CTLA4promoter hypomethylation is a negative prognostic biomarker at initial diagnosis but predicts response and favorable outcome to anti-PD-1 based immunotherapy in clear cell renal cell carcinoma

Abstract

BackgroundIn metastatic clear cell renal cell carcinoma (ccRCC), different combination therapies, each including anti-PD-1 immune checkpoint blockade (ICB), are applied as first-line treatment. Robust predictive biomarkers for rational upfront therapy decisions are lacking, although they are urgently needed. Recently, we showed that CTLA4 promoter methylation predicts response to ICB in melanoma. Here, we aimed to investigate CTLA4 methylation in ccRCC and its utility to serve as a predictive biomarker for anti-PD-1 based ICB in metastatic ccRCC.MethodsCTLA4 methylation was analyzed with regard to transcriptional gene activity (mRNA expression), intratumoral immune cell composition, and clinical course in two ccRCC cohorts obtained from The Cancer Genome Atlas (TCGA cohort, n=533) and the University Hospital Bonn (UHB Non-ICB Cohort, n=116). In addition, CTLA4 methylation as well as CD8+ T cell infiltrates and PD-L1 expression were evaluated in pre-treatment samples from a multicenter cohort (RCC-ICB Cohort, n=71). Patients included in the RCC-ICB Cohort were treated with either first line anti-PD-1 based combination therapy (n=25) or monotherapy post–tyrosine kinase inhibition in second line or later. Analyses were performed with regard to treatment response according to RECIST, progression-free survival (PFS), event-free survival (EFS), and overall survival (OS) following treatment initiation.ResultsCTLA4 promoter hypomethylation was significantly correlated with CTLA4 mRNA expression, lymphocyte infiltration, and poor OS in both primary ccRCC cohorts (TCGA: HR 0.30 (95% CI 0.18 to 0.49), p<0.001; UHB Non-ICB: HR 0.35 (95% CI 0.16 to 0.75), p=0.007). In contrast, CTLA4 promoter hypomethylation predicted response and, accordingly, favorable outcomes (PFS and OS) in patients with ICB-treated ccRCC, overcompensating the negative prognostic value of CTLA4 hypomethylation at initial diagnosis. Moreover, in multivariable Cox regression, CTLA4 promoter hypomethylation remained an independent predictor of improved outcome in ICB-treated ccRCC after co-adjustment of the International Metastatic Renal Cell Carcinoma Database Consortium score (HR 3.00 (95% CI 1.47 to 6.28), p=0.003).ConclusionsOur study suggests CTLA4 methylation as a powerful predictive biomarker for immunotherapy response in metastatic RCC.

Identification of Survival Risk and Immune-Related Characteristics of Kidney Renal Clear Cell Carcinoma

“…Immunity_H had lower tumor purity and higher immune score than Immunity_L, indicating that immune cells exerted critical role in inhibiting tumor progression. These findings supported previous researches that the activation of immune-related responses can effectively control the progression of KIRC [ 28 , 29 ]. Additionally, Immunity_H had higher levels of HLA genes expression and immune cells infiltration than Immunity_L, indicating that Immunity_H had stronger immunogenicity.…”

Expression of immune checkpoint regulators, programmed death-ligand 1 (PD-L1/PD-1), cytotoxic T lymphocyte antigen 4 (CTLA-4), and indolaimine-2, 3-deoxygenase (IDO) in uterine mesenchymal tumors

“…In the past decade, numerous studies have shown the effectiveness of immune checkpoint therapeutics in tackling several malignancies, particularly carcinomas [13,14,38,[45][46][47][48] and melanomas [16,49,50]. Several recent studies are actively investigating the potential role of targeted immunotherapy in a wide range of sarcomas [51].…”

T cell proliferation-related genes: Predicting prognosis, identifying the cold and hot tumors, and guiding treatment in clear cell renal cell carcinoma

“…Previous studies have proved that tumors divided into different subtypes often have different immune microenvironments and respond differently to immunotherapy. For the subtypes of ccRCC, the increased infiltration of immune cells suggests that these tumors are immune "hot tumors", otherwise they are called "cold tumors" (Galon and Bruni, 2019;Klumper, et al, 2021). To distinguish cold and hot tumors in ccRCC, patients were regrouped into two clusters by R package "ConensusClusterPlus" based on the expression levels of the 8 TRGs involved in modeling (Figure 8A; Supplementary Table S6).…”

“…For example, anti-programmed cell death protein 1(PD1) combined with anti-cytotoxic T lymphocyte antigen 4 (CTLA4) has become the first-line treatment of metastatic renal cell carcinoma. Although new targeted and immune agents continue to emerge and improve the prognosis of some patients, these drugs are still not suitable for all patients (Linehan and Ricketts, 2019;Samstein, et al, 2019;Kim, et al, 2021;Klumper, et al, 2021;Wu, et al, 2021;Wu, et al, 2022). Antineoplastic drugs are less effective in immunosuppressive tumor microenvironment (TME) (Lai, et al, 2021).…”

“…Related to the proliferation and function of immune cells or tumor progression, T cell proliferation-related genes (TRGs) involve hundreds of protein-coding genes which include CTLA4, HHLA2, PRKCQ, IL4I1, IL20RB, HOMER1, DHPS, and so on. The ccRCC subgroup with hypomethylated CTLA4 promoter was characterized by increased infiltration of immune cells, especially CD8+T cells (Klumper, et al, 2021). IL4I1 inhibited the proliferation of T cells including CD8 + anti-tumor T cells and recruited suppressor immune cells such as Tregs by activating Aryl hydrocarbon receptor (AHR).…”