Identification Of Molecular Markers Based On Integrative Analysis Of DNA Copy Number And MRNA Expression Profile In Gastric Cancer

Using high throughput biochip technology, based on DNA copy number andmRNA expression analysis in gastric cancer (GC), in order to discover new genes forGC diagnosis and classification, prognosis and treatment, laying a foundation forfurther insight into carcinogenesis and progression of GC. After strict pathologicalexamination of27GC and matched adjacent noncancerous tissues, we applied lasercapture microdissection (LCM) to obtain high purity GC and adjacent noncancerouscells for microarray experiments and profiled DNA copy number and gene expressionusing244K CGH Microarray and Human Exon1.0ST Microarray, and performedintegrative analysis of mRNA and array-based comparative genomic hybridization(aCGH) data.From aCGH, gain at8q11.1-q24.3was detected at the highest frequency (70%)and20q11.21-q12at the second (52%). Meanwhile the highest frequent copy numberloss was observed on6p25.3(33%). This study also found diverse chromosomalregion alterations for different TNM-stages or histological subtypes of GC. Withexpression analysis,260genes showed>2-fold changes in significantly differentialexpression (false discovery rate <0.01, frequency>50%samples). Interestingly, theoverexpression of CTHRC1was associated with tumor invasion. Integrative analysisof the CGH and expression data identified163genes with significant correlationsbetween DNA copy number and gene expression. Moreover, the C20orf11amplification and gain at20q13.33almost separated moderately differentiated (MD) GC from poorly differentiated (PD) type. The study applied stepwise logisticregression analysis to identify the best combination of the32biomarkers atchromosome8q and revealed a panel of SULF1, INTS8, ATP6V1C1, and GPR172Awith a prediction accuracy of98.0%for discriminating carcinomas from adjacentnoncancerous tissues (AUC=0.995). Besides, SULF1was related to tumor invasionand metastasis, and this was the first study to report cancer-associated copy numberamplification and overexpression of GPR172A gene. Annotated functions of the4-marker panel suggested that acidification of intracellular compartments may playimportant roles in the progression of GC. In addition, it was the first time for thisfinding that expression of MCM4, PRKDC, and UBE2V2at8q11.21, or YWHAZ,ANKRD46, ZNF706, and GRHL2at8q22.3was co-regulation and was concordantlyup-regulated in the samples of GC with amplification at8q11.21or8q22.3.Through integrative analysis of copy number and expression data, this studyrevealed diverse chromosomal region alterations for different TNM-stages orhistological subtypes of GC, which is helpful in researching clinicopathologicalclassification, and provided a4-marker panel that may improve the diagnosticaccuracy of GC. Moreover, it was the first time to find that C20orf11was inassociation with differentiation, and verified the previous reports of SULF1andCTHRC1associated with invasion and metastasis. Besides, the research also pointedout some candidate markers (GPR172A, UNQ473, MCM4, YWHAZ, etc.) anddeepened the understanding of GC.