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Prada-Luengo I, Schuster V, Liang Y, Terkelsen T, Sora V, Krogh A. N-of-one differential gene expression without control samples using a deep generative model. Genome Biol 2023; 24:263. [PMID: 37974217 PMCID: PMC10655485 DOI: 10.1186/s13059-023-03104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls, trained solely on healthy tissues. The unsupervised model learns a low-dimensional representation and can identify the closest normal representation for a given disease sample. This enables control-free, single-sample differential expression analysis. In breast cancer, we demonstrate how our approach selects marker genes and outperforms a state-of-the-art method. Furthermore, significant genes identified by the model are enriched in driver genes across cancers. Our results show that the in silico closest normal provides a more favorable comparison than control samples.
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Affiliation(s)
- Iñigo Prada-Luengo
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Viktoria Schuster
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Yuhu Liang
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Thilde Terkelsen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Valentina Sora
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Anders Krogh
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark.
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Clemente-Suárez VJ, Martín-Rodríguez A, Redondo-Flórez L, López-Mora C, Yáñez-Sepúlveda R, Tornero-Aguilera JF. New Insights and Potential Therapeutic Interventions in Metabolic Diseases. Int J Mol Sci 2023; 24:10672. [PMID: 37445852 DOI: 10.3390/ijms241310672] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Endocrine homeostasis and metabolic diseases have been the subject of extensive research in recent years. The development of new techniques and insights has led to a deeper understanding of the mechanisms underlying these conditions and opened up new avenues for diagnosis and treatment. In this review, we discussed the rise of metabolic diseases, especially in Western countries, the genetical, psychological, and behavioral basis of metabolic diseases, the role of nutrition and physical activity in the development of metabolic diseases, the role of single-cell transcriptomics, gut microbiota, epigenetics, advanced imaging techniques, and cell-based therapies in metabolic diseases. Finally, practical applications derived from this information are made.
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Affiliation(s)
- Vicente Javier Clemente-Suárez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain
- Grupo de Investigación en Cultura, Educación y Sociedad, Universidad de la Costa, Barranquilla 080002, Colombia
| | | | - Laura Redondo-Flórez
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Tajo Street s/n, 28670 Villaviciosa de Odon, Spain
| | - Clara López-Mora
- Facultad de Ciencias Biomédicas y de la Salud, Universidad Europea de Valencia, Pg. de l'Albereda, 7, 46010 València, Spain
| | - Rodrigo Yáñez-Sepúlveda
- Faculty of Education and Social Sciences, Universidad Andres Bello, Viña del Mar 2520000, Chile
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3
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Sokouti B. A systems biology approach for investigating significantly expressed genes among COVID-19, hepatocellular carcinoma, and chronic hepatitis B. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:146. [PMID: 37521843 PMCID: PMC9584277 DOI: 10.1186/s43042-022-00360-3] [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: 05/02/2022] [Accepted: 10/12/2022] [Indexed: 01/08/2023] Open
Abstract
Background Worldwide, COVID-19's death rate is about 2%, considering the incidence and mortality. However, the information on its complications in other organs, specifically the liver and its disorders, is limited in mild or severe cases. In this study, we aimed to computationally investigate the typical relationships between liver-related diseases [i.e., hepatocellular carcinoma (HCC), and chronic hepatitis B (CHB)] and COVID-19, considering the involved significant genes and their molecular mechanisms. Methods We investigated two GEO microarray datasets (GSE164805 and GSE58208) to identify differentially expressed genes (DEGs) among the generated four datasets for mild/severe COVID-19, HCC, and CHB. Then, the overlapping genes among them were identified for GO and KEGG enrichment analyses, protein-protein interaction network construction, hub genes determination, and their associations with immune cell infiltration. Results A total of 22 significant genes (i.e., ACTB, ATM, CDC42, DHX15, EPRS, GAPDH, HIF1A, HNRNPA1, HRAS, HSP90AB1, HSPA8, IL1B, JUN, POLR2B, PTPRC, RPS27A, SFRS1, SMARCA4, SRC, TNF, UBE2I, and VEGFA) were found to play essential roles among mild/severe COVID-19 associated with HCC and CHB. Moreover, the analysis of immune cell infiltration revealed that these genes are mostly positively correlated with tumor immune and inflammatory responses. Conclusions In summary, the current study demonstrated that 22 identified DEGs might play an essential role in understanding the associations between the mild/severe COVID-19 patients with HCC and CHB. So, the HCC and CHB patients involved in different types of COVID-19 can benefit from immune-based targets for therapeutic interventions. Supplementary Information The online version contains supplementary material available at 10.1186/s43042-022-00360-3.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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4
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Epigenetically-regulated RPN2 gene influences lymphocyte activation and is involved in pathogenesis of rheumatoid arthritis. Gene 2021; 810:146059. [PMID: 34740730 DOI: 10.1016/j.gene.2021.146059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND To identify RA-associated genes and to ascertain epigenetic factors and functional mechanisms underlying RA pathogenesis. METHODS Peripheral blood mononuclear cells (PBMC) transcriptome- and proteome- wide gene expressions were profiled in a case-control study sample. Differentially expressed genes (DEGs) were discovered and validated independently. In-house PBMC genome-wide SNP genotyping data, miRNA expression data and DNA methylation data in the same sample were utilized to identify SNPs [expression quantitative trait locus (eQTLs) and protein quantitative trait locus (pQTLs)], miRNAs, and DNA methylation positions (DMPs) regulating key DEG of interest. Lentivirus transfection was conducted to study the effects of RPN2 on T lymphocyte activation, proliferation, apoptosis, and inflammatory cytokine expression. Rpn2 protein level in plasma was quantitated by ELISA to assess its performance in discriminating RA cases and controls. RESULTS Twenty-two DEGs were discovered in PBMCs. The most significant DEG, i.e., RPN2, was validated to be up-regulated with RA in PBMCs. A complex regulatory network for RPN2 gene expression in PBMCs was constructed, which consists of 38 eQTL and 53 pQTL SNPs, 3 miRNAs and 2 DMPs. Besides, RPN2 expression was significantly up-regulated with RA in primary T lymphocytes, as well as in PHA-activated T lymphocytes. RPN2 over-expression in T lymphocytes significantly inhibited apoptosis and IL-4 expression and promoted proliferation and activation. PBMCs-expressed RPN2 mRNA and plasma Rpn2 protein demonstrated superior and modest performances in discriminating RA cases and controls, respectively. CONCLUSIONS RPN2 gene influences T lymphocyte growth and activation and is involved in the pathogenesis of RA. Rpn2 may serve as a novel protein biomarker for RA diagnosis.
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Harrison SR, Burska AN, Emery P, Marzo-Ortega H, Ponchel F. Interferon-related gene expression in response to TNF inhibitor treatment in ankylosing spondylitis patients: a pilot study. Rheumatology (Oxford) 2021; 60:3607-3616. [PMID: 33393636 DOI: 10.1093/rheumatology/keaa817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/07/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE Ankylosing spondylitis (AS) is a chronic inflammatory arthritis primarily affecting the spine and sacroiliac joints. TNF inhibitor (TNFi) drugs are recommended for patients not responding to NSAIDs; however, there is a significant need for biomarkers of response. IFN-regulated genes (IRGs) and other cytokines/chemokines are linked to autoimmune diseases and have been associated with treatment response. Our objective was to explore whether IRGs and cytokines/chemokines can be associated with response to TNFiagents in AS. METHODS Peripheral blood mononuclear cells were obtained from 26 AS patients who were to receive a TNFi (I, n = 15) or placebo (P, n = 11) at week 0 and week 22. Response (R)/non-response (NR) was defined as reduction in ASDAS ≥ 1.2 points or reduction in sacroiliac/vertebral MRI lesions. The expression of 96 genes was quantified using TaqMan assays. Finally, ELISA was used to measure IL-6 in serum samples from another 38 AS patients. RESULTS Analysis of gene expression in 26 baseline samples segregated patients into four groups defined by a signature of 15 genes (mainly IRGs). ASDAS response was associated with one group independently of treatment received. We then analysed response to the TNFi (n = 15) and identified a 12-gene signature associated with MRI response. A third IRG signature was also associated with a reduction in IRGs expression post-TNFi samples (n = 10 pairs). Finally, decreased circulating IL-6 was associated with BASDAI-R. CONCLUSION This pilot study suggests an association between IRG expression and response to TNFi in AS. These findings require validation in a larger cohort in order to construct predictive algorithms for patient stratification.
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Affiliation(s)
- Stephanie R Harrison
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - Agata N Burska
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - Paul Emery
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Helena Marzo-Ortega
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Frederique Ponchel
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
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Bai H, Wang Y, Liu H, Lu J. Development of a Four-mRNA Expression-Based Prognostic Signature for Cutaneous Melanoma. Front Genet 2021; 12:680617. [PMID: 34335689 PMCID: PMC8320537 DOI: 10.3389/fgene.2021.680617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 01/22/2023] Open
Abstract
We aim to find a biomarker that can effectively predict the prognosis of patients with cutaneous melanoma (CM). The RNA sequencing data of CM was downloaded from The Cancer Genome Atlas (TCGA) database and randomly divided into training group and test group. Survival statistical analysis and machine-learning approaches were performed on the RNA sequencing data of CM to develop a prognostic signature. Using univariable Cox proportional hazards regression, random survival forest algorithm, and receiver operating characteristic (ROC) in the training group, the four-mRNA signature including CD276, UQCRFS1, HAPLN3, and PIP4P1 was screened out. The four-mRNA signature could divide patients into low-risk and high-risk groups with different survival outcomes (log-rank p < 0.001). The predictive efficacy of the four-mRNA signature was confirmed in the test group, the whole TCGA group, and the independent GSE65904 (log-rank p < 0.05). The independence of the four-mRNA signature in prognostic prediction was demonstrated by multivariate Cox analysis. ROC and timeROC analyses showed that the efficiency of the signature in survival prediction was better than other clinical variables such as melanoma Clark level and tumor stage. This study highlights that the four-mRNA model could be used as a prognostic signature for CM patients with potential clinical application value.
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Affiliation(s)
- Haiya Bai
- Department of Female Plastic Surgery, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Youliang Wang
- Department of Pediatric Surgery, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Huimin Liu
- Department of Female Plastic Surgery, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Junyang Lu
- Department of Female Plastic Surgery, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
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7
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Zhang Q, Liu W, Luo SB, Xie FC, Liu XJ, Xu RA, Chen L, Su Z. Development of a Prognostic Five-Gene Signature for Diffuse Lower-Grade Glioma Patients. Front Neurol 2021; 12:633390. [PMID: 34295296 PMCID: PMC8291287 DOI: 10.3389/fneur.2021.633390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/02/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Diffuse lower-grade gliomas (LGGs) are infiltrative and heterogeneous neoplasms. Gene signature including multiple protein-coding genes (PCGs) is widely used as a tumor marker. This study aimed to construct a multi-PCG signature to predict survival for LGG patients. Methods: LGG data including PCG expression profiles and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). Survival analysis, receiver operating characteristic (ROC) analysis, and random survival forest algorithm (RSFVH) were used to identify the prognostic PCG signature. Results: From the training (n = 524) and test (n = 431) datasets, a five-PCG signature which can classify LGG patients into low- or high-risk group with a significantly different overall survival (log rank P < 0.001) was screened out and validated. In terms of prognosis predictive performance, the five-PCG signature is stronger than other clinical variables and IDH mutation status. Moreover, the five-PCG signature could further divide radiotherapy patients into two different risk groups. GO and KEGG analysis found that PCGs in the prognostic five-PCG signature were mainly enriched in cell cycle, apoptosis, DNA replication pathways. Conclusions: The new five-PCG signature is a reliable prognostic marker for LGG patients and has a good prospect in clinical application.
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Affiliation(s)
- Qiang Zhang
- Department of Clinical Laboratory, The People's Hospital of Lishui, Lishui, China
| | - Wenhao Liu
- Guangdong-Hong Kong-Macao Greater Bay Area (GBA) Research Innovation Institute for Nanotechnology, Guangzhou, China
| | - Shun-Bin Luo
- Department of Clinical Pharmacy, The People's Hospital of Lishui, Lishui, China
| | - Fu-Chen Xie
- Department of Urinary Surgery, The People's Hospital of Lishui, Lishui, China
| | - Xiao-Jun Liu
- Pathology Department, The People's Hospital of Lishui, Lishui, China
| | - Ren-Ai Xu
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lixi Chen
- Department of Gynecology in Xiahe Branch, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Zhilin Su
- Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
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8
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Duderstadt EL, Sanders MA, Samuelson DJ. A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscope. J Mammary Gland Biol Neoplasia 2021; 26:113-120. [PMID: 33866475 DOI: 10.1007/s10911-021-09484-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022] Open
Abstract
RNAscope is a quantitative in situ gene expression measurement technique that preserves the spatial aspect of intact tissue; thus, allowing for comparison of specific cell populations and morphologies. Reliable and accurate measurement of gene expression in tissue is dependent on preserving RNA integrity and the quantitative nature of RNAscope. The purpose of this study was to determine if the quantitative nature of RNAscope was retained following processing and carmine staining of mammary gland whole-mounts, which are commonly used to identify lesions, such as hyperplasia and ductal carcinoma in situ (DCIS). We were concerned that handling and procedures required to visualize microscopic disease lesions might compromise RNA integrity and the robustness of RNAscope. No effect on the quantitative abilities of RNAscope was detected when mammary gland whole-mounts were pre-screened for lesions of interest prior to RNAscope. This was determined in comparison to tissue that had been formalin-fixed and paraffin embedded (FFPE) immediately after collection. The ability to pre-screen whole-mounts allowed unpalpable diseased lesions to be identified without labor-intensive serial sectioning of tissue samples to find diseased tissue. This method is applicable to evaluate mammary gland whole-mounts during normal mammary gland development, function, and disease progression.
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MESH Headings
- 9,10-Dimethyl-1,2-benzanthracene/administration & dosage
- 9,10-Dimethyl-1,2-benzanthracene/toxicity
- Animals
- Carcinogens/administration & dosage
- Carcinogens/toxicity
- Carcinoma, Intraductal, Noninfiltrating/chemically induced
- Carcinoma, Intraductal, Noninfiltrating/diagnosis
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Disease Models, Animal
- Female
- Gene Expression Profiling/methods
- Mammary Glands, Animal/pathology
- Mammary Neoplasms, Experimental/chemically induced
- Mammary Neoplasms, Experimental/diagnosis
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/pathology
- RNA/metabolism
- Rats
- Tissue Preservation/methods
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Affiliation(s)
- Emily L Duderstadt
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mary Ann Sanders
- Department of Pathology, University of Louisville School of Medicine, Louisville, KY, USA
| | - David J Samuelson
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
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Guo JC, Wei QS, Dong L, Fang SS, Li F, Zhao Y. Prognostic Value of an Autophagy-Related Five-Gene Signature for Lower-Grade Glioma Patients. Front Oncol 2021; 11:644443. [PMID: 33768004 PMCID: PMC7985555 DOI: 10.3389/fonc.2021.644443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Molecular characteristics can be good indicators of tumor prognosis and have been introduced into the classification of gliomas. The prognosis of patients with newly classified lower-grade gliomas (LGGs, including grade 2 and grade 3 gliomas) is highly heterogeneous, and new molecular markers are urgently needed. Methods: Autophagy related genes (ATGs) were obtained from Human Autophagy Database (HADb). From the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), gene expression profiles including ATG expression information and patient clinical data were downloaded. Cox regression analysis, receiver operating characteristic (ROC) analysis, Kaplan–Meier analysis, random survival forest algorithm (RSFVH) and stratification analysis were performed. Results: Through univariate Cox regression analysis, we found a total of 127 ATGs associated with the prognosis of LGG patients from TCGA dataset and a total of 131 survival-related ATGs from CGGA dataset. Using TCGA dataset as the training group (n = 524), we constructed a five-ATG signature (including BAG1, BID, MAP1LC3C, NRG3, PTK6), which could divide LGG patients into two risk groups with significantly different overall survival (Log Rank P < 0.001). Then we confirmed in the independent CGGA dataset that the five-ATG signature had the ability to predict prognosis (n = 431, Log Rank P < 0.001). We further discovered that the predictive ability of the five-ATG signature was better than the existing clinical indicators and IDH mutation status. In addition, the five-ATG signature could further classify patients after receiving radiotherapy or chemotherapy into groups with different prognosis. Conclusions: We identified a five-ATG signature that could be a reliable prognostic marker and might be therapeutic targets for autophagy therapy for LGG patients.
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Affiliation(s)
- Jin-Cheng Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qing-Shuang Wei
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Dong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Shuang-Sang Fang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Feng Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yi Zhao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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10
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Alolga RN, Opoku-Damoah Y, Alagpulinsa DA, Huang FQ, Ma G, Chavez Leon MASC, Kudzai C, Yin X, Ding Y. Metabolomic and transcriptomic analyses of the anti-rheumatoid arthritis potential of xylopic acid in a bioinspired lipoprotein nanoformulation. Biomaterials 2020; 268:120482. [PMID: 33307367 DOI: 10.1016/j.biomaterials.2020.120482] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/18/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023]
Abstract
Xylopic acid (XA), a diterpene kaurene and the major active ingredient of the African spice Xylopia aethiopica (Annonaceae), is reported to possess anti-inflammatory and analgesic properties. Here, we investigated the therapeutic potential of XA for rheumatoid arthritis (RA), a debilitating autoimmune inflammatory disease characterized by joint damage, in the complete Freund's adjuvant (CFA)-induced arthritis model in rats. We synthesized bioinspired reconstituted high-density lipoprotein (rHDL) nanoparticles loaded with purified XA crystals (rHDL/XA) that passively accumulate in inflamed joints of CFA-induced arthritic rats. Treatment with rHDL/XA minimized mononuclear cell infiltration of CFA-induced arthritic sites and ameliorated disease burden. Metabolomic and transcriptomic analyses revealed that the major molecular pathways perturbed following CFA-induced arthritis correlated with amino acid and lipid metabolism, which were restored to normal states by rHDL/XA treatment. This work demonstrates the anti-RA potential of XA in a nanoformulation and uncovers its underlying therapeutic mechanisms at the transcript and metabolite levels.
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Affiliation(s)
- Raphael N Alolga
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Yaw Opoku-Damoah
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David A Alagpulinsa
- Massachusetts General Hospital Vaccine & Immunotherapy Center, Harvard Medical School, Boston, MA, 02129, USA
| | - Feng-Qing Huang
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Gaoxiang Ma
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Maria A S C Chavez Leon
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Chifodya Kudzai
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Xiaojian Yin
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China.
| | - Yang Ding
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
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Pacheco C, Ceccatto VM, Maia CM, Rosa SDSRF, Leite CRM. Pesquisa translacional na era pós-genômica: avanços na área da transcriptômica. SAÚDE EM DEBATE 2019. [DOI: 10.1590/0103-11042019s213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
RESUMO A pesquisa translacional envolve a interface entre a pesquisa básica e a clínica médica com o intuito de gerar produtos ou processos inovadores para introduzi-los nos protocolos clínicos e nos sistemas de saúde. O objetivo desse ensaio foi apresentar uma visão geral dos avanços da transcriptômica, subsidiados pela disponibilidade e utilização das novas tecnologias da informação e biologia molecular. Na busca pelo diagnóstico preciso e menos invasivo, testes transcriptômicos utilizam assinaturas de expressão gênica visando detectar doenças neurodegenerativas (Parkinson e Alzheimer), autoimunes (lúpus eritematoso sistêmico, granulomatose de Wegener), insuficiência cardíaca, autismo e câncer (de mama, colorretal, hepático e de pulmão). No sistema de saúde inglês as diretrizes clínicas incorporam oito testes transcriptômicos, todos com foco no câncer. No Brasil testes genômicos com base nas sequências de DNA são regulamentados para diagnosticar anomalias congênitas, tanto no Sistema Único de Saúde, como na saúde suplementar, mas os testes moleculares não avançaram no âmbito da transcriptômica diagnóstica. O sistema de saúde brasileiro deveria ir além dos testes de análise genômica e iniciar o processo de regulamentação das tecnologias transcriptômicas de diagnóstico. No futuro, testes diagnósticos avaliando múltiplos perfis de expressão gênica podem se transformar em exames de rotina numa forma de triagem molecular.
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Karagianni N, Kranidioti K, Fikas N, Tsochatzidou M, Chouvardas P, Denis MC, Kollias G, Nikolaou C. An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis. PLoS Comput Biol 2019; 15:e1006933. [PMID: 31071076 PMCID: PMC6508611 DOI: 10.1371/journal.pcbi.1006933] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/09/2019] [Indexed: 12/22/2022] Open
Abstract
Anti-TNF agents have been in the first line of treatment of various inflammatory diseases such as Rheumatoid Arthritis and Crohn’s Disease, with a number of different biologics being currently in use. A detailed analysis of their effect at transcriptome level has nevertheless been lacking. We herein present a concise analysis of an extended transcriptomics profiling of four different anti-TNF biologics upon treatment of the established hTNFTg (Tg197) mouse model of spontaneous inflammatory polyarthritis. We implement a series of computational analyses that include clustering of differentially expressed genes, functional analysis and random forest classification. Taking advantage of our detailed sample structure, we devise metrics of treatment efficiency that take into account changes in gene expression compared to both the healthy and the diseased state. Our results suggest considerable variability in the capacity of different biologics to modulate gene expression that can be attributed to treatment-specific functional pathways and differential preferences to restore over- or under-expressed genes. Early intervention appears to manage inflammation in a more efficient way but is accompanied by increased effects on a number of genes that are seemingly unrelated to the disease. Administration at an early stage is also lacking in capacity to restore healthy expression levels of under-expressed genes. We record quantifiable differences among anti-TNF biologics in their efficiency to modulate over-expressed genes related to immune and inflammatory pathways. More importantly, we find a subset of the tested substances to have quantitative advantages in addressing deregulation of under-expressed genes involved in pathways related to known RA comorbidities. Our study shows the potential of transcriptomic analyses to identify comprehensive and distinct treatment-specific gene signatures combining disease-related and unrelated genes and proposes a generalized framework for the assessment of drug efficacy, the search of biosimilars and the evaluation of the efficacy of TNF small molecule inhibitors. A number of anti-TNF drugs are being used in the treatment of inflammatory autoimmune diseases, such as Rheumatoid Arthritis and Crohn’s Disease. Despite their wide use there has been, to date, no detailed analysis of their effect on the affected tissues at a transcriptome level. In this work we applied four different anti-TNF drugs on an established mouse model of inflammatory polyarthritis and collected a large number of independent biological replicates from the synovial tissue of healthy, diseased and treated animals. We then applied a series of bioinformatics analyses in order to define the sets of genes, biological pathways and functions that are affected in the diseased animals and modulated by each of the different treatments. Our dataset allowed us to focus on previously overlooked aspects of gene regulation. We found that the majority of differentially expressed genes in disease are under-expressed and that they are also associated with functions related to Rheumatoid Arthritis comorbidities such as cardiovascular disease. We were also able to define gene and pathway subsets that are not changed in the disease but are, nonetheless, altered under various treatments and to use these subsets in drug classification and assessment. Through the application of machine learning approaches we created quantitative efficiency profiles for the tested drugs, which showed some to be more efficiently addressing changes in the inflammatory pathways, while others being quantitatively superior in restoring gene expression changes associated to disease comorbidities. We thus, propose a concise computational pipeline that may be used in the assessment of drug efficacy and biosimilarity and which may form the basis of evaluation protocols for small molecule TNF inhibitors.
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Affiliation(s)
| | | | - Nikolaos Fikas
- Department of Biology, University of Crete, Heraklion, Greece
| | | | - Panagiotis Chouvardas
- Institute of Immunology, Biomedical Sciences Research Center (BSRC), ‘Alexander Fleming’, Vari, Greece
- Department of Physiology, School of Medicine, National Kapodistrian University, Athens, Greece
| | | | - George Kollias
- Institute of Immunology, Biomedical Sciences Research Center (BSRC), ‘Alexander Fleming’, Vari, Greece
- Department of Physiology, School of Medicine, National Kapodistrian University, Athens, Greece
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology (FORTH), Heraklion, Greece
- * E-mail: (NK); (CN)
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13
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Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients. Clin Immunol 2019; 202:1-10. [PMID: 30831253 DOI: 10.1016/j.clim.2019.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023]
Abstract
Rheumatoid arthritis (RA) is therapeutically challenging due to patient heterogeneity and variability. Herein we describe a novel integration of RA synovial genome-scale transcriptomic profiling of different patient cohorts that can be used to provide predictive insights on drug responses. A normalized compendium consisting of 256 RA synovial samples that cover an intersection of 11,769 genes from 11 datasets was build and compared with similar datasets derived from OA patients and healthy controls. Differentially expression genes (DEGs) that were identified in three independent methods were fed into functional network analysis, with subsequent grouping of the samples based on a non-negative matrix factorization method. RA-relevant pathway activation scores and four machine learning classification techniques supported the generation of a predictive model of patient treatment response. We identified 876 up-regulated DEGs including 24 known genetic risk factors and 8 drug targets. DEG-based subgrouping revealed 3 distinct RA patient clusters with distinct activity signatures for RA-relevant pathways. In the case of infliximab, we constructed a classifier of drug response that was highly accurate with an AUC/AUPR of 0.92/0.86. The most informative pathways in achieving this performance were the NFκB-, FcεRI- TCR-, and TNF signaling pathways. Similarly, the expression of the HMMR, PRPF4B, EVI2A, RAB27A, MALT1, SNX6, and IFIH1 genes contributed in predicting the patient outcome. Construction and analysis of normalized synovial transcriptomic compendia can provide useful insights for understanding RA-related pathway involvement and drug responses for individual patients.
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14
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Long NP, Park S, Anh NH, Min JE, Yoon SJ, Kim HM, Nghi TD, Lim DK, Park JH, Lim J, Kwon SW. Efficacy of Integrating a Novel 16-Gene Biomarker Panel and Intelligence Classifiers for Differential Diagnosis of Rheumatoid Arthritis and Osteoarthritis. J Clin Med 2019; 8:E50. [PMID: 30621359 PMCID: PMC6352223 DOI: 10.3390/jcm8010050] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022] Open
Abstract
Introducing novel biomarkers for accurately detecting and differentiating rheumatoid arthritis (RA) and osteoarthritis (OA) using clinical samples is essential. In the current study, we searched for a novel data-driven gene signature of synovial tissues to differentiate RA from OA patients. Fifty-three RA, 41 OA, and 25 normal microarray-based transcriptome samples were utilized. The area under the curve random forests (RF) variable importance measurement was applied to seek the most influential differential genes between RA and OA. Five algorithms including RF, k-nearest neighbors (kNN), support vector machines (SVM), naïve-Bayes, and a tree-based method were employed for the classification. We found a 16-gene signature that could effectively differentiate RA from OA, including TMOD1, POP7, SGCA, KLRD1, ALOX5, RAB22A, ANK3, PTPN3, GZMK, CLU, GZMB, FBXL7, TNFRSF4, IL32, MXRA7, and CD8A. The externally validated accuracy of the RF model was 0.96 (sensitivity = 1.00, specificity = 0.90). Likewise, the accuracy of kNN, SVM, naïve-Bayes, and decision tree was 0.96, 0.96, 0.96, and 0.91, respectively. Functional meta-analysis exhibited the differential pathological processes of RA and OA; suggested promising targets for further mechanistic and therapeutic studies. In conclusion, the proposed genetic signature combined with sophisticated classification methods may improve the diagnosis and management of RA patients.
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Affiliation(s)
- Nguyen Phuoc Long
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Seongoh Park
- Department of Statistics, Seoul National University, Seoul 08826, Korea.
| | - Nguyen Hoang Anh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Jung Eun Min
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Sang Jun Yoon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Hyung Min Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Tran Diem Nghi
- School of Medicine, Vietnam National University, Ho Chi Minh 700000, Vietnam.
| | - Dong Kyu Lim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Jeong Hill Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul 08826, Korea.
| | - Sung Won Kwon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
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15
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Ashton MP, Eugster A, Dietz S, Loebel D, Lindner A, Kuehn D, Taranko AE, Heschel B, Gavrisan A, Ziegler AG, Aringer M, Bonifacio E. Association of Dendritic Cell Signatures With Autoimmune Inflammation Revealed by Single-Cell Profiling. Arthritis Rheumatol 2018; 71:817-828. [PMID: 30511817 DOI: 10.1002/art.40793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/29/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To identify single-cell transcriptional signatures of dendritic cells (DCs) that are associated with autoimmunity, and determine whether those DC signatures are correlated with the clinical heterogeneity of autoimmune disease. METHODS Blood-derived DCs were single-cell sorted from the peripheral blood of patients with rheumatoid arthritis, systemic lupus erythematosus, or type 1 diabetes as well as healthy individuals. DCs were analyzed using single-cell gene expression assays, performed immediately after isolation or after in vitro stimulation of the cells. In addition, protein expression was measured using fluorescence-activated cell sorting. RESULTS CD1c+ conventional DCs and plasmacytoid DCs from healthy individuals exhibited diverse transcriptional signatures, while the DC transcriptional signatures in patients with autoimmune disease were altered. In particular, distinct DC clusters, characterized by up-regulation of TAP1, IRF7, and IFNAR1, were abundant in patients with systemic autoimmune disease, whereas DCs from patients with type 1 diabetes had decreased expression of the regulatory genes PTPN6, TGFB, and TYROBP. The frequency of CD1c+ conventional DCs that expressed a systemic autoimmune profile directly correlated with the extent of disease activity in patients with rheumatoid arthritis (Spearman's r = 0.60, P = 0.03). CONCLUSION DC transcriptional signatures are altered in patients with autoimmune disease and are associated with the level of disease activity, suggesting that immune cell transcriptional profiling could improve our ability to detect and understand the heterogeneity of these diseases, and could guide treatment choices in patients with a complex autoimmune disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Anette-Gabriele Ziegler
- Forschergruppe Diabetes e.V., Institute of Diabetes Research, Helmholtz Zentrum München, and DZD, Neuherberg, Germany
| | | | - Ezio Bonifacio
- TU Dresden, Dresden, Germany, Forschergruppe Diabetes e.V., and DZD, Neuherberg, Germany
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16
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Coras R, Narasimhan R, Guma M. Liquid biopsies to guide therapeutic decisions in rheumatoid arthritis. Transl Res 2018; 201:1-12. [PMID: 30092207 PMCID: PMC6309446 DOI: 10.1016/j.trsl.2018.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 12/18/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic, immune-mediated inflammatory disease that has transitioned from a debilitating disease to a chronic, controllable disease. This has been possible due to the introduction of new treatment strategies like "treat-to-target," in which the clinician treats the patient aggressively enough to reach low disease activity or remission, and the introduction of new therapeutic agents, such as biological therapies, which can lead to the prevention of damage by early diagnosis and initiation of treatment. Attention is now being directed toward identifying the optimal treatment for each patient, one that will be the most efficient and have the least number of side effects. Much work has been done to find serologic and synovial biomarkers of response to various RA treatments. Proteomics, genomics and, in the past few years, metabolomics, have all been used in the quest of identifying these biomarkers. Blood-based liquid biopsies provide a minimally invasive alternative to synovial biopsies to identify cellular and molecular signatures that can be used to longitudinally monitor response and allow for personalized medicine approach. Liquid biopsies are comprised of cell-free DNA, immune circulating cells, and extracellular vesicles, and are being increasingly and successfully used in the field of oncology for diagnosis, progression, prognosis, and prediction of response to treatment. Recently, researchers have also begun investigating the usefulness of liquid biopsies in the field of rheumatology; in this review, we will focus on the potential of liquid biopsy blood samples as biomarkers of response to treatment in patients with RA.
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Affiliation(s)
- Roxana Coras
- Department of Medicine, School of Medicine, La Jolla, California; University of California San Diego, San Diego, California; Department of Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Rekha Narasimhan
- Department of Medicine, School of Medicine, La Jolla, California; University of California San Diego, San Diego, California
| | - Monica Guma
- Department of Medicine, School of Medicine, La Jolla, California; University of California San Diego, San Diego, California; Department of Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain.
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17
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Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis. Arthritis Res Ther 2018; 20:164. [PMID: 30075744 PMCID: PMC6091066 DOI: 10.1186/s13075-018-1655-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022] Open
Abstract
Background Metabolomics is an emerging field of biomedical research that may offer a better understanding of the mechanisms of underlying conditions including inflammatory arthritis. Perturbations caused by inflamed synovial tissue can lead to correlated changes in concentrations of certain metabolites in the synovium and thereby function as potential biomarkers in blood. Here, we explore the hypothesis of whether characterization of patients’ metabolomic profiles in blood, utilizing 1H-nuclear magnetic resonance (NMR), predicts synovial marker profiling in rheumatoid arthritis (RA). Methods Nineteen active, seropositive patients with RA, on concomitant methotrexate, were studied. One of the involved joints was a knee or a wrist appropriate for arthroscopy. A Bruker Avance 700 MHz spectrometer was used to acquire NMR spectra of serum samples. Gene expression in synovial tissue obtained by arthroscopy was analyzed by real-time PCR. Data processing and statistical analysis were performed in Python and SPSS. Results Analysis of the relationships between each synovial marker-metabolite pair using linear regression and controlling for age and gender revealed significant clustering within the data. We observed an association of serine/glycine/phenylalanine metabolism and aminoacyl-tRNA biosynthesis with lymphoid cell gene signature. Alanine/aspartate/glutamate metabolism and choline-derived metabolites correlated with TNF-α synovial expression. Circulating ketone bodies were associated with gene expression of synovial metalloproteinases. Discriminant analysis identified serum metabolites that classified patients according to their synovial marker levels. Conclusion The relationship between serum metabolite profiles and synovial biomarker profiling suggests that NMR may be a promising tool for predicting specific pathogenic pathways in the inflamed synovium of patients with RA. Electronic supplementary material The online version of this article (10.1186/s13075-018-1655-3) contains supplementary material, which is available to authorized users.
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18
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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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19
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Cuppen BVJ, Rossato M, Fritsch-Stork RDE, Concepcion AN, Linn-Rasker SP, Bijlsma JWJ, van Laar JM, Lafeber FPJG, Radstake TR. RNA sequencing to predict response to TNF-α inhibitors reveals possible mechanism for nonresponse in smokers. Expert Rev Clin Immunol 2018; 14:623-633. [PMID: 29808722 DOI: 10.1080/1744666x.2018.1480937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Several studies have employed microarray-based profiling to predict response to tumor necrosis factor-alpha inhibitors (TNFi) in rheumatoid arthritis (RA); yet efforts to validate these targets have failed to show predictive abilities acceptable for clinical practice. METHODS The eighty most extreme responders and nonresponders to TNFi therapy were selected from the observational BiOCURA cohort. RNA sequencing was performed on mRNA from peripheral blood mononuclear cells (PBMCs) collected before initiation of treatment. The expression of pathways as well as individual gene transcripts between responders and nonresponders was investigated. Promising targets were technically replicated and validated in n = 40 new patients using qPCR assays. RESULTS Before therapy initiation, nonresponders had lower expression of pathways related to interferon and cytokine signaling, while also showing higher levels of two genes, GPR15 and SEMA6B (p = 0.02). The two targets could be validated, however, additional analyses revealed that GPR15 and SEMA6B did not independently predict response, but were rather dose-dependent markers of smoking (p < 0.0001). CONCLUSIONS The study did not identify new transcripts ready to use in clinical practice, yet GPR15 and SEMA6B were recognized as candidate explanatory markers for the reduced treatment success in RA smokers.
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Affiliation(s)
- Bart V J Cuppen
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Marzia Rossato
- b Laboratory of Translational Immunology , University Medical Center Utrecht , Utrecht , The Netherlands.,c Department of Biotechnology , University of Verona , Verona , Italy
| | - Ruth D E Fritsch-Stork
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands.,d 1st Medical Department & Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling , Hanusch Hospital , Vienna , Austria.,e Sigmund Freud University , Vienna , Austria
| | - Arno N Concepcion
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | | | - Johannes W J Bijlsma
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Jacob M van Laar
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Floris P J G Lafeber
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Timothy R Radstake
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands.,b Laboratory of Translational Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
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20
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Bullock J, Rizvi SA, Saleh AM, Ahmed SS, Do DP, Ansari RA, Ahmed J. Rheumatoid Arthritis: A Brief Overview of the Treatment. Med Princ Pract 2018; 27:501-507. [PMID: 30173215 PMCID: PMC6422329 DOI: 10.1159/000493390] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 09/02/2018] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory, systemic autoimmune disease, affecting the joints with varying severity among patients. The risk factors include age, gender, genetics, and environmental exposure (cigarette smoking, air pollutants, and occupational). Many complications can follow, such as permanent joint damage requiring arthroplasty, rheumatoid vasculitis, and Felty syndrome requiring splenectomy if it remains unaddressed. As there is no cure for RA, the treatment goals are to reduce the pain and stop/slow further damage. Here, we present a brief summary of various past and present treatment modalities to address the complications associated with RA.
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Affiliation(s)
| | - Syed A.A. Rizvi
- School of Pharmacy, Hampton University, Hampton, Virginia, USA
- *Dr. Syed A.A. Rizvi, Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA 23668 (USA), E-Mail , Dr. Sultan S. Ahmed, College of Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328 (USA), E-Mail , Dr. Ayman M. Saleh, King Saud bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center (KAIMRC), Jeddah, 21423 (Saudi Arabia), E-Mail ,
| | - Ayman M. Saleh
- King Saud bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center (KAIMRC), Jeddah, Saudi Arabia
| | | | - Duc P. Do
- University of Georgia, Athens, Georgia, USA
| | - Rais A. Ansari
- Nova Southeastern University, Fort Lauderdale, Florida, USA
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21
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Lee PH, Lee C, Li X, Wee B, Dwivedi T, Daly M. Principles and methods of in-silico prioritization of non-coding regulatory variants. Hum Genet 2018; 137:15-30. [PMID: 29288389 PMCID: PMC5892192 DOI: 10.1007/s00439-017-1861-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Over a decade of genome-wide association, studies have made great strides toward the detection of genes and genetic mechanisms underlying complex traits. However, the majority of associated loci reside in non-coding regions that are functionally uncharacterized in general. Now, the availability of large-scale tissue and cell type-specific transcriptome and epigenome data enables us to elucidate how non-coding genetic variants can affect gene expressions and are associated with phenotypic changes. Here, we provide an overview of this emerging field in human genomics, summarizing available data resources and state-of-the-art analytic methods to facilitate in-silico prioritization of non-coding regulatory mutations. We also highlight the limitations of current approaches and discuss the direction of much-needed future research.
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Affiliation(s)
- Phil H Lee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA.
- Quantitative Genomics Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Christian Lee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- Department of Life Sciences, Harvard University, Cambridge, MA, USA
| | - Xihao Li
- Quantitative Genomics Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brian Wee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
| | - Tushar Dwivedi
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Mark Daly
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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22
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Tchetina EV. Current and future trends in Russian Rheumatology Care and Research. Mediterr J Rheumatol 2017; 28:201-205. [PMID: 32185283 PMCID: PMC7046001 DOI: 10.31138/mjr.28.4.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/14/2017] [Accepted: 11/28/2017] [Indexed: 11/28/2022] Open
Abstract
This short article provides a description of the present state of rheumatology care and research in Russia and discusses opportunities for development and co-operation.
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Affiliation(s)
- Elena V Tchetina
- Immunology and Molecular Biology Laboratory, Nasonova Research Institute of Rheumatology, Moscow, Russia
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23
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Romão VC, Vital EM, Fonseca JE, Buch MH. Right drug, right patient, right time: aspiration or future promise for biologics in rheumatoid arthritis? Arthritis Res Ther 2017; 19:239. [PMID: 29065909 PMCID: PMC5655983 DOI: 10.1186/s13075-017-1445-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Individualising biologic disease-modifying anti-rheumatic drugs (bDMARDs) to maximise outcomes and deliver safe and cost-effective care is a key goal in the management of rheumatoid arthritis (RA). Investigation to identify predictive tools of bDMARD response is a highly active and prolific area of research. In addition to clinical phenotyping, cellular and molecular characterisation of synovial tissue and blood in patients with RA, using different technologies, can facilitate predictive testing. This narrative review will summarise the literature for the available bDMARD classes and focus on where progress has been made. We will also look ahead and consider the increasing use of ‘omics’ technologies, the potential they hold as well as the challenges, and what is needed in the future to fully realise our ambition of personalised bDMARD treatment.
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Affiliation(s)
- Vasco C Romão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal.,Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Professor Egas Moniz, 1649-035, Lisboa, Portugal
| | - Edward M Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - João Eurico Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal.,Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Professor Egas Moniz, 1649-035, Lisboa, Portugal
| | - Maya H Buch
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK. .,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
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24
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Tchetina EV, Demidova NV, Markova GA, Taskina EA, Glukhova SI, Karateev DE. Increased baseline RUNX2, caspase 3 and p21 gene expressions in the peripheral blood of disease-modifying anti-rheumatic drug-naïve rheumatoid arthritis patients are associated with improved clinical response to methotrexate therapy. Int J Rheum Dis 2017; 20:1468-1480. [PMID: 28741869 DOI: 10.1111/1756-185x.13131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the potential of the baseline gene expression in the whole blood of disease-modifying anti-rheumatic drug-naïve rheumatoid arthritis (RA) patients for predicting the response to methotrexate (MTX) treatment. METHODS Twenty-six control subjects and 40 RA patients were examined. Clinical, immunological and radiographic parameters were assessed before and after 24 months of follow-up. The gene expressions in the whole blood were measured using real-time reverse transcription polymerase chain reaction. The protein concentrations in peripheral blood mononuclear cells were quantified using enzyme-linked immunosorbent assay. Receiver operating characteristic curve analyses were used to suggest thresholds that were associated with the prediction of the response. RESULTS Decreases in the disease activity at the end of the study were accompanied by significant increases in joint space narrowing score (JSN). Positive correlations between the expressions of the Unc-51-like kinase 1 (ULK1) and matrix metalloproteinase 9 (MMP-9) genes with the level of C-reactive protein and MMP-9 expression with Disease Activity Score of 28 joints (DAS28) and swollen joint count were noted at baseline. The baseline tumor necrosis factor (TNF)α gene expression was positively correlated with JSN at the end of the follow-up, whereas p21, caspase 3, and runt-related transcription factor (RUNX)2 were correlated with the ΔDAS28 values. CONCLUSIONS Our results suggest that the expressions of MMP-9 and ULK1 might be associated with disease activity. Increased baseline gene expressions of RUNX2, p21 and caspase 3 in the peripheral blood might predict better responses to MTX therapy.
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Affiliation(s)
- Elena V Tchetina
- Immunology & Molecular Biology Laboratory, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Natalia V Demidova
- Early Rheumatoid Arthritis Department, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Galina A Markova
- Immunology & Molecular Biology Laboratory, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Elena A Taskina
- Osteoarthritis Laboratory, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Svetlana I Glukhova
- Statistics Department, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Dmitry E Karateev
- Early Rheumatoid Arthritis Department, Nasonova Research Institute of Rheumatology, Moscow, Russia
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Derambure C, Dzangue-Tchoupou G, Berard C, Vergne N, Hiron M, D'Agostino MA, Musette P, Vittecoq O, Lequerré T. Pre-silencing of genes involved in the electron transport chain (ETC) pathway is associated with responsiveness to abatacept in rheumatoid arthritis. Arthritis Res Ther 2017; 19:109. [PMID: 28545499 PMCID: PMC5445375 DOI: 10.1186/s13075-017-1319-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background In the current context of personalized medicine, one of the major challenges in the management of rheumatoid arthritis (RA) is to identify biomarkers that predict drug responsiveness. From the European APPRAISE trial, our main objective was to identify a gene expression profile associated with responsiveness to abatacept (ABA) + methotrexate (MTX) and to understand the involvement of this signature in the pathophysiology of RA. Methods Whole human genome microarrays (4 × 44 K) were performed from a first subset of 36 patients with RA. Data validation by quantitative reverse-transcription (qRT)-PCR was performed from a second independent subset of 32 patients with RA. Gene Ontology and WikiPathways database allowed us to highlight the specific biological mechanisms involved in predicting response to ABA/MTX. Results From the first subset of 36 patients with RA, a combination including 87 transcripts allowed almost perfect separation between responders and non-responders to ABA/MTX. Next, the second subset of patients 32 with RA allowed validation by qRT-PCR of a minimal signature with only four genes. This latter signature categorized 81% of patients with RA with 75% sensitivity, 85% specificity and 85% negative predictive value. This combination showed a significant enrichment of genes involved in electron transport chain (ETC) pathways. Seven transcripts from ETC pathways (NDUFA6, NDUFA4, UQCRQ, ATP5J, COX7A2, COX7B, COX6A1) were significantly downregulated in responders versus non-responders to ABA/MTX. Moreover, dysregulation of these genes was independent of inflammation and was specific to ABA response. Conclusion Pre-silencing of ETC genes is associated with future response to ABA/MTX and might be a crucial key to susceptibility to ABA response. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1319-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Derambure
- Normandie Univ, UNIROUEN, Inserm U 1245, F 76000, Rouen, France
| | | | - C Berard
- LITIS EA 4108, Computer science, information processing and systems laboratory, Normandy University, Institute for Research and Innovation in Biomedicine, 76451, Mont-Saint-Aignan, France
| | - N Vergne
- LMRS UMR 6085 CNRS, Raphaël Salem laboratory, Normandy University, 76575, Saint Étienne du Rouvray, France
| | - M Hiron
- Normandie Univ, UNIROUEN, Inserm U 905, F 76000, Rouen, France
| | - M A D'Agostino
- Departement of Rheumatology, AP-HP Ambroise Paré Hospital, University of Versailles Saint Quentin en Yvelines, 92100, Boulogne-Billancourt, France
| | - P Musette
- Normandie Univ, UNIROUEN, Inserm U 1234, Rouen University Hospital, Department of Dermatology, F 76000, Rouen, France
| | - O Vittecoq
- Normandie Univ, UNIROUEN, Inserm U 1234, Inserm CIC-CRB 1404, Rouen University Hospital, Department of Dermatology, F 76000, Rouen, France
| | - T Lequerré
- Normandie Univ, UNIROUEN, Inserm U 1234, Inserm CIC-CRB 1404, Rouen University Hospital, Department of Dermatology, F 76000, Rouen, France.
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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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Banchereau R, Cepika AM, Banchereau J, Pascual V. Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics. Annu Rev Immunol 2017; 35:337-370. [PMID: 28142321 PMCID: PMC5937945 DOI: 10.1146/annurev-immunol-051116-052225] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.
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Affiliation(s)
| | | | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030;
| | - Virginia Pascual
- Baylor Institute for Immunology Research, Dallas, Texas 75204; , ,
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Kłak A, Paradowska-Gorycka A, Kwiatkowska B, Raciborski F. Personalized medicine in rheumatology. Reumatologia 2016; 54:177-186. [PMID: 27826172 PMCID: PMC5090026 DOI: 10.5114/reum.2016.62472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/12/2016] [Indexed: 12/27/2022] Open
Abstract
In the era of the 21st century, rheumatoid arthritis (RA) is still poorly characterized. Rheumatoid arthritis is a common but heterogeneous disease, not only in the course and clinical symptoms, but also in the clinical response to treatment. Now it is known that early, correct diagnosis and starting treatment with disease-modifying drugs (DMARDs), of which methotrexate (MTX) remains the gold standard in the treatment of RA, is crucial in order to prevent joint destruction, functional disability and an unfavourable disease outcome. Early diagnosis of rheumatoid arthritis is significant in so much as the primary treatment can be started better. Pharmacogenetic and pharmacogenomic studies, which help determine the genetic profile of individual patients, may bring us closer to personalized medicine. Further studies on RA should allow for the identification of disease-specific genes at the stage when their tolerance by the organism is still preserved (before auto-aggression develops).
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Affiliation(s)
- Anna Kłak
- Department of Gerontology and Public Health, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Biochemistry and Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Brygida Kwiatkowska
- Clinic of Early Arthritis, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Filip Raciborski
- Department of Gerontology and Public Health, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
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Molecular probing of TNF: From identification of therapeutic target to guidance of therapy in inflammatory diseases. Cytokine 2016; 101:64-69. [PMID: 27633266 DOI: 10.1016/j.cyto.2016.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022]
Abstract
Therapy by blocking tumor necrosis factor (TNF) activity is highly efficacious and profoundly changed the paradigm of several inflammatory diseases. However, a significant proportion of patients with inflammatory diseases do not respond to TNF inhibitors (TNFi). Prediction of therapeutic response is required for TNFi therapy. Isotope labeled anti-TNF antibodies or TNF receptor have been investigated to localize TNF production at inflammatory tissue in animal models and in patients with inflammatory diseases. The in vivo detection of TNF has been associated with treatment response. Recently, fluorophore labeled anti-TNF antibody in combination with confocal laser endomicroscopy in patients with Crohn's disease yielded more accurate and quantitative in vivo detection of TNF in the diseased mucosa. More importantly, this method demonstrated high therapeutic predication value. Fluorophore labeled TNF binding aptamers in combination with modern imaging technology offers additional tools for in vivo TNF probing.
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Anaya JM, Duarte-Rey C, Sarmiento-Monroy JC, Bardey D, Castiblanco J, Rojas-Villarraga A. Personalized medicine. Closing the gap between knowledge and clinical practice. Autoimmun Rev 2016; 15:833-42. [DOI: 10.1016/j.autrev.2016.06.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/07/2016] [Indexed: 12/22/2022]
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31
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Nakamura S, Suzuki K, Iijima H, Hata Y, Lim CR, Ishizawa Y, Kameda H, Amano K, Matsubara K, Matoba R, Takeuchi T. Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study. Arthritis Res Ther 2016; 18:159. [PMID: 27435242 PMCID: PMC4952232 DOI: 10.1186/s13075-016-1052-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/20/2016] [Indexed: 12/20/2022] Open
Abstract
Background According to EULAR recommendations, biologic DMARDs (bDMARDs) such as tumor necrosis factor inhibitor, tocilizumab (TCZ), and abatacept (ABT) are in parallel when prescribing to rheumatoid arthritis (RA) patients who have shown insufficient response to conventional synthetic DMARDs. However, most prediction studies of therapeutic response to bDMARDs using gene expression profiles were focused on a single bDMARD, and consideration of the results from the perspective of RA pathophysiology was insufficient. The aim of this study was to identify the specific molecular biological features predicting the therapeutic outcomes of three bDMARDs (infliximab [IFX], TCZ, and ABT) by studying blood gene expression signatures of patients before biologic treatment in a unified test platform. Methods RA patients who responded inadequately to methotrexate and were later commenced on any one of IFX (n = 140), TCZ (n = 38), or ABT (n = 31) as their first biologic between May 2007 and November 2011 were enrolled. Whole-blood gene expression data were obtained before biologic administration. Patients were categorized into remission (REM) and nonremission (NON-REM) groups according to CDAI at 6 months of biologic therapy. We employed Gene Set Enrichment Analysis (GSEA) to identify functional gene sets differentially expressed between these two groups for each biologic. Then, we compiled “signature scores” for these gene sets, and the prediction performances were assessed. Results GSEA showed that inflammasome genes were significantly upregulated with IFX in the NON-REM group compared with the REM group. With TCZ in the REM group, B-cell-specifically expressed genes were upregulated. RNA elongation, apoptosis-related, and NK-cell-specifically expressed genes were upregulated with ABT in the NON-REM group. Logistic regression analyses showed that “signature scores” of inflammasomes, B-cell-specifically expressed, and NK-cell-specifically expressed genes were significant, independently predictive factors for treatment outcome with IFX, TCZ, and ABT, respectively. The AUCs of ROC curves of these signature scores were 0.637, 0.796, and 0.768 for IFX, TCZ, and ABT, respectively. Conclusions We have identified original gene expression predictive signatures uniquely underlying the therapeutic effects of IFX, TCZ, and ABT. This is, to our knowledge, the first attempt to predict therapeutic effects of three drugs concomitantly using a unified gene expression test platform. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-1052-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seiji Nakamura
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan.
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroshi Iijima
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan
| | - Yuko Hata
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan
| | - Chun Ren Lim
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan
| | - Yohei Ishizawa
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan
| | - Hideto Kameda
- Division of Rheumatology, Department of Internal Medicine, Toho University Ohashi Medical Center, 2-17-6 Ohashi, Muguro-ku, Tokyo, 153-8515, Japan
| | - Koichi Amano
- Department of Rheumatology and Clinical Immunology, Saitama Medical Center, Saitama Medical University, 1981 Tsujido-machi Kamoda, Kawagoe-shi, Saitama, 350-8550, Japan
| | - Kenichi Matsubara
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan
| | - Ryo Matoba
- DNA Chip Research Inc., 1-15-1 Kaigan, Suzuebaydium 5F, Minato-ku, Tokyo, 105-0022, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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32
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Yang H, Li S, Cao H, Zhang C, Cui Y. Predicting disease trait with genomic data: a composite kernel approach. Brief Bioinform 2016; 18:591-601. [DOI: 10.1093/bib/bbw043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 01/17/2023] Open
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Mina-Osorio P. Review: basics of drug development in rheumatology. Arthritis Rheumatol 2016; 67:2581-90. [PMID: 26138901 DOI: 10.1002/art.39253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
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Genetic data: The new challenge of personalized medicine, insights for rheumatoid arthritis patients. Gene 2016; 583:90-101. [PMID: 26869316 DOI: 10.1016/j.gene.2016.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 01/18/2016] [Accepted: 02/05/2016] [Indexed: 01/15/2023]
Abstract
Rapid advances in genotyping technology, analytical methods, and the establishment of large cohorts for population genetic studies have resulted in a large new body of information about the genetic basis of human rheumatoid arthritis (RA). Improved understanding of the root pathogenesis of the disease holds the promise of improved diagnostic and prognostic tools based upon this information. In this review, we summarize the nature of new genetic findings in human RA, including susceptibility loci and gene-gene and gene-environment interactions, as well as genetic loci associated with sub-groups of patients and those associated with response to therapy. Possible uses of these data are discussed, such as prediction of disease risk as well as personalized therapy and prediction of therapeutic response and risk of adverse events. While these applications are largely not refined to the point of clinical utility in RA, it seems likely that multi-parameter datasets including genetic, clinical, and biomarker data will be employed in the future care of RA patients.
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35
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Clavarino G, Adriouach S, Quesada JL, Clay M, Chevreau M, Trocmé C, Grange L, Gaudin P, Gatti E, Pierre P, Cesbron JY, Dumestre-Pérard C. Unfolded protein response gene GADD34 is overexpressed in rheumatoid arthritis and related to the presence of circulating anti-citrullinated protein antibodies. Autoimmunity 2016; 49:172-8. [DOI: 10.3109/08916934.2016.1138220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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36
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Bilgic T, Klok HA. Oligonucleotide Immobilization and Hybridization on Aldehyde-Functionalized Poly(2-hydroxyethyl methacrylate) Brushes. Biomacromolecules 2015; 16:3657-65. [PMID: 26441148 DOI: 10.1021/acs.biomac.5b01116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA biosensing requires high oligonucleotide binding capacity interface chemistries that can be tuned to maximize probe presentation as well as hybridization efficiency. This contribution investigates the feasibility of aldehyde-functionalized poly(2-hydroxyethyl methacrylate) (PHEMA) brush-based interfaces for oligonucleotide binding and hybridization. These polymer brushes, which allow covalent immobilization of oligonucleotides, are prepared by surface-initiated atom transfer radical polymerization (SI-ATRP) of HEMA followed by a postpolymerization oxidation step to generate side chain aldehyde groups. A series of polymer brushes covering a range of film thicknesses and grafting densities was investigated with regard to their oligonucleotide binding capacity as well as their ability to support oligonucleotide hybridization. Densely grafted brushes were found to have probe oligonucleotide binding capacities of up to ∼30 pmol/cm(2). Increasing the thickness of these densely grafted brush films, however, resulted in a decrease in the oligonucleotide binding capacity. Less densely grafted brushes possess binding capacities of ∼10 pmol/cm(2), which did not significantly depend on film thickness. The oligonucleotide hybridization efficiencies, however, were highest (93%) on those brushes that present the lowest surface concentration of the probe oligonucleotide. These results highlight the importance of optimizing the probe oligonucleotide surface concentration and binding interface chemistry. The versatility and tunability of the PHEMA-based brushes presented herein makes these films a very attractive platform for the immobilization and hybridization of oligonucleotides.
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Affiliation(s)
- Tugba Bilgic
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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Song YJ, Li G, He JH, Guo Y, Yang L. Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes. PLoS One 2015; 10:e0137551. [PMID: 26359667 PMCID: PMC4567271 DOI: 10.1371/journal.pone.0137551] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/19/2015] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) act as epigenetic markers and regulate the expression of their target genes, including those characterized as regulators in autoimmune diseases. Rheumatoid arthritis (RA) is one of the most common autoimmune diseases. The potential roles of miRNA-regulated genes in RA pathogenesis have greatly aroused the interest of clinicians and researchers in recent years. In the current study, RA-related miRNAs records were obtained from PubMed through conditional literature retrieval. After analyzing the selected records, miRNA targeted genes were predicted. We identified 14 RA-associated miRNAs, and their sub-analysis in 5 microarray or RNA sequencing (RNA-seq) datasets was performed. The microarray and RNA-seq data of RA were also downloaded from NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA), analyzed, and annotated. Using a bioinformatics approach, we identified a series of differentially expressed genes (DEGs) by comparing studies on RA and the controls. The RA-related gene expression profile was thus obtained and the expression of miRNA-regulated genes was analyzed. After functional annotation analysis, we found GO molecular function (MF) terms significantly enriched in calcium ion binding (GO: 0005509). Moreover, some novel dysregulated target genes were identified in RA through integrated analysis of miRNA/mRNA expression. The result revealed that the expression of a number of genes, including ROR2, ABI3BP, SMOC2, etc., was not only affected by dysregulated miRNAs, but also altered in RA. Our findings indicate that there is a close association between negatively correlated mRNA/miRNA pairs and RA. These findings may be applied to identify genetic markers for RA diagnosis and treatment in the future.
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Affiliation(s)
- Yi-Jiang Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Guiling Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jian-Hua He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Yao Guo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Li Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
- * E-mail:
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Ermann J, Rao DA, Teslovich NC, Brenner MB, Raychaudhuri S. Immune cell profiling to guide therapeutic decisions in rheumatic diseases. Nat Rev Rheumatol 2015; 11:541-51. [PMID: 26034835 PMCID: PMC4898649 DOI: 10.1038/nrrheum.2015.71] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomarkers are needed to guide treatment decisions for patients with rheumatic diseases. Although the phenotypic and functional analysis of immune cells is an appealing strategy for understanding immune-mediated disease processes, immune cell profiling currently has no role in clinical rheumatology. New technologies, including mass cytometry, gene expression profiling by RNA sequencing (RNA-seq) and multiplexed functional assays, enable the analysis of immune cell function with unprecedented detail and promise not only a deeper understanding of pathogenesis, but also the discovery of novel biomarkers. The large and complex data sets generated by these technologies--big data--require specialized approaches for analysis and visualization of results. Standardization of assays and definition of the range of normal values are additional challenges when translating these novel approaches into clinical practice. In this Review, we discuss technological advances in the high-dimensional analysis of immune cells and consider how these developments might support the discovery of predictive biomarkers to benefit the practice of rheumatology and improve patient care.
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Affiliation(s)
- Joerg Ermann
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Smith Building, 1 Jimmy Fund Way, Boston, MA 02115, USA
| | - Deepak A Rao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Smith Building, 1 Jimmy Fund Way, Boston, MA 02115, USA
| | - Nikola C Teslovich
- 'Division of Genetics, Brigham and Women's Hospital, New Research Building NRB, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Michael B Brenner
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Smith Building, 1 Jimmy Fund Way, Boston, MA 02115, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, New Research Building (NRB), 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Hayashi J, Kihara M, Kato H, Nishimura T. A proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritis. Clin Proteomics 2015; 12:20. [PMID: 26251654 PMCID: PMC4527102 DOI: 10.1186/s12014-015-9091-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/15/2015] [Indexed: 12/13/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial joints. Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear. Regardless of numerous investigations of RA by means of genomic and proteomic approaches, proteins interplaying in RA synovial tissues that contain various types of synoviocytes, are not yet sufficiently understood. Hence we have conducted an HPLC/mass spectrometry-based exploratory proteomic analysis focusing on synoviocyte lesions laser-microdissected (LMD) from formalin-fixed paraffin-embedded (FFPE) synovial tissues (RA, n = 15; OA, n = 5), where those of Osteoarthritis (OA) were used as the control. Results A total of 508 proteins were identified from the RA and OA groups. With the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (RSC) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues. These include stromelysin-1 (MMP3), proteins S100-A8 and S100-A9, plastin-2, galectin-3, calreticulin, cathepsin Z, HLA-A, HLA-DRB1, ferritin, neutrophil defensin 1, CD14, MMP9 etc. Conclusions Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1. Network analyses of protein–protein interaction for those proteins significant to RA revealed a dominant participation of ribosome pathway (p = 5.91 × 10−45), and, interestingly, the associations of the p53 signaling (p = 2.34 × 10−5). An involvement of proteins including CD14, S100-A8/S100-A9 seems to suggest an activation of the NF-kB/MAPK signaling pathway. Our strategy of laser-microdissected FFPE-tissue proteomic analysis in Rheumatoid Arthritis thus demonstrated its technical feasibility in profiling proteins expressed in synovial tissues, which may play important roles in the RA pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12014-015-9091-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Harubumi Kato
- Niizashiki Central General Hospital, Saitama, Japan ; Department of Thoracic and Thyroid Surgery, Tokyo Medical University, Tokyo, Japan
| | - Toshihide Nishimura
- Department of Thoracic and Thyroid Surgery, Tokyo Medical University, Tokyo, Japan
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Giannopoulou EG, Elemento O, Ivashkiv LB. Use of RNA sequencing to evaluate rheumatic disease patients. Arthritis Res Ther 2015; 17:167. [PMID: 26126608 PMCID: PMC4488125 DOI: 10.1186/s13075-015-0677-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the detection of non-coding transcripts and alternative splicing events. In this review, we describe how RNA sequencing enables unbiased interrogation of the abundance and complexity of the transcriptome, and present a typical experimental workflow and bioinformatics tools that are often used for RNA sequencing analysis. We also discuss different uses of this next-generation sequencing technology to evaluate rheumatic disease patients and investigate the pathogenesis of rheumatic diseases such as rheumatoid arthritis, systemic lupus erythematosus, juvenile idiopathic arthritis and Sjögren’s syndrome.
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Affiliation(s)
- Eugenia G Giannopoulou
- Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, 11201, USA. .,Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10021, USA.
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
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Ponchel F, Burska AN, Vital EM. Pharmacogenomics in rheumatoid arthritis: how close are we to the clinic? Pharmacogenomics 2015; 15:1275-9. [PMID: 25155929 DOI: 10.2217/pgs.14.79] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Frederique Ponchel
- Leeds Institute of Rheumatic & Musculoskeletal Medicine, University of Leeds, Leeds, UK
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Avila-Pedretti G, Tornero J, Fernández-Nebro A, Blanco F, González-Alvaro I, Cañete JD, Maymó J, Alperiz M, Fernández-Gutiérrez B, Olivé A, Corominas H, Erra A, Aterido A, López Lasanta M, Tortosa R, Julià A, Marsal S. Variation at FCGR2A and functionally related genes is associated with the response to anti-TNF therapy in rheumatoid arthritis. PLoS One 2015; 10:e0122088. [PMID: 25848939 PMCID: PMC4388501 DOI: 10.1371/journal.pone.0122088] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/18/2015] [Indexed: 11/29/2022] Open
Abstract
Objective Anti-TNF therapies have been highly efficacious in the management of rheumatoid arthritis (RA), but 25–30% of patients do not show a significant clinical response. There is increasing evidence that genetic variation at the Fc receptor FCGR2A is associated with the response to anti-TNF therapy. We aimed to validate this genetic association in a patient cohort from the Spanish population, and also to identify new genes functionally related to FCGR2A that are also associated with anti-TNF response. Methods A total of 348 RA patients treated with an anti-TNF therapy were included and genotyped for FCGR2A polymorphism rs1081274. Response to therapy was determined at 12 weeks, and was tested for association globally and independently for each anti-TNF drug (infliximab, etanercept and adalimumab). Using gene expression profiles from macrophages obtained from synovial fluid of RA patients, we searched for genes highly correlated with FCGR2A expression. Tag SNPs were selected from each candidate gene and tested for association with the response to therapy. Results We found a significant association between FCGR2A and the response to adalimumab (P=0.022). Analyzing the subset of anti-CCP positive RA patients (78%), we also found a significant association between FCGR2A and the response to infliximab (P=0.035). DHX32 and RGS12 were the most consistently correlated genes with FCGR2A expression in RA synovial fluid macrophages (P<0.001). We found a significant association between the genetic variation at DHX32 (rs12356233, corrected P=0.019) and a nominally significant association between RGS12 and the response to adalimumab (rs4690093, uncorrected P=0.040). In the anti-CCP positive group of patients, we also found a nominally significant association between RGS12 and the response to infliximab (rs2857859, uncorrected P=0.042). Conclusions In the present study we have validated the FCGR2A association in an independent population, and we have identified new genes associated with the response to anti-TNF therapy in RA.
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Affiliation(s)
| | - Jesús Tornero
- Hospital Universitario De Guadalajara, Rheumatology Department, Guadalajara, Spain
| | - Antonio Fernández-Nebro
- UGC Reumatología, Instituto de Investigación Biomédica en Málaga, Hospital Regional Universitario de Málaga, Universidad de Málaga, Málaga, Spain
| | - Francisco Blanco
- INIBIC-Hospital Universitario A Coruña, Rheumatology Department, A Coruña, Spain
| | - Isidoro González-Alvaro
- Hospital Universitario de La Princesa, IIS La Princesa, Rheumatology Department, Madrid, Spain
| | - Juan D Cañete
- Hospital Clínic de Barcelona, Rheumatology Department, Barcelona, Spain
| | - Joan Maymó
- Hospital del Mar, Barcelona, Rheumatology Department, Barcelona, Spain
| | - Mercedes Alperiz
- Hospital Universitario Central de Asturias, Rheumatology Department, Oviedo, Spain
| | | | - Alex Olivé
- Hospital Universitari Germans Trias i Pujol, Rheumatology Department, Barcelona, Spain
| | - Héctor Corominas
- Hospital Moisès Broggi, Rheumatology Department, Barcelona, Spain
| | - Alba Erra
- Hospital Sant Rafael, Rheumatology Department, Barcelona, Spain
| | - Adrià Aterido
- Vall d'Hebron Hospital Research Institute, Rheumatology Research Group. Barcelona, Spain
| | - María López Lasanta
- Vall d'Hebron Hospital Research Institute, Rheumatology Research Group. Barcelona, Spain
| | - Raül Tortosa
- Vall d'Hebron Hospital Research Institute, Rheumatology Research Group. Barcelona, Spain
| | - Antonio Julià
- Vall d'Hebron Hospital Research Institute, Rheumatology Research Group. Barcelona, Spain
| | - Sara Marsal
- Vall d'Hebron Hospital Research Institute, Rheumatology Research Group. Barcelona, Spain
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Ye H, Zhang J, Wang J, Gao Y, Du Y, Li C, Deng M, Guo J, Li Z. CD4 T-cell transcriptome analysis reveals aberrant regulation of STAT3 and Wnt signaling pathways in rheumatoid arthritis: evidence from a case-control study. Arthritis Res Ther 2015; 17:76. [PMID: 25880754 PMCID: PMC4392874 DOI: 10.1186/s13075-015-0590-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 02/25/2015] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is a systemic autoimmune disease in which T cells play a pivotal role in the pathogenesis. Knowledge in terms of the CD4 T-cell transcriptome in RA is limited. The aim of this study was to examine the whole-genome transcription profile of CD4 T cells in RA by comparing patients with RA to healthy controls. METHODS Peripheral blood CD4 T cells were isolated from 53 RA patients with active disease and 45 healthy individuals; 13 cases and 10 controls were enrolled in microarray analysis. The remaining 40 cases and 35 controls were recruited as an independent cohort for the validation study. Bioinformatics was performed on Gene Ontology (GO), gene-gene interaction networks, and pathway analysis. The gene modules, by combining the results from GO, gene networks, and pathway analysis, were selected for further validation. RESULTS The CD4 T cells showed 1,496 differentially expressed (DE) genes in RA patients relative to healthy individuals. GO analysis revealed that the DE genes were enriched in immune response, T-cell response, apoptosis process, and Wnt receptor signaling. Pathway analysis also identified that 'Wnt signaling pathway' was differentially regulated between two groups (P=2.78×10(-10)). By gene-gene network analysis, we found that the DE genes were enriched in T-cell receptor (TCR), JAK-STAT signaling, and Wnt signaling pathway. By gene module analysis, we found that a number of DE genes overlapped in the three different analyses. In total, 23 genes were selected for further validation, and nine genes were confirmed. Of these, four genes (SOCS3, CBL, IFNAR1, and PIK3CA) were involved in STAT3 (signal transducer and activator of transcription 3) signaling, and three genes (CBL, KLF9, and CSNK2A1) were involved in the Wnt signaling pathway. Additionally, several zinc finger transcription factors (ZEB1, ZNF292, and ZNF644) were confirmed. CONCLUSIONS We report here the first case-control study of the CD4 T-cell transcriptome profile in RA. Our data provide evidence that CD4 T cells from patients with RA have abnormal functional networks in STAT3 signaling and Wnt signaling. Our results also suggest that the aberrant expression of several zinc finger transcription factors (ZEB1, ZNF292, and ZNF644) may be potential pathogenic factors for RA.
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Affiliation(s)
- Hua Ye
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
| | - Jing Zhang
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
| | - Jun Wang
- School of Mathematical Sciences, Center for Quantitative Biology, Peking University, 136 North Zhong-guan-cun Street, Beijing, 100871, China.
| | - Yanyan Gao
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
| | - Yan Du
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
| | - Chun Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
| | - Minghua Deng
- School of Mathematical Sciences, Center for Quantitative Biology, Peking University, 136 North Zhong-guan-cun Street, Beijing, 100871, China.
| | - Jianping Guo
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, 11 South Xizhimen Street, Beijing, 100044, China.
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Serum interferon-related microRNAs as biomarkers to predict the response to interferon therapy in chronic hepatitis C genotype 4. PLoS One 2015; 10:e0121524. [PMID: 25811198 PMCID: PMC4374907 DOI: 10.1371/journal.pone.0121524] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/03/2015] [Indexed: 12/31/2022] Open
Abstract
Background Hepatitis C virus genotype 4 (HCV-4) infection is common in the Middle East and Africa, with an extraordinarily high prevalence in Egypt. MicroRNAs (miRNAs) play an important role in various diseases, including HCV infection. The aim of the present study was to assess serum miR-122, miR-221 and miR-21 expression profiles in HCV-4 patients prior to treatment with HCV-4 combination therapy (pegylated alpha interferon and ribavirin) and to determine whether the miRNAs were associated with the drug response. Methods RNA was extracted from pretreatment serum samples, and miR-122, miR-221 and miR-21 levels were measured by quantitative PCR. The results were compared among patients with sustained virological responses (SVR) and non-responders (NR). Results The expression levels of miR-21 and miR-122 were significantly different between the SVR and NR groups. Receiver operator characteristic (ROC) analysis revealed that the sensitivity, specificity and positive predictive values of miR-21 were 82.2%, 77.3% and 88.1%, respectively, with a cut-off value of 1.7. The sensitivity, specificity and positive predictive values of miR-122 were 68.9%, 59.1% and 77.5%, respectively, with a cut-off value of 3.5. Conclusion and Significance miR-21 and miR-122 might be useful predictors for SVR in HCV-4 patients prior to the administration of combination therapy. A higher predictive response power was obtained for miR-21 than for miR-122. These results should reduce ineffective treatments.
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Serum interferon-related microRNAs as biomarkers to predict the response to interferon therapy in chronic hepatitis C genotype 4. PLoS One 2015; 10:e0120794. [PMID: 25790297 PMCID: PMC4366211 DOI: 10.1371/journal.pone.0120794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are messengers during interferon-virus interplay and are involved in antiviral immunity, however, little is known about interferon-related microRNAs regarding their detection in serum and their potential use as non-invasive diagnostic and prognostic biomarkers in chronic hepatitis C (CHC). To elucidate some of the molecular aspects underlying failure of pegylated interferon-α/ribavirin therapy, we investigated pretreatment expression profiles of seven selected interferon-related microRNAs (miR-146a, miR-34a, miR-130a, miR-19a, miR-192, miR-195, and miR-296) by quantitative RT-PCR custom array technology in serum of Egyptian CHC genotype 4 patients and whether their pretreatment levels would predict patient response to the combination therapy. One hundred and six CHC patients and forty matched healthy controls were included. Patients were divided into sustained virological response (SVR) and non-responder (NR) groups. Serum miR-34a, miR-130a, miR-19a, miR-192, miR-195, and miR-296 were upregulated, whereas serum miR-146a was downregulated in CHC compared to controls. Significant correlations were found between expression levels of studied microRNAs and also with clinical data. Pretreatment levels of miR-34a, miR-130a, and miR-195 were significantly higher, whereas miR-192 and miR-296 levels were significantly lower in SVR than NR patients. miR-19a and miR-146a levels were not significantly different between the two groups. miR-34a was superior to differentiate CHC from controls, whereas miR-296 was superior to discriminate SVR from NR patients by receiver operating characteristic analysis. Multivariate logistic analysis revealed miR-34a and miR-195 as independent predictors for SVR and miR-192 as an independent variable for non-response. In conclusion, pretreatment expression profiles of five interferon-related microRNAs are associated with treatment outcome in CHC. Of these, miR-34a, miR-195, and miR-192 could predict treatment response. The profiling results could be used as novel non-invasive diagnostic and prognostic pharmacogenetic biomarkers for treatment personalization in CHC and could help to identify new microRNA-based antivirals.
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Toro-Domínguez D, Carmona-Sáez P, Alarcón-Riquelme ME. Shared signatures between rheumatoid arthritis, systemic lupus erythematosus and Sjögren's syndrome uncovered through gene expression meta-analysis. Arthritis Res Ther 2014; 16:489. [PMID: 25466291 PMCID: PMC4295333 DOI: 10.1186/s13075-014-0489-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 11/10/2014] [Indexed: 01/01/2023] Open
Abstract
Introduction Systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and Sjögren’s syndrome (SjS) are inflammatory systemic autoimmune diseases (SADs) that share several clinical and pathological features. The shared biological mechanisms are not yet fully characterized. The objective of this study was to perform a meta-analysis using publicly available gene expression data about the three diseases to identify shared gene expression signatures and overlapping biological processes. Methods Previously reported gene expression datasets were selected and downloaded from the Gene Expression Omnibus database. Normalization and initial preprocessing were performed using the statistical programming language R and random effects model–based meta-analysis was carried out using INMEX software. Functional analysis of over- and underexpressed genes was done using the GeneCodis tool. Results The gene expression meta-analysis revealed a SAD signature composed of 371 differentially expressed genes in patients and healthy controls, 187 of which were underexpressed and 184 overexpressed. Many of these genes have previously been reported as significant biomarkers for individual diseases, but others provide new clues to the shared pathological state. Functional analysis showed that overexpressed genes were involved mainly in immune and inflammatory responses, mitotic cell cycles, cytokine-mediated signaling pathways, apoptotic processes, type I interferon–mediated signaling pathways and responses to viruses. Underexpressed genes were involved primarily in inhibition of protein synthesis. Conclusions We define a common gene expression signature for SLE, RA and SjS. The analysis of this signature revealed relevant biological processes that may play important roles in the shared development of these pathologies. Electronic supplementary material The online version of this article (doi:10.1186/s13075-014-0489-x) contains supplementary material, which is available to authorized users.
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Townsend MJ. Molecular and cellular heterogeneity in the Rheumatoid Arthritis synovium: Clinical correlates of synovitis. Best Pract Res Clin Rheumatol 2014; 28:539-49. [DOI: 10.1016/j.berh.2014.10.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Biomarkers in rheumatoid arthritis. Mediators Inflamm 2014; 2014:379310. [PMID: 25061261 PMCID: PMC4100293 DOI: 10.1155/2014/379310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 05/07/2014] [Indexed: 11/18/2022] Open
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