative Complement Pathway Signature Determines Immunosuppression and Resistance to Immunotherapy Plus Tyrosine Kinase Inhibitor Combinations in Renal Cell Carcinoma

• Alternative complement pathway signature (ACPS) was a biomarker for TKI+IO therapy. • ACPS predicted TKI+IO benefit vs. TKI monotherapy. • ACPS was associated with exhausted T cell infiltration and immunosuppression. Latest guidelines recommended immunotherapy (IO) plus tyrosine kinase inhibitor (TKI) combination as standard first-line therapy in renal cell carcinoma (RCC), with no predictive biomarker being applied. Complement system shapes tumor microenvironment, which may influence TKI+IO benefit. Two cohorts from our institute and 2 external cohorts were enrolled. RNA-sequencing was performed for each sample, and alternative complement pathway signature (ACPS) was defined by single sample gene set enrichment analysis. Immune infiltration and function were assessed by immunohistochemistry and flow cytometry. Under TKI+IO therapy, ACPS was elevated in non-responders ( P <0.01), and high-ACPS predicted lower response rate and shorter progression-free survival ( P =0.040). Moreover, TKI+IO, rather than TKI monotherapy, may benefit patients of low-ACPS combined with SETD2-wild type (HR=0.55, P <0.001). In RCC, ACPS was associated with increased tumor-infiltrating T cells (Spearman's ρ=0.50, P =0.001). However, in high-ACPS samples, CD8+ T cells revealed an exhausted phenotype with decreased GZMB ( P <0.001) and increased PD1 ( P =0.008) expression. Elevated PD1 expression in high-ACPS samples was confirmed by immunohistochemistry ( P =0.046). Besides, macrophage infiltration was increased in high-ACPS samples ( P =0.045), along with suppressive cytokines. Under TKI+IO, high-ACPS was linked to immunosuppression and treatment resistance. ACPS might be used as a biomarker for better treatment strategy between TKI+IO or TKI monotherapy.