Multi-omics pan-cancer analyses identify MCM4 as a promising prognostic and diagnostic biomarker

Abstract

Minichromosome Maintenance Complex Component 4 (MCM4) is a vital component of the mini-chromosome maintenance complex family, crucial for initiating the replication of eukaryotic genomes. Recently, there has been a growing interest in investigating the significance of MCM4 in different types of cancer. Despite the existing research on this topic, a comprehensive analysis of MCM4 across various cancer types has been lacking. This study aims to bridge this knowledge gap by presenting a thorough pan-cancer analysis of MCM4, shedding light on its functional implications and potential clinical applications. The study utilized multi-omics samples from various databases. Bioinformatic tools were employed to explore the expression profiles, genetic alterations, phosphorylation states, immune cell infiltration patterns, immune subtypes, functional enrichment, disease prognosis, as well as the diagnostic potential of MCM4 and its responsiveness to drugs in a range of cancers. Our research demonstrates that MCM4 is closely associated with the oncogenesis, prognosis and diagnosis of various tumors and proposes that MCM4 may function as a potential biomarker in pan-cancer, providing a deeper understanding of its potential role in cancer development and treatment.

Keywords: Bioinformatics; Biomarker; Immune infiltration; MCM4; Multi-omics; Pan-cancer; Prognosis.

Figure 1

Structural characteristics and phylogenetic tree of MCM4. (A) The MCM4 gene is localized to the q11.21 region of chromosome 8; (B) The structural features of MCM4 proteins across different species; (C) Phylogenetic tree of MCM4.

Figure 2

MCM4 expression across various cancers and pathological stages. (A) The transcription levels of MCM4 in various kinds of human cancers. Statistical significance was indicated as *P < .05, **P < .01, and ***P < .001. (B) In the TCGA project, for the types of LGG, DLBC, OV, SKCM, THYM, SARC and UCS, we used the corresponding normal tissues from the GTEx database as controls. (C) The expression levels of the MCM4 gene according to different pathological stages (stage I, II, III, and IV) in KICH, LUAD, OV, KIRP, LIHC and UCS. (D) The expression levels of total MCM4 protein between normal tissue and primary tumor tissue in KIRC, COAD, BRCA, GBM, LIHC, HNSC, LUSC, LUAD, OV, PAAD and UCEC.

Figure 3

Single cell analysis of MCM4 in cancer and normal cell lines. (A) The overall essentiality of MCM4 in various cancer cell lines was demonstrated through CRISPR-Cas9 technology. (B) The overall essentiality of MCM4 in various cancer cell lines was demonstrated through RNAi assay. The Chronos and DEMETER2 dependency scores are derived from data obtained through a cellular depletion assay. In this context, a score of 0 indicates the non-essentiality of the gene, while a score of -1 corresponds to the median among all pan-essential genes, represented by the red line. (C) Normal cell line expression of MCM4. (D) MCM4 protein expression levels in various normal tissues. (E) Subcellular localization of MCM4 in the nucleus of A-431, A-549, U20S, and U-251MG cell lines. (F) The correlation between MCM4 transcript expression and progression of the cell cycle.

Figure 4

MCM4 gene mutation and post-translational phosphralation in diverse cancers. (A) Mutation rates and types of MCM4 in various cancers. (B) The three-dimensional structure refers to the spatial arrangement and conformation of the MCM protein. (C) Subtypes and distribution of somatic mutations in MCM4 gene. VUS, Variants of uncertain significance. (D) Phosphorylation site and level of MCM4 protein in BRCA, (E) LUAD, (F) LIHC, (G) GBM, (H) COAD, (I) OV, (J) HNSC and (K) LUSC.

Figure 5

Associations between MCM4 expression and molecular subtypes and immune subtypes in TCGA cancers. (A) The relationship between MCM4 gene expression and various molecular subtypes in 11 types of TCGA cancers. (B) The association between MCM4 gene expression and immune subtypes in 14 types of TCGA cancers. CIN chromosomal instability, GS genomically stable, POLE Polymerase ε, EBV Epstein-Barr virus, C1 wound healing, C2IFN gamma dominant, C3 inflammatory, C4 lymphocyte depleted, C5 immunologically quiet, C6 TGF-b dominant.

Figure 6

Correlation between MCM4 expression and immune cell infiltration in TCGA cancers. (A) Correlation between MCM4 expression and immune infiltration of cancer-associated fibroblasts, presented by heatmap. (B) Correlation between MCM4 expression and cancer-associated fibroblast infiltration in TGCT, BRCA-LumA, ACC, ESCA, HNSC(HPV-), LGG, MESO, PAAD, LIHC and THCA. (C) MCM4 expression exhibits a positive correlation with the infiltration of MDSCs and (D) top 5 tumors were ACC, ESCA, LUAD, UCEC and LIHC. (E) MCM4 expression shows a negative correlation with the infiltration of NKT cells and (F) top 5 tumors were UVM, THYM, CHOL, BRCA-Her2 and PRAD.

Figure 7

Functional and Pathway Enrichment Analysis of MCM4. (A) PPI network: 50 proteins interacting with MCM4 and their interaction networks. The darker the color of a node means that the node is more influential in the network. (B) Twenty-one genes with high correlation coefficients (R > 0.7) among a set of 100 genes known to be associated with MCM4 and (C) corresponding heatmap plot for various types of cancer. (D) Cross analysis between MCM4 binding genes and related genes, 12 identical genes are identified. (E) KEGG enrichment analysis. (F) GO enrichment analysis. BP Biological process, CC cellular component, MF molecular function.

Figure 8

Clinical Value of MCM4. (A) Kaplan–Meier curves of overall survival rate and (B) disease-free survival rate exhibiting the association between MCM4 gene expression and cancer survival outcomes in TCGA. (C) The ROC curve of MCM4 for the diagnosis of different cancers. AUC of ROC curves verified the diagnosis performance of MCM4 in the TCGA cohort.