Identification of EMT-related alternative splicing event of TMC7 to promote invasion and migration of pancreatic cancer

Objective Epithelial-to-mesenchymal transition (EMT) is tightly associated with the invasion and metastasis of pancreatic cancer with rapid progression and poor prognosis. Notably, gene alternative splicing (AS) event plays a critical role in regulating the progression of pancreatic cancer. Therefore, this study aims to identify the EMT-related AS event in pancreatic cancer. Methods The EMT-related gene sets, transcriptomes, and matched clinical data were obtained from the MSigDB, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. Key gene AS events associated with liver metastasis were identified by prognostic analysis, gene set variation analysis (GSVA), and correlation analysis in pancreatic cancer. The cell line and organoid model was constructed to evaluate these key gene AS events in regulating pancreatic cancer in vitro. Furthermore, we established an EMT-related gene set consisting of 13 genes by prognostic analysis, the role of which was validated in two other databases. Finally, the human pancreatic cancer tissue and organoid model was used to evaluate the correlation between the enrichment of this gene set and liver metastasis. Results Prognostic analysis and correlation analysis revealed that eight AS events were closely associated with the prognosis of pancreatic cancer. Furthermore, the expression of TMC7 and CHECK1 AS events was increased in the metastatic lesions of the human tissue and organoid model. Additionally, the knockdown of exon 17 of TMC7 significantly inhibited the proliferation, invasion, and migration of pancreatic cancer cells in 2D and 3D cell experiments. Finally, the expression of exon 17 of TMC17 exhibited a significant correlation with the poor prognosis in pancreatic ductal adenocarcinoma (PDAC). Conclusion The AS events of TMC7 and CHECK1 were associated with liver metastasis in pancreatic cancer. Moreover, exon 17 of TMC7 could be a potential therapeutic target in pancreatic cancer.

[1]  Jiang Chang,et al.  Aberrant RNA splicing is a primary link between genetic variation and pancreatic cancer risk. , 2022, Cancer Research.

[2]  C. Ghigna,et al.  A ligand-insensitive UNC5B splicing isoform regulates angiogenesis by promoting apoptosis , 2021, Nature Communications.

[3]  N. Yin,et al.  Signature of gene aberrant alternative splicing events in pancreatic adenocarcinoma prognosis , 2021, Journal of Cancer.

[4]  Xiao Jiang,et al.  Long non-coding RNA MIR4713HG aggravates malignant behaviors in oral tongue squamous cell carcinoma via binding with microRNA let-7c-5p , 2021, International Journal of Molecular Medicine.

[5]  I. Endo,et al.  Annexin A1 Expression Is Associated with Epithelial–Mesenchymal Transition (EMT), Cell Proliferation, Prognosis, and Drug Response in Pancreatic Cancer , 2021, Cells.

[6]  G. Rätsch,et al.  Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3. , 2021, Genomics.

[7]  Jia Bi,et al.  Prognostic alternative splicing signature reveals the landscape of immune infiltration in Pancreatic Cancer , 2020, Journal of Cancer.

[8]  J. Valle,et al.  Pancreatic cancer , 2020, The Lancet.

[9]  J. Mayerle,et al.  Current Strategies and Future Perspectives for Precision Medicine in Pancreatic Cancer , 2020, Cancers.

[10]  Bo Chen,et al.  The lncRNA ENSG00000254041.1 promotes cell invasiveness and associates with poor prognosis of pancreatic ductal adenocarcinoma , 2020, Aging.

[11]  A. Jemal,et al.  Cancer statistics, 2020 , 2020, CA: a cancer journal for clinicians.

[12]  T. Donahue,et al.  Pancreatic Cancer. , 2019, JAMA.

[13]  Weifeng Hong,et al.  Genome-Wide Profiling of Prognostic Alternative Splicing Pattern in Pancreatic Cancer , 2019, Front. Oncol..

[14]  Yuanchi Weng,et al.  Long non-coding RNA LINC01133 silencing exerts antioncogenic effect in pancreatic cancer through the methylation of DKK1 promoter and the activation of Wnt signaling pathway , 2019, Cancer biology & therapy.

[15]  Chonghui Cheng,et al.  CD44 splice isoform switching determines breast cancer stem cell state , 2019, Genes & development.

[16]  S. Gong,et al.  Identification of candidate diagnostic and prognostic biomarkers for pancreatic carcinoma , 2019, EBioMedicine.

[17]  P. Vigneri,et al.  Insulin Receptor Isoforms in Cancer , 2018, International journal of molecular sciences.

[18]  N. Lee,et al.  Aberrant RNA Splicing in Cancer and Drug Resistance , 2018, Cancers.

[19]  Steven J. M. Jones,et al.  Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients , 2018, Cancer cell.

[20]  Adam Godzik,et al.  The Functional Impact of Alternative Splicing in Cancer. , 2017, Cell reports.

[21]  Icgc,et al.  Pan-cancer analysis of whole genomes , 2017, bioRxiv.

[22]  Qian Wang,et al.  The epithelial to mesenchymal transition (EMT) and cancer stem cells: implication for treatment resistance in pancreatic cancer , 2017, Molecular Cancer.

[23]  Gloria M. Sheynkman,et al.  Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing , 2016, Cell.

[24]  Jaime Rodriguez-Canales,et al.  A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition , 2015, Clinical Cancer Research.

[25]  Mark Rosenzweig,et al.  Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. , 2015, Cancer discovery.

[26]  K. Lillemoe,et al.  Pancreatic Ductal Adenocarcinoma: Is There a Survival Difference for R1 Resections Versus Locally Advanced Unresectable Tumors? What Is a “True” R0 Resection? , 2013, Annals of surgery.

[27]  Michael Peyton,et al.  An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance , 2012, Clinical Cancer Research.

[28]  C. Rinker-Schaeffer,et al.  Metastasis-suppressor genes: a review and perspective on an emerging field. , 2000, Journal of the National Cancer Institute.

[29]  Yi Pan,et al.  miR-193a-5p promotes pancreatic cancer cell metastasis through SRSF6-mediated alternative splicing of OGDHL and ECM1. , 2020, American journal of cancer research.