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Updated: Mar 17, 2026
An In Vitro Protocol for Evaluating MicroRNA Levels, Functions, and Associated Target Genes in Tumor Cells
Published on: May 21, 2019
Integrative microRNA-mRNA and protein-protein interaction analysis in pancreatic neuroendocrine tumors
1Department of Anesthesia, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China. gscfwid@gmail.com.
Objective:
Pancreatic neuroendocrine tumors are relatively rare pancreatic neoplasms over the world. Investigations of the molecular biology of PNETs are insufficient for nowadays. We aimed to explore the expression of microRNA and messenger RNA and regulatory processes underlying pancreatic neuroendocrine tumors.
Materials And Methods:
The messenger RNA and microRNA expression profile of GSE43796 were downloaded, including 6 samples with pancreatic neuroendocrine tumors and 5 healthy samples. First, the Limma package was utilized to distinguish the differentially expressed messenger RNA and microRNA separately. Then we used microRNA Walk databases to predict the target genes of the differentially expressed microRNAs (DE-microRNAs), and selected differentially expressed target genes whose expression was reversely correlated with microRNAs. Gene Ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed to explore the functions and pathways of target genes. In addition, we constructed a regulatory miRNAs-target genes network and a protein-protein interaction network.
Results:
There were 28 differentially expressed microRNAs and 859 differentially expressed messenger RNAs, including 253 potential target genes. These target genes mainly enriched in ABC transporters pathway. In this network, hsa-miR-7-2-3p demonstrated the highest connectivities whereas KLF12 was the mRNAs with the highest connectivities. CXCL12 was identified as the hub of the protein-protein interaction sub-network.
Conclusions:
The genes involved in ABC transporters and Type II diabetes mellitus pathway, KLF12 and CXCL12 may play an important role in the progression of pancreatic neuroendocrine tumors. However, more experimental studies are required.
Insights
This study investigated microRNA and messenger RNA in pancreatic neuroendocrine tumors (PNETs). Key genes KLF12 and CXCL12, and the ABC transporters pathway, are implicated in PNET progression.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Pancreatic neuroendocrine tumors (PNETs) are rare and their molecular biology is not well understood.
- Current research lacks comprehensive molecular profiling of PNETs.
Purpose of the Study:
- To explore microRNA (miRNA) and messenger RNA (mRNA) expression in PNETs.
- To identify regulatory networks and pathways involved in PNET development.
Main Methods:
- Downloaded miRNA and mRNA expression profiles (GSE43796) from PNET and healthy samples.
- Utilized Limma package for differential expression analysis.
- Predicted miRNA-target gene interactions and constructed regulatory and protein-protein interaction networks.
Main Results:
- Identified 28 differentially expressed miRNAs and 859 differentially expressed mRNAs.
- Discovered 253 target genes, predominantly enriched in the ABC transporters pathway.
- Identified hsa-miR-7-2-3p, KLF12, and CXCL12 as key regulatory molecules.
Conclusions:
- KLF12 and CXCL12, along with the ABC transporters pathway, may be crucial in PNET progression.
- Further experimental validation is necessary to confirm these findings.
