Gene expression profiling of gastric cancer by microarray combined with laser capture microdissection (2005)

AIM:To examine the gene expression profile of gastric cancer (GC) by combination of laser capture microdissection (LCM) and microarray and to correlate the profiling with histological subtypes. METHODS:Using LCM, pure cancer cells were procured from 45 cancerous tissues.After procurement of about 5 000 cells, total RNA was extracted and the quality of RNA was determined before further amplification and hybridization.One microgram of amplified RNA was converted to cDNA and hybridized to cDNA microarray.RESULTS: Among 45 cases, only 21 were qualified for their RNAs.A total of 62 arrays were performed.These included 42 arrays for cancer (21 cases with dyeswab duplication) and 20 arrays for non-tumorous cells (10 cases with dye-swab duplication) with universal reference.Analyzed data showed 504 genes were differentially expressed and could distinguish cancerous and non-cancerous groups with more than 99% accuracy.Of the 504 genes, trefoil factors 1, 2, and 3 were in the list and their expression patterns were consistent with previous reports.Immunohistochemical staining of trefoil factor 1 was also consistent with the array data.Analyses of the tumor group with these 504 genes showed that there were 3 subgroups of GC that did not correspond to any current classification system, including Lauren's classification.CONCLUSION: By using LCM, linear amplification of RNA, and cDNA microarray, we have identified a panel of genes that have the power to discriminate between GC and non-cancer groups.The new molecular classification Table 1 Up-regulated genes noted in gastric cancer Biosynthesis Argininosuccinate synthetase [BC009243], hydroxymethylbilane synthase [BC000520], hypothetical protein CL640 [BC008804], methylenetetrahydrofolate dehydrogenase (NADP + -dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase [BC001014] Cell adhesion Collagen, type XVIII, alpha 1 [AF01808], mesothelin [U40434], CD9 antigen (p24) (X60111), collagen, type VI, alpha 3 [X52022], thrombospondin 2 [L12350], immunoglobulin superfamily containing leucine-rich repeat [AB003184] Cell death Nerve growth factor receptor (TNFR superfamily, member 16) [M14764], phosphoprotein enriched in astrocytes 15 [AF153274], programmed cell death 5 [AF014955] Cell growth and/or maintenance Cell division cycle 25B [S78187], cyclin D2 [D13639], hippocalcin [BC001777], anillin, actin binding protein (scraps homolog, Drosophila) [AF273437], afamin [L32140], chromosome 14 open reading frame 58 [AK000378], C1q and tumor necrosis factor related protein 1 [AF32984], low density lipoprotein receptorrelated protein 8, apolipoprotein e receptor [D86407], enhancer of rudimentary homolog (Drosophila) [U66871], tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) [D11139], insulin receptor substrate 2 [AF073310], low density lipoprotein receptor-related protein 8, apolipoprotein e receptor [D50678], thyroid hormone receptor interactor 10 [AJ000414], collagen, type I, alpha 1 [Z74615], ATPase, Na + /K + transporting, beta 3 polypeptide [AF005896], T-LAK cell-originated protein kinase [AB027249], platelet-derived growth factor receptor, beta polypeptide [J03278], nucleolar protein 1 120 ku [BC000656], keratin 7 [BC002700], oncostatin M receptor [BC010943], tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) [BC000866], insulin-like growth factor 2 (somatomedin A) [S77035], karyopherin (importin) beta 1 [L38951], nuclear transport factor 2 (NTF-2) (Placental protein 15) (PP15) [X07315], nucleolar protein 1 120ku [X55504], thymosin beta-10 [S54005] Cell motility Hyaluronan-mediated motility receptor (RHAMM) [AF03286], sorcin [M32886], troponin T1, skeletal, slow [BC010963] Cell-cell signaling Ephrin-A2 [U92896], midkine (neurite growth-promoting factor 2) [X55110], prostaglandin I2 (prostacyclin) receptor (IP) [D25418] Immune response Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) [X14831], Human 1-8D gene from interferon-inducible gene family [X57351], GTP binding protein over-expressed in skeletal muscle [U10550], indoleamine-pyrrole 2,3 dioxygenase [M34455], interferon induced transmembrane protein 1 (9-27) [J04164] Macromolecule metabolism Cathepsin L2 [AB001928], PAK2 [AF09213], ribosomal protein, large P2 [M17887], hypothetical protein FLJ22761 [AK026414], KIAA0205 [D86960], proteasome (prosome, macropain) subunit, alpha type, 1 [D00759], protein tyrosine phosphatase type IVA, member 1 [U48296], peptidylprolyl isomerase (cyclophilin)-like 1 [BC003048], ribosomal protein L14 [BC009294], pyruvate kinase, muscle [BC007952], proteasome (prosome, macropain) subunit, alpha type, 7 [BC001895], isocitrate dehydrogenase 3 (NAD+) alpha [U07681], transglutaminase 4 (prostate) [U31905] Organogenesis Secreted protein, acidic, cysteine-rich (osteonectin) [M25743], caudal type homeo box transcription factor 2(CDX2) [AJ278434], transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) [M36711] Regulation of metabolism Homeo box B7 [BC015345], B-cell receptor-associated protein 37 [AF126021], Mediterranean fever [AJ003147], homeo box B7 [M16937], homeo box D4 [X17360], TIP49 [AB012122], sin3-associated polypeptide, 18 ku [AF153608] Response to stress Complement component 2 [X04481], complement component 3 [K02765], inhibin, beta A (activin A, activin AB alpha polypeptide) [X57579], serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 [K02212], serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) [D83174], meiotic recombination (S. cerevisiae) 11 homolog A [AF073362], RecQ protein-like 4 [BC013277] Signal transduction Secreted frizzled-related protein 4 [AF026692], lymphocyte antigen 6 complex, locus E(RIG-E) [Z68179], dimethylarginine dimethylaminohydrolase 2 [BC001435] Unclassified Angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 [BI826471], apolipoprotein C-I [AV709433], argininosuccinate synthetase [BF305206], ATPase, Ca ++ transporting, plasma membrane 4 [AI885833], ATPase, Na + /K + transporting, beta 3 polypeptide [AU151263], B-cell associated protein [BG771222], BTG family, member 2 [BG750101], cadherin 3, type 1, P-cadherin (placental) [NM001793], calcium modulating ligand [AW474551], carbonyl reductase 3 [AI658832], cathepsin Z [AI913006], CDC-like kinase 2 [BG286233], cell division cycle 25B [BF976307], CGI-01 protein [AK027886], chloride intracellular channel 1 [AA291390], claudin 4 [BI760179], claudin 7 [AI279608], collagen, type I, alpha 1 [AW577407], collagen, type X, alpha 1 (Schmid metaphyseal chondrodysplasia) [NM000493], core-binding factor, beta subunit [NM001755], D123 gene product [BE792735], deoxythymidylate kinase (thymidylate kinase) [BF312526], diubiquitin [AW270961], DKFZP566C134 protein [BG621382], E2F transcription factor 3 [AU153511], epithelial protein lost in neoplasm alpha [AAF23756], exostoses (multiple) 1 [BF057267], FK506-binding protein 4 (59 ku) [NM002014], follistatin-like 3 (secreted glycoprotein) [NM005860], forkhead box M1 [AL525810], glutamine-fructose-6-phosphate transaminase 2 [AK001242], GTP-binding protein over-expressed in skeletal muscle [AW297828], guanylate cyclase 2C (heat stable enterotoxin receptor) [NM004963], heme oxygenase (decycling) 1 [BI596354], HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2 [BG167159], Homo sapiens cDNA FLJ11796 fis, clone HEMBA1006158, highly similar to Homo sapiens transcription factor forkhead-like 7 [FKHL7] gene [BI914918], homo sapiens mRNA for short form of beta II spectrin, partial [AA131993], human cDNA: FLJ22528 fis, clone HRC12825 [AK026181], human cDNA: FLJ22998 fis, clone KAT11985, highly similar to AB000712 Human hCPE-R mRNA for CPE-receptor [AK026651], human chromosome 20 clone h119, complete sequence [AF312913], human claudin 3 [CLDN3] gene, [AF007189], regenerating islet-derived family, member 4 [AF254415], human genomic DNA, chromosome 22q11.2,clone KB1125A3 [AP000350], likely ortholog of mouse membrane bound C2 domain containing protein [AB018290], KIAA0930 protein [AB02314], hypothetical protein LOC90499 [AL137712], fuse-binding protein-interacting repressor [AF190744], Thy-1 cell surface antigen [M11749], biglycan [BC002416], CK2 interacting protein 1; HQ0024c protein [BC010149], hypothetical protein FLJ12436 [BC011993], tissue inhibitor of metalloprotease 1 (erythroid potentiating activity, collagenase inhibitor) [BC000866], hypothetical protein FLJ20277 [M11749], hypothetical protein FLJ22393 [H45848],hypothetical protein PRO1489 [AI536671], interferon induced transmembrane protein 1 (9-27) [BG506643], interferon induced transmembrane protein 3 (1-8U) [BE886918], interleukin 13 [NM002188], interleukin 8 [BG777366], JM4 protein [BI818455], keratin 7 [BI094014], keratin 7 [AA307373], KIAA0747 protein [BG744628], low density lipoprotein receptor-related protein 8, apolipoprotein e receptor [BF110337], lymphocyte antigen 6 complex, locus E [BM101706], matrix metalloproteinase 7 (matrilysin, uterine) [NM002423], membrane protein of cholingeric synaptic vesicles [BG760616], mesothelin [AI813749], midkine (neurite growth-promoting factor) [AI784469], msh (Drosophila) homeo box homolog 1 [AI912103], MyoD family inhibitor [BG675569], neural precursor cell expressed, developmentally down-regulated 5 [AU131176], neuromedin U [BG661038], NIPSNAP, C. elegans, homolog 1 [BC006473], nucleolar and coiled-body phosphoprotein [AL553791], platelet-derived growth factor receptor, beta polypeptide [BI755841], procollagen-lysine, 2-oxogutarate 5-dioxygenase 3 [AL544817], proliferating cell nuclear antigen [AA523378], proliferation-associated 2G4, 38KD [BI088072], protein C receptor, endothelial (EPCR) [BG831881], pyruvate kinase, muscle [BF690275], rhoG [BG338917], regulatory factor X, 5 [AW027312], ribosomal protein L23 [AI349581], ribosomal protein L35 [BF310946], ribosomal protein L37 [BG032793], ribosomal protein S16 [BG765030], ribosomal protein S3 [AA593872], S100 calciumbinding protein A4 [AV713821], serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin) [BG567810], sigma receptor (SR31747 binding protein 1) [AL571572], small inducible cytokine subfamily A (Cys-Cys), member 19 [W07401], superoxide dismutase 2, mitochondrial [BG773219], survival of motor neuron 1, telomeric [AA029190], thymosin, beta 10 [AV707021], thyroid hormone receptor interactor 10 [N98668], transKetolase [BI195990], translocase of outer mitochondrial membrane 34 [BE798732], trefoil factor 3 (intestinal) [AA633399], tumor suppressing subtransferable candidate 3 [BE670374], zinc finger protein 267 [AU128446] [ ]: GeneBank accession numberTable 2 Down-regulated genes noted cancer Biosynthesis 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase [D89976], adenosine monophosphate deaminase 1 (isoform M) [M60092], histidine decarboxylase [D16583], Human histidine decarboxylase (HDC) [M60445] Catabolism Human bilirubin UDP-glucuronosyltransferase isozyme 1 [M57899], Human placental cDNA coding for 5'nucleotidase (EC 3.1.3.5)[X55740] Cell adhesion Collagen, type IV, alpha 6 [D21337], collagen, type XVII, alpha 1[U76585], tenascin C (hexabrachion) [X78565], dermatopontin [AL049455], Human pancreatitis associated protein [M84337], sialic acid binding Ig-like lectin 11 [AF337818], Macaque brain cDNA clone:QflA-14173, full insert sequence [AB062939] Cell death Baculoviral IAP repeat-containing 1 [U80017], CD3E antigen, epsilon polypeptide (TiT3 complex) [X03884], programmed cell death 4 (neoplastic transformation inhibitor) [U96628] Cell growth and/or maintenance Core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related [S69002], ATPase, Ca++ transporting, ubiquitous [Z69881], ATPbinding cassette, sub-family C (CFTR/MRP), member 5 [AB005659], B-cell CLL/lymphoma 3 [M31732], CDC7 (cell division cycle 7, S. cerevisiae, homolog)like 1 [AF015592], gastrokine 1 [AB039886], Human chondroadherin mRNA, complete cds [AF371328], CDC28 protein kinase regulatory subunit 2 [X54942], solute