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Rodriguez-Gil JL, Watkins-Chow DE, Baxter LL, Elliot G, Harper UL, Wincovitch SM, Wedel JC, Incao AA, Huebecker M, Boehm FJ, Garver WS, Porter FD, Broman KW, Platt FM, Pavan WJ. Genetic background modifies phenotypic severity and longevity in a mouse model of Niemann-Pick disease type C1. Dis Model Mech 2020; 13:dmm042614. [PMID: 31996359 PMCID: PMC7075069 DOI: 10.1242/dmm.042614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022] Open
Abstract
Niemann-Pick disease type C1 (NPC1) is a rare, fatal neurodegenerative disorder characterized by lysosomal accumulation of unesterified cholesterol and glycosphingolipids. These subcellular pathologies lead to phenotypes of hepatosplenomegaly, neurological degeneration and premature death. NPC1 is extremely heterogeneous in the timing of clinical presentation and is associated with a wide spectrum of causative NPC1 mutations. To study the genetic architecture of NPC1, we have generated a new NPC1 mouse model, Npc1em1PavNpc1em1Pav/em1Pav mutants showed notably reduced NPC1 protein compared to controls and displayed the pathological and biochemical hallmarks of NPC1. Interestingly, Npc1em1Pav/em1Pav mutants on a C57BL/6J genetic background showed more severe visceral pathology and a significantly shorter lifespan compared to Npc1em1Pav/em1Pav mutants on a BALB/cJ background, suggesting that strain-specific modifiers contribute to disease severity and survival. QTL analysis for lifespan of 202 backcross N2 mutants on a mixed C57BL/6J and BALB/cJ background detected significant linkage to markers on chromosomes 1 and 7. The discovery of these modifier regions demonstrates that mouse models are powerful tools for analyzing the genetics underlying rare human diseases, which can be used to improve understanding of the variability in NPC1 phenotypes and advance options for patient diagnosis and therapy.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
- Medical Scientist Training Program, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53726, USA
| | - Dawn E Watkins-Chow
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura L Baxter
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gene Elliot
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ursula L Harper
- Genomics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen M Wincovitch
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia C Wedel
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arturo A Incao
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mylene Huebecker
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
| | - Frederick J Boehm
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William S Garver
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Forbes D Porter
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
| | - William J Pavan
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Watkins-Chow DE, Varshney GK, Garrett LJ, Chen Z, Jimenez EA, Rivas C, Bishop KS, Sood R, Harper UL, Pavan WJ, Burgess SM. Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection. G3 (Bethesda) 2017; 7:719-722. [PMID: 28040780 PMCID: PMC5295614 DOI: 10.1534/g3.116.038091] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/20/2016] [Indexed: 01/12/2023]
Abstract
Cpf1 has emerged as an alternative to the Cas9 RNA-guided nuclease. Here we show that gene targeting rates in mice using Cpf1 can meet, or even surpass, Cas9 targeting rates (approaching 100% targeting), but require higher concentrations of mRNA and guide. We also demonstrate that coinjecting two guides with close targeting sites can result in synergistic genomic cutting, even if one of the guides has minimal cutting activity.
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Affiliation(s)
- Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gaurav K Varshney
- Functional and Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104
| | - Lisa J Garrett
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Erin A Jimenez
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Cecilia Rivas
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Kevin S Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Ursula L Harper
- Genomics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
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Huang B, Gomez-Rodriguez J, Preite S, Garrett LJ, Harper UL, Schwartzberg PL. CRISPR-Mediated Triple Knockout of SLAMF1, SLAMF5 and SLAMF6 Supports Positive Signaling Roles in NKT Cell Development. PLoS One 2016; 11:e0156072. [PMID: 27258160 PMCID: PMC4892526 DOI: 10.1371/journal.pone.0156072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/08/2016] [Indexed: 01/04/2023] Open
Abstract
The SLAM family receptors contribute to diverse aspects of lymphocyte biology and signal via the small adaptor molecule SAP. Mutations affecting SAP lead to X-linked lymphoproliferative syndrome Type 1, a severe immunodysregulation characterized by fulminant mononucleosis, dysgammaglobulinemia, and lymphoproliferation/lymphomas. Patients and mice having mutations affecting SAP also lack germinal centers due to a defect in T:B cell interactions and are devoid of invariant NKT (iNKT) cells. However, which and how SLAM family members contribute to these phenotypes remains uncertain. Three SLAM family members: SLAMF1, SLAMF5 and SLAMF6, are highly expressed on T follicular helper cells and germinal center B cells. SLAMF1 and SLAMF6 are also implicated in iNKT development. Although individual receptor knockout mice have limited iNKT and germinal center phenotypes compared to SAP knockout mice, the generation of multi-receptor knockout mice has been challenging, due to the genomic linkage of the genes encoding SLAM family members. Here, we used Cas9/CRISPR-based mutagenesis to generate mutations simultaneously in Slamf1, Slamf5 and Slamf6. Genetic disruption of all three receptors in triple-knockout mice (TKO) did not grossly affect conventional T or B cell development and led to mild defects in germinal center formation post-immunization. However, the TKO worsened defects in iNKT cells development seen in SLAMF6 single gene-targeted mice, supporting data on positive signaling and potential redundancy between these receptors.
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Affiliation(s)
- Bonnie Huang
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Julio Gomez-Rodriguez
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Silvia Preite
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Lisa J. Garrett
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Ursula L. Harper
- Genomics Core, National Human Genome Research Institute, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Pamela L. Schwartzberg
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
- * E-mail:
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Sei Y, Zhao X, Forbes J, Szymczak S, Li Q, Trivedi A, Voellinger M, Joy G, Feng J, Whatley M, Jones MS, Harper UL, Marx SJ, Venkatesan AM, Chandrasekharappa SC, Raffeld M, Quezado MM, Louie A, Chen CC, Lim RM, Agarwala R, Schäffer AA, Hughes MS, Bailey-Wilson JE, Wank SA. A Hereditary Form of Small Intestinal Carcinoid Associated With a Germline Mutation in Inositol Polyphosphate Multikinase. Gastroenterology 2015; 149:67-78. [PMID: 25865046 PMCID: PMC4858647 DOI: 10.1053/j.gastro.2015.04.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 03/26/2015] [Accepted: 04/02/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Small intestinal carcinoids are rare and difficult to diagnose and patients often present with advanced incurable disease. Although the disease occurs sporadically, there have been reports of family clusters. Hereditary small intestinal carcinoid has not been recognized and genetic factors have not been identified. We performed a genetic analysis of families with small intestinal carcinoids to establish a hereditary basis and find genes that might cause this cancer. METHODS We performed a prospective study of 33 families with at least 2 cases of small intestinal carcinoids. Affected members were characterized clinically and asymptomatic relatives were screened and underwent exploratory laparotomy for suspected tumors. Disease-associated mutations were sought using linkage analysis, whole-exome sequencing, and copy number analyses of germline and tumor DNA collected from members of a single large family. We assessed expression of mutant protein, protein activity, and regulation of apoptosis and senescence in lymphoblasts derived from the cases. RESULTS Familial and sporadic carcinoids are clinically indistinguishable except for the multiple synchronous primary tumors observed in most familial cases. Nearly 34% of asymptomatic relatives older than age 50 were found to have occult tumors; the tumors were cleared surgically from 87% of these individuals (20 of 23). Linkage analysis and whole-exome sequencing identified a germline 4-bp deletion in the gene inositol polyphosphate multikinase (IPMK), which truncates the protein. This mutation was detected in all 11 individuals with small intestinal carcinoids and in 17 of 35 family members whose carcinoid status was unknown. Mutant IPMK had reduced kinase activity and nuclear localization, compared with the full-length protein. This reduced activation of p53 and increased cell survival. CONCLUSIONS We found that small intestinal carcinoids can occur as an inherited autosomal-dominant disease. The familial form is characterized by multiple synchronous primary tumors, which might account for 22%-35% of cases previously considered sporadic. Relatives of patients with familial carcinoids should be screened to detect curable early stage disease. IPMK haploinsufficiency promotes carcinoid tumorigenesis.
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Affiliation(s)
- Yoshitatsu Sei
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xilin Zhao
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Joanne Forbes
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Silke Szymczak
- Computational and Statistical Genomics Branch, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Qing Li
- Computational and Statistical Genomics Branch, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Apurva Trivedi
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Mark Voellinger
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Grishma Joy
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Jianying Feng
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Millie Whatley
- Nuclear Medicine Division, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - MaryPat Sussex Jones
- Genomics Core/Genome Technology Branch, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Ursula L. Harper
- Genomics Core/Genome Technology Branch, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J. Marx
- Metabolic Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Aradhana M. Venkatesan
- Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Mark Raffeld
- Laboratory of Pathology, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Martha M. Quezado
- Laboratory of Pathology, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Adeline Louie
- Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Clara C. Chen
- Nuclear Medicine Division, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Ramona M. Lim
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Richa Agarwala
- Information Engineering Branch, NCBI, NLM, National Institutes of Health, Bethesda, MD, USA
| | - Alejandro A. Schäffer
- Computational Biology Branch, NCBI, NLM, National Institutes of Health, Bethesda, MD, USA
| | | | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Stephen A. Wank
- Digestive Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA,To whom correspondence should be addressed: Stephen A. Wank, M.D., Address: DDB/NIDDK/NIH, 10/9C-101, Bethesda, MD 20892, , Phone: (301) 402-3704, Fax: (301) 480-7476
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Gartside MG, Chen H, Ibrahimi OA, Byron SA, Curtis AV, Wellens CL, Bengston A, Yudt LM, Eliseenkova AV, Ma J, Curtin JA, Hyder P, Harper UL, Riedesel E, Mann GJ, Trent JM, Bastian BC, Meltzer PS, Mohammadi M, Pollock PM. Loss-of-function fibroblast growth factor receptor-2 mutations in melanoma. Mol Cancer Res 2009; 7:41-54. [PMID: 19147536 DOI: 10.1158/1541-7786.mcr-08-0021] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report that 10% of melanoma tumors and cell lines harbor mutations in the fibroblast growth factor receptor 2 (FGFR2) gene. These novel mutations include three truncating mutations and 20 missense mutations occurring at evolutionary conserved residues in FGFR2 as well as among all four FGFRs. The mutation spectrum is characteristic of those induced by UV radiation. Mapping of these mutations onto the known crystal structures of FGFR2 followed by in vitro and in vivo studies show that these mutations result in receptor loss of function through several distinct mechanisms, including loss of ligand binding affinity, impaired receptor dimerization, destabilization of the extracellular domains, and reduced kinase activity. To our knowledge, this is the first demonstration of loss-of-function mutations in a class IV receptor tyrosine kinase in cancer. Taken into account with our recent discovery of activating FGFR2 mutations in endometrial cancer, we suggest that FGFR2 may join the list of genes that play context-dependent opposing roles in cancer.
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Affiliation(s)
- Michael G Gartside
- Division of Cancer and Cell Biology, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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Baird K, Davis S, Antonescu CR, Harper UL, Walker RL, Chen Y, Glatfelter AA, Duray PH, Meltzer PS. Gene Expression Profiling of Human Sarcomas: Insights into Sarcoma Biology. Cancer Res 2005; 65:9226-35. [PMID: 16230383 DOI: 10.1158/0008-5472.can-05-1699] [Citation(s) in RCA: 276] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sarcomas are a biologically complex group of tumors of mesenchymal origin. By using gene expression microarray analysis, we aimed to find clues into the cellular differentiation and oncogenic pathways active in these tumors as well as potential biomarkers and therapeutic targets. We examined 181 tumors representing 16 classes of human bone and soft tissue sarcomas on a 12,601-feature cDNA microarray. Remarkably, 2,766 probes differentially expressed across this sample set clearly delineated the various tumor classes. Several genes of potential biological and therapeutic interest were associated with each sarcoma type, including specific tyrosine kinases, transcription factors, and homeobox genes. We also identified subgroups of tumors within the liposarcomas, leiomyosarcomas, and malignant fibrous histiocytomas. We found significant gene ontology correlates for each tumor group and identified similarity to normal tissues by Gene Set Enrichment Analysis. Mutation analysis done on 275 tumor samples revealed that the high expression of epidermal growth factor receptor (EGFR) in certain tumors was not associated with gene mutations. Finally, to further the investigation of human sarcoma biology, we have created an online, publicly available, searchable database housing the data from the gene expression profiles of these tumors (http://watson.nhgri.nih.gov/sarcoma), allowing the user to interactively explore this data set in depth.
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Affiliation(s)
- Kristin Baird
- Cancer Genetics Branch, National Human Genome Research Institute
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Pollock PM, Harper UL, Hansen KS, Yudt LM, Stark M, Robbins CM, Moses TY, Hostetter G, Wagner U, Kakareka J, Salem G, Pohida T, Heenan P, Duray P, Kallioniemi O, Hayward NK, Trent JM, Meltzer PS. High frequency of BRAF mutations in nevi. Nat Genet 2003; 33:19-20. [PMID: 12447372 DOI: 10.1038/ng1054] [Citation(s) in RCA: 1169] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2002] [Accepted: 10/29/2002] [Indexed: 11/08/2022]
Abstract
To evaluate the timing of mutations in BRAF (v-raf murine sarcoma viral oncogene homolog B1) during melanocytic neoplasia, we carried out mutation analysis on microdissected melanoma and nevi samples. We observed mutations resulting in the V599E amino-acid substitution in 41 of 60 (68%) melanoma metastases, 4 of 5 (80%) primary melanomas and, unexpectedly, in 63 of 77 (82%) nevi. These data suggest that mutational activation of the RAS/RAF/MAPK pathway in nevi is a critical step in the initiation of melanocytic neoplasia but alone is insufficient for melanoma tumorigenesis.
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Affiliation(s)
- Pamela M Pollock
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA
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