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Jin DX, Jia CY, Yang B, Wu YH, Chen L, Liu R, Wu MG, Yu H, Ge QF. The ameliorative mechanism of Lactiplantibacillus plantarum NJAU-01 against D-galactose induced oxidative stress: a hepatic proteomics and gut microbiota analysis. Food Funct 2024; 15:6174-6188. [PMID: 38770619 DOI: 10.1039/d4fo00406j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Probiotic intervention is an effective strategy to alleviate oxidative stress-related diseases. Our previous studies found that Lactiplantibacillus plantarum NJAU-01 (NJAU-01) exhibited antioxidant effects in a D-galactose (D-gal)-induced aging mouse model. However, the underlying mechanism remains to be unveiled. This study was aimed to investigate the ameliorative effect and mechanism of NJAU-01 against oxidative stress induced by D-gal. The results showed that NJAU-01 could reverse the tendency of a slow body weight gain induced by D-gal. NJAU-01 relieved hepatic oxidative stress via increasing the hepatic total antioxidant capacity and antioxidant enzyme activities including superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT). Moreover, the malondialdehyde (MDA) level was reversed after NJAU-01 supplementation. The proteomic results showed that there were 201 differentially expressed proteins (DEPs) between NJAU-01 and D-gal groups. NJAU-01 regulated the expressions of glutathione S-transferase Mu 5 (Gstm5), glutathione S-transferase P2 (Gstp2) and NADH dehydrogenase 1α subcomplex subunit 7 (Ndufa7) related to oxidative stress, and autophagy protein 5 (Atg5) and plasma alpha-L-fucosidase (Fuca2) involved in autophagy, etc. 16S rDNA sequencing results showed that NJAU-01 supplementation could regulate the gut microbiota dysbiosis induced by D-gal via increasing the relative abundances of the phylum Firmicutes and the genus Lactobacillus and reducing the relative abundances of the phylum Bacteroidetes and the genera Lachnospiraceae_NK4A136_group as well as Prevotellaceae_UCG-001, etc.. Spearman correlation analysis results showed that the altered gut microbiota composition had a significant correlation with antioxidant enzyme activities and the DEPs related to oxidative stress. Overall, NJAU-01 alleviated hepatic oxidative stress induced by D-gal via manipulating the gut microbiota composition and hepatic protein expression profile.
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Affiliation(s)
- Du-Xin Jin
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Chao-Yang Jia
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Bo Yang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Yue-Hao Wu
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Lei Chen
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Rui Liu
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Man-Gang Wu
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Hai Yu
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
| | - Qing-Feng Ge
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, P. R. China.
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2
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Veyssiere M, Rodriguez Ordonez MDP, Chalabi S, Michou L, Cornelis F, Boland A, Olaso R, Deleuze JF, Petit-Teixeira E, Chaudru V. MYLK* FLNB and DOCK1* LAMA2 gene-gene interactions associated with rheumatoid arthritis in the focal adhesion pathway. Front Genet 2024; 15:1375036. [PMID: 38803542 PMCID: PMC11128622 DOI: 10.3389/fgene.2024.1375036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA.
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Affiliation(s)
- Maëva Veyssiere
- Institut National de la Santé et de la Recherche Médicale, Université de Paris, Paris, France
| | | | - Smahane Chalabi
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
| | - Laetitia Michou
- Division of Rheumatology, Department of Medicine, CHU de Québec-Université Laval, Québec City, QC, Canada
| | - François Cornelis
- Génétiqe-Oncogénétique Adulte-Prévention, Institut National de la Santé et de la Recherche Médicale, Clermont-Auvergne University and CHU, Clermont-Ferrand, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | | | - Valérie Chaudru
- Institut National de la Santé et de la Recherche Médicale, Université de Paris, Paris, France
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
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3
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Malik S, Chakraborty D, Agnihotri P, Sharma A, Biswas S. Mitochondrial functioning in Rheumatoid arthritis modulated by estrogen: Evidence-based insight into the sex-based influence on mitochondria and disease. Mitochondrion 2024; 76:101854. [PMID: 38403096 DOI: 10.1016/j.mito.2024.101854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Alteration of immune response and synovium microvasculature in Rheumatoid arthritis (RA) progression has been suggested to be associated with mitochondrial functioning. Mitochondria, with maternally inherited DNA, exhibit differential response to the female hormone estrogen. Various epidemiological evidence has also shown the prominence of RA in the female population, depicting the role of estrogen in modulating the pathogenesis of RA. As estrogen regulates the expression of differential proteins and associated signaling pathways of RA, its influence on mitochondrial functioning seems evident. Thus, in this review, the studies related to mitochondria and their relation with estrogen and Rheumatoid arthritis were retrieved. We analyzed the different mitochondrial activities that are altered in RA and the possibility of their estrogenic control. The study expands to in silico analysis, revealing the differential mitochondrial proteins expressed in RA and examining these proteins as potential estrogenic targets. It was found that ALDH2, CASP3, and SOD2 are the major mitochondrial proteins involved in RA progression and are also potent estradiol targets. The analysis establishes the role of mitochondrial proteins in RA progression, which were found to be direct or indirect targets of estrogen, depicting its potential for regulating mitochondrial functions in RA.
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Affiliation(s)
- Swati Malik
- Department of Integrative and Functional Biology, CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Debolina Chakraborty
- Department of Integrative and Functional Biology, CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Prachi Agnihotri
- Department of Integrative and Functional Biology, CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Alankrita Sharma
- Department of Integrative and Functional Biology, CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Sagarika Biswas
- Department of Integrative and Functional Biology, CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India.
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4
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Kronzer VL, Sparks JA, Raychaudhuri S, Cerhan JR. Low-frequency and rare genetic variants associated with rheumatoid arthritis risk. Nat Rev Rheumatol 2024; 20:290-300. [PMID: 38538758 DOI: 10.1038/s41584-024-01096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Rheumatoid arthritis (RA) has an estimated heritability of nearly 50%, which is particularly high in seropositive RA. HLA alleles account for a large proportion of this heritability, in addition to many common single-nucleotide polymorphisms with smaller individual effects. Low-frequency and rare variants, such as those captured by next-generation sequencing, can also have a large role in heritability in some individuals. Rare variant discovery has informed the development of drugs such as inhibitors of PCSK9 and Janus kinases. Some 34 low-frequency and rare variants are currently associated with RA risk. One variant (19:10352442G>C in TYK2) was identified in five separate studies, and might therefore represent a promising therapeutic target. Following a set of best practices in future studies, including studying diverse populations, using large sample sizes, validating RA and serostatus, replicating findings, adjusting for other variants and performing functional assessment, could help to ensure the relevance of identified variants. Exciting opportunities are now on the horizon for genetics in RA, including larger datasets and consortia, whole-genome sequencing and direct applications of findings in the management, and especially treatment, of RA.
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Affiliation(s)
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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5
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McGovern AJ, Arevalo MA, Ciordia S, Garcia-Segura LM, Barreto GE. Respirasome Proteins Are Regulated by Sex-Hormone Interactions in the Brain. Int J Mol Sci 2022; 23:ijms232314754. [PMID: 36499081 PMCID: PMC9741126 DOI: 10.3390/ijms232314754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
The existence of sex differences in disease incidence is attributed, in part, to sex differences in metabolism. Uncovering the precise mechanism driving these differences is an extraordinarily complex process influenced by genetics, endogenous hormones, sex-specific lifetime events, individual differences and external environmental/social factors. In fact, such differences may be subtle, but across a life span, increase susceptibility to a pathology. Whilst research persists in the hope of discovering an elegant biological mechanism to underpin sex differences in disease, here, we show, for the first time, that such a mechanism may be subtle in nature but influenced by multiple sex-specific factors. A proteomic dataset was generated from a gonadectomized mouse model treated with Tibolone, a menopausal hormone therapy. Following functional enrichment analysis, we identified that Alzheimer's disease and the electron transport chain-associated pathways were regulated by sex-hormone interactions. Specifically, we identified that the expression of three respirasome proteins, NDUFA2, NDUFA7 and UQCR10, is significantly altered by compounding factors that contribute to sex differences. These proteins function in bioenergetics and produce reactive oxygen species, which are each dysregulated in many diseases with sex differences in incidence. We show sex-specific reprogrammed responses to Tibolone following gonadectomy, which primarily influence the expression of proteins contributing to metabolic pathways. This further infers that metabolic differences may underpin the observed sex differences in disease, but also that hormone therapy research now has potential in exploring sex-specific interventions to produce an effective method of prevention or treatment.
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Affiliation(s)
- Andrew J. McGovern
- Department of Biological Sciences, Faculty of Science and Engineering, University of Limerick, V94 T9PX Limerick, Ireland
| | - Maria Angeles Arevalo
- Instituto Cajal, CSIC, 28002 Madrid, Spain
- CIBERFES, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sergio Ciordia
- Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Luis Miguel Garcia-Segura
- Instituto Cajal, CSIC, 28002 Madrid, Spain
- CIBERFES, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - George E. Barreto
- Department of Biological Sciences, Faculty of Science and Engineering, University of Limerick, V94 T9PX Limerick, Ireland
- Correspondence: ; Tel.: +353-(0)-61-202676
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6
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Silva Santos Ribeiro P, Willemen HLDM, Eijkelkamp N. Mitochondria and sensory processing in inflammatory and neuropathic pain. FRONTIERS IN PAIN RESEARCH (LAUSANNE, SWITZERLAND) 2022; 3:1013577. [PMID: 36324872 PMCID: PMC9619239 DOI: 10.3389/fpain.2022.1013577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023]
Abstract
Rheumatic diseases, such as osteoarthritis and rheumatoid arthritis, affect over 750 million people worldwide and contribute to approximately 40% of chronic pain cases. Inflammation and tissue damage contribute to pain in rheumatic diseases, but pain often persists even when inflammation/damage is resolved. Mechanisms that cause this persistent pain are still unclear. Mitochondria are essential for a myriad of cellular processes and regulate neuronal functions. Mitochondrial dysfunction has been implicated in multiple neurological disorders, but its role in sensory processing and pain in rheumatic diseases is relatively unexplored. This review provides a comprehensive understanding of how mitochondrial dysfunction connects inflammation and damage-associated pathways to neuronal sensitization and persistent pain. To provide an overall framework on how mitochondria control pain, we explored recent evidence in inflammatory and neuropathic pain conditions. Mitochondria have intrinsic quality control mechanisms to prevent functional deficits and cellular damage. We will discuss the link between neuronal activity, mitochondrial dysfunction and chronic pain. Lastly, pharmacological strategies aimed at reestablishing mitochondrial functions or boosting mitochondrial dynamics as therapeutic interventions for chronic pain are discussed. The evidence presented in this review shows that mitochondria dysfunction may play a role in rheumatic pain. The dysfunction is not restricted to neuronal cells in the peripheral and central nervous system, but also includes blood cells and cells at the joint level that may affect pain pathways indirectly. Pre-clinical and clinical data suggest that modulation of mitochondrial functions can be used to attenuate or eliminate pain, which could be beneficial for multiple rheumatic diseases.
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7
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Ma C, Wang J, Hong F, Yang S. Mitochondrial Dysfunction in Rheumatoid Arthritis. Biomolecules 2022; 12:biom12091216. [PMID: 36139055 PMCID: PMC9496243 DOI: 10.3390/biom12091216] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/14/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Rheumatoid arthritis, a chronic autoimmune disease with complex etiology, is characterized by excessive proliferation of synovial cells, massive production of inflammatory cells and cartilage destruction. Studies have shown that mitochondrial dysfunction plays an important role in promoting the occurrence of RA. Mitochondria with normal structure and function are essential for the normal survival of chondrocytes and synovial cells. Once mitochondrial function is destroyed, it will affect the survival, activation and differentiation of immune cells and non-immune cells involved in the pathogenesis of RA, thus leading to the occurrence of RA. However, the mechanism of mitochondrial dysfunction in RA remains unclear. This article reviews the method of mitochondrial dysfunction leading to RA, the effects of mitochondrial dysfunction on immune cells, the etiology of mitochondrial dysfunction in RA, and the pathology of mitochondrial dysfunction in RA. We also outline some drugs that can exert therapeutic effects on RA which are associated with modulating mitochondrial activity. The understanding and summary of mitochondrial dysfunction in RA may provide new research directions for pathological intervention and prevention of RA.
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Affiliation(s)
- Chen Ma
- Experimental Center of Pathogen Biology, College of Medicine, Nanchang University, Nanchang 330006, China
- Queen Mary School, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Jie Wang
- Department of Graduate, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Fenfang Hong
- Experimental Center of Pathogen Biology, College of Medicine, Nanchang University, Nanchang 330006, China
- Correspondence: (F.H.); or (S.Y.)
| | - Shulong Yang
- Key Laboratory of Chronic Diseases, Fuzhou Medical College, Nanchang University, Fuzhou 344099, China
- Department of Physiology, Fuzhou Medical College, Nanchang University, Fuzhou 344099, China
- Correspondence: (F.H.); or (S.Y.)
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8
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Kan S, Duan M, Liu Y, Wang C, Xie J. Role of Mitochondria in Physiology of Chondrocytes and Diseases of Osteoarthritis and Rheumatoid Arthritis. Cartilage 2021; 13:1102S-1121S. [PMID: 34894777 PMCID: PMC8804744 DOI: 10.1177/19476035211063858] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PURPOSE OF REVIEW Mitochondria are recognized to be one of the most important organelles in chondrocytes for their role in triphosphate (ATP) generation through aerobic phosphorylation. Mitochondria also participate in many intracellular processes involving modulating reactive oxygen species (ROS), responding to instantaneous hypoxia stress, regulating cytoplasmic transport of calcium ion, and directing mitophagy to maintain the homeostasis of individual chondrocytes. DESIGNS To summarize the specific role of mitochondria in chondrocytes, we screened related papers in PubMed database and the search strategy is ((mitochondria) AND (chondrocyte)) AND (English [Language]). The articles published in the past 5 years were included and 130 papers were studied. RESULTS In recent years, the integrity of mitochondrial structure has been regarded as a prerequisite for normal chondrocyte survival and defect in mitochondrial function has been found in cartilage-related diseases, such as osteoarthritis (OA) and rheumatoid arthritis (RA). However, the understanding of mitochondria in cartilage is still largely limited. The mechanism on how the changes in mitochondrial structure and function directly lead to the occurrence and development of cartilage-related diseases remains to be elusive. CONCLUSION This review aims to summarize the role of mitochondria in chondrocytes under the physiological and pathological changes from ATP generation, calcium homeostasis, redox regulation, mitophagy modulation, mitochondria biogenesis to immune response activation. The enhanced understanding of molecular mechanisms in mitochondria might offer some new cues for cartilage remodeling and pathological intervention.
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Affiliation(s)
- Shiyi Kan
- State Key Laboratory of Oral Diseases,
West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mengmeng Duan
- State Key Laboratory of Oral Diseases,
West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yang Liu
- State Key Laboratory of Oral Diseases,
West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chunli Wang
- “111” Project Laboratory of
Biomechanics and Tissue Repair, Bioengineering College, Chongqing University,
Chongqing, China
| | - Jing Xie
- State Key Laboratory of Oral Diseases,
West China Hospital of Stomatology, Sichuan University, Chengdu, China,“111” Project Laboratory of
Biomechanics and Tissue Repair, Bioengineering College, Chongqing University,
Chongqing, China,Lab of Bone & Joint Disease, State
Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan
University, Chengdu, China,Jing Xie, Lab of Bone & Joint Disease,
State Key Laboratory of Oral Diseases, West China Hospital of Stomatology,
Sichuan University, Chengdu 610064, Sichuan, China.
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9
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Han S, Na Y, Koh I, Nho K, Lee Y. Alternative Splicing Regulation of Low-Frequency Genetic Variants in Exon 2 of TREM2 in Alzheimer's Disease by Splicing-Based Aggregation. Int J Mol Sci 2021; 22:ijms22189865. [PMID: 34576031 PMCID: PMC8471326 DOI: 10.3390/ijms22189865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 01/02/2023] Open
Abstract
TREM2 is among the most well-known Alzheimer’s disease (AD) risk genes; however, the functional roles of its AD-associated variants remain to be elucidated, and most known risk alleles are low-frequency variants whose investigation is challenging. Here, we utilized a splicing-guided aggregation method in which multiple low-frequency TREM2 variants were bundled together to investigate the functional impact of those variants on alternative splicing in AD. We analyzed whole genome sequencing (WGS) and RNA-seq data generated from cognitively normal elderly controls (CN) and AD patients in two independent cohorts, representing three regions in the frontal lobe of the human brain: the dorsolateral prefrontal cortex (CN = 213 and AD = 376), frontal pole (CN = 72 and AD = 175), and inferior frontal (CN = 63 and AD = 157). We observed an exon skipping event in the second exon of TREM2, with that exon tending to be more frequently skipped (p = 0.0012) in individuals having at least one low-frequency variant that caused loss-of-function for a splicing regulatory element. In addition, genes differentially expressed between AD patients with high vs. low skipping of the second exon (i.e., loss of a TREM2 functional domain) were significantly enriched in immune-related pathways. Our splicing-guided aggregation method thus provides new insight into the regulation of alternative splicing of the second exon of TREM2 by low-frequency variants and could be a useful tool for further exploring the potential molecular mechanisms of multiple, disease-associated, low-frequency variants.
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Affiliation(s)
- Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA;
| | - Yirang Na
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul 03080, Korea;
| | - Insong Koh
- Department of Physiology, Hanyang University, Seoul 04763, Korea
- Correspondence: (I.K.); (K.N.); (Y.L.)
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Correspondence: (I.K.); (K.N.); (Y.L.)
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA;
- Correspondence: (I.K.); (K.N.); (Y.L.)
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10
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Clayton SA, MacDonald L, Kurowska-Stolarska M, Clark AR. Mitochondria as Key Players in the Pathogenesis and Treatment of Rheumatoid Arthritis. Front Immunol 2021; 12:673916. [PMID: 33995417 PMCID: PMC8118696 DOI: 10.3389/fimmu.2021.673916] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Mitochondria are major energy-producing organelles that have central roles in cellular metabolism. They also act as important signalling hubs, and their dynamic regulation in response to stress signals helps to dictate the stress response of the cell. Rheumatoid arthritis is an inflammatory and autoimmune disease with high prevalence and complex aetiology. Mitochondrial activity affects differentiation, activation and survival of immune and non-immune cells that contribute to the pathogenesis of this disease. This review outlines what is known about the role of mitochondria in rheumatoid arthritis pathogenesis, and how current and future therapeutic strategies can function through modulation of mitochondrial activity. We also highlight areas of this topic that warrant further study. As producers of energy and of metabolites such as succinate and citrate, mitochondria help to shape the inflammatory phenotype of leukocytes during disease. Mitochondrial components can directly stimulate immune receptors by acting as damage-associated molecular patterns, which could represent an initiating factor for the development of sterile inflammation. Mitochondria are also an important source of intracellular reactive oxygen species, and facilitate the activation of the NLRP3 inflammasome, which produces cytokines linked to disease symptoms in rheumatoid arthritis. The fact that mitochondria contain their own genetic material renders them susceptible to mutation, which can propagate their dysfunction and immunostimulatory potential. Several drugs currently used for the treatment of rheumatoid arthritis regulate mitochondrial function either directly or indirectly. These actions contribute to their immunomodulatory functions, but can also lead to adverse effects. Metabolic and mitochondrial pathways are attractive targets for future anti-rheumatic drugs, however many questions still remain about the precise role of mitochondrial activity in different cell types in rheumatoid arthritis.
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Affiliation(s)
- Sally A Clayton
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Birmingham, United Kingdom
| | - Lucy MacDonald
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Glasgow, United Kingdom.,Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Mariola Kurowska-Stolarska
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Glasgow, United Kingdom.,Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Andrew R Clark
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), Birmingham, United Kingdom
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11
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Metabolic Shifts as the Hallmark of Most Common Diseases: The Quest for the Underlying Unity. Int J Mol Sci 2021; 22:ijms22083972. [PMID: 33921428 PMCID: PMC8068795 DOI: 10.3390/ijms22083972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/13/2022] Open
Abstract
A hyper-specialization characterizes modern medicine with the consequence of classifying the various diseases of the body into unrelated categories. Such a broad diversification of medicine goes in the opposite direction of physics, which eagerly looks for unification. We argue that unification should also apply to medicine. In accordance with the second principle of thermodynamics, the cell must release its entropy either in the form of heat (catabolism) or biomass (anabolism). There is a decreased flow of entropy outside the body due to an age-related reduction in mitochondrial entropy yield resulting in increased release of entropy in the form of biomass. This shift toward anabolism has been known in oncology as Warburg-effect. The shift toward anabolism has been reported in most diseases. This quest for a single framework is reinforced by the fact that inflammation (also called the immune response) is involved in nearly every disease. This strongly suggests that despite their apparent disparity, there is an underlying unity in the diseases. This also offers guidelines for the repurposing of old drugs.
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12
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Wu C, Tan S, Liu L, Cheng S, Li P, Li W, Liu H, Zhang F, Wang S, Ning Y, Wen Y, Zhang F. Transcriptome-wide association study identifies susceptibility genes for rheumatoid arthritis. Arthritis Res Ther 2021; 23:38. [PMID: 33482886 PMCID: PMC7821659 DOI: 10.1186/s13075-021-02419-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
Objective To identify rheumatoid arthritis (RA)-associated susceptibility genes and pathways through integrating genome-wide association study (GWAS) and gene expression profile data. Methods A transcriptome-wide association study (TWAS) was conducted by the FUSION software for RA considering EBV-transformed lymphocytes (EL), transformed fibroblasts (TF), peripheral blood (NBL), and whole blood (YBL). GWAS summary data was driven from a large-scale GWAS, involving 5539 autoantibody-positive RA patients and 20,169 controls. The TWAS-identified genes were further validated using the mRNA expression profiles and made a functional exploration. Results TWAS identified 692 genes with PTWAS values < 0.05 for RA. CRIPAK (PEL = 0.01293, PTF = 0.00038, PNBL = 0.02839, PYBL = 0.0978), MUT (PEL = 0.00377, PTF = 0.00076, PNBL = 0.00778, PYBL = 0.00096), FOXRED1 (PEL = 0.03834, PTF = 0.01120, PNBL = 0.01280, PYBL = 0.00583), and EBPL (PEL = 0.00806, PTF = 0.03761, PNBL = 0.03540, PYBL = 0.04254) were collectively expressed in all the four tissues/cells. Eighteen genes, including ANXA5, AP4B1, ATIC (PTWAS = 0.0113, downregulated expression), C12orf65, CMAH, PDHB, RUNX3 (PTWAS = 0.0346, downregulated expression), SBF1, SH2B3, STK38, TMEM43, XPNPEP1, KIAA1530, NUFIP2, PPP2R3C, RAB24, STX6, and TLR5 (PTWAS = 0.04665, upregulated expression), were validated with integrative analysis of TWAS and mRNA expression profiles. TWAS-identified genes functionally involved in endoplasmic reticulum organization, regulation of cytokine production, TNF signaling pathway, immune response-regulating signaling pathway, regulation of autophagy, etc. Conclusion We identified multiple candidate genes and pathways, providing novel clues for the genetic mechanism of RA. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02419-9.
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Affiliation(s)
- Cuiyan Wu
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China.
| | - Sijian Tan
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Li Liu
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Shiqiang Cheng
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Peilin Li
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Wenyu Li
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Huan Liu
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng'e Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Sen Wang
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yujie Ning
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yan Wen
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center; Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No.76, Yan Ta West Road, Xi'an, 710061, People's Republic of China.
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Shi X, Zhang Y, Chen R, Gong Y, Zhang M, Guan R, Rotstein OD, Liu X, Wen XY. ndufa7 plays a critical role in cardiac hypertrophy. J Cell Mol Med 2020; 24:13151-13162. [PMID: 32989924 PMCID: PMC7701565 DOI: 10.1111/jcmm.15921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/22/2022] Open
Abstract
Cardiac hypertrophy is a common pathological change in patients with progressive cardiac function failure, which can be caused by hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM) or arterial hypertension. Despite years of study, there is still limited knowledge about the underlying molecular mechanisms for cardiac hypertrophy. NDUFA7, a subunit of NADH:ubiquinone oxidoreductase (complex I), has been reported to be a novel HCM associated gene. However, the biological role of NDUFA7 in heart remains unknown. In this study, we found that NDUFA7 exhibited high expression in the heart, and its level was significantly decreased in mice model of cardiac hypertrophy. Moreover, we demonstrated that ndufa7 knockdown in developing zebrafish embryos resulted in cardiac development and functional defects, associated with increased expression of pathological hypertrophy biomarkers nppa (ANP) and nppb (BNP). Mechanistic study demonstrated that ndufa7 depletion promoted ROS production and calcineurin signalling activation. Moreover, NDUFA7 depletion contributed to cardiac cell hypertrophy. Together, these results report for the first time that ndufa7 is implicated in pathological cardiac hypertrophy.
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Affiliation(s)
- Xingjuan Shi
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Yu Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Ru Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Yijie Gong
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Mingming Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Rui Guan
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, & Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Ori D Rotstein
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, & Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Xiangdong Liu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, & Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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14
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Li M, Luo X, Long X, Jiang P, Jiang Q, Guo H, Chen Z. Potential role of mitochondria in synoviocytes. Clin Rheumatol 2020; 40:447-457. [PMID: 32613391 DOI: 10.1007/s10067-020-05263-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Synoviocytes are located in the synovium lining layer, which is composed of macrophage-like synoviocytes (MLS) and fibroblast-like synoviocytes (FLS) with different characteristics. Mitochondria, which exist in most cells, are two membrane-covered organelles. In addition to providing the necessary ATP for synoviocytes, mitochondria are involved in the regulation of redox homeostasis and the integration of synoviocytes death signals. In recent years, mitochondrial dysfunction has been found in rheumatoid arthritis (RA) and osteoarthritis (OA). Interestingly, recent studies have started uncovering that mitochondria that were previously reported to play a role in chondrocytes or immune cells, but not known to have pronounced roles in synoviocytes, can actually play crucial roles in the regulation of the pathological properties of the synoviocytes. The purpose of this review is to summarize our current understanding of the key role of mitochondria in synoviocytes, including mitochondrial dysfunction in synoviocytes can induce and aggravate inflammatory responses and changes in mitochondrial structure and function with the involvement of multiple cytokines, signal pathway, and hypoxic state of synovial tissue alter the response of synoviocytes to apoptotic stimulation. Also, mitochondrial abnormalities in synoviocytes promote the synoviocytes invasion and proliferation.
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Affiliation(s)
- Muzhe Li
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China
| | - Xuling Luo
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China
| | - Xin Long
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China
| | - Peishi Jiang
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China
| | - Qin Jiang
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China
| | - Heng Guo
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China
| | - Zhiwei Chen
- Department of Orthopedic, the First Affiliated Hospital of University of South China, No. 69, Chuanshan Road, Hengyang City, 421001, Hunan Province, China.
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15
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Du J, Yu S, Wang D, Chen S, Chen S, Zheng Y, Wang N, Chen S, Li J, Shen B. Germline and somatic mtDNA mutation spectrum of rheumatoid arthritis patients in the Taizhou area, China. Rheumatology (Oxford) 2020; 59:2982-2991. [DOI: 10.1093/rheumatology/keaa063] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
AbstractObjectiveReactive oxygen species are believed to be involved in the onset of RA, and the association between nuclear-encoded mitochondrial respiratory chain-related variants and RA has recently been revealed. However, little is known about the landscape of mitochondrial DNA (mtDNA) variants in RA.MethodsNext-generation sequencing was conducted to profile mtDNA germline and somatic variants in 124 RA patients and 123 age- and sex-matched healthy controls in the Taizhou area, China. Fisher’s exact test, SKAT and SKAT-O were used for gene-burden tests to investigate RA-related variants of mitochondrial genes. Predictive tools were applied to evaluate the pathogenicity of mtDNA variants, and mtDNA haplogroups were assigned according to mtDNA mutations recorded in PhyloTree database. The frequency distribution of mtDNA haplogroups between the groups was compared using χ2 analysis.ResultsWe identified 467 RA-unique and 341 healthy control-unique mtDNA variants, with 443 common variants. Only MT-ATP6 with a significant burden of variants was identified by Fisher’s exact test, SKAT and SKAT-O, even after Bonferroni adjustment, and the enrichment variants in MT-ATP6 was mainly driven by m.8830C>A, m.8833G>C and m.8843T>A variants. Besides, four frequently low-heteroplasmic variants including the three variants above and m.14135T>G of MT-ND5 were detected in RA only; except for m.8830C>A, they are considered potential pathogenicity based on functional predictions. χ2 analysis before Bonferroni adjustment revealed haplogroup F1/F1a to be negatively associated with RA (P < 0.05).ConclusionThese results profiled the landscape of germline and somatic mtDNA variants in RA and supported the effects of mitochondrial genes on RA.
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Affiliation(s)
- Juping Du
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Sufei Yu
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Donglian Wang
- Department of Clinical Laboratory, Enze Hospital, Taizhou Enze Medical Centre (Group), Luqiao, Taizhou, Zhejiang Province, China
| | - Shuaishuai Chen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Suyun Chen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Yufen Zheng
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Na Wang
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Shiyong Chen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Jun Li
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
| | - Bo Shen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Taizhou Enze Medical Centre (Group), Linhai
- Department of Clinical Laboratory, Enze Hospital, Taizhou Enze Medical Centre (Group), Luqiao, Taizhou, Zhejiang Province, China
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Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S. Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis. Arthritis Res Ther 2019; 21:288. [PMID: 31842970 PMCID: PMC6915963 DOI: 10.1186/s13075-019-2066-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 11/22/2019] [Indexed: 02/10/2023] Open
Abstract
Background Antibodies and upregulated cytokines and chemokines predate the onset of rheumatoid arthritis (RA) symptoms. We aimed to identify the pathways related to the early processes leading to RA development, as well as potential novel biomarkers, using multiple protein analyses. Methods A case-control study was conducted within the Biobank of northern Sweden. The plasma samples from 118 pre-symptomatic individuals (207 samples; median predating time 4.1 years), 79 early RA patients, and 74 matched controls were analyzed. The levels of 122 unique proteins with an acknowledged relationship to autoimmunity were analyzed using 153 antibodies and a bead-based multiplex system (FlexMap3D; Luminex Corp.). The data were analyzed using multifactorial linear regression model, random forest, and network enrichment analysis (NEA) based on the 10 most significantly differentially expressed proteins for each two-by-two group comparison, using the MSigDB collection of hallmarks. Results There was a high agreement between the different statistical methods to identify the most significant proteins. The adipogenesis and interferon alpha response hallmarks differentiated pre-symptomatic individuals from controls. These two hallmarks included proteins involved in innate immunity. Between pre-symptomatic individuals and RA patients, three hallmarks were identified as follows: apical junction, epithelial mesenchymal transition, and TGF-β signaling, including proteins suggestive of cell interaction, remodulation, and fibrosis. The adipogenesis and heme metabolism hallmarks differentiated RA patients from controls. Conclusions We confirm the importance of interferon alpha signaling and lipids in the early phases of RA development. Network enrichment analysis provides a tool for a deeper understanding of molecules involved at different phases of the disease progression.
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Affiliation(s)
- Mikael Brink
- Department of Public Health and Clinical Medicine, Rheumatology, Umeå University, 901 87, Umeå, Sweden.
| | - Anders Lundquist
- Department of Clinical Microbiology, Division of Infection and Immunology, Umeå University, 901 87, Umeå, Sweden
| | - Andrey Alexeyenko
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lejon
- Division of Infection and Immunology, Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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17
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Vaamonde-García C, López-Armada MJ. Role of mitochondrial dysfunction on rheumatic diseases. Biochem Pharmacol 2019; 165:181-195. [DOI: 10.1016/j.bcp.2019.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/07/2019] [Indexed: 02/09/2023]
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18
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Veyssiere M, Perea J, Michou L, Boland A, Caloustian C, Olaso R, Deleuze JF, Cornelis F, Petit-Teixeira E, Chaudru V. A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families. PLoS One 2019; 14:e0213387. [PMID: 30845214 PMCID: PMC6405192 DOI: 10.1371/journal.pone.0213387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/19/2019] [Indexed: 01/31/2023] Open
Abstract
The triggering and development of Rheumatoid Arthritis (RA) is conditioned by environmental and genetic factors. Despite the identification of more than one hundred genetic variants associated with the disease, not all the cases can be explained. Here, we performed Whole Exome Sequencing in 9 multiplex families (N = 30) to identify rare variants susceptible to play a role in the disease pathogenesis. We pre-selected 77 genes which carried rare variants with a complete segregation with RA in the studied families. Follow-up linkage and association analyses with pVAAST highlighted significant RA association of 43 genes (p-value < 0.05 after 106 permutations) and pinpointed their most likely causal variant. We re-sequenced the 10 most significant likely causal variants (p-value ≤ 3.78*10-3 after 106 permutations) in the extended pedigrees and 9 additional multiplex families (N = 110). Only one SNV in SUPT20H: c.73A>T (p.Lys25*), presented a complete segregation with RA in an extended pedigree with early-onset cases. In summary, we identified in this study a new variant associated with RA in SUPT20H gene. This gene belongs to several biological pathways like macro-autophagy and monocyte/macrophage differentiation, which contribute to RA pathogenesis. In addition, these results showed that analyzing rare variants using a family-based approach is a strategy that allows to identify RA risk loci, even with a small dataset.
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Affiliation(s)
- Maëva Veyssiere
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
- * E-mail:
| | - Javier Perea
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
| | - Laetitia Michou
- Division of Rheumatology, Department of Medicine, CHU de Québec-Université Laval, QC, Québec, Canada
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine—François Jacob Institute, CEA, Evry, France
| | - Christophe Caloustian
- Centre National de Recherche en Génomique Humaine—François Jacob Institute, CEA, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine—François Jacob Institute, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine—François Jacob Institute, CEA, Evry, France
| | - François Cornelis
- GenHotel-Auvergne—Auvergne University, Genetic Department, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Valérie Chaudru
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
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Ekim Kocabey A, Kost L, Gehlhar M, Rödel G, Gey U. Mitochondrial Sco proteins are involved in oxidative stress defense. Redox Biol 2018; 21:101079. [PMID: 30593977 PMCID: PMC6307045 DOI: 10.1016/j.redox.2018.101079] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022] Open
Abstract
Members of the evolutionary conserved Sco protein family have been intensively studied regarding their role in the assembly of the mitochondrial cytochrome c oxidase. However, experimental and structural data, specifically the presence of a thioredoxin-like fold, suggest that Sco proteins may also play a role in redox homeostasis. In our study, we addressed this putative function of Sco proteins using Saccharomyces cerevisiae as a model system. Like many eukaryotes, this yeast possesses two SCO homologs (SCO1 and SCO2). Mutants bearing a deletion of either of the two genes are not affected in their growth under oxidative stress. However, the concomitant deletion of the SOD1 gene encoding the superoxide dismutase 1 resulted in a distinct phenotype: double deletion strains lacking SCO1 or SCO2 and SOD1 are highly sensitive to oxidative stress and show dramatically increased ROS levels. The respiratory competent double deletion strain Δsco2Δsod1 paved the way to investigate the putative antioxidant function of SCO homologs apart from their role in respiration by complementation analysis. Sco homologs from Drosophila, Arabidopsis, human and two other yeast species were integrated into the genome of the double deletion mutant and the transformants were analyzed for their growth under oxidative stress. Interestingly, all homologs except for Kluyveromyces lactis K07152 and Arabidopsis thaliana HCC1 were able to complement the phenotype, indicating their role in oxidative stress defense. We further applied this complementation-based system to investigate whether pathogenic point mutations affect the putative antioxidant role of hSco2. Surprisingly, all of the mutant alleles failed to restore the ROS-sensitivity of the Δsco2Δsod1 strain. In conclusion, our data not only provide clear evidence for the function of Sco proteins in oxidative stress defense but also offer a valuable tool to investigate this role for other homologous proteins. Concomitant deletion of SCO and SOD1 leads to a high ROS sensitivity. SCO homologs from higher organisms can rescue the oxidative stress sensitive phenotype of the double deletion mutant. Pathogenic human Sco2 mutations affect the antioxidant function of the protein. The role of the Sco proteins in oxidative stress defense is discussed.
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Affiliation(s)
| | - Luise Kost
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden, Germany
| | - Maria Gehlhar
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden, Germany
| | - Gerhard Rödel
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden, Germany
| | - Uta Gey
- Institute of Genetics, Technische Universität Dresden, 01062 Dresden, Germany.
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Wu W, Yan L, Chen S, Li Q, Gu Z, Xu H, Yin ZQ. Investigating oxidation state-induced toxicity of PEGylated graphene oxide in ocular tissue using gene expression profiles. Nanotoxicology 2018; 12:819-835. [PMID: 29888639 DOI: 10.1080/17435390.2018.1480813] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Wei Wu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, P. R. China
| | - Liang Yan
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Siyu Chen
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, P. R. China
| | - Qiyou Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, P. R. China
| | - Zhanjun Gu
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, P. R. China
| | - Zheng Qin Yin
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, P. R. China
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Duhn PH, Sode J, Hagen CM, Christiansen M, Locht H. Mitochondrial haplogroups in patients with rheumatoid arthritis: No association with disease and disease manifestations. PLoS One 2017; 12:e0188492. [PMID: 29261674 PMCID: PMC5737896 DOI: 10.1371/journal.pone.0188492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE To describe the distribution of specific mitochondrial DNA (mtDNA) haplogroups (hgs) in a cohort of patients with rheumatoid arthritis (RA). METHODS Two-hundred nineteen consecutive patients with RA had mtDNA isolated from their blood, sequenced and haplotyped. Patients were diagnosed according to the American College of Rheumatology (ACR)/European league against Rheumatism (EULAR) criteria. Demographic and clinical data were retrieved from the Danish nationwide database (DANBIO). Logistic regression analyses were performed to test for associations. RESULTS One-hundred eighty-four patients were eligible for analysis. Haplogroup frequencies were: H (n = 88; 47.8%), U (n = 37; 20.1%), T (n = 22; 12.0%), J (n = 16; 8.7%), K (n = 11; 5.9%), HV (n = 6; 3.3%) and V (n = 4; 2.2%). The distribution of individual hgs was identical to the background population. Radiographic erosions were significantly associated with hg clusters JT (OR = 2.37, 95% confidence interval (CI): 1.07-5.53, p = 0.038). Significantly fewer patients from hg cluster JT received biological treatment (OR = 0.17, 95% CI: 0.03-0.87, p = 0.038). Albeit, none of these associations were significant when corrected for multiple tests. CONCLUSION There was no significant association between mtDNA hgs and presence of RA or disease manifestations. There was an, albeit insignificant, overrepresentation of patients with hg JT among patients with erosive disease; however, slightly fewer patients in the JT group were treated with biological drugs.
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Affiliation(s)
- Pernille Hurup Duhn
- Department of Rheumatology Frederiksberg Hospital, Nordre Fasanvej, Frederiksberg, Denmark
- * E-mail:
| | - Jacob Sode
- Department of Rheumatology Frederiksberg Hospital, Nordre Fasanvej, Frederiksberg, Denmark
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej, Copenhagen S, Denmark
- Institute of Regional Health Research, Center Sønderjylland, University of Southern Denmark, Campusvej, Odense M, Denmark
| | - Christian Munch Hagen
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej, Copenhagen S, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej, Copenhagen S, Denmark
- Department of Biomedical Sciences, Faculty of Health and Life Science, University of Copenhagen, Blegdamsvej, Copenhagen N, Denmark
| | - Henning Locht
- Department of Rheumatology Frederiksberg Hospital, Nordre Fasanvej, Frederiksberg, Denmark
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