Gene expression signatures for identifying diffuse-type gastric cancer associated with epithelial-mesenchymal transition

  • Authors:
    • Shihori Tanabe
    • Kazuhiko Aoyagi
    • Hiroshi Yokozaki
    • Hiroki Sasaki
  • View Affiliations

  • Published online on: April 11, 2014     https://doi.org/10.3892/ijo.2014.2387
  • Pages: 1955-1970
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Abstract

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.

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.

Table I.

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

Table I.

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

Probe set IDGene symbolGene titleRatioP-value (non-equal variance)P-value (equal variance)Entrez gene ID
206157_atPTX3Pentraxin 3, long56.91.303E-112.124E-115806
214702_atFN1Fibronectin 143.71.116E-106.76E-102335
215446_s_atLOXLysyl oxidase14.85.836E-106.504E-094015
207558_s_atPITX2Paired-like homeodomain 211.71.076E-095.864E-085308
202952_s_atADAM12ADAM metallopeptidase domain 1219.54.79E-093.948E-078038
214701_s_atFN1Fibronectin 126.63.694E-084.612E-072335
204421_s_atFGF2Fibroblast growth factor 2 (basic)10.96.115E-081.72E-062247
233533_atKRTAP1-5Keratin associated protein 1–5163.76.246E-087.787E-0783895
209946_atVEGFCVascular endothelial growth factor C13.76.864E-081.278E-067424
203438_atSTC2Atanniocalcin 250.26.959E-089.427E-078614
228367_atALPK2α-kinase 221.47.576E-081.14E-06115701
239367_atBDNFBrain-derived neurotrophic factor16.51.442E-073.538E-06627
203439_s_atSTC2Stanniocalcin 254.73.842E-076.59E-068614
201387_s_atUCHL1Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)13.96.127E-071.232E-057345
207345_atFSTFollistatin11.67.941E-071.709E-0510468
204948_s_atFSTFollistatin22.51.041E-062.488E-0510468
204298_s_atLOXLysyl oxidase54.21.615E-063.207E-054015
203851_atIGFBP6Insulin-like growth factor binding protein 610.21.752E-065.669E-053489
226847_atFSTFollistatin23.01.913E-064.582E-0510468
219789_atNPR3Natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)58.12.108E-064.278E-054883
206307_s_atFOXD1Forkhead box D111.12.308E-060.00010042297
236532_atC11orf87Chromosome 11 open reading frame 87181.33.351E-066.966E-05399947
213791_atPENKProenkephalin18.63.43E-069.108E-055179
203440_atCDH2Cadherin 2, type 1, N-cadherin (neuronal)19.86.446E-060.00016631000
219729_atPRRX2Paired related homeobox 216.96.459E-060.000154251450
243813_atLINC00968Long intergenic non-protein coding RNA 96847.08.462E-060.0001846100507632
210261_atKCNK2Potassium channel, subfamily K, member 211.01.158E-050.00034143776
206382_s_atBDNFBrain-derived neurotrophic factor44.61.159E-050.0002555627
1557181_s_atC11orf87Chromosome 11 open reading frame 87293.21.54E-050.0003308399947
219054_atNPR3Natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)28.31.911E-050.00042164883
1557180_atC11orf87Chromosome 11 open reading frame 8721.72.153E-050.0004803399947
235417_atSPOCD1SPOC domain containing 130.22.557E-050.000560390853
223618_atFMN2Formin 222.22.976E-050.000656656776
209905_atHOXA10-HOXA9, HOXA9, MIR196BHOXA10-HOXA9 readthrough, homeobox A9, microRNA 196b11.23.068E-050.0008075100534589, 3205, 442920
210367_s_atPTGESProstaglandin E synthase19.03.112E-050.00068889536
201107_s_atTHBS1Thrombospondin 127.73.53E-050.00076767057
213707_s_atDLX5Distal-less homeobox 511.74.045E-050.00097571749
239202_atRAB3BRAB3B, member RAS oncogene family11.84.595E-050.00109325865
204602_atDKK1Dickkopf 1 homolog (Xenopus laevis)11.74.785E-050.001379822943
210121_atB3GALT2UDP-Gal:βGlcNAc β 1,3-galactosyltransferase, polypeptide 212.44.992E-050.00112948707
232122_s_atVEPH1Ventricular zone expressed PH domai homolog 1 (zebrafish)11.96.254E-050.001556379674
229641_atCCBE1Collagen and calcium binding EGF domains 118.26.7E-050.001394147372
1555471_a_atFMN2Formin 213.86.858E-050.001604556776
219790_s_atNPR3Natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)50.17.041E-050.00141664883
222862_s_atAK5Adenylate kinase 515.37.202E-050.001560126289
1552487_a_atBNC1Basonuclin 111.78.369E-050.0019519646
230112_atMARCH4Membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase15.38.722E-050.001991257574
244623_atKCNQ5Potassium voltage-gated channel, KQT-like subfamily, member 511.39.102E-050.001888856479
213640_s_atLOXLysyl oxidase29.99.205E-050.00184144015
217452_s_atB3GALT2UDP-Gal:βGlcNAc β 1,3-galactosyltransferase, polypeptide 213.09.284E-050.00198098707
235548_atAPCDD1LAdenomatosis polyposis coli downregulated 1-like36.29.734E-050.0019595164284

Table II.

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

Table II.

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

Probe set IDGene symbolGene ontology biological process
202952_s_atADAM12Proteolysis, cell adhesion, epidermal growth factor receptor signaling pathway, myoblast fusion
222862_s_atAK5 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_atALPK2Protein phosphorylation, phosphorylation
235548_atAPCDD1L-
210121_atB3GALT2Protein glycosylation, oligosaccharide biosynthetic process
217452_s_at
239367_atBDNFUreteric 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_atBNC1Transcription, 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_atC11orf87-
1557180_at
1557181_s_at
229641_atCCBE1Angiogenesis, lymphangiogenesis, sprouting angiogenesis, multicellular organismal development, venous blood vessel morphogenesis
203440_atCDH2Cell 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_atDKK1Negative 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_atDLX5Skeletal 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_atFGF2Activation 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_atFMN2Transport, 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_atFN1Angiogenesis, 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_atFOXD1Neural 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_atFSTNegative 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_atHOXA10-HOXA9, HOXA9, MIR196BTranscription, 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_atIGFBP6Regulation of cell growth, signal transduction, negative regulation of cell proliferation, cellular protein metabolic process
210261_atKCNK2Transport, ion transport, potassium ion transport, G-protein coupled receptor signaling pathway, synaptic transmission, regulation of ion transmembrane transport, potassium ion transmembrane transport
244623_atKCNQ5Protein complex assembly, transport, ion transport, potassium ion transport, synaptic transmission, regulation of ion transmembrane transport, transmembrane transport, potassium ion transmembrane transport
233533_atKRTAP1-5-
243813_atLINC00968-
204298_s_atLOXBlood 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_atMARCH4Protein ubiquitination
219054_atNPR3Skeletal 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_atPENKBehavioral fear response, signal transduction, neuropeptide signaling pathway, behavior, sensory perception of pain
207558_s_atPITX2Negative 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_atPRRX2Positive 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_atPTGESProstaglandin 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_atPTX3Response to yeast, inflammatory response, opsonization, positive regulation of nitric oxide biosynthetic process, positive regulation of phagocytosis
239202_atRAB3BGTP catabolic process, transport, intracellular protein transport, nucleocytoplasmic transport, signal transduction, small GTPase mediated signal transduction, protein transport, regulation of exocytosis, peptidyl-cysteine methylation
235417_atSPOCD1Transcription, DNA-dependent, negative regulation of phosphatase activity
203438_atSTC2Cellular 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_atTHBS1Activation 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_atUCHL1Proteolysis, 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_atVEGFCAngiogenesis, 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_atVEPH1-

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).

Table III.

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).

Table III.

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 symbolU95Av2 probe set IDU133Plus2.0 probe set IDRatio of MSCs (12) to GC (5)Entrez gene ID
PENK38291_at213791_at24.45179
VEGFC159_at209946_at18.27424
KCNK234087_at210261_at14.73776
IGFBP61736_at203851_at13.33489
RGS434272_at204338_s_at13.25999
MFAP536513_at209758_s_at11.58076
COMP40162_s_at205713_s_at10.51311
ITGBL140681_at231993_at9.59358
MAP1B39531_at214577_at9.44131
SERPINE241246_at212190_at8.15270
CRYAB32243_g_at209283_at8.11410
TPM232314_g_at212654_at8.07169
NOV39250_at214321_at8.04856
CYP1B1859_at202435_s_at7.41545
TUSC336851_g_at209228_x_at7.37991
LTBP237906_at204682_at7.34053
LEPR34267_r_at211354_s_at7.23953
FBN132535_at202765_s_at6.82200
PPP1R3C39366_at204284_at6.65507
LOXL136811_at203570_at6.34016
PRKD1123_at205880_at6.05587
CXCL1233834_at203666_at5.56387
GAS61597_at202177_at5.42621
NUPR138754_at209230_s_at5.426471
NNMT37032_at202238_s_at5.34837
CALD141739_s_at201615_x_at5.3800
ARMCX236057_at203404_at5.09823
SGCB37223_at205120_s_at5.06443
FGF71380_at205782_at5.02252
MXRA741273_at235836_at4.9439921
AXL1278_at202686_s_at4.9558
CDH112087_s_at207172_s_at4.91009
ACTC139063_at205132_at4.870
NAV333235_at204823_at4.789795
THBS2658_at203083_at4.57058
ELN39098_at212670_at3.82006
STAC40024_at205743_at3.86769
TPM136792_at206117_at3.87168
RECK35234_at205407_at3.68434
DDR21319_at227561_at3.54921
DOK540401_at214844_s_at3.455816
PRUNE233442_at212806_at3.4158471
GLRB39665_at205280_at3.32743
DZIP136521_at204556_s_at3.322873
SGCD41378_at214492_at3.36444
PCOLCE31609_s_at202465_at3.35118
COX7A139031_at204570_at3.21346
EFEMP132551_at201843_s_at3.22202
PTRF34320_at208789_at3.2284119
ACTN139330_s_at211160_x_at3.187
PTGIS36533_at208131_s_at3.05740
FEZ137743_at203562_at3.09638
EYA235226_at209692_at3.02139
CAP2693_g_at212554_at3.010486
FERMT236577_at214212_x_at3.010979
TMEM4737958_at209655_s_at2.983604
FAM127A33856_at201828_x_at2.98933
RHOBTB332216_r_at202976_s_at2.822836
FAP39945_at209955_s_at2.82191
LTBP11495_at202728_s_at2.74052
COL8A137459_at226237_at2.71295
BICC139506_at213429_at2.680114
CAV136119_at203065_s_at2.6857
NAP1L3743_at204749_at2.64675
CLIP336095_at212358_at2.525999
ZNF42334950_at214761_at2.523090
GAS1661_at204457_s_at2.52619
OBSL135781_g_at212776_s_at2.323363
IGFBP41737_s_at201508_at2.33487
COL6A234802_at213290_at2.21292
NR3C1706_at216321_s_at2.22908
THY139395_at208850_s_at2.27070
KCNMA140737_at221584_s_at2.13778
SLC16A439260_at205234_at2.19122
SORBS239295_s_at204288_s_at2.18470
CDK51206_at204247_s_at2.11020
PALLD41191_at200906_s_at2.023022
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 (2022). 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.

Acknowledgements

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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June-2014
Volume 44 Issue 6

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Tanabe S, Aoyagi K, Yokozaki H and Sasaki H: Gene expression signatures for identifying diffuse-type gastric cancer associated with epithelial-mesenchymal transition. Int J Oncol 44: 1955-1970, 2014
APA
Tanabe, S., Aoyagi, K., Yokozaki, H., & Sasaki, H. (2014). Gene expression signatures for identifying diffuse-type gastric cancer associated with epithelial-mesenchymal transition. International Journal of Oncology, 44, 1955-1970. https://doi.org/10.3892/ijo.2014.2387
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Tanabe, S., Aoyagi, K., Yokozaki, H., Sasaki, H."Gene expression signatures for identifying diffuse-type gastric cancer associated with epithelial-mesenchymal transition". International Journal of Oncology 44.6 (2014): 1955-1970.
Chicago
Tanabe, S., Aoyagi, K., Yokozaki, H., Sasaki, H."Gene expression signatures for identifying diffuse-type gastric cancer associated with epithelial-mesenchymal transition". International Journal of Oncology 44, no. 6 (2014): 1955-1970. https://doi.org/10.3892/ijo.2014.2387