Project description:Tumor-adjacent noncancerous tissues often exhibited abnormalities on molecular levels, which is described as field effect of cancerization. Accumulated evidence demonstrated that filed effect may also play important role in cancer progression. In the present study, we found that the gene expression profile in noncancerous lung tissues adjacent to lung squamous cell carcinoma (SCC) was significantly associated with regional lymph node status of patients. Significance Analysis of Microarrays (SAM) showed that 121 genes were significantly associated with lymph node metastasis (delta=0.75, FDR=0.069). Interestingly, all of the significant genes were up-regulated in the lymph node positive samples. For these genes, the most significant biological GO terms were extracellular structure organization, cell adhesion, regulation of cell motion/migration, and vessel development, etc, which were also involved in EMT process supported by another experiment in vitro. Tumor-adjacent histologically normal lung tissues were collected from 60 primary lung SCC patients, of whom 34 (56.7%) suffered regional lymph node metastasis. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray (G4112F).
Project description:Affymetrix exon array data set (HuEx-1.0_st) derived from matched pairs of non-small cell lung cancer (NSCLC) and normal adjacent lung tissue (NAT). This data set includes both the adenocarcinoma (AdCa) as well as the squamous cell carcinoma (SCC) subtype of NSCLC.
Project description:Tumor-adjacent noncancerous tissues often exhibited abnormalities on molecular levels, which is described as field effect of cancerization. Accumulated evidence demonstrated that filed effect may also play important role in cancer progression. In the present study, we found that the gene expression profile in noncancerous lung tissues adjacent to lung squamous cell carcinoma (SCC) was significantly associated with regional lymph node status of patients. Significance Analysis of Microarrays (SAM) showed that 121 genes were significantly associated with lymph node metastasis (delta=0.75, FDR=0.069). Interestingly, all of the significant genes were up-regulated in the lymph node positive samples. For these genes, the most significant biological GO terms were extracellular structure organization, cell adhesion, regulation of cell motion/migration, and vessel development, etc, which were also involved in EMT process supported by another experiment in vitro.
Project description:Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series. We analyzed genome-wide expression at the exon-level for two independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform. This series of samples represents the validation series.
Project description:Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series. We analyzed genome-wide expression at the exon-level for two independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform. This series of samples represents the test series.