Mining of prognosis-related genes in cervical squamous cell carcinoma immune microenvironment

RNA sequencing and multiplexed immunohistochemistry reveal the factors for postoperative recurrence of stage IB-IIA cervical squamous cell carcinoma

BACKGROUND

Stage IB-IIA Cervical Squamous Cell Carcinoma (CSCC) presents diverse clinical outcomes, the mechanisms that cause recurrence in CC patients remain unclear. The goal of this study was to identify predictive biomarkers leading to tumor recurrence in IB-IIA CSCC after surgical treatment by comparing the transcriptional and immune landscape between the recurrence and non-recurrence group.

METHODS

We performed mRNA sequencing and multiplexed immunohistochemistry (mIHC) analysis among stage IB-IIA patients with or without recurrence after surgical resection and were followed-up for a median of three years.

RESULTS

Integrated analysis indicates that the upregulated gene expression in zinc finger proteins, the activation of the PI3K/Akt pathway, and the low infiltration level of T follicular helper cells and B-cells may serve as potential recurrent biomarkers for CSCC. We also observed significant differences in the immune and genomic landscape between two groups.

CONCLUSIONS

These findings provide new insights into the relapse mechanisms of CSCC, which could potentially guide clinical exploration of drug targets.

Construction of a New Immune-Related Competing Endogenous RNA Network with Prognostic Value in Lung Adenocarcinoma

Tumor microenvironment has significant influence on the gene expression of tumor tissues and on the clinical outcomes in lung adenocarcinoma. Infiltrating immune and stromal cells not only perturb the tumor signal in molecular studies, but also play crucial roles in cancer biology. The competing endogenous RNAs (ceRNAs) are useful to explain the post-transcriptional layer regulated by gene translation and play an important role in the occurrence and progression of lung adenocarcinoma. Therefore, identifying novel molecular markers by constructing ceRNA associated with immune infiltration is of great significance to guide the treatment of lung adenocarcinoma in the future. According to the immune and stromal scores of lung adenocarcinoma samples in The Cancer Genome Atlas (TCGA) database calculated by the ESTIMATE algorithm, we identified differentially expressed lncRNAs, miRNAs and mRNAs associated with immune infiltration, including 60 dysregulated lncRNAs, 38 dysregulated mRNAs, and 29 dysregulated miRNAs. Based on the PPI network and Cox regression analysis, 5 mRNAs including CNR2, P2RY12, ZNF831, RSPO1, and F2 were identified to be related to immune infiltration and prognosis in lung adenocarcinoma, and their differential expression, prognosis and correlation with immune cells were verified. Next, through target binding prediction, pearson correlation analysis and expression analysis, a novel immune-related ceRNA network containing 6 lncRNAs, 4 miRNAs, and 3 mRNAs was finally constructed. The present study constructed a novel immune-associated lncRNA-miRNA-mRNA ceRNA network, which deepens our understanding on the molecular network mechanism of lung adenocarcinoma and provides potential prognostic markers and novel therapeutic targets for the patients with lung adenocarcinoma.

Eight Aging-Related Genes Prognostic Signature for Cervical Cancer

This study searched for aging-related genes (ARGs) to predict the prognosis of patients with cervical cancer (CC). All data were obtained from Molecular Signatures Database, Cancer Genome Atlas, Gene Expression Integration, and Genotype Organization Expression. The R software was used to screen out the differentially expressed ARGs (DE-ARGs) between CC and normal tissues. A protein-protein interaction network was established by the DE-ARGs. The univariate and multivariate Cox regression analyses were conducted on the first extracted Molecular Complex Detection component, and a prognostic model was constructed. The prognostic model was further validated in the testing set and GSE44001 dataset. Prognosis was analyzed by Kaplan-Meier curves, and accuracy of the prognostic model was assessed by receiver operating characteristic area under the curve analysis. An independent prognostic analysis of risk score and some clinicopathological factors of CC was also performed. The copy-number variant (CNV) and single-nucleotide variant (SNV) of prognostic ARGs were analyzed by the BioPortal database. A clinical practical nomogram was established to predict individual survival probability. Finally, we carried out cell experiment to further verify the prognostic model. An eight-ARG prognostic signature for CC was constructed. High-risk CC patients had significantly shorter overall survival than low-risk patients. The receiver operating characteristic (ROC) curve validated the good performance of the signature in survival prediction. The Figo_stage and risk score served as independent prognostic factors. The eight ARGs mainly enriched in growth factor regulation and cell cycle pathway, and the deep deletion of FN1 was the most common CNV. An eight-ARG prognostic signature for CC was successfully constructed.

Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment

The cross-talk between tumor cells and the tumor microenvironment (TME) is an important factor in determining the tumorigenesis and progression of cervical cancer (CC). However, clarifying the potential mechanisms which trigger the above biological processes remains a challenge. The present study focused on immune-relevant differences at the transcriptome and somatic mutation levels through an integrative multi-omics analysis based on The Cancer Genome Atlas database. The objective of the study was to recognize the specific immune-related prognostic factors predicting the survival and response to immunotherapy of patients with CC. Firstly, eight hub immune-related prognostic genes were ultimately identified through construction of a protein–protein interaction network and Cox regression analysis. Secondly, 32 differentially mutated genes were simultaneously identified based on the different levels of immune infiltration. As a result, an immune gene-related prognostic model (IGRPM), including six factors (chemokine receptor 7 [CCR7], CD3d molecule [CD3D], CD3e molecule [CD3E], and integrin subunit beta 2 [ITGB2], family with sequence similarity 133 member A [FAM133A], and tumor protein p53 [TP53]), was finally constructed to forecast clinical outcomes of CC. Its predictive capability was further assessed and validated using the Gene Expression Omnibus validation set. In conclusion, IGRPM may be a promising prognostic signature to predict the prognoses and responses to immunotherapy of patients with CC. Moreover, the multi-omics study showed that IGRPM could be a novel therapeutic target for CC, which is a promising biomarker for indicating the immune-dominant status of the TME and revealing the potential mechanisms responsible for the tumorigenesis and progression of CC.

An Innovative Immune Score-Based Prognostic Nomogram for Patients with Cervical Cancer

Background

In the past few years, the immune system and tumor immune microenvironment are becoming increasingly popular as more work has been accomplished in this field. However, nomograms based on immune-related characteristics for prognosis prediction of cervical cancer have not been fully explored to our knowledge. We constructed a novel immune score-based nomogram to predict patients with high risk and poor prognosis.

Materials and Methods

198 patients with cervical cancer from The Cancer Genome Atlas (TCGA) database were included in our study. Immune scores were generated with Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm, and clinic-pathological characteristics were also included for subsequent analysis. Cox proportional hazards regression models were performed for univariate and multivariate analyses to screen the significant factors, and a prognostic nomogram was built. Bootstrap resampling analysis was used for internal validation. The calibration curve and concordance index (C-index) were used to assess the predictive performance of the nomogram.

Results

Patients were split into three subgroups based on immune scores. We found that patients with high immune scores conferred significantly better overall survival (OS) compared with those with medium and low immune scores (hazard ratio (HR), 0.305; 95% confidence interval (CI), 0.108-0.869). A nomogram with a C-index of 0.720 had a favorable performance for predicting survival rate for clinical use by combining immune scores with other clinical features. The calibration curves at 3 and 5 years suggested a good consistency between the predicted OS and the actual OS probability.

Conclusions

Our work highlights the potential clinical application significance of immune score-based nomogram in predicting the OS of cervical cancer patients.