Clinicopathologic Correlation of Up-regulated Genes Identified Using cDNA Microarray and Real-time Reverse Transcription-PCR in Human Colorectal Cancer

Chiu, Sou-Tyau; Hsieh, Fon‐Jou; Chen, Shiwen; Chen, Chun-Lieh; Shu, Hwei-Fan; Li, Hung

doi:10.1158/1055-9965.epi-04-0396

Cited by 72 publications

(60 citation statements)

References 24 publications

(22 reference statements)

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“…Likewise, the up-regulation of THY1 in colon cancer microarray study together with real-time reverse transcription-PCR validation has been reported before (26), but there is also a report on the down-regulation of THY1 in metastatic nasopharyngeal carcinoma (27). Up-regulations of INHBA in pancreatic cancer (28) and oral tongue squamous cell carcinoma (OTSCC) (29) and of SERPINH1 in ductal adenocarcinomas (30,31) compared with corresponding matching non-tumor tissues are also in line with the expression pattern of these genes in gastric cancer as is shown in this report.…”

Section: Discussionsupporting

confidence: 56%

An 8-gene signature, including methylated and down-regulated glutathione peroxidase 3, of gastric cancer

Zhang

Yang²,

Kim³

et al. 2009

Int J Oncol

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Abstract.We have identified an 8-gene signature with significant expression differences between gastric cancer and normal gastric tissues. This 8-gene set can predict the normal and cancer status of gastric tissues with more than 96% accuracy in a totally independent microarray dataset. The 8 genes are composed of down-regulated KLF4, GPX3, SST and LIPF, together with up-regulated SERPINH1, THY1 and INHBA in gastric cancer. To corroborate the differential gene expression pattern, we chose GPX3 and examined its expression pattern in detail. A comparison of GPX3 expression pattern shows a broader down-regulated pattern in multiple types of cancers, including cervical, thyroid, head and neck, lung cancers and melanoma than in healthy controls. An immuno-histostaining analysis in tissue microarrays confirms GPX3 down-regulation in gastric cancer. Mechanism-wise GPX3 down-regulation in gastric cancer is due to promoter hypermethylation. Collectively, these results show a correct identification of 8 genes as gastric cancer biomarkers.

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Section: Discussionsupporting

confidence: 56%

An 8-gene signature, including methylated and down-regulated glutathione peroxidase 3, of gastric cancer

Zhang

Yang²,

Kim³

et al. 2009

Int J Oncol

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“…The microarray data were further validated by quantitative real-time PCR assay (Table 3; Fig. 3), as suggested by the conclusions of earlier studies (9,10).…”

Section: Discussionmentioning

confidence: 67%

A Susceptibility Gene Set for Early Onset Colorectal Cancer That Integrates Diverse Signaling Pathways: Implication for Tumorigenesis

Hong

et al. 2007

Clinical Cancer Research

165

142

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Purpose: The causative genes for autosomal dominantly inherited familial adenomatous polyposis (FAP) and hereditary nonpolyposis colorectal cancer have been well characterized. There is, however, another 10% to 15% of early onset colorectal cancers (CRC) in which the genetic components are unclear. In this study, we used microarray technology to systematically search for differentially expressed genes in early onset CRC. Experimental Design: Young patients with non^FAP or non^hereditary nonpolyposis colorectal cancer, and healthy controls were age-(V50 years old), ethnicity-(Chinese), and tissuematched. RNAs extracted from colonic mucosa specimens were analyzed using GeneChip U133-Plus 2.0 Array. Results: Seven genes, CYR61, UCHL1, FOS, FOS B, EGR1,VIP, and KRT24, were consistently upregulated in the mucosa of all six patients compared with the mucosa from four healthy controls. The overexpression of these genes was independently validated with a testing set of six patients and six healthy controls. Principal component analysis clustered the healthy control specimens separately from the patient specimens. Real-time PCR quantification with SYBR-Green on nine other patient specimens not previously used in microarray assays confirmed the up-regulation of these seven genes. These genes function in a multitude of biological processes ranging from transcription, angiogenesis, adhesion, and inflammatory regulation to protein catabolism in various cellular compartments, from extracellular to the nucleus.They integrate known tumorigenesis (Wnt, PI3K, MAP kinase, hypoxia, G protein^coupled receptor), neurologic, insulin-signaling, and NFAT-immune pathways into an intricate biological network. Conclusions: The data suggest that the patient's mucosa is primed for tumorigenesis when cellular homeostasis is disrupted, and that the seven overexpressed genes could potentially predict early onset CRC.

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“…Reactions were performed in triplicate, and relative quantification of gene expression was achieved using the efficiency-corrected method according to Pfaffl (2001). Primer sequences of the housekeeping genes ACTB, GAPDH, HPRT1, RPL13A, SDHA, B2M and YWHAZ were used as reported elsewhere (Chiu et al 2005;Pattyn et al 2003). …”

Section: Qrt-pcrmentioning

confidence: 99%

Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa

et al. 2012

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Significant health benefits have been demonstrated for certain probiotic strains through intervention studies; however, there is a shortage of experimental evidence relative to the mechanisms of action. Here, noninvasive experimental procedure based on a colon organ culture system has been used that, in contrast to most experimental in vitro models reported, can preserve natural immunohistochemical features of the human mucosa. This system has been used to test whether commensal lactobacilli (Lactobacillus paracasei BL23, Lactobacillus plantarum 299v and L. plantarum 299v (A -)) were able to hinder inflammation-like signals induced by phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO). Whole genome microarrays have been applied to analyze expression differences, from which mRNA markers could be inferred to monitor the effect of putative probiotic strains under such conditions. Regarding the gene expression, PMA/IO treatment induced not only interleukin (IL)-2 and interferon gamma (IFN-c), as expected, but also other relevant genes related to immune response and inflammation, such as IL-17A, chemokine (C-X-C motif) ligand (CXCL) 9 and CXCL11. The ex vivo culturing did not modify the pattern of expression of those genes or others related to inflammation. Interestingly, this study demonstrated that lactobacilli downregulated those genes and triggered a global change of the transcriptional profile that indicated a clear homeostasis restoring effect and a decrease in signals produced by activated T cells.

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Clinicopathologic Correlation of Up-regulated Genes Identified Using cDNA Microarray and Real-time Reverse Transcription-PCR in Human Colorectal Cancer

Cited by 72 publications

References 24 publications

An 8-gene signature, including methylated and down-regulated glutathione peroxidase 3, of gastric cancer

An 8-gene signature, including methylated and down-regulated glutathione peroxidase 3, of gastric cancer

A Susceptibility Gene Set for Early Onset Colorectal Cancer That Integrates Diverse Signaling Pathways: Implication for Tumorigenesis

Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa

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