Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma

Chaoran Zheng,Shicheng Yu

doi:10.1186/s12920-021-00878-2

Abstract

BackgroundSmall nucleolar RNA host gene 1 (SNHG1), a long noncoding RNA (lncRNA), is a transcript that negatively regulates tumour suppressor genes, such as p53. Abnormal SNHG1 expression is associated with cell proliferation and cancer. We used sequencing data downloaded from Genomic Data Commons to analyse the expression and interaction networks of SNHG1 in hepatocellular carcinoma (HCC).MethodsExpression was examined using the limma package of R and verified by Gene Expression Profiling Interactive Analysis. We also obtained miRNA expression data from StarBase to determine the lncRNA-miRNA-mRNA–related RNA regulatory network in HCC. Kaplan–Meier (KM) analysis was performed using the survival package of R. Gene Ontology annotation of genes was carried out using Metascape.ResultsWe found that SNHG1 was overexpressed and often amplified in HCC patients. In addition, SNHG1 upregulation was associated with the promotion of several primary biological functions, including cell proliferation, transcription and protein binding. Moreover, we found similar trends of small nucleolar RNA host gene 1 (SNHG1), E2F8 (E2F transcription factor 8), FANCE (FA complementation group E) and LMNB2 (encodes lamin B2) expression. In the SNHG1-associated network, high expression levels of SNHG1 (log-rank P value = 0.0643), E2F8 (log-rank P value = 0.000048), FANCE (log-rank P value = 0.00125) and LMNB2 (log-rank P value = 0.0392) were significantly associated with poor survival. Single-cell analysis showed that E2F8 may play an important role in tumorigenesis or cancer development.ConclusionsOur results highlight the benefit of utilizing multiple datasets to understand the functional potential regulatory networks of SNHG1 and the role of SNHG1 in tumours.

Highlights

Small nucleolar RNA host gene 1 (SNHG1), a long noncoding RNA, is a transcript that negatively regulates tumour suppressor genes, such as p53
Biological interaction networks in hepatocellular carcinoma (HCC) We sought to determine the biological interaction networks in HCC by using internally incorporated miRNA-messenger RNAs (mRNAs) and miRNA-long noncoding RNA (lncRNA) interactions, and we identified seven mRNA-miRNA-lncRNA networks (Fig. 2)
All the Competing endogenous RNAs (ceRNAs) networks share similar regulation of all miRNAs interacting with the lncRNA-mRNA pairs

Summary

Introduction

Small nucleolar RNA host gene 1 (SNHG1), a long noncoding RNA (lncRNA), is a transcript that negatively regulates tumour suppressor genes, such as p53. Abnormal SNHG1 expression is associated with cell proliferation and cancer. We used sequencing data downloaded from Genomic Data Commons to analyse the expression and interaction networks of SNHG1 in hepatocellular carcinoma (HCC). Hepatocellular carcinoma (HCC) is the most common histological type of primary liver cancer, occurring in 75–85% of patients with primary liver cancer, and Africa and Asia have the highest incidences [1, 2]. Medical practice has changed rapidly in the last few years with the aid of rapidly expanding genome sequencing techniques [5], and precision medicine is gradually becoming an emerging field in the treatment and prevention of diseases. Medical researchers have overcome the challenges of assessing large amounts of data, the application of genetic testing in cancer treatment is progressing slowly. A primary reason for this slow progress is that large amounts of accumulated patient data are independent and discrete.

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