Choong-Chin Liew

Blood-based biomarkers can differentiate ulcerative colitis from Crohn's disease and noninflammatory diarrhea.

Background: Blood gene expression profiling has been used in several studies to identify patients with a number of conditions and diseases. A blood test with the ability to differentiate Crohns disease (CD) from ulcerative colitis (UC) and noninflammatory diarrhea would be useful in the clinical management of these diseases. Methods: Affymetrix U133Plus 2.0 GeneChip oligonucleotide arrays were used to generate whole blood gene expression profiles for 21 patients with UC, 24 patients with CD, and 10 control patients with diarrhea, but without colonic pathology. Results: A supervised learning method (logistic regression) was used to identify specific panels of probe sets which were able to discriminate between UC and CD and from controls. The UC panel consisted of the four genes, CD300A, KPNA4, IL1R2, and ELAVL1; the CD panel comprised the four genes CAP1, BID, NIT2, and NPL. These panels clearly differentiated between CD and UC. Conclusions: Gene expression profiles from blood can differentiate patients with CD from those with UC and from noninflammatory diarrheal disorders. (Inflamm Bowel Dis 2011;)

Differential regulation of peripheral leukocyte genes in patients with active Crohn's disease and Crohn's disease in remission.

Goals Assessment of disease severity is a frequent challenge in the management of Crohns disease. Noninvasive, accurate markers for monitoring disease activity are urgently required. Specific gene expression patterns and molecular biomarkers associated with active Crohns disease could serve as such markers, thereby providing a novel approach to disease activity monitoring. Background Gene expression profiling in circulating leukocytes has shown promise in several medical conditions and blood may provide an easily accessible surrogate tissue for using gene expression profiling to assess activity of Crohns disease. Study In this study, we compared genome-wide transcription profiles of circulating leukocytes in patients with active and quiescent Crohns disease. Results We observed complex changes in blood gene expression patterns in active Crohns disease: genes of various functional categories were differentially regulated between active and inactive Crohns disease. We specifically identified a number of inflammatory molecules overexpressed or underexpressed in active Crohns disease and validated a subset of these genes by real-time reverse transcription-polymerase chain reaction. Conclusions The genes differentially regulated in peripheral leukocytes represent potential new biomarkers for assessing the activity of Crohns disease.

Blood-based Biomarkers Used to Predict Disease Activity in Crohnʼs Disease and Ulcerative Colitis

Background:Identifying specific genes that are differentially expressed during inflammatory bowel disease flares may help stratify disease activity. The aim of this study was to identify panels of genes to be able to distinguish disease activity in Crohns disease (CD) and ulcerative colitis (UC). Methods:Patients were grouped into categories based on disease and severity determined by histological grading. Whole blood was collected by PAXgene Blood RNA collection tubes, (PreAnalytiX) and gene expression analysis using messenger RNA was conducted. Logistic regression was performed on multiple combinations of common probe sets, and data were evaluated in terms of discrimination by computing the area under the receiving operator characteristic curve (ROC–AUC). Results:Nine inactive CD, 8 mild CD, 10 moderate-to-severe CD, 9 inactive UC, 8 mild UC, 10 moderate-to-severe UC, and 120 controls were hybridized to Affymetrix U133 Plus 2 microarrays. Panels of 6 individual genes discriminated the stages of disease activity: CD with mild severity {ROC–AUC, 0.89 (95% confidence interval [CI], 0.84%–0.95%)}, CD with moderate-to-severe severity (ROC–AUC 0.98 [95% CI, 0.97–1.0]), UC with mild severity (ROC–AUC 0.92 [95% CI, 0.87–0.96]), and UC with moderate-to-severe severity (ROC–AUC 0.99 [95% CI, 0.97–1.0]). Validation by real-time reverse transcription–PCR confirmed the Affymetrix microarray data. Conclusions:The specific whole blood gene panels reliably distinguished CD and UC and determined the activity of disease, with high sensitivity and specificity in our cohorts of patients. This simple serological test has the potential to become a biomarker to determine the activity of disease.

Blood RNA biomarker panel detects both left- and right-sided colorectal neoplasms: a case-control study

BackgroundColonoscopy is widely regarded to be the gold standard for colorectal cancer (CRC) detection. Recent studies, however, suggest that the effectiveness of colonoscopy is mostly confined to tumors on the left side of the colon (descending, sigmoid, rectum), and that the technology has poor tumor detection for right-sided (cecum, ascending, transverse) lesions. A minimally invasive test that can detect both left-sided and right-sided lesions could increase the effectiveness of screening colonoscopy by revealing the potential presence of neoplasms in the right-sided “blind spot”.MethodsWe previously reported on a seven-gene, blood-based biomarker panel that effectively stratifies a patient’s risk of having CRC. For the current study, we assessed the effectiveness of the seven-gene panel for the detection of left- and right-sided CRC lesions. Results were evaluated for 314 patients with CRC (left-sided: TNM I, 65; TNM II, 57; TNM III, 60; TNM IV, 17; unknown, 9. right-sided: TNM I, 28; TNM II, 29; TNM III, 38; TNM IV, 12; unknown, 1 and including two samples with both left and right lesions) and 328 control samples. Blood samples were obtained prior to clinical staging and therapy. Most CRC subjects had localized disease (stages I and II, 58%); regional (stage III) and systemic (stage IV) disease represented 32% and 9%, respectively, of the study population.ResultsThe panel detected left-sided (74%, 154/208) and right-sided (85%, 92/108) lesions with an overall sensitivity of 78% (215/316) at a specificity of 66% (215/328). Treatable cancer (stages I to III) was detected with left-sided lesion sensitivity of 76% (138/182) and right-sided sensitivity of 84% (80/95).ConclusionThis seven-gene biomarker panel detected right-sided CRC lesions across all cancer stages with a sensitivity that is at least equal to that for left-sided lesions. This study supports the use of this panel as the basis for a patient-friendly, blood-based test that can be easily incorporated into a routine physical examination in advance of colonoscopy to provide a convenient companion diagnostic and a pre-screening alert, ultimately leading to enhanced CRC screening effectiveness.

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

Despite significant improvements in our understanding of Crohns 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.

Application of a Blood-based Dynamic Genome Signature: How MAS5/RMA/PLIER Normalization Batches Affect Measured Gene Expression Profiling Stability in Clinical Diagnosis

Objective: A number of studies compare the microarray normalization methods MAS5 (Microarray Suite Version 5), RMA (Robust Multi-array Average) and PLIER (Probe Logarithmic Error Intensity Estimate) with respect to the rate at which genes of interest are identified. Here we evaluate and compare the stability of the measured gene expression when identical or technical replicate arrays are analyzed in batches of differing sizes and composition. These variations in measured gene expression have implications for clinical applications, which have requirements that differ significantly from those of research applications.Methods: We evaluated the samples from data set E-MTAB-1532, available on ArrayExpress, a public repository of microarray data using the MAS5, RMA, and PLIER methods. We then evaluated a sample run as triplicate arrays and compared results among the different normalization methods.Results and conclusion: Our study found that for some applications MAS5 is superior to the other methods, although the MAQC (Micro Array Quality Control) project, which extensively evaluated the performance of the platforms, reached a different conclusion.