[Identification of colorectal cancer, adenoma, and inflammatory bowel disease specific gene expression patterns using whole genomic oligonucleotide microarray system]

Use of blood based biomarkers in the evaluation of Crohn’s disease and ulcerative colitis

Despite significant improvements in our understanding of Crohn’s disease (CD) and ulcerative colitis (UC) in recent years, questions remain regarding the best approaches to assessment and management of these chronic diseases during periods of both relapse and remission. Various serologic biomarkers have been used in the evaluation of patients with both suspected and documented inflammatory bowel disease (IBD), and while each has potential utility in the assessment of patients with IBD, potential limitation remain with each method of assessment. Given these potential shortcomings, there has been increased interest in other means of evaluation of patients with IBD, including an expanding interest in the role of gene expression profiling. Among patients with IBD, gene expression profiles obtained from whole blood have been used to differentiate active from inactive CD, as well as to differentiate between CD, UC, and non-inflammatory diarrheal conditions. There are many opportunities for a non-invasive, blood based test to aid in the assessment of patients with IBD, particularly when considering more invasive means of evaluation including endoscopy with biopsy. Furthermore, as the emphasis on personalized medicine continues to increase, the potential ability of gene expression analysis to predict patient response to individual therapies offers great promise. While whole blood gene expression analysis may not completely replace more traditional means of evaluating patients with suspected or known IBD, it does offer significant potential to expand our knowledge of the underlying genes involved in the development of these diseases.

De Novo proteome analysis of genetically modified tumor cells by a metabolic labeling/azide-alkyne cycloaddition approach

Activin receptor type II (ACVR2) is a member of the transforming growth factor type II receptor family and controls cell growth and differentiation, thereby acting as a tumor suppressor. ACVR2 inactivation is known to drive colorectal tumorigenesis. We used an ACVR2-deficient microsatellite unstable colon cancer cell line (HCT116) to set up a novel experimental design for comprehensive analysis of proteomic changes associated with such functional loss of a tumor suppressor. To this end we combined two existing technologies. First, the ACVR2 gene was reconstituted in an ACVR2-deficient colorectal cancer (CRC) cell line by means of recombinase-mediated cassette exchange, resulting in the generation of an inducible expression system that allowed the regulation of ACVR2 gene expression in a doxycycline-dependent manner. Functional expression in the induced cells was explicitly proven. Second, we used the methionine analog azidohomoalanine for metabolic labeling of newly synthesized proteins in our cell line model. Labeled proteins were tagged with biotin via a Click-iT chemistry approach enabling specific extraction of labeled proteins by streptavidin-coated beads. Tryptic on-bead digestion of captured proteins and subsequent ultra-high-performance LC coupled to LTQ Orbitrap XL mass spectrometry identified 513 proteins, with 25 of them differentially expressed between ACVR2-deficient and -proficient cells. Among these, several candidates that had already been linked to colorectal cancer or were known to play a key role in cell growth or apoptosis control were identified, proving the utility of the presented experimental approach. In principle, this strategy can be adapted to analyze any gene of interest and its effect on the cellular de novo proteome.

Significance and expression of aquaporin 1, 3, 8 in cervical carcinoma in Xinjiang Uygur women of China

Overexpression of several aquaporins (AQPs) has been reported in different types of human cancer but their role in carcinogenesis, for example in the cervix, have yet to be clearly defined. In this study, expression of AQPs in cervical carcinomawas investigated by real-time PCR, immunofluorescent and immunohistochemical assays and evaluated for correlations with clinicopathologic variables. AQP1, 3, 8 exhibited differential expression in cervical carcinoma, corresponding CIN and mild cervicitis. AQP1 was predominantly localized in the microvascular endothelial cell in the stroma of mild cervicitis, CIN and cervical carcinoma. AQP3 and AQP8 were localized in the membrane of normal squamous epithelium and carcinoma cells, local signals being more common than diffuse staining. AQP1 and AQP3 expression was remarkably stronger in cervical cancer than in mild cervicitis and CIN2-3 (P<0.05). AQP8 expression was highest in CIN2-3 (91.7%), but levels in cervical carcinoma were also higher than in mild cervicitis. AQP1, AQP3, AQP8 expression significantly increased in advanced stage, deeper infiltration, metastatic lymph nodes and larger tumor volume (P<0.05). Our findings showed that AQPs might play important roles in cervical carcinogenesis and tumour progression in Uygur women.

Linking obesity to colorectal cancer: application of nutrigenomics

Diet is one of the most affective environmental factors in cancer development. Due to complicated nature of the diet, it has been very difficult to provide clear explanations for the role of dietary components in carcinogenesis. However, as high-throughput omics techniques became available, researchers are now able to analyze large sets of gene transcripts, proteins, and metabolites to identify molecules involved in disease development. Bioinformatics uses these data to perform network analyses and suggest possible interactions between metabolic processes and environmental factors. Obesity is known as one of the most closely related risk factors of colorectal cancer (CRC). Metabolic disturbances due to a positive energy balance may trigger and accelerate CRC development. In this review, we have summarized reports on genes, proteins and metabolites that are related to either obesity or CRC, and suggested candidate molecules linking obesity and CRC based on currently available literature. Possible application of bioinformatics for a large scale network analysis in studying cause-effect relationship between dietary components and CRC are suggested.

A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes

Sequence tag count-based gene expression analysis is potent for the identification of candidate genes relevant to the cancerous phenotype. With the public availability of count-based data, the computational approaches for differentially expressed genes, which are mainly based on Binomial or beta-Binomial distribution, become practical and important in cancer biology. It remains a permanent need to select a proper statistical model for these methods. In this study, we developed a novel Bayesian algorithm-based method, Electronic Differential Gene Expression Screener (EDGES), in which a statistical model was determined by geometric averaging of 12 common housekeeping genes. EDGES identified a set of differentially expressed genes in lung, breast and colorectal cancers by using publically available Serial Analysis of Gene Expression (SAGE) and Expressed Sequence Tag (EST data). Gene expression microarray analysis and quantitative reverse transcription real-time PCR demonstrated the effectiveness of this procedure. We conclude that current normalization of calibrators provides a new insight into count-based digital subtraction in cancer research.

[mRNA expression analysis and classification of colonic biopsy samples using oligonucleotide and cDNA microarray techniques]

Despite tremendous progress in the past few decades, certain important aspects regarding the diagnosis, therapy, and follow-up of colorectal cancer still remain unsolved. In our work we searched for biomarkers of the development of colorectal carcinoma, and performed gene expression analysis for colorectal disease classification. We have established that the oligonucleotide microarray analyses of biopsy samples wholly fulfil the Affymetrix quality requirements, are highly standard and reproducible and the Taqman microfluidic card system is suitable for high-throughput, quick and cost efficient real-time-PCR validation of gene expression changes. We have shown that the sequential overexpression of osteopontin and osteonectin mRNAs and proteins significantly correlates with the progression of the colorectal adenoma-dysplasia-carcinoma sequence. We have identified and validated ten novel markers with continuously increasing mRNA expression in line with the adenoma-dysplasia-carcinoma transition. We have identified the top 27, 13 and 10 genes associated with adenoma, colorectal cancer, and inflammatory bowel diseases.