PCBP1 regulates the transcription and alternative splicing of metastasis\u2011related genes and pathways in hepatocellular carcinoma

Shuai Huang,Li Jiang,Kai Luo,Xu-Dong Zhang,Ren-Feng Li,Ying-Hao Lv

doi:10.1038/s41598-021-02642-z

Shuai Huang, Li Jiang + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-02642-z

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Abstract

PCBP1 is a multifunctional RNA-binding protein (RBP) expressed in most human cells and is involved in posttranscriptional gene regulation. PCBP1 regulates the alternative splicing, translation and RNA stability of many cancer-related genes and has been identified as a potential tumour suppressor gene. PCBP1 inhibits the invasion of hepatocellular carcinoma (HCC) cells, but there are few studies on the specific regulatory target and mechanism of RBPs in HCC, and it is unclear whether PCBP1 plays a role in tumour metastasis as a splicing factor. We analysed the regulation of gene expression by PCBP1 at the transcriptional level. We obtained and analysed PCBP1-knockdown RNA-seq data and eCLIP-seq data of PCBP1 in HepG2 cells and found that PCBP1 widely regulates the alternative splicing and expression of genes enriched in cancer-related pathways, including extracellular matrix, cell adhesion, small molecule metabolic process and apoptosis. We validated five regulated alternative splicing events affected by PCBP1 using RT-qPCR and found that there was a significant difference in the expression of APOC1 and SPHK1 between tumour and normal tissues. In this study, we provided convincing evidence that human PCBP1 profoundly regulates the splicing of genes associated with tumour metastasis. These findings provide new insight into potential markers or therapeutic targets for HCC treatment.

Highlights

PCBP1 is a multifunctional RNA-binding protein (RBP) expressed in most human cells and is involved in posttranscriptional gene regulation
We downloaded original RNA sequencing (RNA-seq) reads of sh-PCBP1 cells (the PCBP1 gene was silenced by short-hairpin RNA) and control cells detected by RNA-seq from the ENCODE database[9]
As a feature-rich RBP, PCBP1 participates in mRNA metabolism regulation[16], and alterations in PCBP1 function accelerate tumour metastasis and p rogression[29]

Summary

Introduction

PCBP1 is a multifunctional RNA-binding protein (RBP) expressed in most human cells and is involved in posttranscriptional gene regulation. We provided convincing evidence that human PCBP1 profoundly regulates the splicing of genes associated with tumour metastasis These findings provide new insight into potential markers or therapeutic targets for HCC treatment. ES Exon skipping A5SS Alternative 5′ splice site A3SS Alternative 3′ splice site IR Intron retention MXE Mutually exclusive exons 5pMXE Mutually exclusive 5′UTRs 3pMXE Mutually exclusive 3′UTRs cDNA Complementary deoxyribonucleic acid GO Gene ontology KEGG Kyoto encyclopedia of genes and genomes RT-qPCR Quantitative reverse-transcription polymerase chain reaction PCA Principal component analysis TPM Tags per million TNF Tumor necrosis factor ECM Extracellular matrix CAMs Cell adhesion molecules ANOVA Analysis of variance HOMER Hypergeometric optimization of motif enrichment APOC1 Apolipoprotein C1 SPHK1 Sphingosine kinase-1 IP6K2 The inositol hexakisphosphate kinase[6] TCGA The cancer genome atlas program CKB Creatine kinase, brain-type PTK2 Protein tyrosine kinase 2 EGFR Epidermal growth factor receptor TRAF2 TNF receptor associated factor 2 NIR Non-intron-retention regulated. There is an urgent need to deeply analyse the pathogenesis of HCC and explore molecular markers and therapeutic targets to improve the therapeutic effect[5,6]

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