Multi-omics analysis of MRPL-13 as a tumor-promoting marker from pan-cancer to lung adenocarcinoma

Comparative analysis of MRPL13 expression across cancers

We utilized the UCSC dataset (https://xenabrowser.net/datapages/) to examine the comparative expression of MRPL13 in 33 cancers and normal tissues. This dataset is primarily designed for the analysis of specific gene expression in tumors and normal tissues and provides visualization of contrast data as needed. Specifically, initially, the homogenized and standardized pan-cancer dataset was downloaded from TCGA. Subsequently, the expression data for the ENSG00000172172 (MRPL13) gene were extracted from each sample. Additionally, we screened the sample sources and transformation on each expression value. Finally, we eliminated any cancer type with fewer than 3 samples, resulting in a dataset of 33 cancer type expression data.

Survival prognosis analysis

In addition to extracting the pan-cancer dataset and MRPL13 gene expression data from UCSC, we also extracted and transformed the data about the prognosis of pan-cancer from a prognosis study published in the journal Cell [8]. Subsequently, we obtained and transformed the data of TARGET’s follow-up time of more than 30 days from UCSC as a supplement. The exclusion criteria were cancers with fewer than 10 samples in total. Finally, according to the consensus, the relationship between gene expression and prognosis in each tumor was analyzed by constructing a Cox proportional hazard regression model, and the significance of prognosis was obtained by using the log-rank test. The overall survival and progression-free interval data of the top ten cancer types with differential MRPL13 expression were selected for visualization.

After dividing the patients equally according to the expression level, a Kaplan-Meier curve was used to draw the prognosis (OS, PFI) of cancer patients who expressed MRPL13 to different degrees. Finally, we utilized the GEO database (GSE81538/GSE68465/GSE65858/GSE66229) to verify the influence of MRPL13 expression level on prognosis in four types of cancer patients (BRCA/LUAD/HNSC/STAD).

Diagnostic value of MRPL13 across cancers

We obtained the receiver operating characteristic (ROC) curve through the R package pROC to evaluate the diagnostic value of MRPL13 in 13 cancers with different expression levels [9]. The area under the ROC curve is directly proportional to the diagnostic accuracy. In detail, by setting multiple critical values with differences for genetic variables and then calculating the evaluation index corresponding to each critical value in real time, the most efficient variable is selected, and then a curve with sensitivity as the ordinate and 1-specificity as the abscissa is drawn.

Protein level analysis

We obtained the protein expression data of MRPL13 in BRCA, LUAD, HNSC and their corresponding normal tissues from the CPTAC database [10]. Since the CPTAC database does not provide data on gastric adenocarcinoma and its corresponding normal tissue, we utilized samples with high and low microsatellite instability as substitutes. Additionally, we selected representative immunohistochemistry (IHC) images of BRCA, LUAD, HNSC, and STAD and representative immunohistochemical images of corresponding normal tissues in the HPA database. This database contains a vast number of IHC images of tumors and normal tissues.

Coexpression gene network and enrichment analysis

The correlation between MRPL13 and other genes was analyzed through the “STAT” package [version 4.2.2] (basic package) in R language. The top 30 positively and negatively related genes were selected for thermal map display. Then, the genes coexpressed in two or more cancers were enriched and analyzed, mainly including KEGG (http://www.genome.jp/kegg/) and Gene Ontology (http://pantherdb.org/). The Cluster Profiler package in R language was used for enrichment analysis, and the visualization of the results was completed by the ggplot2 package.

Genomic alterations of MRPL13 in pan-cancer

The protein structure of MRPL13 was visualized by PYMOL (https://pymol.org/2/). Genetic variation of MRPL13 in different tumor types was analyzed by cBioProtal (cBioPortal for Cancer Genomics). The mutation landscape of MRPL13 was shown by the processed pan-cancer SNV data. The MRPL13 protein structure diagram and the mutation’s precise location were analyzed by the “mutations” module. In addition, according to the mutation grouping, the prognosis of patients with four candidate cancers (BRCA, LUAD, HANC, and STAD) was analyzed. In addition, we also compared the somatic gene mutation rates of LUAD patients with high and low MRPL13 expression, and 426 (83.0%) of 513 mutation samples were used to draw graphs. Finally, the chi-square test was used to evaluate the difference in gene mutation frequencies in each group of samples. Furthermore, by downloading and transforming the tumor dryness score calculated by methylation characteristics of each tumor in previous studies and the expression of MRPL13 in pan-cancer, we drew a Lollipop Chart of their correlation [11]. Finally, we analyzed the pan-cancer correlation of MRPL13 in TBM, MSI, HRD, and PLO to find out which patients are the most sensitive and beneficial to immunotherapy.

Differential gene screening and gene enrichment analysis

LUAD patients were divided into two groups according to the median overall expression as the critical point. (Supplementary Table 1). Then, the differentially expressed genes of the two groups of patients were extracted and visualized by using the R language DEseq2 and GGPLOT2 volcanic map. (Log FC > 1, P < 0.05) (Supplementary Material 1) [5]. Then, the differential genes were subjected to GSEA enrichment analysis (Supplementary Material 2).

Immune infiltration analysis and immune checkpoints

In this study, we utilized three algorithms from various databases, TIMER, QUANTISEQ, and XCELL, to investigate the relationship between MRPL13 and immune cell infiltration patterns in different types of cancer. Moreover, we utilized the ssGSEA algorithm embedded in the GSVA package in R language to analyze the immune cell infiltration model based on the high and low expression of MRPL13 in BRCA, LUAD, HNSC, and STAD in TCGA. The data on immune cells were obtained from a published article [12]. Additionally, we used TISIDB analysis to identify five immune subtypes in BRCA, LUAD, STAD, and HNSC.

Chemokine genes, chemokine receptor genes, MHC-related immune pathway marker genes, immunosuppressant genes, and immunostimulant genes were collected from a standardized ubiquitin gene expression dataset. The coexpression relationship between MRPL13 and immune genes in pan-cancer was inferred using the R package “limma” and determined using the Pearson statistical method.

By downloading and transforming the uniform and standardized pan-cancer dataset and screening the sample sources, the expression profile of MRPL13 in each tumor was extracted, and then the expression profile was mapped to Gene-Symbol. Furthermore, the stromal, immune and ESTIMATE scores of each patient were counted, transformed and charted [13].

Protein-protein interaction network and enrichment analysis

We screened for interacting proteins of MRPL13 in the IMEX database and visualized the protein-protein interaction (PPI) network using Cytoscape. Moreover, we performed KEGG/GO enrichment analysis on the binding proteins associated with MRPL13. We used the Cluster Profiler package (version 3.14.3) and the ggplot2 package (version 3.3.3) for enrichment analysis and visualization, respectively.

Drug sensitivity analysis of MRPL13

We downloaded drug activity data and RNA-seq expression profiles from CellMiner™ to analyze the sensitivity of MRPL13 to drugs across cancers [14]. Moreover, to further investigate the possibility of MRPL13 as a new target for tumor treatment, we selected a group of genes related to MRPL13 and analyzed their relationship with drug sensitivity. For our analysis, we only considered FDA-approved drugs or drugs currently undergoing clinical trials.

RNA modification analysis

We screened, extracted and homogenized the expression data of the ENSG00000172172 (MRPL13) gene and three RNA modification marker genes in each sample from the UCSC database. Then, we calculated the correlation between ENSG00000172172 (MRPL13) and five immune pathway marker genes by the Pearson correlation algorithm. The correlation heatmap is drawn. The three RNA methylation patterns analyzed in this work include m1A, m5C, and m6A. The three types of genes related to modification are writers, readers, and erasers.

Correlation between MRPL13 and cuproptosis-related genes in LUAD

The standardized pan cancer dataset was downloaded from the TCGA database, and the expression data of MRPL13 and 13 cuproptosis-related genes expressed in BRCA, CHOL, ESCA, HNSC, LUAD, PPAD, and STAD were extracted. Moreover, the expression data of MRPL13-related genes and 13 cuproptosis-related genes expressed in LUAD were extracted. The Pearson correlation was calculated by log2(x+1) transformation of each expression value.

Effects of MRPL13 on 14 functional states in cancer

The single-cell sequence data from the Cancer-SEA website were extracted [15], and the functional status changes in 14 cancers caused by MRPL13 were analyzed in pan-cancer by the Xiantao academic online tool. The effects of MRPL13 expression on tumor metastasis, EMT, the cell cycle, DNA repair, invasion, DNA damage, proliferation, hypoxia, and inflammation were extracted and shown.

The result of querying candidate causal perturbations of MRPL13

A creative database of the human perturbation database (GPSAdb, https://www.gpsadb.com/) was used for genetic perturbation similarity analysis (GPSA) [16]. GPSA compared the DGE of 3048 disturbed datasets from GPSAdb to determine which genes lead to a similar trend of MRPL13 expression changes after knockout. To put it more succinctly, through the GPSAdb database, we found a gene that leads to changes in the expression of MRPL13 after knockout. To clarify the possible upstream regulatory factors of MRPL13.

Specimen collection

We collected twenty fresh LUAD samples and twenty fresh normal lung tissues adjacent to the tumor from Zhejiang Provincial People’s Hospital (Hangzhou, China). The extracted sample was first placed at the liquid nitrogen lock temperature. This was followed by cell extraction, fragmentation, RNA and protein extraction, and other related steps. We employed qRT-PCR assays and Western blot analysis to analyze the samples. In addition, we obtained 50 IHC samples from the Pathology Department of Zhejiang Provincial People’s Hospital (Supplementary Table 2). All human samples were solely used for research purposes and were approved by the Ethics Committee of Zhejiang Provincial People’s Hospital (QT2023121).

In vitro experiment

We used a qRT-PCR assay, immunohistochemistry (IHC) staining, and WB analysis to investigate the expression of MRPL13 in LUAD samples versus normal samples. Furthermore, we used CCK-8 reagent to evaluate the cell proliferation characteristics and cytotoxicity of each group and flow cytometry to evaluate apoptosis and cell cycle progression in the control and experimental groups. Finally, the distant metastasis ability of tumor cells was determined by the number difference of the same cells passing through the Transwell chamber at the same time. Please refer to Supplementary Material 3 for technical details.

Statistical methods

Bioinformatics analysis was performed using R software and bioinformatics tools, including the Cancer-SEA database (CancerSEA - Database Commons (cncb.ac.cn)) and GPSAdb database (https://www.gpsadb.com/). Statistical analysis was performed with SPSS software version 25.0 (IBM Corp., Armonk, NY, USA) and GraphPad Prism version 7.0 (GraphPad Software Inc., USA). The differential expression of MRPL13 among different samples and groups was determined by t tests. The “survival” and “forest-plot” packages were used to determine the HRs of MRPL13 across cancers. Kaplan-Meier curve reveals the relationship between MRPL13 expression and prognosis of patients with pan-cancer. The correlation coefficient is quantified by Pearson or Spearman. The Wilcox test was used to analyze immune infiltration genes. P-values less than 0.05 (*p < 0.05) were considered significant.

Availability of data and material

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Differential expression of MRPL13 between tumor and normal tissue samples

By comparing cancer and normal tissue data from TCGA, we identified differential expression of MRPL13 in 18 types of cancer, except for cancers lacking comparative data or differences. Compared with normal tissues, the expression of MRPL13 in BLCA, BRCA, CESC, CHOL, COAD, ESCA, GBM, HNSC, LIHC, LUAD, LUSC, PRAD, STAD, and UCEC is completely opposite to that in KICH, KIRC, PCPG, and THCA. The former was higher than that in normal tissue, while the latter was lower than that in normal tissue (Figure 1A). Paired samples showed similar results to unmatched samples in BLCA, BRCA, CHOL, ESCA, HNSC, KICH, KIRC, LIHC, LUAD, LUSC, STAD, UCEC, and THCA (Figure 1B). Additionally, to verify these findings at the protein expression level, we analyzed relevant immunohistochemical images from HPA data (Supplementary Figure 1A–1H).

Figure 1. Differential expression of MRPL13 in pan-cancer and the relationship between MRPL13 expression and prognosis of pan-cancer. (A) Comparison of MRPL13 expression between tumor and normal samples. (B) Comparison of MRPL13 expression between tumor and paired normal samples. (C) Forest plot of OS associations in 33 types of tumor. (D) Forest plot of PFI associations in 33 types of tumor. (E, F) Kaplan–Meier analysis of the association between MRPL13 expression and OS/PFI. *p < 0.05, **p < 0.01, ***p < 0.001. ns, not statistically significant.

Prognostic significance of MRPL13 in cancer

To explore the influence of MRPL13 expression level on the prognosis of patients with pan-cancer from the macro level and to narrow the scope of our investigation, we analyzed the influence of MRPL13 as a single factor on the prognosis of each cancer by two indicators: overall survival (OS) and progression-free interval (PFI). The Cox proportional hazard model analysis revealed that the increased expression level of MRPL13 leads to poor prognosis in patients with BRCA and LUAD, and the result was statistically significant (P = 2.3e-5) (p=5.3e-4). MRPL13 was identified as a higher risk factor (Figure 1C). This result is consistent with the Kaplan-Meier survival analysis (Figure 1E).

The relationship between MRPL13 and PFI revealed that an increase in MRPL13 expression leads to an increase in adverse events in HNSC patients. (p = 1.8e-3), while it acted as a protective factor for STAD (p = 0.02) (Figure 1D). Kaplan-Meier survival analysis confirmed this trend (Figure 1F). Finally, using Kaplan-Meier survival analysis of the validated dataset in GEO, we confirmed that MRPL13 is a reliable factor for predicting the prognosis of cancer (Supplementary Figure 1I).

Diagnostic value of MRPL13 across cancers

Evaluation of the receiver operating characteristic (ROC) curve confirmed the diagnostic value of MRPL13 across cancers. The AUC value, ranging from 0.5 to 1, measures the accuracy of the diagnostic effect. An AUC of 1 indicates a better diagnostic effect. Analyzing the ROC curve of 13 cancers with differential MRPL13 expression obtained from the TCGA analysis of matched and unmatched samples, we found that the diagnostic accuracy of the AUC analyzed by this model was high in 9 cancers, relatively high in 1 cancer, and low in 2 cancers (Figure 2A). Finally, we constructed a Venn diagram to compare the cancer model with differences among unmatched sample comparison, matched sample comparison, ROC diagnosis model, and survival analysis, which identified BRCA, LUAD, STAD, and HNSC as significant cancers (Figure 2B).

Figure 2. AUC of ROC curves verified the diagnosis performance of MRPL13 in the TCGA cohort. (A) ROC curve shows the value of MRPL13 in the diagnosis of patients with Pan-cancer, including UCEC, THCA, STAD, LUSC, LUAD, LIHC, KIRC, KICH, ESCA, CHOL, BRCA, BLCA, HNSC. (B) Venn diagram showed the intersection of cancer in pan-cancer, which was significant in expression, diagnostic performance and prognosis analysis.

Coexpression network analysis of MRPL13 across cancers and coexpression network enrichment analysis

We analyzed the sequencing data of BRCA, LUAD, HNSC, and STAD in TCGA using R language, and the genes related to the expression of MRPL13 in each cancer were identified. We then generated a heatmap based on the log value of the top 30 genes (Figure 3A). Further analysis of the intersection of the genes that co-occur in at least two cancers was performed using the Cluster Profiler package in R, with GO terminology and KEGG pathway analysis. The results showed that genes were mainly related to the regulation of mitotic cell cycle phase transition, mitochondrial inner membrane, translation factor activity, and RNA binding in GO enrichment analysis. In KEGG enrichment analysis, the genes were mainly enriched in amyotrophic lateral sclerosis, Huntington disease, and prion disease (Figure 3B), which was visualized with the ggplot2 R language pack (Figure 3C). Crossing the genes related to MRPL13 in each cancer resulted in a gene set of 40 genes (Figure 3D) and (Supplementary Material 4). Finally, we performed a variety of enrichment analyses of these 40 genes in Metascape, and the results showed that in GO analysis, the top three were neddylation, ribonucleoprotein complex biogenesis and gastric cancer network 2. The cell cycle ranked fifth, which is consistent with the fact that MRPL13 may promote the growth of cancer cells by affecting the cell cycle. In addition, in the summary of enrichment analysis in cell type signatures, TRAVAGLINI LUNG PROLIFERATING NK T CELL ranks second. In the summary of enrichment analysis in DisGeNET, Monosomy is the closest. In the final summary of enrichment analysis in Transcription Factor Targets, the top three are PPARGC1A TARGET GENES, ZNF581 TARGET GENES and HSF2 TARGET GENES. Enrichment analysis revealed the common biological function of these 40 genes, which provides useful value for expounding the role of MRPL13 (Supplementary Figure 1J–1M).

Figure 3. Co-expression network analysis of MRPL13 in pan-cancer and co-expression network enrichment analysis. (A) The top 30 positive and negative genes related to the expression of MRPL13 in BRCA, LUAD, HNSC and STAD. (B) GO and KEGG analyses for genes related to the expression of MRPL13 in at least two cancers (C) the result of GO and KEGG analyses visualize with R language pack ggplot2(red: molecular: blue: enrichment results). (D) Veen map shows the intersection of genes related to the expression of MRPL13 in BRCA, LUAD, HNSC and STAD.

The genetic alterations of MRPL13

Initially, the protein structure of MRPL13 was visualized using the PYMOL website (Figure 4A). The cBioPortal database revealed that the highest incidence of gene alterations in MRPL13 is in ovarian cancer, while it is also amplified in the majority of pan-cancer patients, including those with breast cancer, esophageal cancer, liver cancer, uterine cancer, pancreatic cancer, gastric adenocarcinoma, prostate cancer, head and neck squamous cell carcinoma, bladder cancer, and lung adenocarcinoma. Amplification, deletion mutation, and deep deletion are the most common types of genetic variation observed in MRPL13 (Figure 4B). The types, sites, and cases of MRPL13 gene modification are presented, with MRPL13 missense mutation being the most common mutation type and P8 mutation detected in 2 cases of SKCM and 1 case of LUAD (Figure 4C). Subsequently, we conducted an analysis of the patient prognosis across four types of cancer based on mutation groups, revealing a poor prognosis for patients in the MRPL13 mutation group in STAD (Figure 4D–4G). Moreover, to further explore the gene mutation caused by MRPL13 in patients with LUAD, we divided the patients into two groups and compared the mutation frequency differences between groups. The results showed that the top three gene mutation rates of cells with high and low expression of MRPL13 were TP53 (54.0%), TTN (51.3%) and CSMD3 (41.7%) (Supplementary Figure 2A) and (Supplementary Material 5).

Figure 4. The genetic alterations of MRPL13. (A) The protein structure of MRPL13. (B) Analysis of MRPL13 alteration frequency in different tumor types according to cBioPortal dataset. (C) The mutation types, number, and sites of MRPL13 in pan-cancer analysis according to cBioPortal dataset. (D–G) Relationship between MRPL13 mutation status and Overall survival in BRCA, LUAD, HNSC and STAD. (H–K) the association of TMB, MSI, HRD, PLOIDY with MRPL13 in pan-cancer.

We compared the correlation of TMB, MSI, HRD, and PLOIDY with MRPL13 across various cancer types. TMB was positively correlated with MRPL13 in six cancers, GBM, LUAD, STES, UCEC, STAD, and DLBC, but negatively correlated with MRPL13 in UVM, COADREAD, COAD, and READ (Figure 4H). MSI analysis showed that MRPL13 had a significant positive correlation with eight types of cancers. UVM, DLBCM UCS, STES, TGCT, HNSC, STAD, and CHOL were negatively correlated in six cancers, namely, GBMLGG, COADREAD, COAD, READ, PCPG, and ACC (Figure 4I). In addition, we observed that MRPL13 was significantly associated with HRD in 23 cancers, with a positive correlation in ESCA, UVM, KIRC, DLBC, KIPAN, STAD, STES, ACC, KIRP, GBM, CESC, LUSC, BLCA, PRAD, GBMLGG, LUAD, HNSC, SARC, BRCA, OV, PAAD, LGG, and THYM and a negative correlation with UCS (Figure 4J). Moreover, polyploidy, an indicator of cancer, was positively correlated with 19 cancers, including DLBC, LUAD, HNSC, MESO, PRAD, LUSC, CHOL, SKCM, THYM, UCS, ESCA, SARC, COAD, STES, STAD, COADREAD, READ, LIHC, and BRCA, but negatively correlated with seven cancers, including OV, UVM, UCEC, PCPG, TGCT, GBMLGG, and KICH (Figure 4K). Furthermore, the correlation between MRPL13 and the tumor dryness score in pan-cancer showed that MRPL13 was positively correlated with the tumor dryness score in most cancers (Supplementary Figure 2B–2G).

Finally, to obtain the alterations of MRPL13 and its expression data in pan-cancer, the expression difference of MRPL13 in different samples in each tumor was calculated by R software (version 4.1.3). The copy number data and gene expression data of each tumor sample were integrated, and the difference between two samples was analyzed by using unpaired Wilcoxon rank sum and signed rank tests. The difference between multiple groups of samples was tested by the Kruskal-Wallis test. Significant differences were observed in 23 tumors, including BRCA, LUAD, STAD and HNSC. MRPL13 mutation and gene expression significantly affect many cancer types (Supplementary Figure 3A). The mutation of MRPL13 in individual tumors analyzed by Sanger-Box is shown in Supplementary Figure 3B.

In general, MRPL13 acts as a potential marker of genomic stability in a variety of cancer species, including LUAD, and affects patient prognosis and therapeutic responses.

GSEA enrichment analysis of differentially expressed genes in patients with different degrees of MRPL13 expression

After analyzing the MPRL13 expression count of LUAD patients in the TCGA database. All LUAD patients were divided into high and low expression groups with the median MRPL13 expression as the critical point. By using R language DEseq2, the differentially expressed genes of the two groups were extracted (Log FC > 1, P < 0.05) and visualized by using a GGPLOT2 volcanic map (Figure 5A). Second, the differentially expressed genes were subjected to GSEA. The differentially expressed genes between the two groups were significantly enriched in several biological pathways, including REACTOME SIGNALING by RHO GTPASES, REACTOME TRANSCRIPTIONAL REGULATION by TP53, REACTOME CELL CYCLE CHECKPOINTS, REACTOME MITOTIC G2/G2 M PHASES, and KEGG CELL CYCLE (Figure 5B–5G). Based on the above results, we speculate that MRPL13 may participate in the regulation of tumor occurrence and development by affecting the cell cycle.

Figure 5. DEGs between MRPL13 high and low expression groups in LUAD. (A) The volcano map of DEGs (red: upregulation; blue: downregulation). (B) GSEA enrichment analysis results of high and low MRPL13 differential genes visualized in Ridgeline plot. (C–G) GO and KEGG analyses for samples with high and low MAZ expression in LUAD.

Relationship of MRPL13 expression with immune infiltration analysis

To reveal the change in the immune cell infiltration pattern caused by MRPL13 in patients, we analyzed immune cell infiltration data extracted from various databases and algorithms. Using TIMER, QUANTISEQ, and XCELL, we mapped the MRPL13 gene expression of pan-cancer patients in the TCGA dataset to the corresponding immune cell infiltration and constructed a correlation heatmap. Infiltration of immune cells, including B cells and T cells from lymphocytes, monocytes, macrophages and dendritic cells from the myeloid system, appeared in four cancers (BRCA, LUAD, HNSC, and STAD). The results indicate a negative correlation between MRPL13 expression and the infiltration of various immune cells, such as CD8⁺ T cells, macrophages, and B cells (Figure 6). In addition, in a more detailed comparison, there were significant differences in the composition of immune cell infiltration, including CD8 T cells and NK cells, and the group with low expression of MRPL13 had a better antitumor immune cell infiltration microenvironment. (Supplementary Figure 4A–4D). These findings suggest that MRPL13 may affect tumor prognosis by modulating the host immune response.

Figure 6. The relationship between MRPL13 and tumor immune infiltrating cells in BRCA, LUAD, HNSC and STAD. (A–C) The correlation between MRPL13 expression and immune cell infiltration was analyzed by XCELL, QUANTISEQ and TIMER algorithm. *p < 0.05, **p < 0.01, ns, not statistically significant.

We also analyzed the relationship between MRPL13 and immune infiltration-related genes by a coexpression algorithm. The results indicated that MRPL13 and most immune-related genes had the same change trend in specific cancer types. such as UVM, GBML GG, SKCM, KIHC, LGG, OV, ACC, PAAD, and BLCA. However, in BRCA, STAD, STES, LUAD, ESCA, HNSC, and LUSC, it was negatively correlated. In particular, chemokines, including CXCL8, CXCL10, CXCL11, CXCL16, CCL26, and CCL7, as well as chemokine receptors, including CXCR3, CCR2, CCR5, and CCR1, were positively correlated with MRPL13 expression in various cancer types. (Figure 7A, 7B). MHC genes and MRPL13 were coexpressed in almost all tumor types, except TGCT, STAD, STES, LUAD, ESCA, HNSC, and LUSC (Figure 7C). Furthermore, immune-stimulating factors and immunosuppressive factors were closely associated with the expression of MRPL13 across cancers. Almost all cancers showed a significant relationship between MRPL13 and immune checkpoint suppressor genes, such as VEGFA, CD274 (PD-L1), and CTLA4 (Figure 7D, 7E). Finally, TISIDB analysis demonstrated that MRPL13 expression was considerably enriched in six immune subtypes, including wound healing, IFN dominance, inflammation, lymphocyte depletion, immune calm, and TGFβ dominance, in BRCA, LUAD, HNSC, and STAD (Supplementary Figure 4E–4H).

Figure 7. Heatmaps indicating the co-expression of MRPL13 with immune-relevant genes in pan-cancer. (A) Co-expression between MRPL13 and chemokine genes. (B) Co-expression between MRPL13 and chemokine receptor genes (C), Co-expression between MRPL13 and MHC genes. (D) Co-expression between MRPL13 and Immunoinhibitors genes. (E) Co-expression between MRPL13 and Immunostimulators gene. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001, and ****p-value < 0.0001.

Furthermore, MRPL13 was negatively correlated with the infiltration of various stromal immune cells in the immune microenvironment. Specific B cells, CD4+ T cells, macrophages, and neutrophils are shown in Supplementary Figure 5A.

Finally, we extracted and mapped the expression profile of MRPL13 in patients with LUAD according to the coordination relationship between MRPL13 and immune gene expression. The results were counted and converted into related scores by using the R language package. It was concluded that the expression of MRPL13 in patients with LUAD was inversely proportional to these three scores (Supplementary Figure 5B–5D). Overall, the above results show that MRPL13 is closely associated with the biological functions of several immune-related cells and genes.

PPI network and enrichment analysis of MRPL13-binding proteins

We used the IMEX database to identify the targeted binding protein of MRPL13 (Figure 8A). Subsequently, we analyzed the KEGG/GO enrichment of these targeted binding proteins and found that they mainly participate in several biological processes for instance mitochondrial gene expression, protein complex disassembly, and mitochondrial translation. The molecular function analysis revealed involvement in nuclear-transcribed mRNA catabolic process and protein targeting to the endoplasmic reticulum. The cellular component analysis indicated an association with ribosomes and mitochondrial protein complexes. Moreover, KEGG analysis showed that MRPL13 binding proteins were mainly involved in cellular respiration and the acetyl-CoA biosynthetic process from pyruvate (Figure 8B, 8C).

Figure 8. PPI network and enrichment analysis of MRPL13-binding proteins. (A) PPI network; (B) visual network of GO analysis (red: molecular; blue: enrichment results). (C) KEGG/GO analysis.

Drug sensitivity analysis of MRPL13

Using the Cell Miner database, we conducted further screening for therapeutic drugs related to MRPL13 and analyzed the effect of MRPL13 expression on the sensitivity of patients to molecular drugs. Our results showed that the expression of the MRPL13 gene in patients with LUAD was positively correlated with patients’ sensitivity to tramadol, CI-1040, navitoclax, TGX221 and nutlin-3A. Conversely, the expression of MRPL13 was negatively correlated with sensitivity to vorinostat, SB590885, VX-11e and bleomycin. (Figure 9A–9I). These findings suggest that high MRPL13 expression may significantly impact the effectiveness of drug treatment for cancer patients, including immunotherapy.

Figure 9. Drug sensitivity analysis of PNPO and the genes that MRPL13-related. (A) Trametinib. (B) Vorinostat. (C) SB590885. (D) VX−11e. (E) Bleomycin. (F) CI-1040. (G) Navitoclax. (H) TGX221. (I) Nutlin-3A. (J) Correlation between GDSC drug sensitivity and the genes that MRPL13-related.

Furthermore, by drawing a correlation heatmap between MRPL13-related genes and the sensitivity to 20 common drugs, we found a direct proportion between MRPL13 and most related gene expression levels and the sensitivity to TGX221, trametinib, and selumetinib and an inverse proportion to navitoclax, NPK76-II-72-1, vorinostat, and other drugs (Figure 9J). These findings demonstrate the crucial role that MRPL13 and its related genes play in influencing drug treatment sensitivity, which suggests potential targeted therapies for cancer through MRPL13 and related genes.

MRPL13 and RNA methylation modification markers

The expression data (UCSC database) of MRPL13 and 44 marker genes of three RNA modification genes in each sample of the pan cancer dataset were extracted and converted by formula. Then, we drew a heatmap between MRPL13 and the marker genes of five immune pathways through the results of the Pearson correlation algorithm. The results demonstrate a strong positive correlation between MRPL13 and most genes involved in modifying RNA methylation in some types of cancer, including ACC, KICH, BRCA, LUAD, and STAD. However, there is no obvious correlation between MRPL13 and methylation genes in other types of cancer, for instance UCS, DLBC, LIHC, GBM, and CHOL. These results provide direct evidence that MRPL13 is involved in the regulatory network and complexity of multiple cancers (Supplementary Figure 6). The alteration of RNA methylation is highly significant in cancer development and treatment response.

Correlation between MRPL13 and cuproptosis-related genes in LUAD

We used the expression data of MRPL13 and cuproptosis-related genes in the TCGA database to study the relationship between them through a correlation algorithm. Our analysis revealed that in CHOL, there was no correlation between MRPL13 and most cuproptosis-related genes. However, in BRCA, HNSC, LUAD, PPAD, and STAD, MRPL13 showed a significant correlation with GCSH, FDX1, DLST, and DLD (Figure 10A). To further discuss the relationship between MRPL13 and cuproptosis in detail, we also drew a correlation heatmap between MRPL13-related genes and cuproptosis-related genes. Our findings indicate that except for ATP7A and ATP7B, most cuproptosis-related genes are directly proportional to MRPL13-related genes (Figure 10B). These results indicate that MRPL13 regulates cancer cell status in some types of cancer through cuproptosis-related mechanisms.

Figure 10. Correlation between MRPL13 and the genes that MRPL13-related with cuproptosis related genes in pan-cancer. (A) Correlation between the expression levels of MRPL13 and cuproptosis related genes in pan-cancer. (B) Correlation between the expression levels of the genes that MRPL13-related and cuproptosis related genes. * p < 0.05 ** p < 0.01.

Effects of MRPL13 on 14 functional states in cancer

By downloading the single-cell sequencing data from the CancerSEA database and using Xiantao Academic’s online mapping service, we explained the influence of MRPL13 on the functional status of 14 kinds of cancers. In most cancers, MRPL13 is directly proportional to most cell cycle-related marker genes. Among CML and LUAD, MRPL13 is most closely related to all fourteen cancer functional states. Interestingly, MRPL13 was negatively associated with hypoxia in most tumors (Figure 11A). In LUAD, the expression of MRPL13 was directly proportional to metastasis (r=0.476), EMT (r=0.382), the cell cycle (r=0.631), DNA repair (r=0.601), invasion (r=0.576), and DNA damage (r=0.424). However, it was inversely proportional to hypoxia (r=-0.622) and inflammation (r=-0.427) (Figure 11B).

Figure 11. The correlation between MRPL13 expression and 14 cancer functional states using single-cell sequence data from the Cancer-SEA database. (A) The correlation between MRPL13 expression and 14 cancer functional states in pan-cancer. (B) The expression of MRPL13 is positively correlated to Metastasis, Cell-Cycle, DNA-repair, Invasion, DNA-damage, Proliferation of LUAD. The expression of CENPL is negatively correlated to the Hypoxia, Inflammation of LUAD.

The result of querying candidate causal perturbations of MRPL13

In GPSAdb, we collected 3048 RNA-seq datasets of gene knockdown/knockout and analyzed them for differences. Using the query tool in GPSAdb, we identified the genes regulating MRPL13 from the 3048 RNAseq datasets with genetic perturbations. We found that FOXM1 knockout caused changes in MRPL13 expression in LUAD. Subsequently, we analyzed the correlation between FOXM1 and MRPL13 across various cancers and created a correlation map. The results showed that MRPL13 was directly proportional to FOXM1 in BLCA (r=0.468), BRCA (r=0.406), LGG (r=0.318), LUAD (r=0.349), OV (r=0.487), PAAD (r=0.567), PRAD (r=0.28), STAD (r=0.5), and TGCT (r=0.694) (Supplementary Figure 7).

MRPL13 expression and functional analysis in LUAD

The above analysis results show that the expression level of MRPL13 is not only different between various tumor samples and normal tissues but also leads to the occurrence and development of many cancers. Given the comprehensive nature of these findings and the replication of previous studies, we deemed it necessary to conduct additional experiments to explore its differential expression in lung adenocarcinoma and normal tissues, as well as its general function in lung adenocarcinoma.

We began by investigating whether MRPL13 functions as a tumor-promoting factor in lung adenocarcinoma. Real-time fluorescence quantitative PCR was employed to examine the expression of 20 clinical samples of lung adenocarcinoma, confirming once more that compared with the normal tissue group, the expression of MRPL13 in the LUAD group was higher (Figure 12A). To confirm these results at the protein level, we employed western blotting to assess three representative specimens and immunohistochemistry to assess 50 pathological sections. The comprehensive evaluation score of MRPL13 protein was significantly different between the cancer tissue group and adjacent normal tissue group (Supplementary Material 6). The former is obviously higher than the latter (Figure 12B–12E). The expression score was independently assessed by three experienced pathologists and confirmed through independent inspection and analysis.

Figure 12. Expression of MRPL13 in cancer and normal tissues. (A) Fluorescence real-time quantitative PCR was used to detect the expression of MRPL13 in tumor tissues and normal tissues adjacent to cancer. (B) Western blot to verify the expression of MRPL13 in cancer and normal tissues adjacent to cancer (the experiment was repeated thrice). (C) immunohistochemistry score to verify the expression of MRPL13 in cancer and normal tissues adjacent to cancer. (D) Western blot representative picture. (E) Immunohistochemical representative pictures of cancer patients and normal patients (panorama above, detail below). *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001, and ****p-value < 0.0001.

We chose A549 and NCI-H1975 lung cancer cell lines for further experiments based on their expression of MRPL13 and experimental feasibility. We successfully knocked down MRPL13 expression in these cell lines using siRNA, as confirmed by RT-PCR analysis (Figure 13A).

Figure 13. Effect of MRPL13 down-regulation on the proliferation, cellcycle, apoptosis of LUAD. (A) MRPL13 knockdown validation in A549 and NCI-H1975. (B, C) CCK8 and Colony formation detection of the effect of down-regulation of MRPL13 expression on the proliferation of LUAD cells. (D) The percentage of apoptosis in control group and MRPL13 down-regulated group was analyzed by flow cytometry. (E) The effect of low expression of MRPL13 on cell cycle distribution was detected by flow cytometry. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001, and ****p-value < 0.0001.

CCK8 assays and colony-forming tests showed that MRPL13 knockdown significantly reduced the proliferation of both A549 and NCI-H1975 cells compared to the control groups (Figure 13B, 13C).

Additionally, MRPL13 knockdown led to a significantly higher percentage of apoptotic cells in both cell lines (Figure 13D). Flow cytometry analysis revealed that MRPL13 knockdown altered the cell cycle distribution in both A549 and NCI-H1975 cells. The percentage of cells in G1 phase in the MRPL13 knockout group increased, while the percentage of cells in S and G2 phases decreased. (Figure 13E). These results revealed that MRPL13 can promote the growth of tumor tissue by regulating the proliferation and apoptosis of lung adenocarcinoma cells.

The migration and invasion abilities of lung adenocarcinoma cells were evaluated by comparing the number of cells passing through the Transwell chamber, which demonstrated that MRPL13 knockout significantly reduced the ability of A549 and NCI-H1975 cells to migrate and invade. This finding was further confirmed by the scratch wound healing assay (Figure 14 and Supplementary Materials 7–10).

Figure 14. Effect of MRPL 13 down-regulation on the migration of LUAD. (A, B) The cell migration ability of MRPL13 knockout group and control group was compared by wound healing test (scale bar = 200 μm). (C–E) The cell migration ability of MRPL13 knockout group and control group was compared by transwell test (scale bar = 200 μm). (D–F) The cell invasion ability of MRPL 13 knockout group and control group was compared by transwell test (scale bar = 200 μm). **p-value < 0.01 and ****p-value < 0.0001.

Our findings demonstrate that MRPL13 knockout negatively impacted the cell activity, proliferation, periodic differentiation, apoptosis, migration, and invasion of lung adenocarcinoma cells. Thus, MRPL13 represents a potential therapeutic target for lung adenocarcinoma and other cancers.