Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features.

Russi Russi,Zoppoli Zoppoli,Musto Musto,Felice Felice,Laurino Laurino,Rocca Rocca,Lapadula Lapadula,Ruggieri Ruggieri,Amendola Amendola,Falco Falco,Compare Compare,Calice Calice,Nardone Nardone

doi:10.3390/cancers11091248

Abstract

Gastric cancer (GC) is a leading cause of cancer-related deaths in the world. Molecular heterogeneity is a major determinant for the clinical outcomes and an exhaustive tumor classification is currently missing. Histologically normal tissue adjacent to the tumor (NAT) is commonly used as a control in cancer studies, nevertheless a recently published paper described the unique characteristics of the NAT in several tumor types. Little is known about the global gene expression profile of gastric NAT (gNAT) which could be an effective tool for a more realistic definition of GC molecular signature. Here, we integrated data of 512 samples from the Genotype-Tissue Expression project (GETx) and The Cancer Genome Atlas (TCGA) to analyze the transcriptome of healthy gastric tissues, gNAT, and GC samples. We validated TCGA-GETx data mining through inHouse gNAT and GC expression dataset. Differential gene expression together with pathway enrichment analyses, indeed, led to different results when using the gNAT or the healthy tissue as control. Based on our analyses, gNAT showed a peculiar gene signature and biological features, like the estrogen receptor pathways activation, suggesting a molecular behavior partially different from both healthy and GC tissues. Therefore, using gNAT as healthy control tissue in the characterization of tumor associated biological processes and pathways could lead to suboptimal results.

Highlights

Gastric cancer (GC) was the third leading cause of cancer mortality in 2018, responsible for783,000 deaths and of a poor 5-year survival in case of an advanced stage diagnosis or metastatic disease [1,2]
We assessed differential batch effects and we verified datasets comparability by evaluating the expression and variation of housekeeping genes [18]. We correlated their median expression levels across all samples and we found a high degree of agreement between the two datasets (Pearson R = 0.95, p-value
We considered statistically significant the gene sets resulting from the analysis of The Cancer Genome Atlas (TCGA)-Genotype-Tissue Expression project (GETx) data with a FDR adjusted p-value < 0.05 while, to compensate the relative lower number of samples in the inHouse dataset, we accepted p-value < 0.05 as threshold. single sample gene set enrichment analysis (ssGSEA) implemented in the GSVA [41] package was used to score samples according to the normalized counts of the genes on MSigDB Hallmark and GO gene sets

Summary

Introduction

Gastric cancer (GC) was the third leading cause of cancer mortality in 2018, responsible for783,000 deaths (http://www.who.int/news-room/fact-sheets/detail/cancer) and of a poor 5-year survival in case of an advanced stage diagnosis or metastatic disease [1,2]. This assumption could not be applied to histologically normal adjacent tumor (NAT). It is well known that many molecular differences (versus normal tissues) characterize NAT such as allelic imbalance, telomere length [5], as well as transcriptomic and epigenetic aberrations [6]. The NAT tissue can be considered an intermediate, morphologically normal but molecularly altered pre-neoplastic state and these changes are evident up to 1 cm from the margins of the tumor [7]. About breast NAT, recent studies reported that the tumor microenvironment is essential for recurrence prediction and surgical strategies setting [8] and that, interestingly, NAT tissue is enriched for stromal [9] and wound response pathways [10]. It has been highlighted that breast NAT tissue undergoes wound healing-like processes, extracellular matrix remodeling and an epithelial-to-mesenchymal transition (EMT) [11]

Methods

Results

Discussion

Conclusion