Expression Signature of the AT-Rich Interactive Domain Gene Family Identified in Digestive Cancer.

Yongqu Lu,Wendong Wang,Xin Chen,Wei Fu,Xin Zhou,Zhenzhen Liu

doi:10.3389/fmed.2021.775357

Yongqu Lu, Wendong Wang + Show 4 more

Open Access

https://doi.org/10.3389/fmed.2021.775357

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Abstract

BackgroundThe AT-rich interactive domain (ARID) gene family of 15 proteins has an important role in development and proliferation. Gene expression alterations of the ARID family are correlated with the pathogenesis of digestive cancer, but systematic research has not been conducted.MethodsWe obtained transcriptome sequencing data, clinical characteristics and stemness indices of the seven main types of digestive cancer (cholangiocarcinoma, colon adenocarcinoma, oesophageal carcinoma, liver hepatocellular carcinoma, pancreatic adenocarcinoma, rectum adenocarcinoma and stomach adenocarcinoma) from public pan-cancer data to combine the analysis of the expression and prognostic signature of the ARID gene family. The stromal and immune scores for each sample were calculated to explore the correlations between the ARID gene family members and the tumour microenvironment.ResultsAfter screening, 1,920 digestive cancer samples were included in our study. ARID3C was expressed at low levels throughout the digestive cancer samples. The expression levels of ARID1A and JARID1C were relatively high, but there was striking heterogeneity across the different cancer types for specific family members. The survival analysis indicated that many genes were significantly related to the prognosis of patients with liver hepatocellular carcinoma. The stemness indices, stromal score, and immune score analysis showed that the expression of a single ARID gene had characteristic consistency in each tumour, but the levels among the different genes still varied.ConclusionOur systematic study of the ARID gene family and its association with the immune infiltrate, tumour microenvironment and outcomes of digestive cancer patients focus on the complex relations and indicate the need to study each ARID member as an individual in a specific cancer type.

Highlights

Proteins with AT-rich interactive domains (ARIDs), which are helix–turn–helix motif-based DNA-binding domains spanning ∼100 amino acid residues, constitute a highly conserved family
The expression profiles, including the RNA sequencing data, and the corresponding clinical data, including tumour-nodemetastasis (TNM) stage, stemness scores based on mRNA (RNAss), stemness scores based on DNA methylation (DNAss), and immune subtypes of cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), oesophageal carcinoma (ESCA), liver hepatocellular carcinoma (LIHC), pancreatic adenocarcinoma (PAAD), rectum adenocarcinoma (READ) and stomach adenocarcinoma (STAD) patients, were downloaded from the Xena platform, which integrates cancer genomic and clinical resources [17]
To better understand the intrinsic expression pattern of the ARID genes, we explored the expression levels of the ARID family members in seven digestive cancer types that were available in the The Cancer Genome Atlas (TCGA) RNA sequencing profile

Summary

Introduction

Proteins with AT-rich interactive domains (ARIDs), which are helix–turn–helix motif-based DNA-binding domains spanning ∼100 amino acid residues, constitute a highly conserved family. ARID Family in Digestive Cancer range of DNA interactions [2]. Members of the ARID family are involved in the modification of chromatin structure and regulate the expression of specific genes that are directly associated with cellular growth, differentiation, and development [5, 6]. The AT-rich interactive domain (ARID) gene family of 15 proteins has an important role in development and proliferation. Gene expression alterations of the ARID family are correlated with the pathogenesis of digestive cancer, but systematic research has not been conducted

Methods

Results

Conclusion