Identification of EGFR-Related LINC00460/mir-338-3p/MCM4 Regulatory Axis as Diagnostic and Prognostic Biomarker of Lung Adenocarcinoma Based on Comprehensive Bioinformatics Analysis and Experimental Validation

Abstract

Background: Lung adenocarcinoma (LUAD) is one of the most aggressive and lethal tumor types and requires effective diagnostic and therapeutic targets. Though the epidermal growth factor receptor (EGFR) is an important target for LUAD therapy, acquired resistance is still inevitable. In recent years, the regulation of the EGFR by competing endogenous RNAs (ceRNAs) has been extensively studied and significant progress has been made. Therefore, we aim to find new targets for the diagnosis and treatment of LUAD by analyzing the EGFR-related ceRNA network in LUAD and expect to address the problem of EGFR resistance. Methods: We identified differentially expressed lncRNAs, miRNAs and mRNAs closely associated with the EGFR by analyzing transcriptome data from LUAD samples. Comprehensive bioinformatics analysis strongly suggests that the LINC00460—mir-338-3p—MCM4 ceRNA network plays an important role in the diagnosis and prognosis of LUAD. The effects of different patterns of the LINC00460/MCM4 axis on the overall survival of patients with LUAD were analyzed by a polygene regulation model. We also verified the expression of these genes in LUAD cell lines and tumor tissues by RT-PCR and immunohistochemistry. The functional enrichment analysis and targeted drug prediction of the MCM4 gene were performed. Results: Survival analysis indicated that high expressions of LINC00460 and MCM4 predict a shorter survival period for patients. Univariate and multivariate regression analyses demonstrated that higher expressions of LINC00460 and MCM4 were significantly associated with tumor size, lymph node metastasis, distant metastasis and TNM stage. A multi-gene regulation model analysis revealed that the LINC00460 (downregulation)—mir-338-3p (upregulation)—MCM4 (downregulation) pattern significantly improved the overall survival of LUAD patients (p = 0.0093). RT-PCR and immunohistochemical experiments confirmed our analytical results. In addition, the functional enrichment analysis indicated that MCM4-related genes were mainly enriched in the cell cycle and cell division. A functional association network analysis showed that MCM4 was closely related to the EGFR. Finally, the possible targeted drugs of MCM4 were queried through the drug database platform, hoping to solve its drug resistance problem by targeting EGFR-related genes. Conclusions: In summary, the LINC00460/MCM4 axis can be used as a potential new perspective for targeting EGFR genes in precision medicine and is expected to serve as a diagnostic, prognostic and drug target for LUAD.

MCM4 expression is associated with high-grade histology, tumor progression and poor prognosis in urothelial carcinoma

“…In UTUC, the overexpression of HER2 and EGFR are associated with a high tumor stage, high histological grade, and poor survival [5]. Interestingly, a recent study has demonstrated that a relationship between EGFR and MCM4 is observed in lung adenocarcinoma [30]. In addition, our previous study has con rmed the MCM4 was associated with AKT, ERK and EGFR pathways by functional analysis using GC cell lines [13].…”

LncRNAs in non-small cell lung cancer: novel diagnostic and prognostic biomarkers

“…There are three main ways in which lncRNAs regulate genes: epigenetic regulation, transcriptional and post-transcriptional regulation, and their biological function depends on their location in the cell ( Jia et al, 2022 ). In the nucleus, some lncRNAs can become histone modifiers through methylation or demethylation, thereby regulating the chromatin state and ultimately promoting or repressing gene transcription ( Herman et al, 2022 ).…”

In silico functional, structural and pathogenicity analysis of missense single nucleotide polymorphisms in human MCM6 gene

“…The MCM3 gene is essential for the initiation of DNA replication and is involved in ensuring the precise initiation of DNA replication once per cell cycle 9 . The MCM4 gene is mainly enriched in the cell cycle and cell division and is also significantly associated with tumor size and, lymph node metastasis 10 . The MCM5 gene is associated with malignant status and poor prognosis in cervical adenocarcinoma patients, modulates cervical adenocarcinoma cells proliferation, inhibits the cell cycle and promotes colorectal cancer cells in vitro 11 , 12 .…”