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1.  Validation of a Novel Multi-Biomarker Test to Assess Rheumatoid Arthritis Disease Activity 
Arthritis care & research  2012;64(12):1794-1803.
Objective
Quantitative assessment of disease activity in rheumatoid arthritis (RA) is important for patient management, and additional objective information may aid rheumatologists in clinical decision-making. We validated a recently-developed multi-biomarker disease activity (MBDA) test relative to clinical disease activity in diverse RA cohorts.
Methods
Serum samples were obtained from the InFoRM, BRASS, and Leiden Early Arthritis Clinic cohorts. Levels of 12 biomarkers were measured and combined according to a pre-specified algorithm to generate the composite MBDA score. The relationship of the MBDA score to clinical disease activity was characterized separately in seropositive and seronegative patients using Pearson correlations and area under the receiver operator characteristic curve (AUROC) to discriminate between patients with low and moderate/high disease activity. Associations between changes in MBDA score and clinical responses 6–12 weeks after initiation of anti-TNF or methotrexate treatment were evaluated by AUROC.
Results
The MBDA score was significantly associated with DAS28-CRP in both seropositive (AUROC=0.77; P<0.001) and seronegative patients (AUROC=0.70; P<0.001). In subgroups based on age, sex, body-mass index, and treatment, the MBDA score was associated with DAS28-CRP (P<0.05) in all seropositive and most seronegative subgroups. Changes in MBDA score at 6–12 weeks could discriminate both ACR50 responses (P=0.03) and DAS28-CRP improvement (P=0.002). Changes in MBDA score at 2 weeks were also associated with subsequent DAS28-CRP response (P=0.02).
Conclusion
Our findings establish the criterion and discriminant validity of a novel multi-biomarker test as an objective measure of RA disease activity to aid in the management of RA patients.
doi:10.1002/acr.21767
PMCID: PMC3508159  PMID: 22736476
2.  A multi-biomarker score measures rheumatoid arthritis disease activity in the BeSt study 
Rheumatology (Oxford, England)  2013;52(7):1202-1207.
Objective. To evaluate a multi-biomarker disease activity (MBDA) score, a novel index based on 12 serum proteins, as a tool to guide management of RA patients.
Methods. A total of 125 patients with RA from the Behandel Strategieën study were studied. Clinical data and serum samples were available from 179 visits, 91 at baseline and 88 at year 1. In each serum sample, 12 biomarkers were measured by quantitative multiplex immunoassays and the concentrations were used as input to a pre-specified algorithm to calculate MBDA scores.
Results. MBDA scores had significant correlation with DAS28-ESR (Spearman’s ρ = 0.66, P < 0.0001) and also correlated with simplified disease activity index, clinical disease activity index and HAQ Disability Index (all P < 0.0001). Changes in MBDA between baseline and year 1 were also correlated with changes in DAS28-ESR (ρ = 0.55, P < 0.0001). Groups stratified by European League Against Rheumatism disease activity (DAS28-ESR ≤ 3.2, 3.2–5.1 and > 5.1) had significantly different MBDA scores (P < 0.0001) and MBDA score could discriminate ACR/EULAR Boolean remission with an area under the receiver operating characteristic curve of 0.83 (P < 0.0001).
Conclusion: The MBDA score reflects current clinical disease activity and can track changes in disease activity over time.
doi:10.1093/rheumatology/kes362
PMCID: PMC3685330  PMID: 23392591
rheumatoid arthritis; biomarkers; disability evaluation; outcome measures; bioinformatics; molecular biology; cytokines and inflammatory mediators
4.  Development of a Multi-Biomarker Disease Activity Test for Rheumatoid Arthritis 
PLoS ONE  2013;8(4):e60635.
Background
Disease activity measurement is a key component of rheumatoid arthritis (RA) management. Biomarkers that capture the complex and heterogeneous biology of RA have the potential to complement clinical disease activity assessment.
Objectives
To develop a multi-biomarker disease activity (MBDA) test for rheumatoid arthritis.
Methods
Candidate serum protein biomarkers were selected from extensive literature screens, bioinformatics databases, mRNA expression and protein microarray data. Quantitative assays were identified and optimized for measuring candidate biomarkers in RA patient sera. Biomarkers with qualifying assays were prioritized in a series of studies based on their correlations to RA clinical disease activity (e.g. the Disease Activity Score 28-C-Reactive Protein [DAS28-CRP], a validated metric commonly used in clinical trials) and their contributions to multivariate models. Prioritized biomarkers were used to train an algorithm to measure disease activity, assessed by correlation to DAS and area under the receiver operating characteristic curve for classification of low vs. moderate/high disease activity. The effect of comorbidities on the MBDA score was evaluated using linear models with adjustment for multiple hypothesis testing.
Results
130 candidate biomarkers were tested in feasibility studies and 25 were selected for algorithm training. Multi-biomarker statistical models outperformed individual biomarkers at estimating disease activity. Biomarker-based scores were significantly correlated with DAS28-CRP and could discriminate patients with low vs. moderate/high clinical disease activity. Such scores were also able to track changes in DAS28-CRP and were significantly associated with both joint inflammation measured by ultrasound and damage progression measured by radiography. The final MBDA algorithm uses 12 biomarkers to generate an MBDA score between 1 and 100. No significant effects on the MBDA score were found for common comorbidities.
Conclusion
We followed a stepwise approach to develop a quantitative serum-based measure of RA disease activity, based on 12-biomarkers, which was consistently associated with clinical disease activity levels.
doi:10.1371/journal.pone.0060635
PMCID: PMC3621826  PMID: 23585841
5.  External Qi of Yan Xin Qigong induces cell death and gene expression alterations promoting apoptosis and inhibiting proliferation, migration and glucose metabolism in small-cell lung cancer cells 
Molecular and cellular biochemistry  2011;363(1-2):245-255.
Small-cell lung cancer (SCLC) is a highly malignant carcinoma with poor long-term survival. Effective treatment remains highly demanded. In the present study, we demonstrated that External Qi of Yan Xin Qigong (YXQ-EQ) exerted potent cytotoxic effect towards SCLC cell line NCI-H82 via induction of apoptosis. Global gene expression profiling identified 39 genes whose expression was altered by YXQ-EQ in NCI-82 cells. Among them, semi-quantitative RT-PCR and real-time qPCR analyses confirmed that the gene expression levels of apoptotic proteins death-associated protein kinase 2 and cell death-inducing DFFA-like effector b were upregulated, whereas that of oncoproteins DEK and MYCL1, cell migration-promoting proteins CD24 and integrin-alpha 9, and glycolytic enzyme aldolase A were downregulated. These findings suggest that YXQ-EQ may exert anticancer effect through modulating gene expression in a way that facilitates cancer cell apoptosis while represses proliferation, metastasis, and glucose metabolism.
doi:10.1007/s11010-011-1176-8
PMCID: PMC3567610  PMID: 22160803
Small-cell lung cancer; Gene expression; Cell death; Anti-cancer effect
6.  Performance of a multi-biomarker score measuring rheumatoid arthritis disease activity in the CAMERA tight control study 
Annals of the Rheumatic Diseases  2012;71(10):1692-1697.
Objectives
To evaluate the performance of individual biomarkers and a multi-biomarker disease activity (MBDA) score in the early rheumatoid arthritis (RA) patient population from the computer assisted management in early rheumatoid arthritis (CAMERA) study.
Methods
Twenty biomarkers were measured in the CAMERA cohort, in which patients were treated with either intensive or conventional methotrexate-based treatment strategies. The MBDA score was calculated using the concentrations of 12 biomarkers (SAA, IL-6, TNF-RI, VEGF-A, MMP-1, YKL-40, MMP-3, EGF, VCAM-1, leptin, resistin and CRP) according to a previously trained algorithm. The performance of the scores was evaluated relative to clinical disease activity assessments. Change in MBDA score over time was assessed by paired Wilcoxon rank sum test. Logistic regression was used to evaluate the ability of disease activity measures to predict radiographic progression.
Results
The MBDA score had a significant correlation with the disease activity score based on 28 joints-C reactive protein (DAS28-CRP) (r=0.72; p<0.001) and an area under the receiver operating characteristic curve for distinguishing remission/low from moderate/high disease activity of 0.86 (p<0.001) using a DAS28-CRP cut-off of 2.7. In multivariate analysis the MBDA score, but not CRP, was an independent predictor of disease activity measures. Additionally, mean (SD) MBDA score decreased from 53 (18) at baseline to 39 (16) at 6 months in response to study therapy (p<0.0001). Neither MBDA score nor clinical variables were predictive of radiographic progression.
Conclusions
This multi-biomarker test performed well in the assessment of disease activity in RA patients in the CAMERA study. Upon further validation, this test could be used to complement currently available disease activity measures and improve patient care and outcomes.
doi:10.1136/annrheumdis-2011-200963
PMCID: PMC3439649  PMID: 22596166
7.  Anthrax Lethal Toxin-Induced Gene Expression Changes in Mouse Lung 
Toxins  2011;3(9):1111-1130.
A major virulence factor of Bacillus anthracis is the anthrax Lethal Toxin (LeTx), a bipartite toxin composed of Protective Antigen and Lethal Factor. Systemic administration of LeTx to laboratory animals leads to death associated with vascular leakage and pulmonary edema. In this study, we investigated whether systemic exposure of mice to LeTx would induce gene expression changes associated with vascular/capillary leakage in lung tissue. We observed enhanced susceptibility of A/J mice to death by systemic LeTx administration compared to the C57BL/6 strain. LeTx-induced groups of both up- and down-regulated genes were observed in mouse lungs 6 h after systemic administration of wild type toxin compared to lungs of mice exposed to an inactive mutant form of the toxin. Lungs of the less susceptible C57BL/6 strain showed 80% fewer differentially expressed genes compared to lungs of the more sensitive A/J strain. Expression of genes known to regulate vascular permeability was modulated by LeTx in the lungs of the more susceptible A/J strain. Unexpectedly, the largest set of genes with altered expression was immune specific, characterized by the up-regulation of lymphoid genes and the down-regulation of myeloid genes. Transcripts encoding neutrophil chemoattractants, modulators of tumor regulation and angiogenesis were also differentially expressed in both mouse strains. These studies provide new directions for the investigation of vascular leakage and pulmonary edema induced by anthrax LeTx.
doi:10.3390/toxins3091111
PMCID: PMC3202878  PMID: 22039574
Lethal Toxin; lung; gene expression
8.  Idiopathic inflammatory myopathies, signified by distinctive peripheral cytokines, chemokines and the TNF family members B-cell activating factor and a proliferation inducing ligand 
Rheumatology (Oxford, England)  2010;49(10):1867-1877.
Objective. Serum cytokines play an important role in the pathogenesis of myositis by initiating and perpetuating various cellular and humoral autoimmune processes. The aim of the present study was to describe a broad spectrum of T- and B-cell cytokines, growth factors and chemokines in patients with idiopathic inflammatory myopathies (IIMs) and healthy individuals.
Methods. A protein array system, denoted as multiplex cytokine assay was utilized to measure simultaneously the levels of 24 circulating cytokines, including B-cell activating factor (BAFF) and a proliferation inducing ligand (APRIL) of patients with IIMs and healthy individuals. Additionally, correlational clustering and discriminant function analysis (DFA), two multivariate, supervised analysis methods were employed to identify a subset of biomarkers in order to describe potential functional interrelationships among these pathological cytokines.
Results. Univariate analysis demonstrated that a complex set of immune and inflammatory modulating cytokines are significantly up-regulated in patients with IIMs relative to unaffected controls including IL-10, IL-13, IFN-α, epidermal growth factor (EGF), VEGF, fibroblast growth factor (FGF), CCL3 [macrophage inflammatory protein (MIP-1α)], CCL4 (MIP-1β) and CCL11 (eotaxin), whereas G-CSF was significantly reduced in IIM patients. Correlational clustering was able to discriminate between, and hence sub-classify patients with IIMs. DFA identified EGF, IFN-α, VEGF, CCL3 (MIP-1α) and IL-12p40, as analytes with the strongest discriminatory power among various myositis patients and controls.
Conclusions. Our findings suggest that these factors modulate myositis pathology and help to identify differences between subsets of the disease.
doi:10.1093/rheumatology/keq151
PMCID: PMC2936946  PMID: 20591831
Idiopathic inflammatory myopathies; Circulating cytokines; B-cell activating factor; A proliferation inducing ligand
9.  Anthrax Lethal Toxin-Induced Gene Expression Changes in Mouse Lung 
Toxins  2011;3(9):1111-1130.
A major virulence factor of Bacillus anthracis is the anthrax Lethal Toxin (LeTx), a bipartite toxin composed of Protective Antigen and Lethal Factor. Systemic administration of LeTx to laboratory animals leads to death associated with vascular leakage and pulmonary edema. In this study, we investigated whether systemic exposure of mice to LeTx would induce gene expression changes associated with vascular/capillary leakage in lung tissue. We observed enhanced susceptibility of A/J mice to death by systemic LeTx administration compared to the C57BL/6 strain. LeTx-induced groups of both up- and down-regulated genes were observed in mouse lungs 6 h after systemic administration of wild type toxin compared to lungs of mice exposed to an inactive mutant form of the toxin. Lungs of the less susceptible C57BL/6 strain showed 80% fewer differentially expressed genes compared to lungs of the more sensitive A/J strain. Expression of genes known to regulate vascular permeability was modulated by LeTx in the lungs of the more susceptible A/J strain. Unexpectedly, the largest set of genes with altered expression was immune specific, characterized by the up-regulation of lymphoid genes and the down-regulation of myeloid genes. Transcripts encoding neutrophil chemoattractants, modulators of tumor regulation and angiogenesis were also differentially expressed in both mouse strains. These studies provide new directions for the investigation of vascular leakage and pulmonary edema induced by anthrax LeTx.
doi:10.3390/toxins3091111
PMCID: PMC3202878  PMID: 22039574
Lethal Toxin; lung; gene expression
10.  Oxidative Stress and Inflammation in Renal Patients and Healthy Subjects 
PLoS ONE  2011;6(7):e22360.
The first goal of this study was to measure the oxidative stress (OS) and relate it to lipoprotein variables in 35 renal patients before dialysis (CKD), 37 on hemodialysis (HD) and 63 healthy subjects. The method for OS was based on the ratio of cholesteryl esters (CE) containing C18/C16 fatty acids (R2) measured by gas chromatography (GC) which is a simple, direct, rapid and reliable procedure. The second goal was to investigate and identify a triacylglycerol peak on GC, referred to as TG48 (48 represents the sum of the three fatty acids carbon chain lengths) which was markedly increased in renal patients compared to healthy controls. We measured TG48 in patients and controls. Mass spectrometry (MS) and MS twice in tandem were used to analyze the fatty acid composition of TG48. MS showed that TG48 was abundant in saturated fatty acids (SFAs) that were known for their pro-inflammatory property. TG48 was significantly and inversely correlated with OS. Renal patients were characterized by higher OS and inflammation than healthy subjects. Inflammation correlated strongly with TG, VLDL-cholesterol, apolipoprotein (apo) C-III and apoC-III bound to apoB-containing lipoproteins, but not with either total cholesterol or LDL-cholesterol.
In conclusion, we have discovered a new inflammatory factor, TG48. It is characterized with TG rich in saturated fatty acids. Renal patients have increased TG48 than healthy controls.
doi:10.1371/journal.pone.0022360
PMCID: PMC3145638  PMID: 21829457
11.  Internal standard-based analysis of microarray data2—Analysis of functional associations between HVE-genes 
Nucleic Acids Research  2011;39(18):7881-7899.
In this work we apply the Internal Standard-based analytical approach that we described in an earlier communication and here we demonstrate experimental results on functional associations among the hypervariably-expressed genes (HVE-genes). Our working assumption was that those genetic components, which initiate the disease, involve HVE-genes for which the level of expression is undistinguishable among healthy individuals and individuals with pathology. We show that analysis of the functional associations of the HVE-genes is indeed suitable to revealing disease-specific differences. We show also that another possible exploit of HVE-genes for characterization of pathological alterations is by using multivariate classification methods. This in turn offers important clues on naturally occurring dynamic processes in the organism and is further used for dynamic discrimination of groups of compared samples. We conclude that our approach can uncover principally new collective differences that cannot be discerned by individual gene analysis.
doi:10.1093/nar/gkr503
PMCID: PMC3185418  PMID: 21715372
12.  Gene Expression Profiling in Neutrophils From Children With Polyarticular Juvenile Idiopathic Arthritis 
Arthritis and rheumatism  2009;60(5):1488-1495.
Objective
We have previously reported a defect in neutrophil activation in children with polyarticular juvenile idiopathic arthritis (JIA). The current study was undertaken to determine whether gene expression abnormalities persist in JIA in remission and to use systems biology analysis to elucidate pathologic pathways in polyarticular JIA.
Methods
We performed gene expression profiling on neutrophils from children with polyarticular JIA. Children were grouped according to disease status. We studied 14 children with active disease who were taking medication, 8 children with clinical remission of disease who were taking medication (CRM status), and 6 children with clinical remission of disease who were not taking medication (CR status). We also studied 13 healthy children whose age ranges overlapped those of the patients.
Results
Neutrophil abnormalities persisted in children with polyarticular JIA even after disease remission was achieved. Children with active disease and those with CRM status showed no differences in expression of specific genes, although they could be separated on cluster analysis. A comparison of children with CR status and healthy control children revealed networks of pro- and antiinflammatory genes that suggested that remission is a state of homeostasis and balance rather than a return to normal immune function. Furthermore, gene overexpression in patients with CR status supports the hypothesis that neutrophils play a role in regulating adaptive immunity in this disease.
Conclusion
Neutrophil gene profiling in polyarticular JIA suggests important roles for neutrophils in disease pathogenesis. These findings suggest the presence of complex interactions between innate and adaptive immunity, that are not easily modeled in conventional, linear, reductionist systems.
doi:10.1002/art.24450
PMCID: PMC3063001  PMID: 19404961
13.  Genome-wide expression profiling and Real-time PCR identify RGS1 as a candidate biomarker for undifferentiated spondyloarthritis 
Arthritis and rheumatism  2009;60(11):3269-3279.
Objective
To compare gene expression profiles between ankylosing spondylitis (AS) and undifferentiated spondyloarthritis (USpA) patients with inflammatory low back pain.
Methods
Peripheral blood mononuclear cells (PBMC) from AS, USpA and healthy subjects were screened with genome-wide microarrays, followed by validation with Real-time PCR.
Results
Microarray profiling and Real-time PCR assays showed that any differences between AS and healthy subjects were only minor. In contrast, 20 genes were strikingly more highly expressed in USpA. The “regulator of G-protein signaling 1” (RGS1) was identified as the most useful biomarker distinguishing especially USpA patients and to a lesser extent AS patients, from control subjects (p= 2.3×10-7 and 6.7×10-3 respectively). All these findings were verified with an independent cohort of patients, which also included rheumatoid arthritis and patients with mechanical low back pain. The Receiver-operator-characteristics (ROC) area under the curve (AUC) values in the first and second cohorts of USpA patients were 0.98 and 0.93 respectively (p=1×10-4). To evaluate the possible derivation of RGS1, we cultured a monocyte-derived cell line with a panel of cytokines and chemokines. RGS1 was significantly induced either by TNF-α or by IL-17.
Conclusion
(1) The PBMC of USpA carry strikingly more highly expressed genes compared to AS or healthy subjects. (2) TNF-α and IL-17 – inducible RGS1 is a potential biomarker for USpA patients and to a lesser extent for AS patients, with inflammatory low back pain.
doi:10.1002/art.24968
PMCID: PMC2936922  PMID: 19877080
14.  Gene Network Analysis of Bone Marrow Mononuclear Cells Reveals Activation of Multiple Kinase Pathways in Human Systemic Lupus Erythematosus 
PLoS ONE  2010;5(10):e13351.
Background
Gene profiling studies provide important information for key molecules relevant to a disease but are less informative of protein-protein interactions, post-translational modifications and regulation by targeted subcellular localization. Integration of genomic data and construction of functional gene networks may provide additional insights into complex diseases such as systemic lupus erythematosus (SLE).
Methodology/Principal Findings
We analyzed gene expression microarray data of bone marrow mononuclear cells (BMMCs) from 20 SLE patients (11 with active disease) and 10 controls. Gene networks were constructed using the bioinformatic tool Ingenuity Gene Network Analysis. In SLE patients, comparative analysis of BMMCs genes revealed a network with 19 central nodes as major gene regulators including ERK, JNK, and p38 MAP kinases, insulin, Ca2+ and STAT3. Comparison between active versus inactive SLE identified 30 central nodes associated with immune response, protein synthesis, and post-transcriptional modification. A high degree of identity between networks in active SLE and non-Hodgkin's lymphoma (NHL) patients was found, with overlapping central nodes including kinases (MAPK, ERK, JNK, PKC), transcription factors (NF-kappaB, STAT3), and insulin. In validation studies, western blot analysis in splenic B cells from 5-month-old NZB/NZW F1 lupus mice showed activation of STAT3, ITGB2, HSPB1, ERK, JNK, p38, and p32 kinases, and downregulation of FOXO3 and VDR compared to normal C57Bl/6 mice.
Conclusions/Significance
Gene network analysis of lupus BMMCs identified central gene regulators implicated in disease pathogenesis which could represent targets of novel therapies in human SLE. The high similarity between active SLE and NHL networks provides a molecular basis for the reported association of the former with lymphoid malignancies.
doi:10.1371/journal.pone.0013351
PMCID: PMC2954787  PMID: 20976278
15.  The Meaning of Clinical Remission in Polyarticular Juvenile Idiopathic Arthritis: Gene Expression Profiling in Peripheral Blood Mononuclear Cells Identifies Distinct Disease States 
Arthritis and rheumatism  2009;60(3):892-900.
Objective
The development of biomarkers to predict response to therapy in polyarticular juvenile idiopathic arthritis (JIA) is an important issue in pediatric rheumatology. An critical step in this process is determining whether there is biological meaning to clinically derived terms such as “active disease” and “remission.” We used a systems biology approach to address this question.
Methods
We performed gene transcriptional profiling on children who fit criteria for specific disease states as defined by consensus criteria developed by Wallace et al. (J Rheumatol 2005). Children with active disease (AD, n=14), clinical remission on medication (CRM, n=9) and clinical remission off medication (CR, n=6) were studied, in addition to healthy control children (n=13). Transcriptional profiles in peripheral blood mononuclear cells (PBMC) were obtained using Affymetrix U133 Plus 2.0 Arrays.
Results
Hierarchical cluster analysis and predictive modeling demonstrated that the clinically-derived criteria represent biologically-distinct states. Minimal differences were seen between children with AD and those with CRM. Thus, underlying immune/inflammatory abnormalities persist despite response to therapy. The PBMC transcriptional profiles of children in remission did not return to normal, but revealed networks of pro- and anti-inflammatory genes suggesting that “remission” is a state of homeostasis, not a return to normal.
Conclusions
Gene transcriptional profiling of PBMC reveals that clinically-derived criteria for JIA disease states reflect underlying biology. We also demonstrate that neither CRM nor CR states result in resolution of the underlying inflammatory process, but are more likely to be states of balanced homeostasis between pro- and anti-inflammatory mechanisms.
doi:10.1002/art.24298
PMCID: PMC2758237  PMID: 19248118
16.  Distinct Cytokine Patterns Identified from Multiplex Profiles of Murine DSS and TNBS-Induced Colitis 
Inflammatory bowel diseases  2009;15(3):341-352.
The cytokine network in inflammatory bowel disease (IBD) is a complex, dynamic system that plays an important role in regulating mucosal innate and adaptive immune responses. While several studies have been done to evaluate immunomodulatory profiles in murine IBD, they have been limited to a relatively small number of cytokines that do not take into account its dependency of the interplay of multiple factors, and therefore the diagnostic potential of their cytokine profiles have been inconclusive. Herein we demonstrate a novel approach of comprehensive serum multiplex cytokine profiling to describe the modulation of 16 Th1, Th2, Th17 cytokines and chemokines in both acute and chronic murine models of DSS and TNBS-induced colitis. Distinctive disease-specific cytokine profiles were identified with significant correlations to disease activity and duration of disease. TNBS colitis exhibits heightened Th1-Th17 response (increased IL-12 and IL-17) as the disease becomes chronic. In contrast, DSS colitis switches from a Th1-Th17-mediated acute inflammation (increased TNFα, IL6, IL-17 and KC) to a predominant Th2-mediated inflammatory response (increase in IL-4 and IL-10 and concomitant decrease in TNFα, IL6, IL-17 and KC) in the chronic state. Profiles of multiple cytokines seen systemically were also validated locally in colonic mucosa. Moreover, advanced multivariate analyses identified discriminatory cytokine profiles that can be sufficiently used to distinguish unaffected controls from diseases, and one disease type from another. IL-6 and IL-12 stratified gender-associated disease activity in chronic colitis. Our studies provide insight into disease immunopathogenesis and illustrate the significant potential of utilizing multiplex cytokine profiles and bioinformatics as diagnostic tools in IBD.
doi:10.1002/ibd.20753
PMCID: PMC2643312  PMID: 18942757
Cytokines; Multiplex ELISA; DSS Colitis; TNBS Colitis; Inflammatory Bowel Disease
17.  FOXP3 Inhibits Activation-Induced NFAT2 Expression in T Cells Thereby Limiting Effector Cytokine Expression 
The forkhead DNA-binding protein FOXP3 is critical for the development and suppressive function of CD4+CD25+ regulatory T cells (TREG), which play a key role in maintaining self-tolerance. Functionally, FOXP3 is capable of repressing transcription of cytokine genes regulated by the Nuclear Factor of Activated T cells (NFAT). Various mechanisms have been proposed by which FOXP3 mediates these effects. Using novel cell lines that inducibly express either wild-type (WT) or mutant FOXP3, we have identified NFAT2 as an early target of FOXP3-mediated transcriptional repression. NFAT2 is typically expressed at low levels in resting T cells, but is upregulated by NFAT1 upon cellular activation. We demonstrate that transcription from the NFAT2 promoter is significantly suppressed by FOXP3, and NFAT2 protein expression is markedly diminished in activated CD4+CD25+FOXP3+ TREG compared to CD4+CD25negFOXP3neg T cells. Chromatin immunoprecipitation experiments indicate that FOXP3 competes with NFAT1 for binding to the endogenous NFAT2 promoter. This antagonism of NFAT2 activity by FOXP3 is important for the anergic phenotype of TREG, as ectopic expression of NFAT2 from a retroviral LTR partially restores expression of IL-2 in FOXP3+ TREG. These data suggest that FOXP3 functions not only to suppress the first wave of NFAT-mediated transcriptional responses, but may also affect sustained NFAT-mediated inflammatory gene expression through suppression of inducible NFAT2 transcription.
doi:10.4049/jimmunol.0800216
PMCID: PMC2778477  PMID: 19564342
T cells; Transcription Factors; Gene Regulation; Cytokines
18.  Gene expression in human lupus: bone marrow differentiates active from inactive patients and displays apoptosis and granulopoiesis signatures 
Arthritis and rheumatism  2008;58(11):3541-3549.
Objective
The cells of the immune system originate from the bone marrow (BM), where many of them also mature. To better understand the aberrant immune response in systemic lupus erythematosus (SLE), we examined the BM in lupus patients using DNA microarrays and compared it to the peripheral blood (PB).
Patients and Methods
Bone marrow mononuclear cells (BMMCs) from 20 SLE patients (11 with active disease and 9 with inactive disease) and peripheral blood mononuclear cells (PBMCs) from 27 patients (16 active/ 11 inactive); BMMCs and PBMCs from 7 healthy individuals and 3 osteoarthritis patients served as controls. Samples were analyzed on genome-scale microarrays with 21,329 genes represented.
Results
We found 102 differentially expressed genes between patients’ and controls’ BMMCs (unpaired student t-test), involved in various biologic processes; 53 of them are involved in major networks including cell death, growth, signaling and proliferation. Comparative analysis between BM and PB of patients identified 88 genes differentially expressed; 61 out of 88 participate in cell growth and differentiation, cellular movement and morphology, immune response and other hematopoietic cell functions. Unsupervised clustering of highly expressed genes revealed two major SLE patient clusters (active and inactive) in BM, but not in PB. The upregulated genes in the bone marrow of active patients included genes involved in cell death and granulopoiesis.
Conclusion
Microarray analysis of the bone marrow differentiates active from inactive lupus patients and provides further evidence for the role of apoptosis and granulocytes in the pathogenesis of the disease.
doi:10.1002/art.23961
PMCID: PMC2760826  PMID: 18975309
19.  Transcriptional modulation of TCR, Notch and Wnt signaling pathways in SEB Anergized CD4+ T cells 
Genes and immunity  2005;6(7):596-608.
Gene expression changes in CD4+Vβ8+ T cells anergized by in vivo exposure to staphylococcal enterotoxin B (SEB) bacterial superantigen compared to CD4+Vβ8+ non-anergic T cells were assessed using DNA microarrays containing 5,184 murine cDNAs. Anergy in splenic T cells of SEB-immunized BALB/c mice was verified by dramatically reduced proliferative capacity and an 8X overexpression of GRAIL mRNA in CD4+Vβ8+ T cells taken from mice 7 d after injection. At an associative t-test threshold of p<0.0005, 96 genes were over-expressed or detected only in anergic T cells, while 256 genes were suppressed or not detected in anergic T cells. Six of eight differential expressions tested using real-time quantitative PCR were validated. Message for B-raf was detected only in non-anergic cells, while expression of the TCR signaling modulator Slap and the TCR ζ-chain specific phosphatase Ptpn3 was enhanced. Modulation of multiple genes suggests down-regulation of Wnt/β-catenin signaling and enhanced Notch signaling in the anergic cells. Consistent with previous reports in a non-superantigen in vivo anergy model, mRNA for CD18 and the transcription factor SATB1 was increased in SEB-anergized T cells. This is the first report of global transcriptional changes in CD4+ T cells made anergic by superantigen exposure.
doi:10.1038/sj.gene.6364245
PMCID: PMC2593626  PMID: 16034473
T cell; anergy; superantigen; rodent; microarray
20.  From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells 
BMC Bioinformatics  2008;9(Suppl 9):S4.
A statistically robust and biologically-based approach for analysis of microarray data is described that integrates independent biological knowledge and data with a global F-test for finding genes of interest that minimizes the need for replicates when used for hypothesis generation. First, each microarray is normalized to its noise level around zero. The microarray dataset is then globally adjusted by robust linear regression. Second, genes of interest that capture significant responses to experimental conditions are selected by finding those that express significantly higher variance than those expressing only technical variability. Clustering expression data and identifying expression-independent properties of genes of interest including upstream transcriptional regulatory elements (TREs), ontologies and networks or pathways organizes the data into a biologically meaningful system. We demonstrate that when the number of genes of interest is inconveniently large, identifying a subset of "beacon genes" representing the largest changes will identify pathways or networks altered by biological manipulation. The entire dataset is then used to complete the picture outlined by the "beacon genes." This allow construction of a structured model of a system that can generate biologically testable hypotheses. We illustrate this approach by comparing cells cultured on plastic or an extracellular matrix which organizes a dataset of over 2,000 genes of interest from a genome wide scan of transcription. The resulting model was confirmed by comparing the predicted pattern of TREs with experimental determination of active transcription factors.
doi:10.1186/1471-2105-9-S9-S4
PMCID: PMC2537575  PMID: 18793468
21.  A Template-Driven Gene Selection Procedure * 
Systems biology  2006;153(1):4-12.
The hierarchical clustering and statistical techniques usually used to analyze microarray data do not inherently represent the underlying biology. Herein we present a hybrid approach involving characteristics of both supervised and unsupervised learning. This approach is based on template matching in which the interaction of the variables of inherent malignancy and the ability to express the malignant phenotype are modelled. Immortalized normal urothelial cells and bladder cancer cells of different malignancy were grown in conventional two-dimensional tissue culture and in three dimensions on extracellular matrices that were either permissive or restrictive for expression of the malignant phenotype. The transcriptome represents the effects of two variables--inherent malignancy and the modulatory effect of extracellular matrix. By assigning values to each of the biological variables of inherent malignancy and the ability to express the malignant phenotype, a template was constructed that encapsulated the interaction between them. Gene expression correlating both positively and negatively with the template were observed, but when iterative correlations were carried out, the different models for the template converged to the same actual template. A subset of 21 genes was identified that correlated with two a priori models or an optimized model above the 95% confidence limits identified in a bootstrap resampling with 5,000 permutations of the data set. The correlation coefficients of expression of several genes were > 0.8. Analysis of upstream transcriptional regulatory elements (TREs) confirmed these genes were not a randomly selected set of genes. Several TREs were identified as significantly over-expressed in the sample of 20 genes for which TREs were identified, and the high correlations of several genes were consistent with transcriptional co-regulation. We suggest the template method can be used to identify a unique set of genes for further investigation.
PMCID: PMC1618795  PMID: 16983830
Bladder cancer; phenotype; transcriptomics; extracellular matrix; malignancy; SIS-small intestine submucosa; ECM-extracellular matrix; TCC-transitional cell carcinoma
22.  Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis 
BMC Bioinformatics  2007;8(Suppl 7):S2.
Background
To better understand the response of urinary epithelial (urothelial) cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtained as a time series from urothelial cells growing as a layered 3-dimensional culture similar to normal urothelium. We herein describe a novel means of analysis that is based on deconvolution of gene variability into technical and biological components.
Results
Analysis of the expression of 21,521 genes from 30 minutes to 10 hours post infection, showed 9553 genes were expressed 3 standard deviations (SD) above the system zero-point noise in at least 1 time point. The asymmetric distribution of relative variances of the expressed genes was deconvoluted into technical variation (with a 6.5% relative SD) and biological variation components (>3 SD above the mode technical variability). These 1409 hypervariable (HV) genes encapsulated the effect of infection on gene expression. Pathway analysis of the HV genes revealed an orchestrated response to infection in which early events included initiation of immune response, cytoskeletal rearrangement and cell signaling followed at the end by apoptosis and shutting down cell metabolism. The number of poorly annotated genes in the earliest time points suggests heretofore unknown processes likely also are involved.
Conclusion
Enterococcus infection produced an orchestrated response by the host cells involving several pathways and transcription factors that potentially drive these pathways. The early time points potentially identify novel targets for enhancing the host response. These approaches combine rigorous statistical principles with a biological context and are readily applied by biologists.
doi:10.1186/1471-2105-8-S7-S2
PMCID: PMC2099488  PMID: 18047719
23.  Neutrophils: the forgotten cell in JIA disease pathogenesis 
Juvenile idiopathic arthritis (JIA) has long been assumed to be an autoimmune disease, triggered by aberrant recognition of "self" antigens by T-cells. However, systems biology approaches to this family of diseases have suggested complex interactions between innate and adaptive immunity that underlie JIA. In particular, new data suggest an important role for neutrophils in JIA pathogenesis. In this short review, we will discuss the new data that support a role for neutrophils in JIA, discuss regulatory functions that link neutrophils to adaptive immune responses, and discuss future areas of investigation. Above all else, we invite the reader to re-consider the use of the term "autoimmunity" as applied to the family of illnesses we collectively call JIA.
doi:10.1186/1546-0096-5-13
PMCID: PMC1904449  PMID: 17567896
24.  Discriminators of mouse bladder response to intravesical Bacillus Calmette-Guerin (BCG) 
BMC Immunology  2007;8:6.
Background
Intravesical Bacillus Calmette-Guerin (BCG) is an effective treatment for bladder superficial carcinoma and it is being tested in interstitial cystitis patients, but its precise mechanism of action remains poorly understood. It is not clear whether BCG induces the release of a unique set of cytokines apart from its pro-inflammatory effects. Therefore, we quantified bladder inflammatory responses and alterations in urinary cytokine protein induced by intravesical BCG and compared the results to non-specific pro-inflammatory stimuli (LPS and TNF-α). We went further to determine whether BCG treatment alters cytokine gene expression in the urinary bladder.
Methods
C57BL/6 female mice received four weekly instillations of BCG, LPS, or TNF-α. Morphometric analyses were conducted in bladders isolated from all groups and urine was collected for multiplex analysis of 18 cytokines. In addition, chromatin immune precipitation combined with real-time polymerase chain reaction assay (CHIP/Q-PCR) was used to test whether intravesical BCG would alter bladder cytokine gene expression.
Results
Acute BCG instillation induced edema which was progressively replaced by an inflammatory infiltrate, composed primarily of neutrophils, in response to weekly administrations. Our morphological analysis suggests that these polymorphonuclear neutrophils are of prime importance for the bladder responses to BCG. Overall, the inflammation induced by BCG was higher than LPS or TNF-α treatment but the major difference observed was the unique granuloma formation in response to BCG. Among the cytokines measured, this study highlighted the importance of IL-1β, IL-2, IL-3, IL-4, IL-6, IL-10, IL-17, GM-CSF, KC, and Rantes as discriminators between generalized inflammation and BCG-specific inflammatory responses. CHIP/Q-PCR indicates that acute BCG instillation induced an up-regulation of IL-17A, IL-17B, and IL-17RA, whereas chronic BCG induced IL-17B, IL-17RA, and IL-17RB.
Conclusion
To the best of our knowledge, the present work is the first to report that BCG induces an increase in the IL-17 family genes. In addition, BCG induces a unique type of persisting bladder inflammation different from TNF-α, LPS, and, most likely, other classical pro-inflammatory stimuli.
doi:10.1186/1471-2172-8-6
PMCID: PMC1891101  PMID: 17506885
25.  Temporal dynamics of gene expression in the lung in a baboon model of E. coli sepsis 
BMC Genomics  2007;8:58.
Background
Bacterial invasion during sepsis induces disregulated systemic responses that could lead to fatal lung failure. The purpose of this study was to relate the temporal dynamics of gene expression to the pathophysiological changes in the lung during the first and second stages of E. coli sepsis in baboons.
Results
Using human oligonucleotide microarrays, we have explored the temporal changes of gene expression in the lung of baboons challenged with sublethal doses of E. coli. Temporal expression pattern and biological significance of the differentially expressed genes were explored using clustering and pathway analysis software. Expression of selected genes was validated by real-time PCR. Cytokine levels in tissue and plasma were assayed by multiplex ELISA. Changes in lung ultrastructure were visualized by electron microscopy. We found that genes involved in primary inflammation, innate immune response, and apoptosis peaked at 2 hrs. Inflammatory and immune response genes that function in the stimulation of monocytes, natural killer and T-cells, and in the modulation of cell adhesion peaked at 8 hrs, while genes involved in wound healing and functional recovery were upregulated at 24 hrs.
Conclusion
The analysis of gene expression modulation in response to sepsis provides the baseline information that is crucial for the understanding of the pathophysiology of systemic inflammation and may facilitate the development of future approaches for sepsis therapy.
doi:10.1186/1471-2164-8-58
PMCID: PMC1819384  PMID: 17324256

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