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

Jisup Kim,Jee-Young Park,Su-Jin Shin,Heounjeong Go,Beom Jin Lim

doi:10.3390/cancers13061199

Abstract

Simple SummaryAlthough 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.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.

Highlights

Frameshift insertions and deletions have gained considerable attention owing to the fact that numerous neoantigens with high specificity for the major histocompatibility complex (MHC) are produced upon the accumulation of such mutations, thereby contributing to antitumor immunity [1]
Clear cell renal cell carcinoma (RCC), accounting for 65-70% of all renal malignancies [2], harbors the highest proportion of coding indels across all tumor types; this phenomenon accounts for its immunogenicity and a high response to immunotherapy despite low non-synonymous single-nucleotide variant (SNV) burden [1]
Upon using the American Joint Committee on Cancer (AJCC) cancer staging system, the clear cell RCC population was found to consist of 473 patients with pT1 (74.1%), 23 patients with pT2 (3.6%), 136 patients with pT3 (21.3%), and six patients with pT4 disease (0.9%)

Summary

Introduction

Frameshift insertions and deletions (indels) have gained considerable attention owing to the fact that numerous neoantigens with high specificity for the major histocompatibility complex (MHC) are produced upon the accumulation of such mutations, thereby contributing to antitumor immunity [1]. 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. 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

Methods

Results

Conclusion