Leukocyte Transcriptome Research Articles

Leukocyte transcript alterations in West-African girls following a booster vaccination with diphtheria-tetanus-pertussis vaccine

Background. Observational studies from low-income countries have shown that the vaccination against diphtheria, tetanus and pertussis (DTP) is associated with excess female mortality due to infectious diseases. Methods. To investigate possible changes in gene expression after DTP vaccination, we identified a group of nine comparable West African girls, from a biobank of 356 children, who were due to receive DTP booster vaccine at age 18 months. As a pilot experiment we extracted RNA from blood samples before, and 6 weeks after, vaccination to analyze the coding transcriptome in leukocytes using expression microarrays, and ended up with information from eight girls. The data was further analyzed using dedicated array pathway and network software. We aimed to study whether DTP vaccination introduced a systematic alteration in the immune system in girls. Results. We found very few transcripts to alter systematically. Those that did mainly belonged to the Interferon (IFN) signalling pathway. We scrutinized this pathway as well as the Interleukin (IL) pathways. Two out of eight showed a down-regulated IFN pathway and two showed an up-regulated IFN pathway. The two with down-regulated IFN pathway had also down-regulated IL-6 pathway. In the study of networks, two of the girls stood out as not having the inflammatory response as top altered network. Conclusion. The transcriptome changes following DTP booster vaccination were subtle, but although the material was small, it was possible to identify sub groups that deviate from each other, mainly in the IFN response.

Age related changes in mTOR-related gene expression in two primary human cell lines

Background: Leukocyte transcriptomics studies suggest disrupted mTOR gene expression is a feature of human aging. We aimed to establish whether gene expression is also disrupted in other human tissues senesced in vitro. Methods: We aged two primary cell types (fibroblasts and endothelial cells) in vitro, by repeated passage until growth arrest, and measured the expression of an mTOR-related transcript set by quantitative real-time PCR in low passage (‘young’) and high passage (‘old’) cells. Results: We identified expression differences for 7/28 mTOR-related transcripts in senescent fibroblasts, which included up-regulation of mTORC1 inhibitory transcripts (DEPTOR, TSC1, TSC2; p=0.047, 0.007, and 0.024 respectively) with concurrent up-regulation of down-stream transcripts usually inhibited by mTOR activation (NFKB1, PRKCA, EIF4G3 and FOXO1; p=0.047, 0.007 0.005 and 0.038 respectively). Endothelial cells demonstrated 2 significant expression changes between senescent and non-senescent cells (PRCKA and SGK1; p<0.001 and p=0.0031 respectively), transcripts involved in mTORC2 signaling. Conclusions: Our preliminary study suggests that age-related gene expression changes noted in human population studies also occur with senescence in some primary human tissue types. Age-related expression changes in primary human fibroblasts involve mainly mTORC1 transcripts, whilst in human endothelial cells, expression changes are less apparent and involve mTORC2-related transcripts.

Hypoxia Inducible Factor (HIF)-Dependent Regulation of TH1 CD41 T Cells in Inflammatory Bowel Disease

Hypoxia and inflammation share an interdependent relationship. During inflammatory bowel disease (IBD) the inflamed intestinal mucosa becomes hypoxic due to increased metabolic demand and a paucity of available oxygen. Stabilization of hypoxia-inducible factors (HIF) occur within the cellular milieu of the inflamed intestine and directly affects the leukocyte transcriptome. While effector TH1 CD4+ T cells infiltrating the intestinal lamina propria have been implicated in driving induction and perpetuation of the inflammatory processes in Crohns' Disease (CD), the effect of hypoxia signaling on effector TH1 T cells remains unknown. To address this, we examined the role of hypoxia signaling on the regulation of TH1 CD4+ T cells by differentiating murine TH1 T cells ex vivo and exposed them to ambient hypoxia in vitro (1% P02). The effect of hypoxia on transcriptional machinery and cytokine production was assessed by QPCR, flow cytometry, western immunoblotting and ELISA. Using the CD45Rbhigh murine model of ileocolitis we assessed the localization of T cells infiltrating hypoxic lesions within the inflamed mucosa and the stabilization of T cell-HIF. Lastly, using targeted pharmacological treatment or T cells with and intrinsic genetic deletion of HIF, we further assessed the impact of HIF stabilization or deletion on CD45Rbhigh ileocolitis. Using the CD45Rbhigh murine model of ileocolitis, we show that lamina propria-infiltrating CD4+ T cells are exposed to regions of fulminant hypoxia and express stabilized hypoxia-inducible factor compared to colonic CD4+ T cells from uninflamed mice. Building on these preliminary studies we differentiated murine TH1 CD4+ T cells ex vivo and exposed them to ambient hypoxia in vitro (1% P02). Experimental hypoxia induced a marked repression of the transcription factor Tbet (Tbx21; the master regulator of TH1 T cells) at both the mRNA and protein levels. This was paralleled with a functional effect as hypoxia further suppressed IFNc secretion (the predominant Tbet-responsive TH1 effector cytokine). These findings were also mirrored with pharmacological stabilization of HIF using the prolyl-hydroxylase inhibitor, DMOG. In an effort to define the molecular mechanism employed by hypoxia to repress Tbet, both lentiviral knock-down and genetic deletion of T cell-intrinsic HIF, revealed a redundant role HIF-1a whereas hypoxic-repression of Tbet and IFNc was attenuated in HIF-2a deficient T cells. Lastly, in a proof of principal in vivo experiment, pharmacological stabilization of HIF attenuated all indices of CD45Rbhigh colitis while conversely, selective T cell-HIF-2a deletion exacerbated disease compared to WT counterparts. Based on these preliminary studies, we hypothesize that HIF-2a critically regulates mucosal TH1 CD4+ T cell function and may highlight a novel targeted therapeutic option for the treatment of inflammatory bowel disease.

141. Short-term selective upregulation of natural killer cell genes in response to a first- time tandem skydive

Acute stress induces the activation and mobilization of natural killer (NK) cells into peripheral blood, but the genomic response is unknown. The entire transcriptome of leukocytes was temporally profiled in participants experiencing acute psychological stress through a first-time tandem skydive. Gene expression was examined at baseline, pre-boarding, landing and 1 h post-jump. A peak in expression of a subset of NK cell related genes was observed that complements previously shown peaks in anxiety and sympathetic adrenal response just before and during jump. The expression of these genes returned to baseline levels 1 h post-jump. This selective upregulation of NK genes demonstrates a genomic response to acute stress not accounted solely by an influx of NK cells.

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

BackgroundWeaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.ResultsThe leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.ConclusionsThis study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.

Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds

In this study, mRNA-Seq was used to characterize and compare the leukocyte transcriptomes from two taurine breeds (Holstein and Jersey), and one indicine breed (Cholistani). At the genomic level, we identified breed-specific base changes in protein coding regions. Among 7,793,425 coding bases, only 165 differed between Holstein and Jersey, and 3,383 (0.04%) differed between Holstein and Cholistani, 817 (25%) of which resulted in amino acid changes in 627 genes. At the transcriptional level, we assembled transcripts and estimated their abundances including those from more than 3,000 unannotated intergeneic regions. Differential gene expression analysis showed a high similarity between Holstein and Jersey, and a much greater difference between the taurine breeds and the indicine breed. We identified gene ontology pathways that were systematically altered, including the electron transport chain and immune response pathways that may contribute to different levels of heat tolerance and disease resistance in taurine and indicine breeds. At the post-transcriptional level, sequencing mRNA allowed us to identify a number of genes undergoing differential alternative splicing among different breeds. This study provided a high-resolution survey of the variation between bovine transcriptomes at different levels and may provide important biological insights into the phenotypic differentiation among cattle breeds.

Leukocyte transcriptome from chickens infected with avian pathogenic Escherichia coli identifies pathways associated with resistance

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which is responsible for morbidity and mortality in chickens. Gene expression patterns have previously been demonstrated to differ between chicken populations that are resistant vs. susceptible to bacterial infection, but little is currently known about gene expression response to APEC. Increased understanding of gene expression patterns associated with resistance will facilitate genetic selection to increase resistance to APEC. Male broiler chicks were vaccinated at 2 weeks of age and challenged with APEC at 4 weeks of age. Peripheral blood leukocytes were collected at 1 and 5 day post-infection. Lesions on the liver, pericardium, and air sacs were used to assign a mild or severe pathology status to non-vaccinated, challenged chicks. Ten treatment groups were therefore generated with a priori factors of vaccination, challenge, day post-infection, and the a posteriori factor of pathology status. Global transcriptomic response was evaluated using the Agilent 44K chicken microarray. APEC infection resulted in more up-regulation than down-regulation of differentially expressed genes. Immune response and metabolic processes were enriched with differentially expressed genes. Although vaccination significantly reduced lesions in challenged bird, there was no detectable effect of vaccination on gene expression. This study investigated the transcriptomic differences in host responses associated with mild vs. severe pathology, in addition to the effects of vaccination and challenge, thus revealing genes and networks associated with response to APEC and providing a foundation for future studies on, and genetic selection for, genetic resistance to APEC.

Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes

BackgroundMycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better understand the molecular mechanisms governing the host immune response to M. bovis infection. Furthermore, these studies may enable the identification of novel transcriptional markers of BTB that can augment current diagnostic tests and surveillance programmes. In the present study, we have analysed the transcriptome of peripheral blood leukocytes (PBL) from eight M. bovis-infected and eight control non-infected age-matched and sex-matched Holstein-Friesian cattle using the Affymetrix® GeneChip® Bovine Genome Array with 24,072 gene probe sets representing more than 23,000 gene transcripts.ResultsControl and infected animals had similar mean white blood cell counts. However, the mean number of lymphocytes was significantly increased in the infected group relative to the control group (P = 0.001), while the mean number of monocytes was significantly decreased in the BTB group (P = 0.002). Hierarchical clustering analysis using gene expression data from all 5,388 detectable mRNA transcripts unambiguously partitioned the animals according to their disease status. In total, 2,960 gene transcripts were differentially expressed (DE) between the infected and control animal groups (adjusted P-value threshold ≤ 0.05); with the number of gene transcripts showing decreased relative expression (1,563) exceeding those displaying increased relative expression (1,397). Systems analysis using the Ingenuity® Systems Pathway Analysis (IPA) Knowledge Base revealed an over-representation of DE genes involved in the immune response functional category. More specifically, 64.5% of genes in the affects immune response subcategory displayed decreased relative expression levels in the infected animals compared to the control group.ConclusionsThis study demonstrates that genome-wide transcriptional profiling of PBL can distinguish active M. bovis-infected animals from control non-infected animals. Furthermore, the results obtained support previous investigations demonstrating that mycobacterial infection is associated with host transcriptional suppression. These data support the use of transcriptomic technologies to enable the identification of robust, reliable transcriptional markers of active M. bovis infection.

A genomic storm in critically injured humans

Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose bacterial endotoxin, and show that these severe stresses produce a global reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected "genomic storm." In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore, complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization. The similarities in gene expression patterns between different injuries reveal an apparently fundamental human response to severe inflammatory stress, with genomic signatures that are surprisingly far more common than different. Based on these transcriptional data, we propose a new paradigm for the human immunological response to severe injury.

Screening for colorectal cancer: established and emerging modalities

It has been estimated that >95% of cases of colorectal cancer (CRC) would benefit from curative surgery if diagnosis was made at an early or premalignant polyp stage of disease. Over the past 10 years, most developed nation states have implemented mass population screening programs, which are typically targeted at the older (at-risk) age group (>50-60 years old). Conventional screening largely relies on periodic patient-centric investigation, particularly involving colonoscopy and flexible sigmoidoscopy, or else on the fecal occult blood test. These methods are compromised by either low cost-effectiveness or limited diagnostic accuracy. Advances in the development of diagnostic molecular markers for CRC have yielded an expanding list of potential new screening modalities based on investigations of patient stool (for colonocyte DNA mutations, epigenetic changes or microRNA expression) or blood specimens (for plasma DNA mutations, epigenetic changes, heteroplasmic mitochondrial DNA mutations, leukocyte transcriptome profile, plasma microRNA expression or protein and autoantibody expression). In this Review, we present a critical evaluation of the performance data and relative merits of these various new potential methods. None of these molecular diagnostic methods have yet been evaluated beyond the proof-of-principle and pilot-scale study stage and it could be some years before they replace existing methods for population screening in CRC.

Maternal Influences on the Transmission of Leukocyte Gene Expression Profiles in Population Samples from Brisbane, Australia

Two gene expression profiling studies designed to identify maternal influences on development of the neonate immune system and to address the population structure of the leukocyte transcriptome were carried out in Brisbane, Australia. In the first study, a comparison of 19 leukocyte samples obtained from mothers in the last three weeks of pregnancy with 37 umbilical cord blood samples documented differential expression of 7,382 probes at a false discovery rate of 1%, representing approximately half of the expressed transcriptome. An even larger component of the variation involving 8,432 probes, notably enriched for Vitamin E and methotrexate-responsive genes, distinguished two sets of individuals, with perfect transmission of the two profile types between each of 16 mother-child pairs in the study. A minor profile of variation was found to distinguish the gene expression profiles of obese mothers and children of gestational diabetic mothers from those of children born to obese mothers. The second study was of adult leukocyte profiles from a cross-section of Red Cross blood donors sampled throughout Brisbane. The first two axes in this study are related to the third and fourth axes of variation in the first study and also reflect variation in the abundance of CD4 and CD8 transcripts. One of the profiles associated with the third axis is largely excluded from samples from the central portion of the city. Despite enrichment of insulin signaling and aspects of central metabolism among the differentially expressed genes, there was little correlation between leukocyte expression profiles and body mass index overall. Our data is consistent with the notion that maternal health and cytokine milieu directly impact gene expression in fetal tissues, but that there is likely to be a complex interplay between cultural, genetic, and other environmental factors in the programming of gene expression in leukocytes of newborn children.

Development and assessment of oligonucleotide microarrays for Atlantic salmon ( Salmo salar L.)

The cDNA microarrays have played a major role in functional genomics of fish and contributed substantially to different areas of aquaculture research. However at present these platforms are gradually substituted with oligonucleotide microarrays (ONM), which represent the most cost-efficient, flexible, powerful and accurate tool for multiple gene expression profiling, especially in species with rich genomic resources. This paper describes the development and assessment of ONM platforms for Atlantic salmon. The process started with the establishment of a bioinformatic system, selection of a low redundancy set of nucleotide sequences providing coverage of transcriptomes of several fish species, their identification by protein products and annotations. Pilot experiments were performed to address issues that are essential for development of ONM: gene composition, quality assessment, hybridization success of homologous and heterologous probes, optimum numbers of spot replicates and processing, management and mining of gene expression data. Performance of microarrays was evaluated in two experiments with Atlantic salmon. Comparison of peripheral blood leukocytes with a mixture of other tissues was conducted for characterization of the leukocyte transcriptome. Analyses of salmon infected with different viral diseases identified virus-responsive genes that can be used as markers for diagnostics of infected status of fish. Data mining with functional annotations confirmed the relevance of these findings.

Prolonged Genomic Changes Characterize the Human Response to Burn Injury

Context: The response to a major burn injury is characterized by systemic inflammation, hypermetabolism, and immune suppression involving a reprioritization of energy metabolism and protein synthesis, which persists for up to 60 days post-injury. Objective: Determine changes in the leukocyte transcriptome to obtain unique insights into the initiation and resolution of severe burn injury; to facilitate this, an interactive web site was designed that allows investigators to examine gene expression patterns and the associated signaling pathways.

ORIGINAL ARTICLE: The Transcriptome of the Fetal Inflammatory Response Syndrome

Problem The fetal inflammatory response syndrome (FIRS) is considered the counterpart of the systemic inflammatory response syndrome (SIRS), but similarities in their regulatory mechanisms are unclear. This study characterizes the fetal mRNA transcriptome of peripheral leukocytes to identify key biological processes and pathways involved in FIRS.Method of study Umbilical cord blood from preterm neonates with FIRS (funisitis, plasma IL‐6 &gt;11 pg/mL; n = 10) and neonates with no evidence of inflammation (n = 10) was collected at birth.Results Microarray analysis of leukocyte RNA revealed differential expression of 541 unique genes, changes confirmed by qRT‐PCR for 41 or 44 genes tested. Similar to SIRS and sepsis, ontological and pathway analyses yielded significant enrichment of biological processes including antigen processing and presentation, immune response, and processes critical to cellular metabolism. Results are comparable with microarray studies of endotoxin challenge models and pediatric sepsis, identifying 25 genes across all studies.Conclusion This study is the first to profile genome‐wide expression in FIRS, which demonstrates a substantial degree of similarity with SIRS despite differences in fetal and adult immune systems.

Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases

BackgroundIdentification of molecular classifiers from genome-wide gene expression analysis is an important practice for the investigation of biological systems in the post-genomic era - and one with great potential for near-term clinical impact. The 'Top-Scoring Pair' (TSP) classification method identifies pairs of genes whose relative expression correlates strongly with phenotype. In this study, we sought to assess the effectiveness of the TSP approach in the identification of diagnostic classifiers for a number of human diseases including bacterial and viral infection, cardiomyopathy, diabetes, Crohn's disease, and transformed ulcerative colitis. We examined transcriptional profiles from both solid tissues and blood-borne leukocytes.ResultsThe algorithm identified multiple predictive gene pairs for each phenotype, with cross-validation accuracy ranging from 70 to nearly 100 percent, and high sensitivity and specificity observed in most classification tasks. Performance compared favourably with that of pre-existing transcription-based classifiers, and in some cases was comparable to the accuracy of current clinical diagnostic procedures. Several diseases of solid tissues could be reliably diagnosed through classifiers based on the blood-borne leukocyte transcriptome. The TSP classifier thus represents a simple yet robust method to differentiate between diverse phenotypic states based on gene expression profiles.ConclusionTwo-transcript classifiers have the potential to reliably classify diverse human diseases, through analysis of both local diseased tissue and the immunological response assayed through blood-borne leukocytes. The experimental simplicity of this method results in measurements that can be easily translated to clinical practice.

Gene expression in peripheral blood leukocytes in monozygotic twins discordant for chronic fatigue: no evidence of a biomarker.

BackgroundChronic fatiguing illness remains a poorly understood syndrome of unknown pathogenesis. We attempted to identify biomarkers for chronic fatiguing illness using microarrays to query the transcriptome in peripheral blood leukocytes.MethodsCases were 44 individuals who were clinically evaluated and found to meet standard international criteria for chronic fatigue syndrome or idiopathic chronic fatigue, and controls were their monozygotic co-twins who were clinically evaluated and never had even one month of impairing fatigue. Biological sampling conditions were standardized and RNA stabilizing media were used. These methodological features provide rigorous control for bias resulting from case-control mismatched ancestry and experimental error. Individual gene expression profiles were assessed using Affymetrix Human Genome U133 Plus 2.0 arrays.FindingsThere were no significant differences in gene expression for any transcript.ConclusionsContrary to our expectations, we were unable to identify a biomarker for chronic fatiguing illness in the transcriptome of peripheral blood leukocytes suggesting that positive findings in prior studies may have resulted from experimental bias.

In vivo profile of the human leukocyte microRNA response to endotoxemia

To gain insight into microRNAs (miRNAs) involved in the regulation of the human innate immune response, we screened for differentially expressed miRNAs in circulating leukocytes in an in vivo model of acute inflammation triggered by Escherichia coli lipopolysaccharide (LPS) infusion. Leukocyte RNA was isolated from venous blood samples obtained from healthy male volunteers before and 4 h after LPS-infusion. After fluorescence labeling, RNA samples were hybridized to microarrays containing capture probes for measuring the abundance of more than 600 human miRNAs. Target genes were predicted for differentially expressed miRNAs and then compared to changes in genome-wide expression levels, which had been established in a previous study. Data analysis revealed that five miRNAs consistently responded to LPS-infusion, four of which were down-regulated (miR-146b, miR-150, miR-342, and let-7g) and one was up-regulated (miR-143). The miR-150 and mir-342 response was confirmed by real-time PCR. By correlating to measured LPS-induced changes of the leukocyte transcriptome, we next searched for predicted target genes, whose stability might be under (co-) control by these miRNAs. We found that the rapid transcriptional activation during acute inflammation of select genes, such as the gene encoding interleukin-1 receptor-associated kinase 2 ( IRAK2) might be facilitated by decreased levels of LPS-responsive miRNAs. The increased level of miR-143 might be associated with the pronounced down-regulation of the B-cell CLL/lymphoma 2 ( BCL2) gene expression during LPS endotoxemia, and could further be involved in the translational silencing of several other predicted inflammation-related target genes. This is the first in vivo study to demonstrate relative abundance of miRNA levels in peripheral blood leukocytes during acute LPS-induced inflammation. The miRNAs and their potential target genes identified herein contribute to the understanding of the complex transcriptional program of innate immunity initiated by pathogens.

In vivo profile of the human leukocyte microRNA response to endotoxemia

To gain insight into microRNAs (miRNAs) involved in the regulation of the human innate immune response, we screened for differentially expressed miRNAs in circulating leukocytes in an in vivo model of acute inflammation triggered by Escherichia coli lipopolysaccharide (LPS) infusion. Leukocyte RNA was isolated from venous blood samples obtained from healthy male volunteers before and 4h after LPS-infusion. After fluorescence labeling, RNA samples were hybridized to microarrays containing capture probes for measuring the abundance of more than 600 human miRNAs. Target genes were predicted for differentially expressed miRNAs and then compared to changes in genome-wide expression levels, which had been established in a previous study. Data analysis revealed that five miRNAs consistently responded to LPS-infusion, four of which were down-regulated (miR-146b, miR-150, miR-342, and let-7g) and one was up-regulated (miR-143). The miR-150 and mir-342 response was confirmed by real-time PCR. By correlating to measured LPS-induced changes of the leukocyte transcriptome, we next searched for predicted target genes, whose stability might be under (co-) control by these miRNAs. We found that the rapid transcriptional activation during acute inflammation of select genes, such as the gene encoding interleukin-1 receptor-associated kinase 2 (IRAK2) might be facilitated by decreased levels of LPS-responsive miRNAs. The increased level of miR-143 might be associated with the pronounced down-regulation of the B-cell CLL/lymphoma 2 (BCL2) gene expression during LPS endotoxemia, and could further be involved in the translational silencing of several other predicted inflammation-related target genes. This is the first in vivo study to demonstrate relative abundance of miRNA levels in peripheral blood leukocytes during acute LPS-induced inflammation. The miRNAs and their potential target genes identified herein contribute to the understanding of the complex transcriptional program of innate immunity initiated by pathogens.

A Genome-Wide Gene Expression Signature of Environmental Geography in Leukocytes of Moroccan Amazighs

The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence. Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression. Genetic network analysis further implies that specific aspects of immune function are strongly affected by regional factors and may influence susceptibility to respiratory and inflammatory disease. Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

Application of leukocyte transcriptomes to assess systemic consequences of risk factors for cardiovascular disease

Prevention of cardiovascular disease (CVD) remains a major health issue in the Western world. The diagnostic and therapeutic approach is currently based on risk factor assessment and treatment, which adequately predicts CVD at population level, but not at the level of a single individual. This may arise from the fact that the stage and activity of complex disease states are not likely to be captured by a single parameter or a small set of markers and thus may need a more complex representation. The aim of this review is to explore the possibility of pursuing the use of high-throughput gene expression profiling as a way to improve diagnosis, prognosis and monitoring of the disease. Novel chip-based techniques such as oligo- and cDNA microarrays can measure the abundance of thousands of mRNA transcripts in parallel and thus provide a comprehensive picture of the cell phenotype. Circulating white blood cells (WBCs), which are exposed to the systemic environment (including the risk factors) and are directly involved in the low-grade chronic inflammation related to CVD, have the potential to be used in this context to improve phenotyping of the patient. The paper reviews conceptual limitations in the use of risk factors and biomarkers, and shows the rationale beyond the possible use of circulating WBCs or subpopulations as representative cells to monitor systemic consequences of CVD. Methodological issues in performing microarray analysis of WBCs are also addressed, including controversies related to the choice of adequate cell populations and reference samples. Reproducibility and challenges occurring in the definition of a disease-specific gene panel are also discussed. The available proofs of principle from the literature presented in the last section of the review further support exploration of the application of circulating cell transcriptomics in CVD.