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Zhong X, Peddada N, Moresco JJ, Wang J, Jiang Y, Rios JJ, Moresco EMY, Choi JH, Beutler B. Viable mutations of mouse midnolin suppress B cell malignancies. J Exp Med 2024; 221:e20232132. [PMID: 38625151 PMCID: PMC11022886 DOI: 10.1084/jem.20232132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/20/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
In a genetic screen, we identified two viable missense alleles of the essential gene Midnolin (Midn) that were associated with reductions in peripheral B cells. Causation was confirmed in mice with targeted deletion of four of six MIDN protein isoforms. MIDN was expressed predominantly in lymphocytes where it augmented proteasome activity. We showed that purified MIDN directly stimulated 26S proteasome activity in vitro in a manner dependent on the ubiquitin-like domain and a C-terminal region. MIDN-deficient B cells displayed aberrant activation of the IRE-1/XBP-1 pathway of the unfolded protein response. Partial or complete MIDN deficiency strongly suppressed Eμ-Myc-driven B cell leukemia and the antiapoptotic effects of Eμ-BCL2 on B cells in vivo and induced death of Sp2/0 hybridoma cells in vitro, but only partially impaired normal lymphocyte development. Thus, MIDN is required for proteasome activity in support of normal lymphopoiesis and is essential for malignant B cell proliferation over a broad range of differentiation states.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
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2
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Zegeye Y, Aredo B, Yuksel S, Kirman DC, Kumar A, Chen B, Turpin E, Shresta S, He YG, Gautron L, Tang M, Li X, DiCesare SM, Hulleman JD, Xing C, Ludwig S, Moresco EMY, Beutler BA, Ufret-Vincenty RL. E3 ubiquitin ligase Herc3 deficiency leads to accumulation of subretinal microglia and retinal neurodegeneration. Sci Rep 2024; 14:3010. [PMID: 38321224 PMCID: PMC10847449 DOI: 10.1038/s41598-024-53731-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/04/2024] [Indexed: 02/08/2024] Open
Abstract
Activated microglia have been implicated in the pathogenesis of age-related macular degeneration (AMD), diabetic retinopathy, and other neurodegenerative and neuroinflammatory disorders, but our understanding of the mechanisms behind their activation is in infant stages. With the goal of identifying novel genes associated with microglial activation in the retina, we applied a semiquantitative fundus spot scoring scale to an unbiased, state-of-the-science mouse forward genetics pipeline. A mutation in the gene encoding the E3 ubiquitin ligase Herc3 led to prominent accumulation of fundus spots. CRISPR mutagenesis was used to generate Herc3-/- mice, which developed prominent accumulation of fundus spots and corresponding activated Iba1 + /CD16 + subretinal microglia, retinal thinning on OCT and histology, and functional deficits by Optomotory and electrophysiology. Bulk RNA sequencing identified activation of inflammatory pathways and differentially expressed genes involved in the modulation of microglial activation. Thus, despite the known expression of multiple E3 ubiquitin ligases in the retina, we identified a non-redundant role for Herc3 in retinal homeostasis. Our findings are significant given that a dysregulated ubiquitin-proteasome system (UPS) is important in prevalent retinal diseases, in which activated microglia appear to play a role. This association between Herc3 deficiency, retinal microglial activation and retinal degeneration merits further study.
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Affiliation(s)
- Yeshumenesh Zegeye
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bogale Aredo
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Seher Yuksel
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dogan Can Kirman
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ashwani Kumar
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bo Chen
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Emily Turpin
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sangita Shresta
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yu-Guang He
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Laurent Gautron
- Center for Hypothalamic Research and Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sophia M DiCesare
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - John D Hulleman
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sara Ludwig
- Center for Hypothalamic Research and Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce A Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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3
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Hu Y, Zhang Z, Mao Q, Zhang X, Hao A, Xun Y, Wang Y, Han L, Zhan W, Liu Q, Yin Y, Peng C, Moresco EMY, Chen Z, Beutler B, Sun L. Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3 KBTBD2. Nat Struct Mol Biol 2024; 31:336-350. [PMID: 38332366 DOI: 10.1038/s41594-023-01182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/16/2023] [Indexed: 02/10/2024]
Abstract
Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. Cellular levels of the regulatory p85α subunit are tightly controlled by regulated proteasomal degradation. In adipose tissue and growth plates, failure of K48-linked p85α ubiquitination causes diabetes, lipodystrophy and dwarfism in mice, as in humans with SHORT syndrome. Here we elucidated the structures of the key ubiquitin ligase complexes regulating p85α availability. Specificity is provided by the substrate receptor KBTBD2, which recruits p85α to the cullin3-RING E3 ubiquitin ligase (CRL3). CRL3KBTBD2 forms multimers, which disassemble into dimers upon substrate binding (CRL3KBTBD2-p85α) and/or neddylation by the activator NEDD8 (CRL3KBTBD2~N8), leading to p85α ubiquitination and degradation. Deactivation involves dissociation of NEDD8 mediated by the COP9 signalosome and displacement of KBTBD2 by the inhibitor CAND1. The hereby identified structural basis of p85α regulation opens the way to better understanding disturbances of glucose regulation, growth and cancer.
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Affiliation(s)
- Yuxia Hu
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qiyu Mao
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiang Zhang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Aihua Hao
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Xun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yeda Wang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lin Han
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wuqiang Zhan
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qianying Liu
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhenguo Chen
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Lei Sun
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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Zhong X, Moresco JJ, Diedrich JK, Pinto AM, SoRelle JA, Wang J, Keller K, Ludwig S, Moresco EMY, Beutler B, Choi JH. Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis. Proc Natl Acad Sci U S A 2023; 120:e2314429120. [PMID: 38055739 PMCID: PMC10723049 DOI: 10.1073/pnas.2314429120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023] Open
Abstract
We detected ENU-induced alleles of Mfsd1 (encoding the major facilitator superfamily domain containing 1 protein) that caused lymphopenia, splenomegaly, progressive liver pathology, and extramedullary hematopoiesis (EMH). MFSD1 is a lysosomal membrane-bound solute carrier protein with no previously described function in immunity. By proteomic analysis, we identified association between MFSD1 and both GLMP (glycosylated lysosomal membrane protein) and GIMAP5 (GTPase of immunity-associated protein 5). Germline knockout alleles of Mfsd1, Glmp, and Gimap5 each caused lymphopenia, liver pathology, EMH, and lipid deposition in the bone marrow and liver. We found that the interactions of MFSD1 and GLMP with GIMAP5 are essential to maintain normal GIMAP5 expression, which in turn is critical to support lymphocyte development and liver homeostasis that suppresses EMH. These findings identify the protein complex MFSD1-GLMP-GIMAP5 operating in hematopoietic and extrahematopoietic tissues to regulate immunity and liver homeostasis.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Antonio M. Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Jeffrey A. SoRelle
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX75390
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5
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Zhong X, Peddada N, Wang J, Moresco JJ, Zhan X, Shelton JM, SoRelle JA, Keller K, Lazaro DR, Moresco EMY, Choi JH, Beutler B. OVOL2 sustains postnatal thymic epithelial cell identity. Nat Commun 2023; 14:7786. [PMID: 38012144 PMCID: PMC10682436 DOI: 10.1038/s41467-023-43456-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Distinct pathways and molecules may support embryonic versus postnatal thymic epithelial cell (TEC) development and maintenance. Here, we identify a mechanism by which TEC numbers and function are maintained postnatally. A viable missense allele (C120Y) of Ovol2, expressed ubiquitously or specifically in TECs, results in lymphopenia, in which T cell development is compromised by loss of medullary TECs and dysfunction of cortical TECs. We show that the epithelial identity of TECs is aberrantly subverted towards a mesenchymal state in OVOL2-deficient mice. We demonstrate that OVOL2 inhibits the epigenetic regulatory BRAF-HDAC complex, specifically disrupting RCOR1-LSD1 interaction. This causes inhibition of LSD1-mediated H3K4me2 demethylation, resulting in chromatin accessibility and transcriptional activation of epithelial genes. Thus, OVOL2 controls the epigenetic landscape of TECs to enforce TEC identity. The identification of a non-redundant postnatal mechanism for TEC maintenance offers an entry point to understanding thymic involution, which normally begins in early adulthood.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Xiaowei Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8821, USA
| | - John M Shelton
- Intermal Medicine-Histopathology Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8573, USA
| | - Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9072, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9063, USA
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Danielle Renee Lazaro
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
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6
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Zhong X, Moresco JJ, Keller K, Lazaro DR, Ely C, Moresco EMY, Beutler B, Choi JH. Essential requirement for IER3IP1 in B cell development. Proc Natl Acad Sci U S A 2023; 120:e2312810120. [PMID: 37934820 PMCID: PMC10655558 DOI: 10.1073/pnas.2312810120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
In a forward genetic screen of mice with N-ethyl-N-nitrosourea-induced mutations for aberrant immune function, we identified animals with low percentages of B220+ cells in the peripheral blood. The causative mutation was in Ier3ip1, encoding immediate early response 3 interacting protein 1 (IER3IP1), an endoplasmic reticulum membrane protein mutated in an autosomal recessive neurodevelopmental disorder termed Microcephaly with simplified gyration, Epilepsy and permanent neonatal Diabetes Syndrome (MEDS) in humans. However, no immune function for IER3IP1 had previously been reported. The viable hypomorphic Ier3ip1 allele uncovered in this study, identical to a reported IER3IP1 variant in a MEDS patient, reveals an essential hematopoietic-intrinsic role for IER3IP1 in B cell development and function. We show that IER3IP1 forms a complex with the Golgi transmembrane protein 167A and limits activation of the unfolded protein response mediated by inositol-requiring enzyme-1α and X-box binding protein 1 in B cells. Our findings suggest that B cell deficiency may be a feature of MEDS.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Danielle Renee Lazaro
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Claire Ely
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX75390-8505
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX75390
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7
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Song R, Fond A, Li X, Tang M, Zhan X, Gordillo R, Moresco EMY, Beutler B, Turer EE. The dual lipid desaturase/hydroxylase DEGS2 controls phytoceramide levels necessary to counter intestinal inflammation. Dis Model Mech 2023; 16:dmm050043. [PMID: 37589563 PMCID: PMC10499023 DOI: 10.1242/dmm.050043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Intestinal immunity is dependent on barrier function to maintain quiescence. The mechanisms for the maintenance of this barrier are not fully understood. Delta 4-desaturase, sphingolipid 2 (DEGS2) is a lipid desaturase and hydroxylase that catalyzes the synthesis of ceramide and phytoceramide from dihydroceramide. Using a forward genetic approach, we found and validated a mutation in Degs2 as causative of increasing susceptibility to colitis and altering the phytoceramide balance in the colon. DEGS2 is expressed in the intestinal epithelium, and the colitis phenotype is dependent on the non-hematopoietic compartment of the mouse. In the absence of DEGS2, the colon lacks phytoceramides and accumulates large amounts of the precursor lipid dihydroceramide. In response to dextran sodium sulfate (DSS)-induced colitis, colonic epithelial cells in DEGS2-deficient mice had increased cell death and decreased proliferation compared to those in wild-type mice. These findings demonstrate that DEGS2 is needed to maintain epithelial integrity, protect against DSS-induced colitis and maintain lipid balance in vivo.
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Affiliation(s)
- Ran Song
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Aaron Fond
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Ruth Gordillo
- Department of Internal Medicine, Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Emre E. Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
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8
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Song R, McAlpine W, Fond AM, Nair-Gill E, Choi JH, Nyström EEL, Arike L, Field S, Li X, SoRelle JA, Moresco JJ, Moresco EMY, Yates JR, Azadi P, Ni J, Birchenough GMH, Beutler B, Turer EE. Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation. Nat Commun 2023; 14:3652. [PMID: 37339972 PMCID: PMC10282085 DOI: 10.1038/s41467-023-39398-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/09/2023] [Indexed: 06/22/2023] Open
Abstract
A key feature in intestinal immunity is the dynamic intestinal barrier, which separates the host from resident and pathogenic microbiota through a mucus gel impregnated with antimicrobial peptides. Using a forward genetic screen, we have found a mutation in Tvp23b, which conferred susceptibility to chemically induced and infectious colitis. Trans-Golgi apparatus membrane protein TVP23 homolog B (TVP23B) is a transmembrane protein conserved from yeast to humans. We found that TVP23B controls the homeostasis of Paneth cells and function of goblet cells, leading to a decrease in antimicrobial peptides and more penetrable mucus layer. TVP23B binds with another Golgi protein, YIPF6, which is similarly critical for intestinal homeostasis. The Golgi proteomes of YIPF6 and TVP23B-deficient colonocytes have a common deficiency of several critical glycosylation enzymes. TVP23B is necessary for the formation of the sterile mucin layer of the intestine and its absence disturbs the balance of host and microbe in vivo.
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Affiliation(s)
- Ran Song
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Aaron M Fond
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Elisabeth E L Nyström
- Institute of Biochemistry, University of Kiel, 24118, Kiel, Schleswig-Holstein, Germany
| | - Liisa Arike
- The Wallenberg Centre for Molecular & Translational Medicine, Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Sydney Field
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Jeffrey A SoRelle
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Josephine Ni
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - George M H Birchenough
- The Wallenberg Centre for Molecular & Translational Medicine, Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Emre E Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA.
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9
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Zhang Z, Jiang Y, Su L, Ludwig S, Zhang X, Tang M, Li X, Anderton P, Zhan X, Choi M, Russell J, Bu CH, Lyon S, Xu D, Hildebrand S, Scott L, Quan J, Simpson R, Sun Q, Qin B, Collie T, Tadesse M, Moresco EMY, Beutler B. Obesity caused by an OVOL2 mutation reveals dual roles of OVOL2 in promoting thermogenesis and limiting white adipogenesis. Cell Metab 2022; 34:1860-1874.e4. [PMID: 36228616 PMCID: PMC9633419 DOI: 10.1016/j.cmet.2022.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/30/2022] [Accepted: 09/17/2022] [Indexed: 01/11/2023]
Abstract
Using random germline mutagenesis in mice, we identified a viable hypomorphic allele (boh) of the transcription-factor-encoding gene Ovol2 that resulted in obesity, which initially developed with normal food intake and physical activity but decreased energy expenditure. Fat weight was dramatically increased, while lean weight was reduced in 12-week-old boh homozygous mice, culminating by 24 weeks in massive obesity, hepatosteatosis, insulin resistance, and diabetes. The Ovol2boh/boh genotype augmented obesity in Lepob/ob mice, and pair-feeding failed to normalize obesity in Ovol2boh/boh mice. OVOL2-deficient mice were extremely cold intolerant. OVOL2 is essential for brown/beige adipose tissue-mediated thermogenesis. In white adipose tissues, OVOL2 limited adipogenesis by blocking C/EBPα engagement of its transcriptional targets. Overexpression of OVOL2 in adipocytes of mice fed with a high-fat diet reduced total body and liver fat and improved insulin sensitivity. Our data reveal that OVOL2 plays dual functions in thermogenesis and adipogenesis to maintain energy balance.
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Affiliation(s)
- Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuechun Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mihwa Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chun-Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stephen Lyon
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darui Xu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rochelle Simpson
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qihua Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Baifang Qin
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tiffany Collie
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Meron Tadesse
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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10
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Zhang Z, Xun Y, Rong S, Yan L, SoRelle JA, Li X, Tang M, Keller K, Ludwig S, Moresco EMY, Beutler B. Loss of immunity-related GTPase GM4951 leads to nonalcoholic fatty liver disease without obesity. Nat Commun 2022; 13:4136. [PMID: 35842425 PMCID: PMC9288484 DOI: 10.1038/s41467-022-31812-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/05/2022] [Indexed: 11/30/2022] Open
Abstract
Obesity and diabetes are well known risk factors for nonalcoholic fatty liver disease (NAFLD), but the genetic factors contributing to the development of NAFLD remain poorly understood. Here we describe two semi-dominant allelic missense mutations (Oily and Carboniferous) of Predicted gene 4951 (Gm4951) identified from a forward genetic screen in mice. GM4951 deficient mice developed NAFLD on high fat diet (HFD) with no changes in body weight or glucose metabolism. Moreover, HFD caused a reduction in the level of Gm4951, which in turn promoted the development of NAFLD. Predominantly expressed in hepatocytes, GM4951 was verified as an interferon inducible GTPase. The NAFLD in Gm4951 knockout mice was associated with decreased lipid oxidation in the liver and no defect in hepatic lipid secretion. After lipid loading, hepatocyte GM4951 translocated to lipid droplets (LDs), bringing with it hydroxysteroid 17β-dehydrogenase 13 (HSD17B13), which in the absence of GM4951 did not undergo this translocation. We identified a rare non-obese mouse model of NAFLD caused by GM4951 deficiency and define a critical role for GTPase-mediated translocation in hepatic lipid metabolism.
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Affiliation(s)
- Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Yu Xun
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Shunxing Rong
- grid.267313.20000 0000 9482 7121Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Lijuan Yan
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jeffrey A. SoRelle
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Xiaohong Li
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Miao Tang
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Katie Keller
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Sara Ludwig
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Eva Marie Y. Moresco
- grid.267313.20000 0000 9482 7121Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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11
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Yang MH, Russell JL, Mifune Y, Wang Y, Shi H, Moresco EMY, Siegwart DJ, Beutler B, Boger DL. Next-Generation Diprovocims with Potent Human and Murine TLR1/TLR2 Agonist Activity That Activate the Innate and Adaptive Immune Response. J Med Chem 2022; 65:9230-9252. [PMID: 35767437 DOI: 10.1021/acs.jmedchem.2c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diprovocims, a new class of toll-like receptor (TLR) agonists, bear no similarity to prior TLR agonists, act through a well-defined mechanism (TLR1/TLR2 agonist), exhibit exquisite structure-activity relationships, and display in vivo adjuvant activity. They possess potent and efficacious agonist activity toward human TLR1/TLR2 but modest agonism toward the murine receptor. A manner by which diprovocims can be functionalized without impacting hTLR1/TLR2 activity is detailed, permitting future linkage to antigenic, targeting, or delivery moieties. Improvements in both potency and its low efficacy in the murine system were also achieved, permitting more effective use in animal models while maintaining the hTLR1/TLR2 activity. The prototypical member diprovocim-X exhibits the excellent potency/efficacy of diprovocim-1 in human cells, displays substantially improved potency/efficacy in mouse macrophages, and serves as an adjuvant in mice when coadministered with a nonimmunogenic antigen, indicating stimulation of the adaptive as well as innate immune response.
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Affiliation(s)
- Ming-Hsiu Yang
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Jamie L Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yuto Mifune
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Daniel J Siegwart
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
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12
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Chatenoud L, Marquet C, Valette F, Scott L, Quan J, Bu CH, Hildebrand S, Moresco EMY, Bach JF, Beutler B. Modulation of autoimmune diabetes by N-ethyl-N-nitrosourea- induced mutations in non-obese diabetic mice. Dis Model Mech 2022; 15:275575. [PMID: 35502705 PMCID: PMC9178510 DOI: 10.1242/dmm.049484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
Genetic association studies of type 1 diabetes (T1D) in humans, and in congenic non-obese diabetic (NOD) mice harboring DNA segments from T1D-resistant mice, face the challenge of assigning causation to specific gene variants among many within loci that affect disease risk. Here, we created random germline mutations in NOD/NckH mice and used automated meiotic mapping to identify mutations modifying T1D incidence and age of onset. In contrast with association studies in humans or congenic NOD mice, we analyzed a relatively small number of genetic changes in each pedigree, permitting implication of specific mutations as causative. Among 844 mice from 14 pedigrees bearing 594 coding/splicing changes, we identified seven mutations that accelerated T1D development, and five that delayed or suppressed T1D. Eleven mutations affected genes not previously known to influence T1D (Xpnpep1, Herc1, Srrm2, Rapgef1, Ppl, Zfp583, Aldh1l1, Col6a1, Ccdc13, Cd200r1, Atrnl1). A suppressor mutation in Coro1a validated the screen. Mutagenesis coupled with automated meiotic mapping can detect genes in which allelic variation influences T1D susceptibility in NOD mice. Variation of some of the orthologous/paralogous genes may influence T1D susceptibility in humans.
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Affiliation(s)
- Lucienne Chatenoud
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Cindy Marquet
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Fabrice Valette
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jean-François Bach
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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13
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Xu D, Lyon S, Bu CH, Hildebrand S, Choi JH, Zhong X, Liu A, Turer EE, Zhang Z, Russell J, Ludwig S, Mahrt E, Nair-Gill E, Shi H, Wang Y, Zhang D, Yue T, Wang KW, SoRelle JA, Su L, Misawa T, McAlpine W, Sun L, Wang J, Zhan X, Choi M, Farokhnia R, Sakla A, Schneider S, Coco H, Coolbaugh G, Hayse B, Mazal S, Medler D, Nguyen B, Rodriguez E, Wadley A, Tang M, Li X, Anderton P, Keller K, Press A, Scott L, Quan J, Cooper S, Collie T, Qin B, Cardin J, Simpson R, Tadesse M, Sun Q, Wise CA, Rios JJ, Moresco EMY, Beutler B. Thousands of induced germline mutations affecting immune cells identified by automated meiotic mapping coupled with machine learning. Proc Natl Acad Sci U S A 2021; 118:e2106786118. [PMID: 34260399 PMCID: PMC8285956 DOI: 10.1073/pnas.2106786118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Forward genetic studies use meiotic mapping to adduce evidence that a particular mutation, normally induced by a germline mutagen, is causative of a particular phenotype. Particularly in small pedigrees, cosegregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the identification of mutations causing immune phenotypes in mice by creating Candidate Explorer (CE), a machine-learning software program that integrates 67 features of genetic mapping data into a single numeric score, mathematically convertible to the probability of verification of any putative mutation-phenotype association. At this time, CE has evaluated putative mutation-phenotype associations arising from screening damaging mutations in ∼55% of mouse genes for effects on flow cytometry measurements of immune cells in the blood. CE has therefore identified more than half of genes within which mutations can be causative of flow cytometric phenovariation in Mus musculus The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.
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Affiliation(s)
- Darui Xu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Stephen Lyon
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aijie Liu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Emre E Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Elena Mahrt
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Duanwu Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tao Yue
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jeffrey A SoRelle
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Takuma Misawa
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lei Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mihwa Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Roxana Farokhnia
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Andrew Sakla
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Schneider
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hannah Coco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Gabrielle Coolbaugh
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Braden Hayse
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara Mazal
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Dawson Medler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Brandon Nguyen
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Edward Rodriguez
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Andrew Wadley
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Katie Keller
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Amanda Press
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sydney Cooper
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tiffany Collie
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Baifang Qin
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jennifer Cardin
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Rochelle Simpson
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Meron Tadesse
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Qihua Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390;
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14
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Yue T, Zhan X, Zhang D, Jain R, Wang KW, Choi JH, Misawa T, Su L, Quan J, Hildebrand S, Xu D, Li X, Turer E, Sun L, Moresco EMY, Beutler B. SLFN2 protection of tRNAs from stress-induced cleavage is essential for T cell-mediated immunity. Science 2021; 372:372/6543/eaba4220. [PMID: 33986151 PMCID: PMC8442736 DOI: 10.1126/science.aba4220] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/02/2020] [Accepted: 03/25/2021] [Indexed: 01/05/2023]
Abstract
Reactive oxygen species (ROS) increase in activated T cells because of metabolic activity induced to support T cell proliferation and differentiation. We show that these ROS trigger an oxidative stress response that leads to translation repression. This response is countered by Schlafen 2 (SLFN2), which directly binds transfer RNAs (tRNAs) to protect them from cleavage by the ribonuclease angiogenin. T cell-specific SLFN2 deficiency results in the accumulation of tRNA fragments, which inhibit translation and promote stress-granule formation. Interleukin-2 receptor β (IL-2Rβ) and IL-2Rγ fail to be translationally up-regulated after T cell receptor stimulation, rendering SLFN2-deficient T cells insensitive to interleukin-2's mitogenic effects. SLFN2 confers resistance against the ROS-mediated translation-inhibitory effects of oxidative stress normally induced by T cell activation, permitting the robust protein synthesis necessary for T cell expansion and immunity.
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Affiliation(s)
- Tao Yue
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duanwu Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ruchi Jain
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kuan-wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takuma Misawa
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darui Xu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Emre Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Correspondence to:
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15
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SoRelle JA, Chen Z, Wang J, Yue T, Choi JH, Wang K, Zhong X, Hildebrand S, Russell J, Scott L, Xu D, Zhan X, Bu CH, Wang T, Choi M, Tang M, Ludwig S, Zhan X, Li X, Moresco EMY, Beutler B. Dominant atopy risk mutations identified by mouse forward genetic analysis. Allergy 2021; 76:1095-1108. [PMID: 32810290 DOI: 10.1111/all.14564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Atopy, the overall tendency to become sensitized to an allergen, is heritable but seldom ascribed to mutations within specific genes. Atopic individuals develop abnormally elevated IgE responses to immunization with potential allergens. To gain insight into the genetic causes of atopy, we carried out a forward genetic screen for atopy in mice. METHODS We screened mice carrying homozygous and heterozygous N-ethyl-N-nitrosourea (ENU)-induced germline mutations for aberrant antigen-specific IgE and IgG1 production in response to immunization with the model allergen papain. Candidate genes were validated by independent gene mutation. RESULTS Of 31 candidate genes selected for investigation, the effects of mutations in 23 genes on papain-specific IgE or IgG1 were verified. Among the 20 verified genes influencing the IgE response, eight were necessary for the response, while 12 repressed IgE. Nine genes were not previously implicated in the IgE response. Fifteen genes encoded proteins contributing to IgE class switch recombination or B-cell receptor signaling. The precise roles of the five remaining genes (Flcn, Map1lc3b, Me2, Prkd2, and Scarb2) remain to be determined. Loss-of-function mutations in nine of the 12 genes limiting the IgE response were dominant or semi-dominant for the IgE phenotype but did not cause immunodeficiency in the heterozygous state. Using damaging allele frequencies for the corresponding human genes and in silico simulations (Monte Carlo) of undiscovered atopy mutations, we estimated the percentage of humans with heterozygous atopy risk mutations. CONCLUSIONS Up to 37% of individuals may be heterozygous carriers for at least one dominant atopy risk mutation.
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Affiliation(s)
- Jeffrey A. SoRelle
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
- Department of Pathology University of Texas Southwestern Medical Center Dallas TX USA
| | - Zhe Chen
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Tao Yue
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
- Department of Immunology University of Texas Southwestern Medical Center Dallas TX USA
| | - Kuan‐wen Wang
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Xue Zhong
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Jamie Russell
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Lindsay Scott
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Darui Xu
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Xiaowei Zhan
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Chun Hui Bu
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Tao Wang
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
- Department of Population and Data Sciences Quantitative Biomedical Research Center University of Texas Southwestern Medical Center Dallas TX USA
| | - Mihwa Choi
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Miao Tang
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense University of Texas Southwestern Medical Center Dallas TX USA
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16
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Shi H, Sun L, Wang Y, Liu A, Zhan X, Li X, Tang M, Anderton P, Hildebrand S, Quan J, Ludwig S, Moresco EMY, Beutler B. N4BP1 negatively regulates NF-κB by binding and inhibiting NEMO oligomerization. Nat Commun 2021; 12:1379. [PMID: 33654074 PMCID: PMC7925594 DOI: 10.1038/s41467-021-21711-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/08/2021] [Indexed: 02/07/2023] Open
Abstract
Many immune responses depend upon activation of NF-κB, an important transcription factor in the elicitation of a cytokine response. Here we show that N4BP1 inhibits TLR-dependent activation of NF-κB by interacting with the NF-κB signaling essential modulator (NEMO, also known as IκB kinase γ) to attenuate NEMO-NEMO dimerization or oligomerization. The UBA-like (ubiquitin associated-like) and CUE-like (ubiquitin conjugation to ER degradation-like) domains in N4BP1 mediate interaction with the NEMO COZI domain. Both in vitro and in mice, N4bp1 deficiency specifically enhances TRIF-independent (TLR2, TLR7, or TLR9-mediated) but not TRIF-dependent (TLR3 or TLR4-mediated) NF-κB activation, leading to increased production of proinflammatory cytokines. In response to TLR4 or TLR3 activation, TRIF causes activation of caspase-8, which cleaves N4BP1 distal to residues D424 and D490 and abolishes its inhibitory effect. N4bp1-/- mice also have diminished numbers of T cells in the peripheral blood. Our work identifies N4BP1 as an inhibitory checkpoint protein that must be overcome to activate NF-κB, and a TRIF-initiated caspase-8-dependent mechanism by which this is accomplished.
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Affiliation(s)
- Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aijie Liu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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17
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Misawa T, SoRelle JA, Choi JH, Yue T, Wang KW, McAlpine W, Wang J, Liu A, Tabeta K, Turer EE, Evers B, Nair-Gill E, Poddar S, Su L, Ou F, Yu L, Russell J, Ludwig S, Zhan X, Hildebrand S, Li X, Tang M, Murray AR, Moresco EMY, Beutler B. Mutual inhibition between Prkd2 and Bcl6 controls T follicular helper cell differentiation. Sci Immunol 2020; 5:5/43/eaaz0085. [PMID: 31980486 DOI: 10.1126/sciimmunol.aaz0085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/06/2020] [Indexed: 12/11/2022]
Abstract
T follicular helper cells (TFH) participate in germinal center (GC) development and are necessary for B cell production of high-affinity, isotype-switched antibodies. In a forward genetic screen, we identified a missense mutation in Prkd2, encoding the serine/threonine kinase protein kinase D2, which caused elevated titers of immunoglobulin E (IgE) in the serum. Subsequent analysis of serum antibodies in mice with a targeted null mutation of Prkd2 demonstrated polyclonal hypergammaglobulinemia of IgE, IgG1, and IgA isotypes, which was exacerbated by the T cell-dependent humoral response to immunization. GC formation and GC B cells were increased in Prkd2-/- spleens. These effects were the result of excessive cell-autonomous TFH development caused by unrestricted Bcl6 nuclear translocation in Prkd2-/- CD4+ T cells. Prkd2 directly binds to Bcl6, and Prkd2-dependent phosphorylation of Bcl6 is necessary to constrain Bcl6 to the cytoplasm, thereby limiting TFH development. In response to immunization, Bcl6 repressed Prkd2 expression in CD4+ T cells, thereby committing them to TFH development. Thus, Prkd2 and Bcl6 form a mutually inhibitory positive feedback loop that controls the stable transition from naïve CD4+ T cells to TFH during the adaptive immune response.
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Affiliation(s)
- Takuma Misawa
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Jeffrey A SoRelle
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Yue
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - William McAlpine
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aijie Liu
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Koichi Tabeta
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Science, Niigata, Japan
| | - Emre E Turer
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bret Evers
- Division of Neuropathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Subhajit Poddar
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lijing Su
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Feiya Ou
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Liyang Yu
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anne R Murray
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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18
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Choi JH, Zhong X, Zhang Z, Su L, McAlpine W, Misawa T, Liao TC, Zhan X, Russell J, Ludwig S, Li X, Tang M, Anderton P, Moresco EMY, Beutler B. Essential cell-extrinsic requirement for PDIA6 in lymphoid and myeloid development. J Exp Med 2020; 217:133654. [PMID: 31985756 PMCID: PMC7144532 DOI: 10.1084/jem.20190006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/06/2019] [Accepted: 12/20/2019] [Indexed: 01/21/2023] Open
Abstract
In a forward genetic screen of N-ethyl-N-nitrosourea (ENU)–induced mutant mice for aberrant immune function, we identified mice with a syndromic disorder marked by growth retardation, diabetes, premature death, and severe lymphoid and myeloid hypoplasia together with diminished T cell–independent (TI) antibody responses. The causative mutation was in Pdia6, an essential gene encoding protein disulfide isomerase A6 (PDIA6), an oxidoreductase that functions in nascent protein folding in the endoplasmic reticulum. The immune deficiency caused by the Pdia6 mutation was, with the exception of a residual T cell developmental defect, completely rescued in irradiated wild-type recipients of PDIA6-deficient bone marrow cells, both in the absence or presence of competition. The viable hypomorphic allele uncovered in these studies reveals an essential role for PDIA6 in hematopoiesis, but one extrinsic to cells of the hematopoietic lineage. We show evidence that this role is in the proper folding of Wnt3a, BAFF, IL-7, and perhaps other factors produced by the extra-hematopoietic compartment that contribute to the development and lineage commitment of hematopoietic cells.
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Affiliation(s)
- Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Takuma Misawa
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Tzu-Chieh Liao
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
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19
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Choi JH, Zhong X, McAlpine W, Liao TC, Zhang D, Fang B, Russell J, Ludwig S, Nair-Gill E, Zhang Z, Wang KW, Misawa T, Zhan X, Choi M, Wang T, Li X, Tang M, Sun Q, Yu L, Murray AR, Moresco EMY, Beutler B. LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling. Science 2019; 364:364/6440/eaau0812. [PMID: 31073040 DOI: 10.1126/science.aau0812] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 11/06/2018] [Accepted: 03/11/2019] [Indexed: 12/26/2022]
Abstract
Precise control of Wnt signaling is necessary for immune system development. In this study, we detected severely impaired development of all lymphoid lineages in mice, resulting from an N-ethyl-N-nitrosourea-induced mutation in the limb region 1-like gene (Lmbr1l), which encodes a membrane-spanning protein with no previously described function in immunity. The interaction of LMBR1L with glycoprotein 78 (GP78) and ubiquitin-associated domain-containing protein 2 (UBAC2) attenuated Wnt signaling in lymphocytes by preventing the maturation of FZD6 and LRP6 through ubiquitination within the endoplasmic reticulum and by stabilizing "destruction complex" proteins. LMBR1L-deficient T cells exhibited hallmarks of Wnt/β-catenin activation and underwent apoptotic cell death in response to proliferative stimuli. LMBR1L has an essential function during lymphopoiesis and lymphoid activation, acting as a negative regulator of the Wnt/β-catenin pathway.
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Affiliation(s)
- Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tzu-Chieh Liao
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duanwu Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beibei Fang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takuma Misawa
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mihwa Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qihua Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Liyang Yu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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20
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Su L, Wang Y, Wang J, Mifune Y, Morin MD, Jones BT, Moresco EMY, Boger DL, Beutler B, Zhang H. Structural Basis of TLR2/TLR1 Activation by the Synthetic Agonist Diprovocim. J Med Chem 2019; 62:2938-2949. [PMID: 30829478 PMCID: PMC6537610 DOI: 10.1021/acs.jmedchem.8b01583] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Diprovocim is a recently discovered exceptionally potent, synthetic small molecule agonist of TLR2/TLR1 and has shown significant adjuvant activity in anticancer vaccination against murine melanoma. Since Diprovocim bears no structural similarity to the canonical lipopeptide ligands of TLR2/TLR1, we investigated how Diprovocim interacts with TLR2/TLR1 through in vitro biophysical, structural, and computational approaches. We found that Diprovocim induced the formation of TLR2/TLR1 heterodimers as well as TLR2 homodimers in vitro. We determined the crystal structure of Diprovocim in a complex with a TLR2 ectodomain, which revealed, unexpectedly, two Diprovocim molecules bound to the ligand binding pocket formed between two TLR2 ectodomains. Extensive hydrophobic interactions and a hydrogen-bonding network between the protein and Diprovocim molecules are observed within the defined ligand binding pocket and likely underlie the high potency of Diprovocim. Our work shed first light into the activation mechanism of TLR2/TLR1 by a noncanonical agonist. The structural information obtained here may be exploited to manipulate TLR2/TLR1-dependent signaling.
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Affiliation(s)
- Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Yuto Mifune
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Matthew D. Morin
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brian T. Jones
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Hong Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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21
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Morin MD, Wang Y, Jones BT, Mifune Y, Su L, Shi H, Moresco EMY, Zhang H, Beutler B, Boger DL. Diprovocims: A New and Exceptionally Potent Class of Toll-like Receptor Agonists. J Am Chem Soc 2018; 140:14440-14454. [PMID: 30272974 DOI: 10.1021/jacs.8b09223] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A screen conducted with nearly 100000 compounds and a surrogate functional assay for stimulation of an immune response that measured the release of TNF-α from treated human THP-1 myeloid cells differentiated along the macrophage line led to the discovery of the diprovocims. Unique to these efforts and of special interest, the screening leads for this new class of activators of an immune response came from a compound library designed to promote cell-surface receptor dimerization. Subsequent comprehensive structure-activity relationship studies improved the potency 800-fold over that of the screening leads, providing diprovocim-1 and diprovocim-2. The diprovocims act by inducing cell-surface toll-like receptor (TLR)-2 dimerization and activation with TLR1 (TLR1/TLR2 agonist), bear no structural similarity to any known natural or synthetic TLR agonist, and are easy to prepare and synthetically modify, and selected members are active in both human and murine systems. The most potent diprovocim (3, diprovocim-1) elicits full agonist activity at extraordinarily low concentrations (EC50 = 110 pM) in human THP-1 cells, being more potent than the naturally derived TLR1/TLR2 agonist Pam3CSK4 or any other known small molecule TLR agonist.
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Affiliation(s)
- Matthew D Morin
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Ying Wang
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Brian T Jones
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Yuto Mifune
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Lijing Su
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Hexin Shi
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Hong Zhang
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
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22
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McAlpine W, Wang KW, Choi JH, San Miguel M, McAlpine SG, Russell J, Ludwig S, Li X, Tang M, Zhan X, Choi M, Wang T, Bu CH, Murray AR, Moresco EMY, Turer EE, Beutler B. The class I myosin MYO1D binds to lipid and protects against colitis. Dis Model Mech 2018; 11:11/9/dmm035923. [PMID: 30279225 PMCID: PMC6176994 DOI: 10.1242/dmm.035923] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/02/2018] [Indexed: 12/12/2022] Open
Abstract
Myosin ID (MYO1D) is a member of the class I myosin family. We screened 48,649 third generation (G3) germline mutant mice derived from N-ethyl-N-nitrosourea-mutagenized grandsires for intestinal homeostasis abnormalities after oral administration of dextran sodium sulfate (DSS). We found and validated mutations in Myo1d as a cause of increased susceptibility to DSS-induced colitis. MYO1D is produced in the intestinal epithelium, and the colitis phenotype is dependent on the nonhematopoietic compartment of the mouse. Moreover, MYO1D appears to couple cytoskeletal elements to lipid in an ATP-dependent manner. These findings demonstrate that MYO1D is needed to maintain epithelial integrity and protect against DSS-induced colitis. Summary: Using random germline mutagenesis and screening of mice, we determined that loss of MYO1D function in nonhematopoietic tissues renders mice susceptible to colitis induced by dextran sodium sulfate challenge.
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Affiliation(s)
- William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Miguel San Miguel
- Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505 USA
| | - Sarah Grace McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Mihwa Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Tao Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA.,Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
| | - Emre E Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505 USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505, USA
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23
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Wang T, Bu CH, Hildebrand S, Jia G, Siggs OM, Lyon S, Pratt D, Scott L, Russell J, Ludwig S, Murray AR, Moresco EMY, Beutler B. Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database. Nat Commun 2018; 9:441. [PMID: 29382827 PMCID: PMC5789985 DOI: 10.1038/s41467-017-02806-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022] Open
Abstract
Computational inference of mutation effects is necessary for genetic studies in which many mutations must be considered as etiologic candidates. Programs such as PolyPhen-2 predict the relative severity of damage caused by missense mutations, but not the actual probability that a mutation will reduce/eliminate protein function. Based on genotype and phenotype data for 116,330 ENU-induced mutations in the Mutagenetix database, we calculate that putative null mutations, and PolyPhen-2-classified “probably damaging”, “possibly damaging”, or “probably benign” mutations have, respectively, 61%, 17%, 9.8%, and 4.5% probabilities of causing phenotypically detectable damage in the homozygous state. We use these probabilities in the estimation of genome saturation and the probability that individual proteins have been adequately tested for function in specific genetic screens. We estimate the proportion of essential autosomal genes in Mus musculus (C57BL/6J) and show that viable mutations in essential genes are more likely to induce phenotype than mutations in non-essential genes. Programs such as PolyPhen-2 predict the relative severity of damage by missense mutations. Here, Wang et al estimate probabilities that putative null or missense alleles would reduce protein function to cause detectable phenotype by analyzing data from ENU-induced mouse mutations.
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Affiliation(s)
- Tao Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gaoxiang Jia
- Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Department of Statistical Science, Southern Methodist University, Dallas, TX, 75205, USA
| | - Owen M Siggs
- Immunology Division, Garvan Institute for Medical Research, Sydney, NSW, 2010, Australia
| | - Stephen Lyon
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - David Pratt
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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24
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Sun L, Jiang Z, Acosta-Rodriguez VA, Berger M, Du X, Choi JH, Wang J, Wang KW, Kilaru GK, Mohawk JA, Quan J, Scott L, Hildebrand S, Li X, Tang M, Zhan X, Murray AR, La Vine D, Moresco EMY, Takahashi JS, Beutler B. HCFC2 is needed for IRF1- and IRF2-dependent Tlr3 transcription and for survival during viral infections. J Exp Med 2017; 214:3263-3277. [PMID: 28970238 PMCID: PMC5679162 DOI: 10.1084/jem.20161630] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 07/13/2017] [Accepted: 08/16/2017] [Indexed: 01/08/2023] Open
Abstract
Sun et al. show that host cell factor C2 (HCFC2) is necessary for basal and induced Tlr3 transcription; deficiency of HCFC2 compromises survival during influenza virus and herpes simplex virus 1 infections in mice. Transcriptional regulation of numerous interferon-regulated genes, including Toll-like receptor 3 (Tlr3), which encodes an innate immune sensor of viral double-stranded RNA, depends on the interferon regulatory factor 1 (IRF1) and IRF2 transcription factors. We detected specific abrogation of macrophage responses to polyinosinic-polycytidylic acid (poly(I:C)) resulting from three independent N-ethyl-N-nitrosourea–induced mutations in host cell factor C2 (Hcfc2). Hcfc2 mutations compromised survival during influenza virus and herpes simplex virus 1 infections. HCFC2 promoted the binding of IRF1 and IRF2 to the Tlr3 promoter, without which inflammatory cytokine and type I IFN responses to the double-stranded RNA analogue poly(I:C) are reduced in mouse macrophages. HCFC2 was also necessary for the transcription of a large subset of other IRF2-dependent interferon-regulated genes. Deleterious mutations of Hcfc2 may therefore increase susceptibility to diverse infectious diseases.
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Affiliation(s)
- Lei Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Zhengfan Jiang
- Department of Genetics, The Scripps Research Institute, La Jolla, CA
| | - Victoria A Acosta-Rodriguez
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Michael Berger
- Department of Genetics, The Scripps Research Institute, La Jolla, CA
| | - Xin Du
- Department of Genetics, The Scripps Research Institute, La Jolla, CA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Gokhul K Kilaru
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jennifer A Mohawk
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Diantha La Vine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
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25
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WANG YING, Su L, Morin M, Jones B, Whitby L, Surakattula M, Huang H, Shi H, Choi JH, Wang KW, Moresco EMY, Berger M, Zhan X, Zhan H, Boger D, Beutler B. Identification of novel and potent synthetic TLR agonists. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.129.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Agonists and antagonists of Toll-like receptors (TLRs) may be useful as vaccine adjuvants or suppressors of inflammation, respectively. In an effort to identify compounds capable of activating macrophages via TLRs or other sensors, a synthetic compound library was screened using mouse peritoneal macrophages and human THP-1 cells. Through extensive SAR studies of initial hits, we developed two strong synthetic agonists: Neoseptin-3 and Diprovocim. Genetic studies established that neoseptin-3 is a mouse TLR4/MD-2 agonist with no structural similarity to LPS. It activates mTLR4/MD-2 independently of CD14 and triggers canonical MyD88- and TRIF-dependent signaling. Diprovocim was found by a combination of genetic and antibody blockade analyses to be a TLR1/2 agonist, active on both mouse and human receptors. Its EC50 in human THP-1 cells is 110 pM. Diprovocim showed TLR1/2 dependent adjuvant activity when co-administered with ovalbumin (OVA). It not only promoted antigen-specific humoral responses but also activated cytotoxic T lymphocyte responses in a TLR1/2 dependent manner. Since neither Neoseptin-3 nor Diprovocim resemble the natural ligands for TLR4/MD-2 nor TLR1/2, respectively, we surmise that other “unconventional” ligands for these TLRs may exist in nature. However, the exquisite SAR of both compounds makes it clear that TLRs are not highly promiscuous receptors; on the contrary, they are activated only by compounds that fulfill strict structural rules. In finding these agonists, we also identified antagonists that bind the TLR complexes but do not activate them. The parent compounds Neoseptin-3 and Diprovocim will be used to develop new agonists and antagonists optimized for clinical application.
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Affiliation(s)
- YING WANG
- 1Univ. of Texas Southwestern Med. Ctr
| | - Lijing Su
- 1Univ. of Texas Southwestern Med. Ctr
| | | | | | | | | | | | - Hexin Shi
- 1Univ. of Texas Southwestern Med. Ctr
| | | | | | | | | | | | - Hong Zhan
- 1Univ. of Texas Southwestern Med. Ctr
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26
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Su L, WANG YING, Morin MD, Jones BT, Whitby LR, Surakattula MM, Huang H, Shi H, Choi JH, Wang KW, Moresco EMY, Berger M, Zhan X, Beutler B, Boger D, Zhang H. Structural characterization of TLRs with novel agonists. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.129.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Small molecule TLR4 and TLR2 agonists have been reported, but no structural data reveals their activation mechanism and detailed interactions with the TLRs. We have developed two small molecule agonists, Neoseptin-3 and Diprovocim, that activate TLR4/MD-2 and TLR1/TLR2 complexes, respectively, with exquisitely specific structure activity relationships. These two molecules bear no structural similarity to the natural ligands, lipopolysaccharide (LPS) and tri-acylated lipopeptide (Pam3CSK4). The crystal structures of Neoseptin-3 in complex with mouse TLR4/MD-2 and Diprovocim in complex with human TLR2 provide the first glimpse of how these TLRs bind to unconventional agonists, revealing unique and unexpected binding modes. Neoseptin-3 binds as an asymmetrical dimer within the hydrophobic pocket of MD-2, and induces an active receptor complex (a dimer of TLR4/MD-2) similar to that induced by lipid A. However, Neoseptin-3 and lipid A form different molecular contacts with TLR4/MD-2 to achieve receptor activation. Diprovocim forms a symmetrical dimer and interacts with the same hydrophobic pocket of TLR2 as Pam3CSK4, inducing homodimerization of TLR2 that has a different conformation than the active TLR1/TLR2 heterodimer. Diprovocim binds to TLR2 through an extensive intermolecular hydrogen bonding network that is not observed in the Pam3CSK4/TLR2/TLR1 structure. These two structures are now guiding us in optimization of TLR4/MD-2 and TLR1/TLR2 agonists and antagonists for clinical applications.
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Affiliation(s)
- Lijing Su
- 1Univ. of Texas Southwestern Med. Ctr
| | - YING WANG
- 1Univ. of Texas Southwestern Med. Ctr
| | | | | | | | | | | | - Hexin Shi
- 1Univ. of Texas Southwestern Med. Ctr
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27
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Shi H, Wang Y, Li X, Zhan X, Tang M, Fina M, Su L, Pratt D, Bu CH, Hildebrand S, Lyon S, Scott L, Quan J, Sun Q, Russell J, Arnett S, Jurek P, Chen D, Kravchenko VV, Mathison JC, Moresco EMY, Monson NL, Ulevitch RJ, Beutler B. NLRP3 activation and mitosis are mutually exclusive events coordinated by NEK7, a new inflammasome component. Nat Immunol 2015; 17:250-8. [PMID: 26642356 PMCID: PMC4862588 DOI: 10.1038/ni.3333] [Citation(s) in RCA: 489] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]
Abstract
The NLRP3 inflammasome responds to microbes and danger signals by processing and activating proinflammatory cytokines, including interleukin 1β (IL-1β) and IL-18. We found here that activation of the NLRP3 inflammasome was restricted to interphase of the cell cycle by NEK7, a serine-threonine kinase previously linked to mitosis. Activation of the NLRP3 inflammasome required NEK7, which bound to the leucine-rich repeat domain of NLRP3 in a kinase-independent manner downstream of the induction of mitochondrial reactive oxygen species (ROS). This interaction was necessary for the formation of a complex containing NLRP3 and the adaptor ASC, oligomerization of ASC and activation of caspase-1. NEK7 promoted the NLRP3-dependent cellular inflammatory response to intraperitoneal challenge with monosodium urate and the development of experimental autoimmune encephalitis in mice. Our findings suggest that NEK7 serves as a cellular switch that enforces mutual exclusivity of the inflammasome response and cell division.
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Affiliation(s)
- Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Maggy Fina
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lijing Su
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David Pratt
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Stephen Lyon
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qihua Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Stephanie Arnett
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Peter Jurek
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ding Chen
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Vladimir V Kravchenko
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, USA
| | - John C Mathison
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Nancy L Monson
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Richard J Ulevitch
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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28
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Simon MM, Moresco EMY, Bull KR, Kumar S, Mallon AM, Beutler B, Potter PK. Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome 2015; 26:486-500. [PMID: 26449678 PMCID: PMC4602060 DOI: 10.1007/s00335-015-9603-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to ‘finding a needle in a haystack’. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation.
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Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Saumya Kumar
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Paul K Potter
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
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29
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Zeng M, Hu Z, Shi X, Li X, Zhan X, Li XD, Wang J, Choi JH, Wang KW, Purrington T, Tang M, Fina M, DeBerardinis RJ, Moresco EMY, Pedersen G, McInerney GM, Karlsson Hedestam GB, Chen ZJ, Beutler B. MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses. Science 2015; 346:1486-92. [PMID: 25525240 DOI: 10.1126/science.346.6216.1486] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multivalent molecules with repetitive structures including bacterial capsular polysaccharides and viral capsids elicit antibody responses through B cell receptor (BCR) crosslinking in the absence of T cell help. We report that immunization with these T cell-independent type 2 (TI-2) antigens causes up-regulation of endogenous retrovirus (ERV) RNAs in antigen-specific mouse B cells. These RNAs are detected via a mitochondrial antiviral signaling protein (MAVS)-dependent RNA sensing pathway or reverse-transcribed and detected via the cGAS-cGAMP-STING pathway, triggering a second, sustained wave of signaling that promotes specific immunoglobulin M production. Deficiency of both MAVS and cGAS, or treatment of MAVS-deficient mice with reverse transcriptase inhibitors, dramatically inhibits TI-2 antibody responses. These findings suggest that ERV and two innate sensing pathways that detect them are integral components of the TI-2 B cell signaling apparatus.
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Affiliation(s)
- Ming Zeng
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Zeping Hu
- Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiaolei Shi
- Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Xiao-Dong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Kuan-wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Tiana Purrington
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Maggy Fina
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Ralph J DeBerardinis
- Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA
| | - Gabriel Pedersen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77 Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77 Stockholm, Sweden
| | - Gunilla B Karlsson Hedestam
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, SE-171 77 Stockholm, Sweden
| | - Zhijian J Chen
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA.
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Moresco EMY, Li X, Beutler B. Going forward with genetics: recent technological advances and forward genetics in mice. Am J Pathol 2014; 182:1462-73. [PMID: 23608223 DOI: 10.1016/j.ajpath.2013.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/05/2013] [Indexed: 12/24/2022]
Abstract
Forward genetic analysis is an unbiased approach for identifying genes essential to defined biological phenomena. When applied to mice, it is one of the most powerful methods to facilitate understanding of the genetic basis of human biology and disease. The speed at which disease-causing mutations can be identified in mutagenized mice has been markedly increased by recent advances in DNA sequencing technology. Creating and analyzing mutant phenotypes may therefore become rate-limiting in forward genetic experimentation. We review the forward genetic approach and its future in the context of recent technological advances, in particular massively parallel DNA sequencing, induced pluripotent stem cells, and haploid embryonic stem cells.
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Affiliation(s)
- Eva Marie Y Moresco
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75235-8505, USA
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Moresco EMY, Brandl K. Linking membrane trafficking and intestinal homeostasis. Tissue Barriers 2014; 1:e23119. [PMID: 24665373 PMCID: PMC3875636 DOI: 10.4161/tisb.23119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/02/2012] [Accepted: 12/04/2012] [Indexed: 01/05/2023] Open
Abstract
A major challenge for the human body is to maintain symbiotic relationships with bacterial communities that colonize their intestines. Although several molecules important for intestinal homeostasis have been discovered, the vast array still needs to be identified. We approached this task using a forward genetic approach, which revealed several molecules essential for intestinal homeostasis. One recently identified molecule is Ypt1p-interacting protein 1 domain family, member 6 (Yipf6). Mice with a null mutation in Yipf6 are hypersensitive to dextran sulfate sodium (DSS) induced colitis and develop spontaneous intestinal inflammation. Members of the Yip1 family are believed to be involved in ER to Golgi membrane transport.
In this review we summarize recent advances in the understanding of genes involved in intestinal homeostasis with a specific focus on the Yip family members. We speculate on how deficiency or dysfunction of Yip molecules may dysregulate intestinal homeostasis leading to pathogenic states.
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Affiliation(s)
- Eva Marie Y Moresco
- Center for Genetics of Host Defense; UT Southwestern Medical Center; Dallas, TX USA
| | - Katharina Brandl
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA USA
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Arnold CN, Barnes MJ, Berger M, Blasius AL, Brandl K, Croker B, Crozat K, Du X, Eidenschenk C, Georgel P, Hoebe K, Huang H, Jiang Z, Krebs P, La Vine D, Li X, Lyon S, Moresco EMY, Murray AR, Popkin DL, Rutschmann S, Siggs OM, Smart NG, Sun L, Tabeta K, Webster V, Tomisato W, Won S, Xia Y, Xiao N, Beutler B. ENU-induced phenovariance in mice: inferences from 587 mutations. BMC Res Notes 2012; 5:577. [PMID: 23095377 PMCID: PMC3532239 DOI: 10.1186/1756-0500-5-577] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022] Open
Abstract
Background We present a compendium of N-ethyl-N-nitrosourea (ENU)-induced mouse mutations, identified in our laboratory over a period of 10 years either on the basis of phenotype or whole genome and/or whole exome sequencing, and archived in the Mutagenetix database. Our purpose is threefold: 1) to formally describe many point mutations, including those that were not previously disclosed in peer-reviewed publications; 2) to assess the characteristics of these mutations; and 3) to estimate the likelihood that a missense mutation induced by ENU will create a detectable phenotype. Findings In the context of an ENU mutagenesis program for C57BL/6J mice, a total of 185 phenotypes were tracked to mutations in 129 genes. In addition, 402 incidental mutations were identified and predicted to affect 390 genes. As previously reported, ENU shows strand asymmetry in its induction of mutations, particularly favoring T to A rather than A to T in the sense strand of coding regions and splice junctions. Some amino acid substitutions are far more likely to be damaging than others, and some are far more likely to be observed. Indeed, from among a total of 494 non-synonymous coding mutations, ENU was observed to create only 114 of the 182 possible amino acid substitutions that single base changes can achieve. Based on differences in overt null allele frequencies observed in phenotypic vs. non-phenotypic mutation sets, we infer that ENU-induced missense mutations create detectable phenotype only about 1 in 4.7 times. While the remaining mutations may not be functionally neutral, they are, on average, beneath the limits of detection of the phenotypic assays we applied. Conclusions Collectively, these mutations add to our understanding of the chemical specificity of ENU, the types of amino acid substitutions it creates, and its efficiency in causing phenovariance. Our data support the validity of computational algorithms for the prediction of damage caused by amino acid substitutions, and may lead to refined predictions as to whether specific amino acid changes are responsible for observed phenotypes. These data form the basis for closer in silico estimations of the number of genes mutated to a state of phenovariance by ENU within a population of G3 mice.
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Affiliation(s)
- Carrie N Arnold
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
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Affiliation(s)
- Eva Marie Y Moresco
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
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Affiliation(s)
- Eva Marie Y Moresco
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Diantha La Vine
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce Beutler
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
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Moresco EMY, Beutler B. Resisting viral infection: the gene by gene approach. Curr Opin Virol 2011; 1:513-8. [PMID: 22440911 DOI: 10.1016/j.coviro.2011.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 01/18/2023]
Abstract
This review focuses on genes required for resistance to mouse cytomegalovirus (MCMV), as identified through unbiased genetic screening. Components of the developmental, sensing, and effector pathways, functioning in multiple cell types, were detected by infecting 22,000 G3 mutant mice with MCMV at an inoculum easily contained by WT animals. Merging these findings with discoveries from hypothesis-based studies, we present a cohesive picture of the essential elements utilized by the mouse innate immune system to counter MCMV. We believe that many breakthrough discoveries will yet be made using a classical genetic approach.
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Affiliation(s)
- Eva Marie Y Moresco
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
Foreign DNA activates the innate immune response through Toll-like receptor 9 (TLR9). In this issue of Immunity, Park et al. (2011) present evidence that granulin is a cofactor for TLR9 activation, delivering CpG-oligodeoxynucleotides to TLR9 in endolysosomes.
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Affiliation(s)
- Eva Marie Y Moresco
- Department of Genetics, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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Du X, She E, Gelbart T, Truksa J, Lee P, Xia Y, Khovananth K, Mudd S, Mann N, Moresco EMY, Beutler E, Beutler B. The serine protease TMPRSS6 is required to sense iron deficiency. Science 2008; 320:1088-92. [PMID: 18451267 DOI: 10.1126/science.1157121] [Citation(s) in RCA: 427] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepcidin, a liver-derived protein that restricts enteric iron absorption, is the key regulator of body iron content. Several proteins induce expression of the hepcidin-encoding gene Hamp in response to infection or high levels of iron. However, mechanism(s) of Hamp suppression during iron depletion are poorly understood. We describe mask: a recessive, chemically induced mutant mouse phenotype, characterized by progressive loss of body (but not facial) hair and microcytic anemia. The mask phenotype results from reduced absorption of dietary iron caused by high levels of hepcidin and is due to a splicing defect in the transmembrane serine protease 6 gene Tmprss6. Overexpression of normal TMPRSS6 protein suppresses activation of the Hamp promoter, and the TMPRSS6 cytoplasmic domain mediates Hamp suppression via proximal promoter element(s). TMPRSS6 is an essential component of a pathway that detects iron deficiency and blocks Hamp transcription, permitting enhanced dietary iron absorption.
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Affiliation(s)
- Xin Du
- Department of Genetics, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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