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other·oncology, gastroenterology, molecular biology, bioinformatics, immunology·PMC10041708

Integrated pan-cancer analysis and experimental verification of the roles of tropomyosin 4 in gastric cancer

Frontiers in Immunology · 9 authors, 2 centres

AI SUMMARY

FIDELITY 100%

POPULATIONPatients with pan-cancer (including gastric cancer) from TCGA, GTEx, and other public databases; in vitro experiments used AGS and BGC-823 human gastric cancer cell lines.

INTERVENTIONBioinformatics analysis of TPM4 expression, genetic/epigenetic alterations, immune infiltration, drug sensitivity; in vitro TPM4 knockdown via shRNA lentivirus.

COMPARISONHigh vs. low TPM4 expression groups; tumor vs. normal tissues; TPM4 knockdown vs. control in cell lines.

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TL;DR

This study investigates tropomyosin 4 (TPM4) across multiple cancer types using bioinformatics, with a focus on gastric cancer (GC). TPM4 is upregulated in most cancers, correlates with poor prognosis in several digestive tract malignancies including GC, and is associated with immune infiltration, DNA methylation, and drug sensitivity. Experimental validation shows that TPM4 knockdown reduces GC cell migration and invasion, suggesting it promotes tumor progression potentially through extracellular matrix remodeling.

Full summary

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**Background:** Gastric cancer (GC) is the fifth most common cancer and third leading cause of cancer death globally. Tropomyosin 4 (TPM4), an actin-binding protein, has been implicated in several malignancies including breast, colon, and liver cancers, but its role in GC and across cancer types was not comprehensively characterized. This study aimed to perform a pan-cancer analysis of TPM4 and validate its function in GC.

**Methods:** The authors used multiple public databases: UCSC Xena, TCGA, GTEx, TIMER2.0, GEPIA, cBioPortal, UALCAN, and others. TPM4 mRNA expression was analyzed in 15,776 samples (TCGA+GTEx) and 15,043 paired tumor-normal samples. Prognostic value was assessed using Cox regression and Kaplan-Meier analysis. Diagnostic value was evaluated by ROC curves. Genetic alterations were examined in 2,565 pan-cancer patients via cBioPortal. DNA methylation was analyzed using UALCAN and MethSurv. mRNA modification correlations with 45 regulators (m1A, m5C, m6A) were assessed. Immune infiltration was evaluated using EPIC, ESTIMATE, and TIMER2.0. Correlations with immune checkpoint genes, TMB, MSI, and neoantigens were computed. A lncRNA-miRNA-TPM4 regulatory network was constructed using RNA22, miRWalk, miRDB, Starbase 2.0, and Cytoscape. Drug sensitivity was analyzed via GSCALite, GDSC, CTRP, and CMap. Gene Ontology and KEGG enrichment were performed on co-expressed genes. In vitro, AGS and BGC-823 GC cells were used with TPM4 knockdown via shRNA lentivirus (knockdown efficiency 71.1%). Wound healing and Matrigel transwell assays assessed migration and invasion.

**Key Results:** TPM4 was significantly upregulated (P<0.05) in 19 cancer types including STAD, and downregulated in 11 types. High TPM4 expression was associated with poor overall survival in ACC, CESC, CHOL, DLBC, ESCC, HNSC, KIRC, KIRP, LIHC, LUAD, LUSC, MESO, PAAD, STAD, UCEC, and UVM (HR>1, P<0.05). In digestive cancers, TPM4 had certain diagnostic accuracy for COAD (AUC=0.807), COADREAD (AUC=0.837), ESCA (AUC=0.725), LIHC (AUC=0.739), STAD (AUC=0.795), and high accuracy for PAAD (AUC=0.972). Genetic alterations in TPM4 occurred in 5% of pan-cancer samples (131/2565), with the highest mutation rate in ovarian cancer (>60%). TPM4 was hypomethylated in STAD, and 25 CpG sites were identified. TPM4 expression positively correlated with most m1A, m5C, and m6A methylation regulators across cancers. In STAD, top correlated regulators included METTL14 (r=0.403), YTHDF3 (r=0.421), and FTO (r=0.399). TPM4 expression correlated with immune cell infiltration in multiple cancers and was positively associated with ESTIMATE scores in STAD. TPM4 positively correlated with eight immune checkpoint genes (CD274, CTLA4, HAVCR2, LAG3, PDCD1, TIGIT, etc.) in multiple cancers. TPM4 expression was positively associated with TMB in ACC, UCSC, GBM, PAAD, and STAD; with MSI in TGCT, SARC, ACC, UVM, and STAD; and with neoantigens in ACC, TGCT, DLBC, PCPG, and THCA. A ceRNA network was constructed with four miRNAs (hsa-miR-338-3p, hsa-miR-30e-5p, hsa-miR-30b-5p, hsa-miR-206) and their target lncRNAs. Drug sensitivity analysis showed TPM4 expression correlated with sensitivity to docetaxel and 5-fluorouracil. Eight small molecule drugs were identified from CMap, with rucaparib having the highest absolute connectivity score. GO and KEGG enrichment revealed ECM-related pathways. Top hub genes included COL1A2, COL3A1, FN1, MMP2, and LUM. In vitro, TPM4 knockdown significantly inhibited migration (P<0.01) and invasion (P<0.01) in both AGS and BGC-823 cells.

**Clinical Implications:** TPM4 is a promising biomarker for diagnosis, prognosis, and immunotherapy response prediction across multiple cancers including GC. Its association with docetaxel and 5-fluorouracil sensitivity suggests potential as a chemotherapy response predictor. The identified ceRNA network provides insight into GC regulatory mechanisms. TPM4's role in promoting migration and invasion, likely through ECM remodeling, identifies it as a potential therapeutic target. However, clinical trial validation is needed before clinical application.

PICO

PPOPULATION

Patients with pan-cancer (including gastric cancer) from TCGA, GTEx, and other public databases; in vitro experiments used AGS and BGC-823 human gastric cancer cell lines.

IINTERVENTION

Bioinformatics analysis of TPM4 expression, genetic/epigenetic alterations, immune infiltration, drug sensitivity; in vitro TPM4 knockdown via shRNA lentivirus.

OOUTCOME

TPM4 expression levels, overall survival, diagnostic accuracy (AUC), immune cell infiltration, TMB, MSI, NEO, drug sensitivity, cell migration and invasion.

STUDY TYPE

other

SPECIALTY

oncology

SUMMARISED BY

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FIDELITY CHECK

100% · A

ORIGINAL PAPER

PMC10041708

Integrated pan-cancer analysis and experimental verification of the roles of tropomyosin 4 in gastric cancer

Frontiers in Immunology

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ABSTRACT

Abstract Objective To investigate the function of tropomyosin 4 (TPM4) using pan-cancer data, especially in gastric cancer (GC), using comprehensive bioinformatics analysis and molecular experiments. Methods We used UCSC Xena, The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), TIMER2.0, GEPIA, cBioPortal, Xiantao tool, and UALCAN websites and databases for the extraction of pan-cancer data on TPM4. TPM4 expression was investigated with respect to prognosis, genetic alterations, epigenetic alterations, and immune infiltration. RNA22, miRWalk, miRDB, Starbase 2.0, and Cytoscape were used for identifying and constructing the regulatory networks of lncRNAs, miRNAs, and TPM4 in GC. Data from GSCALite, drug bank databases, and Connectivity Map (CMap) were used to analyze the sensitivity of drugs dependent on TPM4 expression. Gene Ontology (GO), enrichment analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG), wound healing assays, and (Matrigel) transwell experiments were used to investigate the biological functions of TPM4 in GC. Result The findings of the comprehensive pan-cancer analysis revealed that TPM4 has a certain diagnostic and prognosis value in most cancers. Alterations in the expression of TPM4, including duplications and deep mutations, and epigenetic alterations revealed that TPM4 expression is related to the expression of DNA methylation inhibitors and RNA methylation regulators at high concentrations. Besides, TPM4 expression was found to correlate with immune cell infiltration, immune checkpoint (ICP) gene expression, the tumor mutational burden (TMB), and microsatellite instability (MSI). Neoantigens (NEO) were also found to influence its response to immunotherapy. A lncRNA-miRNA -TPM4 network was found to regulate GC development and progression. TPM4 expression was related to docetaxel,5-fluorouracil, and eight small molecular targeted drugs sensitivity. Gene function enrichment analyses revealed that genes that were co-expressed with TPM4 were enriched within the extracellular matrix (ECM)-related pathways. Wound-healing and (Matrigel) transwell assays revealed that TPM4 promotes cell migration and invasion. TPM4, as an oncogene, plays a biological role, perhaps via ECM remodeling in GC. Conclusions TPM4 is a prospective marker for the diagnosis, treatment outcome, immunology, chemotherapy, and small molecular drugs targeted for pan-cancer treatment, including GC treatment. The lncRNA-miRNA-TPM4network regulates the mechanism underlying GC progression. TPM4 may facilitate the invasion and migration of GC cells, possibly through ECM remodeling. Keywords: tropomyosin 4, pan-cancer, gastric cancer, integrative analysis, immune infiltrating, experiment

CITATION EXPORT

Qijing Guo, Linglin Zhao, Nan Yan et al.. Integrated pan-cancer analysis and experimental verification of the roles of tropomyosin 4 in gastric cancer. Frontiers in Immunology. (2023). https://doi.org/10.3389/fimmu.2023.1148056

AUTHORS

9 · 2 CENTRES

Qijing Guo, Linglin Zhao, Nan Yan, Yan Li, Cuiping Guo, Shengyan Dang, Xianliang Shen, Jianfang Han, Yushuang Luo

1 Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinhai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, China
2 Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China