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Montorsi L, Pitcher MJ, Zhao Y, Dionisi C, Demonti A, Tull TJ, Dhami P, Ellis RJ, Bishop C, Sanderson JD, Jain S, D'Cruz D, Gibbons DL, Winkler TH, Bemark M, Ciccarelli FD, Spencer J. Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue. Nat Commun 2024; 15:4051. [PMID: 38744839 PMCID: PMC11094119 DOI: 10.1038/s41467-024-48267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides. We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.
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Affiliation(s)
- Lucia Montorsi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Michael J Pitcher
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Yuan Zhao
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Chiara Dionisi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Alicia Demonti
- School of Immunology and Microbial Sciences, King's College London, London, UK
- École Normale Supérieure de Lyon, Claude Bernard Lyon 1 University, Lyon, France
| | - Thomas J Tull
- St. John's Institute of Dermatology, King's College London, London, UK
| | - Pawan Dhami
- Genomics Research Platform and Single Cell Laboratory at Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Richard J Ellis
- Advanced Cytometry Platform (Flow Core), Research and Development Department at Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Cynthia Bishop
- Advanced Cytometry Platform (Flow Core), Research and Development Department at Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jeremy D Sanderson
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Department of Gastroenterology, Guy's and St Thomas' Foundation Trust, London, UK
| | - Sahil Jain
- Louise Coote Lupus Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - David D'Cruz
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Louise Coote Lupus Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Deena L Gibbons
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas H Winkler
- Division of Genetics, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Mats Bemark
- Department of Translational Medicine - Human Immunology, Lund University, Malmö, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Jo Spencer
- School of Immunology and Microbial Sciences, King's College London, London, UK.
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Yeo NKW, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus. Front Genet 2024; 15:1341272. [PMID: 38501057 PMCID: PMC10944961 DOI: 10.3389/fgene.2024.1341272] [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: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.
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Affiliation(s)
- Nicholas Kim-Wah Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Che Kang Lim
- Duke-NUS Medical School, Singapore, Singapore
- Department of Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Kim Huat Khoo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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Egleston M, Dong L, Howlader AH, Bhat S, Orris B, Bianchet MA, Greenberg MM, Stivers JT. Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding. ACS Chem Biol 2023; 18:2200-2210. [PMID: 37233733 PMCID: PMC10596003 DOI: 10.1021/acschembio.3c00118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase that exists in monomeric, dimeric, and tetrameric forms. It is activated by GTP binding to an A1 allosteric site on each monomer subunit, which induces dimerization, a prerequisite for dNTP-induced tetramerization. SAMHD1 is a validated drug target stemming from its inactivation of many anticancer nucleoside drugs leading to drug resistance. The enzyme also possesses a single-strand nucleic acid binding function that promotes RNA and DNA homeostasis by several mechanisms. To discover small molecule inhibitors of SAMHD1, we screened a custom ∼69 000-compound library for dNTPase inhibitors. Surprisingly, this effort yielded no viable hits and indicated that exceptional barriers for discovery of small molecule inhibitors existed. We then took a rational fragment-based inhibitor design approach using a deoxyguanosine (dG) A1 site targeting fragment. A targeted chemical library was synthesized by coupling a 5'-phosphoryl propylamine dG fragment (dGpC3NH2) to 376 carboxylic acids (RCOOH). Direct screening of the products (dGpC3NHCO-R) yielded nine initial hits, one of which (R = 3-(3'-bromo-[1,1'-biphenyl]), 5a) was investigated extensively. Amide 5a is a competitive inhibitor against GTP binding to the A1 site and induces inactive dimers that are deficient in tetramerization. Surprisingly, 5a also prevented ssDNA and ssRNA binding, demonstrating that the dNTPase and nucleic acid binding functions of SAMHD1 can be disrupted by a single small molecule. A structure of the SAMHD1-5a complex indicates that the biphenyl fragment impedes a conformational change in the C-terminal lobe that is required for tetramerization.
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Affiliation(s)
- Matthew Egleston
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Linghao Dong
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - A. Hasan Howlader
- Department
of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Shridhar Bhat
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Benjamin Orris
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Mario A. Bianchet
- Department
of Neurology and Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Marc M. Greenberg
- Department
of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - James T. Stivers
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
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