The Role of lncRNA-Mediated ceRNA Network in Penile Squamous Cell Carcinoma

Academic Background

Penile Squamous Cell Carcinoma (PSCC) is a relatively rare but life-threatening malignancy that poses a significant health risk to men, particularly in developing countries. Despite advancements in medical diagnosis and treatment, the overall survival rate of PSCC patients has not significantly improved. The pathogenesis of PSCC remains incompletely understood, especially the role of long non-coding RNAs (lncRNAs) in its progression. lncRNAs are a class of non-coding RNAs longer than 200 nucleotides, which have been shown to play important roles in tumor proliferation, metastasis, drug resistance, and immune response in various cancers. However, the specific functions and molecular mechanisms of lncRNAs in PSCC have not been thoroughly investigated.

To address this gap, this study aims to construct a competing endogenous RNA (ceRNA) network in PSCC using lncRNA sequencing technology, revealing the potential regulatory mechanisms of lncRNAs in PSCC progression and providing new strategies for its treatment.

Source of the Paper

This paper was co-authored by Jian Cao, Lin Du, Xueheng Zhao, Zhizhong Liu, Junbin Yuan, Yanwei Luo, Shanshan Zhang, Zailong Qin, and Jie Guo, affiliated with multiple research institutions including the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, and the Third Xiangya Hospital of Central South University. The paper was published in Genes & Immunity in 2024.

Research Process and Results

1. Sample Collection and lncRNA Sequencing

The study began by collecting 5 normal tissue samples and 6 PSCC tumor tissue samples, followed by lncRNA sequencing. RNA quality control and quantification were performed, and the NEB Next® Strand-Specific Library Construction Kit was used to construct the lncRNA library. Sequencing was conducted on the Illumina platform. After quality control, expression profiles of 16,749 lncRNAs and 20,391 mRNAs were obtained.

2. Differential Expression Analysis and Functional Enrichment Analysis

Differential expression analysis of lncRNAs and mRNAs between tumor and normal tissues was performed using DESeq2 software, identifying 1065 differentially expressed lncRNAs (519 downregulated, 546 upregulated) and 3398 differentially expressed mRNAs (1429 downregulated, 1969 upregulated). Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these differentially expressed mRNAs were primarily involved in immune response, cell cycle regulation, and other biological processes.

3. Construction of the ceRNA Network

Using databases such as miRcode, lncBase, miRTarBase, miRWalk, and TargetScan, the regulatory relationships between differentially expressed lncRNAs, miRNAs, and mRNAs were predicted, ultimately constructing a ceRNA network consisting of 4 lncRNAs, 18 miRNAs, and 38 mRNAs. Among these, the lncRNAs MIR205HG, MIAT, HCP5, and PVT1 were significantly upregulated in PSCC and were found to regulate downstream miRNAs and mRNAs involved in tumor proliferation and the formation of an immunosuppressive microenvironment.

4. Immunohistochemical Validation

Immunohistochemical staining confirmed the significant overexpression of cell proliferation-related genes TFAP2C, MKI67, and TP63 in tumor tissues. Additionally, immune infiltration analysis revealed a significant increase in macrophage and exhausted T cell infiltration in PSCC tumor tissues, further supporting the important role of the ceRNA network in the immunosuppressive microenvironment of PSCC.

5. Survival Analysis

Survival analysis using the GSE85730 dataset showed that the genes DUSP2 and WNT5A in the ceRNA network were significantly associated with PSCC patient survival. High expression of DUSP2 was associated with better survival, while high expression of WNT5A indicated a poorer prognosis.

Conclusions and Significance

This study is the first to construct an lncRNA-mediated ceRNA network in PSCC, revealing the critical regulatory role of lncRNAs in PSCC progression. Specifically, the lncRNA MIR205HG was found to promote tumor cell proliferation and the formation of an immunosuppressive microenvironment by regulating downstream miRNAs and mRNAs. This discovery provides new insights into the molecular mechanisms of PSCC and offers potential biomarkers and therapeutic targets for future targeted and immune therapies.

Research Highlights

1. First Construction of a ceRNA Network in PSCC: This study is the first to construct an lncRNA-miRNA-mRNA ceRNA network in PSCC, revealing the regulatory mechanisms of lncRNAs in this cancer.
2. Identification of Key lncRNAs: The lncRNA MIR205HG was identified as playing a crucial role in PSCC and may serve as a potential therapeutic target.
3. Revelation of the Immunosuppressive Microenvironment: The study found significant infiltration of macrophages and exhausted T cells in PSCC tumor tissues, providing new directions for immunotherapy in PSCC.

Other Valuable Information

This study also revealed an increase in B cells and dendritic cells in the tumor microenvironment of PSCC through immune infiltration analysis, highlighting the need for further research into the roles of these cells in tumor progression. Additionally, the ceRNA network constructed in this study provides a theoretical foundation for future research into the molecular mechanisms and therapeutic strategies for PSCC.

Summary

Through lncRNA sequencing and the construction of a ceRNA network, this study delves into the regulatory mechanisms of lncRNAs in PSCC, revealing their crucial roles in tumor proliferation and the formation of an immunosuppressive microenvironment. This research offers new perspectives on the molecular mechanisms of PSCC and provides potential biomarkers and therapeutic targets for future targeted and immune therapies.