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Elangeeb ME, Elfaki I, Eleragi AMS, Ahmed EM, Mir R, Alzahrani SM, Bedaiwi RI, Alharbi ZM, Mir MM, Ajmal MR, Tayeb FJ, Barnawi J. Molecular Dynamics Simulation of Kir6.2 Variants Reveals Potential Association with Diabetes Mellitus. Molecules 2024; 29:1904. [PMID: 38675722 PMCID: PMC11054064 DOI: 10.3390/molecules29081904] [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: 03/07/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Diabetes mellitus (DM) represents a problem for the healthcare system worldwide. DM has very serious complications such as blindness, kidney failure, and cardiovascular disease. In addition to the very bad socioeconomic impacts, it influences patients and their families and communities. The global costs of DM and its complications are huge and expected to rise by the year 2030. DM is caused by genetic and environmental risk factors. Genetic testing will aid in early diagnosis and identification of susceptible individuals or populations using ATP-sensitive potassium (KATP) channels present in different tissues such as the pancreas, myocardium, myocytes, and nervous tissues. The channels respond to different concentrations of blood sugar, stimulation by hormones, or ischemic conditions. In pancreatic cells, they regulate the secretion of insulin and glucagon. Mutations in the KCNJ11 gene that encodes the Kir6.2 protein (a major constituent of KATP channels) were reported to be associated with Type 2 DM, neonatal diabetes mellitus (NDM), and maturity-onset diabetes of the young (MODY). Kir6.2 harbors binding sites for ATP and phosphatidylinositol 4,5-diphosphate (PIP2). The ATP inhibits the KATP channel, while the (PIP2) activates it. A Kir6.2 mutation at tyrosine330 (Y330) was demonstrated to reduce ATP inhibition and predisposes to NDM. In this study, we examined the effect of mutations on the Kir6.2 structure using bioinformatics tools and molecular dynamic simulations (SIFT, PolyPhen, SNAP2, PANTHER, PhD&SNP, SNP&Go, I-Mutant, MuPro, MutPred, ConSurf, HOPE, and GROMACS). Our results indicated that M199R, R201H, R206H, and Y330H mutations influence Kir6.2 structure and function and therefore may cause DM. We conclude that MD simulations are useful techniques to predict the effects of mutations on protein structure. In addition, the M199R, R201H, R206H, and Y330H variant in the Kir6.2 protein may be associated with DM. These results require further verification in protein-protein interactions, Kir6.2 function, and case-control studies.
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Affiliation(s)
- Mohamed E. Elangeeb
- Department of Basic Medical Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Ali M. S. Eleragi
- Department of Microbiology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Elsadig Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia;
- Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti 27711, Sudan
| | - Rashid Mir
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Salem M. Alzahrani
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Ruqaiah I. Bedaiwi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Zeyad M. Alharbi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Mohammad Muzaffar Mir
- Department of Clinical Biochemistry, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Mohammad Rehan Ajmal
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Faris Jamal Tayeb
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Jameel Barnawi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
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Zervou MI, Goulielmos GN. Comment on: Reduced digestion of circulating genomic DNA in systemic sclerosis patients with the DNASE1L3 R206C variant. Rheumatology (Oxford) 2023; 62:e325-e326. [PMID: 36971567 DOI: 10.1093/rheumatology/kead147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 11/09/2023] Open
Affiliation(s)
- Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine (5D17), School of Medicine, University of Crete, Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine (5D17), School of Medicine, University of Crete, Heraklion, Greece
- Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Greece
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3
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Yudhani RD, Pakha DN, Suyatmi S, Irham LM. Identifying pathogenic variants related to systemic lupus erythematosus by integrating genomic databases and a bioinformatic approach. Genomics Inform 2023; 21:e37. [PMID: 37813633 PMCID: PMC10584638 DOI: 10.5808/gi.23002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 08/09/2023] [Indexed: 10/11/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an inflammatory-autoimmune disease with a complex multi-organ pathogenesis, and it is known to be associated with significant morbidity and mortality. Various genetic, immunological, endocrine, and environmental factors contribute to SLE. Genomic variants have been identified as potential contributors to SLE susceptibility across multiple continents. However, the specific pathogenic variants that drive SLE remain largely undefined. In this study, we sought to identify these pathogenic variants across various continents using genomic and bioinformatic-based methodologies. We found that the variants rs35677470, rs34536443, rs17849502, and rs13306575 are likely damaging in SLE. Furthermore, these four variants appear to affect the gene expression of NCF2, TYK2, and DNASE1L3 in whole blood tissue. Our findings suggest that these genomic variants warrant further research for validation in functional studies and clinical trials involving SLE patients. We conclude that the integration of genomic and bioinformatic-based databases could enhance our understanding of disease susceptibility, including that of SLE.
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Affiliation(s)
- Ratih Dewi Yudhani
- Department of Pharmacology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta 57126, Indonesia
| | - Dyonisa Nasirochmi Pakha
- Department of Pharmacology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta 57126, Indonesia
| | - Suyatmi Suyatmi
- Department of Histology, Faculty of Medicine, Universitas Sebelas Maret, Surakarta 57126, Indonesia
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Jia X, Tan L, Chen S, Tang R, Chen W. Monogenic lupus: Tracing the therapeutic implications from single gene mutations. Clin Immunol 2023; 254:109699. [PMID: 37481012 DOI: 10.1016/j.clim.2023.109699] [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: 04/19/2023] [Revised: 06/21/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Monogenic lupus, a distinctive variant of systemic lupus erythematosus (SLE), is characterized by early onset, family-centric clustering, and heightened disease severity. So far, over thirty genetic variations have been identified as single-gene etiology of SLE and lupus-like phenotypes. The critical role of these gene mutations in disrupting various immune pathways is increasingly recognized. In particular, single gene mutation-driven dysfunction within the innate immunity, notably deficiencies in the complement system, impedes the degradation of free nucleic acid and immune complexes, thereby promoting activation of innate immune cells. The accumulation of these components in various tissues and organs creates a pro-inflammatory microenvironment, characterized by a surge in pro-inflammatory cytokines, chemokines, reactive oxygen species, and type I interferons. Concurrently, single gene mutation-associated defects in the adaptive immune system give rise to the emergence of autoreactive T cells, hyperactivated B cells and plasma cells. The ensuing spectrum of cytokines and autoimmune antibodies drives systemic disease manifestations, primarily including kidney, skin and central nervous system-related phenotypes. This review provides a thorough overview of the single gene mutations and potential consequent immune dysregulations in monogenic lupus, elucidating the pathogenic mechanisms of monogenic lupus. Furthermore, it discusses the recent advances made in the therapeutic interventions for monogenic lupus.
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Affiliation(s)
- Xiuzhi Jia
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Li Tan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Sixiu Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Ruihan Tang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China.
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China.
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5
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Al Khatib I, Deng J, Lei Y, Torres-Odio S, Rojas GR, Newman LE, Chung BK, Symes A, Zhang H, Huang SYN, Pommier Y, Khan A, Shadel GS, West AP, Gibson WT, Shutt TE. Activation of the cGAS-STING innate immune response in cells with deficient mitochondrial topoisomerase TOP1MT. Hum Mol Genet 2023; 32:2422-2440. [PMID: 37129502 PMCID: PMC10360396 DOI: 10.1093/hmg/ddad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 03/22/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
The recognition that cytosolic mitochondrial DNA (mtDNA) activates cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) innate immune signaling has unlocked novel disease mechanisms. Here, an uncharacterized variant predicted to affect TOP1MT function, P193L, was discovered in a family with multiple early onset autoimmune diseases, including Systemic Lupus Erythematosus (SLE). Although there was no previous genetic association between TOP1MT and autoimmune disease, the role of TOP1MT as a regulator of mtDNA led us to investigate whether TOP1MT could mediate the release of mtDNA to the cytosol, where it could then activate the cGAS-STING innate immune pathway known to be activated in SLE and other autoimmune diseases. Through analysis of cells with reduced TOP1MT expression, we show that loss of TOP1MT results in release of mtDNA to the cytosol, which activates the cGAS-STING pathway. We also characterized the P193L variant for its ability to rescue several TOP1MT functions when expressed in TOP1MT knockout cells. We show that the P193L variant is not fully functional, as its re-expression at high levels was unable to rescue mitochondrial respiration deficits, and only showed partial rescue for other functions, including repletion of mtDNA replication following depletion, nucleoid size, steady state mtDNA transcripts levels and mitochondrial morphology. Additionally, expression of P193L at endogenous levels was unable to rescue mtDNA release-mediated cGAS-STING signaling. Overall, we report a link between TOP1MT and mtDNA release leading to cGAS-STING activation. Moreover, we show that the P193L variant has partial loss of function that may contribute to autoimmune disease susceptibility via cGAS-STING mediated activation of the innate immune system.
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Affiliation(s)
- Iman Al Khatib
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Jingti Deng
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Yuanjiu Lei
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M University, Bryan, TX, USA
| | - Sylvia Torres-Odio
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M University, Bryan, TX, USA
| | - Gladys R Rojas
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Laura E Newman
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Brian K Chung
- Norwegian PSC Research Center, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andrew Symes
- Department of Geomatics Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shar-yin N Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aneal Khan
- Discovery DNA, Calgary, Alberta T2L 1Y8, Canada
- M.A.G.I.C. Clinic Ltd. (Metabolics and Genetics in Calgary)
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Alberta Children's Hospital Research Institute, Calgary, Alberta T2M OL6, Canada
| | - Gerald S Shadel
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Andrew Phillip West
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M University, Bryan, TX, USA
| | - William T Gibson
- Department of Medical Genetics, Faculty of Medicine, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Timothy E Shutt
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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6
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Lacey KA, Serpas L, Makita S, Wang Y, Rashidfarrokhi A, Soni C, Gonzalez S, Moreira A, Torres VJ, Reizis B. Secreted mammalian DNases protect against systemic bacterial infection by digesting biofilms. J Exp Med 2023; 220:e20221086. [PMID: 36928522 PMCID: PMC10037111 DOI: 10.1084/jem.20221086] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/18/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Extracellular DNase DNASE1L3 maintains tolerance to self-DNA in humans and mice, whereas the role of its homolog DNASE1 remains controversial, and the overall function of secreted DNases in immunity is unclear. We report that deletion of murine DNASE1 neither caused autoreactivity in isolation nor exacerbated lupus-like disease in DNASE1L3-deficient mice. However, combined deficiency of DNASE1 and DNASE1L3 rendered mice susceptible to bloodstream infection with Staphylococcus aureus. DNASE1/DNASE1L3 double-deficient mice mounted a normal innate response to S. aureus and did not accumulate neutrophil extracellular traps (NETs). However, their kidneys manifested severe pathology, increased bacterial burden, and biofilm-like bacterial lesions that contained bacterial DNA and excluded neutrophils. Furthermore, systemic administration of recombinant DNASE1 protein during S. aureus infection rescued the mortality of DNase-deficient mice and ameliorated the disease in wild-type mice. Thus, DNASE1 and DNASE1L3 jointly facilitate the control of bacterial infection by digesting extracellular microbial DNA in biofilms, suggesting the original evolutionary function of secreted DNases as antimicrobial agents.
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Affiliation(s)
- Keenan A. Lacey
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sohei Makita
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yueyang Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ali Rashidfarrokhi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sandra Gonzalez
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Andre Moreira
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
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7
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MacLauchlan S, Fitzgerald KA, Gravallese EM. Intracellular Sensing of DNA in Autoinflammation and Autoimmunity. Arthritis Rheumatol 2022; 74:1615-1624. [PMID: 35656967 PMCID: PMC9529773 DOI: 10.1002/art.42256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/25/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022]
Abstract
Evidence has shown that DNA is a pathogen-associated molecular pattern, posing a unique challenge in the discrimination between endogenous and foreign DNA. This challenge is highlighted by certain autoinflammatory diseases that arise from monogenic mutations and result in periodic flares of inflammation, typically in the absence of autoantibodies or antigen-specific T lymphocytes. Several autoinflammatory diseases arise due to mutations in genes that normally prevent the accrual of endogenous DNA or are due to mutations that cause activation of intracellular DNA-sensing pathway components. Evidence from genetically modified murine models further support an ability of endogenous DNA and DNA sensing to drive disease pathogenesis, prompting the question of whether endogenous DNA can also induce inflammation in human autoimmune diseases. In this review, we discuss the current understanding of intracellular DNA sensing and downstream signaling pathways as they pertain to autoinflammatory disease, including the development of monogenic disorders such as Stimulator of interferon genes-associated vasculopathy with onset in infancy and Aicardi-Goutières syndrome. In addition, we discuss systemic rheumatic diseases, including certain forms of systemic lupus erythematosus, familial chilblain lupus, and other diseases with established links to intracellular DNA-sensing pathways, and highlight the lessons learned from these examples as they apply to the development of therapies targeting these pathways.
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Affiliation(s)
- Susan MacLauchlan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School
| | - Ellen M. Gravallese
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
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8
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Dhawan UK, Margraf A, Lech M, Subramanian M. Hypercholesterolemia promotes autoantibody production and a lupus-like pathology via decreased DNase-mediated clearance of DNA. J Cell Mol Med 2022; 26:5267-5276. [PMID: 36098213 PMCID: PMC9575094 DOI: 10.1111/jcmm.17556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022] Open
Abstract
Hypercholesterolemia exacerbates autoimmune response and accelerates the progression of several autoimmune disorders, but the mechanistic basis is not well understood. We recently demonstrated that hypercholesterolemia is associated with increased serum extracellular DNA levels secondary to a defect in DNase-mediated clearance of DNA. In this study, we tested whether the impaired DNase response plays a causal role in enhancing anti-nuclear antibody levels and renal immune complex deposition in an Apoe-/- mouse model of hypercholesterolemia. We demonstrate that hypercholesterolemic mice have enhanced anti-ds-DNA and anti-nucleosome antibody levels which is associated with increased immune complex deposition in the renal glomerulus. Importantly, treatment with DNase1 led to a decrease in both the autoantibody levels as well as renal pathology. Additionally, we show that humans with hypercholesterolemia have decreased systemic DNase activity and increased anti-nuclear antibodies. In this context, our data suggest that recombinant DNase1 may be an attractive therapeutic strategy to lower autoimmune response and disease progression in patients with autoimmune disorders associated with concomitant hypercholesterolemia.
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Affiliation(s)
- Umesh Kumar Dhawan
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Andreas Margraf
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Maciej Lech
- LMU Hospital Department of Medicine, Munich, Germany
| | - Manikandan Subramanian
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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9
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McCord JJ, Engavale M, Masoumzadeh E, Villarreal J, Mapp B, Latham MP, Keyel PA, Sutton RB. Structural features of Dnase1L3 responsible for serum antigen clearance. Commun Biol 2022; 5:825. [PMID: 35974043 PMCID: PMC9381713 DOI: 10.1038/s42003-022-03755-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.
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Affiliation(s)
- Jon J McCord
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Minal Engavale
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Elahe Masoumzadeh
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Johanna Villarreal
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Britney Mapp
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Michael P Latham
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Peter A Keyel
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - R Bryan Sutton
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA.
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10
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Mathapathi S, Chu CQ. Contribution of Impaired DNASE1L3 Activity to Anti-DNA Autoantibody Production in Systemic Lupus Erythematosus. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2022; 3:17-22. [PMID: 36467024 PMCID: PMC9524810 DOI: 10.2478/rir-2022-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/05/2022] [Indexed: 06/17/2023]
Abstract
Anti-DNA autoantibodies are pathogenic in systemic lupus erythematosus (SLE). Cell-free chromatin associated long DNA fragments are antigens for anti-DNA antibodies. In health state, released by cell death and actively secreted by live cells, these cell-free DNA are cleared by deoxyribonucleases (DNASES). In SLE, cell-free DNA are accumulated. The defective clearance of long fragments of cell-free DNA in SLE is largely attributed to impaired deoxyribonuclease 1 like 3 (DNASE1L3). DNASE1L3 null mutation results in monogenic SLE. The SLE risk single-nucleotide polymorphism (rs35677470) encodes R260C variant DNASE1L3, which is defective in secretion, leading to reduced levels of DNASE1L3. In addition, neutralizing autoantibodies to DNASE1L3 are produced in SLE to inhibit its enzymatic activity.
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Affiliation(s)
- Samarth Mathapathi
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Section of Rheumatology, VA Portland Health Care System, Portland, Oregon, USA
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Section of Rheumatology, VA Portland Health Care System, Portland, Oregon, USA
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11
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Hinchcliff M, Garcia-Milian R, Di Donato S, Dill K, Bundschuh E, Galdo FD. Cellular and Molecular Diversity in Scleroderma. Semin Immunol 2021; 58:101648. [PMID: 35940960 DOI: 10.1016/j.smim.2022.101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the increasing armamentarium of high-throughput tools available at manageable cost, it is attractive and informative to determine the molecular underpinnings of patient heterogeneity in systemic sclerosis (SSc). Given the highly variable clinical outcomes of patients labelled with the same diagnosis, unravelling the cellular and molecular basis of disease heterogeneity will be crucial to predicting disease risk, stratifying management and ultimately informing a patient-centered precision medicine approach. Herein, we summarise the findings of the past several years in the fields of genomics, transcriptomics, and proteomics that contribute to unraveling the cellular and molecular heterogeneity of SSc. Expansion of these findings and their routine integration with quantitative analysis of histopathology and imaging studies into clinical care promise to inform a scientifically driven patient-centred personalized medicine approach to SSc in the near future.
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Affiliation(s)
- Monique Hinchcliff
- Yale School of Medicine, Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, USA.
| | | | - Stefano Di Donato
- Raynaud's and Scleroderma Programme, Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, UK
| | | | - Elizabeth Bundschuh
- Yale School of Medicine, Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, USA
| | - Francesco Del Galdo
- Raynaud's and Scleroderma Programme, Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, UK.
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12
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Santa P, Garreau A, Serpas L, Ferriere A, Blanco P, Soni C, Sisirak V. The Role of Nucleases and Nucleic Acid Editing Enzymes in the Regulation of Self-Nucleic Acid Sensing. Front Immunol 2021; 12:629922. [PMID: 33717156 PMCID: PMC7952454 DOI: 10.3389/fimmu.2021.629922] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of microbial nucleic acids by the innate immune system is mediated by numerous intracellular nucleic acids sensors. Upon the detection of nucleic acids these sensors induce the production of inflammatory cytokines, and thus play a crucial role in the activation of anti-microbial immunity. In addition to microbial genetic material, nucleic acid sensors can also recognize self-nucleic acids exposed extracellularly during turn-over of cells, inefficient efferocytosis, or intracellularly upon mislocalization. Safeguard mechanisms have evolved to dispose of such self-nucleic acids to impede the development of autoinflammatory and autoimmune responses. These safeguard mechanisms involve nucleases that are either specific to DNA (DNases) or RNA (RNases) as well as nucleic acid editing enzymes, whose biochemical properties, expression profiles, functions and mechanisms of action will be detailed in this review. Fully elucidating the role of these enzymes in degrading and/or processing of self-nucleic acids to thwart their immunostimulatory potential is of utmost importance to develop novel therapeutic strategies for patients affected by inflammatory and autoimmune diseases.
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Affiliation(s)
- Pauline Santa
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Anne Garreau
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | | | - Patrick Blanco
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Immunology and Immunogenetic Department, Bordeaux University Hospital, Bordeaux, France
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
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13
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Coke LN, Wen H, Comeau M, Ghanem MH, Shih A, Metz CN, Li W, Langefeld CD, Gregersen PK, Simpfendorfer KR. Arg206Cys substitution in DNASE1L3 causes a defect in DNASE1L3 protein secretion that confers risk of systemic lupus erythematosus. Ann Rheum Dis 2021; 80:782-787. [PMID: 33455918 PMCID: PMC8142439 DOI: 10.1136/annrheumdis-2020-218810] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To determine if the polymorphism encoding the Arg206Cys substitution in DNASE1L3 explains the association of the DNASE1L3/PXK gene locus with systemic lupus erythematosus (SLE) and to examine the effect of the Arg206Cys sequence change on DNASE1L3 protein function. METHODS Conditional analysis for rs35677470 was performed on cases and controls with European ancestry from the SLE Immunochip study, and genotype and haplotype frequencies were compared. DNASE1L3 protein levels were measured in cells and supernatants of HEK293 cells and monocyte-derived dendritic cells expressing recombinant and endogenous 206Arg and 206Cys protein variants. RESULTS Conditional analysis on rs35677470 eliminated the SLE risk association signal for lead single-nucleotide polymorphisms (SNPs) rs180977001 and rs73081554, which are found to tag the same risk haplotype as rs35677470. The modest effect sizes of the SLE risk genotypes (heterozygous risk OR=1.14 and homozygous risk allele OR=1.68) suggest some DNASE1L3 endonuclease enzyme function is retained. An SLE protective signal in PXK (lead SNP rs11130643) remained following conditioning on rs35677470. The DNASE1L3 206Cys risk variant maintained enzymatic activity, but secretion of the artificial and endogenous DNASE1L3 206Cys protein was substantially reduced. CONCLUSIONS SLE risk association in the DNASE1L3 locus is dependent on the missense SNP rs35677470, which confers a reduction in DNASE1L3 protein secretion but does not eliminate its DNase enzyme function.
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Affiliation(s)
- Latanya N Coke
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Hongxiu Wen
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Mary Comeau
- Department of Biostatistics and Data Science, Division of Public Health Sciences, School of Medicine, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Mustafa H Ghanem
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Andrew Shih
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Christine N Metz
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Wentian Li
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, School of Medicine, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Peter K Gregersen
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Kim R Simpfendorfer
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA .,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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