1
|
Fan A, Li Y, Zhang Y, Meng W, Pan W, Chen M, Ma Z, Chen W. Loss of AR-regulated AFF3 contributes to prostate cancer progression and reduces ferroptosis sensitivity by downregulating ACSL4 based on single-cell sequencing analysis. Apoptosis 2024; 29:1679-1695. [PMID: 38478171 DOI: 10.1007/s10495-024-01941-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2024] [Indexed: 09/25/2024]
Abstract
Prostate cancer (PCa) is one of the most common cancers affecting the health of men worldwide. Castration-resistant prostate cancer (CRPC), the advanced and refractory phase of prostate cancer, has multiple mechanisms of resistance to androgen deprivation therapy (ADT) such as AR mutations, aberrant androgen synthase, and abnormal expression of AR-related genes. Based on the research of the AR pathway, new drugs for the treatment of CRPC have been developed in clinical practice, such as Abiraterone and enzalutamide. However, many areas in this pathway are still worth exploring. In this study, single-cell sequencing analysis was utilized to scrutinize significant genes in the androgen receptor (AR) pathway related to CRPC. Our analysis of single-cell sequencing combined with bulk-cell sequencing revealed a substantial downregulation of AR-regulated AFF3 in CRPC. Overexpression of AFF3 restricted the proliferation and migration of prostate cancer cells whilst also increasing their sensitivity towards enzalutamide, while knockdown of AFF3 had the opposite effect. To elucidate the mechanism of tumor inhibition by AFF3, we applied GSVA and GSEA to investigate the metabolic pathways related to AFF3 and revealed that AFF3 had an impact on fatty acids metabolism and ferroptosis through the regulation of ACSL4 protein expression. Based on correlation analysis and flow cytometry, we can speculate that AFF3 can impact the sensitivity of the CRPC cell lines to the ferroptosis inducer (RSL3) by regulating ACSL4. Therefore, our findings may provide new insights into the mechanisms of drug resistance in CRPC, and AFF3 may serve as a novel prognostic biomarker in prostate cancer.
Collapse
Affiliation(s)
- Aoyu Fan
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
| | - Yunpeng Li
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
| | - Yunyan Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
| | - Wei Meng
- Lab for Noncoding RNA and Cancer, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Wei Pan
- Lab for Noncoding RNA and Cancer, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Meixi Chen
- Lab for Noncoding RNA and Cancer, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zhongliang Ma
- Lab for Noncoding RNA and Cancer, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Wei Chen
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200030, China.
| |
Collapse
|
2
|
Chen S, Zhao W, Du J, Chen S, Li J, Shen B, Zhou Y, Chen S. The expression of RBPJ and its potential role in rheumatoid arthritis. BMC Genomics 2024; 25:899. [PMID: 39350019 PMCID: PMC11441141 DOI: 10.1186/s12864-024-10804-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Recombination signal-binding protein for immunoglobulin kappa J region (RBPJ) is a transcriptional regulator that plays an important role in maintaining immune homeostasis. This study aimed to estimate the expression of RBPJ in rheumatoid arthritis (RA) patients and investigate its relationship with RA. METHODS A total of 83 newly diagnosed RA patients and 70 healthy controls were included. mRNA was extracted from peripheral blood mononuclear cells (PBMCs), and the expression of RBPJ was detected using quantitative real-time PCR (qRT‒PCR). An RA dataset (GSE89408) was obtained from the Gene Expression Omnibus (GEO) database, and RA synovial tissues were divided into two groups. The differentially expressed genes (DEGs) were selected with the "DESeq2" R package. RESULTS RBPJ expression was lower in RA patients than in health controls and was negatively correlated with the DAS28 score, C-reactive protein (CRP) level and erythrocyte sedimentation rate (ESR). RA synovial tissues from GSE89408 were classified into RBPJ-low (≤ 25%) and RBPJ-high (≥ 75%) groups according to RBPJ expression, and 562 DEGs were identified. Gene Ontology (GO) enrichment analyses revealed that the DEGs significantly affected the regulation of T cell activation and lymphocyte/mononuclear cell differentiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the most enriched pathways of DEGs were the T cell receptor signaling pathway, Th1/2 and Th17 cell differentiation, the PI3K - Akt signaling pathway and cytokine‒cytokine receptor interaction. CytoHubba Plugin revealed that most of the top 10 genes were involved in osteoclast differentiation, the T cell receptor signaling pathway and cytokine‒cytokine receptor interaction. CONCLUSIONS RBPJ expression was significantly lower in RA patients and negatively correlated with disease activity. GEO dataset analysis demonstrated that RBPJ may be involved in osteoclast differentiation, T cell activation and differentiation, and the T cell receptor signaling pathway. Our research may contribute to understanding the potential mechanisms by which RBPJ regulates T cell differentiation and cytokine‒cytokine receptor interaction in RA patients.
Collapse
Affiliation(s)
- Shuaishuai Chen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Luqiao, China
| | - Weibo Zhao
- Department of Orthopedics, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China
| | - Juping Du
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Luqiao, China
| | - Suyun Chen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Luqiao, China
| | - Jun Li
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Luqiao, China
| | - Bo Shen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Luqiao, China
| | - Yuanlin Zhou
- Department of Neurology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China.
| | - Shiyong Chen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, 150 Ximen Street of Linhai City, Linhai, 317000, China.
- Key Laboratory of System Medicine and Precision Diagnosis and Treatment of Taizhou, Luqiao, China.
| |
Collapse
|
3
|
Gao KX, Yang YH, Liang Q, Mei LY, Liang YB, Wang MJ, Chen XM, Huang QC, Wen ZH, Huang RY. Targeting Therapeutic Windows for Rheumatoid Arthritis Prevention. Chin J Integr Med 2024; 30:842-851. [PMID: 38753276 DOI: 10.1007/s11655-024-3760-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 08/25/2024]
Abstract
Rheumatoid arthritis (RA) is a worldwide public health problem. Interventions to delay or prevent the onset of RA have attracted much attention in recent years, and researchers are now exploring various prevention strategies. At present, there is still no unified consensus for RA prevention, but targeting therapeutic windows and implementing interventions for at-risk individuals are extremely important. Due to the limited number of clinical trials on pharmacologic interventions, further studies are needed to explore and establish optimal intervention regimens and effective measures to prevent progression to RA. In this review, we introduce the RA disease process and risk factors, and present research on the use of both Western and Chinese medicine from clinical perspectives regarding RA prevention. Furthermore, we describe several complete and ongoing clinical studies on the use of Chinese herbal formulae for the prevention of RA.
Collapse
Affiliation(s)
- Kai-Xin Gao
- Section of Rheumatology and Immunology Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Yi-Hong Yang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Qi Liang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Li-Yan Mei
- Section of Rheumatology and Immunology Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - You-Bang Liang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Mao-Jie Wang
- Section of Rheumatology and Immunology Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, 510120, China
| | - Xiu-Min Chen
- Section of Rheumatology and Immunology Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, 510120, China
| | - Qing-Chun Huang
- Section of Rheumatology and Immunology Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
- Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, 510120, China
| | - Ze-Huai Wen
- The Key Unit of Methodology of Clinical Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Run-Yue Huang
- Section of Rheumatology and Immunology Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, 510120, China.
| |
Collapse
|
4
|
Lamba A, Taneja V. Gut microbiota as a sensor of autoimmune response and treatment for rheumatoid arthritis. Immunol Rev 2024; 325:90-106. [PMID: 38867408 PMCID: PMC11338721 DOI: 10.1111/imr.13359] [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] [Indexed: 06/14/2024]
Abstract
Rheumatoid arthritis (RA) is considered a multifactorial condition where interaction between the genetic and environmental factors lead to immune dysregulation causing autoreactivity. While among the various genetic factors, HLA-DR4 and DQ8, have been reported to be the strongest risk factors, the role of various environmental factors has been unclear. Though events initiating autoreactivity remain unknown, a mucosal origin of RA has gained attention based on the recent observations with the gut dysbiosis in patients. However, causality of gut dysbiosis has been difficult to prove in humans. Mouse models, especially mice expressing RA-susceptible and -resistant HLA class II genes have helped unravel the complex interactions between genetic factors and gut microbiome. This review describes the interactions between HLA genes and gut dysbiosis in sex-biased preclinical autoreactivity and discusses the potential use of endogenous commensals as indicators of treatment efficacy as well as therapeutic tool to suppress pro-inflammatory response in rheumatoid arthritis.
Collapse
Affiliation(s)
| | - Veena Taneja
- Department of Immunology and Division of Rheumatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| |
Collapse
|
5
|
Chasov V, Ganeeva I, Zmievskaya E, Davletshin D, Gilyazova E, Valiullina A, Bulatov E. Cell-Based Therapy and Genome Editing as Emerging Therapeutic Approaches to Treat Rheumatoid Arthritis. Cells 2024; 13:1282. [PMID: 39120313 PMCID: PMC11312096 DOI: 10.3390/cells13151282] [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: 06/17/2024] [Revised: 07/19/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation of the joints. Although much remains unknown about the pathogenesis of RA, there is evidence that impaired immune tolerance and the development of RA are related. And it is precisely the restoration of immune tolerance at the site of the inflammation that is the ultimate goal of the treatment of RA. Over the past few decades, significant progress has been made in the treatment of RA, with higher rates of disease remission and improved long-term outcomes. Unfortunately, despite these successes, the proportion of patients with persistent, difficult-to-treat disease remains high, and the task of improving our understanding of the basic mechanisms of disease development and developing new ways to treat RA remains relevant. This review focuses on describing new treatments for RA, including cell therapies and gene editing technologies that have shown potential in preclinical and early clinical trials. In addition, we discuss the opportunities and limitations associated with the use of these new approaches in the treatment of RA.
Collapse
Affiliation(s)
- Vitaly Chasov
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Irina Ganeeva
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Ekaterina Zmievskaya
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Damir Davletshin
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Elvina Gilyazova
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Aygul Valiullina
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Emil Bulatov
- Laboratory of Biomedical Technologies, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119048, Russia
| |
Collapse
|
6
|
Terashima A, Ono K, Omata Y, Tanaka S, Saito T. Inflammatory diseases causing joint and bone destruction: rheumatoid arthritis and hemophilic arthropathy. J Bone Miner Metab 2024; 42:455-462. [PMID: 38856919 DOI: 10.1007/s00774-024-01520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/20/2024] [Indexed: 06/11/2024]
Abstract
Various diseases and conditions cause joint disorders. Osteoarthritis (OA) is characterized by the degeneration of articular cartilage, synovitis, and anabolic changes in surrounding bone tissues. In contrast, rheumatoid arthritis (RA) and hemophilic arthropathy (HA) display marked destruction of bone tissues caused by synovitis. RA is a representative autoimmune disease. The primary tissue of RA pathogenesis is the synovial membrane and involves various immune cells that produce catabolic cytokines and enzymes. Hemophilia is a genetic disorder caused by a deficiency in blood clotting factors. Recurrent intra-articular bleeding leads to chronic synovitis through excessive iron deposition and results in the destruction of affected joints. Although the triggers for these two joint diseases are completely different, many cytokines and enzymes are common in the pathogenesis of both RA and HA. This review focuses on the similarities between joint and bone destruction in RA and HA. The insights may be useful in developing better treatments for hemophilia patients with arthropathy and osteoporosis by leveraging advanced therapeutics for RA.
Collapse
Affiliation(s)
- Asuka Terashima
- Bone and Cartilage Regenerative Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Kumiko Ono
- Department of Joint Surgery, Research Hospital, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo, 108-8639, Japan
- Orthopaedic Surgery, Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Yasunori Omata
- Bone and Cartilage Regenerative Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
- Orthopaedic Surgery, Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Sakae Tanaka
- Orthopaedic Surgery, Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Taku Saito
- Orthopaedic Surgery, Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
| |
Collapse
|
7
|
Carpio Alvarez M, Cintado Benitez A, Diaz Argudin T, Nodarse Cuni H, Dominguez Horta MDC, Fernández Massó JR. Association between COMMD1 gene polymorphism rs11125908 and rheumatoid arthritis in the Cuban population. Reumatismo 2024; 76. [PMID: 38916163 DOI: 10.4081/reumatismo.2024.1691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/09/2024] [Indexed: 06/26/2024] Open
Abstract
OBJECTIVE To evaluate the association of the rs11125908 polymorphism in the COMMD1 gene in the Cuban population with rheumatoid arthritis (RA). METHODS In this case-control study, 161 RA patients and 150 control subjects were genotyped for rs11125908 by the allele-specific polymerase chain reaction method. DNA sequencing was used to verify the assignation of the polymorphism. The odds ratios (OR) and their 95% confidence interval were calculated by logistic regression to determine the associations between genotypes and RA using the SNPStats software. RESULTS An association of the single nucleotide polymorphism with the disease was found in the overdominant model (p=0.025; OR=1.91) for the AG genotype. Our analyses revealed an association between rs11125908 and the subgroup of patients with swollen joints < median under the codominant model for AG (p=0.034; OR=2.30) and GG genotype (p=0.034; OR=0.82) and with the overdominant model (p=0.01; OR=2.38). The subgroup of patients with an age of onset lower than the mean and AG genotype showed an association in the overdominant model (p=0.027; OR=2.27). Disease activity score 28 with erythrocyte sedimentation rate and disease duration variables were not associated with the rs11125908 polymorphism. CONCLUSIONS rs11125908 was associated with RA and with the number of swollen joints and age of onset subgroup analyses. We provide concepts for treatments for RA, based on pharmacological management of COMMD1 expression.
Collapse
Affiliation(s)
- M Carpio Alvarez
- Pharmaceutical Department, Center for Genetic Engineering and Biotechnology, Havana.
| | - A Cintado Benitez
- Pharmacogenomics Department, Center for Genetic Engineering and Biotechnology, Havana.
| | - T Diaz Argudin
- Pharmacogenomics Department, Center for Genetic Engineering and Biotechnology, Havana.
| | - H Nodarse Cuni
- Clinical Research Direction, Center for Genetic Engineering and Biotechnology, Havana.
| | - M D C Dominguez Horta
- Pharmaceutical Department, Center for Genetic Engineering and Biotechnology, Havana.
| | - J R Fernández Massó
- Pharmaceutical Department, Center for Genetic Engineering and Biotechnology, Havana.
| |
Collapse
|
8
|
Hu X, Zhang P, Gao Y, Ding WW, Cheng XE, Shi QQ, Li S, Zhu YY, Pan HF, Wang P. Identification of lipid-modifying drug targets for autoimmune diseases: insights from drug target mendelian randomization. Lipids Health Dis 2024; 23:193. [PMID: 38909219 PMCID: PMC11193261 DOI: 10.1186/s12944-024-02181-2] [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: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUNDS A growing body of evidence has highlighted the interactions of lipids metabolism and immune regulation. Nevertheless, there is still a lack of evidence regarding the causality between lipids and autoimmune diseases (ADs), as well as their possibility as drug targets for ADs. OBJECTIVES This study was conducted to comprehensively understand the casual associations between lipid traits and ADs, and evaluate the therapeutic possibility of lipid-lowering drug targets on ADs. METHODS Genetic variants for lipid traits and variants encoding targets of various lipid-lowering drugs were derived from Global Lipid Genetics Consortium (GLGC) and verified in Drug Bank. Summary data of ADs were obtained from MRC Integrative Epidemiology Unit (MER-IEU) database and FinnGen consortium, respectively. The causal inferences between lipid traits/genetic agents of lipid-lowering targets and ADs were evaluated by Mendelian randomization (MR), summary data-based MR (SMR), and multivariable MR (MVMR) analyses. Enrichment analysis and protein interaction network were employed to reveal the functional characteristics and biological relevance of potential therapeutic lipid-lowering targets. RESULTS There was no evidence of causal effects regarding 5 lipid traits and 9 lipid-lowering drug targets on ADs. Genetically proxied 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) inhibition was associated with a reduced risk of rheumatoid arthritis (RA) in both discovery (OR [odds ratio] = 0.45, 95%CI: 0.32, 0.63, P = 6.79 × 10- 06) and replicate datasets (OR = 0.37, 95%CI: 0.23, 0.61, P = 7.81 × 10- 05). SMR analyses supported that genetically proxied HMGCR inhibition had causal effects on RA in whole blood (OR = 0.48, 95%CI: 0.29, 0.82, P = 6.86 × 10- 03) and skeletal muscle sites (OR = 0.75, 95%CI: 0.56, 0.99, P = 4.48 × 10- 02). After controlling for blood pressure, body mass index (BMI), smoking and drinking alchohol, HMGCR suppression showed a direct causal effect on a lower risk of RA (OR = 0.33, 95%CI: 0.40, 0.96, P = 0.042). CONCLUSIONS Our study reveals causal links of genetically proxied HMGCR inhibition (lipid-lowering drug targets) and HMGCR expression inhibition with a decreased risk of RA, suggesting that HMGCR may serve as candidate drug targets for the treatment and prevention of RA.
Collapse
Affiliation(s)
- Xiao Hu
- Department of Health Promotion and Behavioral Sciences, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Peng Zhang
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Yuan Gao
- Health Services and Management, School of Health Management, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Wen-Wen Ding
- The Second Clinical School of Medicine, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Xue-Er Cheng
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Qian-Qian Shi
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Sheng Li
- Department of Health Promotion and Behavioral Sciences, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Yan-Yu Zhu
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Hai-Feng Pan
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.
| | - Peng Wang
- Department of Health Promotion and Behavioral Sciences, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, China.
| |
Collapse
|
9
|
Ding Q, Xu Q, Hong Y, Zhou H, He X, Niu C, Tian Z, Li H, Zeng P, Liu J. Integrated analysis of single-cell RNA-seq, bulk RNA-seq, Mendelian randomization, and eQTL reveals T cell-related nomogram model and subtype classification in rheumatoid arthritis. Front Immunol 2024; 15:1399856. [PMID: 38962008 PMCID: PMC11219584 DOI: 10.3389/fimmu.2024.1399856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
Objective Rheumatoid arthritis (RA) is a systemic disease that attacks the joints and causes a heavy economic burden on humans worldwide. T cells regulate RA progression and are considered crucial targets for therapy. Therefore, we aimed to integrate multiple datasets to explore the mechanisms of RA. Moreover, we established a T cell-related diagnostic model to provide a new method for RA immunotherapy. Methods scRNA-seq and bulk-seq datasets for RA were obtained from the Gene Expression Omnibus (GEO) database. Various methods were used to analyze and characterize the T cell heterogeneity of RA. Using Mendelian randomization (MR) and expression quantitative trait loci (eQTL), we screened for potential pathogenic T cell marker genes in RA. Subsequently, we selected an optimal machine learning approach by comparing the nine types of machine learning in predicting RA to identify T cell-related diagnostic features to construct a nomogram model. Patients with RA were divided into different T cell-related clusters using the consensus clustering method. Finally, we performed immune cell infiltration and clinical correlation analyses of T cell-related diagnostic features. Results By analyzing the scRNA-seq dataset, we obtained 10,211 cells that were annotated into 7 different subtypes based on specific marker genes. By integrating the eQTL from blood and RA GWAS, combined with XGB machine learning, we identified a total of 8 T cell-related diagnostic features (MIER1, PPP1CB, ICOS, GADD45A, CD3D, SLFN5, PIP4K2A, and IL6ST). Consensus clustering analysis showed that RA could be classified into two different T-cell patterns (Cluster 1 and Cluster 2), with Cluster 2 having a higher T-cell score than Cluster 1. The two clusters involved different pathways and had different immune cell infiltration states. There was no difference in age or sex between the two different T cell patterns. In addition, ICOS and IL6ST were negatively correlated with age in RA patients. Conclusion Our findings elucidate the heterogeneity of T cells in RA and the communication role of these cells in an RA immune microenvironment. The construction of T cell-related diagnostic models provides a resource for guiding RA immunotherapeutic strategies.
Collapse
Affiliation(s)
- Qiang Ding
- The First School of Clinical Medicine, Guangxi Traditional Chinesen Medical University, Nanning, China
| | - Qingyuan Xu
- The First School of Clinical Medicine, Guangxi Traditional Chinesen Medical University, Nanning, China
| | - Yini Hong
- Gynecology Department, The First People’s Hospital of Guangzhou, Guangzhou, China
| | - Honghai Zhou
- Faculty of Orthopedics and Traumatology, Guangxi University of Chinese Medicine, Nanning, China
| | - Xinyu He
- The First School of Clinical Medicine, Guangxi Traditional Chinesen Medical University, Nanning, China
| | - Chicheng Niu
- The First School of Clinical Medicine, Guangxi Traditional Chinesen Medical University, Nanning, China
| | - Zhao Tian
- The First School of Clinical Medicine, Guangxi Traditional Chinesen Medical University, Nanning, China
| | - Hao Li
- The First School of Clinical Medicine, Guangxi Traditional Chinesen Medical University, Nanning, China
| | - Ping Zeng
- Department of Orthopedics and Traumatology, The First Affiliated Hospital of Guangxi University of Traditional Chinese Medicine, Guangxi, China
| | - Jinfu Liu
- Department of Orthopedics and Traumatology, The First Affiliated Hospital of Guangxi University of Traditional Chinese Medicine, Guangxi, China
| |
Collapse
|
10
|
Kozlowska J, Humphryes-Kirilov N, Pavlovets A, Connolly M, Kuncheva Z, Horner J, Manso AS, Murray C, Fox JC, McCarthy A. Unveiling new genetic insights in rheumatoid arthritis for drug discovery through Taxonomy3 analysis. Sci Rep 2024; 14:14153. [PMID: 38898196 PMCID: PMC11186831 DOI: 10.1038/s41598-024-64970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/14/2024] [Indexed: 06/21/2024] Open
Abstract
Genetic support for a drug target has been shown to increase the probability of success in drug development, with the potential to reduce attrition in the pharmaceutical industry alongside discovering novel therapeutic targets. It is therefore important to maximise the detection of genetic associations that affect disease susceptibility. Conventional statistical methods such as genome-wide association studies (GWAS) only identify some of the genetic contribution to disease, so novel analytical approaches are required to extract additional insights. C4X Discovery has developed Taxonomy3, a unique method for analysing genetic datasets based on mathematics that is novel in drug discovery. When applied to a previously published rheumatoid arthritis GWAS dataset, Taxonomy3 identified many additional novel genetic signals associated with this autoimmune disease. Follow-up studies using tool compounds support the utility of the method in identifying novel biology and tractable drug targets with genetic support for further investigation.
Collapse
Affiliation(s)
- Justyna Kozlowska
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK.
| | | | - Anastasia Pavlovets
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - Martin Connolly
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - Zhana Kuncheva
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - Jonathan Horner
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - Ana Sousa Manso
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - Clare Murray
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - J Craig Fox
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| | - Alun McCarthy
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, UK
| |
Collapse
|
11
|
Kaplan MJ. Navigating an enigma: the continuing journey of autoimmunity discoveries. J Clin Invest 2024; 134:e182287. [PMID: 38828730 PMCID: PMC11142729 DOI: 10.1172/jci182287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
|
12
|
Dorans E, Jagadeesh K, Dey K, Price AL. Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307813. [PMID: 38826240 PMCID: PMC11142273 DOI: 10.1101/2024.05.24.24307813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown great promise in linking regulatory elements to genes. However, existing methods differ in their modeling assumptions and approaches to account for biological and technical noise-leading to low concordance in their linking scores-and do not capture the effects of genomic distance. We propose pgBoost, an integrative modeling framework that trains a non-linear combination of existing linking strategies (including genomic distance) on fine-mapped eQTL data to assign a probabilistic score to each candidate SNP-gene link. We applied pgBoost to single-cell multiome data from 85k cells representing 6 major immune/blood cell types. pgBoost attained higher enrichment for fine-mapped eSNP-eGene pairs (e.g. 21x at distance >10kb) than existing methods (1.2-10x; p-value for difference = 5e-13 vs. distance-based method and < 4e-35 for each other method), with larger improvements at larger distances (e.g. 35x vs. 0.89-6.6x at distance >100kb; p-value for difference < 0.002 vs. each other method). pgBoost also outperformed existing methods in enrichment for CRISPR-validated links (e.g. 4.8x vs. 1.6-4.1x at distance >10kb; p-value for difference = 0.25 vs. distance-based method and < 2e-5 for each other method), with larger improvements at larger distances (e.g. 15x vs. 1.6-2.5x at distance >100kb; p-value for difference < 0.009 for each other method). Similar improvements in enrichment were observed for links derived from Activity-By-Contact (ABC) scores and GWAS data. We further determined that restricting pgBoost to features from a focal cell type improved the identification of SNP-gene links relevant to that cell type. We highlight several examples where pgBoost linked fine-mapped GWAS variants to experimentally validated or biologically plausible target genes that were not implicated by other methods. In conclusion, a non-linear combination of linking strategies, including genomic distance, improves power to identify target genes underlying GWAS associations.
Collapse
|
13
|
Kalnapenkis A, Jõeloo M, Lepik K, Kukuškina V, Kals M, Alasoo K, Mägi R, Esko T, Võsa U. Genetic determinants of plasma protein levels in the Estonian population. Sci Rep 2024; 14:7694. [PMID: 38565889 PMCID: PMC10987560 DOI: 10.1038/s41598-024-57966-3] [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: 06/22/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing the effects of common genetic variations on the proteome. Here, we assessed the impact of the common and rare genetic variations as well as the copy number variants (CNVs) on 326 plasma proteins measured in up to 500 individuals. We identified 184 cis and 94 trans signals for 157 protein traits, which were further fine-mapped to credible sets for 101 cis and 87 trans signals for 151 proteins. Rare genetic variation contributed to the levels of 7 proteins, with 5 cis and 14 trans associations. CNVs were associated with the levels of 11 proteins (7 cis and 5 trans), examples including a 3q12.1 deletion acting as a hub for multiple trans associations; and a CNV overlapping NAIP, a sensor component of the NAIP-NLRC4 inflammasome which is affecting pro-inflammatory cytokine interleukin 18 levels. In summary, this work presents a comprehensive resource of genetic variation affecting the plasma protein levels and provides the interpretation of identified effects.
Collapse
Affiliation(s)
- Anette Kalnapenkis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
| | - Maarja Jõeloo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kaido Lepik
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Viktorija Kukuškina
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| |
Collapse
|
14
|
Dudek G, Sakowski S, Brzezińska O, Sarnik J, Budlewski T, Dragan G, Poplawska M, Poplawski T, Bijak M, Makowska J. Machine learning-based prediction of rheumatoid arthritis with development of ACPA autoantibodies in the presence of non-HLA genes polymorphisms. PLoS One 2024; 19:e0300717. [PMID: 38517871 PMCID: PMC10959370 DOI: 10.1371/journal.pone.0300717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
Machine learning (ML) algorithms can handle complex genomic data and identify predictive patterns that may not be apparent through traditional statistical methods. They become popular tools for medical applications including prediction, diagnosis or treatment of complex diseases like rheumatoid arthritis (RA). RA is an autoimmune disease in which genetic factors play a major role. Among the most important genetic factors predisposing to the development of this disease and serving as genetic markers are HLA-DRB and non-HLA genes single nucleotide polymorphisms (SNPs). Another marker of RA is the presence of anticitrullinated peptide antibodies (ACPA) which is correlated with severity of RA. We use genetic data of SNPs in four non-HLA genes (PTPN22, STAT4, TRAF1, CD40 and PADI4) to predict the occurrence of ACPA positive RA in the Polish population. This work is a comprehensive comparative analysis, wherein we assess and juxtapose various ML classifiers. Our evaluation encompasses a range of models, including logistic regression, k-nearest neighbors, naïve Bayes, decision tree, boosted trees, multilayer perceptron, and support vector machines. The top-performing models demonstrated closely matched levels of accuracy, each distinguished by its particular strengths. Among these, we highly recommend the use of a decision tree as the foremost choice, given its exceptional performance and interpretability. The sensitivity and specificity of the ML models is about 70% that are satisfying. In addition, we introduce a novel feature importance estimation method characterized by its transparent interpretability and global optimality. This method allows us to thoroughly explore all conceivable combinations of polymorphisms, enabling us to pinpoint those possessing the highest predictive power. Taken together, these findings suggest that non-HLA SNPs allow to determine the group of individuals more prone to develop RA rheumatoid arthritis and further implement more precise preventive approach.
Collapse
Affiliation(s)
- Grzegorz Dudek
- Electrical Engineering Faculty, Czestochowa University of Technology, Czestochowa, Poland
- Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland
- Centre for Data Analysis, Modelling and Computational Sciences, University of Lodz, Lodz, Poland
| | - Sebastian Sakowski
- Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland
- Centre for Data Analysis, Modelling and Computational Sciences, University of Lodz, Lodz, Poland
| | - Olga Brzezińska
- Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| | - Joanna Sarnik
- Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| | - Tomasz Budlewski
- Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| | - Grzegorz Dragan
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Marta Poplawska
- Biobank, Department of Immunology and Allergy, Medical University of Lodz, Lodz, Poland
| | - Tomasz Poplawski
- Department of Pharmaceutical Microbiology and Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Michał Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Joanna Makowska
- Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| |
Collapse
|
15
|
Cho J, Kim J, Song JS, Uh Y, Lee JH, Lee HS. Whole-Exome Sequencing and Analysis of the T Cell Receptor β and γ Repertoires in Rheumatoid Arthritis. Diagnostics (Basel) 2024; 14:529. [PMID: 38473001 DOI: 10.3390/diagnostics14050529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
This study investigated the potential genetic variants of rheumatoid arthritis (RA) using whole-exome sequencing (WES) and evaluated the disease course using T cell receptor (TCR) repertoire analysis. Fourteen patients with RA and five healthy controls (HCs) were enrolled. For the RA patient group, only treatment-naïve patients were recruited, and data were collected at baseline as well as at 6 and 12 months following the initiation of the disease-modifying antirheumatic drug (DMARD) treatment. Laboratory data and disease parameters were also collected. Genetic variants were detected using WES, and the diversity of the TCR repertoire was assessed using the Shannon-Wiener diversity index. While some variants were detected by WES, their clinical significance should be confirmed by further studies. The diversity of the TCR repertoire in the RA group was lower than that in the HCs; however, after DMARD treatment, it increased significantly. The diversity was negatively correlated with the laboratory findings and disease measures with statistical significance. Variants with a potential for RA pathogenesis were identified, and the clinical significance of the TCR repertoire was evaluated in Korean patients with RA. Further studies are required to confirm the findings of the present study.
Collapse
Affiliation(s)
- Jooyoung Cho
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Juwon Kim
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Ju Sun Song
- GC Genome, GC Labs, Yongin 16924, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Jong-Han Lee
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Hyang Sun Lee
- Division of Rheumatology, Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| |
Collapse
|
16
|
Gao Y, Zhang Y, Liu X. Rheumatoid arthritis: pathogenesis and therapeutic advances. MedComm (Beijing) 2024; 5:e509. [PMID: 38469546 PMCID: PMC10925489 DOI: 10.1002/mco2.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by the unresolved synovial inflammation for tissues-destructive consequence, which remains one of significant causes of disability and labor loss, affecting about 0.2-1% global population. Although treatments with disease-modifying antirheumatic drugs (DMARDs) are effective to control inflammation and decrease bone destruction, the overall remission rates of RA still stay at a low level. Therefore, uncovering the pathogenesis of RA and expediting clinical transformation are imminently in need. Here, we summarize the immunological basis, inflammatory pathways, genetic and epigenetic alterations, and metabolic disorders in RA, with highlights on the abnormality of immune cells atlas, epigenetics, and immunometabolism. Besides an overview of first-line medications including conventional DMARDs, biologics, and small molecule agents, we discuss in depth promising targeted therapies under clinical or preclinical trials, especially epigenetic and metabolic regulators. Additionally, prospects on precision medicine based on synovial biopsy or RNA-sequencing and cell therapies of mesenchymal stem cells or chimeric antigen receptor T-cell are also looked forward. The advancements of pathogenesis and innovations of therapies in RA accelerates the progress of RA treatments.
Collapse
Affiliation(s)
- Ying Gao
- Department of RheumatologyChanghai HospitalNaval Medical UniversityShanghaiChina
| | - Yunkai Zhang
- Naval Medical CenterNaval Medical UniversityShanghaiChina
| | - Xingguang Liu
- National Key Laboratory of Immunity & InflammationNaval Medical UniversityShanghaiChina
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
| |
Collapse
|
17
|
Zhang Q, Liu A, Huang C, Xiong Z, Cheng Q, Zhang J, Lin J, Yang H. Effect of basal metabolic rate on rheumatoid arthritis: a Mendelian randomization study. Postgrad Med J 2024; 100:187-195. [PMID: 37978228 DOI: 10.1093/postmj/qgad105] [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: 08/11/2023] [Revised: 09/23/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE Basal metabolic rate (BMR) as one of the most basic and significant indicators of metabolism has been associated with human health. Previous studies showed that the development of rheumatoid arthritis (RA) is linked to BMR; however, the causal relationship between BMR and RA is unknown. Thus, we aimed to explore the causal relationship between BMR and RA as well as RA-related factors. METHODS Mendelian randomization (MR) analysis was performed on collected genome-wide association studies information. The effect of horizontal pleiotropy was detected by MR-PRESSO and MR-Radial. Five MR analysis methods were applied, including inverse variance weighted, MR-Egger, weighted median, weighted mode, and simple mode. Four sensitivity analysis methods were used for the validation of the significant MR analysis results. A two-component mixture of regressions method was additionally used to validate single nucleotide polymorphisms and to verify results. RESULTS Genetically, there is a causal effect of BMR on overall RA (odds ratio = 1.25, 95% confidence interval: 1.07-1.47, PIVW = .006), seropositive RA (odds ratio = 1.20, 95% confidence interval: 1.01-1.44, PIVW = .035), and seronegative RA (odds ratio = 1.36, 95% confidence interval: 1.04-1.78, PIVW = .023). Sensitivity analyses validated the robustness of the above associations. No evidence supported the effect of RA on BMR. Moreover, BMR showed no causal relationship with rheumatoid factor, C-reactive protein, erythrocyte sedimentation rate, interleukin-1β, tumor necrosis factor-α, and matrix metallopeptidase 3. CONCLUSION MR results implied the causal effect of BMR on RA and raised our attention to the importance of BMR in RA's pathology.
Collapse
Affiliation(s)
- Qin Zhang
- Department of Orthopaedics, First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, P.R. China
- Department of Orthopaedics, Suzhou Dushu Lake Hospital, Dushu Lake Hospital Affiliated to Soochow University, Medical Centre of Soochow University, Suzhou, 215001, Jiangsu, China
| | - Ang Liu
- Department of Orthopaedics, First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, P.R. China
- Department of Orthopaedics, Suzhou Dushu Lake Hospital, Dushu Lake Hospital Affiliated to Soochow University, Medical Centre of Soochow University, Suzhou, 215001, Jiangsu, China
| | - Cheng Huang
- Department of Orthopaedics, China-Japan Friendship Hospital, Beijing 100029, P.R. China
| | - ZhenCheng Xiong
- Department of Orthopedic Surgery, West China Medical School, Sichuan University, West China Hospital, Chengdu, Sichuan 610041, P.R. China
- Department of Trauma Center, West China Medical School, Sichuan University, West China Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Qi Cheng
- Department of Orthopaedics, First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jun Zhang
- Suzhou Institute of Trade & Commerce, Suzhou, Jiangsu 215006, P.R. China
| | - Jun Lin
- Department of Orthopaedics, First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, P.R. China
- Department of Orthopaedics, Suzhou Dushu Lake Hospital, Dushu Lake Hospital Affiliated to Soochow University, Medical Centre of Soochow University, Suzhou, 215001, Jiangsu, China
| | - Huilin Yang
- Department of Orthopaedics, First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, P.R. China
| |
Collapse
|
18
|
Bravo-Villagra KM, Muñoz-Valle JF, Baños-Hernández CJ, Cerpa-Cruz S, Navarro-Zarza JE, Parra-Rojas I, Aguilar-Velázquez JA, García-Arellano S, López-Quintero A. STAT4 Gene Variant rs7574865 Is Associated with Rheumatoid Arthritis Activity and Anti-CCP Levels in the Western but Not in the Southern Population of Mexico. Genes (Basel) 2024; 15:241. [PMID: 38397230 PMCID: PMC10887563 DOI: 10.3390/genes15020241] [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: 11/26/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Rheumatoid Arthritis (RA) is a multifactorial autoimmune disease. Currently, several genes play an important role in the development of the disease. The objective was to evaluate the association of the STAT4 rs7574865 and rs897200 gene variants with RA susceptibility, DAS28, RF, and anti-CCP in Western and Southern Mexico populations. Genotyping was performed on 476 samples (cases = 240; controls = 236) using the Taqman® system and qPCR probes. Disease activity was assessed using DAS28 and HAQ DI. CRP, ESR, RF, and anti-CCP were determined for clinical assessment. Our study showed there is a statistically significant association with susceptibility to RA for the rs7574865 variant in the Western population for the GT and TT genotypes. The same genotypes also showed a moderate-to-high activity according to DAS28 and positive anti-CCP compared to the control group. This association was not found in the Southern population. This work confirms the association of the rs7574865 variant with RA, as well as a moderate-to-high activity and positive anti-CCP in the Western population but not in the Southern population. No association of the rs897200 variant was found in any of the studied populations.
Collapse
Affiliation(s)
- Karla Mayela Bravo-Villagra
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Christian Johana Baños-Hernández
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Sergio Cerpa-Cruz
- Antiguo Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44200, Mexico;
| | | | - Isela Parra-Rojas
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de Bravo 39086, Mexico;
| | - José Alonso Aguilar-Velázquez
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Samuel García-Arellano
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico; (J.F.M.-V.); (C.J.B.-H.); (S.G.-A.)
| | - Andres López-Quintero
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UdeG), Guadalajara 44340, Mexico;
| |
Collapse
|
19
|
Heutz JW, Rogier C, Niemantsverdriet E, van den Eeden SJF, de Jong PHP, Lubberts E, Geluk A, van der Helm-van Mil AHM. The course of cytokine and chemokine gene expression in clinically suspect arthralgia patients during progression to inflammatory arthritis. Rheumatology (Oxford) 2024; 63:563-570. [PMID: 37280058 PMCID: PMC10836970 DOI: 10.1093/rheumatology/kead238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/14/2023] [Accepted: 05/13/2023] [Indexed: 06/08/2023] Open
Abstract
OBJECTIVES Autoantibody responses increase years before the onset of inflammatory arthritis (IA) and are stable during transitioning from clinically suspect arthralgia (CSA) to IA. Cytokine and chemokine levels also increase years before IA onset. However, the course in the at-risk stage of CSA during progression to disease or non-progression is unknown. To increase the understanding of processes mediating disease development, we studied the course of cytokine, chemokine and related receptors gene expression in CSA patients during progression to IA and in CSA patients who ultimately did not develop IA. METHODS Whole-blood RNA expression of 37 inflammatory cytokines, chemokines and related receptors was determined by dual-colour reverse transcription multiplex ligation-dependent probe amplification in paired samples of CSA patients at CSA onset and either at IA development or after 24 months without IA development. ACPA-positive and ACPA-negative CSA patients developing IA were compared at CSA onset and during progression to IA. Generalised estimating equations tested changes over time. A false discovery rate approach was applied. RESULTS None of the cytokine/chemokine genes significantly changed in expression between CSA onset and IA development. In CSA patients without IA development, G-CSF expression decreased (P = 0.001), whereas CCR6 and TNIP1 expression increased (P < 0.001 and P = 0.002, respectively) over a 2 year period. Expression levels in ACPA-positive and ACPA-negative CSA patients who developed IA were similar. CONCLUSION Whole-blood gene expression of assessed cytokines, chemokines and related receptors did not change significantly from CSA to IA development. This suggests that changes in expression of these molecules may not be related to the final process of developing chronicity and may have occurred preceding CSA onset. Changes in gene expression in CSA patients without IA development may provide clues for processes related to resolution.
Collapse
Affiliation(s)
- Judith W Heutz
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cleo Rogier
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Susan J F van den Eeden
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Pascal H P de Jong
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik Lubberts
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Annette H M van der Helm-van Mil
- Department of Rheumatology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
20
|
Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
Collapse
Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| |
Collapse
|
21
|
Wang Y, Yang Y, Jia X, Zhao C, Yang C, Fan J, Wang N, Shi X. Identification of the shared genetic architecture underlying seven autoimmune diseases with GWAS summary statistics. Front Immunol 2024; 14:1303675. [PMID: 38259487 PMCID: PMC10800382 DOI: 10.3389/fimmu.2023.1303675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Background The common clinical symptoms and immunopathological mechanisms have been observed among multiple autoimmune diseases (ADs), but the shared genetic etiology remains unclear. Methods GWAS summary statistics of seven ADs were downloaded from Open Targets Genetics and Dryad. Linkage disequilibrium score regression (LDSC) was applied to estimate overall genetic correlations, bivariate causal mixture model (MiXeR) was used to qualify the polygenic overlap, and stratified-LDSC partitioned heritability to reveal tissue and cell type specific enrichments. Ultimately, we conducted a novel adaptive association test called MTaSPUsSet for identifying pleiotropic genes. Results The high heritability of seven ADs ranged from 0.1228 to 0.5972, and strong genetic correlations among certain phenotypes varied between 0.185 and 0.721. There was substantial polygenic overlap, with the number of shared SNPs approximately 0.03K to 0.21K. The specificity of SNP heritability was enriched in the immune/hematopoietic related tissue and cells. Furthermore, we identified 32 pleiotropic genes associated with seven ADs, 23 genes were considered as novel genes. These genes were involved in several cell regulation pathways and immunologic signatures. Conclusion We comprehensively explored the shared genetic architecture across seven ADs. The findings progress the exploration of common molecular mechanisms and biological processes involved, and facilitate understanding of disease etiology.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Xuezhong Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
22
|
Joseph J, Mathew J, Alexander J. Scaffold Proteins in Autoimmune Disorders. Curr Rheumatol Rev 2024; 20:14-26. [PMID: 37670692 DOI: 10.2174/1573397119666230904151024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Cells transmit information to the external environment and within themselves through signaling molecules that modulate cellular activities. Aberrant cell signaling disturbs cellular homeostasis causing a number of different diseases, including autoimmunity. Scaffold proteins, as the name suggests, serve as the anchor for binding and stabilizing signaling proteins at a particular locale, allowing both intra and intercellular signal amplification and effective signal transmission. Scaffold proteins play a critical role in the functioning of tight junctions present at the intersection of two cells. In addition, they also participate in cleavage formation during cytokinesis, and in the organization of neural synapses, and modulate receptor management outcomes. In autoimmune settings such as lupus, scaffold proteins can lower the cell activation threshold resulting in uncontrolled signaling and hyperactivity. Scaffold proteins, through their binding domains, mediate protein- protein interaction and play numerous roles in cellular communication and homeostasis. This review presents an overview of scaffold proteins, their influence on the different signaling pathways, and their role in the pathogenesis of autoimmune and auto inflammatory diseases. Since these proteins participate in many roles and interact with several other signaling pathways, it is necessary to gain a thorough understanding of these proteins and their nuances to facilitate effective target identification and therapeutic design for the treatment of autoimmune disorders.
Collapse
Affiliation(s)
- Josna Joseph
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - John Mathew
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - Jessy Alexander
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University of Buffalo, New York, USA
| |
Collapse
|
23
|
Xu Y, Wu Q. Genome-wide polygenic risk score for rheumatoid arthritis prediction in postmenopausal women. J Gene Med 2024; 26:e3659. [PMID: 38282146 PMCID: PMC10823178 DOI: 10.1002/jgm.3659] [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: 06/01/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA), a common autoimmune disease, exhibits a vital genetic component. Polygenic risk scores (PRS) derived from genome-wide association studies (GWAS) offer potential utility in predicting disease susceptibility. The present study aimed to develop and validate a PRS for predicting RA risk in postmenopausal women. METHODS The study developed a novel PRS using 225,000 genetic variants from a GWAS dataset. The PRS was developed in a cohort of 8967 postmenopausal women and validated in an independent cohort of 6269 postmenopausal women. Among the development cohort, approximately 70% were Hispanic and approximately 30% were African American. The testing cohort comprised approximately 50% Hispanic and 50% Caucasian individuals. Stratification according to PRS quintiles revealed a pronounced gradient in RA prevalence and odds ratios. RESULTS High PRS was significantly associated with increased RA risk in individuals aged 60-70 years, ≥ 70 years, and overweight and obese participants. Furthermore, at age 65 years, individuals in the bottom 5% of the PRS distribution have an absolute risk of RA at 30.6% (95% confidence interval = 18.5%-42.6%). The risk increased to 53.8% (95% confidence interval = 42.8%-64.9%) for those in the top 5% of the PRS distribution. CONCLUSIONS The PRS developed in the present study is significantly associated with RA risk, showing the potential for early screening of RA in postmenopausal women. This work demonstrates the feasibility of personalized medicine in identifying high-risk individuals for RA, indicating the need for further studies to test the utility of PRS in other populations.
Collapse
Affiliation(s)
- Yingke Xu
- Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, NV, USA
- Department of Epidemiology and Biostatistics, School of Public Health, the University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Qing Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
24
|
Vyawahare A, Ansari MM, Kumar A, Ahmad A, Mishra RK, Jori C, Nadeem A, Siddiqui N, Raza SS, Khan R. Enzyme targeted delivery of sivelestat loaded nanomicelle inhibits arthritic severity in experimental arthritis. Life Sci 2023; 334:122206. [PMID: 37879159 DOI: 10.1016/j.lfs.2023.122206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/21/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
AIMS Rheumatoid arthritis (RA) is chronic inflammatory disorder mainly affects the lining of articular cartilage of synovial joints characterized by severe inflammation and joint damage. The expression of proteolytic enzymes like MMP-2 and Neutrophil Elastase (NE) worsens the RA condition. To address this concern, we have synthesized dual enzyme targeted chlorotoxin conjugated nanomicelles loaded with sivelestat as broad spectrum treatment for RA. MATERIALS AND METHODS Conjugation of the chlorotoxin over nanomicelle and incorporation of sivelestat in nanomicelle provide it dual targeting potential. The sivelestat loaded nanomicelle (SLM) evaluated for the drug release and in-vitro cytocompatibility. Further, investigated its in-vivo anti-arthritic potential on collagen-induced arthritis in wistar rats. KEY FINDINGS The microscopic observation of SLM showed spherical ball like appearance with size ranging from 190 to 230 nm. SLM showed good drug loading and encapsulation efficiency along with no cytotoxicity against healthy cell lines. In-vivo therapeutic assessment on collagen induced arthritis rat model showed potential chondroprotection. The microscopic visualization of articular cartilage by staining showed that it restores the cartilage integrity and lowers the expression of pro-inflammatory enzymes showed by Immunohistochemistry and Immunofluorescence. We observed that, it restrain the mediators of synovial inflammation by simultaneous inhibition of the proteolytic enzymes involved in swelling, cartilage destruction and joint damage which provides strong chondroprotection. SIGNIFICANCE We report that significant alleviation of inflammation and inhibition of proteolytic enzymes together might provide enhanced potential for the treatment and management of RA.
Collapse
Affiliation(s)
- Akshay Vyawahare
- Department of Chemical Biology, Institute of Nano Science and Technology, Sector 81, Knowledge city, Sahibzada Ajit Singh Nagar, Mohali, Punjab 140306, India
| | - Md Meraj Ansari
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Ajay Kumar
- Department of Chemical Biology, Institute of Nano Science and Technology, Sector 81, Knowledge city, Sahibzada Ajit Singh Nagar, Mohali, Punjab 140306, India
| | - Anas Ahmad
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Rakesh Kumar Mishra
- Department of Chemical Biology, Institute of Nano Science and Technology, Sector 81, Knowledge city, Sahibzada Ajit Singh Nagar, Mohali, Punjab 140306, India
| | - Chandrashekhar Jori
- Department of Chemical Biology, Institute of Nano Science and Technology, Sector 81, Knowledge city, Sahibzada Ajit Singh Nagar, Mohali, Punjab 140306, India
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nahid Siddiqui
- Amity Institute of Biotechnology, Amity University, Noida 201303, India
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Department of Biotechnology, Era's Lucknow Medical College and Hospital, Sarfarazganj, Lucknow 226003, Uttar Pradesh, India
| | - Rehan Khan
- Department of Chemical Biology, Institute of Nano Science and Technology, Sector 81, Knowledge city, Sahibzada Ajit Singh Nagar, Mohali, Punjab 140306, India.
| |
Collapse
|
25
|
Fumeron F, Velho G, Alzaid F, El Boustany R, Vandiedonck C, Bonnefond A, Froguel P, Potier L, Marre M, Balkau B, Roussel R, Venteclef N. Genetic variants of interferon-response factor 5 are associated with the incidence of chronic kidney disease: the D.E.S.I.R. study. Genes Immun 2023; 24:303-308. [PMID: 37978231 PMCID: PMC10721545 DOI: 10.1038/s41435-023-00229-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Inflammation has been associated with renal diseases. The Interferon Regulatory Factor (IRF)-5 is a key transcription factor in the pro-inflammatory polarization of M1-like macrophages. GWAS have reported that the IRF5 locus is associated with autoimmune diseases and with the estimated glomerular filtration rate (eGFR). We study whether allelic variations in IRF5 are associated with the incidence of chronic kidney disease (CKD) in a general population. We genotyped eleven IRF5 SNPs in the French D.E.S.I.R. cohort from the general population (n = 4820). Associations of SNPs with baseline renal parameters were assessed. Data were analyzed for three endpoints during a 9-year follow-up, incidence of:at least stage 3 CKD, the KDIGO criterion "certain drop in eGFR", and incidence of micro/macro albuminuria. In the cross-sectional analysis, rs10954213 and rs10954214 were associated with eGFR and rs1874328 with urinary albumin/creatinine ratio (ACR). Rs3807306, rs11761199, rs78658945, rs1874328, rs10954213 and rs11770589 were associated with the incidence of stage 3 CKD in multi-adjusted models. Rs4731532, rs3807306, and rs11761199 were associated with the incidence of CKD defined by the KDIGO. Rs4731532, rs3807306, rs11761199 and rs79288514 were associated with the incidence of micro/macro albuminuria. Our results support the hypothesis of the importance of IRF5 mediated macrophage polarization in the etiology of CKD.
Collapse
Affiliation(s)
- Frédéric Fumeron
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France.
| | - Gilberto Velho
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
| | - Fawaz Alzaid
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
- Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Ray El Boustany
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
| | - Claire Vandiedonck
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
| | - Amélie Bonnefond
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Philippe Froguel
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Louis Potier
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
- Department of Diabetology, Endocrinology and Nutrition, Assistance Publique-Hôpitaux de Paris, Bichat Hospital, DHU FIRE, Paris, France
| | - Michel Marre
- Clinique Ambroise Paré, Neuilly-sur-Seine, France
| | - Beverley Balkau
- Centre for Research in Epidemiology and Population Health (CESP), INSERM, UMR-S 1018, University Paris-Sud, University Versailles Saint-Quentin, Villejuif, France
| | - Ronan Roussel
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
- Department of Diabetology, Endocrinology and Nutrition, Assistance Publique-Hôpitaux de Paris, Bichat Hospital, DHU FIRE, Paris, France
| | - Nicolas Venteclef
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
| |
Collapse
|
26
|
Wang Q, Martínez-Bonet M, Kim T, Sparks JA, Ishigaki K, Chen X, Sudman M, Aguiar V, Sim S, Hernandez MC, Chiu DJ, Wactor A, Wauford B, Marion MC, Gutierrez-Arcelus M, Bowes J, Eyre S, Nordal E, Prahalad S, Rygg M, Videm V, Raychaudhuri S, Weirauch MT, Langefeld CD, Thompson SD, Nigrovic PA. Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant. CELL GENOMICS 2023; 3:100420. [PMID: 38020975 PMCID: PMC10667332 DOI: 10.1016/j.xgen.2023.100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/16/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023]
Abstract
TRAF1/C5 was among the first loci shown to confer risk for inflammatory arthritis in the absence of an associated coding variant, but its genetic mechanism remains undefined. Using Immunochip data from 3,939 patients with juvenile idiopathic arthritis (JIA) and 14,412 control individuals, we identified 132 plausible common non-coding variants, reduced serially by single-nucleotide polymorphism sequencing (SNP-seq), electrophoretic mobility shift, and luciferase studies to the single variant rs7034653 in the third intron of TRAF1. Genetically manipulated experimental cells and primary monocytes from genotyped donors establish that the risk G allele reduces binding of Fos-related antigen 2 (FRA2), encoded by FOSL2, resulting in reduced TRAF1 expression and enhanced tumor necrosis factor (TNF) production. Conditioning on this JIA variant eliminated attributable risk for rheumatoid arthritis, implicating a mechanism shared across the arthritis spectrum. These findings reveal that rs7034653, FRA2, and TRAF1 mediate a pathway through which a non-coding functional variant drives risk of inflammatory arthritis in children and adults.
Collapse
Affiliation(s)
- Qiang Wang
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marta Martínez-Bonet
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory of Immune-regulation, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Taehyeung Kim
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey A. Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoting Chen
- Center of Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Marc Sudman
- Center of Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Vitor Aguiar
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sangwan Sim
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Darren J. Chiu
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexandra Wactor
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Wauford
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Miranda C. Marion
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Center of Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Ellen Nordal
- University Hospital of North Norway and UIT The Arctic University of Norway, Tromsø, Norway
| | - Sampath Prahalad
- Emory University Department of Pediatrics and Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Marite Rygg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Pediatrics, St. Olav’s University Hospital, Trondheim, Norway
| | - Vibeke Videm
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Data Science, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Matthew T. Weirauch
- Center of Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Divisions of Human Genetics, Biomedical Informatics, and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Susan D. Thompson
- Center of Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Peter A. Nigrovic
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
27
|
Garg U, Jain N, Kaul S, Nagaich U. Role of Albumin as a Targeted Drug Carrier in the Management of Rheumatoid Arthritis: A Comprehensive Review. Mol Pharm 2023; 20:5345-5358. [PMID: 37870420 DOI: 10.1021/acs.molpharmaceut.3c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
An endogenous transporter protein called albumin interacts with the Fc receptor to provide it with multiple substrate-binding domains, cell membrane receptor activation, and an extended circulating half-life. Albumin has the remarkable ability to bind with receptors viz. secreted protein acidic and rich in cysteine (SPARC) and scavenger protein-A (SR-A) that are overexpressed during rheumatoid arthritis (RA), enabling active targeting of the disease site instead of requiring specialized substrates to be added to the nanocarrier. RA, a chronic autoimmune illness, is characterized by the presence of a severe inflammatory response. RA patients have low serum albumin concentration, which signifies the high uptake of albumin at the inflammatory sites, giving a rationale to use albumin as a drug carrier for RA therapy. Albumin has the capacity for both passive and active targeting. It is an abundantly available protein in the bloodstream showing excellent cellular compatibility, degradability in biological tissues, nonantigenicity, and safety. There are three strategies of albumin mediated drug delivery as encapsulating therapeutics in albumin nanoparticles, chemically conjugating drugs with functional proteins, and albumin itself which is used as a targeting ligand to deliver drugs specifically to cells or tissues that express albumin-binding receptors. In the current review, an attempt has been made to highlight the significant evidence of albumin as a drug delivery carrier for the safe and effective management of RA. Evidence has been provided in the form of recent research advances, clinical trials, and patents. Additionally, this review will outline the prospective for the potential utilization of albumin as a drug vehicle for RA and suggest possible future avenues to provide the perspective for subsequent studies.
Collapse
Affiliation(s)
- Unnati Garg
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| | - Neha Jain
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| | - Shreya Kaul
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| | - Upendra Nagaich
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| |
Collapse
|
28
|
Ye W, Yu Y, Zhu X, Wan W, Liu Y, Zou H, Zhu Z. A Common Functional Variant at the Enhancer of the Rheumatoid Arthritis Risk Gene ORMDL3 Regulates its Expression Through Allele-Specific JunD Binding. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:485-495. [PMID: 37881318 PMCID: PMC10593690 DOI: 10.1007/s43657-023-00107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 10/27/2023]
Abstract
Genome-wide association studies (GWASs) have identified over 100 loci associated with rheumatoid arthritis (RA); however, the functionally affected genes and the underlying molecular mechanisms contributing to these associations are often unknown. In this study, we conducted an integrative genomic analysis incorporating multiple "omics" data and identified a functional regulatory DNA variant, rs56199421, and a plausible mechanism by which it regulates the expression of a putative RA risk gene, ORMDL Sphingolipid Biosynthesis Regulator 3 (ORMDL3). The T allele of rs56199421, located in the enhancer region of ORMDL3, exhibited stronger direct binding ability than the other C allele of rs56199421 did in vitro with the transcription factor JunD and demonstrated higher transcriptional activity. Moreover, the T allele of rs56199421 is associated with elevated RA risk, and ORMDL3 expression is increased in RA patients. Thus, these findings suggest that the T allele of rs56199421 enhances JunD transcription factor binding, increases enhancer activity, and elevates the expression of the RA risk gene ORMDL3. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00107-z.
Collapse
Affiliation(s)
- Wenjing Ye
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Yiyun Yu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Xiaoxia Zhu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Weiguo Wan
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Yun Liu
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Hejian Zou
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Zaihua Zhu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| |
Collapse
|
29
|
Ali Y, Kausar M, Farooq M, Farooqi N, Ul Islam Z, Khan S, Aman A, Khan N, Kamil A, Jalil F. Association of IL-17F rs2397084 (E126G), rs11465553 (V155I) and rs763780 (H161R) variants with rheumatoid arthritis and their effects on the stability of protein. PLoS One 2023; 18:e0285874. [PMID: 37751416 PMCID: PMC10522029 DOI: 10.1371/journal.pone.0285874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/03/2023] [Indexed: 09/28/2023] Open
Abstract
Interleukin-17F (IL-17F), considered a pro-inflammatory cytokine, has been shown to contribute to skeletal tissue degradation and hence chronic inflammation in rheumatoid arthritis (RA). In this study we utilized bioinformatics tools to analyze the effect of three exonic SNPs (rs2397084, rs11465553, and rs763780) on the structure and function of the IL-17F gene, and evaluated their association with RA in Pakistani patients. The predicted deleterious and damaging effects of identified genetic variants were assessed through the utilization of multiple bioinformatics tools including PROVEAN, SNP&GO, SIFT, and PolyPhen2. Structural and functional effects of these variants on protein structures were evaluated through the use of additional tools such as I-Mutant, MutPred, and ConSurf. Three-dimensional (3D) models of both the wild-type and mutant proteins were constructed through the utilization of I-TASSER software, with subsequent structural comparisons between the models conducted through the use of the TM-align score. A total of 500 individuals, 250 cases and 250 controls, were genotyped through Tri-ARMS-PCR method and the resultant data was statistically analyzed using various inheritance models. Our bioinformatics analysis showed significant structural differences for wild type and mutant protein (TM-scores and RMSD values were 0.85934 and 2.34 for rs2397084 (E126G), 0.87388 and 2.49 for rs11465553 (V155I), and 0.86572 and 0.86572 for rs763780 (H161R) with decrease stability for the later. Overall, these tools enabled us to predict that these variants are crucial in causing disease phenotypes. We further tested each of these single nucleotide variants for their association with RA. Our analysis revealed a strong positive association between the genetic variant rs763780 and the risk of developing rheumatoid arthritis (RA) at both the genotypic and allelic levels. The genotypic association was statistically significant[χ2 = 111.8; P value <0.0001], as was the allelic level [OR 3.444 (2.539-4.672); P value 0.0008]. These findings suggest that the presence of this genetic variant may increase the susceptibility to RA. Similarly, we observed a significant distribution of the genetic variant rs11465553 at the genotypic level [χ2 = 25.24; P value = 0.0001]. However, this variant did not show a significant association with RA at the allelic level [OR = 1.194 (0.930-1.531); P value = 0.183]. However, the distribution of variant rs2397084 was more or less random across our sample with no significant association either at genotypic and or allelic level. Put together, our association study and in silico prediction of decreasing of IL17-F protein stabilty confirmed that two SNPs, rs11465553 and rs763780 are crucial to the suscetibility of and showed that these RA in Pakistani patients.
Collapse
Affiliation(s)
- Yasir Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
- School of Biomedical Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Masood Kausar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Mazhar Farooq
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Nadia Farooqi
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ul Islam
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Suleman Khan
- Consultant Rheumatologists, Lady Reading Hospital-MTI Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Aisha Aman
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Naveed Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Atif Kamil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| |
Collapse
|
30
|
Slaufova M, Karakaya T, Di Filippo M, Hennig P, Beer HD. The gasdermins: a pore-forming protein family expressed in the epidermis. Front Immunol 2023; 14:1254150. [PMID: 37771587 PMCID: PMC10523161 DOI: 10.3389/fimmu.2023.1254150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
Gasdermins comprise a family of pore-forming proteins, which play critical roles in (auto)inflammatory diseases and cancer. They are expressed as self-inhibited precursor proteins consisting of an aminoterminal cytotoxic effector domain (NT-GSDM) and a carboxyterminal inhibitor domain (GSDM-CT) separated by an unstructured linker region. Proteolytic processing in the linker region liberates NT-GSDM, which translocates to membranes, forms oligomers, and induces membrane permeabilization, which can disturb the cellular equilibrium that can lead to cell death. Gasdermin activation and pore formation are associated with inflammation, particularly when induced by the inflammatory protease caspase-1 upon inflammasome activation. These gasdermin pores allow the release of the pro-inflammatory cytokines interleukin(IL)-1β and IL-18 and induce a lytic type of cell death, termed pyroptosis that supports inflammation, immunity, and tissue repair. However, even at the cellular level, the consequences of gasdermin activation are diverse and range from induction of programmed cell death - pyroptosis or apoptosis - to poorly characterized protective mechanisms. The specific effects of gasdermin activation can vary between species, cell types, the membrane that is being permeabilized (plasma membrane, mitochondrial membrane, etc.), and the overall biological state of the local tissue/cells. In epithelia, gasdermins seem to play crucial roles. Keratinocytes represent the main cell type of the epidermis, which is the outermost skin layer with an essential barrier function. Compared to other tissues, keratinocytes express all members of the gasdermin family, in part in a differentiation-specific manner. That raises questions regarding the specific roles of individual GSDM family members in the skin, the mechanisms and consequences of their activation, and the potential crosstalk between them. In this review, we summarize the current knowledge about gasdermins with a focus on keratinocytes and the skin and discuss the possible roles of the different family members in immunity and disease.
Collapse
Affiliation(s)
- Marta Slaufova
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Tugay Karakaya
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Michela Di Filippo
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Paulina Hennig
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Hans-Dietmar Beer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| |
Collapse
|
31
|
Cao Y, Yang Y, Hu Q, Wei G. Identification of potential drug targets for rheumatoid arthritis from genetic insights: a Mendelian randomization study. J Transl Med 2023; 21:616. [PMID: 37697373 PMCID: PMC10496392 DOI: 10.1186/s12967-023-04474-z] [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: 05/22/2023] [Accepted: 08/27/2023] [Indexed: 09/13/2023] Open
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is a chronic inflammatory illness that mostly affects the joints of the hands and feet and can reduce life expectancy by an average of 3 to 10 years. Although tremendous progress has been achieved in the treatment of RA, a large minority of patients continue to respond poorly to existing medications, owing in part to a lack of appropriate therapeutic targets. METHODS To find therapeutic targets for RA, a Mendelian randomization (MR) was performed. Cis-expression quantitative trait loci (cis-eQTL, exposure) data were obtained from the eQTLGen Consortium (sample size 31,684). Summary statistics for RA (outcome) were obtained from two largest independent cohorts: sample sizes of 97,173 (22,350 cases and 74,823 controls) and 269,377 (8279 cases and 261,098), respectively. Colocalisation analysis was used to test whether RA risk and gene expression were driven by common SNPs. Drug prediction and molecular docking was further used to validate the medicinal value of drug targets. RESULTS Seven drug targets were significant in both cohorts in MR analysis and supported by localization. PheWAS at the gene level showed only ATP2A1 associated with other traits. These genes are strongly associated with immune function in terms of biological significance. Molecular docking showed excellent binding for drugs and proteins with available structural data. CONCLUSION This study identifies seven potential drug targets for RA. Drugs designed to target these genes have a higher chance of success in clinical trials and is expected to help prioritise RA drug development and save on drug development costs.
Collapse
Affiliation(s)
- Yu Cao
- Department of Orthopedics, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, No. N1, Shangcheng Avenue, Yiwu City, Zhejiang Province, China
- Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Ying Yang
- Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Qingfeng Hu
- Department of Orthopedics, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, No. N1, Shangcheng Avenue, Yiwu City, Zhejiang Province, China.
| | - Guojun Wei
- Department of Orthopedics, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, No. N1, Shangcheng Avenue, Yiwu City, Zhejiang Province, China.
| |
Collapse
|
32
|
Xu M, Wu T, Li Z, Xin G. Influence of genetically predicted autoimmune diseases on NAFLD. Front Immunol 2023; 14:1229570. [PMID: 37767101 PMCID: PMC10520707 DOI: 10.3389/fimmu.2023.1229570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction Non-alcoholic fatty liver disease (NAFLD), the emerging cause of end-stage liver disease, is the most common liver disease. Determining the independent risk factors of NAFLD and patients who need more monitoring is important. Methods Two-Sample Mendelian randomization (MR) was performed in the analysis to investigate the causal association of different autoimmune diseases with NAFLD using summary level data. Genome-wide association study (GWAS) of 5 autoimmune diseases including celiac disease (CeD), Crohn's disease (CD), multiple sclerosis (MS), rheumatoid arthritis (RA), and type 1 diabetes (T1D) were selected for Instrument variables (IVs). NAFLD was included as outcome. Result After adjusting for confounding factors, genetic predisposition of CeD (OR= 0.973, [0.949,0.997], IVW p-value=0.026), MS (OR= 1.048, [1.012,1.085], IVW p-value= 0.008), RA (OR= 1.036, [1.006,1.066], IVW p-value=0.019), T1D (OR= 1.039, [1.002,1.079], IVW p-value= 0.041) is causally associated with NAFLD. No causal effect was found between CD and NAFLD. Conclusion CeD itself may be a protective factor for NAFLD, the results of previous observational studies have been influenced by confounding factors, and the morbidity of NAFLD may be higher in patients with MS, RA, and T1D than in common populations, and monitoring the prevalence of NAFLD in these populations is considerable.
Collapse
|
33
|
Machaj F, Rosik J, Szostak B, Malinowski D, Safranow K, Olędzka G, Wiechec E, Pawlik A. The association between CYB5A gene rs1790834 polymorphism and clinical improvement after 6 months of leflunomide treatment in women with rheumatoid arthritis. Clin Rheumatol 2023; 42:2477-2483. [PMID: 37289314 DOI: 10.1007/s10067-023-06653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
INTRODUCTION/OBJECTIVES Rheumatoid arthritis (RA) is a disease affecting around 1% of the population in developed countries and can be treated with leflunomide. The higher prevalence of RA among women and numerous previous studies suggested the crucial role of sex hormones. Cytochrome CYB5A regulates the synthesis of androgens. Therefore, the aim of this study was to determine the association between common CYB5A gene polymorphism and the response to leflunomide in women with RA. METHODS This study included 111 patients. All of them received oral leflunomide monotherapy at a dose of 20 mg daily. Women were genotyped for the presence of CYB5A rs1790834 polymorphism and evaluated monthly for 6 months following the initiation of treatment. RESULTS After 6 months of therapy, patients with the GG genotype had higher DAS28 values and less improvement in DAS28 compared to patients with the GA and AA genotypes (p = 0.04). No statistically significant differences were found in relation to other disease activity parameters. CONCLUSIONS The results of the current study suggest a possible association of the CYB5A rs1790834 polymorphism with some disease activity parameters in RA patients treated with leflunomide during the initial therapy period. However, confirmation of the effect of this polymorphism on the efficacy of leflunomide treatment requires further studies. Key Points • Leflunomide is the synthetic disease-modifying anti-rheumatic drug used in the therapy of rheumatoid arthritis. • CYB5A rs1790834 gene polymorphism may influence the clinical improvement after 6 months of leflunomide treatment in women with rheumatoid arthritis.
Collapse
Affiliation(s)
- Filip Machaj
- Department of Physiology, Pomeranian Medical University, 70-111, Szczecin, Poland
- Department of Medical Biology, Medical University of Warsaw, 00-575, Warsaw, Poland
| | - Jakub Rosik
- Department of Physiology, Pomeranian Medical University, 70-111, Szczecin, Poland
| | - Bartosz Szostak
- Department of Physiology, Pomeranian Medical University, 70-111, Szczecin, Poland
| | - Damian Malinowski
- Department of Pharmacokinetics and Therapeutic Drug Monitoring, Pomeranian Medical University, 70-111, Szczecin, Poland
| | - Krzysztof Safranow
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-111, Szczecin, Poland
| | - Gabriela Olędzka
- Department of Medical Biology, Medical University of Warsaw, 00-575, Warsaw, Poland
| | - Emilia Wiechec
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, 581 85, Linköping, Sweden
- Faculty of Medicine, Academy of Silesia, 40-555, Katowice, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111, Szczecin, Poland.
| |
Collapse
|
34
|
Renauer P, Park JJ, Bai M, Acosta A, Lee WH, Lin GH, Zhang Y, Dai X, Wang G, Errami Y, Wu T, Clark P, Ye L, Yang Q, Chen S. Immunogenetic Metabolomics Reveals Key Enzymes That Modulate CAR T-cell Metabolism and Function. Cancer Immunol Res 2023; 11:1068-1084. [PMID: 37253111 PMCID: PMC10527769 DOI: 10.1158/2326-6066.cir-22-0565] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/26/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
Immune evasion is a critical step of cancer progression that remains a major obstacle for current T cell-based immunotherapies. Hence, we investigated whether it is possible to genetically reprogram T cells to exploit a common tumor-intrinsic evasion mechanism whereby cancer cells suppress T-cell function by generating a metabolically unfavorable tumor microenvironment (TME). In an in silico screen, we identified ADA and PDK1 as metabolic regulators. We then showed that overexpression (OE) of these genes enhanced the cytolysis of CD19-specific chimeric antigen receptor (CAR) T cells against cognate leukemia cells, and conversely, ADA or PDK1 deficiency dampened this effect. ADA-OE in CAR T cells improved cancer cytolysis under high concentrations of adenosine, the ADA substrate, and an immunosuppressive metabolite in the TME. High-throughput transcriptomics and metabolomics analysis of these CAR T cells revealed alterations of global gene expression and metabolic signatures in both ADA- and PDK1-engineered CAR T cells. Functional and immunologic analyses demonstrated that ADA-OE increased proliferation and decreased exhaustion in CD19-specific and HER2-specific CAR T cells. ADA-OE improved tumor infiltration and clearance by HER2-specific CAR T cells in an in vivo colorectal cancer model. Collectively, these data unveil systematic knowledge of metabolic reprogramming directly in CAR T cells and reveal potential targets for improving CAR T-cell therapy.
Collapse
Affiliation(s)
- Paul Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
| | - Jonathan J. Park
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
- M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
| | - Meizhu Bai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Arianny Acosta
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Won-Ho Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Guang Han Lin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Yueqi Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Guangchuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Youssef Errami
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Tulane University, New Orleans, LA, USA
| | - Terence Wu
- West Campus Analytical Core, Mass Spectrometry/Proteomics Facility, West Haven, Connecticut, USA
| | - Paul Clark
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Lupeng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Nanjing University, Nanjing, Jiangsu, China
| | - Quanjun Yang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
- M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
- Immunobiology Program, Yale University, New Haven, Connecticut, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Liver Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Wu-Tsai Center, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
35
|
Daghestani M, Othman N, Omair MA, Alenzi F, Omair MA, Alqurtas E, Amin S, Warsy A. Single Nucleotide Polymorphisms Associated with Rheumatoid Arthritis in Saudi Patients. J Clin Med 2023; 12:4944. [PMID: 37568346 PMCID: PMC10419658 DOI: 10.3390/jcm12154944] [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: 06/13/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex, multifactorial disorder with an autoimmune etiology. RA is highly heritable and is associated with both human leucocyte antigen (HLA) and non-HLA genes. We investigated the associations of 33 single nucleotide polymorphisms (SNPs) with RA in the Saudi population. METHODS This study included 105 patients with RA and an equal number of age- and sex-matched controls. The patients with RA attended outpatient clinics at King Khalid University Hospital in Riyadh, Saudi Arabia. Blood samples were collected, and DNA was extracted using Qiagen kits. Primers were designed for the 33 selected SNPs using the MassEXTEND primers program, and samples were genotyped on the Sequenom MassARRAY iPLEX platform. The allele frequencies and genotypes were determined for each SNP, and the results obtained for the patients were compared to those for the controls. RESULTS The allele and genotype frequencies of six SNPs were significantly associated with RA: rs1188934, rs10919563, rs3087243, rs1980422, rs10499194, and rs629326. The minor alleles of rs1188934, rs10919563, rs10499194, and rs629326 were protective, with odds ratios of 0.542, 0.597, 0.589, and 0.625, and p-values of 0.002, 0.023, 0.013 and 0.036, respectively. In addition, the heterozygote frequencies of two SNPs (rs6859219 and rs11586238) were significantly higher in the controls than in the patients. CONCLUSIONS There is considerable heterogeneity in the genetics of RA in different populations, and the SNPs that are associated with RA in some populations are not in others. We studied 33 SNPs and only eight were associated with RA. The remaining SNPs showed no allelic or genotypic associations with RA.
Collapse
Affiliation(s)
- Maha Daghestani
- Department of Zoology, College of Science, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Nashwa Othman
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia; (N.O.); (S.A.); (A.W.)
| | - Mohammed A. Omair
- Rheumatology Unit, Department of Medicine, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia; (M.A.O.); (E.A.)
| | - Fahidah Alenzi
- Department of Clinical Science, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Maha A. Omair
- Department of Statistics and Operations Research, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Eman Alqurtas
- Rheumatology Unit, Department of Medicine, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia; (M.A.O.); (E.A.)
| | - Shireen Amin
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia; (N.O.); (S.A.); (A.W.)
| | - Arjumand Warsy
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh 11451, Saudi Arabia; (N.O.); (S.A.); (A.W.)
| |
Collapse
|
36
|
Ibis B, Aliazis K, Cao C, Yenyuwadee S, Boussiotis VA. Immune-related adverse effects of checkpoint immunotherapy and implications for the treatment of patients with cancer and autoimmune diseases. Front Immunol 2023; 14:1197364. [PMID: 37342323 PMCID: PMC10277501 DOI: 10.3389/fimmu.2023.1197364] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 06/22/2023] Open
Abstract
During the past decade, there has been a revolution in cancer therapeutics by the emergence of antibody-based immunotherapies that modulate immune responses against tumors. These therapies have offered treatment options to patients who are no longer responding to classic anti-cancer therapies. By blocking inhibitory signals mediated by surface receptors that are naturally upregulated during activation of antigen-presenting cells (APC) and T cells, predominantly PD-1 and its ligand PD-L1, as well as CTLA-4, such blocking agents have revolutionized cancer treatment. However, breaking these inhibitory signals cannot be selectively targeted to the tumor microenvironment (TME). Since the physiologic role of these inhibitory receptors, known as immune checkpoints (IC) is to maintain peripheral tolerance by preventing the activation of autoreactive immune cells, IC inhibitors (ICI) induce multiple types of immune-related adverse effects (irAEs). These irAEs, together with the natural properties of ICs as gatekeepers of self-tolerance, have precluded the use of ICI in patients with pre-existing autoimmune diseases (ADs). However, currently accumulating data indicates that ICI might be safely administered to such patients. In this review, we discuss mechanisms of well established and newly recognized irAEs and evolving knowledge from the application of ICI therapies in patients with cancer and pre-existing ADs.
Collapse
Affiliation(s)
- Betul Ibis
- Division of Hematology-Oncology Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Konstantinos Aliazis
- Division of Hematology-Oncology Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Carol Cao
- Division of Hematology-Oncology Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
- Harvard College, Cambridge, MA, United States
| | - Sasitorn Yenyuwadee
- Division of Hematology-Oncology Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Vassiliki A. Boussiotis
- Division of Hematology-Oncology Beth Israel Deaconess Medical Center, Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
- Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
37
|
Gao Y, Fan ZR, Shi FY. Hypothyroidism and rheumatoid arthritis: a two-sample Mendelian randomization study. Front Endocrinol (Lausanne) 2023; 14:1179656. [PMID: 37324262 PMCID: PMC10262846 DOI: 10.3389/fendo.2023.1179656] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Background Meta-analysis of genome-wide association studies (GWAS) data showed that the relationship between hypothyroidism and rheumatoid arthritis (RA) risk remains under debate. This study is conducted to test the causal relationship of hypothyroidism and RA. Methods A two-sample Mendelian randomization (TSMR) analysis was employed to estimate the causality of hypothyroidism and rheumatoid arthritis in European ancestry and Asian ancestry. Integrating the effects generated by TSMR, functional annotations and noncoding variant prediction framework were applied to analyze and interpret the functional instrument variants (IVs). Results The results of the inverse variance weighted method showed a strong significant causal relationship between hypothyroidism and risk of RA in European ancestry [odds ratio (OR) = 1.96; 95% confidence interval (CI) 1.49, 2.58; p < 0.001]. The outcomes of MR-Egger, weighted median, weighted mode, and simple mode also showed that hypothyroidism was significantly associated with increased risk of RA in European ancestry. The MR-PRESSO method also showed significant results [Outlier-corrected Causal Estimate = 0.70; standard error (SE) = 0.06; p < 0.001]. An independent dataset and an Asian ancestry dataset were applied to estimate and obtain the coincident results. Furthermore, we integrated the effect of variants in TSMR analysis, functional annotations, and prediction methods to pinpoint the single-nucleotide polymorphism (SNP) rs4409785 as one of the causal variants, which suggested that this variant could impact the binding of CTCF-cohesin and play a vital role in immune cells. Conclusion In this study, we prove that hypothyroidism is significantly causally associated with increased RA risk, which has not been shown in previous studies. Furthermore, we pinpoint the potential causal variants in RA.
Collapse
Affiliation(s)
- Yang Gao
- School of Medical Technology, North Minzu University, Yinchuan, China
| | - Zheng-Rui Fan
- Orthopedics Department, Tianjin Hospital, Tianjin, China
| | - Fang-Yuan Shi
- School of Information Engineering, Ningxia University, Yinchuan, China
- Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Ningxia University, Yinchuan, China
| |
Collapse
|
38
|
Pudjihartono N, Ho D, Golovina E, Fadason T, Kempa-Liehr AW, O'Sullivan JM. Juvenile idiopathic arthritis-associated genetic loci exhibit spatially constrained gene regulatory effects across multiple tissues and immune cell types. J Autoimmun 2023; 138:103046. [PMID: 37229810 DOI: 10.1016/j.jaut.2023.103046] [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: 03/05/2023] [Revised: 04/04/2023] [Accepted: 04/15/2023] [Indexed: 05/27/2023]
Abstract
Juvenile idiopathic arthritis (JIA) is an autoimmune, inflammatory joint disease with complex genetic etiology. Previous GWAS have found many genetic loci associated with JIA. However, the biological mechanism behind JIA remains unknown mainly because most risk loci are located in non-coding genetic regions. Interestingly, increasing evidence has found that regulatory elements in the non-coding regions can regulate the expression of distant target genes through spatial (physical) interactions. Here, we used information on the 3D genome organization (Hi-C data) to identify target genes that physically interact with SNPs within JIA risk loci. Subsequent analysis of these SNP-gene pairs using data from tissue and immune cell type-specific expression quantitative trait loci (eQTL) databases allowed the identification of risk loci that regulate the expression of their target genes. In total, we identified 59 JIA-risk loci that regulate the expression of 210 target genes across diverse tissues and immune cell types. Functional annotation of spatial eQTLs within JIA risk loci identified significant overlap with gene regulatory elements (i.e., enhancers and transcription factor binding sites). We found target genes involved in immune-related pathways such as antigen processing and presentation (e.g., ERAP2, HLA class I and II), the release of pro-inflammatory cytokines (e.g., LTBR, TYK2), proliferation and differentiation of specific immune cell types (e.g., AURKA in Th17 cells), and genes involved in physiological mechanisms related to pathological joint inflammation (e.g., LRG1 in arteries). Notably, many of the tissues where JIA-risk loci act as spatial eQTLs are not classically considered central to JIA pathology. Overall, our findings highlight the potential tissue and immune cell type-specific regulatory changes contributing to JIA pathogenesis. Future integration of our data with clinical studies can contribute to the development of improved JIA therapy.
Collapse
Affiliation(s)
- N Pudjihartono
- The Liggins Institute, The University of Auckland, Auckland, New Zealand.
| | - D Ho
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - E Golovina
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - T Fadason
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - A W Kempa-Liehr
- Department of Engineering Science, The University of Auckland, Auckland, New Zealand
| | - J M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand; The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand; MRC Lifecourse Epidemiology Unit, University of Southampton, United Kingdom; Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, New South Wales, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; A*STAR Singapore Institute for Clinical Sciences, Singapore, Singapore.
| |
Collapse
|
39
|
Suga K, Suto A, Tanaka S, Sugawara Y, Kageyama T, Ishikawa J, Sanayama Y, Ikeda K, Furuta S, Kagami SI, Iwata A, Hirose K, Suzuki K, Ohara O, Nakajima H. TAp63, a methotrexate target in CD4+ T cells, suppresses Foxp3 expression and exacerbates autoimmune arthritis. JCI Insight 2023; 8:164778. [PMID: 37212280 PMCID: PMC10322677 DOI: 10.1172/jci.insight.164778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/07/2023] [Indexed: 05/23/2023] Open
Abstract
Methotrexate (MTX) is a standard, first-line therapy for rheumatoid arthritis (RA); however, its precise mechanisms of action other than antifolate activity are largely unknown. We performed DNA microarray analyses of CD4+ T cells in patients with RA before and after MTX treatment and found that TP63 was the most significantly downregulated gene after MTX treatment. TAp63, an isoform of TP63, was highly expressed in human IL-17-producing Th (Th17) cells and was suppressed by MTX in vitro. Murine TAp63 was expressed at high levels in Th cells and at lower levels in thymus-derived Treg cells. Importantly, TAp63 knockdown in murine Th17 cells ameliorated the adoptive transfer arthritis model. RNA-Seq analyses of human Th17 cells overexpressing TAp63 and those with TAp63 knockdown identified FOXP3 as a possible TAp63 target gene. TAp63 knockdown in CD4+ T cells cultured under Th17 conditions with low-dose IL-6 increased Foxp3 expression, suggesting that TAp63 balances Th17 cells and Treg cells. Mechanistically, TAp63 knockdown in murine induced Treg (iTreg) cells promoted hypomethylation of conserved noncoding sequence 2 (CNS2) of the Foxp3 gene and enhanced the suppressive function of iTreg cells. Reporter analyses revealed that TAp63 suppressed the activation of the Foxp3 CNS2 enhancer. Collectively, TAp63 suppresses Foxp3 expression and exacerbates autoimmune arthritis.
Collapse
Affiliation(s)
- Kensuke Suga
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
- Institute for Advanced Academic Research, Chiba University, Chiba, Japan
| | - Shigeru Tanaka
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Yutaka Sugawara
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Takahiro Kageyama
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Junichi Ishikawa
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Yoshie Sanayama
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Kei Ikeda
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Shunsuke Furuta
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Shin-Ichiro Kagami
- Research Center for Allergy and Clinical Immunology, Asahi General Hospital, Asahi, Chiba, Japan
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Koichi Hirose
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Kotaro Suzuki
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, and
| |
Collapse
|
40
|
Lee GY, Yao C, Hwang SJ, Ma J, Joehanes R, Lee DH, Ellison RC, Moore LL, Liu C, Levy D. Integrative Mendelian randomization reveals the soluble receptor for advanced glycation end products as protective in relation to rheumatoid arthritis. Sci Rep 2023; 13:8002. [PMID: 37198231 PMCID: PMC10192300 DOI: 10.1038/s41598-023-35098-4] [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: 02/05/2022] [Accepted: 05/12/2023] [Indexed: 05/19/2023] Open
Abstract
Rheumatoid arthritis (RA) is a risk factor for atherosclerotic cardiovascular diseases (CVD). Given the critical roles of the immune system and inflammatory signals in the pathogenesis of CVD, we hypothesized that interrogation of CVD-related proteins using integrative genomics might provide new insights into the pathophysiology of RA. We utilized two-sample Mendelian randomization (MR) for causal inference between circulating protein levels and RA by incorporating genetic variants, followed by colocalization to characterize the causal associations. Genetic variants from three sources were obtained: those associated with 71 CVD-related proteins measured in nearly 7000 Framingham Heart Study participants, a published genome-wide association study (GWAS) of RA (19 234 cases, 61 565 controls), and GWAS of rheumatoid factor (RF) levels from the UK Biobank (n = 30 565). We identified the soluble receptor for advanced glycation end products (sRAGE), a critical inflammatory pathway protein, as putatively causal and protective for both RA (odds ratio per 1-standard deviation increment in inverse-rank normalized sRAGE level = 0.364; 95% confidence interval 0.342-0.385; P = 6.40 × 10-241) and RF levels (β [change in RF level per sRAGE increment] = - 1.318; SE = 0.434; P = 0.002). Using an integrative genomic approach, we highlight the AGER/RAGE axis as a putatively causal and promising therapeutic target for RA.
Collapse
Affiliation(s)
- Gha Young Lee
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
| | - Chen Yao
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
| | - Jiantao Ma
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
- School of Nutrition Science and Policy, Tufts University, Boston, USA
| | - Roby Joehanes
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
| | - Dong Heon Lee
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
| | - R Curtis Ellison
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Lynn L Moore
- Boston University School of Medicine, Boston, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA
- School of Public Health, Boston University, Boston, MA, USA
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
- Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA.
| |
Collapse
|
41
|
Greenwood CS, Wynosky-Dolfi MA, Beal AM, Booty LM. Gasdermins assemble; recent developments in bacteriology and pharmacology. Front Immunol 2023; 14:1173519. [PMID: 37266429 PMCID: PMC10230072 DOI: 10.3389/fimmu.2023.1173519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
The discovery of gasdermin D (GSDMD) as the terminal executioner of pyroptosis provided a large piece of the cell death puzzle, whilst simultaneously and firmly putting the gasdermin family into the limelight. In its purest form, GSDMD provides a connection between the innate alarm systems to an explosive, inflammatory form of cell death to jolt the local environment into immunological action. However, the gasdermin field has moved rapidly and significantly since the original seminal work and novel functions and mechanisms have been recently uncovered, particularly in response to infection. Gasdermins regulate and are regulated by mechanisms such as autophagy, metabolism and NETosis in fighting pathogen and protecting host. Importantly, activators and interactors of the other gasdermins, not just GSDMD, have been recently elucidated and have opened new avenues for gasdermin-based discovery. Key to this is the development of potent and specific tool molecules, so far a challenge for the field. Here we will cover some of these recently discovered areas in relation to bacterial infection before providing an overview of the pharmacological landscape and the challenges associated with targeting gasdermins.
Collapse
Affiliation(s)
- Claudine S. Greenwood
- Chemical Biology, GSK, Stevenage, United Kingdom
- Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | | | - Allison M. Beal
- Immunology Research Unit, GSK, Philadelphia, PA, United States
| | - Lee M. Booty
- Immunology Network, GSK, Stevenage, United Kingdom
| |
Collapse
|
42
|
Mulhearn B, Marshall L, Sutcliffe M, Hannes SK, Fonseka C, Hussell T, Raychaudhuri S, Barton A, Viatte S. Automated clustering reveals CD4 + T cell subset imbalances in rheumatoid arthritis. Front Immunol 2023; 14:1094872. [PMID: 37215131 PMCID: PMC10196473 DOI: 10.3389/fimmu.2023.1094872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Background Despite the report of an imbalance between CD4+ T helper (Th) cell subsets in rheumatoid arthritis (RA), patient stratification for precision medicine has been hindered by the discovery of ever more Th cell subsets, as well as contradictory association results. Objectives To capture previously reported Th imbalance in RA with deep immunophenotyping techniques; to compare hypothesis-free unsupervised automated clustering with hypothesis-driven conventional biaxial gating and explore if Th cell heterogeneity accounts for conflicting association results. Methods Unstimulated and stimulated peripheral blood mononuclear cells from 10 patients with RA and 10 controls were immunophenotyped with a 37-marker panel by mass cytometry (chemokine receptors, intra-cellular cytokines, intra-nuclear transcription factors). First, conventional biaxial gating and standard definitions of Th cell subsets were applied to compare subset frequencies between cases and controls. Second, unsupervised clustering was performed with FlowSOM and analysed using mixed-effects modelling of Associations of Single Cells (MASC). Results Conventional analytical techniques fail to identify classical Th subset imbalance, while unsupervised automated clustering, by allowing for unusual marker combinations, identified an imbalance between pro- and anti-inflammatory subsets. For example, a pro-inflammatory Th1-like (IL-2+ T-bet+) subset and an unconventional but pro-inflammatory IL-17+ T-bet+ subset were significantly enriched in RA (odds ratio=5.7, p=2.2 x 10-3; odds ratio=9.7, p=1.5x10-3, respectively). In contrast, a FoxP3+ IL-2+ HLA-DR+ Treg-like subset was reduced in RA (odds ratio=0.1, p=7.7x10-7). Conclusion Taking an unbiased approach to large dataset analysis using automated clustering algorithms captures non-canonical CD4+ T cell subset imbalances in RA blood.
Collapse
Affiliation(s)
- Ben Mulhearn
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Lysette Marshall
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Megan Sutcliffe
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Susan K. Hannes
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Chamith Fonseka
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
- Research, eGenesis, Cambridge, MA, United States
| | - Tracy Hussell
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Soumya Raychaudhuri
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- NIHR Manchester Musculoskeletal Biomedical Research Centre, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sebastien Viatte
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- NIHR Manchester Musculoskeletal Biomedical Research Centre, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| |
Collapse
|
43
|
Budlewski T, Sarnik J, Galita G, Dragan G, Brzezińska O, Popławska M, Popławski T, Makowska J. SNP in PTPN22, PADI4, and STAT4 but Not TRAF1 and CD40 Increase the Risk of Rheumatoid Arthritis in Polish Population. Int J Mol Sci 2023; 24:ijms24087586. [PMID: 37108746 PMCID: PMC10145319 DOI: 10.3390/ijms24087586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Single nucleotide polymorphisms in non-HLA genes are involved in the development of rheumatoid arthritis (RA). SNPS in genes: PADI4 (rs2240340), STAT4 (rs7574865), CD40 (rs4810485), PTPN22 (rs2476601), and TRAF1 (rs3761847) have been described as risk factors for the development of autoimmune diseases, including RA. This study aimed to assess the prevalence of polymorphisms of these genes in the Polish population of patients with rheumatoid arthritis as compared to healthy controls. 324 subjects were included in the study: 153 healthy subjects and 181 patients from the Department of Rheumatology, Medical University of Lodz who fulfilled the criteria of rheumatoid arthritis diagnosis. Genotypes were determined by Taqman SNP Genotyping Assay. rs2476601 (G/A, OR = 2.16, CI = 1.27-3.66; A/A, OR = 10.35, CI = 1.27-84.21), rs2240340 (C/T, OR = 4.35, CI = 2.55-7.42; T/T, OR = 2.80, CI = 1.43-4.10) and rs7574865 (G/T, OR = 1.97, CI = 1.21-3.21; T/T, OR = 3.33, CI = 1.01-11.02) were associated with RA in the Polish population. Rs4810485 was also associated with RA, however after Bonferroni's correction was statistically insignificant. We also found an association between minor alleles of rs2476601, rs2240340, and rs7574865 and RA (OR = 2.32, CI = 1.47-3.66; OR = 2.335, CI = 1.64-3.31; OR = 1.88, CI = 1.27-2.79, respectively). Multilocus analysis revealed an association between CGGGT and rare (below 0.02 frequency) haplotypes (OR = 12.28, CI = 2.65-56.91; OR = 3.23, CI = 1.63-6.39). In the Polish population, polymorphisms of the PADI4, PTPN22, and STAT4 genes have been detected, which are also known risk factors for RA in various other populations.
Collapse
Affiliation(s)
- Tomasz Budlewski
- Department of Rheumatology, Medical University of Lodz, 92-115 Lodz, Poland
| | - Joanna Sarnik
- Department of Rheumatology, Medical University of Lodz, 92-115 Lodz, Poland
| | - Grzegorz Galita
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland
- Doctoral Study in Molecular Genetics, Cytogenetics and Medical Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Grzegorz Dragan
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland
| | - Olga Brzezińska
- Department of Rheumatology, Medical University of Lodz, 92-115 Lodz, Poland
| | - Marta Popławska
- Biobank, Department of Immunology and Allergy, Medical University of Lodz, 92-213 Lodz, Poland
| | - Tomasz Popławski
- Department of Pharmaceutical Microbiology and Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland
| | - Joanna Makowska
- Department of Rheumatology, Medical University of Lodz, 92-115 Lodz, Poland
| |
Collapse
|
44
|
Martín-Masot R, Herrador-López M, Navas-López VM, Carmona FD, Nestares T, Bossini-Castillo L. Celiac Disease Is a Risk Factor for Mature T and NK Cell Lymphoma: A Mendelian Randomization Study. Int J Mol Sci 2023; 24:ijms24087216. [PMID: 37108375 PMCID: PMC10139431 DOI: 10.3390/ijms24087216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Celiac disease (CeD) is an immune-mediated disorder triggered by gluten ingestion that damages the small intestine. Although CeD has been associated with a higher risk for cancer, the role of CeD as a risk factor for specific malignancies, such as enteropathy-associated T-cell lymphoma (EATL), remains controversial. Using two-sample Mendelian randomization (2SMR) methods and the summarized results of large genome-wide association studies from public repositories, we addressed the causal relationship between CeD and eight different malignancies. Eleven non-HLA SNPs were selected as instrumental variables (IVs), and causality estimates were obtained using four 2SMR methods: random-effects inverse variance-weighted, weighted median estimation, MR-Egger regression, and MR pleiotropy residual sum and outlier (MR-PRESSO). We identified a significant causal relationship between CeD and mature T/NK cell lymphomas. Under a multivariate Mendelian randomization model, we observed that the causal effect of CeD was not dependent on other known lymphoma risk factors. We found that the most instrumental IV was located in the TAGAP locus, suggesting that aberrant T cell activation might be relevant in the T/NK cell malignization process. Our findings provide new insights into the connection between immune imbalance and the development of severe comorbidities, such as EATL, in patients with CeD.
Collapse
Affiliation(s)
- Rafael Martín-Masot
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
- Instituto de Nutrición y Tecnología de los Alimentos "José Mataix Verdú" (INYTA), Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
| | - Marta Herrador-López
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
| | - Víctor Manuel Navas-López
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Reproducción Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnologías Biomédicas, Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Teresa Nestares
- Instituto de Nutrición y Tecnología de los Alimentos "José Mataix Verdú" (INYTA), Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Departamento de Fisiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain
| | - Lara Bossini-Castillo
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Reproducción Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnologías Biomédicas, Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| |
Collapse
|
45
|
Al-Harbi N, Abdulla MH, Vaali-Mohammed MA, Bin Traiki T, Alswayyed M, Al-Obeed O, Abid I, Al-Omar S, Mansour L. Evidence of Association between CTLA-4 Gene Polymorphisms and Colorectal Cancers in Saudi Patients. Genes (Basel) 2023; 14:genes14040874. [PMID: 37107632 PMCID: PMC10138150 DOI: 10.3390/genes14040874] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Cytotoxic T lymphocyte antigen-4 (CTLA-4) has been identified as an immunosuppressive molecule involved in the negative regulation of T cells. It is highly expressed in several types of autoimmune diseases and cancers including colorectal cancer (CRC). (1) Objective: To explore the association between CTLA-4 single nucleotide polymorphisms (SNP) and risk to (CRC) in the Saudi population. (2) Methods: In this case-control study, 100 patients with CRC and 100 matched healthy controls were genotyped for three CTLA-4 SNPs: rs11571317 (-658C > T), rs231775 (+49A > G) and rs3087243 (CT60 G > A), using TaqMan assay method. Associations were evaluated using odds ratios (ORs) and 95% confidence intervals (95% CIs) for five inheritance models (co-dominant, dominant, recessive, over-dominant and log-additive). Furthermore, CTLA-4 expression levels were evaluated using quantitative real-time PCR (Q-RT-PCR) in colon cancer and adjacent colon tissues. (3) Results: Our result showed a significant association of the G allele (OR = 2.337, p < 0.0001) and GG genotype of the missense SNP +49A > G with increased risk of developing CRC in codominant (OR = 8.93, p < 0.0001) and recessive (OR = 16.32, p < 0.0001) models. Inversely, the AG genotype was significantly associated with decreased risk to CRC in the codominant model (OR = 0.23, p < 0.0001). In addition, the CT60 G > A polymorphism exhibited a strong association with a high risk of developing CRC for the AA genotype in codominant (OR = 3.323, p = 0.0053) and in allele models (OR = 1.816, p = 0.005). No significant association was found between -658C > T and CRC. The haplotype analysis showed that the G-A-G haplotype of the rs11571317, rs231775 and rs3087243 was associated with high risk for CRC (OR = 57.66; p < 0.001). The CTLA-4 mRNA gene expression was found significantly higher in tumors compared to normal adjacent colon samples (p < 0.001). (4) Conclusions: Our findings support an association between the CTLA-4 rs231775 (+49A > G) and rs3087243 (CT60 G > A) polymorphisms and CRC risk in the Saudi population. Further validation in a larger cohort size is needed prior to utilizing these SNPs as a potential screening marker in the Saudi population.
Collapse
Affiliation(s)
- Nouf Al-Harbi
- Department of Zoology, College of Science, King Saud University, Riyadh 11472, Saudi Arabia
| | - Maha-Hamadien Abdulla
- Department of Surgery, College of Medicine, King Saud University, Riyadh 11472, Saudi Arabia
| | | | - Thamer Bin Traiki
- Department of Surgery, College of Medicine, King Saud University, Riyadh 11472, Saudi Arabia
| | - Mohammed Alswayyed
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh 11495, Saudi Arabia
| | - Omar Al-Obeed
- Department of Surgery, College of Medicine, King Saud University, Riyadh 11472, Saudi Arabia
| | - Islem Abid
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh 11495, Saudi Arabia
| | - Suliman Al-Omar
- Department of Zoology, College of Science, King Saud University, Riyadh 11472, Saudi Arabia
| | - Lamjed Mansour
- Department of Zoology, College of Science, King Saud University, Riyadh 11472, Saudi Arabia
| |
Collapse
|
46
|
Wang NN, Zhang Y, Jiang F, Zhu DL, Di CX, Hu SY, Chen XF, Zhi LQ, Rong Y, Ke X, Duan YY, Dong SS, Yang TL, Yang Z, Guo Y. Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis. Am J Hum Genet 2023; 110:625-637. [PMID: 36924774 PMCID: PMC10119143 DOI: 10.1016/j.ajhg.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Genome-wide association studies (GWASs) have repeatedly reported multiple non-coding single-nucleotide polymorphisms (SNPs) at 2p14 associated with rheumatoid arthritis (RA), but their functional roles in the pathological mechanisms of RA remain to be explored. In this study, we integrated a series of bioinformatics and functional experiments and identified three intronic RA SNPs (rs1876518, rs268131, and rs2576923) within active enhancers that can regulate the expression of SPRED2 directly. At the same time, SPRED2 and ACTR2 influence each other as a positive feedback signal amplifier to strengthen the protective role in RA by inhibiting the migration and invasion of rheumatoid fibroblast-like synoviocytes (FLSs). In particular, the transcription factor CEBPB preferentially binds to the rs1876518-T allele to increase the expression of SPRED2 in FLSs. Our findings decipher the molecular mechanisms behind the GWAS signals at 2p14 for RA and emphasize SPRED2 as a potential candidate gene for RA, providing a potential target and direction for precise treatment of RA.
Collapse
Affiliation(s)
- Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yan Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Chen-Xi Di
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Li-Qiang Zhi
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China.
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.
| |
Collapse
|
47
|
Fehrenbach DJ, Nguyen B, Alexander MR, Madhur MS. Modulating T Cell Phenotype and Function to Treat Hypertension. KIDNEY360 2023; 4:e534-e543. [PMID: 36951464 PMCID: PMC10278787 DOI: 10.34067/kid.0000000000000090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 01/25/2023] [Indexed: 03/24/2023]
Abstract
Hypertension is the leading modifiable risk factor of worldwide morbidity and mortality because of its effects on cardiovascular and renal end-organ damage. Unfortunately, BP control is not sufficient to fully reduce the risks of hypertension, underscoring the need for novel therapies that address end-organ damage in hypertension. Over the past several decades, the link between immune activation and hypertension has been well established, but there are still no therapies for hypertension that specifically target the immune system. In this review, we describe the critical role played by T cells in hypertension and hypertensive end-organ damage and outline potential therapeutic targets to modulate T-cell phenotype and function in hypertension without causing global immunosuppression.
Collapse
Affiliation(s)
- Daniel J. Fehrenbach
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Bianca Nguyen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Matthew R. Alexander
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee
| | - Meena S. Madhur
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee
| |
Collapse
|
48
|
Wang M, Wu J, Lei S, Mo X. Genome-wide identification of RNA modification-related single nucleotide polymorphisms associated with rheumatoid arthritis. BMC Genomics 2023; 24:153. [PMID: 36973646 PMCID: PMC10045113 DOI: 10.1186/s12864-023-09227-2] [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: 09/21/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND RNA modification plays important roles in many biological processes, such as gene expression control. The aim of this study was to identify single nucleotide polymorphisms related to RNA modification (RNAm-SNPs) for rheumatoid arthritis (RA) as putative functional variants. METHODS We examined the association of RNAm-SNPs with RA in summary data from a genome-wide association study of 19,234 RA cases and 61,565 controls. We performed eQTL and pQTL analyses for the RNAm-SNPs to find associated gene expression and protein levels. Furthermore, we examined the associations of gene expression and circulating protein levels with RA using two-sample Mendelian randomization analysis methods. RESULTS A total of 160 RNAm-SNPs related to m6A, m1A, A-to-I, m7G, m5C, m5U and m6Am modifications were identified to be significantly associated with RA. These RNAm-SNPs were located in 62 protein-coding genes, which were significantly enriched in immune-related pathways. RNAm-SNPs in important RA susceptibility genes, such as PADI2, SPRED2, PLCL2, HLA-A, HLA-B, HLA-DRB1, HLA-DPB1, TRAF1 and TXNDC11, were identified. Most of these RNAm-SNPs showed eQTL effects, and the expression levels of 26 of the modifiable genes (e.g., PADI2, TRAF1, HLA-A, HLA-DRB1, HLA-DPB1 and HLA-B) in blood cells were associated with RA. Circulating protein levels, such as CFB, GZMA, HLA-DQA2, IL21, LRPAP1 and TFF3, were affected by RNAm-SNPs and were associated with RA. CONCLUSION The present study identified RNAm-SNPs in the reported RA susceptibility genes and suggested that RNAm-SNPs may affect RA risk by affecting the expression levels of corresponding genes and proteins.
Collapse
Affiliation(s)
- Mimi Wang
- Center for Genetic Epidemiology and Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Jingyun Wu
- Center for Genetic Epidemiology and Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Shufeng Lei
- Center for Genetic Epidemiology and Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Xingbo Mo
- Center for Genetic Epidemiology and Genomics, Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, Jiangsu, 215123, People's Republic of China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, Suzhou, China.
| |
Collapse
|
49
|
Stankey CT, Lee JC. Translating non-coding genetic associations into a better understanding of immune-mediated disease. Dis Model Mech 2023; 16:297044. [PMID: 36897113 PMCID: PMC10040244 DOI: 10.1242/dmm.049790] [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] [Indexed: 03/11/2023] Open
Abstract
Genome-wide association studies have identified hundreds of genetic loci that are associated with immune-mediated diseases. Most disease-associated variants are non-coding, and a large proportion of these variants lie within enhancers. As a result, there is a pressing need to understand how common genetic variation might affect enhancer function and thereby contribute to immune-mediated (and other) diseases. In this Review, we first describe statistical and experimental methods to identify causal genetic variants that modulate gene expression, including statistical fine-mapping and massively parallel reporter assays. We then discuss approaches to characterise the mechanisms by which these variants modulate immune function, such as clustered regularly interspaced short palindromic repeats (CRISPR)-based screens. We highlight examples of studies that, by elucidating the effects of disease variants within enhancers, have provided important insights into immune function and uncovered key pathways of disease.
Collapse
Affiliation(s)
- Christina T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Institute of Liver and Digestive Health, Royal Free Hospital, University College London, London NW3 2PF, UK
| |
Collapse
|
50
|
Rheumatoid arthritis and non-coding RNAs; how to trigger inflammation. Life Sci 2023; 315:121367. [PMID: 36639050 DOI: 10.1016/j.lfs.2023.121367] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/31/2022] [Accepted: 12/31/2022] [Indexed: 01/12/2023]
Abstract
Rheumatoid arthritis (RA) is a systemic and chronic inflammatory disease categorized by continuous synovitis in the joints and systemic inflammatory responses that can cause lifelong disability. The major cause of RA is the dysregulation of the immune response. The development of RA disease includes multiplex association of several interleukins and cells, which leads to synovial cell growth, cartilage and bone damage. The primary stage of RA disease is related to the modification of both the innate and adaptive immune systems, which leads to the formation of autoantibodies. This process results in many damaged molecules and epitope spreading. Both the innate (e.g., dendritic cells, macrophages, and neutrophils) and acquired immune cells (e.g., T and B lymphocytes) will increase and continue the chronic inflammatory condition in the next stages of the RA disease. In recent years, non-coding RNAs have been proved as significant controllers of biological functions, especially immune cell expansion and reactions. Non-coding RNAs were primarily containing microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). Various studies confirmed non-coding RNAs as hopeful markers for diagnosing and curing RA. This review will describe and cover existing knowledge about RA pathogenesis, which might be favorable for discovering possible ncRNA markers for RA.
Collapse
|