Journal Article

Characterization of tumor microenvironment and tumor immunology based on the double-stranded RNA-binding protein related genes in cervical cancer

Wan, Chong, Li, Xiaoqi, Li, Xiaoqiu, Li, Jin, Quan, Chenlian, Wu, Xiaohua

2023

Overview

Background Cervical cancer is one of the most common gynecological cancers threatening women’s health worldwide. Double-stranded RNA-binding proteins (dsRBPs) regulate innate immunity and are therefore believed to be involved in virus-related malignancies, however, their role in cervical cancer is not well known. Methods We performed RNA-seq of tumor samples from cervical cancer patients in local cohort and also assessed the RNA-seq and clinical data derived from public datasets. By using single sample Gene Set Enrichment Analysis (ssGSEA) and univariate Cox analysis, patients were stratified into distinct dsRBP clusters. Stepwise Cox and CoxBoost were performed to construct a risk model based on optimal dsRBPs clusters-related differentially expressed genes (DEGs), and GSE44001 and CGCI-HTMCP-CC were employed as two external validation cohorts. Single cell RNA sequencing data from GSE168652 and Scissor algorithm were applied to evaluated the signature-related cell population. Results The expression of dsRBP features was found to be associated with HPV infection and carcinogenesis in CESC. However, only Adenosine deaminases acting on RNA (ADAR) and Dicer, Drosha, and Argonautes (DDR) exhibited significant correlations with the overall survival (OS) of CESC patients. Based on these findings, CESC patients were divided into three dsRBP clusters. Cluster 3 showed superior OS but lower levels of ADAR and DDR. Additionally, Cluster 3 demonstrated enhanced innate immunity, with significantly higher activity in cancer immunity cycles, immune scores, and levels of tumor-infiltrating immune cells, particularly CD8+ T cells. Furthermore, a risk model based on nine dsRBP cluster-related DEGs was established. The accuracy of survival prediction for 1 to 5 years was consistently above 0.78, and this model’s robust predictive capacity was confirmed by two external validation sets. The low-risk group exhibited significantly higher levels of immune checkpoints, such as PDCD1 and CTLA4, as well as a higher abundance of CD8+ T cells. Analysis of single-cell sequencing data revealed a significant association between the dsRBP signature and glycolysis. Importantly, low-risk patients showed improved OS and a higher response rate to immunotherapy, along with enduring clinical benefits from concurrent chemoradiotherapy. Conclusions dsRBP played a crucial role in the regulation of prognosis and tumor immunology in cervical cancer, and its prognostic signature provides a strategy for risk stratification and immunotherapy evaluation.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Analysis / Binding proteins / Biomedical and Life Sciences / Biomedicine / Cancer microenvironment / Cancer therapies / Carcinogenesis / CD8 antigen / Cervical cancer / Chemoradiotherapy / Chemotherapy / Complications and side effects / CTLA-4 protein / Datasets / Double-stranded RNA / dsRBP / Gene set enrichment analysis / Genes / Glycolysis / Gynecological cancer / Health aspects / Health risk assessment / Human papillomavirus / Immune checkpoint / Immunology / Immunotherapy / Infections / Innate immunity / Interferon / Kinases / Lymphocytes T / Malignancy / Medicine/Public Health / Methods / Mutation / Papillomavirus infections / Patient outcomes / Prevention / Proteins / Radiation therapy / Risk factors / Risk groups / Risk model / RNA sequencing / RNA-binding protein / Tumor microenvironment / Tumor-infiltrating lymphocytes / Tumors / Women