scholarly journals Micro RNA HSA-486-3P Gene Expression Profiling in the Whole Blood of Patients with Autism

2012 ◽  
Vol 26 (6) ◽  
pp. 3385-3388 ◽  
Author(s):  
Nikolay Todorov Popov ◽  
Nadejda Petrova Madjirova ◽  
Ivan Nikiforov Minkov ◽  
Tihomir Iliev Vachev
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Micro Rna

Novel method for rapid enrichment of high purity circulating tumor cells (CTCs) for prostate cancer (PCa) gene expression profiling.

2018 ◽  
Vol 36 (6_suppl) ◽  
pp. 271-271
Author(s):  
Gareth Morrison ◽  
Nita Jojo ◽  
Alexander Cunha ◽  
Yucheng Xu ◽  
Peggy S. Robinson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Gene Expression Profiling ◽  
High Purity ◽  
Whole Blood ◽  
Expression Profiling ◽  
Cell Recovery ◽  
Enrichment Method ◽  
Qrt Pcr ◽  
Cd45 Depletion

271 Background: CTC RNA analysis currently involves single cell recovery that is laborious and expensive, or alternatively lysis of preserved whole blood which yields RNA predominantly from leukocytes which vastly outnumber CTCs. To effectively characterize gene expression in large patient cohorts, new enrichment methodologies are needed that yield high purity CTC populations while preserving RNA integrity. Here we describe a simple yet robust method for enrichment of prostate CTCs for gene expression analysis. Methods: Blood was drawn with informed consent under an IRB-approved protocol. For initial optimization, CFSE-stained PCa cells were spiked into healthy blood and recovered using various combinations of 2 methods: microfluidic enrichment (Parsortix™ system) and CD45 depletion. For assay qualification, a prostate-specific multiplexed qRT-PCR gene expression panel was developed. Enrichment and gene expression were tested initially using PCa cell lines spiked into healthy blood, then metastatic castrate resistant prostate cancer (mCRPC) blood samples in parallel with CellSearch enumeration. Results: Optimal enrichment of live cells was achieved with CD45 depletion followed by microfluidic enrichment, resulting in an average spiked cell recovery of 30% and approximately 100 contaminating background leukocytes. Using this enrichment method, prostate specific genes were detectable by multiplexed qRT-PCR down to 25 cells spiked into 7.5 ml whole blood, and transcripts were not measurable in matched healthy blood controls. When applied to mCRPC patient blood containing CTCs by CellSearch, multiplexed qRT-PCR successfully detected prostate specific genes in all samples. Conclusions: We developed a novel enrichment method capable of rapidly and efficiently recovering live CTCs with high purity, free of magnetic beads and with very few background leukocytes. Captured cells yielded high-quality RNA with high sensitivity and specificity for prostate-specific transcripts. This approach is applicable to high throughput gene expression profiling assays and offers an alternative to laborious single cell recovery or non-cancer-specific whole blood fixation.

scholarly journals Gene expression profiling in whole blood of patients with coronary artery disease

2010 ◽  
Vol 119 (8) ◽  
pp. 335-343 ◽  
Author(s):  
Chiara Taurino ◽  
William H. Miller ◽  
Martin W. McBride ◽  
John D. McClure ◽  
Raya Khanin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Gene Expression Analysis ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Artery Disease

Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent whole-blood gene expression analysis before and after the completion of a cardiac rehabilitation programme following surgical coronary revascularization. mRNA and miRNA (microRNA) were isolated for expression profiling. Gene expression analysis identified 365 differentially expressed genes in patients with CAD compared with healthy controls (175 up- and 190 down-regulated in CAD), and 645 in CAD rehabilitation patients (196 up- and 449 down-regulated post-rehabilitation). Biological pathway analysis identified a number of canonical pathways, including oxidative phosphorylation and mitochondrial function, as being significantly and consistently modulated across the groups. Analysis of miRNA expression revealed a number of differentially expressed miRNAs, including hsa-miR-140-3p (control compared with CAD, P=0.017), hsa-miR-182 (control compared with CAD, P=0.093), hsa-miR-92a and hsa-miR-92b (post- compared with pre-exercise, P<0.01). Global analysis of predicted miRNA targets found significantly reduced expression of genes with target regions compared with those without: hsa-miR-140-3p (P=0.002), hsa-miR-182 (P=0.001), hsa-miR-92a and hsa-miR-92b (P=2.2×10−16). In conclusion, using whole blood as a ‘surrogate tissue’ in patients with CAD, we have identified differentially expressed miRNAs, differentially regulated genes and modulated pathways which warrant further investigation in the setting of cardiovascular function. This approach may represent a novel non-invasive strategy to unravel potentially modifiable pathways and possible therapeutic targets in cardiovascular disease.

scholarly journals Effects of Storage, RNA Extraction, Genechip Type, and Donor Sex on Gene Expression Profiling of Human Whole Blood

2007 ◽  
Vol 53 (6) ◽  
pp. 1038-1045 ◽  
Author(s):  
Sung Jae Kim ◽  
David J Dix ◽  
Kary E Thompson ◽  
Rachel N Murrell ◽  
Judith E Schmid ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Extraction Technique ◽  
Interindividual Differences ◽  
Human Whole Blood ◽  
Rna Quality

Abstract Background: Gene expression profiling of whole blood may be useful for monitoring toxicological exposure and for diagnosis and monitoring of various diseases. Several methods are available that can be used to transport, store, and extract RNA from whole blood, but it is not clear which procedures alter results. In addition, characterization of interindividual and sex-based variation in gene expression is needed to understand sources and extent of variability. Methods: Whole blood was obtained from adult male and female volunteers (n = 42) and stored at various temperatures for various lengths of time. RNA was isolated and RNA quality analyzed. Affymetrix GeneChips (n = 23) were used to characterize gene expression profiles (GEPs) and to determine the effects on GEP of storage conditions, extraction techniques, types of GeneChip, or donor sex. Hierarchical clustering and principal component analysis were used to assess interindividual differences. Regression analysis was used to assess the relative impact of the studied variables. Results: Storage of blood samples for &gt;1 week at 4 °C diminished subsequent RNA quality. Interindividual GEP differences were seen, but larger effects were observed related to RNA extraction technique, GeneChip, and donor sex. The relative importance of the variables was as follows: storage &lt; genechip &lt; extraction technique &lt; donor sex. Conclusion: Sample storage and extraction methods and interindividual differences, particularly donor sex, affect GEP of human whole blood.

scholarly journals Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods

PLoS ONE ◽  
2019 ◽  
Vol 14 (10) ◽  
pp. e0223065 ◽  
Author(s):  
Duncan E. Donohue ◽  
Aarti Gautam ◽  
Stacy-Ann Miller ◽  
Seshamalini Srinivasan ◽  
Duna Abu-Amara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Comparative Assessment ◽  
Collection Methods

Gene expression profiling of whole blood in ipilimumab-treated patients for identification of potential biomarkers of immune-mediate gastrointestinal adverse events.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 8593-8593 ◽  
Author(s):  
Vafa Shahabi ◽  
David Mark Berman ◽  
Scott D. Chasalow ◽  
Lisu Wang ◽  
Zenta Tsuchihashi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adverse Events ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Repeated Measures ◽  
Predictive Biomarkers ◽  
Activation Markers ◽  
Over Time ◽  
Potential Biomarkers

8593 Background: Treatment with ipilimumab, a fully human anti-CTLA-4 antibody approved for treatment of metastatic melanoma (MM), is associated with a number of immune-mediated Adverse Events (imAEs) such as colitis and skin rash. Predictive biomarkers that can help identify patients (pts) who might experience these imAEs could enhance the management of these toxicities. Methods: Gene expression profiling (using Affymetrix gene chip HT-HG-U133A) was performed on the whole blood samples from 162 MM pts at baseline, 3 and 11 weeks after the start of ipilimumab treatment in two phase II clinical trials (CA184004 and -007). Overall, 49 pts experienced Grade 2 or higher GI-imAE (G2+) during the course of treatment. A repeated measures ANOVA was used to evaluate the differences in mean expression levels between the two groups and at the three time points. Uncorrected p-value of 0.05 was used as a cutoff for this analysis. Results: In baseline samples, 27 probe sets showed differential mean expression (≥ 1.5 fold, p < 0.05) between G2+ pts and others. Most of these genes belonged to three functional categories: immune system, cell cycle or intracellular trafficking. Changes in gene expression over time were also characterized. In the G2+ pts, 58 and 247 genes had a ≥ 1.5 fold (p < 0.05) change in expression from baseline to week 3 and 11 post-treatment, respectively, compared to 17 and 73 in other pts. In particular, the on-treatment increases of the expression of CD177 and CEACAM1, two neutrophil activation markers, were closely associated with G2+ GI-imAE, suggesting a possible role of neutrophils in ipilimumab associated GI-imAEs. In addition, the expression of several Ig genes increased over time, with higher increases in the G2+ pts. These observations were reproduced in another ipilimumab monotherapy study in MM (CA184078). Conclusions: Gene expression profiling of peripheral blood resulted in the identification of a set of potential biomarkers that may be predictive of severe GI-imAEs before, or early in the course of treatment with ipilimumab. Further validation of these biomarkers in a larger patient cohort is warranted.

scholarly journals Prospective Study of Metal Fume-Induced Responses of Global Gene Expression Profiling in Whole Blood

2008 ◽  
Vol 20 (14) ◽  
pp. 1233-1244 ◽  
Author(s):  
Zhaoxi Wang ◽  
Donna Neuberg ◽  
Li Su ◽  
Jee Young Kim ◽  
Jiu-Chiuan Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prospective Study ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Global Gene Expression ◽  
Induced Responses ◽  
Global Gene Expression Profiling

Gene expression profiling in human whole blood samples after controlled testosterone application and exercise

2011 ◽  
Vol 3 (10) ◽  
pp. 652-660 ◽  
Author(s):  
Martin Schönfelder ◽  
Hande Hofmann ◽  
Patricia Anielski ◽  
Detlef Thieme ◽  
Renate Oberhoffer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Whole Blood ◽  
Expression Profiling ◽  
Blood Samples ◽  
Human Whole Blood ◽  
Whole Blood Samples
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