1
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Zhong X, Moresco JJ, SoRelle JA, Song R, Jiang Y, Nguyen MT, Wang J, Bu CH, Moresco EMY, Beutler B, Choi JH. Disruption of the ZFP574-THAP12 complex suppresses B cell malignancies in mice. Proc Natl Acad Sci U S A 2024; 121:e2409232121. [PMID: 39047044 DOI: 10.1073/pnas.2409232121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Despite the availability of life-extending treatments for B cell leukemias and lymphomas, many of these cancers remain incurable. Thus, the development of new molecular targets and therapeutics is needed to expand treatment options. To identify new molecular targets, we used a forward genetic screen in mice to identify genes required for development or survival of lymphocytes. Here, we describe Zfp574, an essential gene encoding a zinc finger protein necessary for normal and malignant lymphocyte survival. We show that ZFP574 interacts with zinc finger protein THAP12 and promotes the G1-to-S-phase transition during cell cycle progression. Mutation of ZFP574 impairs nuclear localization of the ZFP574-THAP12 complex. ZFP574 or THAP12 deficiency results in cell cycle arrest and impaired lymphoproliferation. Germline mutation, acute gene deletion, or targeted degradation of ZFP574 suppressed Myc-driven B cell leukemia in mice, but normal B cells were largely spared, permitting long-term survival, whereas complete lethality was observed in control animals. Our findings support the identification of drugs targeting ZFP574-THAP12 as a unique strategy to treat B cell malignancies.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - James J Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jeffrey A SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ran Song
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mylinh T Nguyen
- Department of Biochemistry, 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
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, 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
| | - 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
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2
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Russell J, Chen L, Liu A, Wang J, Ghosh S, Zhong X, Shi H, Beutler B, Nair-Gill E. Lrp10 suppresses IL7R limiting CD8 T cell homeostatic expansion and anti-tumor immunity. EMBO Rep 2024:10.1038/s44319-024-00191-w. [PMID: 38956225 DOI: 10.1038/s44319-024-00191-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Signals emanating from the T-cell receptor (TCR), co-stimulatory receptors, and cytokine receptors each influence CD8 T-cell fate. Understanding how these signals respond to homeostatic and microenvironmental cues can reveal new ways to therapeutically direct T-cell function. Through forward genetic screening in mice, we discover that loss-of-function mutations in LDL receptor-related protein 10 (Lrp10) cause naive and central memory CD8 T cells to accumulate in peripheral lymphoid organs. Lrp10 encodes a conserved cell surface protein of unknown immunological function. T-cell activation induces Lrp10 expression, which post-translationally suppresses IL7 receptor (IL7R) levels. Accordingly, Lrp10 deletion enhances T-cell homeostatic expansion through IL7R signaling. Lrp10-deficient mice are also intrinsically resistant to syngeneic tumors. This phenotype depends on dense tumor infiltration of CD8 T cells, which display increased memory cell characteristics, reduced terminal exhaustion, and augmented responses to immune checkpoint inhibition. Here, we present Lrp10 as a new negative regulator of CD8 T-cell homeostasis and a host factor that controls tumor resistance with implications for immunotherapy.
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Affiliation(s)
- Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Luming Chen
- Medical Scientist Training Program, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Aijie Liu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Subarna Ghosh
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Hexin Shi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA
| | - Evan Nair-Gill
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA.
- Department of Internal Medicine, Division of Rheumatic Diseases, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-8505, USA.
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3
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Rong R, Denton K, Jin KW, Quan P, Wen Z, Kozlitina J, Lyon S, Wang A, Wise CA, Beutler B, Yang DM, Li Q, Rios JJ, Xiao G. Deep Learning-Based Automated Measurement of Murine Bone Length in Radiographs. Bioengineering (Basel) 2024; 11:670. [PMID: 39061752 PMCID: PMC11273961 DOI: 10.3390/bioengineering11070670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Genetic mouse models of skeletal abnormalities have demonstrated promise in the identification of phenotypes relevant to human skeletal diseases. Traditionally, phenotypes are assessed by manually examining radiographs, a tedious and potentially error-prone process. In response, this study developed a deep learning-based model that streamlines the measurement of murine bone lengths from radiographs in an accurate and reproducible manner. A bone detection and measurement pipeline utilizing the Keypoint R-CNN algorithm with an EfficientNet-B3 feature extraction backbone was developed to detect murine bone positions and measure their lengths. The pipeline was developed utilizing 94 X-ray images with expert annotations on the start and end position of each murine bone. The accuracy of our pipeline was evaluated on an independent dataset test with 592 images, and further validated on a previously published dataset of 21,300 mouse radiographs. The results showed that our model performed comparably to humans in measuring tibia and femur lengths (R2 > 0.92, p-value = 0) and significantly outperformed humans in measuring pelvic lengths in terms of precision and consistency. Furthermore, the model improved the precision and consistency of genetic association mapping results, identifying significant associations between genetic mutations and skeletal phenotypes with reduced variability. This study demonstrates the feasibility and efficiency of automated murine bone length measurement in the identification of mouse models of abnormal skeletal phenotypes.
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Affiliation(s)
- Ruichen Rong
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
| | - Kristin Denton
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; (K.D.); (C.A.W.)
| | - Kevin W. Jin
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
| | - Peiran Quan
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
| | - Zhuoyu Wen
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
| | - Julia Kozlitina
- McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Stephen Lyon
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (S.L.); (B.B.)
| | - Aileen Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; (K.D.); (C.A.W.)
- McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Department of Orthopaedic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (S.L.); (B.B.)
| | - Donghan M. Yang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
| | - Qiwei Li
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX 75083, USA;
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; (K.D.); (C.A.W.)
- McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Department of Orthopaedic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (R.R.); (K.W.J.); (P.Q.); (Z.W.); (A.W.); (D.M.Y.)
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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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] [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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5
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Jakkamsetti V, Ma Q, Angulo G, Scudder W, Beutler B, Pascual JM. Genetic influences on motor learning and performance and superperforming mutants revealed by random mutational survey of the mouse genome. J Physiol 2024; 602:2649-2664. [PMID: 38299894 PMCID: PMC11142877 DOI: 10.1113/jp285505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. In total, 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1408 normal mice for reference. In total, 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least three mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well-characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included, preferentially, histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the remaining mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behaviour influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease. KEY POINTS: We studied the effect of chemically induced random mutations on mouse motor performance. An array of mutations influenced the rate of motor learning. DNA regulation genes predominated among these mutant loci. Several mutations in unsuspected genes led to superperformance. Assuming little-biased mutagenicity, the results allow for an estimation of the probability for any spontaneous mutation to influence a behaviour such as motor learning and ultimate performance.
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Affiliation(s)
- Vikram Jakkamsetti
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Ma
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gustavo Angulo
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Scudder
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan M. Pascual
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth & Development / Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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6
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Teixeira SK, Pontes R, Zuleta LFG, Wang J, Xu D, Hildebrand S, Russell J, Zhan X, Choi M, Tang M, Li X, Ludwig S, Beutler B, Krieger JE. Genetic determinants of blood pressure and heart rate identified through ENU-induced mutagenesis with automated meiotic mapping. SCIENCE ADVANCES 2024; 10:eadj9797. [PMID: 38427739 PMCID: PMC10906923 DOI: 10.1126/sciadv.adj9797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
We used N-ethyl-N-nitrosurea-induced germline mutagenesis combined with automated meiotic mapping to identify specific systolic blood pressure (SBP) and heart rate (HR) determinant loci. We analyzed 43,627 third-generation (G3) mice from 841 pedigrees to assess the effects of 45,378 variant alleles within 15,760 genes, in both heterozygous and homozygous states. We comprehensively tested 23% of all protein-encoding autosomal genes and found 87 SBP and 144 HR (with 7 affecting both) candidates exhibiting detectable hypomorphic characteristics. Unexpectedly, only 18 of the 87 SBP genes were previously known, while 26 of the 144 genes linked to HR were previously identified. Furthermore, we confirmed the influence of two genes on SBP regulation and three genes on HR control through reverse genetics. This underscores the importance of our research in uncovering genes associated with these critical cardiovascular risk factors and illustrate the effectiveness of germline mutagenesis for defining key determinants of polygenic phenotypes that must be studied in an intact organism.
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Affiliation(s)
- Samantha K. Teixeira
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Roberto Pontes
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Fernando G. Zuleta
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jianhui Wang
- 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
| | - 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
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, 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
| | - Xiaohong Li
- 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
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jose E. Krieger
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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7
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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] [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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8
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Russell J, Chen L, Liu A, Wang J, Ghosh S, Zhong X, Shi H, Beutler B, Nair-Gill E. Lrp10 suppresses IL7R limiting CD8 T cell homeostatic expansion and anti-tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570738. [PMID: 38106103 PMCID: PMC10723380 DOI: 10.1101/2023.12.08.570738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Signals emanating from the T cell receptor (TCR), co-stimulatory receptors, and cytokine receptors each influence CD8 T cell fate. Understanding how these signals respond to homeostatic and microenvironmental cues can reveal new ways to therapeutically direct T cell function. Through forward genetic screening in mice, we discovered that loss-of-function mutations in LDL receptor related protein 10 ( Lrp10 ) caused naïve and central memory CD8 T cells to accumulate in peripheral lymphoid organs. Lrp10 encodes a conserved cell surface protein of unknown immunological function. Lrp10 was induced with T cell activation and its expression post-translationally suppressed IL7 receptor (IL7R) levels. Accordingly, Lrp10 deletion enhanced T cell homeostatic expansion through IL7R signaling. Lrp10 -deficient mice were also intrinsically resistant to syngeneic tumors. This phenotype depended on dense tumor infiltration of CD8 T cells that displayed increased memory cell characteristics, reduced terminal exhaustion, and augmented responses to immune checkpoint inhibition. Here, we present Lrp10 as a new negative regulator of CD8 T cell homeostasis and a host factor that controls tumor resistance with implications for immunotherapy.
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9
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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] [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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10
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Jakkamsetti V, Ma Q, Angulo G, Scudder W, Beutler B, Pascual JM. Genetic influences on motor learning and superperformance mutants revealed by random mutational survey of mouse locomotion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546756. [PMID: 37425744 PMCID: PMC10327015 DOI: 10.1101/2023.06.28.546756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1,408 normal mice for reference. 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least 3 mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included preferentially histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the rest of mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behavior influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease.
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Affiliation(s)
- Vikram Jakkamsetti
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Ma
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gustavo Angulo
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Scudder
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan M. Pascual
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth & Development / Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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11
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Yuksel S, Aredo B, Zegeye Y, Zhao CX, Tang M, Li X, Hulleman JD, Gautron L, Ludwig S, Moresco EMY, Butovich IA, Beutler BA, Ufret-Vincenty RL. Forward genetic screening using fundus spot scale identifies an essential role for Lipe in murine retinal homeostasis. Commun Biol 2023; 6:533. [PMID: 37198396 DOI: 10.1038/s42003-023-04870-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Microglia play a role in the pathogenesis of many retinal diseases. Fundus spots in mice often correlate with the accumulation of activated subretinal microglia. Here we use a semiquantitative fundus spot scoring scale in combination with an unbiased, state-of-the-science forward genetics pipeline to identify causative associations between chemically induced mutations and fundus spot phenotypes. Among several associations, we focus on a missense mutation in Lipe linked to an increase in yellow fundus spots in C57BL/6J mice. Lipe-/- mice generated using CRISPR-Cas9 technology are found to develop accumulation of subretinal microglia, a retinal degeneration with decreased visual function, and an abnormal retinal lipid profile. We establish an indispensable role of Lipe in retinal/RPE lipid homeostasis and retinal health. Further studies using this new model will be aimed at determining how lipid dysregulation results in the activation of subretinal microglia and whether these microglia also play a role in the subsequent retinal degeneration.
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Affiliation(s)
- Seher Yuksel
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bogale Aredo
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yeshumenesh Zegeye
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Cynthia X Zhao
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, 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
| | - John D Hulleman
- 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, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eva M Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Igor A Butovich
- Department of Ophthalmology, UT 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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