Integrated Chromatin Accessibility and Transcriptome Landscapes of 5-Fluorouracil-Resistant Colon Cancer Cells.

Bishu Zhang,Xiaxing Deng,Jiaqiang Zhang,Jiewei Lin,Xuelong Wang

doi:10.3389/fcell.2022.838332

Abstract

Background: 5-Fluorouracil (5-FU) is one of the most effective and widely used chemotherapeutic drugs in the treatment of colon cancer, yet chemoresistance is a common feature of colon cancer treatment, resulting in poor prognosis and short survival. Dynamic reprogramming of chromatin accessibility is crucial for proper regulation of gene transcription associated with cancer drug resistance by providing the gene regulatory machinery with rapid access to the open genomic DNA. Methods: Here, we explored the global chromatin accessibility and transcription changes by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with transcriptome sequencing of both parental and 5-FU-resistant HCT15 cells, followed by integrative analysis to better understand the regulatory network underlying 5-FU resistance in colon cancer cells. Results: A total of 3,175 differentially expressed mRNAs (DEGs), lncRNAs (DELs), and miRNAs (DEMs) related to 5-FU resistance were identified, including significantly upregulated IL33, H19, and miR-17-5p; the downregulated AKR1B10, LINC01012, and miR-125b-5p; and chromatin modifiers such as INO80C, HDAC6, and KDM5A. The construction of the ceRNA regulatory network revealed that H19, HOXA11-AS, and NEAT1 might function as ceRNAs associated with 5-FU resistance in HCT15 cells. Moreover, 9,868 differentially accessible regions (DARs) were obtained, which were positively (r = 0.58) correlated with their nearest DEGs and DELs. The upregulated genes related to 4,937 hyper-accessible regions were significantly enriched in signaling pathways of MAPK, FOX, and WNT, while the 4,931 hypo-accessible regions were considered to be involved in declined biosynthesis of amino acids and nucleotide sugars, signaling pathways of Notch, and HIF-1. Analyses of the DAR sequences revealed that besides the AP-1 family, the TF motifs of FOX and KLF family members were highly enriched in hyper- and hypo-accessible regions, respectively. Finally, we obtained several critical TFs and their potential targets associated with DARs and 5-FU resistance, including FOXA1 and KLF3. Conclusion: These data provided clear insights and valuable resources for an improved understanding of the non-genetic landscape of 5-FU-resistant colon cancer cells based on chromatin accessibility and transcript levels, which allowed for genome-wide detection of TF binding sites, potential cis-regulatory elements and therapeutic targets.

Highlights

Colon cancer, a type of cancer that starts in the colon, is the third leading cause of cancer-related deaths worldwide, showing higher morbidity due to its aggressive behavior, poor prognosis, and lack of targeted treatments (Dekker et al, 2019; Sung et al, 2021)
Gene set enrichment analysis (GSEA) using “clusterProfiler” (Yu et al, 2012) and WebGestalt (Wang et al, 2013) revealed that the upregulated Differential expression genes (DEGs) in HCT15FR cells were mainly enriched for gene sets associated with TNFa signaling via the NF-kB, signaling pathways of p53, IL2STAT5, and KRAS, while those of the downregulated DEGs were associated with gene sets linked to mTORC1 signaling, xenobiotic, and glutathione metabolism (Figures 1D–F, Supplementary Figure S2C)
We performed GO analysis to elucidate the biological processes, which indicated that the regulation of secretion, programmed cell death, and epithelial to mesenchymal transition was upregulated, while the protein targeting the membrane, peptide, and the biosynthetic process was downregulated in HCT15-FR cells (Supplementary Figures S2A, B)

Summary

Introduction

A type of cancer that starts in the colon, is the third leading cause of cancer-related deaths worldwide, showing higher morbidity due to its aggressive behavior, poor prognosis, and lack of targeted treatments (Dekker et al, 2019; Sung et al, 2021). Over the past four decades, a more detailed understanding of the mechanisms of 5-FU transport, activation, action, and catabolism have led to the development of strategies that increase its anti-cancer activity (Hu et al, 2016; Blondy et al, 2020; Raskov et al, 2020). Despite these advances, drug resistance after chemotherapy remains a major limitation to the clinical application of 5-FU (Vodenkova et al, 2020; Sethy and Kundu 2021). Overcoming 5-FU resistance would represent a major therapeutic advance

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Discussion

Conclusion