Abstract
MYC is an oncogene responsible for excessive cell growth in cancer, enabling transcriptional activation of genes involved in cell cycle regulation, metabolism, and apoptosis, and is usually overexpressed in gastric cancer (GC). By using siRNA and Next-Generation Sequencing (NGS), we identified MYC-regulated differentially expressed Genes (DEGs) in three Brazilian gastric cancer cell lines representing the histological subtypes of GC (diffuse, intestinal, and metastasis). The DEGs were picked using Sailfish software, followed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using KEGG. We found 11 significantly enriched gene sets by using enrichment score (ES), False Discovery Rate (FDR), and nominal P-values. We identified a total of 5.471 DEGs with correlation over (80%). In diffuse-type and in metastatic GC cell lines, MYC-silencing caused DEGs downregulation, while the intestinal-type GC cells presented overall DEGs upregulation after MYC siRNA depletion. We were able to detect 11 significant gene sets when comparing our samples to the hallmark collection of gene expression, enriched mostly for the following hallmarks: proliferation, pathway, signaling, metabolic, and DNA damage response. When we analyzed our DEGs considering KEGG metabolic pathways, we found 12 common branches covering a wide range of biological functions, and three of them were common to all three cell lines: ubiquitin-mediated proteolysis, ribosomes, and system and epithelial cell signaling in Helicobacter pylori infection. The GC cell lines used in this study share 14 MYC-regulated genes, but their gene expression profile is different for each histological subtype of GC. Our results present a computational analysis of MYC-related signatures in GC, and we present evidence that GC cell lines representing distinct histological subtypes of this disease have different MYC-regulated expression profiles but share a common core of altered genes. This is an important step towards the understanding of MYC's role in gastric carcinogenesis and an indication of probable new drug targets in stomach cancer.
Highlights
Gastric cancer (GC) remains as an important cause of cancerrelated morbidity and mortality worldwide, with recent estimates accounting for over 950.000 new diagnosis and 720.000 deaths each year [1]
We used next-generation sequencing based in semiconductors, as well as RNA-Seq, to quantify the transcripts and its isoforms in three gastric cancer cell lines, ACP02, ACP03, and AGP01, before and after MYC-silencing using Small interfering RNAs (siRNA)
The use of siRNA to reduce MYC expression in the three gastric cancer cell line used in this study was very effective, reducing MYC mRNA expression in 73% for AGP01, in 84% for ACP02, and in 77% for ACP03
Summary
Gastric cancer (GC) remains as an important cause of cancerrelated morbidity and mortality worldwide, with recent estimates accounting for over 950.000 new diagnosis and 720.000 deaths each year [1]. MYC amplification and overexpression are present in 6-58% of all sporadic gastric tumors [4,5,6], being more frequent in Brazilian samples [7,8,9], usually as a result from gene amplification and chromosomal translocations [2, 10]. We established and characterized three GC cell lines, AGP01, ACP02, and ACP03, obtained from intestinal-type GC metastasis, diffuse-type GC, and intestinal-type GC, respectively (Leal et al 2009). Those cell lines carry genetic alterations commonly found in Brazilian GC patients, such as MYC amplification and overexpression and TP53 deletion [7, 13, 16]
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