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Raven N, Klaassen M, Madsen T, Thomas F, Hamede R, Ujvari B. Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 2022; 31:2293-2311. [PMID: 35202488 PMCID: PMC9310804 DOI: 10.1111/mec.16408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Understanding the effects of wildlife diseases on populations requires insight into local environmental conditions, host defence mechanisms, host life‐history trade‐offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils’ capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils’ immune system. By using RT‐qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex ecoevolutionary interactions of not only conventional host‐parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.
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Affiliation(s)
- N Raven
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - M Klaassen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - T Madsen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - F Thomas
- CREEC/CANECEV (CREES), Montpellier, France.,MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - R Hamede
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia.,School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - B Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
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Wright M, Smed MK, Nelson JL, Olsen J, Hetland ML, Zoffmann V, Jawaheer D. Is gene expression among women with rheumatoid arthritis dysregulated during a postpartum flare? Arthritis Res Ther 2021; 23:30. [PMID: 33461591 PMCID: PMC7812735 DOI: 10.1186/s13075-021-02418-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022] Open
Abstract
Background To evaluate our hypotheses that, when rheumatoid arthritis (RA) flares postpartum, gene expression patterns are altered compared to (a) healthy women, (b) RA women whose disease activity is low or in remission postpartum, and (c) pre-pregnancy expression profiles. Methods Twelve women with RA and five healthy women were included in this pilot study. RA disease activity and postpartum flare were assessed using the Clinical Disease Activity Index (CDAI). Total RNA from frozen whole blood was used for RNA sequencing. Differential gene expression within the same women (within-group) over time, i.e., postpartum vs. third trimester (T3) or pre-pregnancy (T0), were examined, using a significance threshold of q < 0.05 and fold-change ≥ 2. Results Nine of the women with RA experienced a flare postpartum (RAFlare), while three had low disease activity or were in remission (RANoFlare) during that time frame. Numerous immune-related genes were differentially expressed postpartum (vs. T3) during a flare. Fold-changes in expression from T3 to postpartum were mostly comparable between the RAFlare and healthy groups. At 3 months postpartum, compared to healthy women, several genes were significantly differentially expressed only among the RAFlare women, and not among the RANoFlare women. Some of these genes were among those whose “normal” expression was significantly modulated postpartum, and the postpartum expression patterns were significantly altered during the RA flare. There were also some genes that were significantly differentially expressed in RAFlare compared to both healthy and RANoFlare women, even though their expression was not significantly modulated postpartum. Furthermore, while postpartum expression profiles were similar to those at pre-pregnancy among healthy women, significant differences were found between those time points among the RAFlare women. Conclusions The large majority of gene expression changes between T3 and 3 months postpartum among RA women who flared postpartum reflected normal postpartum changes also seen among healthy women. Nonetheless, during a postpartum flare, a set of immune-related genes showed dysregulated expression compared to healthy women and women with RA whose disease activity was low or in remission during the same time frame, while other genes demonstrated significant differences in expression compared to RA pre-pregnancy levels. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02418-w.
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Affiliation(s)
- Matthew Wright
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital Oakland, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
| | - Mette K Smed
- Juliane Marie Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J Lee Nelson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,University of Washington, Seattle, WA, USA
| | - Jørn Olsen
- University of California Los Angeles, Los Angeles, CA, USA.,Aarhus University Hospital, Aarhus, Denmark
| | - Merete L Hetland
- DANBIO Registry and Copenhagen Centre for Arthritis Research, Centre for Rheumatology and Spine Diseases VRR, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Vibeke Zoffmann
- Juliane Marie Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Damini Jawaheer
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital Oakland, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA. .,University of California San Francisco, San Francisco, CA, USA.
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The Clinical Use of Curcumin for the Treatment of Rheumatoid Arthritis: A Systematic Review of Clinical Trials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1291:251-263. [PMID: 34331695 DOI: 10.1007/978-3-030-56153-6_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease of the joints, which is prevalent in about 0.5-1.0% of the world population. Newer therapies for RA have only minimal efficacy in some cases and some adverse effects. Curcumin with anti-antioxidant, anti-inflammatory, and immunomodulatory properties might have beneficial effects on RA. We have carried out a systematic review with the main aim of estimating the effect of curcumin supplementation on RA. A systematic search of the medical databases, PubMed, Scopus, ISI, and Google Scholar was performed up to March 21, 2020 to identify clinical trials assessing the effect of turmeric or curcumin on RA. Six studies, comprising 259 patients with RA of 6-12 weeks duration, were included. Disease activity was assessed using 28 joints (DAS-28), visual analog scale (VAS), and American College of Rheumatology (ACR-20) scores. Treatment with curcumin significantly reduced DAS-28 scores in four out of five studies and VAS scores for pain in all three studies and significantly increased ACR-20 scores in all three studies in which it was measured. Erythrocyte sedimentation rate (ESR) and circulating C-reactive protein (CRP) were assessed in six and five studies, respectively, out of which four studies reported significant reductions in these parameters in response to curcumin treatment. Rheumatoid factor (RF) was significantly reduced after consumption of curcumin in all three relevant studies. None of the studies reported serious adverse effects with curcumin consumption. The present systematic review suggests that curcumin could be used as a safe agent to treat RA. Thus, further validation is justified.
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Pathi A, Wright M, Smed MK, Nelson JL, Olsen J, Hetland ML, Zoffmann V, Jawaheer D. The Rheumatoid Arthritis Gene Expression Signature Among Women Who Improve or Worsen During Pregnancy: A Pilot Study. J Rheumatol 2020; 48:985-991. [PMID: 33323535 DOI: 10.3899/jrheum.201128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To assess whether gene expression signatures associated with rheumatoid arthritis (RA) before pregnancy differ between women who improve or worsen during pregnancy, and to determine whether these expression signatures are altered during pregnancy when RA improves or worsens. METHODS Clinical data and blood samples were collected before pregnancy (T0) and at the third trimester (T3) from 11 women with RA and 5 healthy women. RA disease activity was assessed using the Clinical Disease Activity Index (CDAI). At each timepoint, RA-associated gene expression signatures were identified using differential expression analysis of RNA sequencing profiles between women with RA and healthy women. RESULTS Of the women with RA, 6 improved by T3 (RAimproved), 3 worsened (RAworsened),and 2 were excluded. At T0, mean CDAI scores were similar in both groups (RAimproved 11.2 ± 9.8; RAworsened 13.8 ± 6.7; Wilcoxon rank-sum test: P = 0.6). In the RAimproved group, 89 genes were differentially expressed at T0 (q < 0.05 and fold change ≥ 2) compared to healthy women. When RA improved at T3, 65 of 89 (73%) of these genes no longer displayed RA-associated expression. In the RAworsened group, a largely different RA gene expression signature (429 genes) was identified at T0. When RA disease activity worsened at T3, 207 of 429 (48%) genes lost their differential expression, while an additional 151 genes became newly differentially expressed. CONCLUSION In our pilot dataset, pre-pregnancy RA expression signatures differed between women who subsequently improved or worsened during pregnancy, suggesting that inherent genomic differences may influence how pregnancy affects disease activity. Further, these RA signatures were altered during pregnancy as disease activity changed.
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Affiliation(s)
- Amogh Pathi
- A. Pathi, BS, M. Wright, MS, Staff Research Associate II, Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Matthew Wright
- A. Pathi, BS, M. Wright, MS, Staff Research Associate II, Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Mette Kiel Smed
- M.K. Smed, RM, Study Coordinator, Juliane Marie Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J Lee Nelson
- J.L. Nelson, MD, Professor, Fred Hutchinson Cancer Research Center, and University of Washington, Seattle, Washington, USA
| | - Jørn Olsen
- J. Olsen, MD, PhD, Professor, University of California Los Angeles, Los Angeles, California, USA, and Aarhus University Hospital, Aarhus, Denmark
| | - Merete Lund Hetland
- M.L. Hetland, DMSc, Professor, DANBIO Registry and Copenhagen Centre for Arthritis Research, Centre for Rheumatology and Spine Diseases VRR, Rigshospitalet, Copenhagen, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Vibeke Zoffmann
- V. Zoffmann, RN, PhD, Professor, Juliane Marie Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, and Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Damini Jawaheer
- D. Jawaheer, PhD, Associate Scientist, Children's Hospital Oakland Research Institute, Oakland, and University of California San Francisco, San Francisco, California, USA.
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Akhbari P, Richardson SJ, Morgan NG. Type 1 Diabetes: Interferons and the Aftermath of Pancreatic Beta-Cell Enteroviral Infection. Microorganisms 2020; 8:microorganisms8091419. [PMID: 32942706 PMCID: PMC7565444 DOI: 10.3390/microorganisms8091419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) have long been implicated in the pathogenesis of type 1 diabetes (T1D), and accumulating evidence has associated virus-induced autoimmunity with the loss of pancreatic beta cells in T1D. Inflammatory cytokines including interferons (IFN) form a primary line of defence against viral infections, and their chronic elevation is a hallmark feature of many autoimmune diseases. IFNs play a key role in activating and regulating innate and adaptive immune responses, and to do so they modulate the expression of networks of genes and transcription factors known generically as IFN stimulated genes (ISGs). ISGs in turn modulate critical cellular processes ranging from cellular metabolism and growth regulation to endoplasmic reticulum (ER) stress and apoptosis. More recent studies have revealed that IFNs also modulate gene expression at an epigenetic as well as post-transcriptional and post-translational levels. As such, IFNs form a key link connecting the various genetic, environmental and immunological factors involved in the initiation and progression of T1D. Therefore, gaining an improved understanding of the mechanisms by which IFNs modulate beta cell function and survival is crucial in explaining the pathogenesis of virally-induced T1D. This should provide the means to prevent, decelerate or even reverse beta cell impairment.
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Chetina EV, Markova GA. [Upcoming value of gene expression analysis in rheumatology]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:221-232. [PMID: 29964257 DOI: 10.18097/pbmc20186403221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease of unknown etiology, which involves disturbance in immune system signaling pathway functions, damage of other tissues, pain and joint destruction. Modern treatment attempts to improve pathophysiological and biochemical mechanisms damaged by the disease. However, due to the RA patient heterogeneity personalized approach to treatment is required; the choice of personalized treatment is complicated by the variability of patient's response to treatment. Gene expression analysis might serve a tool for the disease control and therapy personification for inhibition of inflammation and pain as well as for prevention of joint destruction.
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Affiliation(s)
- E V Chetina
- Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - G A Markova
- Nasonova Research Institute of Rheumatology, Moscow, Russia
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7
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Song X, Lin Q. Genomics, transcriptomics and proteomics to elucidate the pathogenesis of rheumatoid arthritis. Rheumatol Int 2017; 37:1257-1265. [DOI: 10.1007/s00296-017-3732-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/29/2017] [Indexed: 01/23/2023]
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Common Marker Genes Identified from Various Sample Types for Systemic Lupus Erythematosus. PLoS One 2016; 11:e0156234. [PMID: 27257790 PMCID: PMC4892593 DOI: 10.1371/journal.pone.0156234] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/11/2016] [Indexed: 12/26/2022] Open
Abstract
Objective Systemic lupus erythematosus (SLE) is a complex auto-immune disease. Gene expression studies have been conducted to identify SLE-related genes in various types of samples. It is unknown whether there are common marker genes significant for SLE but independent of sample types, which may have potentials for follow-up translational research. The aim of this study is to identify common marker genes across various sample types for SLE. Methods Based on four public microarray gene expression datasets for SLE covering three representative types of blood-born samples (monocyte; peripheral blood mononuclear cell, PBMC; whole blood), we utilized three statistics (fold-change, FC; t-test p value; false discovery rate adjusted p value) to scrutinize genes simultaneously regulated with SLE across various sample types. For common marker genes, we conducted the Gene Ontology enrichment analysis and Protein-Protein Interaction analysis to gain insights into their functions. Results We identified 10 common marker genes associated with SLE (IFI6, IFI27, IFI44L, OAS1, OAS2, EIF2AK2, PLSCR1, STAT1, RNASE2, and GSTO1). Significant up-regulation of IFI6, IFI27, and IFI44L with SLE was observed in all the studied sample types, though the FC was most striking in monocyte, compared with PBMC and whole blood (8.82–251.66 vs. 3.73–74.05 vs. 1.19–1.87). Eight of the above 10 genes, except RNASE2 and GSTO1, interact with each other and with known SLE susceptibility genes, participate in immune response, RNA and protein catabolism, and cell death. Conclusion Our data suggest that there exist common marker genes across various sample types for SLE. The 10 common marker genes, identified herein, deserve follow-up studies to dissert their potentials as diagnostic or therapeutic markers to predict SLE or treatment response.
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9
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Cui A, Quon G, Rosenberg AM, Yeung RSM, Morris Q. Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis. PLoS One 2016; 11:e0156055. [PMID: 27244050 PMCID: PMC4887077 DOI: 10.1371/journal.pone.0156055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/09/2016] [Indexed: 01/10/2023] Open
Abstract
Gene expression-based signatures help identify pathways relevant to diseases and treatments, but are challenging to construct when there is a diversity of disease mechanisms and treatments in patients with complex diseases. To overcome this challenge, we present a new application of an in silico gene expression deconvolution method, ISOpure-S1, and apply it to identify a common gene expression signature corresponding to response to treatment in 33 juvenile idiopathic arthritis (JIA) patients. Using pre- and post-treatment gene expression profiles only, we found a gene expression signature that significantly correlated with a reduction in the number of joints with active arthritis, a measure of clinical outcome (Spearman rho = 0.44, p = 0.040, Bonferroni correction). This signature may be associated with a decrease in T-cells, monocytes, neutrophils and platelets. The products of most differentially expressed genes include known biomarkers for JIA such as major histocompatibility complexes and interleukins, as well as novel biomarkers including α-defensins. This method is readily applicable to expression datasets of other complex diseases to uncover shared mechanistic patterns in heterogeneous samples.
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Affiliation(s)
- Ang Cui
- Division of Engineering Science, University of Toronto, Toronto, ON, Canada
| | - Gerald Quon
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Alan M. Rosenberg
- Department of Pediatrics, Division of Rheumatology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rae S. M. Yeung
- Divisions of Rheumatology and Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Departments of Paediatrics, Immunology and Medical Sciences, University of Toronto, Toronto, ON, Canada
- * E-mail: (RY); (QM)
| | - Quaid Morris
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- * E-mail: (RY); (QM)
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Niu X, Lu C, Xiao C, Ge N, Jiang M, Li L, Bian Y, Xu G, Bian Z, Zhang G, Lu A. The Crosstalk of Pathways Involved in Immune Response Maybe the Shared Molecular Basis of Rheumatoid Arthritis and Type 2 Diabetes. PLoS One 2015; 10:e0134990. [PMID: 26252209 PMCID: PMC4529222 DOI: 10.1371/journal.pone.0134990] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023] Open
Abstract
Rheumatoid arthritis (RA) and Type 2 diabetes (T2D) are both systemic diseases linked with altered immune response, moderate mortality when present together. The treatment for both RA and T2D are not satisfied, partly because of the linkage between them has not yet been appreciated. A comprehensive study for the potential associations between the two disorders is needed. In this study, we used RNA sequencing to explore the differently expressed genes (DEGs) in peripheral blood mononuclear cells (PBMC) of 10 RA and 10 T2D patients comparing with 10 healthy volunteers (control). We used bioinformatics analysis and the Ingenuity Pathways Analysis (IPA) to predict the commonalities on signaling pathways and molecular networks between those two diseases. 212 DEGs in RA and 114 DEGs in T2D patients were identified compared with healthy controls, respectively. 32 DEGs were shared between the two comparisons. The top 10 shared pathways interacted in cross-talking networks, regulated by 5 shared predicted upstream regulators, leading to the activated immune response were explored, which was considered as partly of the association mechanism of this two disorders. These discoveries would be considered as new understanding on the associations between RA and T2D, and provide novel treatment or prevention strategy.
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Affiliation(s)
- Xuyan Niu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases,School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Cheng Xiao
- China-Japan Friendship Hospital, Beijing, China
| | - Na Ge
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Miao Jiang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanqin Bian
- E-Institute of Chinese Traditional Internal Medicine, Shanghai Municipal Education Commission, Shanghai, China
| | - Gang Xu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases,School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhaoxiang Bian
- Institute for Advancing Translational Medicine in Bone & Joint Diseases,School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases,School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases,School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- E-Institute of Chinese Traditional Internal Medicine, Shanghai Municipal Education Commission, Shanghai, China
- * E-mail:
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Chaussabel D. Assessment of immune status using blood transcriptomics and potential implications for global health. Semin Immunol 2015; 27:58-66. [PMID: 25823891 DOI: 10.1016/j.smim.2015.03.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 12/17/2022]
Abstract
The immune system plays a key role in health maintenance and pathogenesis of a wide range of diseases. Leukocytes that are present in the blood convey valuable information about the status of the immune system. Blood transcriptomics, which consists in profiling blood transcript abundance on genome-wide scales, has gained in popularity over the past several years. Indeed, practicality and simplicity largely makes up for what this approach may lack in terms of cell population-level resolution. An extensive survey of the literature reveals increasingly widespread use across virtually all fields of medicine as well as across a number of different animal species, including model organisms but also animals of economical importance. Dissemination across such a wide range of disciplines holds the promise of adding a new perspective, breadth or context, to the considerable depth afforded by whole genome profiling of blood transcript abundance. Indeed, it is only through such contextualization that a truly global perspective will be gained from the use of systems approaches. Also discussed are opportunities that may arise for the fields of immunology and medicine from using blood transcriptomics as a common denominator for developing interactions and cooperation across fields of research that have traditionally been and largely remain compartmentalized. Finally, an argument is made for building immunology research capacity using blood transcriptomics platforms in low-resource and high-disease burden settings.
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12
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Niu X, Lu C, Xiao C, Zhang Z, Jiang M, He D, Bian Y, Zhang G, Bian Z, Lu A. The shared crosstalk of multiple pathways involved in the inflammation between rheumatoid arthritis and coronary artery disease based on a digital gene expression profile. PLoS One 2014; 9:e113659. [PMID: 25514790 PMCID: PMC4267808 DOI: 10.1371/journal.pone.0113659] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/26/2014] [Indexed: 12/16/2022] Open
Abstract
Rheumatoid arthritis (RA) and coronary artery disease (CAD) are both complex inflammatory diseases, and an increased prevalence of CAD and a high rate of mortality have been observed in RA patients. But the molecular mechanism of inflammation that is shared between the two disorders is unclear. High-throughput techniques, such as transcriptome analysis, are becoming important tools for genetic biomarker discovery in highly complex biological samples, which is critical for the diagnosis, prognosis, and treatment of disease. In the present study, we reported one type of transcriptome analysis method: digital gene expression profiling of peripheral blood mononuclear cells of 10 RA patients, 10 CAD patients and 10 healthy people. In all, 213 and 152 differently expressed genes (DEGs) were identified in RA patients compared with normal controls (RA vs. normal) and CAD patients compared with normal controls (CAD vs. normal), respectively, with 73 shared DEGs between them. Using this technique in combination with Ingenuity Pathways Analysis software, the effects on inflammation of four shared canonical pathways, three shared activated predicted upstream regulators and three shared molecular interaction networks were identified and explored. These shared molecular mechanisms may provide the genetic basis and potential targets for optimizing the application of current drugs to more effectively treat these diseases simultaneously and for preventing one when the other is diagnosed.
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Affiliation(s)
- Xuyan Niu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cheng Xiao
- China-Japan Friendship Hospital, Beijing, 100029, China
| | - Zhiguo Zhang
- Institute of Basic Theory, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Miao Jiang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Dan He
- E-Institute of Chinese Traditional Internal Medicine, Shanghai Municipal Education Commission, Shanghai, 201203, China
| | - Yanqin Bian
- E-Institute of Chinese Traditional Internal Medicine, Shanghai Municipal Education Commission, Shanghai, 201203, China
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhaoxiang Bian
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Aiping Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- E-Institute of Chinese Traditional Internal Medicine, Shanghai Municipal Education Commission, Shanghai, 201203, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- * E-mail:
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13
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Ma D, Li X, Zhang L, Deng C, Zhang T, Wang L, Hu C, Li Y, Zhang F. S100A12 expression in patients with primary biliary cirrhosis. Immunol Invest 2014; 44:13-22. [PMID: 25313445 DOI: 10.3109/08820139.2014.914530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES S100 calcium binding protein A12 (S100A12) has been supposed to be a pro-inflammatory factor associated with non-infectious inflammatory diseases. However, whether S100A12 is involved in the inflammatory process of primary biliary cirrhosis (PBC) has not been shown. METHODS The levels of S100A12 mRNA transcripts in peripheral mononuclear blood cells (PBMCs) of 66 Chinese patients with primary biliary cirrhosis (PBC), 62 healthy controls (HC) and 55 chronic hepatitis B (CHB) were measured by qRT-PCR. S100A12 serum concentrations in 34 PBC patients were measured by ELISA. RESULTS The levels of S100A12 mRNA transcripts in PBMCs of patients with PBC were significantly higher than healthy controls (p < 0.01) and that of patients with CHB (p < 0.01). Importantly, the levels of S100A12 mRNA in PBMCs and S100A12 protein levels in serum were positively correlated with biochemical indicators of bile duct and hepatocyte damage. CONCLUSION S100A12 might participate in the damage of biliary epithelial cells and hepatocytes in PBC, and analysis of S100A12 expression could be useful as a surrogate marker for the evaluation of PBC activity.
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Affiliation(s)
- Danxu Ma
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences , Beijing , China
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Reinhardt K, Foell D, Vogl T, Mezger M, Wittkowski H, Fend F, Federmann B, Gille C, Feuchtinger T, Lang P, Handgretinger R, Andreas Bethge W, Holzer U. Monocyte-induced development of Th17 cells and the release of S100 proteins are involved in the pathogenesis of graft-versus-host disease. THE JOURNAL OF IMMUNOLOGY 2014; 193:3355-65. [PMID: 25187661 DOI: 10.4049/jimmunol.1400983] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Graft-versus-host disease (GvHD) is a major cause of morbidity and mortality after allogeneic hematopoietic cell transplantation. However, the pathophysiology of GvHD remains poorly understood. In this study, we analyzed the induction of Th17 cells by monocytes of patients with GvHD in vitro, demonstrating that monocytes isolated from patients with acute skin and intestinal GvHD stage I-IV and chronic GvHD induce significantly increased levels of Th17 cells compared with patients without GvHD. S100 proteins are known to act as innate amplifier of inflammation. We therefore investigated the presence of S100 proteins in the stool, serum, and bowel tissue of patients with GvHD and the influence of S100 proteins on the induction of Th17 cells. Elevated levels of S100 proteins could be detected in patients with acute GvHD, demonstrating the release of these phagocyte-specific proteins during GvHD. Furthermore, stimulation of monocytes with S100 proteins was found to promote Th17 development, emphasizing the role of S100 proteins in Th17-triggered inflammation. Altogether, our results indicate that induction of Th17 cells by activated monocytes and the stimulatory effects of proinflammatory S100 proteins might play a relevant role in the pathogenesis of acute GvHD. Regarding our data, S100 proteins might be novel markers for the diagnosis and follow-up of GvHD.
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Affiliation(s)
| | - Dirk Foell
- Department of Pediatric Rheumatology and Immunology, University of Muenster, 48149 Muenster, Germany
| | - Thomas Vogl
- Institute of Immunology, University of Muenster, 48149 Muenster, Germany
| | - Markus Mezger
- University Children's Hospital, 72076 Tuebingen, Germany
| | - Helmut Wittkowski
- Department of Pediatric Rheumatology and Immunology, University of Muenster, 48149 Muenster, Germany
| | - Falko Fend
- Institute of Pathology, University of Tuebingen, 72076 Tuebingen, Germany; and
| | - Birgit Federmann
- Institute of Pathology, University of Tuebingen, 72076 Tuebingen, Germany; and
| | | | | | - Peter Lang
- University Children's Hospital, 72076 Tuebingen, Germany
| | | | | | - Ursula Holzer
- University Children's Hospital, 72076 Tuebingen, Germany;
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15
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Kallionpää H, Elo LL, Laajala E, Mykkänen J, Ricaño-Ponce I, Vaarma M, Laajala TD, Hyöty H, Ilonen J, Veijola R, Simell T, Wijmenga C, Knip M, Lähdesmäki H, Simell O, Lahesmaa R. Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility. Diabetes 2014; 63:2402-14. [PMID: 24550192 DOI: 10.2337/db13-1775] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The insult leading to autoantibody development in children who will progress to develop type 1 diabetes (T1D) has remained elusive. To investigate the genes and molecular pathways in the pathogenesis of this disease, we performed genome-wide transcriptomics analysis on a unique series of prospective whole-blood RNA samples from at-risk children collected in the Finnish Type 1 Diabetes Prediction and Prevention study. We studied 28 autoantibody-positive children, out of which 22 progressed to clinical disease. Collectively, the samples covered the time span from before the development of autoantibodies (seroconversion) through the diagnosis of diabetes. Healthy control subjects matched for date and place of birth, sex, and HLA-DQB1 susceptibility were selected for each case. Additionally, we genotyped the study subjects with Immunochip to identify potential genetic variants associated with the observed transcriptional signatures. Genes and pathways related to innate immunity functions, such as the type 1 interferon (IFN) response, were active, and IFN response factors were identified as central mediators of the IFN-related transcriptional changes. Importantly, this signature was detected already before the T1D-associated autoantibodies were detected. Together, these data provide a unique resource for new hypotheses explaining T1D biology.
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Affiliation(s)
- Henna Kallionpää
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandTurku Doctoral Programme of Biomedical Sciences, Turku, FinlandThe Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, Finland
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandBiomathematics Research Group, Department of Mathematics, University of Turku, Turku, Finland
| | - Essi Laajala
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandThe Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, FinlandDepartment of Information and Computer Science, Aalto University School of Science, Aalto, FinlandThe National Graduate School in Informational and Structural Biology, Turku, Finland
| | - Juha Mykkänen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandThe Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, FinlandDepartment of Pediatrics, University of Turku, Turku, FinlandDepartment of Pediatrics, Turku University Hospital, Turku, Finland
| | - Isis Ricaño-Ponce
- Department of Genetics, University of Groningen, University Medical Centre, Groningen, the Netherlands
| | - Matti Vaarma
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Teemu D Laajala
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Heikki Hyöty
- Department of Virology, University of Tampere, Tampere, FinlandFimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, FinlandDepartment of Clinical Microbiology, University of Eastern Finland, Kuopio, Finland
| | - Riitta Veijola
- Department of Pediatrics, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Tuula Simell
- The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, FinlandDepartment of Pediatrics, University of Turku, Turku, Finland
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre, Groningen, the Netherlands
| | - Mikael Knip
- The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, FinlandChildren's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, FinlandFolkhälsan Research Center, Helsinki, FinlandDepartment of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Harri Lähdesmäki
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandThe Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, FinlandDepartment of Information and Computer Science, Aalto University School of Science, Aalto, Finland
| | - Olli Simell
- The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, FinlandDepartment of Pediatrics, University of Turku, Turku, FinlandDepartment of Pediatrics, Turku University Hospital, Turku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandThe Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, Finland
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16
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Burska AN, Roget K, Blits M, Soto Gomez L, van de Loo F, Hazelwood LD, Verweij CL, Rowe A, Goulielmos GN, van Baarsen LGM, Ponchel F. Gene expression analysis in RA: towards personalized medicine. THE PHARMACOGENOMICS JOURNAL 2014; 14:93-106. [PMID: 24589910 PMCID: PMC3992869 DOI: 10.1038/tpj.2013.48] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/29/2013] [Accepted: 11/26/2013] [Indexed: 12/13/2022]
Abstract
Gene expression has recently been at the forefront of advance in personalized medicine, notably in the field of cancer and transplantation, providing a rational for a similar approach in rheumatoid arthritis (RA). RA is a prototypic inflammatory autoimmune disease with a poorly understood etiopathogenesis. Inflammation is the main feature of RA; however, many biological processes are involved at different stages of the disease. Gene expression signatures offer management tools to meet the current needs for personalization of RA patients' care. This review analyses currently available information with respect to RA diagnostic, prognostic and prediction of response to therapy with a view to highlight the abundance of data, whose comparison is often inconclusive due to the mixed use of material source, experimental methodologies and analysis tools, reinforcing the need for harmonization if gene expression signatures are to become a useful clinical tool in personalized medicine for RA patients.
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Affiliation(s)
- A N Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and Leeds Musculoskeletal Biomediacal Research Unit, The University of Leeds, Leeds, UK
| | - K Roget
- TcLand Expression, Huningue, France
| | - M Blits
- Department of Pathology and Rheumatology, Inflammatory Disease Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
| | - L Soto Gomez
- School of law, The University of Leeds, Leeds, UK
| | - F van de Loo
- Department of Rheumatology Research and Advanced Therapeutics, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - L D Hazelwood
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - C L Verweij
- Department of Pathology and Rheumatology, Inflammatory Disease Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
| | - A Rowe
- Janssen Research and Development, High Wycombe, UK
| | - G N Goulielmos
- Molecular Medicine and Human Genetics Section, Department of Medicine, University of Crete, Heraklion, Greece
| | - L G M van Baarsen
- Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - F Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and Leeds Musculoskeletal Biomediacal Research Unit, The University of Leeds, Leeds, UK
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17
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Moura RA, Canhão H, Polido-Pereira J, Rodrigues AM, Navalho M, Mourão AF, Resende C, Campanilho-Marques R, Madruga Dias J, da Silva JAP, Graca L, Fonseca JE. BAFF and TACI gene expression are increased in patients with untreated very early rheumatoid arthritis. J Rheumatol 2013; 40:1293-302. [PMID: 23772083 DOI: 10.3899/jrheum.121110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE B cells play important roles in rheumatoid arthritis (RA). Given the beneficial effect of B cell depletion therapy in RA as well as the observed alterations in B cell subpopulations in this disease, we evaluated whether changes in the expression of genes related to B cell survival and activation were already present in patients with untreated very early RA (VERA; < 6 weeks of disease duration). METHODS The expression of a group of B cell-related activation and survival genes was quantified in peripheral blood mononuclear cells from patients with VERA by real-time PCR and compared with untreated early RA (< 1 year), established treated RA, and other untreated early arthritis conditions. Serum B cell-activating factor belonging to the tumor necrosis factor family (BAFF) was quantified by ELISA. RESULTS BAFF gene expression and serum levels were highest in patients with VERA. The expression of BAFF receptor (BAFF-R) increased with disease progression, while transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI) was elevated since the first weeks of RA onset. Paired box 5 gene expression was also increased at all RA stages. Chemokine (C-X-C motif) receptor 5 was elevated only in established RA. No differences were observed in B cell maturation antigen, activation-induced cytidine deaminase, B lymphocyte-induced maturation protein, and B cell lymphoma 2 expression. CONCLUSION Disturbances in the expression of B cell-related activation and survival genes, particularly BAFF and TACI, occur from the onset of RA and precede changes in BAFF-R. These alterations can lead to the development of autoreactive B cells from the first weeks of RA onset.
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Affiliation(s)
- Rita A Moura
- Rheumatology Research Unit, and the Cellular Immunology Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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18
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Li G, Han N, Li Z, Lu Q. Identification of transcription regulatory relationships in rheumatoid arthritis and osteoarthritis. Clin Rheumatol 2013; 32:609-15. [PMID: 23296645 DOI: 10.1007/s10067-012-2143-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/19/2012] [Accepted: 12/04/2012] [Indexed: 12/17/2022]
Abstract
Rheumatoid arthritis (RA) is recognized as the most crippling or disabling type of arthritis, and osteoarthritis (OA) is the most common form of arthritis. These diseases severely reduce the quality of life, and cause high socioeconomic burdens. However, the molecular mechanisms of RA and OA development remain elusive despite intensive research efforts. In this study, we aimed to identify the potential transcription regulatory relationships between transcription factors (TFs) and differentially co-expressed genes (DCGs) in RA and OA, respectively. We downloaded the gene expression profiles of RA and OA from the Gene Expression Omnibus and analyzed the gene expression using computational methods. We identified a set of 4,076 DCGs in pairwise comparisons between RA and OA patients, RA and normal donors (NDs), or OA and ND. After regulatory network construction and regulatory impact factor analysis, we found that EGR1, NFE2L1, and NFYA were crucial TFs in the regulatory network of RA and NFYA, CBFB, CREB1, YY1 and PATZ1 were crucial TFs in the regulatory network of OA. These TFs could regulate the DCGs expression to involve RA and OA by promoting or inhibiting their expression. Altogether, our work may extend our understanding of disease mechanisms and may lead to an improved diagnosis. However, further experiments are still needed to confirm these observations.
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Affiliation(s)
- Guofeng Li
- Department of Traumatology, East Hospital, Tongji University School of Medicine, Number 150 Jimo Road, Pudong New District, Shanghai 200120, China
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19
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Edwards CK, Green JS, Volk HD, Schiff M, Kotzin BL, Mitsuya H, Kawaguchi T, Sakata KM, Cheronis J, Trollinger D, Bankaitis-Davis D, Dinarello CA, Norris DA, Bevilacqua MP, Fujita M, Burmester GR. Combined anti-tumor necrosis factor-α therapy and DMARD therapy in rheumatoid arthritis patients reduces inflammatory gene expression in whole blood compared to DMARD therapy alone. Front Immunol 2012; 3:366. [PMID: 23264777 PMCID: PMC3525111 DOI: 10.3389/fimmu.2012.00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 11/17/2012] [Indexed: 11/13/2022] Open
Abstract
Periodic assessment of gene expression for diagnosis and monitoring in rheumatoid arthritis (RA) may provide a readily available and useful method to detect subclinical disease progression and follow responses to therapy with disease modifying anti-rheumatic agents (DMARDs) or anti-TNF-α therapy. We used quantitative real-time PCR to compare peripheral blood gene expression profiles in active (“unstable”) RA patients on DMARDs, stable RA patients on DMARDs, and stable RA patients treated with a combination of a disease-modifying anti-rheumatoid drug (DMARD) and an anti-TNF-α agent (infliximab or etanercept) to healthy human controls. The expression of 48 inflammatory genes were compared between healthy controls (N = 122), unstable DMARD patients (N = 18), stable DMARD patients (N = 26), and stable patients on combination therapy (N = 20). Expression of 13 genes was very low or undetectable in all study groups. Compared to healthy controls, patients with unstable RA on DMARDs exhibited increased expression of 25 genes, stable DMARD patients exhibited increased expression of 14 genes and decreased expression of five genes, and combined therapy patients exhibited increased expression of six genes and decreased expression of 10 genes. These findings demonstrate that active RA is associated with increased expression of circulating inflammatory markers whereas increases in inflammatory gene expression are diminished in patients with stable disease on either DMARD or anti-TNF-α therapy. Furthermore, combination DMARD and anti-TNF-α therapy is associated with greater reductions in circulating inflammatory gene expression compared to DMARD therapy alone. These results suggest that assessment of peripheral blood gene expression may prove useful to monitor disease progression and response to therapy.
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Affiliation(s)
- Carl K Edwards
- Department of Dermatology, University of Colorado Denver, Anschutz Medical Campus Aurora, CO, USA ; Department of Rheumatology, University of Colorado Denver, Anschutz Medical Campus Aurora, CO, USA
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20
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Schmidt N, Art J, Forsch I, Werner A, Erkel G, Jung M, Horke S, Kleinert H, Pautz A. The anti-inflammatory fungal compound (S)-curvularin reduces proinflammatory gene expression in an in vivo model of rheumatoid arthritis. J Pharmacol Exp Ther 2012; 343:106-14. [PMID: 22767531 DOI: 10.1124/jpet.112.192047] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In previous studies, we identified the fungal macrocyclic lactone (S)-curvularin (SC) as an anti-inflammatory agent using a screening system detecting inhibitors of the Janus kinase/signal transducer and activator of transcription pathway. The objective of the present study was to investigate whether SC is able to decrease proinflammatory gene expression in an in vivo model of a chronic inflammatory disease. Therefore, the effects of SC and dexamethasone were compared in the model of collagen-induced arthritis (CIA) in mice. Total genomic microarray analyses were performed to identify SC target genes. In addition, in human C28/I2 chondrocytes and MonoMac6 monocytes, the effect of SC on proinflammatory gene expression was tested at the mRNA and protein level. In the CIA model, SC markedly reduced the expression of a number of proinflammatory cytokines and chemokines involved in the pathogenesis of CIA as well as human rheumatoid arthritis (RA). In almost all cases, the effects of SC were comparable with those of dexamethasone. In microarray analyses, we identified additional new therapeutic targets of SC. Some of them, such as S100A8, myeloperoxidase, or cathelicidin, an antimicrobial peptide, are known to be implicated in pathophysiological processes in RA. Similar anti-inflammatory effects of SC were also observed in human C28/I2 chondrocyte cells, which are resistant to glucocorticoid treatment. These data indicate that SC and glucocorticoid effects are mediated via independent signal transduction pathways. In summary, we demonstrate that SC is a new effective anti-inflammatory compound that may serve as a lead compound for the development of new drugs for the therapy of chronic inflammatory diseases.
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Affiliation(s)
- Nadine Schmidt
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
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21
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Catalá-Rabasa A, Ndagire D, Sabio JM, Fedetz M, Matesanz F, Alcina A. High ACSL5 transcript levels associate with systemic lupus erythematosus and apoptosis in Jurkat T lymphocytes and peripheral blood cells. PLoS One 2011; 6:e28591. [PMID: 22163040 PMCID: PMC3232234 DOI: 10.1371/journal.pone.0028591] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/11/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which increased apoptosis and decreased apoptotic cells removal has been described as most relevant in the pathogenesis. Long-chain acyl-coenzyme A synthetases (ACSLs) have been involved in the immunological dysfunction of mouse models of lupus-like autoimmunity and apoptosis in different in vitro cell systems. The aim of this work was to assess among the ACSL isoforms the involvement of ACSL2, ACSL4 and ACSL5 in SLE pathogenesis. FINDINGS With this end, we determined the ACSL2, ACSL4 and ACSL5 transcript levels in peripheral blood mononuclear cells (PBMCs) of 45 SLE patients and 49 healthy controls by quantitative real time-PCR (q-PCR). We found that patients with SLE had higher ACSL5 transcript levels than healthy controls [median (range), healthy controls = 16.5 (12.3-18.0) vs. SLE = 26.5 (17.8-41.7), P = 3.9×10 E-5] but no differences were found for ACSL2 and ACSL4. In in vitro experiments, ACSL5 mRNA expression was greatly increased when inducing apoptosis in Jurkat T cells and PBMCs by Phorbol-Myristate-Acetate plus Ionomycin (PMA+Io). On the other hand, short interference RNA (siRNA)-mediated silencing of ACSL5 decreased induced apoptosis in Jurkat T cells up to the control levels as well as decreased mRNA expression of FAS, FASLG and TNF. CONCLUSIONS These findings indicate that ACSL5 may play a role in the apoptosis that takes place in SLE. Our results point to ACSL5 as a potential novel functional marker of pathogenesis and a possible therapeutic target in SLE.
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Affiliation(s)
- Antonio Catalá-Rabasa
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra-Consejo Superior de Investigaciones Científicas, Granada, Spain
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22
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Santer DM, Wiedeman AE, Teal TH, Ghosh P, Elkon KB. Plasmacytoid dendritic cells and C1q differentially regulate inflammatory gene induction by lupus immune complexes. THE JOURNAL OF IMMUNOLOGY 2011; 188:902-15. [PMID: 22147767 DOI: 10.4049/jimmunol.1102797] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Immune complexes (ICs) play a pivotal role in causing inflammation in systemic lupus erythematosus (SLE). Yet, it remains unclear what the dominant blood cell type(s) and inflammation-related gene programs stimulated by lupus ICs are. To address these questions, we exposed normal human PBMCs or CD14(+) isolated monocytes to SLE ICs in the presence or absence of C1q and performed microarray analysis and other tests for cell activation. By microarray analysis, we identified genes and pathways regulated by SLE ICs that are both type I IFN dependent and independent. We also found that C1q-containing ICs markedly reduced expression of the majority of IFN-response genes and also influenced the expression of multiple other genes induced by SLE ICs. Surprisingly, IC activation of isolated CD14(+) monocytes did not upregulate CD40 and CD86 and only modestly stimulated inflammatory gene expression. However, when monocyte subsets were purified and analyzed separately, the low-abundance CD14(dim) ("patrolling") subpopulation was more responsive to ICs. These observations demonstrate the importance of plasmacytoid dendritic cells, CD14(dim) monocytes, and C1q as key regulators of inflammatory properties of ICs and identify many pathways through which they act.
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Affiliation(s)
- Deanna M Santer
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA 98195, USA
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23
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Rotunno M, Hu N, Su H, Wang C, Goldstein AM, Bergen AW, Consonni D, Pesatori AC, Bertazzi PA, Wacholder S, Shih J, Caporaso NE, Taylor PR, Landi MT. A gene expression signature from peripheral whole blood for stage I lung adenocarcinoma. Cancer Prev Res (Phila) 2011; 4:1599-608. [PMID: 21742797 PMCID: PMC3188352 DOI: 10.1158/1940-6207.capr-10-0170] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Affordable early screening in subjects with high risk of lung cancer has great potential to improve survival from this deadly disease. We measured gene expression from lung tissue and peripheral whole blood (PWB) from adenocarcinoma cases and controls to identify dysregulated lung cancer genes that could be tested in blood to improve identification of at-risk patients in the future. Genome-wide mRNA expression analysis was conducted in 153 subjects (73 adenocarcinoma cases, 80 controls) from the Environment And Genetics in Lung cancer Etiology study using PWB and paired snap-frozen tumor and noninvolved lung tissue samples. Analyses were conducted using unpaired t tests, linear mixed effects, and ANOVA models. The area under the receiver operating characteristic curve (AUC) was computed to assess the predictive accuracy of the identified biomarkers. We identified 50 dysregulated genes in stage I adenocarcinoma versus control PWB samples (false discovery rate ≤0.1, fold change ≥1.5 or ≤0.66). Among them, eight (TGFBR3, RUNX3, TRGC2, TRGV9, TARP, ACP1, VCAN, and TSTA3) differentiated paired tumor versus noninvolved lung tissue samples in stage I cases, suggesting a similar pattern of lung cancer-related changes in PWB and lung tissue. These results were confirmed in two independent gene expression analyses in a blood-based case-control study (n = 212) and a tumor-nontumor paired tissue study (n = 54). The eight genes discriminated patients with lung cancer from healthy controls with high accuracy (AUC = 0.81, 95% CI = 0.74-0.87). Our finding suggests the use of gene expression from PWB for the identification of early detection markers of lung cancer in the future.
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Affiliation(s)
- Melissa Rotunno
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Andrew W. Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
- Center for Health Sciences, SRI International, Menlo Park, California
| | - Dario Consonni
- Unit of Epidemiology, Fondazione IRCCS Ospedale Maggiore Policlinico and Department of Occupational and Environmental Health, Università degli Studi di Milano, Milan, Italy
| | - Angela C Pesatori
- Unit of Epidemiology, Fondazione IRCCS Ospedale Maggiore Policlinico and Department of Occupational and Environmental Health, Università degli Studi di Milano, Milan, Italy
| | - Pier Alberto Bertazzi
- Unit of Epidemiology, Fondazione IRCCS Ospedale Maggiore Policlinico and Department of Occupational and Environmental Health, Università degli Studi di Milano, Milan, Italy
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Joanna Shih
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Phil R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
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25
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Andrés Cerezo L, Mann H, Pecha O, Pleštilová L, Pavelka K, Vencovský J, Senolt L. Decreases in serum levels of S100A8/9 (calprotectin) correlate with improvements in total swollen joint count in patients with recent-onset rheumatoid arthritis. Arthritis Res Ther 2011; 13:R122. [PMID: 21791097 PMCID: PMC3239361 DOI: 10.1186/ar3426] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/28/2011] [Accepted: 07/26/2011] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The aim of this study was to examine the serum levels of S100 proteins and to evaluate their role in patients with recent-onset rheumatoid arthritis (RA). METHODS Serum levels of S100A8/9 and S100A12 were analysed in 43 patients with recent-onset RA, both before and three months after the initiation of conventional treatment, as well as in 32 healthy individuals. Disease activity was assessed based on serum levels of C-reactive protein (CRP), the Disease Activity Score for 28 joints (DAS28) and the total number of swollen joints count for 66 joints (SJC). RESULTS The levels of serum S100A8/9 and S100A12 were significantly higher in patients with recent-onset RA compared to the levels in healthy individuals (P < 0.0001) and normalised after three months of treatment. Using age- and sex-adjusted analysis, S100A8/9 levels were correlated with CRP (r = 0.439, P < 0.01), DAS28 (r = 0.501, P = 0.002) and SJC (r = 0.443, P = 0.007), while S100A12 was less significantly correlated with these parameters. Higher levels of S100A8/9 at baseline predicted improvement in the levels of CRP and SJC over time. Moreover, decreases in serum S100A8/9 were associated with decreased serum levels of CRP (r = 0.459, P = 0.005) and improvements in SJC (r = 0.459, P = 0.005). In multiple linear regression analyses, decreases in S100A8/9 but not CRP were significant predictors for improvements in SJC (P = 0.001). CONCLUSIONS This study is the first to show normalisation of elevated S100 proteins in patients with recent-onset RA after the initiation of conventional treatment. Therefore, S100A8/9 might potentially be a predictive marker for improvement in the total number of swollen joints in patients in the early phase of RA.
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Affiliation(s)
- Lucie Andrés Cerezo
- Institute of Rheumatology, First Medical Faculty, Charles University, Na Slupi 4, 128 50 Prague 2, Czech Republic
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Mesko B, Poliska S, Nagy L. Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases. Trends Mol Med 2011; 17:223-33. [PMID: 21388884 DOI: 10.1016/j.molmed.2010.12.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 12/11/2010] [Accepted: 12/13/2010] [Indexed: 11/28/2022]
Abstract
Gene expression profiling in clinical genomics has yet to deliver robust and reliable approaches for developing diagnostics and contributing to personalized medicine. Owing to technological developments and the recent accumulation of expression profiles, it is a timely and relevant question whether peripheral blood gene expression profiling can be used routinely in clinical decision making. Here, we review the available gene expression profiling data of peripheral blood in autoimmune and chronic inflammatory diseases and suggest that peripheral blood mononuclear cells are suitable for descriptive and comparative gene expression analyses. A gene-disease interaction network in chronic inflammatory diseases, a general protocol for future studies and a decision tree for researchers are presented to facilitate standardization and adoption of this approach.
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Affiliation(s)
- Bertalan Mesko
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Mediicne, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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Meugnier E, Coury F, Tebib J, Ferraro-Peyret C, Rome S, Bienvenu J, Vidal H, Sibilia J, Fabien N. Gene expression profiling in peripheral blood cells of patients with rheumatoid arthritis in response to anti-TNF-alpha treatments. Physiol Genomics 2011; 43:365-71. [PMID: 21266503 DOI: 10.1152/physiolgenomics.00127.2010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The efficacy of anti-TNF-α therapies highlights the role of TNF-α in the pathogenesis of rheumatoid arthritis (RA). However, the mechanism of action of these agents is poorly understood at the molecular level. The aim of this study was to characterize the effects of anti-TNF-α treatment on the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of responder RA patients. Changes in gene expression were determined using oligonucleotide microarrays (25,341 genes) in PBMCs obtained before and after 12 wk of treatment with either etanercept or adalimumab from responder RA patients. Two hundred fifty-one genes displayed significant changes (false discovery rate < 0.1%) in expression level (178 upregulations with mean fold change = 1.5 and 73 downregulations with mean fold change = -1.50) after 12 wk of treatment. Importantly, the expression of several genes, including those coding for the calcium binding proteins S100A12 and A8, CD14 antigen, Selectin P, or ribosomal protein L39, reported to be upregulated in RA patients, were found to be decreased after anti-TNF-α treatment. Globally, inflammation, immune response, apoptosis, protein synthesis, and mitochondrial oxido-reduction were the most affected pathways in response to anti-TNF-α treatment. The obtained gene expression signature in PBMCs provides new information to better understand the mechanisms of action of anti-TNF-α treatment in RA patients.
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Ungethuem U, Haeupl T, Witt H, Koczan D, Krenn V, Huber H, von Helversen TM, Drungowski M, Seyfert C, Zacher J, Pruss A, Neidel J, Lehrach H, Thiesen HJ, Ruiz P, Bläss S. Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis. Physiol Genomics 2010; 42A:267-82. [PMID: 20858714 DOI: 10.1152/physiolgenomics.00004.2010] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced interpatient heterogeneity. To characterize RA at the molecular level and to uncover pathomechanisms, we performed genome-wide gene expression analysis. We identified a set of 1,054 genes significantly deregulated in pair-wise comparisons between RA and osteoarthritis (OA) patients, RA and normal donors (ND), or OA and ND. Correlation analysis revealed gene sets regulated identically in all three groups. As a prominent example secreted phosphoprotein 1 (SPP1) was identified to be significantly upregulated in RA compared with both OA and ND. SPP1 expression was found to correlate with genes expressed during an inflammatory response, T-cell activation and apoptosis, suggesting common underlying regulatory networks. A subclassification of RA patients was achieved on the basis of proteoglycan 4 (PRG4) expression, distinguishing PRG4 high and low expressors and reflecting the heterogeneity of the disease. In addition, we found that low PRG4 expression was associated with a more aggressive disease stage, which is in accordance with PRG4 loss-of-function mutations causing camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Altogether we provide evidence for molecular signatures of RA and RA subclasses, sets of new candidate genes as well as for candidate gene networks, which extend our understanding of disease mechanisms and may lead to an improved diagnosis.
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Affiliation(s)
- U Ungethuem
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, CharitéUniversitätsmedizin Berlin, Germany.
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Grcevic D, Jajic Z, Kovacic N, Lukic IK, Velagic V, Grubisic F, Ivcevic S, Marusic A. Peripheral blood expression profiles of bone morphogenetic proteins, tumor necrosis factor-superfamily molecules, and transcription factor Runx2 could be used as markers of the form of arthritis, disease activity, and therapeutic responsiveness. J Rheumatol 2009; 37:246-56. [PMID: 20008919 DOI: 10.3899/jrheum.090167] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE To assess whether different forms of arthritis and disease activity could be distinguished by peripheral blood expression profiles of bone-regulatory factors including tumor necrosis factor (TNF)-superfamily [TNF-related apoptosis-inducing ligand (TRAIL), the Fas ligand (FasL), and the ligand for herpesvirus entry mediator (LIGHT)] and bone morphogenetic protein (BMP)-family members (BMP-2, BMP-4, BMP-6) as well as osteoblast differentiation gene Runx2. METHODS Blood cells from healthy controls (n = 25) and patients at different disease stages with rheumatoid arthritis (RA; n = 49), osteoarthritis (OA; n = 17), or spondyloarthritis, including ankylosing spondylitis (AS; n = 27) or psoriatic arthritis (PsA; n = 23), were processed for quantitative polymerase chain reaction. Gene expression was assessed in comparison with control samples, correlated with clinical data of different forms of arthritis, and analyzed for discriminative efficacy between groups by receiver-operation characteristic (ROC) curves. Results were confirmed on diagnostic RA (n = 5) and AS (n = 8) samples. RESULTS BMP-4, BMP-6, and Runx2 expressions were significantly decreased in patients with RA and OA versus controls. Patients with RA also had decreased FasL and LIGHT expression, while patients with AS had increased Runx2 expression. Negative correlation with disease activity was found for BMP-4, FasL, and Runx2 in RA and for Runx2 in PsA, while positive correlation was found for BMP-4 in PsA. Gene expression was higher in the therapy-resistant form of AS (for BMP-4, LIGHT, and Runx2) and in methotrexate-treated patients in RA (for BMP-2 and LIGHT). ROC curve analysis confirmed discrimination between groups, particularly decreased LIGHT and Runx2 for RA and increased Runx2 for AS. CONCLUSION Our study identified BMP and Runx2 as possible biomarkers of bone metabolism in several forms of arthritis, while lower FasL and LIGHT were associated with RA. Correlation between gene expression and disease activity may be clinically useful in assessing therapeutic effectiveness and disease monitoring.
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Affiliation(s)
- Danka Grcevic
- Department of Physiology and Immunology, University of Zagreb School of Medicine, Zagreb, Croatia.
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Cytokines and cytokine profiles in human autoimmune diseases and animal models of autoimmunity. Mediators Inflamm 2009; 2009:979258. [PMID: 19884985 PMCID: PMC2768824 DOI: 10.1155/2009/979258] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 07/13/2009] [Accepted: 08/10/2009] [Indexed: 02/08/2023] Open
Abstract
The precise pathomechanisms of human autoimmune diseases are still poorly understood. However, a deepened understanding of these is urgently needed to improve disease prevention and early detection and guide more specific treatment approaches. In recent years, many new genes and signalling pathways involved in autoimmunity with often overlapping patterns between different disease entities have been detected. Major contributions were made by experiments using DNA microarray technology, which has been used for the analysis of gene expression patterns in chronic inflammatory and autoimmune diseases, among which were rheumatoid arthritis, systemic lupus erythematosus, psoriasis, systemic sclerosis, multiple sclerosis, and type-1 diabetes. In systemic lupus erythematosus, a so-called interferon signature has been identified. In psoriasis, researchers found a particular immune signalling cluster. Moreover the identification of a new subset of inflammatory T cells, so-called Th17 T cells, secreting interleukin (IL)-17 as one of their major cytokines and the identification of the IL-23/IL-17 axis of inflammation regulation, have significantly improved our understanding of autoimmune diseases. Since a plethora of new treatment approaches using antibodies or small molecule inhibitors specifically targeting cytokines, cellular receptors, or signalling mechanisms has emerged in recent years, more individualized treatment for affected patients may be within reach in the future.
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Griffin TA, Barnes MG, Ilowite NT, Olson JC, Sherry DD, Gottlieb BS, Aronow BJ, Pavlidis P, Hinze CH, Thornton S, Thompson SD, Grom AA, Colbert RA, Glass DN. Gene expression signatures in polyarticular juvenile idiopathic arthritis demonstrate disease heterogeneity and offer a molecular classification of disease subsets. ACTA ACUST UNITED AC 2009; 60:2113-23. [PMID: 19565504 DOI: 10.1002/art.24534] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To determine whether peripheral blood mononuclear cells (PBMCs) from children with recent-onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures. METHODS Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biologic agents. RNA was extracted from isolated mononuclear cells, fluorescence labeled, and hybridized to commercial gene expression microarrays (Affymetrix HG-U133 Plus 2.0). Data were analyzed using analysis of variance at a 5% false discovery rate threshold after robust multichip analysis preprocessing and distance-weighted discrimination normalization. RESULTS Initial analysis revealed 873 probe sets for genes that were differentially expressed between polyarticular JIA patients and healthy controls. Hierarchical clustering of these probe sets distinguished 3 subgroups within the polyarticular JIA group. Prototypical patients within each subgroup were identified and used to define subgroup-specific gene expression signatures. One of these signatures was associated with monocyte markers, another with transforming growth factor beta-inducible genes, and a third with immediate early genes. Correlation of gene expression signatures with clinical and biologic features of JIA subgroups suggested relevance to aspects of disease activity and supported the division of polyarticular JIA into distinct subsets. CONCLUSION Gene expression signatures in PBMCs from patients with recent-onset polyarticular JIA reflect discrete disease processes and offer a molecular classification of disease.
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Affiliation(s)
- Thomas A Griffin
- William S. Rowe Division of Pediatric Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
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Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S, Jacq L, Oliveira CR, Hilliquin P, Gut I, Cornelis F, Petit-Teixeira E. Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients. PLoS One 2009; 4:e6803. [PMID: 19710928 PMCID: PMC2729373 DOI: 10.1371/journal.pone.0006803] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 08/03/2009] [Indexed: 12/13/2022] Open
Abstract
Background Large-scale gene expression profiling of peripheral blood mononuclear cells from Rheumatoid Arthritis (RA) patients could provide a molecular description that reflects the contribution of diverse cellular responses associated with this disease. The aim of our study was to identify peripheral blood gene expression profiles for RA patients, using Illumina technology, to gain insights into RA molecular mechanisms. Methodology/Principal Findings The Illumina Human-6v2 Expression BeadChips were used for a complete genome-wide transcript profiling of peripheral blood mononuclear cells (PBMCs) from 18 RA patients and 15 controls. Differential analysis per gene was performed with one-way analysis of variance (ANOVA) and P values were adjusted to control the False Discovery Rate (FDR<5%). Genes differentially expressed at significant level between patients and controls were analyzed using Gene Ontology (GO) in the PANTHER database to identify biological processes. A differentially expression of 339 Reference Sequence genes (238 down-regulated and 101 up-regulated) between the two groups was observed. We identified a remarkably elevated expression of a spectrum of genes involved in Immunity and Defense in PBMCs of RA patients compared to controls. This result is confirmed by GO analysis, suggesting that these genes could be activated systemically in RA. No significant down-regulated ontology groups were found. Microarray data were validated by real time PCR in a set of nine genes showing a high degree of correlation. Conclusions/Significance Our study highlighted several new genes that could contribute in the identification of innovative clinical biomarkers for diagnostic procedures and therapeutic interventions.
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Affiliation(s)
- Vitor Hugo Teixeira
- GenHotel-EA3886, Evry University, Paris 7 University Medical School, AutoCure European Consortium member, Evry, France.
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Bovin LF, Brynskov J, Hegedüs L, Jess T, Nielsen CH, Bendtzen K. Gene expression profiling in autoimmune diseases: Chronic inflammation or disease specific patterns? Autoimmunity 2009; 40:191-201. [PMID: 17453718 DOI: 10.1080/08916930701233813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A central issue in autoimmune disease is whether the underlying inflammation is a repeated stereotypical process or whether disease specific gene expression is involved. To shed light on this, we analysed whether genes previously found to be differentially regulated in rheumatoid arthritis (RA) patients and healthy individuals were specific for the arthritic process or likewise altered in other chronic inflammatory diseases such as chronic autoimmune thyroiditis (Hashimoto's thyroiditis, HT) and inflammatory bowel disease (IBD). Using qPCR for 18 RA-discriminative genes, there were no significant differences in peripheral blood mononuclear cell (MNC) gene expression patterns between 15 newly diagnosed HT patients and 15 matched healthy controls. However, the MNC expression levels of five genes were significantly upregulated in 25 IBD patients, compared to 18 matched healthy controls (CD14, FACL2, FCN1, RNASE2, VNN2). There was concordance in the directional change for all genes between IBD and RA patients, i.e. increased expression compared to controls. These data show that one third of the genes significantly upregulated in MNC from RA patients were upregulated in patients with other chronic immunoinflammatory diseases, but only if accompanied by pronounced systemic manifestations. This suggests that at least some of the genes activated in RA are predominantly or solely related to general and disease-nonspecific autoimmune processes.
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Affiliation(s)
- Lone Frier Bovin
- Rigshospitalet National University Hospital, Institute for Inflammation Research, Copenhagen, Denmark
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Hamilton JA, Tak PP. The dynamics of macrophage lineage populations in inflammatory and autoimmune diseases. ACTA ACUST UNITED AC 2009; 60:1210-21. [PMID: 19404968 DOI: 10.1002/art.24505] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- John A Hamilton
- Arthritis and Inflammation Research Centre, University of Melbourne and Department of Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia.
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Chen YS, Yan W, Geczy CL, Brown MA, Thomas R. Serum levels of soluble receptor for advanced glycation end products and of S100 proteins are associated with inflammatory, autoantibody, and classical risk markers of joint and vascular damage in rheumatoid arthritis. Arthritis Res Ther 2009; 11:R39. [PMID: 19284577 PMCID: PMC2688185 DOI: 10.1186/ar2645] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/25/2009] [Accepted: 03/11/2009] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION The receptor for advanced glycation end products (RAGE) is a member of the immunoglobulin superfamily of cell surface receptor molecules. High concentrations of three of its putative proinflammatory ligands, S100A8/A9 complex (calprotectin), S100A8, and S100A12, are found in rheumatoid arthritis (RA) serum and synovial fluid. In contrast, soluble RAGE (sRAGE) may prevent proinflammatory effects by acting as a decoy. This study evaluated the serum levels of S100A9, S100A8, S100A12 and sRAGE in RA patients, to determine their relationship to inflammation and joint and vascular damage. METHODS Serum sRAGE, S100A9, S100A8 and S100A12 levels from 138 patients with established RA and 44 healthy controls were measured by ELISA and compared by unpaired t test. In RA patients, associations with disease activity and severity variables were analyzed by simple and multiple linear regressions. RESULTS Serum S100A9, S100A8 and S100A12 levels were correlated in RA patients. S100A9 levels were associated with body mass index (BMI), and with serum levels of S100A8 and S100A12. S100A8 levels were associated with serum levels of S100A9, presence of anti-citrullinated peptide antibodies (ACPA), and rheumatoid factor (RF). S100A12 levels were associated with presence of ACPA, history of diabetes, and serum S100A9 levels. sRAGE levels were negatively associated with serum levels of C-reactive protein (CRP) and high-density lipoprotein (HDL), history of vasculitis, and the presence of the RAGE 82Ser polymorphism. CONCLUSIONS sRAGE and S100 proteins were associated not just with RA inflammation and autoantibody production, but also with classical vascular risk factors for end-organ damage. Consistent with its role as a RAGE decoy molecule, sRAGE had the opposite effects to S100 proteins in that S100 proteins were associated with autoantibodies and vascular risk, whereas sRAGE was associated with protection against joint and vascular damage. These data suggest that RAGE activity influences co-development of joint and vascular disease in rheumatoid arthritis patients.
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Affiliation(s)
- Yueh-Sheng Chen
- Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Woolloongabba, Australia
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López-Pedrera C, Barbarroja N, Villalba JM. Novel biomarkers of atherosclerosis and cardiovascular risk in autoimmune diseases: Genomics and proteomics approaches. Proteomics Clin Appl 2009; 3:213-25. [DOI: 10.1002/prca.200800147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Indexed: 01/15/2023]
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van Baarsen LGM, Bos CL, van der Pouw Kraan TCTM, Verweij CL. Transcription profiling of rheumatic diseases. Arthritis Res Ther 2009; 11:207. [PMID: 19232067 PMCID: PMC2688218 DOI: 10.1186/ar2557] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Rheumatic diseases are a diverse group of disorders. Most of these diseases are heterogeneous in nature and show varying responsiveness to treatment. Because our understanding of the molecular complexity of rheumatic diseases is incomplete and criteria for categorization are limited, we mainly refer to them in terms of group averages. The advent of DNA microarray technology has provided a powerful tool to gain insight into the molecular complexity of these diseases; this technology facilitates open-ended survey to identify comprehensively the genes and biological pathways that are associated with clinically defined conditions. During the past decade, encouraging results have been generated in the molecular description of complex rheumatic diseases, such as rheumatoid arthritis, systemic lupus erythematosus, Sjögren syndrome and systemic sclerosis. Here, we describe developments in genomics research during the past decade that have contributed to our knowledge of pathogenesis, and to the identification of biomarkers for diagnosis, patient stratification and prognostication.
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Affiliation(s)
- Lisa G M van Baarsen
- Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
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Shiina T, Hosomichi K, Inoko H, Kulski JK. The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet 2009; 54:15-39. [PMID: 19158813 DOI: 10.1038/jhg.2008.5] [Citation(s) in RCA: 471] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The human leukocyte antigen (HLA) super-locus is a genomic region in the chromosomal position 6p21 that encodes the six classical transplantation HLA genes and at least 132 protein coding genes that have important roles in the regulation of the immune system as well as some other fundamental molecular and cellular processes. This small segment of the human genome has been associated with more than 100 different diseases, including common diseases, such as diabetes, rheumatoid arthritis, psoriasis, asthma and various other autoimmune disorders. The first complete and continuous HLA 3.6 Mb genomic sequence was reported in 1999 with the annotation of 224 gene loci, including coding and non-coding genes that were reviewed extensively in 2004. In this review, we present (1) an updated list of all the HLA gene symbols, gene names, expression status, Online Mendelian Inheritance in Man (OMIM) numbers, including new genes, and latest changes to gene names and symbols, (2) a regional analysis of the extended class I, class I, class III, class II and extended class II subregions, (3) a summary of the interspersed repeats (retrotransposons and transposons), (4) examples of the sequence diversity between different HLA haplotypes, (5) intra- and extra-HLA gene interactions and (6) some of the HLA gene expression profiles and HLA genes associated with autoimmune and infectious diseases. Overall, the degrees and types of HLA super-locus coordinated gene expression profiles and gene variations have yet to be fully elucidated, integrated and defined for the processes involved with normal cellular and tissue physiology, inflammatory and immune responses, and autoimmune and infectious diseases.
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Affiliation(s)
- Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.
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Whalen KA, Legault H, Hang C, Hill A, Kasaian M, Donaldson D, Bensch GW, Bensch G, Baker J, Reddy PS, Wood N, Ramarao MK, Ellis DK, Csimma C, McKee C, Clark JD, Ryan J, Dorner AJ, O'Toole M. In vitro allergen challenge of peripheral blood induces differential gene expression in mononuclear cells of asthmatic patients: inhibition of cytosolic phospholipase A2alpha overcomes the asthma-associated response. Clin Exp Allergy 2008; 38:1590-605. [PMID: 18665843 PMCID: PMC2613256 DOI: 10.1111/j.1365-2222.2008.03059.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 05/01/2008] [Accepted: 05/12/2008] [Indexed: 01/14/2023]
Abstract
BACKGROUND Existing treatments for asthma are not effective in all patients and disease exacerbations are common, highlighting the need for increased understanding of disease mechanisms and novel treatment strategies. The leukotriene pathway including the enzyme responsible for arachidonic acid release from cellular phospholipids, cPLA(2)alpha, is a major contributor to asthmatic responses and an attractive target in asthma therapies. OBJECTIVE The study reported here investigates (a) the differential effects of in vitro exposure of peripheral blood mononuclear cells (PBMCs) to allergen between asthma and healthy subjects, and (b) the contribution of cPLA(2)alpha to these differences in gene expression. METHODS In vitro responses of asthma (N=26) and healthy (N=11) subject PBMC samples to allergen stimulation in the presence and absence of cPLA(2)alpha inhibition or 5-lipoxygenase inhibition were compared at the gene expression level using oligonucleotide arrays and at the protein level using ELISA. RESULTS Subject samples within both asthma and healthy groups showed allergen-dependent cytokine production and allergen-dependent gene expression changes, although transcriptional profiling identified 153 genes that were modulated significantly differently by allergen between asthma and healthy subjects. Among these were genes previously associated with asthma, but the majority (about 80%) have not previously been associated with asthma. CONCLUSIONS Transcriptional profiling elucidated novel gene expression differences between the asthmatic and healthy subject samples. Although 5-lipoxygenase inhibition did not significantly affect allergen-modulated gene expression, the inhibition of cPLA(2)alpha activity affected many of the allergen-dependent, asthma-associated gene expression changes.
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Affiliation(s)
- K A Whalen
- Wyeth Research, Cambridge, MA 02140, USA
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Sørensen LK, Havemose-Poulsen A, Sønder SU, Bendtzen K, Holmstrup P. Blood cell gene expression profiling in subjects with aggressive periodontitis and chronic arthritis. J Periodontol 2008; 79:477-85. [PMID: 18315430 DOI: 10.1902/jop.2008.070309] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Microarray analysis of local and peripheral cells in subjects with immune-inflammatory diseases may identify candidate genes associated with these diseases. The present study identified differentially expressed genes in peripheral blood mononuclear cells (PBMCs) from subjects with untreated localized aggressive periodontitis (LAgP) or generalized aggressive periodontitis (GAgP). Differentially expressed genes were validated in groups of subjects with LAgP, GAgP, juvenile idiopathic arthritis (JIA), or rheumatoid arthritis (RA) and controls. METHODS Candidate genes were identified by gene expression profiling of PBMCs using a microarray system in untreated gender-matched subjects with LAgP (N = 2) or GAgP (N = 3) and controls (N = 2) younger than 35 years of age. The microarray results were validated by real-time reverse transcription-polymerase chain reaction (RT-PCR) using PBMCs from 103 individuals, including groups of subjects with LAgP (N = 18), GAgP (N = 27), JIA (N = 10), or RA (N = 23) and controls (N = 25). RESULTS Of 53 differentially expressed candidate genes identified in subjects with LAgP, 14 were involved in immune responses and inflammatory processes. Of these, the RT-PCR validation confirmed that Toll-like receptor 2 gene (TLR2) and myomesin 2 gene had a significantly higher expression in subjects with LAgP than in controls. RT-PCR also showed increased expression of TLR2 in subjects with RA. Comparison of subjects with GAgP to controls using microarray analysis identified only three upregulated genes. CONCLUSION Several genes upregulated in subjects with LAgP were related to immune responses including TLR2 and myomesin 2.
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Affiliation(s)
- Lars K Sørensen
- Department of Periodontology, School of Dentistry, Faculty of Health Sciences, University of Copenhagen, 20 Nørre Allé, Copenhagen, Denmark
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42
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Abstract
Inflammatory rheumatic diseases with their unclear aetiology are a challenge for the routine clinical practice. The dominating inflammatory processes with many facets of autoimmune phenomena have been extensively studied during the last decades. Modern high throughput technologies provide for the first time the opportunity to obtain an insight into the many different molecular aspects in one patient in parallel. Step by step, concepts can be developed to understand the relationships and interdependencies of the molecular processes and to place them in order of importance for each individual separately. Thus, studies have demonstrated that the risk of disease severity can be estimated and the response to therapy can be objectified based on molecular investigations. Exemplarily, the potential has been demonstrated that the therapeutic outcome towards a defined treatment may be predicted. Despite the high cost, it is becoming more and more obvious that an extensive increase of knowledge depends on the detection of a multitude of parameters, a task which will need to be accomplished in the near future.
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Affiliation(s)
- R Guenther
- Institut für Pathologie, Charité Universitätsmedizin Berlin, Berlin, Deutschland
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43
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Ardigo D, Gaillard CAJM, Braam B. Application of leukocyte transcriptomes to assess systemic consequences of risk factors for cardiovascular disease. Clin Chem Lab Med 2008; 45:1109-20. [PMID: 17635069 DOI: 10.1515/cclm.2007.261] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
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Affiliation(s)
- Diego Ardigo
- Department of Internal Medicine and Biomedical Sciences, University of Parma, Italy
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44
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Edwards CJ, Feldman JL, Beech J, Shields KM, Stover JA, Trepicchio WL, Larsen G, Foxwell BM, Brennan FM, Feldmann M, Pittman DD. Molecular profile of peripheral blood mononuclear cells from patients with rheumatoid arthritis. Mol Med 2007; 13:40-58. [PMID: 17515956 PMCID: PMC1869619 DOI: 10.2119/2006-000056.edwards] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 12/07/2006] [Indexed: 11/06/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory arthritis. Currently, diagnosis of RA may take several weeks, and factors used to predict a poor prognosis are not always reliable. Gene expression in RA may consist of a unique signature. Gene expression analysis has been applied to synovial tissue to define molecularly distinct forms of RA; however, expression analysis of tissue taken from a synovial joint is invasive and clinically impractical. Recent studies have demonstrated that unique gene expression changes can be identified in peripheral blood mononuclear cells (PBMCs) from patients with cancer, multiple sclerosis, and lupus. To identify RA disease-related genes, we performed a global gene expression analysis. RNA from PBMCs of 9 RA patients and 13 normal volunteers was analyzed on an oligonucleotide array. Compared with normal PBMCs, 330 transcripts were differentially expressed in RA. The differentially regulated genes belong to diverse functional classes and include genes involved in calcium binding, chaperones, cytokines, transcription, translation, signal transduction, extracellular matrix, integral to plasma membrane, integral to intracellular membrane, mitochondrial, ribosomal, structural, enzymes, and proteases. A k-nearest neighbor analysis identified 29 transcripts that were preferentially expressed in RA. Ten genes with increased expression in RA PBMCs compared with controls mapped to a RA susceptibility locus, 6p21.3. These results suggest that analysis of RA PBMCs at the molecular level may provide a set of candidate genes that could yield an easily accessible gene signature to aid in early diagnosis and treatment.
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Affiliation(s)
- Christopher J Edwards
- The Kennedy Institute of Rheumatology Division, Imperial College School of Medicine, London, UK.
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45
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Galligan CL, Baig E, Bykerk V, Keystone EC, Fish EN. Distinctive gene expression signatures in rheumatoid arthritis synovial tissue fibroblast cells: correlates with disease activity. Genes Immun 2007; 8:480-91. [PMID: 17568789 DOI: 10.1038/sj.gene.6364400] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene expression profiling of rheumatoid arthritis (RA) and osteoarthritis (OA) joint tissue samples provides a unique insight into the gene signatures involved in disease development and progression. Fibroblast-like synovial (FLS) cells were obtained from RA, OA and control trauma joint tissues (non-RA, non-OA) and RNA was analyzed by Affymetrix microarray. Thirty-four genes specific to RA and OA FLS cells were identified (P<0.05). HOXD10, HOXD11, HOXD13, CCL8 and LIM homeobox 2 were highly and exclusively expressed in RA and CLU, sarcoglycan-gamma, GPR64, POU3F3, peroxisome proliferative activated receptor-gamma and tripartite motif-containing 2 were expressed only in OA. The data also revealed expression heterogeneity for patients with the same disease. To address disease heterogeneity in RA FLS cells, we examined the effects of clinical disease parameters (Health Assessment Questionnaire (HAQ) score, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), rheumatoid factor (RF)) and drug therapies (methotrexate/prednisone) on RA FLS cell gene expression. Eight specific and unique correlations were identified: human leukocyte antigen (HLA)-DQA2 with HAQ score; Clec12A with RF; MAB21L2, SIAT7E, HAPLN1 and BAIAP2L1 with CRP level; RGMB and OSAP with ESR. Signature RA FLS cell gene expression profiles may provide insights into disease pathogenesis and have utility in diagnosis, prognosis and drug responsiveness.
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Affiliation(s)
- C L Galligan
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
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46
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Abstract
PURPOSE OF REVIEW There have recently been fewer publications describing novel cytokines in rheumatoid arthritis. In the present review we focus on cytokines not previously implicated in contributing to the pathogenesis of rheumatoid arthritis. RECENT FINDINGS The detection of IL-17 and factors that drive the differentiation and expansion of ThIL-17 cells, particularly in mouse models, clearly place IL-17 as a potential therapeutic target in rheumatoid arthritis. The emergence of other novel cytokines, notably IL-20 and IL-22, is of interest, not least by displaying proinflammatory effects particularly on fibroblasts - in contrast to their family member IL-10, the most potent anti-inflammatory cytokine. IL-32 is also of interest, with proinflammatory effects both on myeloid and nonmyeloid cells. SUMMARY It is unclear whether the novel cytokines described in the present review will influence clinical practise. The involvement of IL-17 in murine arthritis may not translate as effectively to human arthritis - the ultimate test is a clinical trial in humans. The lack of efficacy of a recent anti-MCP-1/CCL-2 trial in rheumatoid arthritis highlights this dilemma. Finally, while technological advances including microarray analysis have broadened the scope for cytokine detection in rheumatoid arthritis, these methods have yet to translate to therapy in the clinic.
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Affiliation(s)
- Fionula Brennan
- Kennedy Institute of Rheumatology Division, Imperial College London, London, UK.
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47
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Baechler EC, Batliwalla FM, Reed AM, Peterson EJ, Gaffney PM, Moser KL, Gregersen PK, Behrens TW. Gene expression profiling in human autoimmunity. Immunol Rev 2007; 210:120-37. [PMID: 16623768 DOI: 10.1111/j.0105-2896.2006.00367.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human autoimmune diseases are well suited for the application of gene expression profiling. Sampling of blood cells and target tissues has already revealed many important pathways contributing to this spectrum of disorders, and many commonalities are emerging. For instance, clinically distinct diseases such as systemic lupus erythematosus, Sjögren's syndrome, dermatomyositis, and psoriasis all show evidence for dysregulation of the type I interferon pathway. These data suggest that autoimmune diseases will eventually be categorized at the level of gene expression. This work has led to advances in our understanding of disease pathogenesis and in the future promises to facilitate assessments of disease activity and improve targeting of therapies. Here, we review the literature on gene profiling in human autoimmune diseases and provide perspective on the current state of the art.
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Affiliation(s)
- Emily C Baechler
- University of Minnesota Medical School, Minneapolis, MN 55455, USA
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48
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Yu X, Bauer K, Koczan D, Thiesen HJ, Ibrahim SM. Combining global genome and transcriptome approaches to identify the candidate genes of small-effect quantitative trait loci in collagen-induced arthritis. Arthritis Res Ther 2007; 9:R3. [PMID: 17244351 PMCID: PMC1860061 DOI: 10.1186/ar2108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 12/05/2006] [Accepted: 01/23/2007] [Indexed: 11/10/2022] Open
Abstract
Quantitative traits such as complex diseases are controlled by many small-effect genes that are difficult to identify. Here we present a novel strategy to identify the candidate genes for small-effect quantitative trait loci (QTL) in collagen induced arthritis (CIA) using global genome and transcriptome approaches. First, we performed genome linkage analysis in F2 progeny of the CIA susceptible and resistant strains to search for small-effect QTL. Second, we detected gene expression patterns of both strains during CIA. The candidate genes were identified using three criteria: they are located in a genomic region linked to CIA; they are disease-specific differentially expressed during CIA; and they are strain-specific differentially expressed regarding the two parental strains. Eight small-effect QTL controlling CIA severity were identified. Of 22,000 screened genes, 117 were both strain-specific and disease-specific differentially expressed during CIA. Of these 117 genes, 21 were located inside the support intervals of the 8 small-effect QTL and thus were considered as candidate genes.
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Affiliation(s)
- Xinhua Yu
- Immunogenetics Group, University of Rostock, Schillingallee, 18055 Rostock, Germany
| | - Kristin Bauer
- Immunogenetics Group, University of Rostock, Schillingallee, 18055 Rostock, Germany
| | - Dirk Koczan
- Institute for Immunology, University of Rostock, Schillingallee, 18055 Rostock, Germany
| | - Hans-Jürgen Thiesen
- Institute for Immunology, University of Rostock, Schillingallee, 18055 Rostock, Germany
| | - Saleh M Ibrahim
- Immunogenetics Group, University of Rostock, Schillingallee, 18055 Rostock, Germany
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49
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Larsen A, Bronstein IB, Dahl O, Wentzel-Larsen T, Kristoffersen EK, Fagerhol MK. Quantification of S100A12 (EN-RAGE) in Blood Varies with Sampling Method, Calcium and Heparin. Scand J Immunol 2007; 65:192-201. [PMID: 17257225 DOI: 10.1111/j.1365-3083.2006.01875.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
S100A12 is a calcium-binding protein predominantly found in neutrophil granulocytes and monocytes. Its usefulness in monitoring inflammatory disease states depends on documentation that assay results are reliable. This study aimed at defining guidelines for blood sampling, selection of optimal material handling and reference intervals in healthy controls while taking into account the basic features of S100A12. An enzyme linked immunosorbent assay was developed based upon antibodies induced in rabbits by injection of recombinant S100A12. Our studies confirm that oligomers of S100A12 are generated in the presence of calcium. Structural changes in S100A12 mediated by calcium influence the interaction with antibody. This is proposed as the background for our very low readings of S100A12 in Ethylene Diamine Tetraacetic Acid (EDTA) plasma. Individual S100A12 levels did not change substantially over a 5-week sampling period. Based upon testing of 150 blood donors we suggest reference intervals of S100A12 in serum to be 49-1340 microg/l for women and 27-1750 microg/l for men. The estimated mean concentrations were 234 microg/l in serum samples (range 12-15791), 114 microg/l (range 3-17282) in re-calcified EDTA plasma and 48 microg/l (range 2-14843) in heparin plasma. Without adding calcium to EDTA plasma before running the assay, concentrations were around 2 microg/l (16 persons). S100A12 quantification is assumed to become relevant for diagnostic use in many disease states. The importance of the handling and analysing conditions for a reliable result was examined. We recommend serum collected in gel-containing tubes as the preferred sample material and have suggested reference intervals for healthy individuals.
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Affiliation(s)
- A Larsen
- Section of Oncology, Institute of Internal Medicine, University of Bergen, Bergen, Norway.
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50
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van der Pouw Kraan TCTM, Wijbrandts CA, van Baarsen LGM, Voskuyl AE, Rustenburg F, Baggen JM, Ibrahim SM, Fero M, Dijkmans BAC, Tak PP, Verweij CL. Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 2007; 66:1008-14. [PMID: 17223656 PMCID: PMC1954704 DOI: 10.1136/ard.2006.063412] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a heterogeneous disease with unknown cause. AIM To identify peripheral blood (PB) gene expression profiles that may distinguish RA subtypes. METHODS Large-scale expression profiling by cDNA microarrays was performed on PB from 35 patients and 15 healthy individuals. Differential gene expression was analysed by significance analysis of microarrays (SAM), followed by gene ontology analysis of the significant genes. Gene set enrichment analysis was applied to identify pathways relevant to disease. RESULTS A substantially raised expression of a spectrum of genes involved in immune defence was found in the PB of patients with RA compared with healthy individuals. SAM analysis revealed a highly significant elevated expression of interferon (IFN) type I regulated genes in patients with RA compared with healthy individuals, which was confirmed by gene ontology and pathway analysis, suggesting that this pathway was activated systemically in RA. A quantitative analysis revealed that increased expression of IFN-response genes was characteristic of approximately half of the patients (IFN(high) patients). Application of pathway analysis revealed that the IFN(high) group was largely different from the controls, with evidence for upregulated pathways involved in coagulation and complement cascades, and fatty acid metabolism, while the IFN(low) group was similar to the controls. CONCLUSION The IFN type I signature defines a subgroup of patients with RA, with a distinct biomolecular phenotype, characterised by increased activity of the innate defence system, coagulation and complement cascades, and fatty acid metabolism.
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Affiliation(s)
- T C T M van der Pouw Kraan
- Department of Molecular and Cellular Biology & Immunology, VU Medical Centre, J295, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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