Neo-Fs Index: A Novel Immunohistochemical Biomarker Panel Predicts Survival and Response to Anti-Angiogenetic Agents in Clear Cell Renal Cell Carcinoma

SIMPLE SUMMARY: Although anti-angiogenetic agents (AAA) are mainstay treatments for clear cell renal cell carcinoma (ccRCC), there are very few histology-based predictive biomarkers applicable in routine clinical practice. Considering that frameshifts contribute to antitumor immunity and ccRCC harbors the highest indel proportion across tumors, we hypothesized that protein markers frequently mutated via frameshift indels could predict prognosis and response to AAA. We evaluated the prognostic impact of the individual protein markers and found five proteins showing independent prognostic value. Utilizing the five proteins, we developed an integrated biomarker—Neo-fs index. High Neo-fs index predicted better prognosis and AAA response. High Neo-fs index, which harbored greater single nucleotide variant and indel mutation, was also associated with antitumor immune gene signature. Neo-fs index could be a practical biomarker to improve risk stratification and predict AAA response in ccRCC patients. ABSTRACT: Background: Frameshift indels have emerged as a predictor of immunotherapy response but were not evaluated yet to predict anti-angiogenetic agent (AAA) response or prognosis in clear cell renal cell carcinoma (ccRCC). Methods: Here, to develop biomarkers that predict survival and response to AAA, we evaluated the immunohistochemical expression of proteins whose genes frequently harbor frameshift indels in 638 ccRCC patients and correlated the individual and integrated markers with prognosis and AAA response. The mutational landscape was evaluated using targeted next-generation sequencing in 12 patients concerning protein markers. Immune gene signatures were retrieved from TCGA RNA seq data. Results: Five proteins (APC, NOTCH1, ARID1A, EYS, and filamin A) were independent adverse prognosticators and were incorporated into the Neo-fs index. Better overall, disease-specific and recurrence-free survival were observed with high Neo-fs index in univariate and multivariate survival analyses. Better AAA responses were observed with a high Neo-fs index, which reflected increased MHC class I, CD8+ T cell, cytolytic activity, and plasmacytoid dendritic cell signatures and decreased type II-IFN response signatures, as well as greater single-nucleotide variant (SNV) and indel counts. Conclusions: Neo-fs index, reflecting antitumor immune signature and more SNVs. and indels, is a powerful predictor of survival and AAA response in ccRCC.