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Tan PR, Lee AJL, Zhao JJ, Chan YH, Fu JH, Ma M, Tay SH. Higher odds of periodontitis in systemic lupus erythematosus compared to controls and rheumatoid arthritis: a systematic review, meta-analysis and network meta-analysis. Front Immunol 2024; 15:1356714. [PMID: 38629069 PMCID: PMC11019014 DOI: 10.3389/fimmu.2024.1356714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction Periodontitis as a comorbidity in systemic lupus erythematosus (SLE) is still not well recognized in the dental and rheumatology communities. A meta-analysis and network meta-analysis were thus performed to compare the (i) prevalence of periodontitis in SLE patients compared to those with rheumatoid arthritis (RA) and (ii) odds of developing periodontitis in controls, RA, and SLE. Methods Pooled prevalence of and odds ratio (OR) for periodontitis were compared using meta-analysis and network meta-analysis (NMA). Results Forty-three observational studies involving 7,800 SLE patients, 49,388 RA patients, and 766,323 controls were included in this meta-analysis. The pooled prevalence of periodontitis in SLE patients (67.0%, 95% confidence interval [CI] 57.0-77.0%) was comparable to that of RA (65%, 95% CI 55.0-75.0%) (p>0.05). Compared to controls, patients with SLE (OR=2.64, 95% CI 1.24-5.62, p<0.01) and RA (OR=1.81, 95% CI 1.25-2.64, p<0.01) were more likely to have periodontitis. Indirect comparisons through the NMA demonstrated that the odds of having periodontitis in SLE was 1.49 times higher compared to RA (OR=1.49, 95% CI 1.09-2.05, p<0.05). Discussion Given that RA is the autoimmune disease classically associated with periodontal disease, the higher odds of having periodontitis in SLE are striking. These results highlight the importance of addressing the dental health needs of patients with SLE. Systematic review registration https://www.crd.york.ac.uk/PROSPERO/ identifier CRD42021272876.
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Affiliation(s)
- Ping Ren Tan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Aaron J. L. Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Joseph J. Zhao
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jia Hui Fu
- Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Margaret Ma
- Division of Rheumatology, Department of Medicine, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sen Hee Tay
- Division of Rheumatology, Department of Medicine, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Khatiwada A, Yilmaz AS, Wolf BJ, Pietrzak M, Chung D. multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results. PLoS Comput Biol 2023; 19:e1011686. [PMID: 38060592 PMCID: PMC10729974 DOI: 10.1371/journal.pcbi.1011686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 12/19/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), most with small or moderate effect sizes, making them difficult to detect. Second, many complex traits share a common genetic basis due to 'pleiotropy' and and though few methods consider it, leveraging pleiotropy can improve statistical power to detect genotype-trait associations with weaker effect sizes. Third, currently available statistical methods are limited in explaining the functional mechanisms through which genetic variants are associated with specific or multiple traits. We propose multi-GPA-Tree to address these challenges. The multi-GPA-Tree approach can identify risk SNPs associated with single as well as multiple traits while also identifying the combinations of functional annotations that can explain the mechanisms through which risk-associated SNPs are linked with the traits. First, we implemented simulation studies to evaluate the proposed multi-GPA-Tree method and compared its performance with existing statistical approaches. The results indicate that multi-GPA-Tree outperforms existing statistical approaches in detecting risk-associated SNPs for multiple traits. Second, we applied multi-GPA-Tree to a systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), and to a Crohn's disease (CD) and ulcertive colitis (UC) GWAS, and functional annotation data including GenoSkyline and GenoSkylinePlus. Our results demonstrate that multi-GPA-Tree can be a powerful tool that improves association mapping while facilitating understanding of the underlying genetic architecture of complex traits and potential mechanisms linking risk-associated SNPs with complex traits.
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Affiliation(s)
- Aastha Khatiwada
- Department of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, United States of America
| | - Ayse Selen Yilmaz
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
| | - Bethany J. Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
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Stafford IS, Ashton JJ, Mossotto E, Cheng G, Mark Beattie R, Ennis S. Supervised Machine Learning Classifies Inflammatory Bowel Disease Patients by Subtype Using Whole Exome Sequencing Data. J Crohns Colitis 2023; 17:1672-1680. [PMID: 37205778 PMCID: PMC10637043 DOI: 10.1093/ecco-jcc/jjad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Inflammatory bowel disease [IBD] is a chronic inflammatory disorder with two main subtypes: Crohn's disease [CD] and ulcerative colitis [UC]. Prompt subtype diagnosis enables the correct treatment to be administered. Using genomic data, we aimed to assess machine learning [ML] to classify patients according to IBD subtype. METHODS Whole exome sequencing [WES] from paediatric/adult IBD patients was processed using an in-house bioinformatics pipeline. These data were condensed into the per-gene, per-individual genomic burden score, GenePy. Data were split into training and testing datasets [80/20]. Feature selection with a linear support vector classifier, and hyperparameter tuning with Bayesian Optimisation, were performed [training data]. The supervised ML method random forest was utilised to classify patients as CD or UC, using three panels: 1] all available genes; 2] autoimmune genes; 3] 'IBD' genes. ML results were assessed using area under the receiver operating characteristics curve [AUROC], sensitivity, and specificity on the testing dataset. RESULTS A total of 906 patients were included in analysis [600 CD, 306 UC]. Training data included 488 patients, balanced according to the minority class of UC. The autoimmune gene panel generated the best performing ML model [AUROC = 0.68], outperforming an IBD gene panel [AUROC = 0.61]. NOD2 was the top gene for discriminating CD and UC, regardless of the gene panel used. Lack of variation in genes with high GenePy scores in CD patients was the best classifier of a diagnosis of UC. DISCUSSION We demonstrate promising classification of patients by subtype using random forest and WES data. Focusing on specific subgroups of patients, with larger datasets, may result in better classification.
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Affiliation(s)
- Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Enrico Mossotto
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Guo Cheng
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University Hospital Southampton, Southampton, UK
| | - Robert Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Sakalyte R, Stropuviene S, Jasionyte G, Bagdonaite L, Venalis A. Association between PYTPN22 rs2476601, VEGF rs833070, TNFAIP3 rs6920220 Polymorphisms and Risk for Rheumatoid Arthritis in Early Undifferentiated Arthritis Patients: A Pilot Study. Medicina (Kaunas) 2023; 59:1824. [PMID: 37893542 PMCID: PMC10607990 DOI: 10.3390/medicina59101824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: About 40% of early undifferentiated arthritis (UA) progresses to rheumatoid (RA) or other chronic arthritis. Novel diagnostic tools predicting the risk for this progression are needed to identify the patients who would benefit from early aggressive treatment. Evidence on the role of single-nucleotide polymorphisms (SNPs) in the development of RA has emerged. The aim of our study was to investigate the association between rs2476601, rs833070, and rs6920220 SNPs and UA progression to RA. Materials and Methods: Ninety-two UA patients were observed for 12 months. At study entry, demographic and clinical characteristics were recorded, musculoskeletal ultrasonography was performed, and blood samples were drawn to investigate levels of inflammatory markers, rheumatoid factor (RF), anti-citrullinated protein antibodies (anti-CCP)detect SNPs. After 12 months, UA outcomes were assessed, and patients were divided into two (RA and non-RA) groups. The association between the risk of progression to chronic inflammatory arthritis and analyzed SNPs was measured by computing odds ratios (OR). Results: After a 12-month follow-up, 27 (29.3%) patients developed RA, and 65 (70.7%) patients were assigned to the non-RA group. The arthritis of 21 patients (22.8%) from the non-RA group resolved completely, while the other 44 (47.2%) patients were diagnosed with another rheumatic inflammatory disease. The patients who developed RA had a significantly greater number of tender and swollen joints (p = 0.010 and p = 0.021 respectively) and were more frequently RF or anti-CCP (p < 0.001), and both RF and anti-CCP positive (p < 0.001) at the baseline as compared with the patients in the non-RA group. No significant association between rs2476601 (OR = 0.99, p = 0.98), rs833070 (OR = 1.0, p = 0.97), and rs6920220 (OR = 0.48, p = 0.13) polymorphisms and the risk of developing RA were found. Conclusions: No association between analyzed SNPs and a greater risk to progress from UA to RA was confirmed, although patients with rs6920220 AA + AG genotypes had fewer tender joints at the disease onset.
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Affiliation(s)
- Regina Sakalyte
- The Clinic of Rheumatology, Traumatology Orthopaedics and Reconstructive Surgery, Institute of Clinical Medicine of the Faculty of Vilnius University, M. K. Čiurlionio Str. 21, 03101 Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Santariškių g. 5, 08406 Vilnius, Lithuania
| | - Sigita Stropuviene
- The Clinic of Rheumatology, Traumatology Orthopaedics and Reconstructive Surgery, Institute of Clinical Medicine of the Faculty of Vilnius University, M. K. Čiurlionio Str. 21, 03101 Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Santariškių g. 5, 08406 Vilnius, Lithuania
| | - Gabija Jasionyte
- The Clinic of Rheumatology, Traumatology Orthopaedics and Reconstructive Surgery, Institute of Clinical Medicine of the Faculty of Vilnius University, M. K. Čiurlionio Str. 21, 03101 Vilnius, Lithuania
| | - Loreta Bagdonaite
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio Str. 21, 03101 Vilnius, Lithuania
| | - Algirdas Venalis
- The Clinic of Rheumatology, Traumatology Orthopaedics and Reconstructive Surgery, Institute of Clinical Medicine of the Faculty of Vilnius University, M. K. Čiurlionio Str. 21, 03101 Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Santariškių g. 5, 08406 Vilnius, Lithuania
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Li Y, Li W, Huang L, Li H, He P, Xue C. Association of ATG4A single nucleotide polymorphism rs807185 on risk of microscopic polyangiitis in Chinese population. Int Immunopharmacol 2023; 123:110659. [PMID: 37494842 DOI: 10.1016/j.intimp.2023.110659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/08/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Microscopic polyangiitis is a type of antineutrophil cytoplasmic antibody-associated vasculitis, characterized by a systemic, pauci-immune, necrotizing, small-vessel vasculitis without clinical or pathological evidence of necrotizing granulomatous inflammation. Many studies have linked autophagy-related gene polymorphisms to the development of immune diseases. However, the association between autophagy-related genes and microscopic polyangiitis remains unclear. OBJECTIVE We investigated the association between microscopic polyangiitis and the single nucleotide polymorphism rs807185 in autophagy-associated gene 4A (ATG4A) in the Chinese population. METHODS ATG4A single nucleotide polymorphism rs807185 frequency was identified using multiplex polymerase chain reaction and high-throughput sequencing in a cohort with microscopic polyangiitis (n = 181) and a healthy control group (n = 209). RESULTS We found that the control cohort had a higher prevalence of allele A of rs807185 compared to the microscopic polyangiitis cohort. The rs807185A allele was therefore linked to a lower risk of microscopic polyangiitis. CONCLUSION The single nucleotide polymorphism rs807185 allele A in ATG4A may have a protective effect against microscopic polyangiitis in the Chinese population, but the molecular mechanisms remain unclear.
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Affiliation(s)
- Yan Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Wei Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Li Huang
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Huijia Li
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Peipeng He
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Chao Xue
- Department of Nephrology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
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Tanwar H, Gnanasekaran JM, Allison D, Chuang LS, He X, Aimetti M, Baima G, Costalonga M, Cross RK, Sears C, Mehandru S, Cho J, Colombel JF, Raufman JP, Thumbigere-Math V. Unraveling the Link between Periodontitis and Inflammatory Bowel Disease: Challenges and Outlook. ArXiv 2023:arXiv:2308.10907v1. [PMID: 37645044 PMCID: PMC10462160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Periodontitis and Inflammatory Bowel Disease (IBD) are chronic inflammatory conditions, characterized by microbial dysbiosis and hyper-immunoinflammatory responses. Growing evidence suggest an interconnection between periodontitis and IBD, implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an "Oral-Gut" axis, marked by a higher prevalence of periodontitis in IBD patients and vice versa. The specific mechanisms linking periodontitis and IBD remain to be fully elucidated, but emerging evidence points to the ectopic colonization of the gut by oral bacteria, which promote intestinal inflammation by activating host immune responses. This review presents an in-depth examination of the interconnection between periodontitis and IBD, highlighting the shared microbiological and immunological pathways, and proposing a "multi-hit" hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.
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Affiliation(s)
- Himanshi Tanwar
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | | | - Devon Allison
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Ling-shiang Chuang
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Massimo Costalonga
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, USA
| | - Raymond K. Cross
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cynthia Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saurabh Mehandru
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Pierre Raufman
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vivek Thumbigere-Math
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
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Afrasiabi A, Ahlenstiel C, Swaminathan S, Parnell GP. The interaction between Epstein-Barr virus and multiple sclerosis genetic risk loci: insights into disease pathogenesis and therapeutic opportunities. Clin Transl Immunology 2023; 12:e1454. [PMID: 37337612 PMCID: PMC10276892 DOI: 10.1002/cti2.1454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic neurodegenerative autoimmune disease, characterised by the demyelination of neurons in the central nervous system. Whilst it is unclear what precisely leads to MS, it is believed that genetic predisposition combined with environmental factors plays a pivotal role. It is estimated that close to half the disease risk is determined by genetic factors. However, the risk of developing MS cannot be attributed to genetic factors alone, and environmental factors are likely to play a significant role by themselves or in concert with host genetics. Epstein-Barr virus (EBV) infection is the strongest known environmental risk factor for MS. There has been increasing evidence that leaves little doubt that EBV is necessary, but not sufficient, for developing MS. One plausible explanation is EBV may alter the host immune response in the presence of MS risk alleles and this contributes to the pathogenesis of MS. In this review, we discuss recent findings regarding how EBV infection may contribute to MS pathogenesis via interactions with genetic risk loci and discuss possible therapeutic interventions.
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Affiliation(s)
- Ali Afrasiabi
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- The Graduate School of Biomedical EngineeringUniversity of New South WalesSydneyNSWAustralia
| | - Chantelle Ahlenstiel
- Kirby InstituteUniversity of New South WalesSydneyNSWAustralia
- RNA InstituteUniversity of New South WalesSydneyNSWAustralia
| | - Sanjay Swaminathan
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- Department of MedicineWestern Sydney UniversitySydneyNSWAustralia
| | - Grant P Parnell
- EBV Molecular Lab, Centre for Immunology and Allergy Research, Westmead Institute for Medical ResearchUniversity of SydneySydneyNSWAustralia
- Biomedical Informatics and Digital Health, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
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Johnson D, Jiang W. Infectious diseases, autoantibodies, and autoimmunity. J Autoimmun 2023; 137:102962. [PMID: 36470769 PMCID: PMC10235211 DOI: 10.1016/j.jaut.2022.102962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 11/27/2022] [Indexed: 12/04/2022]
Abstract
Infections are known to trigger flares of autoimmune diseases in humans and serve as an inciting cause of autoimmunity in animals. Evidence suggests a causative role of infections in triggering antigen-specific autoimmunity, previous thought mainly through antigen mimicry. However, an infection can induce bystander autoreactive T and B cell polyclonal activation, believed to result in non-pathogenic and pathogenic autoimmune responses. Lastly, epitope spreading in autoimmunity is a mechanism of epitope changes of autoreactive cells induced by infection, promoting the targeting of additional self-epitopes. This review highlights recent research findings, emphasizes infection-mediated autoimmune responses, and discusses the possible mechanisms involved.
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Affiliation(s)
- Douglas Johnson
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC, USA; Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - Wei Jiang
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC, USA; Ralph H. Johnson VA Medical Center, Charleston, SC, USA; Divison of Infectious Disease, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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Vaitinadin NS, Stein CM, Mosley JD, Kawai VK. Genetic susceptibility for autoimmune diseases and white blood cell count. Sci Rep 2023; 13:5852. [PMID: 37041293 PMCID: PMC10090175 DOI: 10.1038/s41598-023-32799-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 04/03/2023] [Indexed: 04/13/2023] Open
Abstract
Some autoimmune (AI) conditions affect white blood cell (WBC) counts. Whether a genetic predisposition to AI disease associates with WBC counts in populations expected to have low numbers of AI cases is not known. We developed genetic instruments for 7 AI diseases using genome-wide association study summary statistics. Two-sample inverse variance weighted regression (IVWR) was used to determine associations between each instrument and WBC counts. Effect size represents change in transformed WBC counts per change in log odds-ratio of the disease. For AI diseases with significant associations by IVWR, polygenic risk scores (PRS) were used to test for associations with measured WBC counts in individuals of European ancestry in a community-based (ARIC, n = 8926), and a medical-center derived cohort (BioVU, n = 40,461). The IVWR analyses revealed significant associations between 3 AI diseases and WBC counts: systemic lupus erythematous (Beta = - 0.05 [95% CI, - 0.06, - 0.03]), multiple sclerosis (Beta = - 0.06 [- 0.10, - 0.03]), and rheumatoid arthritis (Beta = 0.02 [0.01, 0.03]). PRS for these diseases showed associations with measured WBC counts in ARIC and BioVU. Effect sizes tended to be larger among females, consistent with the known higher prevalence of these diseases among this group. This study shows that genetic predisposition to systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis was associated with WBC counts, even in populations expected to have very low numbers of disease cases.
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Affiliation(s)
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vivian K Kawai
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Division of Clinical Pharmacology, 536 RRB, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
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Fu Z, Zhao PY, Yang XP, Li H, Hu SD, Xu YX, Du XH. Cannabidiol regulates apoptosis and autophagy in inflammation and cancer: A review. Front Pharmacol 2023; 14:1094020. [PMID: 36755953 PMCID: PMC9899821 DOI: 10.3389/fphar.2023.1094020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/24/2023] Open
Abstract
Cannabidiol (CBD) is a terpenoid naturally found in plants. The purified compound is used in the treatment of mental disorders because of its antidepressive, anxiolytic, and antiepileptic effects. CBD can affect the regulation of several pathophysiologic processes, including autophagy, cytokine secretion, apoptosis, and innate and adaptive immune responses. However, several authors have reported contradictory findings concerning the magnitude and direction of CBD-mediated effects. For example, CBD treatment can increase, decrease, or have no significant effect on autophagy and apoptosis. These variable results can be attributed to the differences in the biological models, cell types, and CBD concentration used in these studies. This review focuses on the mechanism of regulation of autophagy and apoptosis in inflammatory response and cancer by CBD. Further, we broadly elaborated on the prospects of using CBD as an anti-inflammatory agent and in cancer therapy in the future.
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Affiliation(s)
- Ze Fu
- Medical School of Chinese PLA, Beijing, China
| | | | | | - Hao Li
- Medical School of Chinese PLA, Beijing, China
| | - Shi-Dong Hu
- Department of General Surgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ying-Xin Xu
- Department of General Surgery, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiao-Hui Du
- Department of General Surgery, First Medical Center of Chinese PLA General Hospital, Beijing, China,*Correspondence: Xiao-Hui Du,
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Pandey A, L'Yi S, Wang Q, Borkin MA, Gehlenborg N. GenoREC: A Recommendation System for Interactive Genomics Data Visualization. IEEE Trans Vis Comput Graph 2023; 29:570-580. [PMID: 36191105 PMCID: PMC10067538 DOI: 10.1109/tvcg.2022.3209407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Interpretation of genomics data is critically reliant on the application of a wide range of visualization tools. A large number of visualization techniques for genomics data and different analysis tasks pose a significant challenge for analysts: which visualization technique is most likely to help them generate insights into their data? Since genomics analysts typically have limited training in data visualization, their choices are often based on trial and error or guided by technical details, such as data formats that a specific tool can load. This approach prevents them from making effective visualization choices for the many combinations of data types and analysis questions they encounter in their work. Visualization recommendation systems assist non-experts in creating data visualization by recommending appropriate visualizations based on the data and task characteristics. However, existing visualization recommendation systems are not designed to handle domain-specific problems. To address these challenges, we designed GenoREC, a novel visualization recommendation system for genomics. GenoREC enables genomics analysts to select effective visualizations based on a description of their data and analysis tasks. Here, we present the recommendation model that uses a knowledge-based method for choosing appropriate visualizations and a web application that enables analysts to input their requirements, explore recommended visualizations, and export them for their usage. Furthermore, we present the results of two user studies demonstrating that GenoREC recommends visualizations that are both accepted by domain experts and suited to address the given genomics analysis problem. All supplemental materials are available at https://osf.io/y73pt/.
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Abstract
Macroautophagy/autophagy, a fundamental cell process for nutrient recycling and defense against pathogens (termed xenophagy), is crucial to human health. ATG16L2 (autophagy related 16 like 2) is an autophagic protein and a paralog of ATG16L1. Both proteins are implicated in similar diseases such as cancer and other chronic diseases; however, most autophagy studies to date have primarily focused on the function of ATG16L1, with ATG16L2 remaining uncharacterized and understudied. Overexpression of ATG16L2 has been reported in various cancers including colorectal, gastric, and prostate carcinomas, whereas altered methylation of ATG16L2 has been associated with lung cancer formation and poorer response to therapy in leukemia. In addition, ATG16L2 polymorphisms have been implicated in a range of other diseases including inflammatory bowel diseases and neurodegenerative disorders. Despite this likely role in human health, the function of this enigmatic protein in autophagy remains unknown. Here, we review current studies on ATG16L2 and collate evidence that suggests that this protein is a potential modulator of autophagy as well as the implications this has on pathogenesis.Abbreviations: ATG5: autophagy related 5; ATG12: autophagy related 12; ATG16L1: autophagy related 16 like 1; ATG16L2: autophagy related 16 like 2; CD: Crohn disease; IBD: inflammatory bowel diseases; IRGM: immunity related GTPase M; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PE: phosphatidylethanolamine; RB1CC1: RB1 inducible coiled-coil 1; SLE: systemic lupus erythematosus; WIPI2B: WD repeat domain, phosphoinositide interacting 2B.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia,CONTACT Laurence Don Wai Luu School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Nadeem O. Kaakoush
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia,Natalia Castaño-Rodríguez School of Biotechnology and Biomolecular Sciences, Faculty of Science, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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Vaishnav J, Khan F, Yadav M, Parmar N, Buch H, Jadeja SD, Dwivedi M, Begum R. V-set domain containing T-cell activation inhibitor-1 (VTCN1): A potential target for the treatment of autoimmune diseases. Immunobiology 2022; 227:152274. [PMID: 36095871 DOI: 10.1016/j.imbio.2022.152274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022]
Abstract
Autoimmunity eventuates when the immune system attacks self-molecules as a result of the breakdown in immune tolerance. Targeting autoimmune diseases via immunomodulation has become an essential strategy in today's era. A B7 superfamily member immune checkpoint, the V-set domain containing T-cell activation inhibitor-1 (VTCN1), also known as B7-H4, B7S1, and B7x, is involved in negatively regulating T-cell activation. VTCN1 transcript has been reported in various lymphoid and non-lymphoid tissues, but its protein expression is restricted, indicating its translational regulation. Dysregulation of VTCN1 has resulted in the exacerbation of various autoimmune diseases. Moreover, increased soluble form of VTCN1 in the patient's sera positively correlates with the disease progression and severity. The current review summarizes all the reports till date, unfolding the role of VTCN1 in various autoimmune diseases and its therapeutic potential.
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Hasnat MA, Cheang I, Dankers W, Lee JPW, Truong LM, Pervin M, Jones SA, Morand EF, Ooi JD, Harris J. Investigating immunoregulatory effects of myeloid cell autophagy in acute and chronic inflammation. Immunol Cell Biol 2022; 100:605-623. [PMID: 35652357 PMCID: PMC9542007 DOI: 10.1111/imcb.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/26/2022]
Abstract
Studies have highlighted a critical role for autophagy in the regulation of multiple cytokines. Autophagy inhibits the release of interleukin (IL)‐1 family cytokines, including IL‐1α, IL‐1β and IL‐18, by myeloid cells. This, in turn, impacts the release of other cytokines by myeloid cells, as well as other cells of the immune system, including IL‐22, IL‐23, IL‐17 and interferon‐γ. Here, we assessed the impact of genetic depletion of the autophagy gene Atg7 in myeloid cells on acute and chronic inflammation. In a model of acute lipopolysaccharide‐induced endotoxemia, loss of autophagy in myeloid cells resulted in increased release of proinflammatory cytokines, both locally and systemically. By contrast, loss of Atg7 in myeloid cells in the Lyn−/− model of lupus‐like autoimmunity resulted in reduced systemic release of IL‐6 and IL‐10, with no effects on other cytokines observed. In addition, Lyn−/− mice with autophagy‐deficient myeloid cells showed reduced expression of autoantibodies relevant to systemic lupus erythematosus, including anti‐histone and anti‐Smith protein. In vitro, loss of autophagy, through pharmacological inhibition or small interfering RNA against Becn1, inhibited IL‐10 release by human and mouse myeloid cells. This effect was evident at the level of Il10 messenger RNA expression. Our data highlight potentially important differences in the role of myeloid cell autophagy in acute and chronic inflammation and demonstrate a direct role for autophagy in the production and release of IL‐10 by macrophages.
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Affiliation(s)
- Md Abul Hasnat
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - IanIan Cheang
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Wendy Dankers
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Jacinta PW Lee
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Lynda M Truong
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Mehnaz Pervin
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Sarah A Jones
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Eric F Morand
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - Joshua D Ooi
- Regulatory T Cell Therapies Group, Centre for Inflammatory Diseases Department of Medicine, School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
| | - James Harris
- Centre for Inflammatory Diseases, Department of Medicine School of Clinical Sciences at Monash Health Faculty of Medicine, Nursing and Health Sciences Monash University Clayton VIC Australia
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Vaishnav J, Jadeja SD, Singh M, Khan F, Yadav M, Begum R. Altered Levels of Negative Costimulatory Molecule V-Set Domain-Containing T-Cell Activation Inhibitor-1 (VTCN1) and Metalloprotease Nardilysin (NRD1) are Associated with Generalized Active Vitiligo. Immunol Invest 2022; 51:2035-2052. [PMID: 35815687 DOI: 10.1080/08820139.2022.2097091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Vitiligo is characterized by depigmented macules on the skin caused due to autoimmune destruction of melanocytes. V-set domain-containing T-cell activation inhibitor-1 (VTCN1) is a negative costimulatory molecule that plays a vital role in suppressing autoimmunity and tuning immune response. Nardilysin (NRD1), a metalloproteinase, cleaves membrane-tethered VTCN1 resulting in the shedding of soluble-VTCN1 (sVTCN1). However, the role of VTCN1 and NRD1 in vitiligo pathogenesis is unexplored. OBJECTIVES AND METHODS This study was aimed to (i) Investigate the association of VTCN1 intronic polymorphisms (rs10923223 T/C and rs12046117 C/T) with vitiligo susceptibility in Gujarat population by using Polymerase Chain Reaction- Restriction Fragment Length Polymorphism (PCR-RFLP) (ii) Estimate VTCN1 & NRD1 transcript levels from peripheral blood mononuclear cells (PBMCs) and skin samples of vitiligo patients by real-time PCR, (iii) Estimate sVTCN1 and NRD1 protein levels from plasma by ELISA and (iv) Estimate VTCN1 protein levels in the skin samples of vitiligo patients by immunofluorescence. RESULTS The analysis revealed increased VTCN1 and NRD1 transcript levels in the skin (p = .039, p = .021 respectively), increased sVTCN1 and NRD1 levels (p = .026, p = .015 respectively) in the plasma, and decreased VTCN1 protein levels (p = .0002) in the skin of vitiligo patients as compared to healthy controls. The genetic analysis revealed no significant association of VTCN1 intronic polymorphisms rs10923223 T/C and rs12046117 C/T with vitiligo susceptibility in Gujarat population (p = .359, p = .937, respectively). CONCLUSIONS The present study revealed altered VTCN1 and NRD1 expressions in the blood and skin of vitiligo patients, suggesting their potential role in the development and progression of Vitiligo.
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Affiliation(s)
- Jayvadan Vaishnav
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Shahnawaz D Jadeja
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Mala Singh
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Farheen Khan
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Madhu Yadav
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Rasheedunnisa Begum
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
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Ramírez-Bello J, Jiménez-Morales S, Barbosa-Cobos RE, Sánchez-Zauco N, Hernández-Molina G, Luria-Pérez R, Fragoso JM, Cabello-Gutiérrez C, Montúfar-Robles I. TNFSF4 is a risk factor for rheumatoid arthritis but not for primary Sjögren's syndrome in the Mexican population. Immunobiology 2022; 227:152244. [PMID: 35835012 DOI: 10.1016/j.imbio.2022.152244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/04/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Rheumatoid arthritis (RA) and primary Sjögren's syndrome (pSS) are autoimmune diseases (ADs) characterized by joint damage and involvement of the salivary glands, respectively. ADs share some susceptibility loci, such as TNFSF4, which is a classical susceptibility gene associated with systemic lupus erythematosus, but its role in RA and pSS is not yet clear. Thus, the aim of this study was to determine whether three TNFSFS4 polymorphisms are associated with RA and pSS. METHODS Our case-control study included 500 controls, 459 patients with RA, and 210 patients with pSS from Mexico. TNFSF4 single nucleotide polymorphisms (SNPs) rs1234315C/T, rs2205960G/T, and rs704840T/G were genotyped using TaqMan probes and discrimination allelic assay. RESULTS The three TNFSF4 SNPs were associated with susceptibility to RA (rs1234315C/T: odds ratio [OR] 1.4, p = 0.01; rs2205960G/T: OR 1.23, p = 0.03; rs704840T/G: OR 1.24, p = 0.02). An association between TNFSF4 rs1234315C/T and pSS was also observed (OR 1.28, p = 0.04), however, after Bonferroni correction, this association was lost. CONCLUSION Our data suggest that TNFSF4 could be a risk factor in RA but not pSS in a Mexican population.
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Affiliation(s)
- Julian Ramírez-Bello
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico.
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, 14610 Mexico City, Mexico.
| | | | - Norma Sánchez-Zauco
- División de Auxiliares de Diagnóstico y Tratamiento, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, 06720 IMSS, Mexico.
| | - Gabriela Hernández-Molina
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080 Mexico City, Mexico.
| | - Rosendo Luria-Pérez
- Unidad de Investigación en Enfermedades Hemato-Oncológicas, Hospital Infantil de México Federico Gómez, 06720, Mexico.
| | - José M Fragoso
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico.
| | - Carlos Cabello-Gutiérrez
- Departamento de Investigación en Virología y Micología, Instituto Nacional de Enfermedades Respiratorias, 14080 Mexico City, Mexico.
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El-Akhras BA, Ali YB, El-Masry SA, Bassyouni IH, El-Sayed IH, Talaat RM. mir-146a genetic polymorphisms in systemic lupus erythematosus patients: Correlation with disease manifestations. Noncoding RNA Res 2022; 7:142-149. [PMID: 35756164 PMCID: PMC9192690 DOI: 10.1016/j.ncrna.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 11/28/2022] Open
Abstract
This study aimed to investigate the genetic polymorphisms of miR-146a SNPs (rs2910164, rs57095329, and rs2431697) in systemic lupus erythematosus (SLE) patients and their association with clinical manifestations. The implication of SNPs on miR-146a expression level was also evaluated. SLE patients (113) and healthy controls (104) were registered in this study. The miR-146a SNPs were genotyped by polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP). Quantitative real-time PCR was used to measure the miR-146a expression in peripheral blood mononuclear cells (PBMCs). Our results showed that the genotype frequency of miR-146a SNPs didn't deviate significantly from the Hardy–Weinberg equilibrium (HWE). The AG genotype and G allele of miR-146a (rs57095329 A/G) might be considered a risk factor for the disease (OR = 2.27; CI: 0.78–6.57 and OR: 2.35; CI: 0.79–6.92 for AG genotype and G allele, respectively). Although, no statistical significance in the distribution of miR-146a SNPs (rs2910164, rs57095329, and rs2431697) was found, indicating the lack of association between the three SNPs and SLE susceptibility. Significantly, the higher frequency of the AA genotype of miR-146a (rs57095329) was associated with pancytopenia (P < 0.05), while the CT genotype of miR-146a (rs2431697) was associated (P < 0.05) with the antiphospholipid syndrome (APS). SLE patients had significantly higher levels of miR-146a compared to controls (P < 0.05). Elevation of miR-146a was independent of any SNP genotypes. In conclusion, this pilot study shows no association between miR-146a SNPs in our population group and susceptibility to lupus. Studies concerning other miRNAs in larger sample sizes are essential for a better understanding of their role in susceptibility to SLE disease. This study is concerned with genetic polymorphisms of miR-146a in Lupus patients. The AG genotype and G allele of miR-146a (rs57095329 A/G) might be considered a risk factor. No significance in the distribution of miR-146a SNPs (rs2910164, rs57095329, and rs2431697). miR-146a level was significantly elevated in SLE irrespective to any SNP genotypes. AA genotype of rs57095329 was associated with pancytopenia while the CT genotype of rs2431697 was associated with the APS.
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Affiliation(s)
- Basima A. El-Akhras
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), Sadat City University, Egypt
| | - Yasser B.M. Ali
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), Sadat City University, Egypt
| | - Samir A. El-Masry
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), Sadat City University, Egypt
| | - Iman H. Bassyouni
- Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ibrahim H. El-Sayed
- Biochemistry Department, Faculty of Science, Kafr El-Sheikh University, Egypt
| | - Roba M. Talaat
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), Sadat City University, Egypt
- Corresponding author. Molecular Biology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Egypt.
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Papageorgiou L, Alkenaris H, Zervou MI, Vlachakis D, Matalliotakis I, Spandidos DA, Bertsias G, Goulielmos GN, Eliopoulos E. Epione application: An integrated web‑toolkit of clinical genomics and personalized medicine in systemic lupus erythematosus. Int J Mol Med 2021; 49:8. [PMID: 34791504 PMCID: PMC8612305 DOI: 10.3892/ijmm.2021.5063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
Genome wide association studies (GWAS) have identified autoimmune disease-associated loci, a number of which are involved in numerous disease-associated pathways. However, much of the underlying genetic and pathophysiological mechanisms remain to be elucidated. Systemic lupus erythematosus (SLE) is a chronic, highly heterogeneous auto-immune disease, characterized by differences in autoantibody profile, serum cytokines and a multi-system involvement. This study presents the Epione application, an integrated bioinformatics web-toolkit, designed to assist medical experts and researchers in more accurately diagnosing SLE. The application aims to identify the most credible gene variants and single nucleotide polymorphisms (SNPs) associated with SLE susceptibility, by using patient's genomic data to aid the medical expert in SLE diagnosis. The application contains useful knowledge of >70,000 SLE-related publications that have been analyzed, using data mining and semantic techniques, towards extracting the SLE-related genes and the corresponding SNPs. Probable genes associated with the patient's genomic profile are visualized with several graphs, including chromosome ideograms, statistic bars and regulatory networks through data mining studies with relative publications, to obtain a representative number of the most credible candidate genes and biological pathways associated with the SLE. Furthermore, an evaluation study was performed on a patient diagnosed with SLE and is presented herein. Epione has also been expanded in family-related candidate patients to evaluate its predictive power. All the recognized gene variants that were previously considered to be associated with SLE were accurately identified in the output profile of the patient, and by comparing the results, novel findings have emerged. The Epione application may assist and facilitate in early stage diagnosis by using the patients' genomic profile to compare against the list of the most predictable candidate gene variants related to SLE. Its diagnosis-oriented output presents the user with a structured set of results on variant association, position in genome and links to specific bibliography and gene network associations. The overall aim of the present study was to provide a reliable tool for the most effective study of SLE. This novel and accessible webserver tool of SLE is available at http://geneticslab.aua.gr/epione/.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Haris Alkenaris
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Dimitriοs Vlachakis
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Ioannis Matalliotakis
- Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, 71409 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George Bertsias
- Department of Rheumatology and Clinical Immunology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
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Kawai VK, Shi M, Liu G, Feng Q, Wei W, Chung CP, Walunas TL, Gordon AS, Linneman JG, Hebbring SJ, Harley JB, Cox NJ, Roden DM, Stein CM, Mosley JD. Pleiotropy of systemic lupus erythematosus risk alleles and cardiometabolic disorders: A phenome-wide association study and inverse-variance weighted meta-analysis. Lupus 2021; 30:1264-1272. [PMID: 33977795 PMCID: PMC8205989 DOI: 10.1177/09612033211014952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
OBJECTIVES To test the hypothesis that genetic predisposition to systemic lupus erythematosus (SLE) increases the risk of cardiometabolic disorders. METHODS Using 41 single nucleotide polymorphisms (SNPs) associated with SLE, we calculated a weighted genetic risk score (wGRS) for SLE. In a large biobank we tested the association between this wGRS and 9 cardiometabolic phenotypes previously associated with SLE: atrial fibrillation, ischemic stroke, coronary artery disease, type 1 and type 2 diabetes, obesity, chronic kidney disease, hypertension, and hypercholesterolemia. Additionally, we performed a phenome-wide association analysis (pheWAS) to discover novel clinical associations with a genetic predisposition to SLE. Findings were replicated in the Electronic Medical Records and Genomics (eMERGE) Network. To further define the association between SLE-related risk alleles and the selected cardiometabolic phenotypes, we performed an inverse variance weighted regression (IVWR) meta-analysis. RESULTS The wGRS for SLE was calculated in 74,759 individuals of European ancestry. Among the pre-selected phenotypes, the wGRS was significantly associated with type 1 diabetes (OR [95%CI] =1.11 [1.06, 1.17], P-value = 1.05x10-5). In the PheWAS, the wGRS was associated with several autoimmune phenotypes, kidney disorders, and skin neoplasm; but only the associations with autoimmune phenotypes were replicated. In the IVWR meta-analysis, SLE-related risk alleles were nominally associated with type 1 diabetes (P = 0.048) but the associations were heterogeneous and did not meet the adjusted significance threshold. CONCLUSION A weighted GRS for SLE was associated with an increased risk of several autoimmune-related phenotypes including type I diabetes but not with cardiometabolic disorders.
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Affiliation(s)
- Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ge Liu
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - WeiQi Wei
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Cecilia P. Chung
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Rheumatology, Department of Medicine Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System - Nashville Campus
| | - Theresa L. Walunas
- Center for Health Information Partnerships, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Adam S. Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - James G. Linneman
- Office of Research, Computing, and Analytics, Marshfield Clinic Research Institute, Marshfield, WI
| | - Scott J. Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin USA
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dan M. Roden
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - C. Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan D. Mosley
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
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20
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Hurkmans DP, Basak EA, Schepers N, Oomen-De Hoop E, Van der Leest CH, El Bouazzaoui S, Bins S, Koolen SLW, Sleijfer S, Van der Veldt AAM, Debets R, Van Schaik RHN, Aerts JGJV, Mathijssen RHJ. Granzyme B is correlated with clinical outcome after PD-1 blockade in patients with stage IV non-small-cell lung cancer. J Immunother Cancer 2021; 8:jitc-2020-000586. [PMID: 32461348 PMCID: PMC7254154 DOI: 10.1136/jitc-2020-000586] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 01/05/2023] Open
Abstract
Background A minority of patients with advanced non-small-cell lung cancer (NSCLC) benefit from treatment with immune checkpoint inhibitors (ICIs). Ineffective effector function of activated T and NK cells may lead to reduced tumor cell death, even when these activated effector cells are released from their immune checkpoint brake. Hence, in this study we aimed to assess the association of baseline serum granzyme B, as well as germline variation of the GZMB gene, with clinical outcome to programmed cell death protein 1 (PD-1) blockade. Methods A total of 347 patients with stage IV NSCLC who started nivolumab treatment between June 2013 and June 2017 were prospectively included. Baseline serum and whole blood was available, allowing for protein quantification and targeted DNA sequencing. Clinical outcome was based on best overall response (BOR) according to Response Evaluation Criteria in Solid Tumors, V.1.1, progression-free survival (PFS), and overall survival (OS). Results Patients with low serum levels of granzyme B had worse PFS (HR: 1.96; 95% CI: 1.12 to 3.43; p=0.018) and worse OS (HR: 2.08; 95% CI: 1.12 to 3.87; p=0.021) than patients with high baseline serum levels. To validate the findings, germline variation of GZMB rs8192917 was assessed. Patients with homozygous and heterozygous variants of GZMB rs8192917 had worse BOR (OR: 1.60; 95% CI: 1.01 to 2.52; p=0.044) and worse PFS (HR: 1.38; 95% CI:1.02 to 1.87; p=0.036) than wild types. Conclusions A low baseline serum level of granzyme B and germline variation of GZMB was associated with worse clinical outcome in NSCLC, emphasizing the relevance and additional value of monitoring germline genetic variations which mirror cytotoxic functions of T cells in ICI therapy. Trail registration number Dutch Trial Registry (NL6828).
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Affiliation(s)
- Daan P Hurkmans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands .,Department of Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edwin A Basak
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Nina Schepers
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Esther Oomen-De Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Samira El Bouazzaoui
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Bins
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Stijn L W Koolen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.,Departmemt of Hospital Pharmacy, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Astrid A M Van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.,Department of Radiology & Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ron H N Van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim G J V Aerts
- Department of Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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21
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Eid R, Hammad A, Abdelsalam M, Fathy AA, Abd-El Ghafaar DM, Elmarghany EB, El-Hanafy AA, Mostafa N, Niazey NA, Korkor MS, Hamdy N. Tumor necrosis factor receptor II and PTPN22 genes polymorphisms and the risk of systemic lupus erythematosus in Egyptian children. Lupus 2021; 30:1449-1458. [PMID: 34080911 DOI: 10.1177/09612033211020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Many genes have been implicated in the pathogenesis of systemic lupus erythematosus (SLE). Tumor necrosis factor (TNF) is a potent cytokine stimulator acting through 2 cell surface receptors (TNFR I and II). TNFRII gene which controls expression of these receptors has been linked to SLE susceptibility through promoting apoptosis. Also; Protein tyrosine phosphatase non receptor 22 (PTPN22) gene enhances intrinsic phosphatase activity of T lymphocytes leading to their dysregulation and stimulates autoimmune process of lupus and its rs2476601 has been linked to susceptibility to thyroiditis in SLE patients in few studies. OBJECTIVES (i) to investigate the correlation between 2 SNPs of TNFR II and PTPN22 genes and SLE susceptibility in a cohort of Egyptian children compared to controls (ii) and to investigate their possible association with different clinical presentations of the disease in children. SUBJECTS AND METHODS Typing of TNFR II rs1061622 and PTPN22 rs2476601 SNPs were done using polymerase chain reaction-restriction fragment length polymorphism for 74 children with SLE and 100 matched healthy controls. RESULTS Children with SLE had more frequent G allele and GG genotype of TNFR II rs1061622 (p < 0.001) and more T allele and TT genotype of PTPN22 rs2476601 (p = 0.012 and <0.001, respectively) compared to controls. Only 6 patients (8%) had thyroiditis (hypothyroidism) with T allele and TT genotype of PTPN22 1858 T more prevalent in those patients versus those without thyroiditis (p ≤ 0.001). Apart from, thyroiditis, no significant association was found between genotypes and alleles frequencies of the 2 studied SNPs and other clinical manifestations of the disease. CONCLUSION The G allele and GG genotype of TNFR II rs1061622 and T allele and TT genotype of PTPN22 rs2476601 genes polymorphism can be considered as risk factors for the development of SLE. The presence of the T allele of PTPN22 rs2476601 may increase the risk of concomitant thyroiditis in Egyptian children with SLE but further studies are required to confirm this finding as thyroiditis was reported only in few cases in this study.
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Affiliation(s)
- Riham Eid
- Pediatric Nephrology Unit, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Egypt
| | - Ayman Hammad
- Immunology unit, clinical pathology department, Faculty of medicine, Mansoura university, Egypt; Immunology department, Egypt center for research and regenerative medicine, Cairo, Egypt
| | - Maha Abdelsalam
- Public health and community Department, Faculty of Medicine, Mansoura University, Egypt
| | - Aya Ahmed Fathy
- Rheumatology, Rehabilitation and Physical Medicine Department, Faculty of Medicine, Mansoura University, Egypt
| | - Dena M Abd-El Ghafaar
- Rheumatology, Rehabilitation and Physical Medicine Department, Faculty of Medicine, Mansoura University, Egypt
| | - Eman B Elmarghany
- Rheumatology, Rehabilitation and Physical Medicine Department, Faculty of Medicine, Mansoura University, Egypt
| | - Aya A El-Hanafy
- Medical Biochemistry Department, Faculty of Medicine, Mansoura University, Egypt
| | - Nora Mostafa
- Medical Biochemistry Department, Faculty of Medicine, Mansoura University, Egypt
| | - Nermeen A Niazey
- Rheumatology, Rehabilitation and Physical Medicine Department, Faculty of Medicine, Mansoura University, Egypt
| | - Mai S Korkor
- Pediatric Nephrology Unit, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Egypt
| | - Nashwa Hamdy
- Immunology unit, clinical pathology department, Faculty of medicine, Mansoura university, Egypt; Immunology department, Egypt center for research and regenerative medicine, Cairo, Egypt
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22
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Chiou J, Geusz RJ, Okino ML, Han JY, Miller M, Melton R, Beebe E, Benaglio P, Huang S, Korgaonkar K, Heller S, Kleger A, Preissl S, Gorkin DU, Sander M, Gaulton KJ. Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. Nature 2021; 594:398-402. [PMID: 34012112 PMCID: PMC10560508 DOI: 10.1038/s41586-021-03552-w] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 04/14/2021] [Indexed: 02/04/2023]
Abstract
Genetic risk variants that have been identified in genome-wide association studies of complex diseases are primarily non-coding1. Translating these risk variants into mechanistic insights requires detailed maps of gene regulation in disease-relevant cell types2. Here we combined two approaches: a genome-wide association study of type 1 diabetes (T1D) using 520,580 samples, and the identification of candidate cis-regulatory elements (cCREs) in pancreas and peripheral blood mononuclear cells using single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) of 131,554 nuclei. Risk variants for T1D were enriched in cCREs that were active in T cells and other cell types, including acinar and ductal cells of the exocrine pancreas. Risk variants at multiple T1D signals overlapped with exocrine-specific cCREs that were linked to genes with exocrine-specific expression. At the CFTR locus, the T1D risk variant rs7795896 mapped to a ductal-specific cCRE that regulated CFTR; the risk allele reduced transcription factor binding, enhancer activity and CFTR expression in ductal cells. These findings support a role for the exocrine pancreas in the pathogenesis of T1D and highlight the power of large-scale genome-wide association studies and single-cell epigenomics for understanding the cellular origins of complex disease.
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Affiliation(s)
- Joshua Chiou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
- Internal Medicine Research Unit, Pfizer Worldwide Research, Cambridge, MA, USA.
| | - Ryan J Geusz
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Jee Yun Han
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Melton
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Elisha Beebe
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Paola Benaglio
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Serina Huang
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Katha Korgaonkar
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Sandra Heller
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | | | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - David U Gorkin
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Maike Sander
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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23
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Fang Q, Li T, Chen P, Wu Y, Wang T, Mo L, Ou J, Nandakumar KS. Comparative Analysis on Abnormal Methylome of Differentially Expressed Genes and Disease Pathways in the Immune Cells of RA and SLE. Front Immunol 2021; 12:668007. [PMID: 34079550 PMCID: PMC8165287 DOI: 10.3389/fimmu.2021.668007] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
We identified abnormally methylated, differentially expressed genes (DEGs) and pathogenic mechanisms in different immune cells of RA and SLE by comprehensive bioinformatics analysis. Six microarray data sets of each immune cell (CD19+ B cells, CD4+ T cells and CD14+ monocytes) were integrated to screen DEGs and differentially methylated genes by using R package “limma.” Gene ontology annotations and KEGG analysis of aberrant methylome of DEGs were done using DAVID online database. Protein-protein interaction (PPI) network was generated to detect the hub genes and their methylation levels were compared using DiseaseMeth 2.0 database. Aberrantly methylated DEGs in CD19+ B cells (173 and 180), CD4+ T cells (184 and 417) and CD14+ monocytes (193 and 392) of RA and SLE patients were identified. We detected 30 hub genes in different immune cells of RA and SLE and confirmed their expression using FACS sorted immune cells by qPCR. Among them, 12 genes (BPTF, PHC2, JUN, KRAS, PTEN, FGFR2, ALB, SERB-1, SKP2, TUBA1A, IMP3, and SMAD4) of RA and 12 genes (OAS1, RSAD2, OASL, IFIT3, OAS2, IFIH1, CENPE, TOP2A, PBK, KIF11, IFIT1, and ISG15) of SLE are proposed as potential biomarker genes based on receiver operating curve analysis. Our study suggests that MAPK signaling pathway could potentially differentiate the mechanisms affecting T- and B- cells in RA, whereas PI3K pathway may be used for exploring common disease pathways between RA and SLE. Compared to individual data analyses, more dependable and precise filtering of results can be achieved by integrating several relevant data sets.
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Affiliation(s)
- Qinghua Fang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Tingyue Li
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peiya Chen
- Department of Science and Education, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuzhe Wu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Tingting Wang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Lixia Mo
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jiaxin Ou
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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24
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Ali Y, Khan S, Chen Y, Farooqi N, Islam ZU, Akhtar M, Aamir, Aman A, Shah AA, Jamal M, Jalil F. Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort. Genet Res (Camb) 2021; 2021:5544198. [PMID: 34104118 PMCID: PMC8147531 DOI: 10.1155/2021/5544198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is one of the complex diseases with the involvement of the genetic as well as environmental factors in its onset and severity. Different genome-wide association and candidate gene studies have shown the role of several genetic variants in multiple loci/genes with ethnical and geographical variations. This study was designed to detect the association of a single-nucleotide polymorphism (SNP) rs10865035 in the AFF3 gene with the genetic background of rheumatoid arthritis (RA) in the Pakistani cohort. A total of 703 individuals, including 409 RA patients and 294 healthy controls, were genotyped using TaqMan assay and Tri primer ARMS-PCR (amplification-refractory mutation system-polymerase chain reaction) methods. The association of rs10865035 with the RA was statistically determined using different models. Interestingly, besides the homozygous recessive model (G/G vs. A/G + A/A) (OR = 1.693(1.06-2.648); P = 0.025), all other models, which included the codominant (χ 2 = 5.169; P = 0.075), homozygous dominant (A/A vs. G/G + A/G) (OR = 0.867 (0.636-1.187); P = 0.41), heterozygous (A/G vs. A/A + GG) (OR = 0.491 (0.667-1.215); P = 0.49), and additive model (OR = 0.826 (0.665-1.027); P = 0.08) showed insignificant distribution of the genotypes among the cases and controls. These findings suggest that the AFF3 gene (rs10865035) has no significant role in the onset of RA in the Pakistani population.
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Affiliation(s)
- Yasir Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Suleman Khan
- Lady Ready Hospital, MTI Peshawar, Peshawar, Pakistan
| | - Yangchao Chen
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, Pakistan
| | - Nadia Farooqi
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Zia-Ul Islam
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Aamir
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Aisha Aman
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Aftab Ali Shah
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
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25
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Yukina MY, Larina AA, Vasilyev EV, Troshina EA, Dimitrova DA. Search for Genetic Predictors of Adult Autoimmune Polyendocrine Syndrome in Monozygotic Twins. Clin Med Insights Endocrinol Diabetes 2021; 14:11795514211009796. [PMID: 33953634 PMCID: PMC8058797 DOI: 10.1177/11795514211009796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022]
Abstract
Autoimmune polyendocrine syndromes (APS) are a heterogeneous group of diseases characterized by the presence of autoimmune dysfunction of 2 or more endocrine glands and other non-endocrine organs. The components of the syndrome can manifest throughout life: in childhood—APS type 1 (the juvenile type) and in adulthood—APS type 2, 3, and 4 (the adult types). Adult types of APS are more common in clinical practice. It is a polygenic disease associated with abnormalities in genes encoding key regulatory proteins of the major histocompatibility complex (MHC). The search of for candidate genes responsible for mutations in adult APS is continuing. Genetic predisposition is insufficient for the manifestation of the APS of adults, since the penetrance of the disease, even among monozygotic twins, does not approach 100% (30–70%). The article presents the case of isolated Addison’s disease and APS type 2 in monozygotic twins with a revealed compound heterozygosity in the candidate gene VTCN1.
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26
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Nam SW, Lee KS, Yang JW, Ko Y, Eisenhut M, Lee KH, Shin JI, Kronbichler A. Understanding the genetics of systemic lupus erythematosus using Bayesian statistics and gene network analysis. Clin Exp Pediatr 2021; 64:208-222. [PMID: 32683804 PMCID: PMC8103040 DOI: 10.3345/cep.2020.00633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
The publication of genetic epidemiology meta-analyses has increased rapidly, but it has been suggested that many of the statistically significant results are false positive. In addition, most such meta-analyses have been redundant, duplicate, and erroneous, leading to research waste. In addition, since most claimed candidate gene associations were false-positives, correctly interpreting the published results is important. In this review, we emphasize the importance of interpreting the results of genetic epidemiology meta-analyses using Bayesian statistics and gene network analysis, which could be applied in other diseases.
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Affiliation(s)
- Seoung Wan Nam
- Department of Rheumatology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Kwang Seob Lee
- Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Won Yang
- Department of Nephrology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Korea
| | - Michael Eisenhut
- Department of Pediatrics, Luton & Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
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27
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Lu H, Zhang J, Jiang Z, Zhang M, Wang T, Zhao H, Zeng P. Detection of Genetic Overlap Between Rheumatoid Arthritis and Systemic Lupus Erythematosus Using GWAS Summary Statistics. Front Genet 2021; 12:656545. [PMID: 33815486 PMCID: PMC8012913 DOI: 10.3389/fgene.2021.656545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Clinical and epidemiological studies have suggested systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are comorbidities and common genetic etiologies can partly explain such coexistence. However, shared genetic determinations underlying the two diseases remain largely unknown. Methods Our analysis relied on summary statistics available from genome-wide association studies of SLE (N = 23,210) and RA (N = 58,284). We first evaluated the genetic correlation between RA and SLE through the linkage disequilibrium score regression (LDSC). Then, we performed a multiple-tissue eQTL (expression quantitative trait loci) weighted integrative analysis for each of the two diseases and aggregated association evidence across these tissues via the recently proposed harmonic mean P-value (HMP) combination strategy, which can produce a single well-calibrated P-value for correlated test statistics. Afterwards, we conducted the pleiotropy-informed association using conjunction conditional FDR (ccFDR) to identify potential pleiotropic genes associated with both RA and SLE. Results We found there existed a significant positive genetic correlation (rg = 0.404, P = 6.01E-10) via LDSC between RA and SLE. Based on the multiple-tissue eQTL weighted integrative analysis and the HMP combination across various tissues, we discovered 14 potential pleiotropic genes by ccFDR, among which four were likely newly novel genes (i.e., INPP5B, OR5K2, RP11-2C24.5, and CTD-3105H18.4). The SNP effect sizes of these pleiotropic genes were typically positively dependent, with an average correlation of 0.579. Functionally, these genes were implicated in multiple auto-immune relevant pathways such as inositol phosphate metabolic process, membrane and glucagon signaling pathway. Conclusion This study reveals common genetic components between RA and SLE and provides candidate associated loci for understanding of molecular mechanism underlying the comorbidity of the two diseases.
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Affiliation(s)
- Haojie Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Jinhui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Zhou Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Meng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ting Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Huashuo Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ping Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
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28
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de With M, Hurkmans DP, Oomen-de Hoop E, Lalouti A, Bins S, El Bouazzaoui S, van Brakel M, Debets R, Aerts JGJV, van Schaik RHN, Mathijssen RHJ, van der Veldt AAM. Germline Variation in PDCD1 Is Associated with Overall Survival in Patients with Metastatic Melanoma Treated with Anti-PD-1 Monotherapy. Cancers (Basel) 2021; 13:cancers13061370. [PMID: 33803602 PMCID: PMC8002987 DOI: 10.3390/cancers13061370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/06/2021] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
A substantial number of melanoma patients do not benefit from therapy with anti-PD-1. Therefore, we investigated the predictive value of single nucleotide polymorphisms (SNPs) in genes related to the PD-1 axis in patients with metastatic melanoma. From 119 consecutive melanoma patients who were treated with pembrolizumab or nivolumab monotherapy, blood samples were genotyped for 11 SNPs in nine genes. Associations between SNPs and OS were tested using Cox regression analysis and internally validated by bootstrapping. For SNPs with a statistical significance, an expression quantitative trait loci (eQTL) analysis was performed. In a subset of patients, immunophenotyping was performed. Patients with a SNP in PDCD1 (804C > T; rs2227981) had a significantly poorer OS with a 3-year OS rate of 51.8%, as compared to 71% in wild type patients (hazard ratio [HR] 2.37; 95% CI: 1.11-5.04; p = 0.026). eQTL analysis showed that this SNP was associated with decreased gene expression. In addition, PDCD1 804C > T carriers had a reduced fraction of peripheral PD-1+CD4+ T cells. No other associations between SNPs and OS were found. PDCD1 804C > T is associated with poorer OS after anti-PD-1 monotherapy in patients with metastatic melanoma. This SNP may affect clinical benefit from ICIs by decreasing transcription initiation and expression of PD-1 in T cells.
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Affiliation(s)
- Mirjam de With
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (R.H.N.v.S.)
| | - Daan P. Hurkmans
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
- Department of Pulmonology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Correspondence: ; Tel.: +31-10-704-11-12
| | - Esther Oomen-de Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Ayoub Lalouti
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Sander Bins
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Samira El Bouazzaoui
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (R.H.N.v.S.)
| | - Mandy van Brakel
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Joachim G. J. V. Aerts
- Department of Pulmonology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
| | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (R.H.N.v.S.)
| | - Ron H. J. Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Astrid A. M. van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
- Department of Radiology & Nuclear Medicine, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
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Sim H, Jeong D, Kim HI, Pak S, Thapa B, Kwon HJ, Lee K. CD11b Deficiency Exacerbates Methicillin-Resistant Staphylococcus aureus-Induced Sepsis by Upregulating Inflammatory Responses of Macrophages. Immune Netw 2021; 21:e13. [PMID: 33996169 PMCID: PMC8099615 DOI: 10.4110/in.2021.21.e13] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/21/2020] [Accepted: 01/07/2021] [Indexed: 12/14/2022] Open
Abstract
Macrophages are important for the first line of defense against microbial pathogens. Integrin CD11b, which is encoded by Itgam, is expressed on the surface of macrophages and has been implicated in adhesion, migration, and cell-mediated cytotoxicity. However, the functional impact of CD11b on the inflammatory responses of macrophages upon microbial infection remains unclear. Here, we show that CD11b deficiency resulted in increased susceptibility to sepsis induced by methicillin-resistant Staphylococcus aureus (MRSA) infection by enhancing the pro-inflammatory activities of macrophages. Upon infection with MRSA, the mortality of Itgam knockout mice was significantly higher than that of control mice, which is associated with increased production of TNF-α and IL-6. In response to MRSA, both bone marrow-derived macrophages and peritoneal macrophages lacking CD11b produced elevated amounts of pro-inflammatory cytokines and nitric oxide. Moreover, CD11b deficiency upregulated IL-4-induced expression of anti-inflammatory mediators such as IL-10 and arginase-1, and an immunomodulatory function of macrophages to restrain T cell activation. Biochemical and confocal microscopy data revealed that CD11b deficiency augmented the activation of NF-κB signaling and phosphorylation of Akt, which promotes the functional activation of macrophages with pro-inflammatory and immunoregulatory phenotypes, respectively. Overall, our experimental evidence suggests that CD11b is a critical modulator of macrophages in response to microbial infection.
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Affiliation(s)
- Hyunsub Sim
- Department of Biomedical Science, College of Natural Science, Hallym University, Chuncheon 24252, Korea
| | - Daecheol Jeong
- Department of Biomedical Science, College of Natural Science, Hallym University, Chuncheon 24252, Korea
| | - Hye-In Kim
- Department of Biomedical Science, College of Natural Science, Hallym University, Chuncheon 24252, Korea
| | - Seongwon Pak
- Department of Biomedical Science, College of Natural Science, Hallym University, Chuncheon 24252, Korea
| | - Bikash Thapa
- Institute of Bioscience and Biotechnology, Hallym University, Chuncheon 24252, Korea
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Korea
| | - Keunwook Lee
- Department of Biomedical Science, College of Natural Science, Hallym University, Chuncheon 24252, Korea.,Institute of Bioscience and Biotechnology, Hallym University, Chuncheon 24252, Korea
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30
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Karaderi T, Bareke H, Kunter I, Seytanoglu A, Cagnan I, Balci D, Barin B, Hocaoglu MB, Rahmioglu N, Asilmaz E, Taneri B. Host Genetics at the Intersection of Autoimmunity and COVID-19: A Potential Key for Heterogeneous COVID-19 Severity. Front Immunol 2020; 11:586111. [PMID: 33414783 PMCID: PMC7783411 DOI: 10.3389/fimmu.2020.586111] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
COVID-19 presentation is very heterogeneous across cases, and host factors are at the forefront for the variables affecting the disease manifestation. The immune system has emerged as a key determinant in shaping the outcome of SARS-CoV-2 infection. It is mainly the deleterious unconstrained immune response, rather than the virus itself, which leads to severe cases of COVID-19 and the associated mortality. Genetic susceptibility to dysregulated immune response is highly likely to be among the host factors for adverse disease outcome. Given that such genetic susceptibility has also been observed in autoimmune diseases (ADs), a number of critical questions remain unanswered; whether individuals with ADs have a significantly different risk for COVID-19-related complications compared to the general population, and whether studies on the genetics of ADs can shed some light on the host factors in COVID-19. In this perspective, we discuss the host genetic factors, which have been under investigation in association with COVID-19 severity. We touch upon the intricate link between autoimmunity and COVID-19 pathophysiology. We put forth a number of autoimmune susceptibility genes, which have the potential to be additional host genetic factors for modifying the severity of COVID-19 presentation. In summary, host genetics at the intersection of ADs and COVID-19 may serve as a source for understanding the heterogeneity of COVID-19 severity, and hence, potentially holds a key in achieving effective strategies in risk group identification, as well as effective treatments.
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Affiliation(s)
- Tugce Karaderi
- Center for Health Data Science, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Halin Bareke
- Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Imge Kunter
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, Cyprus
| | - Adil Seytanoglu
- Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
| | - Ilgin Cagnan
- Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
| | - Deniz Balci
- Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
| | - Burc Barin
- Vaccines and Infectious Diseases Therapeutic Research Area, The Emmes Company, Rockville, MD, United States
| | - Mevhibe B. Hocaoglu
- Cicely Saunders Institute of Palliative Care, Policy & Rehabilitation, Florence Nightingale Faculty of Nursing, Midwifery & Palliative Care, King’s College London, London, United Kingdom
- Dr Fazil Kucuk Faculty of Medicine, Eastern Mediterranean University, Famagusta, Cyprus
| | - Nilufer Rahmioglu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Esra Asilmaz
- Department of Gastroenterology, Homerton University Hospital, Clapton, United Kingdom
| | - Bahar Taneri
- Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
- Department of Genetics and Cell Biology, Faculty of Health, Medicine & Life Sciences, Institute for Public Health Genomics, Maastricht University, Maastricht, Netherlands
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31
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Thomsen H, Li X, Sundquist K, Sundquist J, Försti A, Hemminki K. Familial risks between giant cell arteritis and Takayasu arteritis and other autoimmune diseases in the population of Sweden. Sci Rep 2020; 10:20887. [PMID: 33257751 PMCID: PMC7705754 DOI: 10.1038/s41598-020-77857-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/13/2020] [Indexed: 02/08/2023] Open
Abstract
Giant cell arteritis (GCA, also called temporal arteritis) is a rare and Takayasu arteritis (TA) is an even rarer autoimmune disease (AID), both of which present with inflammatory vasculitis of large and medium size arteries. The risk factors are largely undefined but disease susceptibility has been associated with human leukocyte antigen locus. Population-level familial risk is not known. In the present nation-wide study we describe familial risk for GCA and for GCA and TA with any other AID based on the Swedish hospital diagnoses up to years 2012. Family relationships were obtained from the Multigeneration Register. Familial standardized incidence ratios (SIRs) were calculated for offspring whose parents or siblings were diagnosed with GCA, TA or any other AID. The number of GCA patients in the offspring generation was 4695, compared to 209 TA patients; for both, familial patients accounted for 1% of all patients. The familial risk for GCA was 2.14, 2.40 for women and non-significant for men. GCA was associated with 10 other AIDs and TA was associated with 6 other AIDs; both shared associations with polymyalgia rheumatica and rheumatoid arthritis. The results showed that family history is a risk factor for GCA. Significant familial associations of both GCA and TA with such a number of other AIDs provide evidence for polyautoimmunity among these diseases.
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Affiliation(s)
- Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- Center for Primary Health Care Research, Lund University, Malmö, Sweden.
- GeneWerk GmbH, Im Neuenheimer Feld 582, 69120, Heidelberg, Germany.
| | - Xinjun Li
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Functional Pathology, School of Medicine, Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, Matsue, Japan
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Functional Pathology, School of Medicine, Center for Community-Based Healthcare Research and Education (CoHRE), Shimane University, Matsue, Japan
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic
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Zervou MI, Andreou A, Matalliotakis M, Spandidos DA, Goulielmos GN, Eliopoulos EE. Association of the DNASE1L3 rs35677470 polymorphism with systemic lupus erythematosus, rheumatoid arthritis and systemic sclerosis: Structural biological insights. Mol Med Rep 2020; 22:4492-4498. [PMID: 33173951 PMCID: PMC7646740 DOI: 10.3892/mmr.2020.11547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/30/2020] [Indexed: 01/29/2023] Open
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of autoimmune disease-associated loci, much of the genetics underlying these diseases remains unknown. In an attempt to identify potential causal variants, previous studies have determined that the rs35677470 missense variant of the Deoxyribonuclease I-like 3 (DNASE1L3) gene was associated with the development of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and systemic sclerosis (SSc). DNase1L3 is a member of the human DNase I family, representing a nuclease that cleaves double-stranded DNA during apoptosis and serving a role in the development of autoimmune diseases. The present study aimed to determine the role of the rs35677470 variant at the DNASE1L3 gene leading to the R206C mutation in SLE, RA and SSc. The underlying mechanism potentially affecting protein structure loss of function was also assessed. DNASE1L3 evolution was investigated to define conservation elements in the protein sequence. Additionally, 3D homology modeling and in silico mutagenesis was performed to localize the polymorphism under investigation. Evolutionary analysis revealed heavily conserved sequence elements among species, indicating structural/functional importance. In silico mutagenesis and 3D protein structural analysis also demonstrated the potentially varied impact of the DNASE1L3 (rs35677470) single nucleotide polymorphism (SNP), providing an explanation for its effect on the R206C variant. Structural analysis demonstrated that the rs35677470 SNP encodes a non-conservative amino acid variation, R206C, which disrupted the conserved electrostatic network holding secondary protein structure elements in position. Specifically, the R206 to E170 interaction forming part of a salt bridge network stabilizing two α-helices was interrupted, thereby affecting the molecular architecture. Previous studies on the effect of this SNP in Caucasian populations demonstrated lower DNAse1L3 activity levels, which is consistent with the current results. The present study comprehensively evaluated the shared autoimmune locus of DNASE1L3 (rs35677470), which produced an inactive form of DNaseIL3. Furthermore, structural analysis explained the potential role of the produced mutation by modifying the placement of structural elements and consequently introducing disorder in protein folding, affecting biological function.
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Affiliation(s)
- Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Athena Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Michail Matalliotakis
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
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Cho KS, Lee JH, Cho J, Cha GH, Song GJ. Autophagy Modulators and Neuroinflammation. Curr Med Chem 2020; 27:955-982. [PMID: 30381067 DOI: 10.2174/0929867325666181031144605] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/20/2018] [Accepted: 10/21/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Neuroinflammation plays a critical role in the development and progression of various neurological disorders. Therefore, various studies have focused on the development of neuroinflammation inhibitors as potential therapeutic tools. Recently, the involvement of autophagy in the regulation of neuroinflammation has drawn substantial scientific interest, and a growing number of studies support the role of impaired autophagy in the pathogenesis of common neurodegenerative disorders. OBJECTIVE The purpose of this article is to review recent research on the role of autophagy in controlling neuroinflammation. We focus on studies employing both mammalian cells and animal models to evaluate the ability of different autophagic modulators to regulate neuroinflammation. METHODS We have mostly reviewed recent studies reporting anti-neuroinflammatory properties of autophagy. We also briefly discussed a few studies showing that autophagy modulators activate neuroinflammation in certain conditions. RESULTS Recent studies report neuroprotective as well as anti-neuroinflammatory effects of autophagic modulators. We discuss the possible underlying mechanisms of action of these drugs and their potential limitations as therapeutic agents against neurological disorders. CONCLUSION Autophagy activators are promising compounds for the treatment of neurological disorders involving neuroinflammation.
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Affiliation(s)
- Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul, Korea
| | - Jang Ho Lee
- Translational Brain Research Center, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
| | - Jeiwon Cho
- Translational Brain Research Center, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea.,Department of Medical Science, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Korea
| | - Guang-Ho Cha
- Department of Medical Science, College of Medicine, Chungnam National University, 35015 Daejeon, Korea
| | - Gyun Jee Song
- Translational Brain Research Center, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea.,Department of Medical Science, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Korea
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34
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Das M, Karnam A, Stephen-Victor E, Gilardin L, Bhatt B, Kumar Sharma V, Rambabu N, Patil V, Lecerf M, Käsermann F, Bruneval P, Narayanaswamy Balaji K, Benveniste O, Kaveri SV, Bayry J. Intravenous immunoglobulin mediates anti-inflammatory effects in peripheral blood mononuclear cells by inducing autophagy. Cell Death Dis 2020; 11:50. [PMID: 31974400 PMCID: PMC6978335 DOI: 10.1038/s41419-020-2249-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Autophagy plays an important role in the regulation of autoimmune and autoinflammatory responses of the immune cells. Defective autophagy process is associated with various autoimmune and inflammatory diseases. Moreover, in many of these diseases, the therapeutic use of normal immunoglobulin G or intravenous immunoglobulin (IVIG), a pooled normal IgG preparation, is well documented. Therefore, we explored if IVIG immunotherapy exerts therapeutic benefits via induction of autophagy in the immune cells. Here we show that IVIG induces autophagy in peripheral blood mononuclear cells (PBMCs). Further dissection of this process revealed that IVIG-induced autophagy is restricted to inflammatory cells like monocytes, dendritic cells, and M1 macrophages but not in cells associated with Th2 immune response like M2 macrophages. IVIG induces autophagy by activating AMP-dependent protein kinase, beclin-1, class III phosphoinositide 3-kinase and p38 mitogen-activated protein kinase and by inhibiting mammalian target of rapamycin. Mechanistically, IVIG-induced autophagy is F(ab')2-dependent but sialylation independent, and requires endocytosis of IgG by innate cells. Inhibition of autophagy compromised the ability of IVIG to suppress the inflammatory cytokines in innate immune cells. Moreover, IVIG therapy in inflammatory myopathies such as dermatomyositis, antisynthetase syndrome and immune-mediated necrotizing myopathy induced autophagy in PBMCs and reduced inflammatory cytokines in the circulation, thus validating the translational importance of these results. Our data provide insight on how circulating normal immunoglobulins maintain immune homeostasis and explain in part the mechanism by which IVIG therapy benefits patients with autoimmune and inflammatory diseases.
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Affiliation(s)
- Mrinmoy Das
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France
| | - Anupama Karnam
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France
| | - Emmanuel Stephen-Victor
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France
| | - Laurent Gilardin
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France.,Département de Médecine Interne et Immunologie Clinique, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Bharat Bhatt
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Varun Kumar Sharma
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France
| | - Naresh Rambabu
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France
| | - Veerupaxagouda Patil
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France
| | - Maxime Lecerf
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Fabian Käsermann
- CSL Behring, Research, CSL Biologics Research Center, 3014, Bern, Switzerland
| | - Patrick Bruneval
- Service d'anatomie pathologique, Hôpital Européen Georges Pompidou, 75015, Paris, France
| | | | - Olivier Benveniste
- Département de Médecine Interne et Immunologie Clinique, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Institut National de la Santé et de la Recherche Médicale Unité 974, Sorbonne Université, 75013, Paris, France
| | - Srini V Kaveri
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France
| | - Jagadeesh Bayry
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe- Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, 75006, Paris, France. .,Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France.
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35
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Thomsen H, Li X, Sundquist K, Sundquist J, Försti A, Hemminki K. Familial associations for rheumatoid autoimmune diseases. Rheumatol Adv Pract 2020; 4:rkaa048. [PMID: 33241174 PMCID: PMC7673201 DOI: 10.1093/rap/rkaa048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/17/2020] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Previous studies have shown a familial component in RA and in some other rheumatic autoimmune diseases (RAIDs), but because of the different study designs the risk estimates for familial risks differ extensively. The objective of this study is to identify familial components for RAIDs. METHODS We collected data on patients diagnosed in Swedish hospitals with RA, AS, PM/DM, SS, SLE and SSc (and scleroderma) and calculated familial standardized incidence ratios (SIRs) for each of these (concordant) and between them (discordant). RESULTS The combined number of RAID patients in the offspring population (for whom SIRs were calculated) was 71 544, and in the whole population the number was 152 714, accounting for 19.8% of all autoimmune diseases in Sweden. AS showed the highest concordant familial risk of 18.42, followed by SLE (14.04), SS (8.63), SSc (4.50), PM/DM (4.03) and RA (3.03). There was no sex difference in SIRs. Risks for AS and SLE were 80.28 and 19.53 for persons whose parents and siblings were affected. Discordant risks were far lower than concordant risks, but they were significant for RA with all the other five RAIDs, for SLE and SSc with four RAIDs, for AS and SS with three RAIDs and for PM/DM with two RAIDs, attesting to extensive polyautoimmunity between RAIDs. CONCLUSION The derived familial risks in this nationwide family study on medically diagnosed RAID are compatible with emerging evidence on the polygenic background of these complex diseases. Novel genetic pathways offer new therapeutic targets that alleviate disease onset optimally in high-risk familial patients and others.
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Affiliation(s)
- Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Bioinformatics and Biostatistics Working Section, GeneWerk GmbH, Heidelberg, Germany
- Correspondence to: Hauke Thomsen, GeneWerk GmbH, Im Neuenheimer Feld 582, D-69120 Heidelberg, Germany. E-mail:
| | - Xinjun Li
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | | | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ)
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK)
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
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Thomsen H, Li X, Sundquist K, Sundquist J, Försti A, Hemminki K. Familial risks between Graves disease and Hashimoto thyroiditis and other autoimmune diseases in the population of Sweden. J Transl Autoimmun 2020; 3:100058. [PMID: 32743538 PMCID: PMC7388361 DOI: 10.1016/j.jtauto.2020.100058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 02/08/2023] Open
Abstract
Genetic and family studies have indicated that Graves disease and Hashimoto thyroiditis have a heritable component which appears to be shared to some extend also with some other autoimmune diseases (AIDs). In the present nation-wide study we describe familial risk for Graves disease and Hashimoto thyroiditis identified from the Swedish Hospital Discharge Register (years 1964 through 2012) and the Outpatient Register (2001 through 2012). Family relationships were obtained from the Multigeneration Register and cancers from the Cancer Registry. Familial standardized incidence ratios (SIRs) were calculated for 29,005 offspring with Graves disease and for 25,607 offspring with Hashimoto thyroiditis depending on any of 43 AIDs in parents or siblings. The concordant familial risks for Graves disease and Hashimoto thyroiditis were 3.85 and 4.75, higher for men than for women. The familial risks were very high (11.35, Graves and 22.06, Hashimoto) when both a parent and a sibling were affected. Spousal familial risks were higher for Hashimoto thyroiditis (1.98/1.93) than for Graves disease (1.48/1.50). For Graves disease, 24 discordant AIDs showed a significant association; for Hashimoto thyroiditis, 20 discordant associations were significant. All significant discordant associations were positive for the two thyroid AIDs, with the exception of Hashimoto thyroiditis with Reiter disease. Overall 8 associations were significant only for Graves disease and 6 Hashimoto thyroiditis. The overall high concordant familial risks for Graves disease and Hashimoto thyroiditis suggest a strong genetic contribution to the familial risk. Significant familial associations among more than half of the 43 AIDs attest to the extensive polyautoimmunity among thyroid AIDs.
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Affiliation(s)
- Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- GeneWerk GmbH, 69120, Heidelberg, Germany
- Corresponding author. Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
| | - Xinjun Li
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | | | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA 94305-5705, USA
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic
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Ramírez-Bello J, Sun C, Valencia-Pacheco G, Singh B, Barbosa-Cobos RE, Saavedra MA, López-Villanueva RF, Nath SK. ITGAM is a risk factor to systemic lupus erythematosus and possibly a protection factor to rheumatoid arthritis in patients from Mexico. PLoS One 2019; 14:e0224543. [PMID: 31774828 PMCID: PMC6881022 DOI: 10.1371/journal.pone.0224543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/15/2019] [Indexed: 12/25/2022] Open
Abstract
Introduction ITGAM has consistently been associated with susceptibility to systemic lupus erythematosus (SLE) in many ethnically diverse populations. However, in populations with higher Amerindian ancestry (like Yucatan) or highly admixed population (like Mexican), ITGAM has seldom been evaluated (except few studies where patients with childhood-onset SLE were included). In addition, ITGAM has seldom been evaluated in patients with rheumatoid arthritis (RA). Here, we evaluated whether four single nucleotide polymorphisms (SNPs), located within ITGAM, were associated with SLE and RA susceptibility in patients from Mexico. Methods Our study consisted of 1,462 individuals, which included 363 patients with SLE (292 from Central Mexico and 71 from Yucatan), and 621 healthy controls (504 from Central Mexico and 117 from Yucatan). Our study also included 478 patients with RA from Central Mexico. TaqMan assays were used to obtain the genotypes of the four SNPs: rs34572943 (G/A), rs1143679 (G/A), rs9888739 (C/T), and rs1143683 (C/T). We also verified the genotypes by Sanger sequencing. Fisher's exact test and permutation test were employed to evaluate the distribution of genotype, allele, and haplotype between patients and controls. Results Our data show that all four ITGAM SNPs are significantly associated with susceptibility to SLE using both genotypic and allelic association tests (corrected for multiple testing, but not for population stratification). A second study carried out in patients from Yucatan, a southeastern part of Mexico (with a high Amerindian ancestry), also replicated SLE association with all four SNPs, including the functional SNP, rs1143679 (OR = 24.6 and p = 9.3X10-6). On the other hand, none of the four SNPs are significant in RA after multiple testing. Interestingly, the GACC haplotype, which carries the ITGAM rs1143679 (A) minor allele, showed an association with protection against RA (OR = 0.14 and p = 3.0x10-4). Conclusion Our data displayed that ITGAM is a risk factor to SLE in individuals of Mexican population. Concurrently, a risk haplotype in ITGAM confers protection against RA.
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Affiliation(s)
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | | | - Bhupinder Singh
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | | | - Miguel A. Saavedra
- Rheumatology Department, Centro Médico Nacional “La Raza”, Mexico City, Mexico
| | | | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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Geginat J, Vasco M, Gerosa M, Tas SW, Pagani M, Grassi F, Flavell RA, Meroni P, Abrignani S. IL-10 producing regulatory and helper T-cells in systemic lupus erythematosus. Semin Immunol 2019; 44:101330. [PMID: 31735515 DOI: 10.1016/j.smim.2019.101330] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Systemic lupus erythematosus (SLE) is a highly heterogeneous autoimmune disease characterised by the production of pathogenic autoantibodies against nuclear self-antigens. The anti-inflammatory and tolerogenic cytokine Interleukin-10 appears to play a paradoxical pathogenic role in SLE and is therefore currently therapeutically targeted in clinical trials. It is generally assumed that the pathogenic effect of IL-10 in SLE is due to its growth and differentiation factor activity on autoreactive B-cells, but effects on other cells might also play a role. To date, a unique cellular source of pathogenic IL-10 in SLE has not been identified. In this review, we focus on the contribution of different CD4+T-cell subsets to IL-10 and autoantibody production in SLE. In particular, we discuss that IL-10 produced by different subsets of adaptive regulatory T-cells, follicular helper T-cells and extra-follicular B-helper T-cells is likely to have different effects on autoreactive B-cell responses. A better understanding of the role of IL-10 in B-cell responses and lupus would allow to identify the most promising therapies for individual SLE patients in the future.
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Affiliation(s)
- J Geginat
- INGM-National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy.
| | - M Vasco
- INGM-National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - M Gerosa
- DISCCO, Department of Clinical Science and Community Health, University of Milan, Italy; ASST Istituto G. Pini, Milan, Italy
| | - S W Tas
- Amsterdam UMC, University of Amsterdam, Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Infection & Immunity Institute and Amsterdam Rheumatology & immunology Center (ARC), Academic Medical Center, Amsterdam, the Netherlands
| | - M Pagani
- INGM-National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy; Amsterdam UMC, University of Amsterdam, Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Infection & Immunity Institute and Amsterdam Rheumatology & immunology Center (ARC), Academic Medical Center, Amsterdam, the Netherlands; Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - F Grassi
- INGM-National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy; Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - R A Flavell
- Department of Immunobiology, and Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, USA
| | - Pl Meroni
- Istituto Auxologico Italiano, Milano, Italy
| | - S Abrignani
- INGM-National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy; DISCCO, Department of Clinical Science and Community Health, University of Milan, Italy
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Aslam MM, John P, Fan KH, Bhatti A, Jahangir S, Feingold E, Demirci FY, Kamboh MI. Exploration of shared genetic susceptibility loci between type 1 diabetes and rheumatoid arthritis in the Pakistani population. BMC Res Notes 2019; 12:544. [PMID: 31455420 PMCID: PMC6712654 DOI: 10.1186/s13104-019-4590-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Type 1 diabetes (T1D) and rheumatoid arthritis (RA) are autoimmune diseases. It is known that certain genetic loci and factors that increase the overall autoimmunity risk can be shared among different autoimmune diseases. We sought to replicate seven T1D-related SNPs (single nucleotide polymorphisms) that have been previously reported to be associated with RA susceptibility in a small set of mixed family-based and case-control Pakistani sample in a relatively large and independent RA case-control sample from the same population. Seven T1D-associated SNPs (GLIS3/rs7020673, BACH2/rs11755527, SKAP2/rs7804356, GDSMB/rs2290400, C6orf173/rs9388489, LOC399716/rs947474 and DLK1-MEG2/rs941576) were genotyped in a large Pakistani RA case-control sample (n = 1959) using TaqMan® SNP genotyping assays. RESULTS None of the tested SNPs showed statistically significant association with RA susceptibility; however, one SNP (GLIS3/rs7020673) showed a trend for association (OR = 0.88, p = 7.99E-02). Our study has failed to replicate the previously reported association of seven T1D-associated SNPs with RA risk in a large sample from the same population. Thus, our results do not support a major role of these T1D SNPs in affecting RA susceptibility in the Pakistani population.
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Affiliation(s)
- Muhammad Muaaz Aslam
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.,Department of Human Genetics, Graduate School of Public Health (GSPH), University of Pittsburgh, Pittsburgh, PA, 15216, USA
| | - Peter John
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Kang-Hsien Fan
- Department of Human Genetics, Graduate School of Public Health (GSPH), University of Pittsburgh, Pittsburgh, PA, 15216, USA
| | - Attya Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sidrah Jahangir
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health (GSPH), University of Pittsburgh, Pittsburgh, PA, 15216, USA
| | - F Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health (GSPH), University of Pittsburgh, Pittsburgh, PA, 15216, USA
| | - M Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health (GSPH), University of Pittsburgh, Pittsburgh, PA, 15216, USA.
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Ciccacci C, Latini A, Perricone C, Conigliaro P, Colafrancesco S, Ceccarelli F, Priori R, Conti F, Perricone R, Novelli G, Borgiani P. TNFAIP3 Gene Polymorphisms in Three Common Autoimmune Diseases: Systemic Lupus Erythematosus, Rheumatoid Arthritis, and Primary Sjogren Syndrome-Association with Disease Susceptibility and Clinical Phenotypes in Italian Patients. J Immunol Res 2019; 2019:6728694. [PMID: 31534975 DOI: 10.1155/2019/6728694] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Autoimmune diseases (AIDs) are complex diseases characterized by persistent or recurrent inflammation, alteration of immune response, and production of specific autoantibodies. It is known that different AIDs share several susceptibility genetic loci. Tumor necrosis factor alpha inducible protein 3 (TNFAIP3) encodes the ubiquitin-modifying enzyme A20, which downregulates inflammation by restricting NF-κB, a transcription factor that regulates expression of various proinflammatory genes. Variants in TNFAIP3 gene have been described as associated with susceptibility to several AIDs. Here, we analyzed two TNFAIP3 polymorphisms in Italian patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and primary Sjogren's syndrome (pSS), to verify if the genetic variability of TNFAIP3 gene is involved in genetic predisposition to AIDs also in the Italian population. We recruited 313 SLE patients, 256 RA patients, 195 pSS patients, and 236 healthy controls. Genotyping of rs2230926 and rs6920220 in TNFAIP3 gene was performed by an allelic discrimination assay. We carried out a case/control association study and a genotype/phenotype correlation analysis. A higher risk to develop SLE was observed for rs2230926 (P = 0.02, OR = 1.92). No association was observed between this SNP and the susceptibility to pSS or RA. However, the rs2230926 variant allele seems to confer a higher risk to develop lymphoma in pSS patients, while in RA patients, the presence of RF resulted significantly associated with the variant allele. Regarding the rs6920220 SNP, we observed a significant association of the variant allele with SLE (P = 0.03, OR = 1.53), pSS (P = 0.016, OR = 1.69), and RA (P = 0.0001, OR = 2.35) susceptibility. Furthermore, SLE patients carrying the variant allele showed a higher risk to develop pericarditis, pleurisy, and kidney complications. Our results support the importance of the TNFAIP3 gene variant role in the development of different autoimmune diseases in the Italian population and furtherly confirm a sharing of genetic predisposing factors among these three pathologies.
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Abstract
Motivation A large proportion of risk regions identified by genome-wide association studies (GWAS) are shared across multiple diseases and traits. Understanding whether this clustering is due to sharing of causal variants or chance colocalization can provide insights into shared etiology of complex traits and diseases. Results In this work, we propose a flexible, unifying framework to quantify the overlap between a pair of traits called UNITY (Unifying Non-Infinitesimal Trait analYsis). We formulate a Bayesian generative model that relates the overlap between pairs of traits to GWAS summary statistic data under a non-infinitesimal genetic architecture underlying each trait. We propose a Metropolis-Hastings sampler to compute the posterior density of the genetic overlap parameters in this model. We validate our method through comprehensive simulations and analyze summary statistics from height and body mass index GWAS to show that it produces estimates consistent with the known genetic makeup of both traits. Availability and implementation The UNITY software is made freely available to the research community at: https://github.com/bogdanlab/UNITY. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruth Johnson
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sriram Sankararaman
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.,Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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Soomro AH, Khan E, Noori S, Lone MA, Syal Z, Sheikh S. Assessment of Cytokine Release against Oral Mucosal Cell Line Culture (TR146) Stimulated by Neutrophil Elastase Associated with Behcet's Disease. Int J Dent 2019; 2019:6095628. [PMID: 31263499 DOI: 10.1155/2019/6095628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/10/2019] [Accepted: 05/06/2019] [Indexed: 12/14/2022] Open
Abstract
Aim Cytokines and chemokines may be involved in the onset of oral ulcer in Behcet's disease. The aim of our study is to assess the cytotoxic effects of proinflammatory cytokines and chemokines on reconstructed oral mucosal cell line (TR146) when treated with different concentrations of neutrophil elastase (NE). Objective For this purpose, a culture of the oral mucosal model (OMM) prepared from a cell line derived from an oral squamous cell carcinoma of buccal mucosa (TR146) is treated with different concentrations of neutrophil elastase. The cultures were incubated for 4- and 24-hour intervals and designed as follows: culture + artificial saliva served as the negative control; culture + 0.01% SLS (sodium lauryl sulphate) served as the positive control; and culture + NE (10, 50, 100, and 200 nM) served as the treated group. Materials and Methods We used sandwich ELISA technique to isolate IL-1β (interleukin 1β), IL-8, and TNF-α (tumor necrosis factor). Results We found no significant level of IL-8 and TNF-α when treated with different concentrations of neutrophil elastase after 4- and 24-hour incubation. The IL-1β level was slightly higher when treated with 100 and 200 nM NE after 24 hours of incubation although a significantly high level was observed at 100 nM NE after 4 hours of incubation. Hence, we found an increase in the level of IL-1β when stimulating the reconstructed oral mucosal model (OMM) with different concentrations of NE. This is a preliminary in vitro study; however, further research is required to evaluate the cytotoxic effects of cytokines and chemokines released when treated with NE. Moreover, high concentrations of NE are recommended to stimulate the release of cytokines and chemokines against the OMM.
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Odhams CA, Roberts AL, Vester SK, Duarte CST, Beales CT, Clarke AJ, Lindinger S, Daffern SJ, Zito A, Chen L, Jones LL, Boteva L, Morris DL, Small KS, Fernando MMA, Cunninghame Graham DS, Vyse TJ. Interferon inducible X-linked gene CXorf21 may contribute to sexual dimorphism in Systemic Lupus Erythematosus. Nat Commun 2019; 10:2164. [PMID: 31092820 PMCID: PMC6520347 DOI: 10.1038/s41467-019-10106-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease, characterised by increased expression of type I interferon (IFN)-regulated genes and a striking sex imbalance towards females. Through combined genetic, in silico, in vitro, and ex vivo approaches, we define CXorf21, a gene of hitherto unknown function, which escapes X-chromosome inactivation, as a candidate underlying the Xp21.2 SLE association. We demonstrate that CXorf21 is an IFN-response gene and that the sexual dimorphism in expression is magnified by immunological challenge. Fine-mapping reveals a single haplotype as a potential causal cis-eQTL for CXorf21. We propose that expression is amplified through modification of promoter and 3'-UTR chromatin interactions. Finally, we show that the CXORF21 protein colocalises with TLR7, a pathway implicated in SLE pathogenesis. Our study reveals modulation in gene expression affected by the combination of two hallmarks of SLE: CXorf21 expression increases in a both an IFN-inducible and sex-specific manner.
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Affiliation(s)
- Christopher A Odhams
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | - Amy L Roberts
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Susan K Vester
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Carolina S T Duarte
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Charlie T Beales
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Alexander J Clarke
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Sonja Lindinger
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- University of Applied Sciences - FH Campus Wien, Favoritenstrasse 226, 1100, Wien, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Samuel J Daffern
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Antonino Zito
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Lingyan Chen
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- MRC/BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Leonardo L Jones
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Lora Boteva
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital, Edinburgh, EH4 2XU, UK
| | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Kerrin S Small
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Michelle M A Fernando
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | | | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK.
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Rizk DV, Maillard N, Julian BA, Knoppova B, Green TJ, Novak J, Wyatt RJ. The Emerging Role of Complement Proteins as a Target for Therapy of IgA Nephropathy. Front Immunol 2019; 10:504. [PMID: 30941137 PMCID: PMC6433978 DOI: 10.3389/fimmu.2019.00504] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/25/2019] [Indexed: 12/28/2022] Open
Abstract
IgA nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide and a common cause of end-stage renal disease. Evaluation of a kidney biopsy is necessary for diagnosis, with routine immunofluorescence microscopy revealing dominant or co-dominant IgA immunodeposits usually with complement C3 and sometimes IgG and/or IgM. IgA nephropathy reduces life expectancy by more than 10 years and leads to kidney failure in 20–40% of patients within 20 years of diagnosis. There is accumulating clinical, genetic, and biochemical evidence that complement plays an important role in the pathogenesis of IgA nephropathy. The presence of C3 differentiates the diagnosis of IgA nephropathy from the subclinical deposition of glomerular IgA. Markers for the activation of the alternative and mannan-binding lectin (MBL) pathways in renal-biopsy specimens are associated with disease activity and portend a worse renal outcome. Complement proteins in the circulation have also been evaluated in IgA nephropathy and found to be of prognostic value. Recently, genetic studies have identified IgA nephropathy-associated loci. Within these loci are genes encoding products involved in complement regulation and interaction with immune complexes. Put together, these data identify the complement cascade as a rational treatment target for this chronic kidney disease. Recent case reports on the successful use of humanized anti-C5 monoclonal antibody eculizumab are consistent with this hypothesis, but a better understanding of the role of complement in IgA nephropathy is needed to guide future therapeutic interventions.
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Affiliation(s)
- Dana V Rizk
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nicolas Maillard
- Department of Nephrology, Dialysis, Transplantation, CHU de Saint-Etienne, GIMAP, EA3064, Université Jean Monnet, COMUE Université de Lyon, Rhône-Alpes, France
| | - Bruce A Julian
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Barbora Knoppova
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States.,Department of Immunology, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc, Czechia
| | - Todd J Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Robert J Wyatt
- Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, United States
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46
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Xu M, Gao W, Wu L, Liu X, Yu D, Shi X, Liu X, Wang Q, Fu X, Yu J, Xu B, Wang S. Functional variants of TNFAIP3 are associated with systemic lupus erythematosus in a cohort of Chinese Han population. Hum Immunol 2018; 80:140-145. [PMID: 30529365 DOI: 10.1016/j.humimm.2018.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
Tumor necrosis factor-alpha-induced protein 3 (TNFAIP3) is a negative regulator of NF-κB activity. We previously reported that the paired tandem polymorphic dinucleotides TT > A (rs148314165, rs200820567 of TNFAIP3) conferred the risk for systemic lupus erythematosus (SLE) in European and Korean populations. We investigated the genetic association of the TT > A variants, as well as the functional coding variant rs2230926 in exon 3 of TNFAIP3 in 1229 Chinese Han SLE patients and 1608 matched population controls. We further evaluated the role of these variants in regulating expression of the TNFAIP3 gene and NF-κB signaling pathway in their peripheral blood mononuclear cells from Chinese SLE patients. The TT > A variants and the TNFAIP3 exon 3 coding variant rs2230926 demonstrated significant associations in SLE (PTT > A = 8.96 × 10-12, odds ratio [OR] = 2.07, 95% confidence interval [CI] = 1.68-2.55). SLE patients carrying the risk A allele showed reduced messenger RNA expression of the TNFAIP3 gene and increased expression of NF-κB1 in PBMCs. Conditional analyses revealed that the TT > A variants are likely to be causal variants in Chinese Han SLE patients. The TT > A variants associated with Chinese Han SLE and negatively regulate the expression of the TNFAIP3 gene resulting in enhanced NF-κB activity.
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Affiliation(s)
- Meng Xu
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China; Department of Pediatric Rheumatology, The First Hospital of Jilin University, Changchun, China
| | - Wenjing Gao
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China
| | - Lan Wu
- Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Xianjun Liu
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China
| | - Di Yu
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xiaoju Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xuhan Liu
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China
| | - Qi Wang
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China
| | - Xueqi Fu
- The College of Life Sciences, The University of Jilin, Changchun, China
| | - Jiaao Yu
- Department of Burn Surgery, The First Hospital of Jilin University, Changchun, China
| | - Baofeng Xu
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China.
| | - Shaofeng Wang
- The Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China.
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47
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Abstract
TNIP1 protein is increasingly being recognized as a key repressor of inflammatory signaling and a potential factor in multiple autoimmune diseases. In addition to earlier foundational reports of TNIP1 SNPs in human autoimmune diseases and TNIP1 protein-protein interaction with receptor regulating proteins, more recent studies have identified new potential interaction partners and signaling pathways likely modulated by TNIP1. Subdomains within the TNIP1 protein as well as how they interact with ubiquitin have not only been mapped but inflammatory cell- and tissue-specific consequences subsequent to their defective function are being recognized and related to human disease states such as lupus, scleroderma, and psoriasis. In this review, we emphasize receptor signaling complexes and regulation of cytoplasmic signaling steps downstream of TLR given their association with some of the same autoimmune diseases where TNIP1 has been implicated. TNIP1 dysfunction or deficiency may predispose healthy cells to the inflammatory response to otherwise innocuous TLR ligand exposure. The recognition of the anti-inflammatory roles of TNIP1 and improved integrated understanding of its physical and functional association with other signaling pathway proteins may position TNIP1 as a candidate target for the design and/or testing of next-generation anti-inflammatory therapeutics.
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Affiliation(s)
- Rambon Shamilov
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
- Stem Cell Institute, University of Connecticut, Storrs, CT 06269-3092, USA
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48
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Abstract
Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, 96 Jonathan Lucas Street, Suite 816, Charleston, SC 29425, USA; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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49
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Smith JA. Regulation of Cytokine Production by the Unfolded Protein Response; Implications for Infection and Autoimmunity. Front Immunol 2018; 9:422. [PMID: 29556237 PMCID: PMC5844972 DOI: 10.3389/fimmu.2018.00422] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Protein folding in the endoplasmic reticulum (ER) is an essential cell function. To safeguard this process in the face of environmental threats and internal stressors, cells mount an evolutionarily conserved response known as the unfolded protein response (UPR). Invading pathogens induce cellular stress that impacts protein folding, thus the UPR is well situated to sense danger and contribute to immune responses. Cytokines (inflammatory cytokines and interferons) critically mediate host defense against pathogens, but when aberrantly produced, may also drive pathologic inflammation. The UPR influences cytokine production on multiple levels, from stimulation of pattern recognition receptors, to modulation of inflammatory signaling pathways, and the regulation of cytokine transcription factors. This review will focus on the mechanisms underlying cytokine regulation by the UPR, and the repercussions of this relationship for infection and autoimmune/autoinflammatory diseases. Interrogation of viral and bacterial infections has revealed increasing numbers of examples where pathogens induce or modulate the UPR and implicated UPR-modulated cytokines in host response. The flip side of this coin, the UPR/ER stress responses have been increasingly recognized in a variety of autoimmune and inflammatory diseases. Examples include monogenic disorders of ER function, diseases linked to misfolding protein (HLA-B27 and spondyloarthritis), diseases directly implicating UPR and autophagy genes (inflammatory bowel disease), and autoimmune diseases targeting highly secretory cells (e.g., diabetes). Given the burgeoning interest in pharmacologically targeting the UPR, greater discernment is needed regarding how the UPR regulates cytokine production during specific infections and autoimmune processes, and the relative place of this interaction in pathogenesis.
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Affiliation(s)
- Judith A Smith
- Department of Pediatrics, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States.,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States
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50
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Wu J, Yang S, Yu D, Gao W, Liu X, Zhang K, Fu X, Bao W, Zhang K, Yu J, Sun L, Wang S. CRISPR/cas9 mediated knockout of an intergenic variant rs6927172 identified IL-20RA as a new risk gene for multiple autoimmune diseases. Genes Immun 2019; 20:103-11. [PMID: 29483615 DOI: 10.1038/s41435-018-0011-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/19/2017] [Accepted: 11/10/2017] [Indexed: 12/19/2022]
Abstract
Genetic variants near the tumor necrosis factor-α-induced protein 3 gene (TNFAIP3) at the chromosomal region 6q23 demonstrated significant associations with multiple autoimmune diseases. The signals of associations have been explained to the TNFAIP3 gene, the most likely causal gene. In this study, we employed CRISPR/cas9 genome-editing tool to generate cell lines with deletions including a candidate causal variant, rs6927172, at 140 kb upstream of the TNFAIP3 gene. Interestingly, we observed alterations of multiple genes including IL-20RA encoding a subunit of the receptor for interleukin 20. Using Electrophoretic mobility shift assay (EMSA), Western blotting, and chromatin conformation capture we characterized the molecular mechanism that the DNA element carrying the variant rs6927172 influences expression of IL-20RA and TNFAIP3 genes. Additionally, we developed a new use of the transcription activator-like effector (TALE) to study the role of the variant in regulating expressions of its target genes. In summary, we generated deletion knockouts that included the candidate causal variant rs6927172 in HEK293T cells provided new evidence and mechanism for IL-20RA gene as a risk factor for multiple autoimmune diseases.
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