1
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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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2
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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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3
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Hauser BM, Luo Y, Nathan A, Al-Moujahed A, Vavvas DG, Comander J, Pierce EA, Place EM, Bujakowska KM, Gaiha GD, Rossin EJ. Structure-based network analysis predicts pathogenic variants in human proteins associated with inherited retinal disease. NPJ Genom Med 2024; 9:31. [PMID: 38802398 PMCID: PMC11130145 DOI: 10.1038/s41525-024-00416-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: 11/15/2023] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
Advances in gene sequencing technologies have accelerated the identification of genetic variants, but better tools are needed to understand which are causal of disease. This would be particularly useful in fields where gene therapy is a potential therapeutic modality for a disease-causing variant such as inherited retinal disease (IRD). Here, we apply structure-based network analysis (SBNA), which has been successfully utilized to identify variant-constrained amino acid residues in viral proteins, to identify residues that may cause IRD if subject to missense mutation. SBNA is based entirely on structural first principles and is not fit to specific outcome data, which makes it distinct from other contemporary missense prediction tools. In 4 well-studied human disease-associated proteins (BRCA1, HRAS, PTEN, and ERK2) with high-quality structural data, we find that SBNA scores correlate strongly with deep mutagenesis data. When applied to 47 IRD genes with available high-quality crystal structure data, SBNA scores reliably identified disease-causing variants according to phenotype definitions from the ClinVar database. Finally, we applied this approach to 63 patients at Massachusetts Eye and Ear (MEE) with IRD but for whom no genetic cause had been identified. Untrained models built using SBNA scores and BLOSUM62 scores for IRD-associated genes successfully predicted the pathogenicity of novel variants (AUC = 0.851), allowing us to identify likely causative disease variants in 40 IRD patients. Model performance was further augmented by incorporating orthogonal data from EVE scores (AUC = 0.927), which are based on evolutionary multiple sequence alignments. In conclusion, SBNA can used to successfully identify variants as causal of disease in human proteins and may help predict variants causative of IRD in an unbiased fashion.
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Affiliation(s)
| | - Yuyang Luo
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Anusha Nathan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Ahmad Al-Moujahed
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Demetrios G Vavvas
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Jason Comander
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Eric A Pierce
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Emily M Place
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Kinga M Bujakowska
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Gaurav D Gaiha
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth J Rossin
- Harvard Medical School, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
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4
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Bakhshalizadeh S, Bird AD, Sreenivasan R, Bell KM, Robevska G, van den Bergen J, Asghari-Jafarabadi M, Kueh AJ, Touraine P, Lokchine A, Jaillard S, Ayers KL, Wilhelm D, Sinclair AH, Tucker EJ. A Human Homozygous HELQ Missense Variant Does Not Cause Premature Ovarian Insufficiency in a Mouse Model. Genes (Basel) 2024; 15:333. [PMID: 38540391 PMCID: PMC10970702 DOI: 10.3390/genes15030333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 04/02/2024] Open
Abstract
Disruption of meiosis and DNA repair genes is associated with female fertility disorders like premature ovarian insufficiency (POI). In this study, we identified a homozygous missense variant in the HELQ gene (c.596 A>C; p.Gln199Pro) through whole exome sequencing in a POI patient, a condition associated with disrupted ovarian function and female infertility. HELQ, an enzyme involved in DNA repair, plays a crucial role in repairing DNA cross-links and has been linked to germ cell maintenance, fertility, and tumour suppression in mice. To explore the potential association of the HELQ variant with POI, we used CRISPR/Cas9 to create a knock-in mouse model harbouring the equivalent of the human HELQ variant identified in the POI patient. Surprisingly, Helq knock-in mice showed no discernible phenotype, with fertility levels, histological features, and follicle development similar to wild-type mice. Despite the lack of observable effects in mice, the potential role of HELQ in human fertility, especially in the context of POI, should not be dismissed. Larger studies encompassing diverse ethnic populations and alternative functional approaches will be necessary to further examine the role of HELQ in POI. Our results underscore the potential uncertainties associated with genomic variants and the limitations of in vivo animal modelling.
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Affiliation(s)
- Shabnam Bakhshalizadeh
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anthony D. Bird
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; (A.D.B.); (D.W.)
- Hudson Institute of Medical Research, Monash Medical Centre, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Rajini Sreenivasan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Katrina M. Bell
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Gorjana Robevska
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Jocelyn van den Bergen
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Mohammad Asghari-Jafarabadi
- Biostatistics Unit, School of Public Health and Preventative Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3004, Australia;
- Department of Psychiatry, School of Clinical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Andrew J. Kueh
- The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Philippe Touraine
- Department of Endocrinology and Reproductive Medicine, Pitie Salpetriere Hospital, AP-HP, Sorbonne University Medicine, 75013 Paris, France;
| | - Anna Lokchine
- IRSET (Institut de Recherche en Santé, Environnement et Travail), INSERM/EHESP/Univ Rennes/CHU Rennes–UMR_S 1085, 35000 Rennes, France; (A.L.); (S.J.)
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, 35033 Rennes, France
| | - Sylvie Jaillard
- IRSET (Institut de Recherche en Santé, Environnement et Travail), INSERM/EHESP/Univ Rennes/CHU Rennes–UMR_S 1085, 35000 Rennes, France; (A.L.); (S.J.)
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, 35033 Rennes, France
| | - Katie L. Ayers
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Dagmar Wilhelm
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; (A.D.B.); (D.W.)
| | - Andrew H. Sinclair
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Elena J. Tucker
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
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5
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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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6
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Hauser BM, Luo Y, Nathan A, Gaiha GD, Vavvas D, Comander J, Pierce EA, Place EM, Bujakowska KM, Rossin EJ. Structure-based network analysis predicts mutations associated with inherited retinal disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.05.23292247. [PMID: 37461650 PMCID: PMC10350150 DOI: 10.1101/2023.07.05.23292247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
With continued advances in gene sequencing technologies comes the need to develop better tools to understand which mutations cause disease. Here we validate structure-based network analysis (SBNA)1,2 in well-studied human proteins and report results of using SBNA to identify critical amino acids that may cause retinal disease if subject to missense mutation. We computed SBNA scores for genes with high-quality structural data, starting with validating the method using 4 well-studied human disease-associated proteins. We then analyzed 47 inherited retinal disease (IRD) genes. We compared SBNA scores to phenotype data from the ClinVar database and found a significant difference between benign and pathogenic mutations with respect to network score. Finally, we applied this approach to 65 patients at Massachusetts Eye and Ear (MEE) who were diagnosed with IRD but for whom no genetic cause was found. Multivariable logistic regression models built using SBNA scores for IRD-associated genes successfully predicted pathogenicity of novel mutations, allowing us to identify likely causative disease variants in 37 patients with IRD from our clinic. In conclusion, SBNA can be meaningfully applied to human proteins and may help predict mutations causative of IRD.
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Affiliation(s)
| | - Yuyang Luo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Anusha Nathan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA
| | - Gaurav D. Gaiha
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA
| | - Demetrios Vavvas
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Jason Comander
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Eric A. Pierce
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Emily M. Place
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Kinga M. Bujakowska
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Elizabeth J. Rossin
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
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7
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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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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] [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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Tzika AC, Ullate-Agote A, Zakany S, Kummrow M, Milinkovitch MC. Somitic positional information guides self-organized patterning of snake scales. SCIENCE ADVANCES 2023; 9:eadf8834. [PMID: 37315141 DOI: 10.1126/sciadv.adf8834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
Two influential concepts in tissue patterning are Wolpert's positional information and Turing's self-organized reaction-diffusion (RD). The latter establishes the patterning of hair and feathers. Here, our morphological, genetic, and functional-by CRISPR-Cas9-mediated gene disruption-characterization of wild-type versus "scaleless" snakes reveals that the near-perfect hexagonal pattern of snake scales is established through interactions between RD in the skin and somitic positional information. First, we show that ventral scale development is guided by hypaxial somites and, second, that ventral scales and epaxial somites guide the sequential RD patterning of the dorsolateral scales. The RD intrinsic length scale evolved to match somite periodicity, ensuring the alignment of ribs and scales, both of which play a critical role in snake locomotion.
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Affiliation(s)
- Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Asier Ullate-Agote
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Szabolcs Zakany
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Maya Kummrow
- Tierspital, University of Zurich, Zurich, Switzerland
| | - Michel C Milinkovitch
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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10
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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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11
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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] [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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12
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Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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13
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Kapur P, Gao M, Zhong H, Chintalapati S, Mitui M, Barnes S, Zhou Q, Miyata J, Carrillo D, Malladi V, Rakheja D, Pedrosa I, Xu L, Kinch L, Brugarolas J. Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney. Mod Pathol 2022; 35:333-343. [PMID: 34538873 PMCID: PMC9817016 DOI: 10.1038/s41379-021-00896-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/11/2023]
Abstract
Low-grade oncocytic tumor (LOT) of the kidney is a recently described entity with poorly understood pathogenesis. Using next-generation sequencing (NGS) and complementary approaches, we provide insight into its biology. We describe 22 LOT corresponding to 7 patients presenting with a median age of 75 years (range 63-86 years) and male to female ratio 2:5. All 22 tumors demonstrated prototypical microscopic features. Tumors were well-circumscribed and solid. They were composed of sheets of tumor cells in compact nests. Tumor cells had eosinophilic cytoplasm, round to oval nuclei (without nuclear membrane irregularities), focal subtle perinuclear halos, and occasional binucleation. Sharply delineated edematous stromal islands were often observed. Tumor cells were positive for PAX8, negative for CD117, and exhibited diffuse and strong cytokeratin-7 expression. Six patients presented with pT1 tumors. At a median follow-up of 29 months, four patients were alive without recurrence (three patients had died from unrelated causes). All tumors were originally classified as chromophobe renal cell carcinoma, eosinophilic variant (chRCC-eo). While none of the patients presented with known syndromic features, one patient with multiple bilateral LOTs was subsequently found to have a likely pathogenic germline TSC1 mutation. Somatic, likely activating, mutations in MTOR and RHEB were identified in all other evaluable LOTs. As assessed by phospho-S6 and phospho-4E-BP1, mTOR complex 1 (mTORC1) was activated across all cases but to different extent. MTOR mutant LOT exhibited lower levels of mTORC1 activation, possibly related to mTORC1 dimerization and the preservation of a wild-type MTOR copy (retained chromosome 1). Supporting its distinction from related entities, gene expression analyses showed that LOT clustered separately from classic chRCC, chRCC-eo, and RO. In summary, converging mTORC1 pathway mutations, mTORC1 complex activation, and a distinctive gene expression signature along with characteristic phenotypic features support LOT designation as a distinct entity with both syndromic and non-syndromic cases associated with an indolent course.
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Affiliation(s)
- Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Ming Gao
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Hua Zhong
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Suneetha Chintalapati
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Midori Mitui
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Spencer Barnes
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Qinbo Zhou
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Jeffrey Miyata
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Deyssy Carrillo
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Venkat Malladi
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Ivan Pedrosa
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Lin Xu
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - Lisa Kinch
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390
| | - James Brugarolas
- Kidney Cancer Program at Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Hematology-Oncology Division of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Affiliation(s)
- Tomokazu Konishi
- Graduate School of Bioresource Sciences, Akita Prefectural University
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15
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Rios JJ, Denton K, Russell J, Kozlitina J, Ferreira CR, Lewanda AF, Mayfield JE, Moresco E, Ludwig S, Tang M, Li X, Lyon S, Khanshour A, Paria N, Khalid A, Li Y, Xie X, Feng JQ, Xu Q, Lu Y, Hammer RE, Wise CA, Beutler B. Germline Saturation Mutagenesis Induces Skeletal Phenotypes in Mice. J Bone Miner Res 2021; 36:1548-1565. [PMID: 33905568 PMCID: PMC8862308 DOI: 10.1002/jbmr.4323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 12/28/2022]
Abstract
Proper embryonic and postnatal skeletal development require coordination of myriad complex molecular mechanisms. Disruption of these processes, through genetic mutation, contributes to variation in skeletal development. We developed a high-throughput N-ethyl-N-nitrosourea (ENU)-induced saturation mutagenesis skeletal screening approach in mice to identify genes required for proper skeletal development. Here, we report initial results from live-animal X-ray and dual-energy X-ray absorptiometry (DXA) imaging of 27,607 G3 mice from 806 pedigrees, testing the effects of 32,198 coding/splicing mutations in 13,020 genes. A total of 39.7% of all autosomal genes were severely damaged or destroyed by mutations tested twice or more in the homozygous state. Results from our study demonstrate the feasibility of in vivo mutagenesis to identify mouse models of skeletal disease. Furthermore, our study demonstrates how ENU mutagenesis provides opportunities to create and characterize putative hypomorphic mutations in developmentally essential genes. Finally, we present a viable mouse model and case report of recessive skeletal disease caused by mutations in FAM20B. Results from this study, including engineered mouse models, are made publicly available via the online Mutagenetix database. © 2021 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kristin Denton
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Jamie Russell
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Julia Kozlitina
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carlos R Ferreira
- Skeletal Genomics Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy F Lewanda
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Joshua E Mayfield
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Eva Moresco
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sara Ludwig
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Miao Tang
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xiaohong Li
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Lyon
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - Anas Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Aysha Khalid
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Yang Li
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Xudong Xie
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Jian Q Feng
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Qian Xu
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Yongbo Lu
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - Robert E Hammer
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
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16
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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: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [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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17
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Rios JJ, Denton K, Yu H, Manickam K, Garner S, Russell J, Ludwig S, Rosenfeld JA, Liu P, Munch J, Sucato DJ, Beutler B, Wise CA. Saturation mutagenesis defines novel mouse models of severe spine deformity. Dis Model Mech 2021; 14:269194. [PMID: 34142127 PMCID: PMC8246263 DOI: 10.1242/dmm.048901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic formation and patterning of the vertebrate spinal column requires coordination of many molecular cues. After birth, the integrity of the spine is impacted by developmental abnormalities of the skeletal, muscular and nervous systems, which may result in deformities, such as kyphosis and scoliosis. We sought to identify novel genetic mouse models of severe spine deformity by implementing in vivo skeletal radiography as part of a high-throughput saturation mutagenesis screen. We report selected examples of genetic mouse models following radiographic screening of 54,497 mice from 1275 pedigrees. An estimated 30.44% of autosomal genes harbored predicted damaging alleles examined twice or more in the homozygous state. Of the 1275 pedigrees screened, 7.4% presented with severe spine deformity developing in multiple mice, and of these, meiotic mapping implicated N-ethyl-N-nitrosourea alleles in 21% of pedigrees. Our study provides proof of concept that saturation mutagenesis is capable of discovering novel mouse models of human disease, including conditions with skeletal, neural and neuromuscular pathologies. Furthermore, we report a mouse model of skeletal disease, including severe spine deformity, caused by recessive mutation in Scube3. By integrating results with a human clinical exome database, we identified a patient with undiagnosed skeletal disease who harbored recessive mutations in SCUBE3, and we demonstrated that disease-associated mutations are associated with reduced transactivation of Smad signaling in vitro. All radiographic results and mouse models are made publicly available through the Mutagenetix online database with the goal of advancing understanding of spine development and discovering novel mouse models of human disease. Summary: We report selected mouse models of spine deformity following mutagenesis across 30% of autosomal genes, results of which are made publicly available to advance understanding of spine development and disease.
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,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.,Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristin Denton
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Hao Yu
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Kandamurugu Manickam
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Shannon Garner
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Baylor Genetics, Houston, TX 77021, USA
| | - Pengfei Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Baylor Genetics, Houston, TX 77021, USA
| | - Jake Munch
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Daniel J Sucato
- Department of Orthopaedics, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,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
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18
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Konishi T. SARS-CoV-2 mutations among minks show reduced lethality and infectivity to humans. PLoS One 2021; 16:e0247626. [PMID: 34038423 PMCID: PMC8153470 DOI: 10.1371/journal.pone.0247626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/16/2021] [Indexed: 01/23/2023] Open
Abstract
SARS-CoV-2 infection in minks has become a serious problem, as the virus may mutate and reinfect humans; some countries have decided to cull minks. Here, the virus sequencing data in minks were analysed and compared to those of human-virus. Although the mink-virus maintained the characteristics of human-virus, some variants rapidly mutated, adapting to minks. Some mink-derived variants infected humans, which accounted for 40% of the total SARS-CoV-2 cases in the Netherlands. These variants appear to be less lethal and infective compared to those in humans. Variants that have mutated further among minks were not found in humans. Such mink-viruses might be suitable for vaccination for humans, such as in the case of the smallpox virus, which is less infective and toxic to humans.
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Affiliation(s)
- Tomokazu Konishi
- Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
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19
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Clark JF, Dinsmore CJ, Soriano P. A most formidable arsenal: genetic technologies for building a better mouse. Genes Dev 2021; 34:1256-1286. [PMID: 33004485 PMCID: PMC7528699 DOI: 10.1101/gad.342089.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this review, Clark et al. summarize the history of mice in genetic studies and the development of classic approaches to genome modification, and how they have been used and improved in recent years. They also discuss the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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20
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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] [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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21
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Impact of an SGLT2-loss of function mutation on renal architecture, histology, and glucose homeostasis. Cell Tissue Res 2021; 384:527-543. [PMID: 33409652 DOI: 10.1007/s00441-020-03358-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/18/2020] [Indexed: 01/14/2023]
Abstract
Inhibitors of sodium/glucose co-transporter 2 (SGLT2) are currently in clinical use for type 2 diabetes (T2D) treatment due to their anti-hyperglycemic effect exerted by the inhibition of glucose reabsorption in the kidney. Inhibition of SGLT2 is associated with improvement of renal outcomes in chronic kidney disease associated with T2D. Our study aimed to describe the renal-specific phenotypic consequences of the SGLT2-loss of function "Jimbee" mutation within the Slc5a2 mouse gene in a non-diabetic/non-obese background. The Jimbee mice displayed reduced body weight, glucosuria, polyuria, polydipsia, and hyperphagia but were normoglycemic, with no signs of baseline insulin resistance or renal dysfunction. Histomorphological analysis of the kidneys revealed a normal architecture and morphology of the renal cortex, but shrinkage of the glomerular and tubular apparatus, including Bowman's space, glomerular tuft, mesangial matrix fraction, and proximal convoluted tubule (PCT). Immunofluorescent analysis of renal sections showed that SGLT2 was absent from the apical membrane of PCT of the Jimbee mice but remnant positive vesicles were detected within the cytosol or at the perinuclear interface. Renal localization and abundance of GLUT1, GLUT2, and SGLT1 were unchanged in the Jimbee genotype. Intriguingly, the mutation did not induce hepatic gluconeogenic gene expression in overnight fasted mice despite a high glucose excretion rate. The Jimbee phenotype is remarkably similar to humans with SLC5A2 mutations and provides a useful model for the study of SGLT2-loss of function effects on renal architecture and physiology, as well as for identifying possible novel roles for the kidneys in glucose homeostasis and metabolic reprogramming.
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22
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Lu T, Park S, Zhu J, Wang Y, Zhan X, Wang X, Wang L, Zhu H, Wang T. Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data. Cell Rep 2021; 34:108589. [PMID: 33406427 DOI: 10.1016/j.celrep.2020.108589] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/04/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023] Open
Abstract
Single-cell lineage tracing provides crucial insights into the fates of individual cells. Single-cell RNA sequencing (scRNA-seq) is commonly applied in modern biomedical research, but genetics-based lineage tracing for scRNA-seq data is still unexplored. Variant calling from scRNA-seq data uniquely suffers from "expressional drop-outs," including low expression and allelic bias in gene expression, which presents significant obstacles for lineage reconstruction. We introduce SClineager, which infers accurate evolutionary lineages from scRNA-seq data by borrowing information from related cells to overcome expressional drop-outs. We systematically validate SClineager and show that genetics-based lineage tracing is applicable for single-cell-sequencing studies of both tumor and non-tumor tissues using SClineager. Overall, our work provides a powerful tool that can be applied to scRNA-seq data to decipher the lineage histories of cells and that could address a missing opportunity to reveal valuable information from the large amounts of existing scRNA-seq data.
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Affiliation(s)
- Tianshi Lu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Seongoh Park
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Statistics, Sungshin Women's University, Seoul 02844, Republic of Korea
| | - James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA
| | - Li Wang
- Department of Mathematics and Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Hao Zhu
- Children's Research Institute, Department of Pediatrics and Department of Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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23
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Tran TN, Schimenti JC. A segregating human allele of SPO11 modeled in mice disrupts timing and amounts of meiotic recombination, causing oligospermia and a decreased ovarian reserve†. Biol Reprod 2020; 101:347-359. [PMID: 31074776 DOI: 10.1093/biolre/ioz089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/29/2019] [Accepted: 05/09/2019] [Indexed: 01/27/2023] Open
Abstract
A major challenge in medical genetics is to characterize variants of unknown significance (VUS). Doing so would help delineate underlying causes of disease and the design of customized treatments. Infertility has presented an especially difficult challenge with respect to not only determining if a given patient has a genetic basis, but also to identify the causative genetic factor(s). Though genome sequencing can identify candidate variants, in silico predictions of causation are not always sufficiently reliable so as to be actionable. Thus, experimental validation is crucial. Here, we describe the phenotype of mice containing a non-synonymous (proline-to-threonine at position 306) change in Spo11, corresponding to human SNP rs185545661. SPO11 is a topoisomerase-like protein that is essential for meiosis because it induces DNA double stranded breaks (DSBs) that stimulate pairing and recombination of homologous chromosomes. Although both male and female Spo11P306T/P306T mice were fertile, they had reduced sperm and oocytes, respectively. Spermatocyte chromosomes exhibited synapsis defects (especially between the X and Y chromosomes), elevated apoptotic cells, persistent markers of DSBs, and most importantly, fewer Type 1 crossovers that causes some chromosomes to have none. Spo11P306T/- mice were sterile and made fewer meiotic DSBs than Spo11+/- animals, suggesting that the Spo11P306T allele is a hypomorph and likely is delayed in making sufficient DSBs in a timely fashion. If the consequences are recapitulated in humans, it would predict phenotypes of premature ovarian failure, reduced sperm counts, and possible increased number of aneuploid gametes. These results emphasize the importance of deep phenotyping in order to accurately assess the impact of VUSs in reproduction genes.
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Affiliation(s)
- Tina N Tran
- Department of Biomedical Sciences and the Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - John C Schimenti
- Department of Biomedical Sciences and the Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
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24
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Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice. Proc Natl Acad Sci U S A 2020; 117:12931-12942. [PMID: 32457148 DOI: 10.1073/pnas.1921224117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retinal disease and loss of vision can result from any disruption of the complex pathways controlling retinal development and homeostasis. Forward genetics provides an excellent tool to find, in an unbiased manner, genes that are essential to these processes. Using N-ethyl-N-nitrosourea mutagenesis in mice in combination with a screening protocol using optical coherence tomography (OCT) and automated meiotic mapping, we identified 11 mutations presumably causative of retinal phenotypes in genes previously known to be essential for retinal integrity. In addition, we found multiple statistically significant gene-phenotype associations that have not been reported previously and decided to target one of these genes, Sfxn3 (encoding sideroflexin-3), using CRISPR/Cas9 technology. We demonstrate, using OCT, light microscopy, and electroretinography, that two Sfxn3 -/- mouse lines developed progressive and severe outer retinal degeneration. Electron microscopy showed thinning of the retinal pigment epithelium and disruption of the external limiting membrane. Using single-cell RNA sequencing of retinal cells isolated from C57BL/6J mice, we demonstrate that Sfxn3 is expressed in several bipolar cell subtypes, retinal ganglion cells, and some amacrine cell subtypes but not significantly in Müller cells or photoreceptors. In situ hybridization confirmed these findings. Furthermore, pathway analysis suggests that Sfxn3 may be associated with synaptic homeostasis. Importantly, electron microscopy analysis showed disruption of synapses and synaptic ribbons in the outer plexiform layer of Sfxn3 -/- mice. Our work describes a previously unknown requirement for Sfxn3 in retinal function.
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25
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Singla N, Xie Z, Zhang Z, Gao M, Yousuf Q, Onabolu O, McKenzie T, Tcheuyap VT, Ma Y, Choi J, McKay R, Christie A, Torras OR, Bowman IA, Margulis V, Pedrosa I, Przybycin C, Wang T, Kapur P, Rini B, Brugarolas J. Pancreatic tropism of metastatic renal cell carcinoma. JCI Insight 2020; 5:134564. [PMID: 32271170 DOI: 10.1172/jci.insight.134564] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022] Open
Abstract
Renal cell carcinoma (RCC) is characterized by a particularly broad metastatic swath, and, enigmatically, when the pancreas is a destination, the disease is associated with improved survival. Intrigued by this observation, we sought to characterize the clinical behavior, therapeutic implications, and underlying biology. While pancreatic metastases (PM) are infrequent, we identified 31 patients across 2 institutional cohorts and show that improved survival is independent of established prognostic variables, that these tumors are exquisitely sensitive to antiangiogenic agents and resistant to immune checkpoint inhibitors (ICIs), and that they are characterized by a distinctive biology. Primary tumors of patients with PM exhibited frequent PBRM1 mutations, 3p loss, and 5q amplification, along with a lower frequency of aggressive features such as BAP1 mutations and loss of 9p, 14q, and 4q. Gene expression analyses revealed constrained evolution with remarkable uniformity, reduced effector T cell gene signatures, and increased angiogenesis. Similar findings were observed histopathologically. Thus, RCC metastatic to the pancreas is characterized by indolent biology, heightened angiogenesis, and an uninflamed stroma, likely underlying its good prognosis, sensitivity to antiangiogenic therapies, and refractoriness to ICI. These data suggest that metastatic organotropism may be an indicator of a particular biology with prognostic and treatment implications for patients.
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Affiliation(s)
- Nirmish Singla
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Urology, and
| | - Zhiqun Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ze Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ming Gao
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
| | | | | | | | | | - Yuanqing Ma
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
| | - Jacob Choi
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, Ohio, USA
| | - Renee McKay
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Internal Medicine
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Division of Biostatistics, Department of Clinical Sciences, and
| | | | - Isaac A Bowman
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Internal Medicine
| | - Vitaly Margulis
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Urology, and
| | - Ivan Pedrosa
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Urology, and.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christopher Przybycin
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
| | - Tao Wang
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Brian Rini
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, Ohio, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center.,Department of Internal Medicine
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26
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Stearman RS, Cornelius AR, Young LR, Conklin DS, Mickler EA, Lu X, Hara N, Fettig LM, Phang TL, Geraci MW. Familial Pulmonary Fibrosis and Hermansky-Pudlak Syndrome Rare Missense Mutations in Context. Am J Respir Crit Care Med 2020; 200:253-256. [PMID: 30985222 DOI: 10.1164/rccm.201902-0457le] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | | | - Lisa R Young
- 3 Vanderbilt University Medical Center Nashville, Tennessee
| | | | | | - Xiao Lu
- 4 St. John Medical Center Westlake, Ohio and
| | - Naoko Hara
- 5 University of Colorado School of Medicine Aurora, Colorado
| | - Lynsey M Fettig
- 5 University of Colorado School of Medicine Aurora, Colorado
| | - Tzu L Phang
- 5 University of Colorado School of Medicine Aurora, Colorado
| | - Mark W Geraci
- 1 Indiana University School of Medicine Indianapolis, Indiana
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27
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Courtney KD, Ma Y, Diaz de Leon A, Christie A, Xie Z, Woolford L, Singla N, Joyce A, Hill H, Madhuranthakam AJ, Yuan Q, Xi Y, Zhang Y, Chang J, Fatunde O, Arriaga Y, Frankel AE, Kalva S, Zhang S, McKenzie T, Reig Torras O, Figlin RA, Rini BI, McKay RM, Kapur P, Wang T, Pedrosa I, Brugarolas J. HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma. Clin Cancer Res 2019; 26:793-803. [PMID: 31727677 DOI: 10.1158/1078-0432.ccr-19-1459] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/16/2019] [Accepted: 11/05/2019] [Indexed: 12/30/2022]
Abstract
PURPOSE The heterodimeric transcription factor HIF-2 is arguably the most important driver of clear cell renal cell carcinoma (ccRCC). Although considered undruggable, structural analyses at the University of Texas Southwestern Medical Center (UTSW, Dallas, TX) identified a vulnerability in the α subunit, which heterodimerizes with HIF1β, ultimately leading to the development of PT2385, a first-in-class inhibitor. PT2385 was safe and active in a first-in-human phase I clinical trial of patients with extensively pretreated ccRCC at UTSW and elsewhere. There were no dose-limiting toxicities, and disease control ≥4 months was achieved in 42% of patients. PATIENTS AND METHODS We conducted a prospective companion substudy involving a subset of patients enrolled in the phase I clinical trial at UTSW (n = 10), who were treated at the phase II dose or above, involving multiparametric MRI, blood draws, and serial biopsies for biochemical, whole exome, and RNA-sequencing studies. RESULTS PT2385 inhibited HIF-2 in nontumor tissues, as determined by a reduction in erythropoietin levels (a pharmacodynamic marker), in all but one patient, who had the lowest drug concentrations. PT2385 dissociated HIF-2 complexes in ccRCC metastases, and inhibited HIF-2 target gene expression. In contrast, HIF-1 complexes were unaffected. Prolonged PT2385 treatment resulted in the acquisition of resistance, and we identified a gatekeeper mutation (G323E) in HIF2α, which interferes with drug binding and precluded HIF-2 complex dissociation. In addition, we identified an acquired TP53 mutation elsewhere, suggesting a possible alternate mechanism of resistance. CONCLUSIONS These findings demonstrate a core dependency on HIF-2 in metastatic ccRCC and establish PT2385 as a highly specific HIF-2 inhibitor in humans. New approaches will be required to target mutant HIF-2 beyond PT2385 or the closely related PT2977 (MK-6482).
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Affiliation(s)
- Kevin D Courtney
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuanqing Ma
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alberto Diaz de Leon
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhiqun Xie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Layton Woolford
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Nirmish Singla
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Allison Joyce
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Haley Hill
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ananth J Madhuranthakam
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Qing Yuan
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yin Xi
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yue Zhang
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jenny Chang
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Oluwatomilade Fatunde
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yull Arriaga
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Arthur E Frankel
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sanjeeva Kalva
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Song Zhang
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tiffani McKenzie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Oscar Reig Torras
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robert A Figlin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Brian I Rini
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Renée M McKay
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tao Wang
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ivan Pedrosa
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas. .,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - James Brugarolas
- Hematology-Oncology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas. .,Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
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28
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Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, Keinan A, Schimenti JC, Clark AG, Yu H. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nat Commun 2019; 10:4141. [PMID: 31515488 PMCID: PMC6742646 DOI: 10.1038/s41467-019-11959-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022] Open
Abstract
Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at > 1% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual's genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.
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Affiliation(s)
- Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shayne D Wierbowski
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jin Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tina N Tran
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Juan F Beltran
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Christen A Rivera-Erick
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kaixiong Ye
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Li Yao
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Xiaomu Wei
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alon Keinan
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - John C Schimenti
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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29
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McAlpine W, Russell J, Murray AR, Beutler B, Turer E. Research Techniques Made Simple: Forward Genetic Screening to Uncover Genes Involved in Skin Biology. J Invest Dermatol 2019; 139:1848-1853.e1. [PMID: 31445571 DOI: 10.1016/j.jid.2019.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022]
Abstract
The primary goals of modern genetics are to identify disease-causing mutations and to define the functions of genes in biological processes. Two complementary approaches, reverse and forward genetics, can be used to achieve this goal. Reverse genetics is a gene-driven approach that comprises specific gene targeting followed by phenotypic assessment. Conversely, forward genetics is a phenotype-driven approach that involves the phenotypic screening of organisms with randomly induced mutations followed by subsequent identification of the causative mutations (i.e., those responsible for phenotype). In this article, we focus on how forward genetics in mice can be used to explore dermatologic disease. We outline mouse mutagenesis with the chemical N-ethyl-N-nitrosourea and the strategy used to instantaneously identify mutations that are causative of specific phenotypes. Furthermore, we summarize the types of phenotypic screens that can be performed to explore various aspects of dermatologic disease.
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Affiliation(s)
- William McAlpine
- 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
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - Emre Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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30
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Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40. Nat Immunol 2019; 20:1322-1334. [PMID: 31427773 DOI: 10.1038/s41590-019-0464-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
Abstract
We report a new immunodeficiency disorder in mice caused by a viable hypomorphic mutation of Snrnp40, an essential gene encoding a subunit of the U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome. Snrnp40 is ubiquitous but strongly expressed in lymphoid tissue. Homozygous mutant mice showed hypersusceptibility to infection by murine cytomegalovirus and multiple defects of lymphoid development, stability and function. Cell-intrinsic defects of hematopoietic stem cell differentiation also affected homozygous mutants. SNRNP40 deficiency in primary hematopoietic stem cells or T cells or the EL4 cell line increased the frequency of splicing errors, mostly intron retention, in several hundred messenger RNAs. Altered expression of proteins associated with immune cell function was also observed in Snrnp40-mutant cells. The immunological consequences of SNRNP40 deficiency presumably result from cumulative, moderate effects on processing of many different mRNA molecules and secondary reductions in the expression of critical immune proteins, yielding a syndromic immune disorder.
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31
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Brommage R, Powell DR, Vogel P. Predicting human disease mutations and identifying drug targets from mouse gene knockout phenotyping campaigns. Dis Model Mech 2019; 12:dmm038224. [PMID: 31064765 PMCID: PMC6550044 DOI: 10.1242/dmm.038224] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two large-scale mouse gene knockout phenotyping campaigns have provided extensive data on the functions of thousands of mammalian genes. The ongoing International Mouse Phenotyping Consortium (IMPC), with the goal of examining all ∼20,000 mouse genes, has examined 5115 genes since 2011, and phenotypic data from several analyses are available on the IMPC website (www.mousephenotype.org). Mutant mice having at least one human genetic disease-associated phenotype are available for 185 IMPC genes. Lexicon Pharmaceuticals' Genome5000™ campaign performed similar analyses between 2000 and the end of 2008 focusing on the druggable genome, including enzymes, receptors, transporters, channels and secreted proteins. Mutants (4654 genes, with 3762 viable adult homozygous lines) with therapeutically interesting phenotypes were studied extensively. Importantly, phenotypes for 29 Lexicon mouse gene knockouts were published prior to observations of similar phenotypes resulting from homologous mutations in human genetic disorders. Knockout mouse phenotypes for an additional 30 genes mimicked previously published human genetic disorders. Several of these models have helped develop effective treatments for human diseases. For example, studying Tph1 knockout mice (lacking peripheral serotonin) aided the development of telotristat ethyl, an approved treatment for carcinoid syndrome. Sglt1 (also known as Slc5a1) and Sglt2 (also known as Slc5a2) knockout mice were employed to develop sotagliflozin, a dual SGLT1/SGLT2 inhibitor having success in clinical trials for diabetes. Clinical trials evaluating inhibitors of AAK1 (neuropathic pain) and SGLT1 (diabetes) are underway. The research community can take advantage of these unbiased analyses of gene function in mice, including the minimally studied 'ignorome' genes.
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Affiliation(s)
- Robert Brommage
- Department of Metabolism Research, Lexicon Pharmaceuticals, 8800 Technology Forest Place, The Woodlands, TX 77381, USA
| | - David R Powell
- Department of Metabolism Research, Lexicon Pharmaceuticals, 8800 Technology Forest Place, The Woodlands, TX 77381, USA
| | - Peter Vogel
- St. Jude Children's Research Hospital, Pathology, MS 250, Room C5036A, 262 Danny Thomas Place, Memphis, TN 38105, USA
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32
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Turer EE, San Miguel M, Wang KW, McAlpine W, Ou F, Li X, Tang M, Zang Z, Wang J, Hayse B, Evers B, Zhan X, Russell J, Beutler B. A viable hypomorphic Arnt2 mutation causes hyperphagic obesity, diabetes and hepatic steatosis. Dis Model Mech 2018; 11:11/12/dmm035451. [PMID: 30563851 PMCID: PMC6307907 DOI: 10.1242/dmm.035451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022] Open
Abstract
Aryl hydrocarbon receptor nuclear translocator 2 (ARNT2) is a member of the basic helix-loop-helix/PER-ARNT-SIM (bHLH/PAS) transcription factor family. ARNT2 heterodimerizes with several members of the family, including single-minded homolog-1 (SIM1) and neuronal PAS domain protein 4 (NPAS4), primarily in neurons of the central nervous system. We screened 64,424 third-generation germline mutant mice derived from N-ethyl-N-nitrosourea (ENU)-mutagenized great-grandsires for weight abnormalities. Among 17 elevated body weight phenotypes identified and mapped, one strongly correlated with an induced missense mutation in Arnt2 using a semidominant model of inheritance. Causation was confirmed by CRISPR/Cas9 gene targeting to recapitulate the original ENU allele, specifying Arg74Cys (R74C). The CRISPR/Cas9-targeted (Arnt2R74C/R74C) mice demonstrated hyperphagia and increased adiposity as well as hepatic steatosis and abnormalities in glucose homeostasis. The mutant ARNT2 protein showed decreased transcriptional activity when coexpressed with SIM1. These findings establish a requirement for ARNT2-dependent genes in the maintenance of the homeostatic feeding response, necessary for prevention of obesity and obesity-related diseases. Summary: A forward genetic approach identified genes involved in maintaining normal body weight. A mutation in Arnt2 caused obesity by regulating food intake.
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Affiliation(s)
- 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
| | - Miguel San Miguel
- 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
| | - Kuan-Wen Wang
- 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
| | - Feiya Ou
- 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
| | - Zhao Zang
- 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
| | - Braden Hayse
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8505, USA
| | - Bret Evers
- Department of Pathology, 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
| | - Jamie Russell
- 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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33
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Tran TN, Schimenti JC. A putative human infertility allele of the meiotic recombinase DMC1 does not affect fertility in mice. Hum Mol Genet 2018; 27:3911-3918. [PMID: 30085085 PMCID: PMC6216207 DOI: 10.1093/hmg/ddy286] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/19/2018] [Accepted: 07/26/2018] [Indexed: 11/13/2022] Open
Abstract
Whole-exome or whole-genome sequencing is becoming routine in clinical situations for identifying mutations underlying presumed genetic causes of disease including infertility. While this is a powerful approach for implicating polymorphisms or de novo mutations in genes plausibly related to the phenotype, a greater challenge is to definitively prove causality. This is a crucial requisite for treatment, especially for infertility, in which validation options are limited. In this study, we created a mouse model of a putative infertility allele, DMC1M200V. DMC1 encodes a RecA homolog essential for meiotic recombination and fertility in mice. This allele was originally implicated as being responsible for the sterility of a homozygous African woman, a conclusion supported by subsequent biochemical analyses of the mutant protein and by studies of yeast with the orthologous amino acid change. Here, we found that Dmc1M200V/M200V male and female mice are fully fertile and do not exhibit any gonadal abnormalities. Detailed immunocytological analysis of meiosis revealed no defects suggestive of compromised fertility. This study serves as a cautionary tale for making conclusions about consequences of genetic variants, especially with respect to infertility, and emphasizes the importance of conducting relevant biological assays for making accurate diagnoses in the era of genomic medicine.
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Affiliation(s)
- Tina N Tran
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
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34
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Wierbowski SD, Fragoza R, Liang S, Yu H. Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 11:107-116. [PMID: 31086831 PMCID: PMC6510504 DOI: 10.1016/j.coisb.2018.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rapid advances in next-generation sequencing technology have resulted in an explosion of whole-exome/genome sequencing data, providing an unprecedented opportunity to identify disease- and trait-associated variants in humans on a large scale. To date, the long-standing paradigm has leveraged fitness-based approximations to translate this ever-expanding sequencing data into causal insights in disease. However, while this approach robustly identifies variants under evolutionary constraint, it fails to provide molecular insights. Moreover, complex disease phenomena often violate standard assumptions of a direct organismal phenotype to overall fitness effect relationship. Here we discuss the potential of a molecular phenotype-oriented paradigm to uniquely identify candidate disease-causing mutations from the human genetic background. By providing a direct connection between single nucleotide mutations and observable organismal and cellular phenotypes associated with disease, we suggest that molecular phenotypes can readily incorporate alongside established fitness-based methodologies to provide complementary insights to the functional impact of human mutations. Lastly, we discuss how integrated approaches between molecular phenotypes and fitness-based perspectives facilitate new insights into the molecular mechanisms underlying disease-associated mutations while also providing a platform for improved interpretation of epistasis in human disease.
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Affiliation(s)
- Shayne D. Wierbowski
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Robert Fragoza
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Siqi Liang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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35
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Unpackaging the genetics of mammalian fertility: strategies to identify the “reproductive genome”†. Biol Reprod 2018; 99:1119-1128. [DOI: 10.1093/biolre/ioy133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022] Open
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36
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Wang Y, Cao L, Lee CY, Matsuo T, Wu K, Asher G, Tang L, Saitoh T, Russell J, Klewe-Nebenius D, Wang L, Soya S, Hasegawa E, Chérasse Y, Zhou J, Li Y, Wang T, Zhan X, Miyoshi C, Irukayama Y, Cao J, Meeks JP, Gautron L, Wang Z, Sakurai K, Funato H, Sakurai T, Yanagisawa M, Nagase H, Kobayakawa R, Kobayakawa K, Beutler B, Liu Q. Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors. Nat Commun 2018; 9:2041. [PMID: 29795268 PMCID: PMC5966455 DOI: 10.1038/s41467-018-04324-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/18/2018] [Indexed: 12/14/2022] Open
Abstract
Innate behaviors are genetically encoded, but their underlying molecular mechanisms remain largely unknown. Predator odor 2,4,5-trimethyl-3-thiazoline (TMT) and its potent analog 2-methyl-2-thiazoline (2MT) are believed to activate specific odorant receptors to elicit innate fear/defensive behaviors in naive mice. Here, we conduct a large-scale recessive genetics screen of ethylnitrosourea (ENU)-mutagenized mice. We find that loss of Trpa1, a pungency/irritancy receptor, diminishes TMT/2MT and snake skin-evoked innate fear/defensive responses. Accordingly, Trpa1 -/- mice fail to effectively activate known fear/stress brain centers upon 2MT exposure, despite their apparent ability to smell and learn to fear 2MT. Moreover, Trpa1 acts as a chemosensor for 2MT/TMT and Trpa1-expressing trigeminal ganglion neurons contribute critically to 2MT-evoked freezing. Our results indicate that Trpa1-mediated nociception plays a crucial role in predator odor-evoked innate fear/defensive behaviors. The work establishes the first forward genetics screen to uncover the molecular mechanism of innate fear, a basic emotion and evolutionarily conserved survival mechanism.
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Affiliation(s)
- Yibing Wang
- National Institute of Biological Sciences, 102206, Beijing, China
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Liqin Cao
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Chia-Ying Lee
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Tomohiko Matsuo
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Kejia Wu
- National Institute of Biological Sciences, 102206, Beijing, China
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Greg Asher
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Lijun Tang
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Tsuyoshi Saitoh
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Jamie Russell
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniela Klewe-Nebenius
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Li Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shingo Soya
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Emi Hasegawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yoan Chérasse
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Jiamin Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yuwenbin Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tao Wang
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiaowei Zhan
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chika Miyoshi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yoko Irukayama
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Jie Cao
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Julian P Meeks
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Laurent Gautron
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zhiqiang Wang
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Katsuyasu Sakurai
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Department of Anatomy, Faculty of Medicine, Toho University, Ota-Ku, Tokyo, 143-8540, Japan
| | - Takeshi Sakurai
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Hiroshi Nagase
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Reiko Kobayakawa
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Ko Kobayakawa
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan.
| | - Bruce Beutler
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Qinghua Liu
- National Institute of Biological Sciences, 102206, Beijing, China.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan.
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China.
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