IJO International Journal of Oncology 1019-6439 1791-2423 D.A. Spandidos 10.3892/ijo.2014.2387 ijo-44-06-1955 Article Gene expression signatures for identifying diffuse-type gastric cancer associated with epithelial-mesenchymal transition TANABESHIHORI1 AOYAGIKAZUHIKO2 YOKOZAKIHIROSHI3 SASAKIHIROKI2 Division of Safety Information on Drug, Food and Chemicals, National Institute of Health Sciences, 1-18-1, Kami-yoga, Setagaya-ku, Tokyo 158-8501; Department of Translational Oncology, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045; Department of Pathology, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan Correspondence to: Dr Shihori Tanabe, Division of Safety Information on Drug, Food and Chemicals, National Institute of Health Sciences, 1-18-1, Kami-yoga, Setagaya-ku, Tokyo 158-8501, Japan, E-mail: stanabe@nihs.go.jp 06 2014 11 04 2014 44 6 1955 1970 07 02 2014 28 03 2014 Copyright © 2014, Spandidos Publications 2014 This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Epithelial-mesenchymal transition (EMT) is associated with tumor malignancy. The hedgehog-EMT pathway is preferentially activated in diffuse-type gastric cancer (GC) compared with intestinal-type GC; however, histological typing is currently the only method for distinguishing these two major types of GC. We compared the gene expression profiles of 12 bone marrow-derived mesenchymal stem cell cultures and 5 diffuse-type GC tissue samples. Numerous upregulated or downregulated genes were identified in diffuse-type GC, including CDH1, CDH2, VIM, WNT4 and WNT5. Among these genes, the mRNA ratio of CDH2 to CDH1 could distinguish the 15 diffuse-type GC samples from the 17 intestinal-type GC samples. Our results suggested that the mesenchymal features were more prominent in diffuse-type GC than in intestinal-type GC, but were weaker in diffuse-type GC than in mesenchymal stem cells. Diffuse-type GC that has undergone extensive EMT, which has a poor prognosis, can be identified by quantitative PCR analysis of only two genes.

 epithelial-mesenchymal transition microarray mesenchymal stem cell gastric cancer gene expression Introduction

Gene expression is dramatically deregulated in tumor development and progression. Various epithelial cell-derived cancers often have mesenchymal features. Epithelial-mesenchymal transition (EMT) is a physiological phenotypic shift in which epithelial cells with cell-cell and cell-extracellular matrix connections transform into mesenchymal cells and then migrate to other locations within the body (1). EMT is a key developmental process that is often activated during cancer invasion and metastasis, and EMT in immortalized human mammary epithelial cells results in the development of mesenchymal cells and the expression of stem-cell markers (2). These insights highlight the need to investigate the relationship between cancer and mesenchymal cells. Cancer genomic landscapes have been revealed, and mutations in cancer-associated genes involved in cell proliferation have been discovered (3). Here, we report that the expression of several genes involved in EMT or stem cell development is altered in cancer cells and mesenchymal stem cells (MSCs).

Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide. Histopathologically, GC can be divided into two major categories: intestinal-type and diffuse-type. Intestinal-type GC develops via sequential stages including Helicobacter pylori (H. pylori)-associated gastritis, intestinal metaplasia (IM) and dysplasia. This type is found predominantly in high-risk geographic areas, such as East Asia, and is strongly correlated with the prevalence of H. pylori infection among the elderly. In contrast, diffuse-type GC appears in half of all GC cases and is more geographically dispersed. Diffuse-type GC typically develops from H. pylori-free, morphologically normal gastric mucosa without atrophic gastritis, or IM, and is both genetically and phenotypically different from intestinal-type GC (4-8). Unlike the decreasing incidence of intestinal-type GC, the prevalence of diffuse-type GC is reportedly increasing worldwide. Therefore, the molecular characterization of diffuse-type GC, with a particular focus on its infiltrating and scattered growth, is important for the development of novel therapeutics for this disease. The infiltrating and scattered growth of diffuse-type GC has been reported to be mediated by the loss of E-cadherin [cadherin 1, type 1, E-cadherin (epithelial) (CDH1)] function through somatic mutation, promoter methylation and cancer-associated down-regulation (9). We previously reported that the activation of hedgehog (Hh) signaling selectively occurs in diffuse-type GC and that blocking the Hh signal inhibits the growth of GC cells in which Hh has been activated (6). We also reported that the EMT regulator ZEB1/SIP1 is a target of Hh signaling in diffuse-type GC and that ZEB1 regulates mesenchymal-related genes WNT5A, CDH2 [cadherin 2, type 1, N-cadherin (neuronal)], PDGFRB, EDNRA, ROBO1, ROR2 (receptor tyrosine kinase-like orphan receptor 2) and MEF2C that are preferentially expressed in diffuse-type GC (7). Thus, the hedgehog-EMT pathway is preferentially activated in diffuse-type GC compared with intestinal-type GC; however, histological typing is currently the only method to distinguish the two major types. Here, we report that diffuse-type GC that has undergone extensive EMT, which has a poor prognosis, was distinguished from intestinal-type GC by quantitative real-time RT-PCR analysis of only two genes.

 Materials and methods Cell culture

Human MSCs from bone marrow (Lonza, Walkersville, MD, USA) were cultured in mesenchymal stem cell growth medium (MSCGM; Lonza #PT-3001; MSC basal medium supplemented with mesenchymal cell growth supplement, L-glutamine, and penicillin/streptomycin) at 37˚C in a 5% CO2 incubator. The cells were passaged according to the manufacturer’s protocol, with a slight modification in the use of trypsin-EDTA solution (Lonza #CC-3232). The following lot numbers of human MSC batches were utilized: #4F1127, #4F0312, #5F0138, #4F1560, #4F0591 and #4F0760. Informed consent was obtained for the development of the Poietics human mesenchymal stem cell systems (Lonza) (10).

 Total RNA purification and extraction

The MSCs were cultured on a 10-cm dish, lysed in 600 μl of buffer RLT (RNeasy lysis buffer) with β-mercaptoethanol, and homogenized using a QIA shredder (Qiagen, Düsseldorf, Germany). Total RNA was purified using RNeasy mini spin columns according to the manufacturer’s protocol (Qiagen). Total RNA was eluted with RNase-free water (10). Cancer samples were lysed with Isogen lysis buffer and total RNA was extracted by precipitation with isopropanol (11).

 Microarray analysis

Total RNA (100 ng) was reverse transcribed and amplified using a GeneChip kit (Affymetrix, Santa Clara, CA, USA). The microarray analysis was performed using GeneChip Human Genome U95Av2 or U133 Plus2.0 (Affymetrix) in accordance with the manufacturer’s instructions (10,11). Human bone marrow-derived MSCs are commercially available from Lonza, and gastric cancer cells were obtained from the National Cancer Center Research Institute. The microarray data on human MSCs and gastric cancer are available to the public in NCBI’s Gene Expression Omnibus (GEO) database and are accessible via GEO Series accession number GSE7888 and GSE42252, respectively (10,12).

 Quantitative real-time RT-PCR analysis

Real-time RT-PCR was performed using primer sets designed for detecting CDH1 (5′-GGGGTAGTGAGGATCTTGAT-3′ and 5′-TCCTTTTCC ACCCCCAAAGA-3′), CDH2 (5′-GGCATAGTCTATGGA GAAGT-3′ and 5′-GCTGTTGTCAGAAGTCTCTC-3′) and VIM (5′-GCTTTCAAGTGCCTTTCTGC-3′ and 5′-GTT GGTTGGATACTTGCTGG-3′). Quantitative real-time PCR was performed using a Bio-Rad iCycler with iQ SYBR-Green Super mix as previously reported (11). The relative mRNA expression level of each gene was normalized to that of ACTB (β-actin: 5′-GAAGTCCCTTGCCATCCTAA-3′ and 5′-GCA CGAAGGCTCATCATTCA-3′) using the ΔΔCt method.

 Statistics

Student’s t-test or Wilcoxon’s U test was performed to calculate the P-values. Microsoft Excel and GeneSpring software (Agilent Technologies, Ltd., CA, USA) were used for the analyses.

 Results Comparing the expression of EMT-related genes in MSCs and diffuse-type GC

The microarray gene expression analysis identified 51 upregulated probe sets that had detectable cells in either all of the 12 MSC samples or all of the 5 diffuse-type GC samples; the average GAPDH-normalized signal intensity of these upregulated probe sets in MSCs was >10-fold higher than the average GAPDH-normalized signal intensity in diffuse-type GC (P<0.0001) (Tables I and II). This class of probe sets contained probes recognizing CDH2, which encodes N-cadherin, a protein that has been reported to be involved in EMT (13). CDH2 was upregulated in 12 MSC samples compared with the 5 diffuse-type GC samples (Fig. 1A). A previous report demonstrated that CDH2 is a marker of EMT (13). E-cadherin stabilizes cellular organization or conformation (14). The expression of CDH1 (E-cadherin), which plays an important role in the cell junctions of epithelial cells, was downregulated in MSCs compared with diffuse-type GC (Fig. 1B). It has been reported that HMLER cancer cells (human mammary epithelial cells transformed with genomic versions of SV40 large-T, hTERT and H-rasV12) have an increased CD44high/CD24low cancer stem cell (CSC) fraction after treatment with small interfering RNA targeting CDH1 (15,16). This report details the involvement of CDH1 in interfering with the CSC phenotype and in inducing stem cell differentiation. Considering the expression patterns of CDH2 and CDH1 in MSCs and diffuse-type GC, most of the cells in diffuse-type GC are likely to have an epithelial-like phenotype, although there is more evidence of EMT in diffuse-type GC than in intestinal-type GC.

We further examined mesenchymal phenotype-related genes in 5 diffuse-type GC samples and identified 1461 upregul ated probe sets with an average signal intensity >500 in the 12 MSC samples and with greater than a 2-fold change in the 12 MSC samples compared with the 5 diffuse-type GC samples using the U133Plus2.0 platform. Of these 1461 probe sets, 983 were aligned with the U95Av2 platform. Using the U95Av2 platform, 94 probe sets were determined to be upregulated in the 13 diffuse-type GC samples compared with the 17 intestinal-type GC samples (Fig. 2). Probe sets that recognized the same symbol were unified in probe sets with a larger fold-change and 77 genes were selected (Table III). FN1 (fibronectin 1) was upregulated in MSCs compared with diffuse-type GC (Fig. 3A). It has been reported that salinomycin has selective toxicity in the stem cells of epithelial cell-derived cancers and that it induces epithelial cell differentiation (17). Salinomycin, a selective breast cancer stem cell inhibitor, has been reported to decrease stem cell-related genes such as CCND1 (cyclin D1), LEF1 and FN1, which are targets of Wnt signaling (17). The role of Wnt signaling in different cell types may be an interesting target for cancer stem cell machinery (18,19). Gene expression was analyzed to investigate whether these stem cell-related genes were involved in the cellular phenotypic changes. FN1 was upregulated in MSCs compared with diffuse-type GC, suggesting that the stem cell phenotype was more typical in MSCs than in diffuse-type GC (Fig. 3A). One of the probe sets recognizing VIM (vimentin) was upregulated in diffuse-type GC compared with MSCs (Fig. 3B).

 Comparing the expression of stem cell-related genes in MSCs and diffuse-type GC

To identify markers of EMT or the stemness phenotype of diffuse-type GC, we compared the expression of stem cell-related genes in MSCs and diffuse-type GC. We first selected stem-cell related genes based on biological processes using gene ontology and then performed a clustering analysis of the signal intensity of 33 stem cell-related genes that had greater than a 5-fold change in the GAPDH-normalized signal intensity in GC compared with MSCs (NCSS2007) (Fig. 4A). Among these 33 stem cell-related genes, 10 were selected that were significantly differentially expressed (more than a 20-fold change; P<0.01 and P<0.05; n=12 MSCs and n=5 diffuse-type GCs) (Fig. 4B). SOX2, which is involved in embryonic and adult tissue stem cell maintenance, was upregulated in diffuse-type GC compared with MSCs. This corresponded with previous reports indicating that SOX2 was overexpressed or mutated in a stage-dependent manner in certain types of cancer (20–22). NOTCH1, which plays a well-known role in cancer development and EMT, was also upregulated in diffuse-type GC compared with MSCs. ID3 was downregulated in diffuse-type GC compared with MSCs. NANOG (Nanog homeobox), which is involved in maintaining the pluripotency of embryonic stem cells, was upregulated in diffuse-type GC compared with MSCs (Fig. 4C). NANOG functions in conjunction with ten-eleven translocation (TET) family proteins, and TET1 enhances the efficacy of reprogramming (23). TET1 was also upregulated in diffuse-type GC compared with MSCs.

These data indicating that embryonic stem cell-related genes may play a role in cancer cells in which EMT occurs, such as in diffuse-type GC rather than in MSCs, are very interesting; however, if particular EMT markers are overexpressed in MSCs, then these genes are unlikely to be useful for distinguishing diffuse-type GC from intestinal-type GC.

 The mRNA ratio of CDH2 to CDH1 distinguished the mesenchymal from the epithelial phenotype

Using the microarray results, the mRNA ratios of CDH2 to CDH1 were compared in 12 MSC samples and 5 diffuse-type GC samples, and in 13 diffuse-type GC samples and 17 intestinal-type GC samples. The results and a diagram showing the phenotypic transition among the samples are shown in Fig. 5A. The mRNA ratio of CDH2/CDH1 was higher in MSCs than in diffuse-type GC. The mRNA ratio of CDH2/CDH1 was also higher in diffuse-type GC samples than in intestinal-type GC samples. The combin ation of the CDH2 and CDH1 mRNA levels may distinguish the mesenchymal cell phenotype from the epithelial cell phenotype. WNT5A upregulation has been reported to be associated with EMT (7). The WNT5A/WNT4 ratio was higher in MSCs than in diffuse-type GC, whereas the WNT5A/WNT4 ratio was similar in the diffuse- and intestinal-type GCs (Fig. 5B). Accordingly, the combination of WNT5A and WNT4 may only distinguish MSCs from GC.

We performed quantitative real-time RT-PCR to detect the expression of CDH1 and CDH2 in 6 MSC samples, 15 diffuse-type GC samples and 17 intestinal-type GC samples. In accordance with the above microarray results, CDH1 was upregulated and CDH2 was downregulated in GC compared with MSCs (Fig. 6). The CDH2/CDH1 mRNA ratio was confirmed to be higher in MSCs than in both types of GC. Most importantly, the CDH2/CDH1 mRNA ratio was perfect at distinguishing the 15 diffuse-type GC samples from the 17 intestinal-type GC samples (Fig. 7); all of the 15 diffuse-type GC samples had ratios that were higher than the intestinal-type GC sample with the highest ratio (I-80).

VIM is one of the most validated EMT markers. Therefore, using quantitative real-time RT-PCR, we investigated the possibility that the combination of VIM and CDH1 could distinguish the mesenchymal phenotype from the epithelial phenotype (Fig. 8). The VIM/CDH1 mRNA ratio was higher in MSCs than in both types of GC. However, the VIM/CDH1 ratio was much more varied among the 32 GC samples than the CDH2/CDH1 ratio. As mentioned above, there was a threshold CDH2/CDH1 ratio that distinguished the 15 diffuse-type GC samples from the 17 intestinal-type GC samples, whereas some intestinal-type GC samples (for example, I-11 and I-15) had a higher VIM/CDH1 ratio than certain diffuse-type GC samples.

 Discussion

We previously compared the expression profiles of 18 intestinal-type GC and 12 diffuse-type GC samples with typical characteristics in terms of cell growth (clustered or scattered) and differentiation (well/moderate or poor), and selected genes based on their expression levels in the two types of cancer (7). A gene was selected using the Wilcoxon U test (P<0.05) from genes with more than a 2-fold change on average. By this procedure, a total of 892 genes were identified (704 genes specific to diffuse-type and 188 genes specific to intestinal-type). The two types of GC were completely separated by two-dimensional hierarchical clustering analysis of the 892 selected genes. In this paper, we reported that an EMT regulator, ZEB1/SIP1, is a target of the primary transcription factor GLI1 in the Hh signaling pathway in diffuse-type GC and that ZEB1/SIP1 further activates NOTCH2 and other EMT regulators [snail family zinc finger 2 (SNAI2) and twist family bHLH transcription factor 2 (TWIST2)]. SNAI2 upregulates CDH2 and WNT5A and downregulates CDH1. TWIST2 upregulates CDH2, ROR2, which is the WNT5A receptor, and other mesenchymal-related genes (PDGFRB, EDNRA, ROBO1 and MEF2C). Accordingly, we concluded that Hh signaling-mediated EMT specifically occurred in diffuse-type GC. This crosstalk between Hh signaling and EMT has been reported in esophageal squamous cell carcinoma (24). However, we were unable to identify a single marker that distinguished the 12 diffuse-type GC samples from the 18 intestinal-type GC samples. Therefore, herein, we searched for such genes by comparing the expression profiles of diffuse-type GC and MSCs, which are typical mesenchymal cells. Among the 1461 probe sets that were significantly upregulated in MSCs, we selected 94 probes (77 genes) that were upregulated in diffuse-type GC compared with intestinal-type GC (Table III).

The typical mesenchymal cell markers FN1, VIM and CDH2 were highly expressed in MSCs. Regarding EMT regulators, it is known that the Snail family transcription factor regulates EMT by repressing CDH1 gene transcription (25). SNAI2 expression was higher in MSCs than in diffuse-type GC. CDH1 gene regulation might be involved in EMT because it was shown that intracellular CDH1 is located at the membrane after treatment with siRNA targeting the EMT regulator ZEB2/SIP1 in esophageal cancer (24). In terms of Wnt signaling, WNT5A was upregulated in MSCs compared with diffuse-type GC; however, its receptor ROR2 was more highly expressed in diffuse-type GC than in MSCs. Regarding Notch signaling, NOTCH1, 3 and 4 were highly expressed in the diffuse-type GC samples, whereas NOTCH2 was upregulated in MSCs. Because NOTCH is related to stem cell maintenance, this alteration in gene expression may reflect transitions or modifications in stem cell features (26). In terms of other stem cell markers, a recent report suggested that Lgr5+ cells in mouse intestinal adenomas acquired the ability for cancerous growth as a stem cell (27). Dclk1 (doublecortin-like kinase 1), which is a candidate marker for intestinal cancer stem cells, did not dramatically differ in expression between diffuse-type GC and MSCs (28).

From these results, we selected FN1, VIM, CDH2, SNAI2, WNT5A and NOTCH2 as EMT-related genes that were upregulated in MSCs. However, all 6 of these genes were included in our previously-selected 704 genes that were upregulated in diffuse-type GC compared with intestinal-type GC. Therefore, we examined the power of the mRNA ratio of each of these 6 mesenchymal-related genes to a typical epithelial marker gene, CDH1. We determined that the mRNA ratio of CDH2 to CDH1 has great potential as a single indicator that distinguishes diffuse-type GC from intestinal-type GC. In the near future, the power of this simple indicator of EMT should be evaluated in a large cohort study of GC as well as other tumor types.

We gratefully acknowledge Dr Ryoji Kushima for the pathological and clinical evaluations. We would also like to thank Ms. Rie Komatsuzaki and Ms. Fumiko Chiwaki for their technical assistance. This study was supported in part by the National Institute of Biomedical Innovation (for the Advanced Research for Medical Products Mining Programme ID10-41, ID12-01), the Ministry of Health, Labour and Welfare of Japan (for the Third Comprehensive 10-Year Strategy for Cancer Control H22-007 and for Cancer Control and Cancer Research 20-12), National Cancer Center Research and Development Fund (23-A-7, 23-B-6, 23-B-18, 25-A-6), the Ministry of Education, Culture, Sports, Science and Technology of Japan (23501322) and the Princess Takamatsu Cancer Research Fund.

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Gene expression of the two cadherins. (A) CDH2 (N-cadherin) gene expression was upregulated in MSCs compared with diffuse-type GC. (B) CDH1 (E-cadherin) gene expression was downregulated in MSCs compared with diffuse-type GC. The data are presented as the mean ± SE of the ratio to the average in the MSCs (***P<0.001 vs. MSCs; n=12 MSCs and n=5 diffuse-type GCs). The data were normalized to GAPDH.

Venn diagram of the extraction of common genes with upregulated probe sets in MSCs and upregulated probe sets in diffuse-type GC. Probe sets with an average signal intensity of >500 in MSCs and greater than a 2-fold change in MSCs compared with diffuse-type GC were selected from the U133Plus2.0 platform and were aligned with the U95Av2 platform. Furthermore, 94 probe sets were extracted that were upregulated in diffuse-type GC compared with intestinal-type GC on the U95Av2 platform.

Gene expression of FN1 (A) and VIM (B). (A) FN1 gene expression was upregulated in MSCs compared with diffuse-type GC. (B) One of the probe sets recognizing VIM was downregulated in MSCs compared with diffuse-type GC. The data are presented as the mean ± SE of the ratio to the average in the MSCs (***P<0.001 and *P<0.05 vs. MSCs; n=12 MSCs and n=5 diffuse-type GC). The data were normalized to GAPDH.

Gene expression of stem cell-related genes in MSCs and diffuse-type GC. (A) The gene expression of 33 stem cell-related genes, which were selected based on biological processes using gene ontology, in MSCs and diffuse-type GC was compared by clustering analysis (fold change >5 in diffuse-type GC compared with MSCs) (NCSS 2007). The amount value is indicated as the ratio to the average GAPDH-normalized signal intensity in the MSCs. (B) From among the 33 stem cell-related genes, 10 probe sets with a >20-fold change in diffuse-type GC compared with MSCs are shown. The data are presented as the mean ± SE of the ratio to the average in the MSCs (**P<0.01, *P<0.05 vs. MSCs; n=12 MSCs and n=5 diffuse-type GC). The data were normalized to GAPDH. (C) NANOG gene expression was upregulated in diffuse-type GC compared with MSCs. The data are presented as the mean ± SE of the ratio to the average in the MSCs (**P<0.01 vs. MSCs; n=12 MSCs and n=5 diffuse-type GC). The data were normalized to GAPDH.

Diagram of the cellular phenotype transition and the mRNA ratios of CDH2 to CDH1 and WNT5A to WNT4 in MSCs and GC. (A) A diagram of the mesenchymal to epithelial transition in MSCs, diffuse-type GC, and intestinal-type GC is shown (upper). The mRNA ratio of CDH2 to CDH1 in MSCs, diffuse-type GC, and intestinal-type GC was compared. (B) The mRNA ratio of WNT5A and WNT4 was also examined. The data are presented as the mean ± SE of the ratio to the average in the MSCs (***P<0.001 vs. MSCs; n=12 MSCs and n=5 diffuse-type GC) or the ratio to the average in diffuse-type GC (#P<0.05 vs. diffuse-type GC; n=13 diffuse-type GC and n=17 intestinal-type GC).

Quantitative real-time RT-PCR analysis of two cadherin genes. (A) CDH1 was upregulated in the 15 diffuse-type and the 17 intestinal-type GC samples compared with the 6 MSC samples. CDH1 mRNA expression was significantly higher in the 17 intestinal-type GC samples than in the 15 diffuse-type GC samples. (B) CDH2 was downregulated in both GC types compared with the 6 MSC samples. CDH2 mRNA expression was significantly lower in the 17 intestinal-type GC samples than in the 15 diffuse-type GC samples. The data are presented as the mean ± SE of the ratio to the average in the MSCs (***P<0.001, **P<0.01 vs. MSCs; n=6 MSCs, n=15 diffuse-type GC and n=17 intestinal-type GC). The data were normalized to ACTB.

The CDH2 to CDH1 mRNA ratio obtained by quantitative real-time RT-PCR in diffuse-type GC and intestinal-type GC. (A) The CDH2 to CDH1 mRNA ratio was significantly higher in diffuse-type GC than in intestinal-type GC. (B) The ratios in the two types of GC were compared. The data are presented as the mean ± SE of the ratio to the average in the diffuse-type GC samples (***P<0.001 vs. diffuse-type GC; n=15 diffuse-type GC and n=17 intestinal-type GC).

The VIM to CDH1 mRNA ratio obtained by quantitative real-time RT-PCR in diffuse-type GC and intestinal-type GC. (A) The VIM to CDH1 mRNA ratio was significantly higher in diffuse-type GC than in intestinal-type GC. (B) The ratios in the two types of GC were compared. The data are presented as the mean ± SE of the ratio to the average in the diffuse-type GC samples (*P<0.05 vs. diffuse-type GC; n=15 diffuse-type GC and n=17 intestinal-type GC).

Upregulated probe sets in MSCs compared with diffuse-type GC.

Probe set ID Gene symbol Gene title Ratio P-value (non-equal variance) P-value (equal variance) Entrez gene ID
206157_at PTX3 Pentraxin 3, long 56.9 1.303E-11 2.124E-11 5806
214702_at FN1 Fibronectin 1 43.7 1.116E-10 6.76E-10 2335
215446_s_at LOX Lysyl oxidase 14.8 5.836E-10 6.504E-09 4015
207558_s_at PITX2 Paired-like homeodomain 2 11.7 1.076E-09 5.864E-08 5308
202952_s_at ADAM12 ADAM metallopeptidase domain 12 19.5 4.79E-09 3.948E-07 8038
214701_s_at FN1 Fibronectin 1 26.6 3.694E-08 4.612E-07 2335
204421_s_at FGF2 Fibroblast growth factor 2 (basic) 10.9 6.115E-08 1.72E-06 2247
233533_at KRTAP1-5 Keratin associated protein 1–5 163.7 6.246E-08 7.787E-07 83895
209946_at VEGFC Vascular endothelial growth factor C 13.7 6.864E-08 1.278E-06 7424
203438_at STC2 Atanniocalcin 2 50.2 6.959E-08 9.427E-07 8614
228367_at ALPK2 α-kinase 2 21.4 7.576E-08 1.14E-06 115701
239367_at BDNF Brain-derived neurotrophic factor 16.5 1.442E-07 3.538E-06 627
203439_s_at STC2 Stanniocalcin 2 54.7 3.842E-07 6.59E-06 8614
201387_s_at UCHL1 Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) 13.9 6.127E-07 1.232E-05 7345
207345_at FST Follistatin 11.6 7.941E-07 1.709E-05 10468
204948_s_at FST Follistatin 22.5 1.041E-06 2.488E-05 10468
204298_s_at LOX Lysyl oxidase 54.2 1.615E-06 3.207E-05 4015
203851_at IGFBP6 Insulin-like growth factor binding protein 6 10.2 1.752E-06 5.669E-05 3489
226847_at FST Follistatin 23.0 1.913E-06 4.582E-05 10468
219789_at NPR3 Natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 58.1 2.108E-06 4.278E-05 4883
206307_s_at FOXD1 Forkhead box D1 11.1 2.308E-06 0.0001004 2297
236532_at C11orf87 Chromosome 11 open reading frame 87 181.3 3.351E-06 6.966E-05 399947
213791_at PENK Proenkephalin 18.6 3.43E-06 9.108E-05 5179
203440_at CDH2 Cadherin 2, type 1, N-cadherin (neuronal) 19.8 6.446E-06 0.0001663 1000
219729_at PRRX2 Paired related homeobox 2 16.9 6.459E-06 0.0001542 51450
243813_at LINC00968 Long intergenic non-protein coding RNA 968 47.0 8.462E-06 0.0001846 100507632
210261_at KCNK2 Potassium channel, subfamily K, member 2 11.0 1.158E-05 0.0003414 3776
206382_s_at BDNF Brain-derived neurotrophic factor 44.6 1.159E-05 0.0002555 627
1557181_s_at C11orf87 Chromosome 11 open reading frame 87 293.2 1.54E-05 0.0003308 399947
219054_at NPR3 Natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 28.3 1.911E-05 0.0004216 4883
1557180_at C11orf87 Chromosome 11 open reading frame 87 21.7 2.153E-05 0.0004803 399947
235417_at SPOCD1 SPOC domain containing 1 30.2 2.557E-05 0.0005603 90853
223618_at FMN2 Formin 2 22.2 2.976E-05 0.0006566 56776
209905_at HOXA10-HOXA9, HOXA9, MIR196B HOXA10-HOXA9 readthrough, homeobox A9, microRNA 196b 11.2 3.068E-05 0.0008075 100534589, 3205, 442920
210367_s_at PTGES Prostaglandin E synthase 19.0 3.112E-05 0.0006888 9536
201107_s_at THBS1 Thrombospondin 1 27.7 3.53E-05 0.0007676 7057
213707_s_at DLX5 Distal-less homeobox 5 11.7 4.045E-05 0.0009757 1749
239202_at RAB3B RAB3B, member RAS oncogene family 11.8 4.595E-05 0.0010932 5865
204602_at DKK1 Dickkopf 1 homolog (Xenopus laevis) 11.7 4.785E-05 0.0013798 22943
210121_at B3GALT2 UDP-Gal:βGlcNAc β 1,3-galactosyltransferase, polypeptide 2 12.4 4.992E-05 0.0011294 8707
232122_s_at VEPH1 Ventricular zone expressed PH domai homolog 1 (zebrafish) 11.9 6.254E-05 0.0015563 79674
229641_at CCBE1 Collagen and calcium binding EGF domains 1 18.2 6.7E-05 0.001394 147372
1555471_a_at FMN2 Formin 2 13.8 6.858E-05 0.0016045 56776
219790_s_at NPR3 Natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 50.1 7.041E-05 0.0014166 4883
222862_s_at AK5 Adenylate kinase 5 15.3 7.202E-05 0.0015601 26289
1552487_a_at BNC1 Basonuclin 1 11.7 8.369E-05 0.0019519 646
230112_at MARCH4 Membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase 15.3 8.722E-05 0.0019912 57574
244623_at KCNQ5 Potassium voltage-gated channel, KQT-like subfamily, member 5 11.3 9.102E-05 0.0018888 56479
213640_s_at LOX Lysyl oxidase 29.9 9.205E-05 0.0018414 4015
217452_s_at B3GALT2 UDP-Gal:βGlcNAc β 1,3-galactosyltransferase, polypeptide 2 13.0 9.284E-05 0.0019809 8707
235548_at APCDD1L Adenomatosis polyposis coli downregulated 1-like 36.2 9.734E-05 0.0019595 164284

Gene ontology of upregulated genes in MSCs compared to diffuse-type GC.

Probe set ID Gene symbol Gene ontology biological process
202952_s_at ADAM12 Proteolysis, cell adhesion, epidermal growth factor receptor signaling pathway, myoblast fusion
222862_s_at AK5 Nucleobase-containing compound metabolic process, nucleoside diphosphate phosphorylation, ADP biosynthetic process, dADP biosynthetic process, signal transduction, nucleoside triphosphate biosynthetic process, pyrimidine ribonucleotide biosynthetic process, nucleobase-containing small molecule interconversion, phosphorylation, small molecule metabolic process, ATP metabolic process, nucleobase-containing small molecule metabolic process
228367_at ALPK2 Protein phosphorylation, phosphorylation
235548_at APCDD1L -
210121_at B3GALT2 Protein glycosylation, oligosaccharide biosynthetic process
217452_s_at
239367_at BDNF Ureteric bud development, behavioral fear response, response to hypoxia, chronic inflammatory response, mitochondrial electron transport, NADH to ubiquinone, nervous system development, negative regulation of neuroblast proliferation, axon guidance, axon target recognition, behavior, learning or memory, feeding behavior, neuron recognition, response to hormone stimulus, glutamate secretion, response to fluoxetine, dendrite development, regulation of metabolic process, nerve development, response to nutrient levels, response to vitamin A, mechanoreceptor differentiation, response to drug, fear response, negative regulation of apoptotic process, regulation of neuron apoptotic process, negative regulation of neuron apoptotic process, positive regulation of neuron differentiation, negative regulation of striated muscle tissue development, regulation of retinal cell programmed cell death, regulation of synaptic plasticity, regulation of long-term neuronal synaptic plasticity, positive regulation of long-term neuronal synaptic plasticity, regulation of short-term neuronal synaptic plasticity, inner ear development, cognition, positive regulation of synapse assembly, response to hyperoxia, regulation of excitatory postsynaptic membrane potential, response to anesthetic
206382_s_at
1552487_a_at BNC1 Transcription, DNA-dependent, regulation of transcription, DNA-dependent, regulation of transcription from RNA polymerase I promoter, regulation of transcription from RNA polymerase II promoter, positive regulation of cell proliferation, epidermis development, wound healing, positive regulation of epithelial cell proliferation, chromosome organization
236532_at C11orf87 -
1557180_at
1557181_s_at
229641_at CCBE1 Angiogenesis, lymphangiogenesis, sprouting angiogenesis, multicellular organismal development, venous blood vessel morphogenesis
203440_at CDH2 Cell adhesion, homophilic cell adhesion, heterophilic cell-cell adhesion, synapse assembly, cell- cell adhesion, calcium-dependent cell-cell adhesion, cell migration, regulation of myelination, regulation of protein localization, cell junction assembly, adherens junction organization, regulation of Rho protein signal transduction, muscle cell differentiation, positive regulation of MAPK cascade, cell-cell junction organization, blood vessel morphogenesis, regulation of axonogenesis, striated muscle cell differentiation, positive regulation of muscle cell differentiation, negative regulation of canonical Wnt receptor signaling pathway
204602_at DKK1 Negative regulation of transcription from RNA polymerase II promoter, cell morphogenesis involved in differentiation, endoderm formation, mesoderm formation, hair follicle development, regulation of receptor internalization, multicellular organismal development, endoderm development, Wnt receptor signaling pathway, regulation of Wnt receptor signaling pathway, negative regulation of Wnt receptor signaling pathway, embryonic limb morphogenesis, negative regulation of BMP signaling pathway, forebrain development, negative regulation of protein complex assembly, response to retinoic acid, negative regulation of peptidyl-serine phosphorylation, negative regulation of mesodermal cell fate specification, regulation of endodermal cell fate specification, negative regulation of skeletal muscle tissue development, head morphogenesis, face morphogenesis, negative regulation of pathway-restricted SMAD protein phosphorylation, positive regulation of heart induction by negative regulation of canonical Wnt receptor signaling pathway, negative regulation of canonical Wnt receptor signaling pathway, Wnt receptor signaling pathway involved in somitogenesis, extracellular negative regulation of signal transduction, negative regulation of canonical Wnt receptor signaling pathway involved in cardiac muscle cell fate commitment, negative regulation of cardiac muscle cell differentiation
213707_s_at DLX5 Skeletal system development, ossification, osteoblast differentiation, endochondral ossification, transcription, DNA-dependent, regulation of transcription, DNA-dependent, multicellular organismal development, nervous system development, axonogenesis, axon guidance, cell proliferation, embryonic limb morphogenesis, BMP signaling pathway, epithelial cell differentiation, inner ear morphogenesis, ear development, positive regulation of osteoblast differentiation, positive regulation of transcription, DNA-dependent, positive regulation of transcription from RNA polymerase II promoter, anatomical structure formation involved in morphogenesis, positive regulation of epithelial cell proliferation, palate development, olfactory pit development, head development, face morphogenesis, bone morphogenesis, cellular response to BMP stimulus, positive regulation of canonical Wnt receptor signaling pathway, positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
204421_s_at FGF2 Activation of MAPKK activity, activation of MAPK activity, MAPK import into nucleus, angiogenesis, branching involved in ureteric bud morphogenesis, organ induction, positive regulation of protein phosphorylation, positive regulation of endothelial cell proliferation, cell migration involved in sprouting angiogenesis, regulation of transcription, DNA-dependent, phosphatidyl-inositol biosynthetic process, C21-steroid hormone biosynthetic process, apoptotic process, chemotaxis, signal transduction, epidermal growth factor receptor signaling pathway, intracellular protein kinase cascade, Ras protein signal transduction, synaptic transmission, multicellular organismal development, nervous system development, positive regulation of cell proliferation, negative regulation of cell proliferation, insulin receptor signaling pathway, fibroblast growth factor receptor signaling pathway, fibroblast growth factor receptor signaling pathway, embryo development, organ morphogenesis, glial cell differentiation, positive regulation of endothelial cell migration, positive regulation of gene expression, negative regulation of fibroblast migration, positive regulation of phospholipase C activity, regulation of calcium ion-dependent exocytosis, substantia nigra development, positive regulation of cerebellar granule cell precursor proliferation, cell differentiation, extracellular matrix organization, hyaluronan catabolic process, negative regulation of cell growth, lung development, inositol phosphate biosynthetic process, Fc-epsilon receptor signaling pathway, wound healing, positive regulation of cell fate specification, positive regulation of blood vessel endothelial cell migration, negative regulation of blood vessel endothelial cell migration, positive regulation of phosphatidylinositol 3-kinase activity, innate immune response, positive regulation of cell differentiation, positive regulation of osteoblast differentiation, regulation of angiogenesis, positive regulation of angiogenesis, negative regulation of transcription, DNA-dependent, positive regulation of transcription, DNA-dependent, positive regulation of transcription from RNA polymerase II promoter, regulation of retinal cell programmed cell death, neurotrophin TRK receptor signaling pathway, phosphatidylinositol-mediated signaling, embryonic morphogenesis, response to axon injury, stem cell development, positive regulation of epithelial cell proliferation, positive chemotaxis, release of sequestered calcium ion into cytosol, regulation of cell cycle, positive regulation of cell division, positive regulation of cardiac muscle cell proliferation, corticotropin hormone secreting cell differentiation, thyroid-stimulating hormone-secreting cell differentiation, negative regulation of cell death, chondroblast differentiation, mammary gland epithelial cell differentiation, negative regulation of wound healing, positive regulation of ERK1 and ERK2 cascade
223618_at FMN2 Transport, apoptotic process, response to stress, response to DNA damage stimulus, meiotic meta-phase I, multicellular organismal development, protein transport, cellular component organization, vesicle-mediated transport, meiotic chromosome movement towards spindle pole, actin cytoskeleton organization, intracellular signal transduction, polar body extrusion after meiotic divisions, negative regulation of protein catabolic process, negative regulation of apoptotic process, actin nucleation, intracellular transport, oogenesis, establishment of meiotic spindle localization, homologous chromosome movement towards spindle pole involved in homologous chromosome segregation, formin-nucleated actin cable assembly, cellular response to hypoxia
1555471_a_at
214701_s_at FN1 Angiogenesis, platelet degranulation, acute-phase response, cell-substrate junction assembly, celladhesion, cell-matrix adhesion, calcium-independent cell-matrix adhesion, blood coagulation, regulation of cell shape, response to wounding, positive regulation of peptidase activity, cell migration, peptide cross-linking, platelet activation, extracellular matrix organization, substrate adhesion-dependent cell spreading, wound healing, leukocyte migration
214702_at
206307_s_at FOXD1 Neural crest cell migration, transcription, DNA-dependent, regulation of transcription, DNA-dependent, pattern specification process, peripheral nervous system development, embryo development, positive regulation of gene expression, melanocyte differentiation, positive regulation of BMP signaling pathway, negative regulation of transcription, DNA-dependent, positive regulation of transcription from RNA polymerase II promoter, enteric nervous system development, sympathetic nervous system development, axon extension involved in axon guidance, lateral line nerve glial cell development, iridophore differentiation, regulation of sequence-specific DNA binding transcription factor activity, cartilage development, dichotomous subdivision of terminal units involved in ureteric bud branching, metanephric capsule development, metanephric capsule specification, positive regulation of kidney development
204948_s_at FST Negative regulation of transcription from RNA polymerase II promoter, hematopoietic progenitor cell differentiation, gamete generation, pattern specification process, female gonad development, BMP signaling pathway, hair follicle morphogenesis, negative regulation of activin receptor signaling pathway, odontogenesis of dentin-containing tooth, keratinocyte proliferation, negative regulation of cell differentiation, negative regulation of follicle-stimulating hormone secretion, positive regulation of hair follicle development
207345_at
226847_at
209905_at HOXA10-HOXA9, HOXA9, MIR196B Transcription, DNA-dependent, regulation of transcription, DNA-dependent, multicellular organismal development, anterior/posterior pattern specification, proximal/distal pattern formation, mammary gland development, embryonic forelimb morphogenesis, endothelial cell activation, negative regulation of myeloid cell differentiation, embryonic skeletal system development, definitive hemopoiesis
203851_at IGFBP6 Regulation of cell growth, signal transduction, negative regulation of cell proliferation, cellular protein metabolic process
210261_at KCNK2 Transport, ion transport, potassium ion transport, G-protein coupled receptor signaling pathway, synaptic transmission, regulation of ion transmembrane transport, potassium ion transmembrane transport
244623_at KCNQ5 Protein complex assembly, transport, ion transport, potassium ion transport, synaptic transmission, regulation of ion transmembrane transport, transmembrane transport, potassium ion transmembrane transport
233533_at KRTAP1-5 -
243813_at LINC00968 -
204298_s_at LOX Blood vessel development, cellular protein modification process, response to hormone stimulus, extracellular matrix organization, collagen fibril organization, lung development, wound healing, response to drug, elastic fiber assembly, response to steroid hormone stimulus, oxidation-reduction process
213640_s_at
215446_s_at
230112_at MARCH4 Protein ubiquitination
219054_at NPR3 Skeletal system development, osteoclast proliferation, adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway, negative regulation of adenylate cyclase activity, phospholipase C-activating G-protein coupled receptor signaling pathway, regulation of blood pressure, regulation of osteoblast proliferation, positive regulation of urine volume, positive regulation of nitric-oxide synthase activity
219789_at
219790_s_at
213791_at PENK Behavioral fear response, signal transduction, neuropeptide signaling pathway, behavior, sensory perception of pain
207558_s_at PITX2 Negative regulation of transcription from RNA polymerase II promoter, patterning of blood vessels, vasculogenesis, in utero embryonic development, neuron migration, extraocular skeletal muscle development, atrioventricular valve development, cardiac neural crest cell migration involved in outflow tract morphogenesis, pulmonary myocardium development, regulation of transcription, DNA-dependent, regulation of transcription from RNA polymerase II promoter, transcription from RNA polymerase II promoter, multicellular organismal development, determination of left/right symmetry, brain development, heart development, skeletal muscle tissue development, myoblast fusion, male gonad development, female gonad development, anatomical structure morphogenesis, response to hormone stimulus, organ morphogenesis, Wnt receptor signaling pathway, subthalamic nucleus development, hypothalamus cell migration, pituitary gland development, neuron differentiation, lung development, regulation of cell migration, embryonic camera-type eye development, response to vitamin A, embryonic hindlimb morphogenesis, hair cell differentiation, vascular smooth muscle cell differentiation, deltoid tuberosity development, regulation of cell proliferation, odontogenesis of dentin-containing tooth, odontogenesis, camera-type eye development, positive regulation of DNA binding, positive regulation of transcription, DNA-dependent, positive regulation of transcription from RNA polymerase II promoter, spleen development, embryonic digestive tract morphogenesis, cardiac muscle tissue development, cardiac muscle cell differentiation, atrial cardiac muscle tissue morphogenesis, ventricular cardiac muscle cell development, digestive system development, somatotropin secreting cell differentiation, prolactin secreting cell differentiation, ventricular septum morphogenesis, left lung morphogenesis, pulmonary vein morphogenesis, superior vena cava morphogenesis, endodermal digestive tract morphogenesis, iris morphogenesis, cell proliferation involved in outflow tract morphogenesis, left/right axis specification, positive regulation of myoblast proliferation
219729_at PRRX2 Positive regulation of mesenchymal cell proliferation, regulation of transcription, DNA-dependent, multicellular organismal development, embryonic limb morphogenesis, inner ear morphogenesis, middle ear morphogenesis, positive regulation of smoothened signaling pathway, embryonic cranial skeleton morphogenesis, embryonic skeletal system morphogenesis, artery morphogenesis, cartilage development
210367_s_at PTGES Prostaglandin biosynthetic process, acute inflammatory response, chronic inflammatory response, lipid metabolic process, fatty acid metabolic process, fatty acid biosynthetic process, prostaglandin metabolic process, signal transduction, negative regulation of cell proliferation, response to organic cyclic compound, arachidonic acid metabolic process, cyclooxygenase pathway, response to lipopolysaccharide, response to retinoic acid, response to cytokine stimulus, small molecule metabolic process, response to calcium ion
206157_at PTX3 Response to yeast, inflammatory response, opsonization, positive regulation of nitric oxide biosynthetic process, positive regulation of phagocytosis
239202_at RAB3B GTP catabolic process, transport, intracellular protein transport, nucleocytoplasmic transport, signal transduction, small GTPase mediated signal transduction, protein transport, regulation of exocytosis, peptidyl-cysteine methylation
235417_at SPOCD1 Transcription, DNA-dependent, negative regulation of phosphatase activity
203438_at STC2 Cellular calcium ion homeostasis, response to oxidative stress, cell surface receptor signaling pathway, cell-cell signaling, embryo implantation, response to nutrient, endoplasmic reticulum unfolded protein response, response to vitamin D, response to endoplasmic reticulum stress, negative regulation of multicellular organism growth, response to peptide hormone stimulus, decidualization, calcium ion homeostasis, cellular response to hypoxia, regulation of store-operated calcium entry
201107_s_at THBS1 Activation of MAPK activity, response to hypoxia, negative regulation of endothelial cell proliferation, negative regulation of cell-matrix adhesion, sprouting angiogenesis, chronic inflammatory response, platelet degranulation, negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, negative regulation of dendritic cell antigen processing and presentation, outflow tract morphogenesis, endocardial cushion development, growth plate cartilage development, induction of apoptosis, inflammatory response, immune response, cell cycle arrest, cell adhesion, blood coagulation, response to glucose stimulus, positive regulation of endothelial cell migration, negative regulation of endothelial cell migration, negative regulation of plasma membrane long-chain fatty acid transport, negative regulation of nitric oxide mediated signal transduction, negative regulation of cGMP-mediated signaling, negative regulation of plasminogen activation, positive regulation of macrophage chemotaxis, positive regulation of fibroblast migration, positive regulation of cell-substrate adhesion, cell migration, negative regulation of angiogenesis, peptide cross-linking, platelet activation, positive regulation of blood coagulation, extracellular matrix organization, positive regulation of cell migration, positive regulation of transforming growth factor beta receptor signaling pathway, response to magnesium ion, response to progesterone stimulus, negative regulation of interleukin-12 production, positive regulation of transforming growth factor beta1 production, cellular response to heat, response to endoplasmic reticulum stress, negative regulation of fibroblast growth factor receptor signaling pathway, positive regulation of phosphorylation, response to drug, positive regulation of tumor necrosis factor biosynthetic process, positive regulation of macrophage activation, negative regulation of apoptotic process, negative regulation of cysteine-type endopeptidase activity involved in apoptotic process, positive regulation of blood vessel endothelial cell migration, negative regulation of blood vessel endothelial cell migration, engulfment of apoptotic cell, positive regulation of translation, positive regulation of angiogenesis, behavioral response to pain, blood vessel morphogenesis, positive regulation of chemotaxis, response to calcium ion, negative regulation of focal adhesion assembly, positive regulation of protein kinase B signaling cascade, negative regulation of fibrinolysis, positive regulation of execution phase of apoptosis, positive regulation of extrinsic apoptotic signaling pathway via death domain receptors, positive regulation of endothelial cell apoptotic process, positive regulation of reactive oxygen species metabolic process, negative regulation of extrinsic apoptotic signaling pathway
201387_s_at UCHL1 Proteolysis, ubiquitin-dependent protein catabolic process, response to stress, axonogenesis, axon target recognition, adult walking behavior, cell death, cell proliferation, protein deubiquitination, sensory perception of pain, axon transport of mitochondrion, eating behavior, negative regulation of MAP kinase activity, muscle fiber development, neuromuscular process
209946_at VEGFC Angiogenesis, positive regulation of neuroblast proliferation, platelet degranulation, substrate-dependent cell migration, signal transduction, multicellular organismal development, blood coagulation, positive regulation of cell proliferation, organ morphogenesis, morphogenesis of embryonic epithelium, cell differentiation, platelet activation, regulation of vascular endothelial growth factor receptor signaling pathway, positive regulation of protein autophosphorylation, response to drug, positive regulation of blood vessel endothelial cell migration, negative regulation of blood pressure, vascular endothelial growth factor receptor signaling pathway, positive regulation of epithelial cell proliferation, positive regulation of protein secretion, positive chemotaxis, induction of positive chemotaxis, positive regulation of cell division, positive regulation of mast cell chemotaxis, positive regulation of lymphangiogenesis
232122_s_at VEPH1 -

Common genes among the upregulated probe sets in MSCs compared with diffuse-type GC (U133Plus2.0) and the upregulated probe sets in diffuse-type GC compared with intestinal-type GC (U95Av2).

Gene symbol U95Av2 probe set ID U133Plus2.0 probe set ID Ratio of MSCs (12) to GC (5) Entrez gene ID
PENK 38291_at 213791_at 24.4 5179
VEGFC 159_at 209946_at 18.2 7424
KCNK2 34087_at 210261_at 14.7 3776
IGFBP6 1736_at 203851_at 13.3 3489
RGS4 34272_at 204338_s_at 13.2 5999
MFAP5 36513_at 209758_s_at 11.5 8076
COMP 40162_s_at 205713_s_at 10.5 1311
ITGBL1 40681_at 231993_at 9.5 9358
MAP1B 39531_at 214577_at 9.4 4131
SERPINE2 41246_at 212190_at 8.1 5270
CRYAB 32243_g_at 209283_at 8.1 1410
TPM2 32314_g_at 212654_at 8.0 7169
NOV 39250_at 214321_at 8.0 4856
CYP1B1 859_at 202435_s_at 7.4 1545
TUSC3 36851_g_at 209228_x_at 7.3 7991
LTBP2 37906_at 204682_at 7.3 4053
LEPR 34267_r_at 211354_s_at 7.2 3953
FBN1 32535_at 202765_s_at 6.8 2200
PPP1R3C 39366_at 204284_at 6.6 5507
LOXL1 36811_at 203570_at 6.3 4016
PRKD1 123_at 205880_at 6.0 5587
CXCL12 33834_at 203666_at 5.5 6387
GAS6 1597_at 202177_at 5.4 2621
NUPR1 38754_at 209230_s_at 5.4 26471
NNMT 37032_at 202238_s_at 5.3 4837
CALD1 41739_s_at 201615_x_at 5.3 800
ARMCX2 36057_at 203404_at 5.0 9823
SGCB 37223_at 205120_s_at 5.0 6443
FGF7 1380_at 205782_at 5.0 2252
MXRA7 41273_at 235836_at 4.9 439921
AXL 1278_at 202686_s_at 4.9 558
CDH11 2087_s_at 207172_s_at 4.9 1009
ACTC1 39063_at 205132_at 4.8 70
NAV3 33235_at 204823_at 4.7 89795
THBS2 658_at 203083_at 4.5 7058
ELN 39098_at 212670_at 3.8 2006
STAC 40024_at 205743_at 3.8 6769
TPM1 36792_at 206117_at 3.8 7168
RECK 35234_at 205407_at 3.6 8434
DDR2 1319_at 227561_at 3.5 4921
DOK5 40401_at 214844_s_at 3.4 55816
PRUNE2 33442_at 212806_at 3.4 158471
GLRB 39665_at 205280_at 3.3 2743
DZIP1 36521_at 204556_s_at 3.3 22873
SGCD 41378_at 214492_at 3.3 6444
PCOLCE 31609_s_at 202465_at 3.3 5118
COX7A1 39031_at 204570_at 3.2 1346
EFEMP1 32551_at 201843_s_at 3.2 2202
PTRF 34320_at 208789_at 3.2 284119
ACTN1 39330_s_at 211160_x_at 3.1 87
PTGIS 36533_at 208131_s_at 3.0 5740
FEZ1 37743_at 203562_at 3.0 9638
EYA2 35226_at 209692_at 3.0 2139
CAP2 693_g_at 212554_at 3.0 10486
FERMT2 36577_at 214212_x_at 3.0 10979
TMEM47 37958_at 209655_s_at 2.9 83604
FAM127A 33856_at 201828_x_at 2.9 8933
RHOBTB3 32216_r_at 202976_s_at 2.8 22836
FAP 39945_at 209955_s_at 2.8 2191
LTBP1 1495_at 202728_s_at 2.7 4052
COL8A1 37459_at 226237_at 2.7 1295
BICC1 39506_at 213429_at 2.6 80114
CAV1 36119_at 203065_s_at 2.6 857
NAP1L3 743_at 204749_at 2.6 4675
CLIP3 36095_at 212358_at 2.5 25999
ZNF423 34950_at 214761_at 2.5 23090
GAS1 661_at 204457_s_at 2.5 2619
OBSL1 35781_g_at 212776_s_at 2.3 23363
IGFBP4 1737_s_at 201508_at 2.3 3487
COL6A2 34802_at 213290_at 2.2 1292
NR3C1 706_at 216321_s_at 2.2 2908
THY1 39395_at 208850_s_at 2.2 7070
KCNMA1 40737_at 221584_s_at 2.1 3778
SLC16A4 39260_at 205234_at 2.1 9122
SORBS2 39295_s_at 204288_s_at 2.1 8470
CDK5 1206_at 204247_s_at 2.1 1020
PALLD 41191_at 200906_s_at 2.0 23022