Gene expression in mononuclear cells from patients with inflammatory bowel disease

Gene expression profiling of indigenous Tharparkar and crossbred Vrindavani cattle affected with lameness using PBMC model

Lameness is an economically significant, production-limiting syndrome that adversely affects the (re)production performance of animals besides deteriorating the quantity and quality aspects of milk in dairy cattle. The present study aimed to explore the potential biomarkers for painful foot lesions in indigenous Tharparkar and crossbred Vrindavani cattle affected with lameness. The differentially expressed genes in lame versus healthy animals were elucidated using microarray analysis and validated them by qRT-PCR. On microarray analysis, 504 genes were differentially expressed in lame crossbred cattle as compared to healthy counterparts. Similarly, 991 genes were differentially expressed in lame crossbred cattle as compared to the healthy Tharparkar animals. Various genes such as BOLA-DQA3, BOLA-DQA1, CCL4, CCR1, CCRL2, CXCL2, CXCL3, CXCL8, IL1A, IL1B, MMP-9 and SLC11A1 were common between both the comparisons (crossbred lame vs. crossbred normal cattle; and crossbred lame vs. normal Tharparkar cattle). The results revealed downregulation of multiple pro-inflammatory cytokines. Validation using qRT-PCR showed high correlation with the microarray results, except for the IRAK1 gene. The functional annotation and gene network analysis revealed involvement of various processes including inflammation, immunology, apoptosis, cell proliferation and cytoskeleton organization. The Ingenuity pathway analysis revealed three inhibited pathways in the comparison between lame and normal (healthy) crossbred cattle i.e., HMGB1-signalling pathway, Aryl hydrocarbon receptor signalling pathway, and Mitotic roles of pol-like kinase. Whereas, on comparison of lame crossbred with healthy Tharparkar cattle, the Situin signalling pathway was inhibited; the LxR/RxR activation pathway was activated. The results from microarray analysis, identifying differential expressed genes provides valuable insights into the development of molecular biomarkers for early detection of lameness-affected animals.

A Putative Blood-Based Biomarker for Autism Spectrum Disorder-Associated Ileocolitis

Gastrointestinal symptoms are common in children with autism spectrum disorder (ASD). A significant proportion of children with ASD and gastrointestinal symptoms have histologic evidence of ileocolitis (inflammation of the terminal ileum and/or colon). We previously reported the molecular characterization of gastrointestinal biopsy tissue from ASD children with ileocolitis (ASD^IC+) compared to anatomically similar inflamed tissue from typically developing children with inflammatory bowel disease (IBD; i.e. Crohn’s disease or ulcerative colitis) and typically developing children with gastrointestinal symptoms but no evidence of gastrointestinal mucosal inflammation (TD^IC−). ASD^IC+ children had a gene expression profile that, while primarily overlapping with known IBD, had distinctive differences. The present study confirms these findings and replicates this molecular characterization in a second cohort of cases (ASD^IC+) and controls (TD^IC−). In these two separate case/control mucosal-based cohorts, we have demonstrated overlap of 59 differentially expressed transcripts (DETs) unique to inflamed ileocolonic tissue from symptomatic ASD^IC+ children. We now report that 9 of these 59 transcripts are also differentially expressed in the peripheral blood of the second cohort of ASD^IC+ children. This set of transcripts represents a putative blood-based biomarker for ASD-associated ileocolonic inflammation.

RNA Biosignatures in Adolescent Patients in a Pediatric Emergency Department With Pelvic Inflammatory Disease

BACKGROUND

Adolescents are at high risk for pelvic inflammatory disease (PID). Because accurate diagnosis of PID is difficult, and complications of untreated PID are significant, novel methods to improve diagnosis are essential.

OBJECTIVES

To determine if patients with PID have unique RNA expression patterns compared to controls.

METHODS

Peripheral blood was collected from adolescent females with PID in the emergency department, and from control patients in the operating room. RNA was isolated, and microarray analysis was performed. Initial analysis involved a training set of 18 patients (9 PID patients with either Neisseria gonorrhoeae or Chlamydia trachomatis infection and 9 control patients). Supervised and unsupervised cluster analyses were performed, followed by network analysis. The training set was used to classify a set of 15 additional PID patients and 2 controls.

RESULTS

Supervised cluster analysis of the training set revealed 170 genes which were differentially expressed in PID patients versus controls. Network analysis indicated that several differentially expressed genes are involved in immune activation. Analysis of additional PID patients based on the training set findings revealed that patients with positive testing for Trichomonas vaginalis partitioned with the PID group, whereas patients with no organism identified partitioned with both groups.

CONCLUSIONS

RNA sample collection from adolescents in the emergency department is feasible. Genes were identified which were differentially expressed in PID patients versus controls, many of which are involved in inflammation. Future studies should confirm the training set findings on a larger sample and may lead to improved accuracy of PID diagnosis.

Involvement of TG-interacting factor in microglial activation during experimental traumatic brain injury

Traumatic brain injury (TBI) is a complex injury involving several physiological alterations, potentially leading to neurological impairment. Previous mouse studies using high-density oligonucleotide array analysis have confirmed the upregulation of transforming growth-interacting factor (TGIF) mRNA in TBI. TGIF is a transcriptional corepressor of transforming growth factor beta (TGF-β) signaling which plays a protective role in TBI. However, the functional roles of TGIF in TBI are not well understood. In this study, we used confocal microscopy after immunofluorescence staining to demonstrate the increase of TGIF levels in the activated microglia of the pericontusional cortex of rats with TBI. Intracerebral knockdown of TGIF in the pericontusional cortex significantly downregulated TGIF expression, attenuated microglial activation, reduced the volume of damaged brain tissue, and facilitated recovery of limb motor function. Collectively, our results indicate that TGIF is involved in TBI-induced microglial activation, resulting in secondary brain injury and motor dysfunction. This study investigated the roles of transforming growth-interacting factor (TGIF) in a traumatic brain injury (TBI)-rat model. We demonstrated the increase of TGIF levels in the activated microglia of the pericontusional cortex of rats with TBI. Intracerebral knockdown of TGIF in the pericontusional cortex of the TBI rats significantly attenuated micoglial activation, reduced the volume of damaged brain tissue, and facilitated recovery of limb motor function. We suggest that inhibition of TGIF might provide a promising therapeutic strategy for TBI.

Expression of genes associated with cholesterol and lipid metabolism identified as a novel pathway in the early pathogenesis of Mycobacterium avium subspecies paratuberculosis-infection in cattle

Johne's disease (JD) is a chronic disease affecting ruminants and other species caused by the pathogenic mycobacterium, Mycobacterium avium subsp. paratuberculosis (MAP). MAP has developed a multitude of mechanisms to persist within the host, and these in turn are counteracted by the host through various immune pathways. Identifying and characterising the different strategies employed by MAP to alter the host immune system in its favour, and thereby persist intracellularly, could hold the key to developing strategies to fight this disease. In this study we analysed a subset of bovine microarray data derived from early time points after experimental infection with MAP. A specifically developed integrated approach was used to identify and validate host genes involved in cholesterol homeostasis (24DHCR, LDLR, SCD-1), calcium homeostasis and anti-bacterial defence mechanisms, (CD38, GIMAP6) which were downregulated in response to MAP exposure. A trend for upregulation of granulysin gene expression in MAP-exposed cattle in comparison to unexposed cattle was also observed. From these analyses, a model of potential pathogen-host interactions involving these novel pathways was developed which indicates an important role for host lipids in mycobacterial survival and persistence.

Dietary selenium deficiency exacerbates DSS-induced epithelial injury and AOM/DSS-induced tumorigenesis

Selenium (Se) is an essential micronutrient that exerts its functions via selenoproteins. Little is known about the role of Se in inflammatory bowel disease (IBD). Epidemiological studies have inversely correlated nutritional Se status with IBD severity and colon cancer risk. Moreover, molecular studies have revealed that Se deficiency activates WNT signaling, a pathway essential to intestinal stem cell programs and pivotal to injury recovery processes in IBD that is also activated in inflammatory neoplastic transformation. In order to better understand the role of Se in epithelial injury and tumorigenesis resulting from inflammatory stimuli, we examined colonic phenotypes in Se-deficient or -sufficient mice in response to dextran sodium sulfate (DSS)-induced colitis, and azoxymethane (AOM) followed by cyclical administration of DSS, respectively. In response to DSS alone, Se-deficient mice demonstrated increased morbidity, weight loss, stool scores, and colonic injury with a concomitant increase in DNA damage and increases in inflammation-related cytokines. As there was an increase in DNA damage as well as expression of several EGF and TGF-β pathway genes in response to inflammatory injury, we sought to determine if tumorigenesis was altered in the setting of inflammatory carcinogenesis. Se-deficient mice subjected to AOM/DSS treatment to model colitis-associated cancer (CAC) had increased tumor number, though not size, as well as increased incidence of high grade dysplasia. This increase in tumor initiation was likely due to a general increase in colonic DNA damage, as increased 8-OHdG staining was seen in Se-deficient tumors and adjacent, non-tumor mucosa. Taken together, our results indicate that Se deficiency worsens experimental colitis and promotes tumor development and progression in inflammatory carcinogenesis.

Gene expression changes in the colon epithelium are similar to those of intact colon during late inflammation in interleukin-10 gene deficient mice

In addition to their role in absorption and secretion, epithelial cells play an important role in the protection of the colon mucosa from the resident microbiota and are important for the maintenance of homeostasis. Microarray analysis of intact colon samples is widely used to gain an overview of the cellular pathways and processes that are active in the colon during inflammation. Laser microdissection of colon epithelial cells allows a more targeted analysis of molecular pathways in the mucosa, preceding and during inflammation, with potentially increased sensitivity to changes in specific cell populations. The aim of this study was to investigate the molecular changes that occur in early and late inflammation stages in colon epithelium of a mouse model of inflammatory bowel diseases. Microarray analysis of intact colon samples and microdissected colon epithelial cell samples from interleukin-10 gene deficient and control mice at 6 and 12 weeks of age was undertaken. Results of gene set enrichment analysis showed that more immune-related pathways were identified between interleukin-10 gene deficient and control mice at 6 weeks of age in epithelial cells than intact colon. This suggests that targeting epithelial cells could increase sensitivity for detecting immune changes that occur early in the inflammatory process. However, in the later stages of inflammation, microarray analyses of intact colon and epithelium both provide a similar overview of gene expression changes in the colon mucosa at the pathway level.

Using gene expression data to identify certain gastro-intestinal diseases

Background

Inflammatory bowel diseases, ulcerative colitis and Crohn’s disease are considered to be of autoimmune origin, but the etiology of irritable bowel syndrome remains elusive. Furthermore, classifying patients into irritable bowel syndrome and inflammatory bowel diseases can be difficult without invasive testing and holds important treatment implications. Our aim was to assess the ability of gene expression profiling in blood to differentiate among these subject groups.

Methods

Transcript levels of a total of 45 genes in blood were determined by quantitative real-time polymerase chain reaction (RT-PCR). We applied three separate analytic approaches; one utilized a scoring system derived from combinations of ratios of expression levels of two genes and two different support vector machines.

Results

All methods discriminated different subject cohorts, irritable bowel syndrome from control, inflammatory bowel disease from control, irritable bowel syndrome from inflammatory bowel disease, and ulcerative colitis from Crohn’s disease, with high degrees of sensitivity and specificity.

Conclusions

These results suggest these approaches may provide clinically useful prediction of the presence of these gastro-intestinal diseases and syndromes.

Molecular Characterization of the Onset and Progression of Colitis in Inoculated Interleukin-10 Gene-Deficient Mice: A Role for PPARalpha

The interleukin-10 gene-deficient (Il10(-/-)) mouse is a model of human inflammatory bowel disease and Ppara has been identified as one of the key genes involved in regulation of colitis in the bacterially inoculated Il10(-/-) model. The aims were to (1) characterize colitis onset and progression using a histopathological, transcriptomic, and proteomic approach and (2) investigate links between PPARalpha and IL10 using gene network analysis. Bacterial inoculation resulted in severe colitis in Il10(-/-) mice from 10 to 12 weeks of age. Innate and adaptive immune responses showed differences in gene expression relating to colitis severity. Actin cytoskeleton dynamics, innate immunity, and apoptosis-linked gene and protein expression data suggested a delayed remodeling process in 12-week-old Il10(-/-) mice. Gene expression changes in 12-week-old Il10(-/-) mice were related to PPARalpha signaling likely to control colitis, but how PPARalpha activation might regulate intestinal IL10 production remains to be determined.

Protein profiles of peripheral blood mononuclear cells are useful for differential diagnosis of ulcerative colitis and Crohn's disease

BACKGROUND

Effective biomarkers for discrimination between ulcerative colitis (UC) and Crohn's disease (CD) have not been established yet. In this study, we analyzed protein profiles of peripheral blood mononuclear cells (PBMCs) of the patients to find such a biomarker.

METHODS

Peripheral blood mononuclear cell proteins from 17 UC patients, 13 CD patients, and 17 healthy controls were separated by two-dimensional gel electrophoresis. The intensities of individual protein spots were subjected to discriminant analysis of UC and CD using the SIMCA-P+program.

RESULTS

We found that 547 protein spots were commonly detected among the UC, CD, and healthy groups. Orthogonal partial least squares-discriminant analysis using 276 protein spots clearly discriminated the UC patients from the CD patients (R (2) 0.994; Q (2) 0.462). A similar analysis using a further selected 58 protein spots showed higher performance for discrimination of the diseases (R (2) 0.948; Q (2) 0.566). Eleven out of the 58 protein spots were successfully identified; these were functionally related to inflammation, oxidation/reduction, the cytoskeleton, endocytotic trafficking, and transcription. In addition, the PBMC protein profiles were useful for the prediction of disease activity in the UC and the CD patients, and they were also useful for predicting disease severity and responses to treatments in the UC patients.

CONCLUSIONS

PBMC protein profiles are useful for the discrimination of UC from CD. The profiles could be a potent biomarker for the differential diagnosis of these diseases. Further investigation of the proteins which contributed to the discrimination could promote elucidation of the pathophysiology of UC and CD.

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 Crohn's disease. Noninvasive, accurate markers for monitoring disease activity are urgently required. Specific gene expression patterns and molecular biomarkers associated with active Crohn's 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 Crohn's disease.

STUDY

In this study, we compared genome-wide transcription profiles of circulating leukocytes in patients with active and quiescent Crohn's disease.

RESULTS

We observed complex changes in blood gene expression patterns in active Crohn's disease: genes of various functional categories were differentially regulated between active and inactive Crohn's disease. We specifically identified a number of inflammatory molecules overexpressed or underexpressed in active Crohn's 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 Crohn's disease.

The future of molecular approaches to inflammatory bowel disease

Technological advances in genomics and transcriptomics have resulted in the introduction of molecular tests into the clinical arena. Despite established uses of such tests in the oncology field, their integration into the management of complex diseases has not been widely evaluated. Progress in the field of inflammatory bowel disease (IBD) genetics has been rapid in recent years, and these advances have provided more urgent impetus to investigating the role of molecular tests in IBD. This article summarizes the current state of molecular testing available for IBD, and the potential utility of such tests as research in the area widens.

Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease

The cause of Crohn's disease (CD) remains poorly understood. Counterintuitively, these patients possess an impaired acute inflammatory response, which could result in delayed clearance of bacteria penetrating the lining of the bowel and predispose to granuloma formation and chronicity. We tested this hypothesis in human subjects by monitoring responses to killed Escherichia coli injected subcutaneously into the forearm. Accumulation of (111)In-labeled neutrophils at these sites and clearance of (32)P-labeled bacteria from them were markedly impaired in CD. Locally increased blood flow and bacterial clearance were dependent on the numbers of bacteria injected. Secretion of proinflammatory cytokines by CD macrophages was grossly impaired in response to E. coli or specific Toll-like receptor agonists. Despite normal levels and stability of cytokine messenger RNA, intracellular levels of tumor necrosis factor (TNF) were abnormally low in CD macrophages. Coupled with reduced secretion, these findings indicate accelerated intracellular breakdown. Differential transcription profiles identified disease-specific genes, notably including those encoding proteins involved in vesicle trafficking. Intracellular destruction of TNF was decreased by inhibitors of lysosomal function. Together, our findings suggest that in CD macrophages, an abnormal proportion of cytokines are routed to lysosomes and degraded rather than being released through the normal secretory pathway.

New bioinformatics approach to analyze gene expressions and signaling pathways reveals unique purine gene dysregulation profiles that distinguish between CD and UC

BACKGROUND

Expression of purine genes is modulated by inflammation or experimental colitis and altered expression leads to disrupted gut function. We studied purine gene dysregulation profiles in inflammatory bowel disease (IBD) and determined whether they can distinguish between Crohn's disease (CD) and ulcerative colitis (UC) using Pathway Analysis and a new Comparative Analysis of Gene Expression and Selection (CAGES) method.

METHODS

Raw datasets for 22 purine genes and 36 probe-sets from National Center for Biotechnology Information (NCBI) GEO (Gene Expression Omnibus) (http://www.ncbi.nlm.nih.gov/projects/geo/) were analyzed by National Cancer Institute (NCI) Biological Resources Branch (BRB) array tools for random-variance of multiple/36 t-tests in colonic mucosal biopsies or peripheral blood mononuclear cells (PBMCs) of CD, UC or control subjects. Dysregulation occurs in 59% of purine genes in IBD including ADORA3, CD73, ADORA2A, ADORA2B, ADAR, AMPD2, AMPD3, DPP4, P2RY5, P2RY6, P2RY13, P2RY14, and P2RX5.

RESULTS

In CD biopsies, expression of ADORA3, AMPD3, P2RY13, and P2RY5 were negatively correlated with acute inflammatory score, Crohn's Disease Activity Index (CDAI) or disease chronicity; P2RY14 was positively correlated in UC. In mucosal biopsies or PBMCs, CD and UC were distinguished by unique patterns of dysregulation (up- or downregulation) in purine genes. Purine gene dysregulation differs between PBMCs and biopsies and possibly between sexes for each disease. Ingenuity Pathway Analysis (IPA) revealed significant associations between alterations in the expression of CD73 (upregulation) or ADORA3 (downregulation) and inflammatory or purine genes (<or=10% of 57 genes) as well as G-protein coupled receptors, cAMP-dependent, and inflammatory pathways; IPA distinguishes CD from UC.

CONCLUSION

CAGES and Pathway Analysis provided novel evidence that UC and CD have distinct purine gene dysregulation signatures in association with inflammation, cAMP, or other signaling pathways. Disease-specific purine gene signature profiles and pathway associations may be of therapeutic, diagnostic, and functional relevance.

Research progress in susceptibility genes of inflammatory bowel disease

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a group of non-specific chronic inflammatory conditions of the gastrointestinal tract with unknown complex etiology. Epidemiologic data indicate genetic contribution to IBD pathogenesis, which include familial aggregation, twin studies, racial and ethnic differences in disease prevalence. The most widely adopted approaches to identifying susceptibility genes in IBD include linkage studies, genome-wide association (GWA) studies and microarray. The first two technologies have confirmed NOD2, IL23R and other genes implicated in IBD pathogenesis and advances in microarray technology makes it possible to diagnose IBD at gene expression level. This article reviewed IBD related genes and introduced application of microarray to IBD research.

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.

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

BACKGROUND

Discrimination and classification of colorectal diseases (adenoma, colorectal cancer, inflammatory bowel disease) using biopsy samples and expression microarrays, has not been solved yet, nevertheless, it can contribute to the understanding of the colonic diseases.

METHODS

Total ribonucleic acid was extracted, amplified and biotinylated from frozen colonic biopsies of 15 patients with colorectal cancer, 15 with adenoma, 14 with inflammatory bowel disease and 8 normal controls. Genome-wide gene expression profile was evaluated by Human Genome U133 Plus 2.0 microarrays. Two independent methods were used for data normalization and "Prediction Analysis of Microarrays" was performed for feature selection. Leave one-out stepwise discriminant analysis was performed. The expression results were verified by real-time polymerase chain reaction.

RESULTS

Top validated genes included CD44 antigen, met proto-oncogene, chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette-A8 genes in adenoma; collagen IValpha1, lipocalin-2, calumenin, aquaporin-8 genes in colorectal cancer; and lipocalin-2, ubiquitin D and interferon induced transmembrane protein 2 genes in inflammatory bowel disease. The discriminant analysis was able to classify the samples in overall 96.2% using 7 discriminatory genes. The expression of 94% of the 52 genes measured by Taqman real-time polymerase chain reaction correlated with the results obtained using Affymetrix microarrays at a significance of p < 0.05.

CONCLUSIONS

We successfully performed whole genomic microarray analysis to identify discriminative signatures using routine biopsy samples. The results set up data warehouse which can be further mined.

The peripheral-blood transcriptome: new insights into disease and risk assessment

Future personalized medicine strategies for assessing an individual's health require, ideally, a noninvasive system that is capable of integrating numerous interactive factors, including gender, age, genetics, behavior, environment and comorbidities. Several microarray-based methods developed to meet this goal are currently under investigation. However, most rely on tissue biopsies, which are not readily available or accessible. As an alternative, several recent studies have investigated the use of human peripheral blood cells as surrogate biopsy material. Such studies are based on the assumption that molecular profiling of circulating blood might reflect physiological and pathological events occurring in different tissues of the body. This has led to the development of novel methods for identifying and monitoring blood biomarkers to probe an individual's health status. Here, we discuss the rationale and clinical potential of profiling the peripheral-blood transcriptome.

Gene expression profiling of peripheral mononuclear cells in lame dairy cows with foot lesions

Lameness is a major health issue and likely the single most common cause of pain and discomfort in dairy cattle. Appropriate treatment is delayed or neglected due, in part, to lack of reliable detection. Assessment of cows with lameness is currently limited to subjective visual scoring systems based on locomotion and posture abnormalities. These systems are unreliable to detect lameness, and therefore, a large number of cows remain undiagnosed. The objective of this research was to search for potential biomarkers for lameness-associated painful inflammatory foot lesions in dairy cattle using microarray-based gene expression profiling of peripheral blood mononuclear cells (PBMC). BOTL5 microarrays spotted in duplicate with cDNA representing bovine immune response genes were interrogated with cDNA samples in an eight-array, balanced complete block design with dye swap. Samples from eight lame cows with inflammatory foot lesions and from eight sound cows were pair-matched by age, weight, days in lactation, and pregnancy status at time of PBMC collection and directly compared with each other on individual arrays. Statistical analysis of resulting fluorescence intensity data revealed 31 genes that were putatively differentially expressed in lame versus sound cows (P<0.05). Of these, BLASTn analysis and gene ontology information showed that 28 genes had high similarity or homology to known human and/or rodent genes. Validation of 15 of these genes known to be important in inflammation and pain was carried out using relative quantitative real-time RT-PCR, which confirmed the up-regulation of interleukin (IL)-2 (12.68+/-1.47-fold increase) and IL-10 (2.39+/-0.55-fold increase), matrix metalloproteinase-13 (MMP-13) (10.44+/-1.14-fold increase), and chemokine C-C motif receptor-5 (CCR5) (5.26+/-1.05-fold increase), in lame relative to sound cows (P< or =0.05). Similarly, granulocyte-macrophage colony-stimulating factor receptor alpha chain precursor (GM-CSF-R-alpha) (2.30+/-0.63-fold increase) and IL-4 (2.06+/-0.59-fold increase) showed a tendency (P=0.10) for up-regulation in lame compared to sound cows. PBMC co-expression of IL-2, MMP-13, CCR5 and IL-10, and potentially IL-4 and GM-CSF-R-alpha appears to be a promising, objective sign of lameness-related inflammatory foot lesions in dairy cattle. In conclusion, this study revealed potential biomarkers of the presence of foot lesions that could boost diagnostic accuracy of lameness and, ultimately, help identify animals in need of pain relief.

Deoxycholate-induced colitis is markedly attenuated in Nos2 knockout mice in association with modulation of gene expression profiles

Nos2 knockout mice were compared to wild-type mice for susceptibility to colitis in response to a diet supplemented with deoxycholate, a bile acid increased in the colon of individuals on a high-fat diet. Wild-type mice fed a fat-related diet, supplemented with 0.2% DOC, develop colonic inflammation associated with increases in nitrosative stress, proliferation, oxidative DNA/RNA damage, and angiogenesis, as well as altered expression of numerous genes. However, Nos2 knockout mice fed a diet supplemented with deoxycholate were resistant to these alterations. In particular, 35 genes were identified whose expression was significantly altered at the mRNA level in deoxycholate-fed Nos2(+/+) mice but not in deoxycholate-fed Nos2(-/-) mice. Some of these alterations in NOS2-dependent gene expression correspond to those reported in human inflammatory bowel disease. Overall, our results indicate that NOS2 expression is necessary for the development of deoxycholate-induced colitis in mice, a unique dietary-related model of colitis.

Comparative analysis of colonic gene expression of three experimental colitis models mimicking inflammatory bowel disease

BACKGROUND

Mouse models of inflammatory bowel diseases (IBD) are used to unravel the pathophysiology of IBD and to study new treatment modalities, but their relationship to Crohn's disease (CD) or ulcerative colitis (UC) is speculative.

METHODS

Using Agilent mouse TOX oligonucleotide microarrays, we analyzed colonic gene expression profiles in three widely used models of experimental colitis. In 2 of the models (TNBS and DSS-induced colitis), exogenous agents induce the colitis. In the third model the colitis is induced after transfer of a T-cell population (CD4(+)CD45RB(high) T cells) that lacks regulatory cells into an immunodeficient host.

RESULTS

Compared with control mice, in DSS, TNBS, and the CD45RB transfer colitis mice, 387, 21, and 582 genes were more than 2-fold upregulated in the intestinal mucosa. Analyses of exclusively shared gene expression profiles between the different models revealed that DSS/transfer colitis share 69 concordantly upregulated genes, DSS/TNBS 6, and TNBS/transfer colitis 1. Seven genes were upregulated in all three models. The CD45RB transfer model expression profile included the most genes that are known to be upregulated in IBD. Of 32 genes that are known to change transcriptional activity in IBD (TNF, IFN-gamma, Ltbeta, IL-6, IL-16, IL-18R1, IL-22, CCR2, 7, CCL2, 3, 4, 5, 7, 11, 17, 20, CXCR3, CXCL1, 5, 10, Mmp3, 7,9, 14, Timp1, Reg3gamma, and Pap, S-100a8, S-100a9, Abcb1, and Ptgs2), 2/32 are upregulated in TNBS, 15/32 are upregulated or downregulated in DSS and 30/32 are upregulated or downregulated in the CD45RB transfer colitis.

CONCLUSION

The pattern of gene expression in the CD45RB transfer model most closely reflects altered gene expression in IBD.

Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells

Ulcerative colitis (UC) and Crohn's disease (CD) are common inflammatory bowel diseases producing intestinal inflammation and tissue damage. Although emerging evidence suggests these diseases are distinct, approximately 10% of patients remain classified as indeterminate inflammatory bowel disease even after invasive colonoscopy intended for diagnosis. A molecular diagnostic assay using a clinically accessible tissue would greatly assist in the classification of these diseases. In the present study we assessed transcriptional profiles in peripheral blood mononuclear cells from 42 healthy individuals, 59 CD patients, and 26 UC patients by hybridization to microarrays interrogating more than 22,000 sequences. Supervised analysis identified a set of 12 genes that distinguished UC and CD patient samples with high accuracy. The alterations in transcript levels observed by microarray were verified by real-time polymerase chain reaction. The results suggest that a peripheral blood mononuclear cell-based gene expression signature can provide a molecular biomarker that can complement the standard diagnosis of UC and CD.

Transcriptional profiling of peripheral blood cells in clinical pharmacogenomic studies

Peripheral blood represents an attractive tissue source in clinical pharmacogenomic studies, given the feasibility of its collection from patients and its potential as a sentinel tissue to monitor perturbations of physiology in many disease states. The hypothesis is that the circulating blood cells monitor the physiological state of the organism and alter their transcriptome in response to this surveillance. However, the successful implementation of transcriptional profiling of peripheral blood cells in clinical trials represents a tremendous technical challenge for several reasons, including controlling the pre-analytical variables associated with sample processing and the interpretation of gene expression signatures generated from the complex mixture of cell types in blood. Multiple approaches for identifying transcriptomes in peripheral blood cells exist and each method is associated with significant advantages and disadvantages. Nonetheless, a growing number of studies are rapidly identifying transcriptional biomarkers in peripheral blood cells that may function as biomarkers of disease, evidence of pharmacodynamic effect, or even predictors of clinical outcomes and risk of toxicity. This review highlights the major approaches employed in global transcriptional profiling of peripheral blood cells and summarizes the available literature of initial studies in the growing field of hemogenomics. The overall purpose of the review is to focus on the development and application of technologies for the use of peripheral blood cells as a sentinel or surrogate tissue to measure disease state and drug response.

Unique dietary-related mouse model of colitis

BACKGROUND

A high-fat diet is a risk factor for the development of inflammatory bowel disease (IBD) in humans. Deoxycholate (DOC) is increased in the colonic contents in response to a high-fat diet. Thus, an elevated level of DOC in the colonic lumen may play a role in the natural course of development of IBD.

METHODS

Wild-type B6.129 mice were fed an AIN-93G diet, either supplemented with 0.2% DOC or unsupplemented and sacrificed at 1 week, 1 month, 3 months, 4 months, and 8 months. Colon samples were assessed by histopathological, immunohistochemical, and cDNA microarray analyses.

RESULTS

Mice fed the DOC-supplemented diet developed focal areas of colonic inflammation associated with increases in angiogenesis, nitrosative stress, DNA/RNA damage, and proliferation. Genes that play a central role in inflammation and angiogenesis and other related processes such as epithelial barrier function, oxidative stress, apoptosis, cell proliferation/cell cycle/DNA repair, membrane transport, and the ubiquitin-proteasome pathway showed altered expression in the DOC-fed mice compared with the control mice. Changes in expression of individual genes (increases or reductions) correlated over time. These changes were greatest 1 month after the start of DOC feeding.

CONCLUSIONS

The results suggest that exposure of the colonic mucosa to DOC may be a key etiologic factor in IBD. The DOC-fed mouse model may reflect the natural course of development of colitis/IBD in humans, and thus may be useful for determining new preventive strategies and lifestyle changes in affected individuals.

Consistent across-tissue signatures of differential gene expression in Crohn's disease

An approach based on analysis of variance was applied to raw expression data on 44,760 transcripts in order to identify those with significant differential expression across ileum and colon in Crohn's disease (CD) and ulcerative colitis (UC). The design treated tissue as a block effect, thereby removing this effect statistically and increasing the power to test for effects of disease states (control, CD, and UC). A significant F-statistic for the disease effect was not correlated with the ratios CD/control or UC/control, evidently because many transcripts with high-expression ratios to the control showed inconsistent patterns across tissues. Of 1,053 transcripts showing a significant effect of disease state at the 1% level by the bootstrap test, 508 showed significant difference at the 1% level in a post hoc test for difference between the mean scores for CD and control. These included a number of genes relevant to the mechanism of pathogenesis of CD and a number of genes mapping to genomic regions that have previously shown linkage to CD in association studies.

Analysis of NOD2-mediated proteome response to muramyl dipeptide in HEK293 cells

NOD2, a cytosolic receptor for the bacterial proteoglycan fragment muramyl dipeptide (MDP), plays an important role in the recognition of intracellular pathogens. Variants in the bacterial sensor domain of NOD2 are genetically associated with an increased risk for the development of Crohn disease, a human chronic inflammatory bowel disease. In the present study, global protein expression changes after MDP stimulation were analyzed by two-dimensional PAGE of total protein extracts of human cultured cells stably transfected with expression constructs encoding for wild type NOD2 (NOD2(WT)) or the disease-associated NOD2 L1007fsinsC (NOD2(SNP13)) variant. Differentially regulated proteins were identified by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) peptide mass fingerprinting and MALDI MS/MS. The limited overlap in the responses of the NOD2-overexpressing cell lines to MDP included a down-regulation of heat shock 70-kDa protein 4. A complex pro-inflammatory program regulated by NOD2(WT) that encompasses a regulation of key genes involved in protein folding, DNA repair, cellular redox homeostasis, and metabolism was observed both under normal growth conditions and after stimulation with MDP. By using the comparison of NOD2(WT) and disease-associated NOD2(SNP13) variant, we have identified a proteomic signature pattern that may further our understanding of the influence of genetic variations in the NOD2 gene in the pathophysiology of chronic inflammatory bowel disease.