Gene Expression In Blood Samples Research Articles

A Machine Learning Approach to Gene Expression in Hypertrophic Cardiomyopathy

Background/Objectives: Hypertrophic cardiomyopathy (HCM) is a common heart disorder characterized by the thickening of the heart muscle, particularly in the left ventricle, which increases the risk of cardiac complications. This study aims to analyze the expression of apoptosis-regulating genes (CASP8, CASP9, CASP3, BAX, and BCL2) in blood samples from HCM patients, to better understand their potential as biomarkers for disease progression. Methods: Quantitative real-time PCR (qPCR) was used to evaluate gene expression in blood samples from 93 HCM patients. The correlation between apoptosis-regulating genes was conducted and clinical parameters were integrated for feature importance and clustering analysis. Results: Most patients exhibited significant downregulation of CASP8, CASP9, and CASP3. In contrast, BAX expression was elevated in 71 out of 93 patients, while BCL2 was increased in 55 out of 93 patients. Correlation analysis revealed weak negative correlations between the BAX/BCL2 ratio and CASP gene expression. Conclusions: These findings suggest that reduced expression of apoptotic genes may indicate a protective cellular mechanism, which could serve as a biomarker for disease progression. Further studies are needed to investigate the potential for therapeutic modulation of these pathways to improve patient outcomes.

FCER1G as a novel immune-associated blood biomarker in cardiogenic stroke

BackgroundCardioembolic stroke (CE) exhibits the highest recurrence rate and mortality rate among all subtypes of cerebral ischemic stroke (CIS), yet its pathogenesis remains uncertain. The immune system plays a pivotal role in the progression of CE. Growing evidence indicates that several immune-associated blood biomarkers may inform the causes of stroke. The study aimed to identify new immune-associated blood biomarkers in patients with CE and create an online predictive tool in distinguishing CE from noncardioembolic stroke (non-CE) in CIS. MethodsGene expression profiles that were publicly available were obtained from the Gene Expression Omnibus (GEO). The identification of differentially expressed genes (DEGs) was conducted using the Limma package. The hub module and hub genes were identified through the application of weighted gene coexpression network analysis (WGCNA). In order to identify potential diagnostic biomarkers for CE, both the random forest (RF) model and least absolute shrinkage and selection operator (LASSO) regression analysis were employed. Concurrently, the CIBERSORT algorithm was employed to evaluate the infiltration of immune cells in CE samples and examine the correlation between the biomarkers and the infiltrating immune cells. The diagnostic gene expression in blood samples was confirmed using qRT-PCR in a self-constructed dataset. Univariate and multiple logistic regression analyses were used to identify the risk factors for CE. Subsequently, the mathematical model of the nomogram was employed via Java's "Spring Boot" framework to develop the corresponding online tool, which was then deployed on a cloud server utilizing "nginx". ResultsEleven differentially expressed genes (DEGs) that were upregulated and seven DEGs that were downregulated were identified. Through bioinformatics analysis and clinical sample verification, it was discovered that Fc Fragment of IgE Receptor Ig (FCER1G) could serve as a novel potential blood biomarker for CE. FCER1G, along with other risk factors associated with CE, were utilized to develop a nomogram. The training and validation sets, which consisted of 65 CIS patients, yielded areas under the curve (AUCs) of 0.9722 and 0.9689, respectively. These results indicate a high level of precision in risk delineation by the nomogram. Furthermore, the associated online predictive platform has the potential to serve as a more efficacious and appropriate predictive instrument (https://www.origingenetic.com/CardiogenicStroke-FCER1G) for distinguishing between CE and non-CE. ConclusionBlood biomarker FCER1G has the potential to identify patients who are at a higher risk of cardioembolism and direct the search for occult AF.The utilization of this online tool is anticipated to yield significant implications in terms of distinguishing between CE and non-CE, as well as enhancing the optimization of treatment decision support.

Differential gene expression of blood-based ABCA9, CNOT8, SESN1, UCP3, MAP2K1 and DDIT4 in Alzheimer’s disease

This study uncovered differential gene expression in blood to distinguish subjects with probable Alzheimer’s disease (AD) from normal elderly participants (non-demented controls, NDC). The participants were recruited via training (Phase 1) and validation cohorts (Phase 2). The changes of gene expression in blood samples from the training cohort (92 AD vs 92 NDC) were assessed using the microarray technology. The Partial Least Square Discrimination Analysis (PLSDA) was then used to develop a disease classifier algorithm (accuracy = 88.3%). Six differentially expressed genes were validated through RT-qPCR using blood samples from the validation cohort [(25 AD, 25 NDC, 12 mild cognitive impairment (MCI) and 12 vascular dementia (VaD) subjects] . The PLSDA model indicated a good separation between AD and NDC [area under the receiver operating characteristic curve (ROC AUC) = 0.88]. ABCA9, CNOT8, SESN1, UCP3, MAP2K1 and DDIT4 were found to be differentially expressed between the two groups. Validation of the panel of six genes gave an overall accuracy of 82.0% (AUC=0.86). The ABCA9 mRNA level, which was significantly (p < 0.05) lower in the AD group, correctly classified 90.9% of all subjects (AUC=0.94). This group of genes may be responsible for dysregulation of pathways related to inflammation, mitochondrial dysfunction, oxidative injury, DNA damage, apoptosis and lipid metabolism. The disease classifier algorithm discriminated probable AD from MCI and VaD at specificity of 83.3% and 75.0%, respectively. These findings warrant further validation of potential blood-based biomarkers in larger samples of clinical AD.

CHEK1 and GFPT1 as Potential Blood-Based Biomarkers for Colorectal Cancer

BACKGROUND: The checkpoint kinase 1 (CHEK1) and glutamine-fructose-6-phosphate aminotransferase 1 (GFPT1) genes have been reported to have a crucial role in carcinogenesis in colorectal cancer (CRC). However, their association with the pathogenesis of CRC remains unclear. This study was conducted to study the expression of CHEK1 and GFPT1 genes in adenoma and adenocarcinoma CRC patients’ whole blood samples compared to the healthy controls.METHODS: A comparative cross‑sectional study to examine the expression of CHEK1 and GFPT1 genes were conducted in 6 colorectal adenoma and 6 colorectal adenocarcinoma patients along with 6 healthy controls. Blood samples were taken from subjects, and CHEK1 and GFPT1 genes were analyzed by using reverse transcription quantitative polymerase chain reaction (RT-qPCR). RESULTS: CHEK1 gene expression in blood samples has the highest in adenoma patients meanwhile for the GFPT1 gene expression has the highest in adenocarcinoma patients. Higher CHEK1 gene expression were also found in adenoma patients compared to healthy controls (p=0.040) and adenocarcinoma patients (p=0.025). Besides, at the 5% level of significance, the median GFPT1 gene expression was higher in colorectal adenocarcinoma patients compared to colorectal adenoma patients and healthy controls.CONCLUSION: CHEK1 and GFPT1 may function as potential regulators in adenoma and adenocarcinoma and measuring their expression might be a potential tool to determine the CRC progression and could be further explored as blood diagnostic biomarkers for CRC patients.KEYWORDS: CHEK1, GFPT1, colorectal cancer, adenoma, adenocarcinoma

Overexpression of the PTEN Gene in Myocardial Tissues of Coronary Bypass Surgery Patients.

Coronary artery disease is a complex disorder that causes death worldwide. One of the genes involved in developing this disease may be PTEN. This study aimed to investigate the PTEN gene and protein expression in tissue and blood samples taken from coronary bypass surgery patients. Molecular studies were performed at Erciyes University Genome and Stem Cell Center (GENKOK). Right atrial appendage and blood samples were taken from the central vein of 22 coronary bypass surgery patients before starting and ending cardiopulmonary bypass. PTEN expression was determined using quantitative real-time PCR and western blot analysis. The significance level was accepted as p<0.05. There was no significant difference in the PTEN gene expression in blood samples taken before and after cardiopulmonary bypass. However, a substantial increase in both protein and gene expression levels of P-PTEN and PTEN was observed in the tissue samples. Myocardial expression of the PTEN gene was significantly increased at the end of the cardiopulmonary bypass. PTEN gene expression in the post-cardiopulmonary bypass period was increased when compared to the pre-bypass period, but it was insignificant when compared to healthy controls. This study first revealed the role of the PTEN gene by analyzing both mRNA and protein expression in coronary bypass patients, appearing in both myocardial tissue and blood samples. Increased levels of PTEN may be a marker in myocardial tissue for patients with coronary artery disease.

Genome-wide screening of sex-biased genetic variants potentially associated with COVID-19 hospitalization.

Sex-biased difference in coronavirus disease 2019 (COVID-19) hospitalization has been observed as that male patients tend to be more likely to be hospitalized than female patients. However, due to the insufficient sample size and existed studies that more prioritized to sex-stratified COVID-19 genome-wide association study (GWAS), the searching for sex-biased genetic variants showing differential association signals between sexes with COVID-19 hospitalization was severely hindered. We hypothesized genetic variants would show potentially sex-biased genetic effects on COVID-19 hospitalization if they display significant differential association effect sizes between male and female COVID-19 patients. By integrating two COVID-19 GWASs, including hospitalized COVID-19 patients vs. general population separated into males (case = 1,917 and control = 221,174) and females (case = 1,343 and control = 262,886), we differentiated the association effect sizes of each common single nucleotide polymorphism (SNP) within the two GWASs. Twelve SNPs were suggested to show differential COVID-19 associations between sexes. Further investigation of genes (n = 58) close to these 12 SNPs resulted in the identification of 34 genes demonstrating sex-biased differential expression in at least one GTEx tissue. Finally, 5 SNPs are mapped to 8 genes, including rs1134004 (GADD45G), rs140657166 (TRIM29 and PVRL1), rs148143613 (KNDC1 and STK32C), rs2443615 (PGAP2 and TRIM21), and rs2924725 (CSMD1). The 8 genes display significantly differential gene expression in blood samples derived from COVID-19 patients compared to healthy controls. These genes are potential genetic factors contributing to sex differences in COVID-19 hospitalization and warranted for further functional studies.

Expression Patterns and Corepressor Function of Retinoic Acid-induced 2 in Prostate Cancer.

Revealing molecular mechanisms linked to androgen receptor activity can help to improve diagnosis and treatment of prostate cancer. Retinoic acid-induced 2 (RAI2) protein is thought to act as a transcriptional coregulator involved in hormonal responses and epithelial differentiation. We evaluated the clinical relevance and biological function of the RAI2 protein in prostate cancer. We assessed RAI2 gene expression in the Cancer Genome Atlas prostate adenocarcinoma PanCancer cohort and protein expression in primary tumors (n = 199) by immunohistochemistry. We studied RAI2 gene expression as part of a multimarker panel in an enriched circulating tumor cell population isolated from blood samples (n = 38) of patients with metastatic prostate cancer. In prostate cancer cell lines, we analyzed the consequences of androgen receptor inhibition on RAI2 protein expression and the consequences of RAI2 depletion on the expression of the androgen receptor and selected target genes. Abundance of the RAI2 protein in adenocarcinomas correlated with the androgen receptor; keratins 8, 18, and 19; and E-cadherin as well as with an early biochemical recurrence. In circulating tumor cells, detection of RAI2 mRNA significantly correlated with gene expression of FOLH1, KLK3, RAI2, AR, and AR-V7. In VCaP and LNCaP cell lines, sustained inhibition of hormone receptor activity induced the RAI2 protein, whereas RAI2 depletion augmented the expression of MME, STEAP4, and WIPI1. The RAI2 protein functions as a transcriptional coregulator of the androgen response in prostate cancer cells. Detection of RAI2 gene expression in blood samples from patients with metastatic prostate cancer indicated the presence of circulating tumor cells.

Assessment of Interleukin-8 in Bronchial Asthma in Iraq.

It has been approved that neutrophils are responsible for many inflammatory lung diseases, such as acute respiratory distress syndrome, chronic obstructive pulmonary disease, and asthma. It is well documented that the CXC chemokine interleukin-8 (IL-8) plays a key role as a potent neutrophil recruiting and activating factor. Asthma is one of the most common major non-contagious diseases and has a substantial impact on the patient's quality of life. The current evidence suggests that asthma is a complex multifactorial disorder, and its etiology is increasingly attributed to interactions between genetic susceptibility, host factors, and environmental exposures. IL-8 plays an important role in respiratory diseases and is a known regulator of pulmonary inflammation and immunity, induced phagocytosis, and promoted angiogenesis. This study aimed to investigate the IL-8 gene expression in blood samples of bronchial asthma patients. Therefore, the blood samples were taken from two groups of participants, including the group of patients with asthma (n=100) in the age range of20-61years and the group of healthy individuals (n=50).The obtained results indicated that the expression of IL-8 mRNA in the group of asthma patients was three times higher than that in the group of healthy individuals. Therefore, it is suggested that the antagonism of IL-8 could be a potent therapeutic strategy in the treatment of asthma.

Ionizing radiation induces epithelial-mesenchymal transition in human bronchial epithelial cells.

Objective: The present study aimed to analyze the mechanism by which long-term occupational exposure of workers to low-dose ionizing irradiation induces epithelial–mesenchymal transition (EMT) of the human bronchial epithelial cells using transcriptome profiling.Methods: RNA-seq transcriptomics was used to determine gene expression in blood samples from radiation-exposed workers followed by bioinformatics analysis. Normal bronchial epithelial cells (16HBE) were irradiated for different durations and subjected to immunofluorescence, Western blotting, scratch healing, and adhesion assays to detect the progression of EMT and its underlying molecular mechanisms.Results: Transcriptomics revealed that exposure to ionizing radiation led to changes in the expression of genes related to EMT, immune response, and migration. At increased cumulative doses, ionizing radiation-induced significant EMT, as evidenced by a gradual decrease in the expression of E-cadherin, increased vimentin, elevated migration ability, and decreased adhesion capability of 16HBE cells. The expression of fibronectin 1 (FN1) showed a gradual increase with the progression of EMT, and may be involved in EMT.Conclusion: Ionizing radiation induces EMT. FN1 may be involved in the progression of EMT and could serve as a potential biomarker for this process.

Considering blood samples for early diagnosis of prostate cancer by evaluating prostate cancer antigen 3 expression values

Background: Prostate cancer antigen 3 (PCA3) is the most specific biomarker for an early diagnosis of prostate cancer (PCa), and it is routinely evaluated in urine samples. Recent investigations consider blood as a reliable source to determine PCA3 expression levels and fast diagnosis of PCa since in addition to bacterial and viral contaminations and the hygienic problems, if the area of the prostatic duct is not involved PCa, the obtained urine samples may not contain any cancerous cells. Materials and Methods: This study investigated blood expression values of the PCA3 gene in patients with PCa and multiple endocrine neoplasia compared with normal volunteers in an Iranian population. A total of 150 blood samples from three groups were assessed for PCA3 expression using real-time polymerase chain reaction. Prostate-specific antigen (PSA) serum levels, age, and family history of PCa were also analyzed. Results: PCA3 expression analysis showed a significant increase in PCa patients and in patients with PSA serum levels higher than 7 ng/ml (P = 0.005 and P= 0.0011, respectively). Analysis of blood samples from men with an older age and positive family history also showed significant PCA3 expression values. Results of this study suggests that evaluating PCA3 gene expression in blood samples is an adequate method for an early diagnosis of PCa. The decision to perform a prostate biopsy should be made more cautiously in patients with a PSA serum level between 4 and 7 ng/ml. Patients with a positive PCa family history and higher age should be considered for PCa diagnostic procedures.Conclusion: Blood samples can be considered for PCA3 evaluating as a promising alternative of urine samples for PCa diagnosis.

Cardioembolic Ischemic Stroke Gene Expression Fingerprint in Blood: a Systematic Review and Verification Analysis.

An accurate etiological classification is key to optimize secondary prevention after ischemic stroke, but the cause remains undetermined in one third of patients. Several studies pointed out the usefulness of circulating gene expression markers to discriminate cardioembolic (CE) strokes, mainly due to atrial fibrillation (AF), while only exploring them in small cohorts. A systematic review of studies analyzing high-throughput gene expression in blood samples to discriminate CE strokes was performed. Significantly dysregulated genes were considered as candidates, and a selection of them was validated by RT-qPCR in 100 patients with defined CE or atherothrombotic (LAA) stroke etiology. Longitudinal performance was evaluated in 12 patients at three time points. Their usefulness as biomarkers for AF was tested in 120 cryptogenic strokes and 100 individuals at high-risk for stroke. Three published studies plus three unpublished datasets were considered for candidate selection. Sixty-seven genes were found dysregulated in CE strokes. CREM, PELI1, and ZAK were verified to be up-regulated in CE vs LAA (p = 0.010, p = 0.003, p < 0.001, respectively), without changes in their expression within the first 24h after stroke onset. The combined up-regulation of these three biomarkers increased the probability of suffering from CE stroke by 23-fold. In cryptogenic strokes with subsequent AF detection, PELI1 and CREM showed overexpression (p = 0.017, p = 0.059, respectively), whereas in high-risk asymptomatic populations, all three genes showed potential to detect AF (p = 0.007, p = 0.007, p = 0.015). The proved discriminatory capacity of these gene expression markers to detect cardioembolism even in cryptogenic strokes and asymptomatic high-risk populations might bring up their use as biomarkers.

Abstract 2263: Prognostic significance of REV3like and TYMS gene expression in blood samples from non-small cell lung patients treated with platinum-based chemotherapy plus pemetrexed

Abstract BACKGROUND: Pemetrexed is an effective antineoplastic agent as monotherapy (second line and maintenance setting) or in platinum-based combination regimes (first-line). Pemetrexed inhibits three key enzymes in the folate metabolic pathway: thymidylate synthase (TS), dihydrofolate reductase (DHFR) and glycinamide ribonucleotide formyl transferase (GARFT). As a consequence, pemetrexed interferes with the synthesis of both pyrimidine and purine, thereby effectively inhibiting both DNA and RNA synthesis. The aim of this study was to investigate the impact of the PBMC (peripheral blood mononuclear cells) expression levels of AEG1, BRCA1, REV3like, ant TYMS mRNA in the clinical outcome in NSCLC patients treated with Pemetrexed-based therapy. MATERIAL AND METHODS: This is a prospective, observational cohort study, of consecutively selected patients. We included patients with non-squamous NSCLC, stage IV, treated with platinum-based chemotherapy plus Pemetrexed. Blood samples from each patient were collected at the beginning of treatment. Quantitative reverse transcription (qRT)-PCR was performed with the use of the TaqMan gene expression assay (Applied Biosystems) according to the manufacturer's instructions. Amplifications were carried out on the Applied Biosystem 7500 RT-PCR system, and relative gene expression values were calculated by the ΔΔCt method (Sequence Detection System 2.0.5). Results from analysis, done in triplicate, are expressed relative to expression levels of GAPDH. RESULTS: We here present preliminary results of 16 patients included in the study: median age was 63.4 (range 52-82); 12 were males. Histological subtypes were 13 adenocarcinomas, and 3 large cell carcinomas. Pemetrexed was combined with Carboplatin in 9 patients and Cisplatin in 7 patients. Best response obtained was partial response in 7 patients, stable disease in 3 patients, and progression in 5 patients. We found significant differences in the REV3like expression levels between patients with PR&amp;SD and patients with PD (0.69 ± 0.14 vs 0.44 ± 0.07; P = 0.003). In addition there were statistically significant differences in disease free survival (3 ± 0.74 vs 13 ± 1.89, P = 0.035; 12 ± 2.32 vs 3 ± 2.19, P = 0.003, months), and overall survival (10 ± 5.21 vs not reached, P = 0.026; not reached vs 12 ± 2.38, P = 0.007, months) between patients with mRNA levels of REV3like and TYMS under mean value of the cohort and patients with levels over mean value of the our cohort. CONCLUSIONS: This study supports the value of the PBMC expression profiling of the REV3like and TYMS genes in the prognosis of NSCLC treated with platinum-based chemotherapy plus Pemetrexed. Citation Format: Maria Teresa Agullo-Ortuño, C.Vanessa Díaz-García, José A. López-Martín, Elena Prieto-García, Santiago Ponce, Jon Zugazagoitia, Lara Iglesias-Docampo, Ana B. Enguita, Luis Paz-Ares, Juan A. Nuñez-Sobrino. Prognostic significance of REV3like and TYMS gene expression in blood samples from non-small cell lung patients treated with platinum-based chemotherapy plus pemetrexed. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2263.

Does elevated peripheral benzodiazepine receptor gene expression relate to cognitive deficits in methamphetamine dependence?

Methamphetamine (METH) is a neurotoxin and psychostimulant drug with potent effects on the central nervous system. With chronic METH administration, an inflammatory glial response is observed as a result of METH-induced neurotoxicity. One inflammatory marker is the peripheral benzodiazepine receptor (PBR). The purpose of the present study was to determine whether PBR expression is changed in METH dependence and whether the changes relate to cognitive deficits. Reverse transcriptase-polymerase chain reaction was used to investigate PBR gene expression in blood samples taken from 14 male subjects with METH dependence and 14 controls. The results showed a significant increase in PBR gene expression in METH dependence, suggestive of a systemic inflammatory response. The increase remained elevated for more than 1 year following abstinence from METH use, but eventually returned to normal. Subjects with elevated PBR also exhibited a deficit in one domain of the Wisconsin Card Sorting Test. The results suggest that systemic inflammatory effects can be associated with chronic METH abuse, and this may relate to the cognitive deficits seen in METH dependence. Copyright © 2016 John Wiley & Sons, Ltd.

Effects of Transport and Storage Conditions on Gene Expression in Blood Samples.

Inappropriate handling of blood samples might induce or repress gene expression and/or lead to RNA degradation affecting downstream analysis. In particular, sample transport is a critical step for biobanking or multicenter studies because of uncontrolled variables (i.e., unstable temperature). We report the results of a pilot study implemented within the EC funded SPIDIA project, aimed to investigate the role of transport and storage of blood samples containing and not containing an RNA stabilizer. Blood was collected from a single donor both in EDTA and in PAXgene Blood RNA tubes. Half of the samples were sent to a second laboratory both at room temperature and at 4°C, whereas the remaining samples were stored at room temperature and at 4°C. Gene expression of selected genes (c-FOS, IL-1β, IL-8, and GAPDH) known to be induced or repressed by ex vivo blood handling and of blood-mRNA quality biomarkers identified and validated within the SPIDIA project, which allow for monitoring changes in unstabilized blood samples after collection and during transport and storage, were analyzed by RT-qPCR. If the shipment of blood in tubes not containing RNA stabilizer is not performed under a stable condition, gene profile studies can be affected by the effects of transport. Moreover, also controlled temperature shipment (4°C) can influence the expression of specific genes if blood is collected in tubes not containing a stabilizer. The use of dedicated biomarkers or time course experiments should be performed in order to verify potential bias on gene expression analysis due to sample shipment and storage conditions. Alternatively, the use of RNA stabilizer containing tubes can represent a reliable option to avoid ex vivo RNA changes.

Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis.

Volatile organic compounds (VOCs) can be easily taken up by humans, leading to various diseases, such as respiratory system and central nervous system disorders. Environmental risk assessment is generally conducted using traditional tests, which may be time-consuming and technically challenging. Therefore, analysis of the effects of VOCs, such as toluene, ethylbenzene, and xylene, may be improved by use of novel, high-throughput methods, such as microarray analysis. In this study, we examined the effects of VOCs exposure in humans on gene expression and methylation using microarray analysis. We recruited participants who had short-term exposure, long-term exposure, or no exposure. We then analyzed changes in gene expression in blood samples from these participants. A total of 866 genes were upregulated, while 366 genes were downregulated in the short-term exposure group. Similarly, in the long-term exposure group, a total of 852 and 480 genes were up- or downregulated, respectively. Hierarchical clustering analysis was used to divide the clustered genes into nine clusters to investigate the expression of variations in accordance with the exposure period. And the methylation microarray was performed at the same time to see whether this expression variation is related to the epigenetic study. Finally, we have 5 genes that were upregulated and 12 genes that were downregulated, gradually and respectively, so these genes are expected to function as biomarkers of the duration of exposure to VOCs. Further research is required to determine the time-dependent effects of VOCs on epigenetic regulation of gene expression. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1563-1570, 2016.

A nutrigenomic approach to detect nutritional stress from gene expression in blood samples drawn from Steller sea lions

Gene expression profiles are increasingly being used as biomarkers to detect the physiological responses of a number of species to disease, nutrition, and other stressors. However, little attention has been given to using gene expression to assess the stressors and physiological status of marine mammals. We sought to develop and validate a nutrigenomic approach to quantify nutritional stress in Steller sea lions (Eumetopias jubatus). We subjected 4 female Steller sea lions to 3 feeding regimes over 70-day trials (unrestricted food intake, acute nutritional stress, and chronic nutritional stress), and drew blood samples from each animal at the end of each feeding regime. We then extracted the RNA of white blood cells and measured the response of 8 genes known to react to diet restriction in terrestrial mammals. Overall, we found that the genomic response of Steller sea lions experiencing nutritional stress was consistent with how terrestrial mammals respond to dietary restrictions. Our nutritionally stressed sea lions down-regulated some cellular processes involved in immune response and oxidative stress, and up-regulated pro-inflammatory responses and metabolic processes. Nutrigenomics appears to be a promising means to monitor nutritional status and contribute to mitigation measures needed to assist in the recovery of Steller sea lions and other at-risk species of marine mammals.

Gene expression profile in cardiovascular disease and preeclampsia: A meta-analysis of the transcriptome based on raw data from human studies deposited in Gene Expression Omnibus

IntroductionCardiovascular disease (CVD) and preeclampsia (PE) share common clinical features. We aimed to identify common transcriptomic signatures involved in CVD and PE in humans. MethodsMeta-analysis of individual raw microarray data deposited in GEO, obtained from blood samples of patients with CVD versus controls and placental samples from women with PE versus healthy women with uncomplicated pregnancies. Annotation of cases versus control samples was taken directly from the microarray documentation. Genes that showed a significant differential expression in the majority of experiments were selected for subsequent analysis. Hypergeometric gene list analysis was performed using Bioconductor GOstats package. Bioinformatic analysis was performed in PANTHER. ResultsSeven studies in CVD and 5 studies in PE were eligible for meta-analysis. A total of 181 genes were found to be differentially expressed in microarray studies investigating gene expression in blood samples obtained from patients with CVD compared to controls and 925 genes were differentially expressed between preeclamptic and healthy placentas. Among these differentially expressed genes, 22 were common between CVD and PE. DiscussionBioinformatic analysis of these genes revealed oxidative stress, p-53 pathway feedback, inflammation mediated by chemokines and cytokines, interleukin signaling, B-cell activation, PDGF signaling, Wnt signaling, integrin signaling and Alzheimer disease pathways to be involved in the pathophysiology of both CVD and PE. Metabolism, development, response to stimulus, immune response and cell communication were the associated biologic processes in both conditions. Gene set enrichment analysis showed the following overlapping pathways between CVD and PE: TGF-β-signaling, apoptosis, graft-versus-host disease, allograft rejection, chemokine signaling, steroid hormone synthesis, type I and II diabetes mellitus, VEGF signaling, pathways in cancer, GNRH signaling, Huntingtons disease and Notch signaling. ConclusionCVD and PE share same common traits in their gene expression profile indicating common pathways in their pathophysiology.

Expression profiling in peripheral blood reveals signature for penetrance in DYT1 dystonia

DYT1 dystonia is an autosomal-dominantly inherited movement disorder, which is usually caused by a GAG deletion in the TOR1A gene. Due to the reduced penetrance of ∼ 30–40%, the determination of the mutation in a subject is of limited use with regard to actual manifestation of symptoms. In the present study, we used Affymetrix oligonucleotide microarrays to analyze global gene expression in blood samples of 15 manifesting and 15 non-manifesting mutation carriers in order to identify a susceptibility profile beyond the GAG deletion which is associated with the manifestation of symptoms in DYT1 dystonia. We identified a genetic signature which distinguished between asymptomatic mutation carriers and symptomatic DYT1 patients with 86.7% sensitivity and 100% specificity. This genetic signature could correctly predict the disease state in an independent test set with a sensitivity of 87.5% and a specificity of 85.7%. Conclusively, this genetic signature might provide a possibility to distinguish DYT1 patients from asymptomatic mutation carriers.

Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease

Huntington's disease (HD) is an autosomal dominant disorder caused by an expansion of glutamine repeats in ubiquitously distributed huntingtin protein. Recent studies have shown that mutant huntingtin interferes with the function of widely expressed transcription factors, suggesting that gene expression may be altered in a variety of tissues in HD, including peripheral blood. Affymetrix and Amersham Biosciences oligonucleotide microarrays were used to analyze global gene expression in blood samples of HD patients and matched controls. We identified 322 mRNAs that showed significantly altered expression in HD blood samples, compared with controls (P < 0.0005), on two different microarray platforms. A subset of up-regulated mRNAs selected from this group was able to distinguish controls, presymptomatic individuals carrying the HD mutation, and symptomatic HD patients. In addition, early presymptomatic subjects showed gene expression profiles similar to those of controls, whereas late presymptomatic subjects showed altered expression that resembled that of symptomatic HD patients. These elevated mRNAs were significantly reduced in HD patients involved in a dose-finding study of the histone deacetylase inhibitor sodium phenylbutyrate. Furthermore, expression of the marker genes was significantly up-regulated in postmortem HD caudate, suggesting that alterations in blood mRNAs may reflect disease mechanisms observed in HD brain. In conclusion, we identified changes in blood mRNAs that clearly distinguish HD patients from controls. These alterations in mRNA expression correlate with disease progression and response to experimental treatment. Such markers may provide clues to the state of HD and may be of predictive value in clinical trials.

Monitoring therapy with gene expression profiling reveals physiological differences in drug action.

Gene expression profiling has become a versatile tool for biomedical research, which allows the assessment of a wide variety of basic questions in cellular regulation, in particular when a large number of molecular parameters have changed. There are various applications in drug research for which gene expression profiling is a very suitable approach. This includes: target identification, target validation, validation of drug specificity and monitoring of drug action during therapy. The focus of this article is the therapy monitoring and the interpretation of the gene expression profiles in respect to physiological differences of drug action. As an example, we will discuss changes in gene expression in blood samples from CML patients treated with the tyrosine kinase inhibitor (imatinib mesylate) and compare the observed effects on gene expression with the effects of IFNalpha treatment. In comparison with other examples of therapy monitoring the potential of this application of gene expression profiling for optimizing individual therapy will be discussed.