**4. Gene-expression signatures as markers for cancer grades and stages**

Cui et al. [43] developed for the first time a computational study aimed to identify a set of genes whose expression patterns can distinguish among gastric cancers of different grades, with the aim of developing a gene expression-based grading system for gastric cancer.

A total of 452 genes were found to be differentially expressed in the 54 gastric cancer specimens studied. It was revealed that genes whose expression changes correlated with the degree of differentiation are highly enriched among secreted/membrane proteins, involved in signaling pathways (ErbB, FAS, NOD-like receptor, PPAR and Wnt signaling), as well as cell adhesion molecules (CAMs) and tight junctions.

The researchers identified a 19-gene group that can distinguish between well versus poorly differentiated tumors (overall agreement at 79.2%), based on the expression fold change in cancer versus control tissues. The protein products of these 19 genes mentioned above are involved in cell growth, differentiation (IL17RB, SMYD1, SHCBP1), and motility (ACTG2), angiogenesis (ADIPOQ), tumorigenesis (ECRG4), matrix protein synthesis (COL3A1, COL6A3), and extracellular communication.

Moreover, there is a 198-gene group which can distinguish among the four different cancer grades (well-, moderate-, poorly-, and un-differentiated) and the control group according to their gene expression (74.2% accuracy). In addition, the functions of the 198-gene group involve cell division, immune response control, signal transduction, and transcription.

There were also analyzed grade-specific gene signatures. LAPTM4B gene has demonstrated a high classification accuracy for tumor and control samples in the well-differentiated group (AUC = 0.97), a gene known to be essential for cell growth and survival; its up-regulation has been previously found to be correlated with the degree of differentiation of hepatocellular carcinoma [15]. Similarly, they have also identified single gene discriminators for each grade group.

Cui et al. have identified two multigene signatures that can distinguish early stage (stages I and II) and advanced stage gastric cancer (stages III and IV), namely a 10-gene group (CPS

1+DEFA5+DES+DMN+GFRA3+MUC17+OR9G1+REEP3+TMED6+TTN) and a 9-gene group (DPT+EIF1AX+FAM26D+IFITM2+ LOC401498+OR2AE1+PRRG1+REEP3+RTKN2). The overall classification accuracy obtained on the three groups, early, advanced stomach cancer, and control, was 71.4%. Among the early-stage signature genes, there are signaling and immunerelated genes that may represent the early changes of tissue cells during carcinogenesis. A few genes were found to be in both the cancer grading and staging signatures (e.g., CPS1, DES, GFRA3, TMED6, and DPT), indicating some functional connection between cancer differentiation and progression. LANCL3, MFAP2, and PPA1 were genes highly correlated with different pathological stages, showing consistent upregulation or downregulation along with tumor progression.

There were found 62 genes with consistent differential expression in gastric cancer versus control tissues, related to extracellular processes such as CAMs, tight junction, cytokinecytokine receptor interaction, and ECM receptor interaction, the plasminogen activation cascade, as well as signaling pathways (Wnt and Integrin signaling) related to the control of cell growth and proliferation.

The study revealed that the differential expression patterns of 15 genes are highly specific to gastric cancer (e.g., GKN2, CLDN7, THY1, GIF, and PGA4), while most others are general to numerous cancer types, including a few members of the collagen gene family, the carcinoembryonic antigen-related cell adhesion molecule, matrix metalloproteinases, topoisomerase, and secreted phosphoprotein. Only three genes, CLDN7, CLDN1, and DPT, were significantly differentiated in all grades and stages of gastric neoplasia; the consistent expression of dysregulation across all the cancer subgroups may indicate their involvement in major biological pathways leading to cancer development and progression. Dermatopontin (DPT) represents an extracellular matrix protein that creates a link between the dermal fibroblast cell surface and its extracellular matrix, previously found to be downregulated in both uterine leiomyomas and keloids [44].
