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Berns HM, Watkins-Chow DE, Lu S, Louphrasitthiphol P, Zhang T, Brown KM, Moura-Alves P, Goding CR, Pavan WJ. Single-cell profiling of MC1R-inhibited melanocytes. Pigment Cell Melanoma Res 2024; 37:291-308. [PMID: 37972124 DOI: 10.1111/pcmr.13141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Abstract
The human red hair color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. While MC1R variants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to define a MC1R-inhibited Gene Signature (MiGS) comprising a large set of previously unidentified genes which may be implicated in melanogenesis and oncogenic transformation. We show that one of the candidate MiGS genes, TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into further mechanisms by which melanocytes with reduced MC1R signaling may regulate pigmentation and offer new candidates of study toward understanding how individuals with the RHC phenotype are predisposed to melanoma.
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Affiliation(s)
- H Matthew Berns
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, PT, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, PT, Portugal
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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2
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Watkins-Chow DE, Incao AA, Rivas C, Elliott G, Garrett LJ, Pavan WJ. The MFSD12 p.Tyr182His common variant is sufficient to alter mouse agouti coat color. Pigment Cell Melanoma Res 2024; 37:259-264. [PMID: 37874775 DOI: 10.1111/pcmr.13144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023]
Abstract
MFSD12 functions as a transmembrane protein required for import of cysteine into melanosomes and lysosomes. The MFSD12 locus has been associated with phenotypic variation in skin color across African, Latin American, and East Asian populations. The frequency of a particular MFSD12 coding variant, rs2240751 (MAF = 0.08), has been reported to correlate with solar radiation and occur at highest frequency in Peruvian (PEL MAF = 0.48) and Han Chinese (CHB MAF = 0.40) populations, suggesting it could be causative for associated phenotypic variation in skin color. We have generated a mouse knock-in allele, Mfsd12Y182H , to model the human missense p.Tyr182His human variant. We demonstrate that the variant transcript is stably expressed and that agouti mice homozygote for the variant allele are viable with an altered coat color. This in vivo data confirms that the MFSD12 p.Tyr182His variant functions as a hypomorphic allele sufficient to alter mammalian pigmentation.
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Affiliation(s)
- Dawn E Watkins-Chow
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Arturo A Incao
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cecelia Rivas
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gene Elliott
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa J Garrett
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William J Pavan
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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3
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Loftus SK, Gillis MF, Lundh L, Baxter LL, Wedel JC, Watkins-Chow DE, Donovan FX, Sergeev YV, Oetting WS, Pavan WJ, Adams DR. Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B. Am J Hum Genet 2023; 110:1123-1137. [PMID: 37327787 PMCID: PMC10357474 DOI: 10.1016/j.ajhg.2023.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023] Open
Abstract
Oculocutaneous albinism (OCA) is a rare disorder of pigment production. Affected individuals have variably decreased global pigmentation and visual-developmental changes that lead to low vision. OCA is notable for significant missing heritability, particularly among individuals with residual pigmentation. Tyrosinase (TYR) is the rate-limiting enzyme in melanin pigment biosynthesis and mutations that decrease enzyme function are one of the most common causes of OCA. We present the analysis of high-depth short-read TYR sequencing data for a cohort of 352 OCA probands, ∼50% of whom were previously sequenced without yielding a definitive diagnostic result. Our analysis identified 66 TYR single-nucleotide variants (SNVs) and small insertion/deletions (indels), 3 structural variants, and a rare haplotype comprised of two common frequency variants (p.Ser192Tyr and p.Arg402Gln) in cis-orientation, present in 149/352 OCA probands. We further describe a detailed analysis of the disease-causing haplotype, p.[Ser192Tyr; Arg402Gln] ("cis-YQ"). Haplotype analysis suggests that the cis-YQ allele arose by recombination and that multiple cis-YQ haplotypes are segregating in OCA-affected individuals and control populations. The cis-YQ allele is the most common disease-causing allele in our cohort, representing 19.1% (57/298) of TYR pathogenic alleles in individuals with type 1 (TYR-associated) OCA. Finally, among the 66 TYR variants, we found several additional alleles defined by a cis-oriented combination of minor, potentially hypomorph-producing alleles at common variant sites plus a second, rare pathogenic variant. Together, these results suggest that identification of phased variants for the full TYR locus are required for an exhaustive assessment for potentially disease-causing alleles.
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Affiliation(s)
- Stacie K Loftus
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Meredith F Gillis
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank X Donovan
- Cancer Genomics Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuri V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Berns HM, Watkins-Chow DE, Lu S, Louphrasitthiphol P, Zhang T, Brown KM, Moura-Alves P, Goding CR, Pavan WJ. Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition. bioRxiv 2023:2023.03.10.532018. [PMID: 37090624 PMCID: PMC10120706 DOI: 10.1101/2023.03.10.532018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The human Red Hair Color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. While MC1R variants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to reveal a Pheomelanin Gene Signature (PGS) comprising genes implicated in melanogenesis and oncogenic transformation. We show that TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, is part of the PGS and binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into mechanisms by which MC1R signaling regulates pigmentation and how individuals with the RHC phenotype are predisposed to melanoma.
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Affiliation(s)
- H. Matthew Berns
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Dawn E. Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, 13 USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, 13 USA
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, PT
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, PT
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Baxter LL, Watkins-Chow DE, Johnson NL, Farhat NY, Platt FM, Dale RK, Porter FD, Pavan WJ, Rodriguez-Gil JL. Correlation of age of onset and clinical severity in Niemann-Pick disease type C1 with lysosomal abnormalities and gene expression. Sci Rep 2022; 12:2162. [PMID: 35140266 PMCID: PMC8828765 DOI: 10.1038/s41598-022-06112-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022] Open
Abstract
Niemann-Pick disease type C1 (NPC1) is a rare, prematurely fatal lysosomal storage disorder which exhibits highly variable severity and disease progression as well as a wide-ranging age of onset, from perinatal stages to adulthood. This heterogeneity has made it difficult to obtain prompt diagnosis and to predict disease course. In addition, small NPC1 patient sample sizes have been a limiting factor in acquiring genome-wide transcriptome data. In this study, primary fibroblasts from an extensive cohort of 41 NPC1 patients were used to validate our previous findings that the lysosomal quantitative probe LysoTracker can be used as a predictor for age of onset and disease severity. We also examined the correlation between these clinical parameters and RNA expression data from primary fibroblasts and identified a set of genes that were significantly associated with lysosomal defects or age of onset, in particular neurological symptom onset. Hierarchical clustering showed that these genes exhibited distinct expression patterns among patient subgroups. This study is the first to collect transcriptomic data on such a large scale in correlation with clinical and cellular phenotypes, providing a rich genomic resource to address NPC1 clinical heterogeneity and discover potential biomarkers, disease modifiers, or therapeutic targets.
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Affiliation(s)
- Laura L Baxter
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 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, USA
| | - Nicholas L Johnson
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Nicole Y Farhat
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Forbes D Porter
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - William J Pavan
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Rodriguez-Gil JL, Baxter LL, Watkins-Chow DE, Johnson NL, Davidson CD, Carlson SR, Incao AA, Wallom KL, Farhat NY, Platt FM, Dale RK, Porter FD, Pavan WJ. Transcriptome of HPβCD-treated Niemann-pick disease type C1 cells highlights GPNMB as a biomarker for therapeutics. Hum Mol Genet 2021; 30:2456-2468. [PMID: 34296265 DOI: 10.1093/hmg/ddab194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/20/2021] [Accepted: 06/29/2021] [Indexed: 11/12/2022] Open
Abstract
The rare, fatal neurodegenerative disorder Niemann-Pick disease type C1 (NPC1) arises from lysosomal accumulation of unesterified cholesterol and glycosphingolipids. These subcellular pathologies lead to phenotypes of hepatosplenomegaly, neurological degeneration and premature death. The timing and severity of NPC1 clinical presentation is extremely heterogeneous. This study analyzed RNA-Seq data from 42 NPC1 patient-derived, primary fibroblast cell lines to determine transcriptional changes induced by treatment with 2-hydroxypropyl-β-cyclodextrin (HPβCD), a compound currently under investigation in clinical trials. A total of 485 HPβCD-responsive genes were identified. Pathway enrichment analysis of these genes showed significant involvement in cholesterol and lipid biosynthesis. Furthermore, immunohistochemistry of the cerebellum as well as measurements of serum from Npc1m1N null mice treated with HPβCD and adeno-associated virus (AAV) gene therapy suggests that one of the identified genes, GPNMB, may serve as a useful biomarker of treatment response in NPC1 disease. Overall, this large NPC1 patient-derived dataset provides a comprehensive foundation for understanding the genomic response to HPβCD treatment.
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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.,Medical Scientist Training Program, University of Wisconsin-Madison School of Medicine and Public Health
| | - Laura L Baxter
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health
| | - Dawn E Watkins-Chow
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health
| | - Nicholas L Johnson
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Cristin D Davidson
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health
| | - Steven R Carlson
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health
| | - Arturo A Incao
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health
| | | | | | - Nicole Y Farhat
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | | | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - Forbes D Porter
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health
| | - William J Pavan
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health
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7
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Loftus SK, Lundh L, Watkins-Chow DE, Baxter LL, Pairo-Castineira E, Nisc Comparative Sequencing Program, Jackson IJ, Oetting WS, Pavan WJ, Adams DR. A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus. Hum Mutat 2021; 42:1239-1253. [PMID: 34246199 DOI: 10.1002/humu.24257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022]
Abstract
Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3-19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.
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Affiliation(s)
- Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | | | - Ian J Jackson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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8
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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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9
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Baxter LL, Watkins-Chow DE, Pavan WJ, Loftus SK. A curated gene list for expanding the horizons of pigmentation biology. Pigment Cell Melanoma Res 2019; 32:348-358. [PMID: 30339321 PMCID: PMC10413850 DOI: 10.1111/pcmr.12743] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/01/2018] [Accepted: 09/29/2018] [Indexed: 12/27/2022]
Abstract
Over the past century, studies of human pigmentary disorders along with mouse and zebrafish models have shed light on the many cellular functions associated with visible pigment phenotypes. This has led to numerous genes annotated with the ontology term "pigmentation" in independent human, mouse, and zebrafish databases. Comparisons among these datasets revealed that each is individually incomplete in documenting all genes involved in integument-based pigmentation phenotypes. Additionally, each database contained inherent species-specific biases in data annotation, and the term "pigmentation" did not solely reflect integument pigmentation phenotypes. This review presents a comprehensive, cross-species list of 650 genes involved in pigmentation phenotypes that was compiled with extensive manual curation of genes annotated in OMIM, MGI, ZFIN, and GO. The resulting cross-species list of genes both intrinsic and extrinsic to integument pigment cells provides a valuable tool that can be used to expand our knowledge of complex, pigmentation-associated pathways.
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Affiliation(s)
- Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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10
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Marshall CA, Watkins-Chow DE, Palladino G, Deutsch G, Chandran K, Pavan WJ, Erickson RP. In Niemann-Pick C1 mouse models, glial-only expression of the normal gene extends survival much further than do changes in genetic background or treatment with hydroxypropyl-beta-cyclodextrin. Gene 2017; 643:117-123. [PMID: 29223359 DOI: 10.1016/j.gene.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/01/2017] [Accepted: 12/06/2017] [Indexed: 11/19/2022]
Abstract
The Npc1nmf164 allele of Npc1 provides a mouse model for Niemann-Pick disease type C1 (NPC1), a genetic disease known to have a widely variable phenotype. The transfer of the Npc1nmf164 mutation from the C57BL/6J inbred strain to the BALB/cJ inbred strain increased the mean lifespan from 117.8days to 153.1days, confirming that the severity of the NPC1 phenotype is strongly influenced by genetic background. The transfer of another Npc1 allele, Npc1nih, to this background also extended survival of the homozygotes indicating that the modifying effect of BALB/cJ is not limited to a single allele of Npc1. The increased longevity due to the BALB/cJ background did not map to a previously mapped modifier on chromosome 19, indicating the presence of additional genes impacting disease severity. The previously studied Glial Fibrillary Acidic Protein promoter-Npc1 cDNA transgene (GFAP-Npc1) which only expresses NPC1 in astrocytes further extended the lifespan of Npc1nmf164 homozygotes on a BALB/cJ background (up to 600days). Hydroxypropyl-β-cyclodextrin (HPβCD) treatment, not previously tested in the Npc1nmf164 mutant, extended life in the Npc1nmf164 homozygotes but not the transgenic, Npc1nmf164 mice on the BALB/cJ background. In all cases, lack of weight gain and early cerebellar symptoms of loss of motor control were found. At termination, the one mouse sacrificed for histological studies showed severe, diffuse pulmonary alveolar proteinosis suggesting that pulmonary abnormalities in NPC1 mouse models are not unique to the Npc1nih allele.
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Affiliation(s)
- Craig A Marshall
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724-5073, United States
| | - Dawn E Watkins-Chow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Giampiero Palladino
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724-5073, United States
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA, United States
| | - Keshav Chandran
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724-5073, United States
| | - William J Pavan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Robert P Erickson
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724-5073, United States.
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11
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Marathe HG, Watkins-Chow DE, Weider M, Hoffmann A, Mehta G, Trivedi A, Aras S, Basuroy T, Mehrotra A, Bennett DC, Wegner M, Pavan WJ, de la Serna IL. BRG1 interacts with SOX10 to establish the melanocyte lineage and to promote differentiation. Nucleic Acids Res 2017; 45:6442-6458. [PMID: 28431046 PMCID: PMC5499657 DOI: 10.1093/nar/gkx259] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in SOX10 cause neurocristopathies which display varying degrees of hypopigmentation. Using a sensitized mutagenesis screen, we identified Smarca4 as a modifier gene that exacerbates the phenotypic severity of Sox10 haplo-insufficient mice. Conditional deletion of Smarca4 in SOX10 expressing cells resulted in reduced numbers of cranial and ventral trunk melanoblasts. To define the requirement for the Smarca4 -encoded BRG1 subunit of the SWI/SNF chromatin remodeling complex, we employed in vitro models of melanocyte differentiation in which induction of melanocyte-specific gene expression is closely linked to chromatin alterations. We found that BRG1 was required for expression of Dct, Tyrp1 and Tyr, genes that are regulated by SOX10 and MITF and for chromatin remodeling at distal and proximal regulatory sites. SOX10 was found to physically interact with BRG1 in differentiating melanocytes and binding of SOX10 to the Tyrp1 distal enhancer temporally coincided with recruitment of BRG1. Our data show that SOX10 cooperates with MITF to facilitate BRG1 binding to distal enhancers of melanocyte-specific genes. Thus, BRG1 is a SOX10 co-activator, required to establish the melanocyte lineage and promote expression of genes important for melanocyte function.
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Affiliation(s)
- Himangi G Marathe
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Dawn E Watkins-Chow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4472, USA
| | - Matthias Weider
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Alana Hoffmann
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Gaurav Mehta
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Archit Trivedi
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Shweta Aras
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Tupa Basuroy
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Aanchal Mehrotra
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Dorothy C Bennett
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - William J Pavan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4472, USA
| | - Ivana L de la Serna
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
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12
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Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J, Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA. Loci associated with skin pigmentation identified in African populations. Science 2017; 358:eaan8433. [PMID: 29025994 PMCID: PMC5759959 DOI: 10.1126/science.aan8433] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/03/2017] [Indexed: 12/13/2022]
Abstract
Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.
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Affiliation(s)
- Nicholas G Crawford
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Derek E Kelly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shanna L Bowman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ethan Jewett
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94704, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94704, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yancy Lo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C Campbell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Farhad Hormozdiari
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | | | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone, Botswana
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jake Haut
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Harriet Rothschild
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard Zon
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Zhou
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Sinclair
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cecilia Rivas
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eugene Elliot
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elena Oceana
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Yun S Song
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94704, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94704, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eleazar Eskin
- Department of Computer Science and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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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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14
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Watkins-Chow DE, Cooke J, Pidsley R, Edwards A, Slotkin R, Leeds KE, Mullen R, Baxter LL, Campbell TG, Salzer MC, Biondini L, Gibney G, Tuy FPD, Chelly J, Morris HD, Riegler J, Lythgoe MF, Arkell RM, Loreni F, Flint J, Pavan WJ, Keays DA. Correction: Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes. PLoS Genet 2015; 11:e1005682. [PMID: 26584186 PMCID: PMC4652907 DOI: 10.1371/journal.pgen.1005682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Saldana-Caboverde A, Perera EM, Watkins-Chow DE, Hansen NF, Vemulapalli M, Mullikin JC, Pavan WJ, Kos L. The transcription factors Ets1 and Sox10 interact during murine melanocyte development. Dev Biol 2015; 407:300-12. [PMID: 25912689 PMCID: PMC4618791 DOI: 10.1016/j.ydbio.2015.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 11/19/2022]
Abstract
Melanocytes, the pigment-producing cells, arise from multipotent neural crest (NC) cells during embryogenesis. Many genes required for melanocyte development were identified using mouse pigmentation mutants. The variable spotting mouse pigmentation mutant arose spontaneously at the Jackson Laboratory. We identified a G-to-A nucleotide transition in exon 3 of the Ets1 gene in variable spotting, which results in a missense G102E mutation. Homozygous variable spotting mice exhibit sporadic white spotting. Similarly, mice carrying a targeted deletion of Ets1 exhibit hypopigmentation; nevertheless, the function of Ets1 in melanocyte development is unknown. The transcription factor Ets1 is widely expressed in developing organs and tissues, including the NC. In the chick, Ets1 is required for the expression of Sox10, a transcription factor critical for the development of various NC derivatives, including melanocytes. We show that Ets1 is required early for murine NC cell and melanocyte precursor survival in vivo. Given the importance of Ets1 for Sox10 expression in the chick, we investigated a potential genetic interaction between these genes by comparing the hypopigmentation phenotypes of single and double heterozygous mice. The incidence of hypopigmentation in double heterozygotes was significantly greater than in single heterozygotes. The area of hypopigmentation in double heterozygotes was significantly larger than would be expected from the addition of the areas of hypopigmentation of single heterozygotes, suggesting that Ets1 and Sox10 interact synergistically in melanocyte development. Since Sox10 is also essential for enteric ganglia development, we examined the distal colons of Ets1 null mutants and found a significant decrease in enteric innervation, which was exacerbated by Sox10 heterozygosity. At the molecular level, Ets1 was found to activate an enhancer critical for Sox10 expression in NC-derived structures. Furthermore, enhancer activation was significantly inhibited by the variable spotting mutation. Together, these results suggest that Ets1 and Sox10 interact to promote proper melanocyte and enteric ganglia development from the NC.
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Affiliation(s)
| | - Erasmo M Perera
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nancy F Hansen
- Comparative Genomics Analysis Unit, CGCGB, National Human Genome Research Institute, Bethesda, MD, USA
| | - Meghana Vemulapalli
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Rockville, MD, USA
| | - James C Mullikin
- Comparative Genomics Analysis Unit, CGCGB, National Human Genome Research Institute, Bethesda, MD, USA; NIH Intramural Sequencing Center, National Human Genome Research Institute, Rockville, MD, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lidia Kos
- Department of Biological Sciences, Florida International University, Miami, FL, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL.
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16
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Fufa TD, Harris ML, Watkins-Chow DE, Levy D, Gorkin DU, Gildea DE, Song L, Safi A, Crawford GE, Sviderskaya EV, Bennett DC, Mccallion AS, Loftus SK, Pavan WJ. Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Hum Mol Genet 2015. [PMID: 26206884 DOI: 10.1093/hmg/ddv267] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
SOX10 is required for melanocyte development and maintenance, and has been linked to melanoma initiation and progression. However, the molecular mechanisms by which SOX10 guides the appropriate gene expression programs necessary to promote the melanocyte lineage are not fully understood. Here we employ genetic and epigenomic analysis approaches to uncover novel genomic targets and previously unappreciated molecular roles of SOX10 in melanocytes. Through global analysis of SOX10-binding sites and epigenetic characteristics of chromatin states, we uncover an extensive catalog of SOX10 targets genome-wide. Our findings reveal that SOX10 predominantly engages 'open' chromatin regions and binds to distal regulatory elements, including novel and previously known melanocyte enhancers. Integrated chromatin occupancy and transcriptome analysis suggest a role for SOX10 in both transcriptional activation and repression to regulate functionally distinct classes of genes. We demonstrate that distinct epigenetic signatures and cis-regulatory sequence motifs predicted to bind putative co-regulatory transcription factors define SOX10-activated and SOX10-repressed target genes. Collectively, these findings uncover a central role of SOX10 as a global regulator of gene expression in the melanocyte lineage by targeting diverse regulatory pathways.
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Affiliation(s)
- Temesgen D Fufa
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melissa L Harris
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Denise Levy
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David U Gorkin
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Derek E Gildea
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA, Department of Pediatrics, Division of Molecular Genetics, Duke University, Durham, NC 27708, USA and
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA, Department of Pediatrics, Division of Molecular Genetics, Duke University, Durham, NC 27708, USA and
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA, Department of Pediatrics, Division of Molecular Genetics, Duke University, Durham, NC 27708, USA and
| | - Elena V Sviderskaya
- Molecular Cell Sciences Research Centre, St George's, University of London, London SW17 0RE, UK
| | - Dorothy C Bennett
- Molecular Cell Sciences Research Centre, St George's, University of London, London SW17 0RE, UK
| | - Andrew S Mccallion
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA,
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17
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Harris ML, Levy DJ, Watkins-Chow DE, Pavan WJ. Ectopic differentiation of melanocyte stem cells is influenced by genetic background. Pigment Cell Melanoma Res 2015; 28:223-8. [PMID: 25495036 DOI: 10.1111/pcmr.12344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/01/2014] [Indexed: 01/13/2023]
Abstract
Hair graying in mouse is attributed to the loss of melanocyte stem cell function and the progressive depletion of the follicular melanocyte population. Single-gene, hair graying mouse models have pointed to a number of critical pathways involved in melanocyte stem cell biology; however, the broad range of phenotypic variation observed in human hair graying suggests that additional genetic variants involved in this process may yet be discovered. Using a sensitized approach, we ask here whether natural genetic variation influences a predominant cellular mechanism of hair graying in mouse, melanocyte stem cell differentiation. We developed an innovative method to quantify melanocyte stem cell differentiation by measuring ectopically pigmented melanocyte stem cells in response to the melanocyte-specific transgene Tg(Dct-Sox10). We make the novel observation that the production of ectopically pigmented melanocyte stem cells varies considerably across strains. The success of sensitizing for melanocyte stem cell differentiation by Tg(Dct-Sox10) sets the stage for future investigations into the genetic basis of strain-specific contributions to melanocyte stem cell biology.
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Affiliation(s)
- Melissa L Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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18
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Hazzard KC, Watkins-Chow DE, Garrett LJ. Method of euthanasia influences the oocyte fertilization rate with fresh mouse sperm. J Am Assoc Lab Anim Sci 2014; 53:641-6. [PMID: 25650969 PMCID: PMC4253576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 02/10/2014] [Accepted: 03/26/2014] [Indexed: 06/04/2023]
Abstract
In vitro fertilization (IVF) is used to produce mouse embryos for a variety of reasons. We evaluated the effect of the method of euthanasia on the fertilization rate in 2 different IVF protocols. Oocytes collected from C57BL/6J female mice euthanized by CO2 inhalation or cervical dislocation were used in IVF with fresh sperm from either wild-type or genetically engineered C57BL/6J. Compared with CO2 inhalation, cervical dislocation improved the resulting rate of fertilization by 18% in an IVF method using Cook media and by 13% in an IVF method using methyl-B cyclodextrin and reduced glutathione. The lower fertilization rate due to euthanasia by CO2 inhalation was accompanied by changes in blood pH and body temperature despite efforts to minimize temperature drops. In our hands, euthanasia by cervical dislocation improved fertilization rates and consequently reduced the number of egg-donor mice required.
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Affiliation(s)
- Karen C Hazzard
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, Bethesda, Maryland, USA.
| | - Dawn E Watkins-Chow
- Mouse Embryology Section, Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Lisa J Garrett
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, Bethesda, Maryland, USA
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Harmacek L, Watkins-Chow DE, Chen J, Jones KL, Pavan WJ, Salbaum JM, Niswander L. A unique missense allele of BAF155, a core BAF chromatin remodeling complex protein, causes neural tube closure defects in mice. Dev Neurobiol 2014; 74:483-97. [PMID: 24170322 DOI: 10.1002/dneu.22142] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 11/08/2022]
Abstract
Failure of embryonic neural tube closure results in the second most common class of birth defects known as neural tube defects (NTDs). While NTDs are likely the result of complex multigenic dysfunction, it is not known whether polymorphisms in epigenetic regulators may be risk factors for NTDs. Here we characterized Baf155(msp3) , a unique ENU-induced allele in mice. Homozygous Baf155(mps3) embryos exhibit highly penetrant exencephaly, allowing us to investigate the roles of an assembled, but malfunctional BAF chromatin remodeling complex in vivo at the time of neural tube closure. Evidence of defects in proliferation and apoptosis were found within the neural tube. RNA-Seq analysis revealed that surprisingly few genes showed altered expression in Baf155 mutant neural tissue, given the broad epigenetic role of the BAF complex, but included genes involved in neural development and cell survival. Moreover, gene expression changes between individual mutants were variable even though the NTD was consistently observed. This suggests that inconsistent gene regulation contributes to failed neural tube closure. These results shed light on the role of the BAF complex in the process of neural tube closure and highlight the importance of studying missense alleles to understand epigenetic regulation during critical phases of development.
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Affiliation(s)
- Laura Harmacek
- Department of Pediatrics and Graduate Program in Molecular Biology, Howard Hughes Medical Institute, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, Colorado, 80045
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20
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Cronin JC, Watkins-Chow DE, Incao A, Hasskamp JH, Schönewolf N, Aoude LG, Hayward NK, Bastian BC, Dummer R, Loftus SK, Pavan WJ. SOX10 ablation arrests cell cycle, induces senescence, and suppresses melanomagenesis. Cancer Res 2013; 73:5709-18. [PMID: 23913827 DOI: 10.1158/0008-5472.can-12-4620] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The transcription factor SOX10 is essential for survival and proper differentiation of neural crest cell lineages, where it plays an important role in the generation and maintenance of melanocytes. SOX10 is also highly expressed in melanoma tumors, but a role in disease progression has not been established. Here, we report that melanoma tumor cell lines require wild-type SOX10 expression for proliferation and SOX10 haploinsufficiency reduces melanoma initiation in the metabotropic glutamate receptor 1 (Grm1(Tg)) transgenic mouse model. Stable SOX10 knockdown in human melanoma cells arrested cell growth, altered cellular morphology, and induced senescence. Melanoma cells with stable loss of SOX10 were arrested in the G1 phase of the cell cycle, with reduced expression of the melanocyte determining factor microphthalmia-associated transcription factor, elevated expression of p21WAF1 and p27KIP2, hypophosphorylated RB, and reduced levels of its binding partner E2F1. As cell-cycle dysregulation is a core event in neoplastic transformation, the role for SOX10 in maintaining cell-cycle control in melanocytes suggests a rational new direction for targeted treatment or prevention of melanoma.
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Affiliation(s)
- Julia C Cronin
- Authors' Affiliations: Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland; Maryland Melanoma Center at Medstar Franklin Square Medical Center, Baltimore, Maryland; Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland; Queensland Institute of Medical Research, Oncogenomics Laboratory, Brisbane, Australia; and Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA
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21
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Fu R, Wassif CA, Yanjanin NM, Watkins-Chow DE, Baxter LL, Incao A, Liscum L, Sidhu R, Firnkes S, Graham M, Ory DS, Porter FD, Pavan WJ. Efficacy of N-acetylcysteine in phenotypic suppression of mouse models of Niemann-Pick disease, type C1. Hum Mol Genet 2013; 22:3508-23. [PMID: 23666527 DOI: 10.1093/hmg/ddt206] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Niemann-Pick disease, type C1 (NPC1), which arises from a mutation in the NPC1 gene, is characterized by abnormal cellular storage and transport of cholesterol and other lipids that leads to hepatic disease and progressive neurological impairment. Oxidative stress has been hypothesized to contribute to the NPC1 disease pathological cascade. To determine whether treatments reducing oxidative stress could alleviate NPC1 disease phenotypes, the in vivo effects of the antioxidant N-acetylcysteine (NAC) on two mouse models for NPC1 disease were studied. NAC was able to partially suppress phenotypes in both antisense-induced (NPC1ASO) and germline (Npc1-/-) knockout genetic mouse models, confirming the presence of an oxidative stress-related mechanism in progression of NPC1 phenotypes and suggesting NAC as a potential molecule for treatment. Gene expression analyses of NAC-treated NPC1ASO mice suggested NAC affects pathways distinct from those initially altered by Npc1 knockdown, data consistent with NAC achieving partial disease phenotype suppression. In a therapeutic trial of short-term NAC administration to NPC1 patients, no significant effects on oxidative stress in these patients were identified other than moderate improvement of the fraction of reduced CoQ10, suggesting limited efficacy of NAC monotherapy. However, the mouse model data suggest that the distinct antioxidant effects of NAC could provide potential treatment of NPC1 disease, possibly in concert with other therapeutic molecules at earlier stages of disease progression. These data also validated the NPC1ASO mouse as an efficient model for candidate NPC1 drug screening, and demonstrated similarities in hepatic phenotypes and genome-wide transcript expression patterns between the NPC1ASO and Npc1-/- models.
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Affiliation(s)
- Rao Fu
- Department of Health and Human Services, 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
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22
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Cronin JC, Watkins-Chow DE, Incao A, Hasskamp JH, Schönewolf N, Hayward NK, Bastian BC, Dummer R, Loftus SK, Pavan WJ. Abstract 1743: SOX10 is required for cell cycle regulation and melanomagenesis. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The transcription factor SOX10 is essential for proper survival and differentiation of neural crest cell lineages, and plays an important role in the establishment and maintenance of melanocytes. SOX10 is also highly expressed in melanoma tumors, however its role in the progression of the disease is not yet understood. Here, we report that melanoma tumor cell lines require wild-type SOX10 expression for proliferation, and detail the rescue of melanoma in the metabotropic glutamate receptor 1 (Grm1Tg) transgenic mouse by Sox10 haploinsufficiency. Stable SOX10 knockdown in human melanoma cells results in arrested growth, altered cellular morphology, and senescence. Cells with a stable loss of SOX10 are arrested in the G1 phase of the cell cycle with elevated cyclin-dependent kinase inhibitor 1A and 1B (p21 and p27) expression. SOX10 loss also results in hypophosphorylation of retinoblastoma protein (RB) and a reduction in the expression of its binding partner E2F1. Previously, the RB-E2F1 pathway has been shown to play a central role in cell cycle regulation, and here we demonstrate that SOX10 expression is required for the maintenance of the RB-E2F1 pathway to promote melanoma cell growth. One of the main events driving cellular transformation is the dysregulation of the cell cycle, therefore the role that SOX10 has in maintaining this process provides great promise for targeted interventions.
Citation Format: Julia C. Cronin, Dawn E. Watkins-Chow, Art Incao, Joanne H. Hasskamp, Nicola Schönewolf, Nicholas K. Hayward, Boris C. Bastian, Reinhard Dummer, Stacie K. Loftus, William J. Pavan. SOX10 is required for cell cycle regulation and melanomagenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1743. doi:10.1158/1538-7445.AM2013-1743
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Affiliation(s)
- Julia C. Cronin
- 1Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD
| | - Dawn E. Watkins-Chow
- 1Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD
| | - Art Incao
- 1Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD
| | - Joanne H. Hasskamp
- 2Maryland Melanoma Center at Medstar Franklin Square Medical Center, Baltimore, MD
| | - Nicola Schönewolf
- 3Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland
| | - Nicholas K. Hayward
- 4Queensland Institute of Medical Research, Oncogenomics Department, Queensland, Australia
| | - Boris C. Bastian
- 5Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA
| | - Reinhard Dummer
- 3Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland
| | - Stacie K. Loftus
- 1Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD
| | - William J. Pavan
- 1Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD
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23
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Cluzeau CVM, Watkins-Chow DE, Fu R, Borate B, Yanjanin N, Dail MK, Davidson CD, Walkley SU, Ory DS, Wassif CA, Pavan WJ, Porter FD. Microarray expression analysis and identification of serum biomarkers for Niemann-Pick disease, type C1. Hum Mol Genet 2012; 21:3632-46. [PMID: 22619379 DOI: 10.1093/hmg/dds193] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Niemann-Pick disease type C (NPC) is a lysosomal storage disorder characterized by liver disease and progressive neurodegeneration. Deficiency of either NPC1 or NPC2 leads to the accumulation of cholesterol and glycosphingolipids in late endosomes and early lysosomes. In order to identify pathological mechanisms underlying NPC and uncover potential biomarkers, we characterized liver gene expression changes in an Npc1 mouse model at six ages spanning the pathological progression of the disease. We identified altered gene expression at all ages, including changes in asymptomatic, 1-week-old mice. Biological pathways showing early altered gene expression included: lipid metabolism, cytochrome P450 enzymes involved in arachidonic acid and drug metabolism, inflammation and immune responses, mitogen-activated protein kinase and G-protein signaling, cell cycle regulation, cell adhesion and cytoskeleton remodeling. In contrast, apoptosis and oxidative stress appeared to be late pathological processes. To identify potential biomarkers that could facilitate monitoring of disease progression, we focused on a subset of 103 differentially expressed genes that encode secreted proteins. Further analysis identified two secreted proteins with increased serum levels in NPC1 patients: galectin-3 (LGALS3), a pro-inflammatory molecule, and cathepsin D (CTSD), a lysosomal aspartic protease. Elevated serum levels of both proteins correlated with neurological disease severity and appeared to be specific for NPC1. Expression of Lgals3 and Ctsd was normalized following treatment with 2-hydroxypropyl-β-cyclodextrin, a therapy that reduces pathological findings and significantly increases Npc1(-/-) survival. Both LGALS3 and CTSD have the potential to aid in diagnosis and serve as biomarkers to monitor efficacy in therapeutic trials.
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Affiliation(s)
- Celine V M Cluzeau
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA
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24
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Silver DL, Watkins-Chow DE, Schreck KC, Pierfelice TJ, Larson DM, Burnetti AJ, Liaw HJ, Myung K, Walsh CA, Gaiano N, Pavan WJ. The exon junction complex component Magoh controls brain size by regulating neural stem cell division. Nat Neurosci 2010; 13:551-8. [PMID: 20364144 PMCID: PMC2860667 DOI: 10.1038/nn.2527] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 03/03/2010] [Indexed: 12/13/2022]
Abstract
Brain structure and size requires precise division of neural stem cells (NSCs), which self-renew and generate intermediate neural progenitors (INPs) and neurons. The factors that regulate NSCs remain poorly understood, as do mechanistic explanations of how aberrant NSC division causes reduced brain size as seen in microcephaly. Here we demonstrate that Magoh, a component of the exon junction complex (EJC) that binds RNA, controls mouse cerebral cortical size by regulating NSC division. Magoh haploinsufficiency causes microcephaly due to INP depletion and neuronal apoptosis. Defective mitosis underlies these phenotypes as depletion of EJC components disrupts mitotic spindle orientation and integrity, chromosome number, and genomic stability. In utero rescue experiments revealed that a key function of Magoh is to control levels of the microcephaly-associated protein, LIS1, during neurogenesis. This study uncovers new requirements for the EJC in brain development, NSC maintenance, and mitosis, thus implicating this complex in the pathogenesis of microcephaly.
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Affiliation(s)
- Debra L Silver
- Genetic Disease Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland, USA
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25
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Abstract
A full understanding of transcriptional regulation requires integration of information obtained from multiple experimental datasets. These include datasets annotating gene expression within the context of an entire organism under normal and genetically perturbed conditions. Here we describe an expression dataset annotating pigment cell-expressed genes of the developing melanocyte and retinal pigmented epithelium lineages. Expression images are annotated and available at http://research.nhgri.nih.gov/manuscripts/Loftus/March2009/. Data are also summarized in a standardized manner using a universal melanoblast scoring scale that accounts for the embryonic location of cells and regional cell density. This approach allowed us to classify 14 pigment genes into four groupings classified by cell lineage expression, temporal-spatial context, and differential alteration in response to altered MITF and SOX10 status. Significant differences in regional populations were also observed across inbred strain backgrounds, highlighting the value of this approach to identify modifier allele influences on melanoblast number and distributions. This analysis revealed novel features of in vivo expression patterns that are not measurable by in vitro-based assays, providing data that in combination with genomic analyses will allow modeling of pigment cell gene expression in development and disease.
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Affiliation(s)
- Stacie K Loftus
- National Institutes of Health, National Human Genome Research Institute, Genetic Disease Research Branch, Bethesda, MD, USA.
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26
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Buac K, Watkins-Chow DE, Loftus SK, Larson DM, Incao A, Gibney G, Pavan WJ. A Sox10 expression screen identifies an amino acid essential for Erbb3 function. PLoS Genet 2008; 4:e1000177. [PMID: 18773073 PMCID: PMC2518866 DOI: 10.1371/journal.pgen.1000177] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 07/18/2008] [Indexed: 11/18/2022] Open
Abstract
The neural crest (NC) is a population of embryonic stem cells that gives rise to numerous cell types, including the glia and neurons of the peripheral and enteric nervous systems and the melanocytes of the skin and hair. Mutations in genes and genetic pathways regulating NC development lead to a wide spectrum of human developmental disorders collectively called neurocristopathies. To identify molecular pathways regulating NC development and to understand how alterations in these processes lead to disease, we established an N-ethyl-N-nitrosourea (ENU) mutagenesis screen utilizing a mouse model sensitized for NC defects, Sox10LacZ/+. Out of 71 pedigrees analyzed, we identified and mapped four heritable loci, called modifier of Sox10 expression pattern 1–4 (msp1–4), which show altered NC patterning. In homozygous msp1 embryos, Sox10LacZ expression is absent in cranial ganglia, cranial nerves, and the sympathetic chain; however, the development of other Sox10-expressing cells appears unaffected by the mutation. Linkage analysis, sequencing, and complementation testing confirmed that msp1 is a new allele of the receptor tyrosine kinase Erbb3, Erbb3msp1, that carries a single amino acid substitution in the extracellular region of the protein. The ENU-induced mutation does not alter protein expression, however, it is sufficient to impair ERBB3 signaling such that the embryonic defects observed in msp1 resemble those of Erbb3 null alleles. Biochemical analysis of the mutant protein showed that ERBB3 is expressed on the cell surface, but its ligand-induced phosphorylation is dramatically reduced by the msp1 mutation. These findings highlight the importance of the mutated residue for ERBB3 receptor function and activation. This study underscores the utility of using an ENU mutagenesis to identify genetic pathways regulating NC development and to dissect the roles of discrete protein domains, both of which contribute to a better understanding of gene function in a cellular and developmental setting. Genome-wide mutagenesis screens provide a valuable tool to identify genes and genetic pathways regulating complex developmental processes. The neural crest is a population of multipotent cells that gives rise to many different tissue and organ systems. Alterations in the pathways coordinating neural crest formation lead to human developmental disorders. To identify genetic components involved in neural crest development, we combined a whole-genome chemical mutagenesis approach with a mouse strain, Sox10LacZ/+, that marks neural crest progenitors during early embryogenesis. We identified and determined the chromosomal location of four mutant lines that display impaired neural crest patterning. One of the mutant lines identified carries a single amino acid change that is sufficient to alter neural crest development and cause embryonic lethality without impeding upon protein expression, highlighting the importance of the mutated residue for gene function. This study demonstrates the feasibility of mutagenesis screens to identify the molecular players required for neural crest development as well as to dissect protein domain functions.
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Affiliation(s)
- Kristina Buac
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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27
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Matera I, Watkins-Chow DE, Loftus SK, Hou L, Incao A, Silver DL, Rivas C, Elliott EC, Baxter LL, Pavan WJ. A sensitized mutagenesis screen identifies Gli3 as a modifier of Sox10 neurocristopathy. Hum Mol Genet 2008; 17:2118-31. [PMID: 18397875 DOI: 10.1093/hmg/ddn110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Haploinsufficiency for the transcription factor SOX10 is associated with the pigmentary deficiencies of Waardenburg syndrome (WS) and is modeled in Sox10 haploinsufficient mice (Sox10(LacZ/+)). As genetic background affects WS severity in both humans and mice, we established an N-ethyl-N-nitrosourea (ENU) mutagenesis screen to identify modifiers that increase the phenotypic severity of Sox10(LacZ/+) mice. Analysis of 230 pedigrees identified three modifiers, named modifier of Sox10 neurocristopathies (Mos1, Mos2 and Mos3). Linkage analysis confirmed their locations on mouse chromosomes 13, 4 and 3, respectively, within regions distinct from previously identified WS loci. Positional candidate analysis of Mos1 identified a truncation mutation in a hedgehog(HH)-signaling mediator, GLI-Kruppel family member 3 (Gli3). Complementation tests using a second allele of Gli3 (Gli3(Xt-J)) confirmed that a null mutation of Gli3 causes the increased hypopigmentation in Sox10(LacZ/+);Gli3(Mos1/)(+) double heterozygotes. Early melanoblast markers (Mitf, Sox10, Dct, and Si) are reduced in Gli3(Mos1/)(Mos1) embryos, indicating that loss of GLI3 signaling disrupts melanoblast specification. In contrast, mice expressing only the GLI3 repressor have normal melanoblast specification, indicating that the full-length GLI3 activator is not required for specification of neural crest to the melanocyte lineage. This study demonstrates the feasibility of sensitized screens to identify disease modifier loci and implicates GLI3 and other HH signaling components as modifiers of human neurocristopathies.
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Affiliation(s)
- Ivana Matera
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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28
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Watkins-Chow DE, Pavan WJ. Genomic copy number and expression variation within the C57BL/6J inbred mouse strain. Genes Dev 2008; 18:60-6. [PMID: 18032724 PMCID: PMC2134784 DOI: 10.1101/gr.6927808] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 10/16/2007] [Indexed: 12/14/2022]
Abstract
The C57BL/6J strain is one of the most widely used animal models for biomedical research, and individual mice within the strain are often assumed to be genetically identical after more than 70 yr of inbreeding. Using a single nucleotide polymorphism (SNP) genotyping panel, we assessed if copy number variations (CNVs) could be detected within the C57BL/6J strain by comparing relative allele frequencies in first generation (F(1)) progeny of C57BL/6J mice. Sequencing, quantitative PCR, breeding, and array comparative genomic hybridization (CGH) together confirmed the presence of two CNVs. Both CNVs span genes encoded on chromosome 19, and quantitative RT-PCR demonstrated that they result in altered expression of the insulin-degrading enzyme (Ide) and fibroblast growth factor binding protein 3 (Fgfbp3) genes. Analysis of 39 different C57BL/6J breeders revealed that 64% of mice from the Jackson Laboratory colony were heterozygous for the CNV spanning Ide. Homozygotes with and without the duplication were present in concordance with Hardy-Weinberg equilibrium (13% and 23%, respectively), and analysis of archived samples from the C57BL/6J colony suggests that the duplication has rapidly reached a high frequency in the colony since 1994. The identification of two CNVs in the small portion of the genome screened demonstrates that individual mice of highly inbred strains are not isogenic and suggests other CNVs may be segregating within C57BL/6J as well as other carefully maintained inbred strains. These differences can influence interpretations of physiological, biomedical, and behavioral experiments and can be exploited to model CNVs apparent in the human genome.
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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, USA
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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29
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Cushman LJ, Watkins-Chow DE, Brinkmeier ML, Raetzman LT, Radak AL, Lloyd RV, Camper SA. Persistent Prop1 expression delays gonadotrope differentiation and enhances pituitary tumor susceptibility. Hum Mol Genet 2001; 10:1141-53. [PMID: 11371507 DOI: 10.1093/hmg/10.11.1141] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 'paired'-like homeodomain transcription factor Prop1 is essential for the expansion of the pituitary primordia and for the differentiation and/or function of the hormone-producing cells of the anterior pituitary gland. Prop1 expression is normally extinguished before transcription of most differentiation markers is initiated. We report that constitutive expression of Prop1 interferes with anterior pituitary cell differentiation and increases the susceptibility for pituitary tumors. The terminal differentiation of pituitary gonadotropes is delayed, resulting in transient hypogonadism and a delay in the onset of puberty. Thyrotrope differentiation occurs normally, but thyrotrope function is impaired resulting in mild hypothyroidism. Aged mice exhibit defects consistent with misregulation of pituitary cell proliferation, including adenomatous hyperplasia with the formation of Rathke's cleft cysts and tumors. Thus, silencing Prop1 is important for normal pituitary development and function. These data suggest that gain-of-function mutations in PROP1 could contribute to the most common human pituitary endocrinopathies and tumors.
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Affiliation(s)
- L J Cushman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-0638, USA
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30
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Stahl JH, Kendall SK, Brinkmeier ML, Greco TL, Watkins-Chow DE, Campos-Barros A, Lloyd RV, Camper SA. Thyroid hormone is essential for pituitary somatotropes and lactotropes. Endocrinology 1999; 140:1884-92. [PMID: 10098528 DOI: 10.1210/endo.140.4.6627] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mice homozygous for a disruption in the alpha-subunit essential for TSH, LH, and FSH activity (alphaGsu-/-) exhibit hypothyroidism and hypogonadism similar to that observed in TSH receptor-deficient hypothyroid mice (hyt) and GnRH-deficient hypogonadal mutants (hpg). Although the five major hormone-producing cells of the anterior pituitary are present in alphaGsu-/- mice, the relative proportions of each cell type are altered dramatically. Thyrotropes exhibit hypertrophy and hyperplasia, and somatotropes and lactotropes are underrepresented. The size and number of gonadotropes in alphaGsu mutants are not remarkable in contrast to the hypertrophy characteristic of gonadectomized animals. The reduction in lactotropes is more severe in alphaGsu mutants (13-fold relative to wild-type) than in hyt or hpg mutants (4.5- and 1.5-fold, respectively). In addition, T4 replacement therapy of alphaGsu mutants restores lactotropes to near-normal levels, illustrating the importance of T4, but not alpha-subunit, for lactotrope proliferation and function. T4 replacement is permissive for gonadotrope hypertrophy in alphaGsu mutants, consistent with the role for T4 in the function of gonadotropes. This study reveals the importance of thyroid hormone in developing the appropriate proportions of anterior pituitary cell types.
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Affiliation(s)
- J H Stahl
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor 48109-0638, USA
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Abstract
The secrets of anterior pituitary development and cell lineage determination have been revealed mostly by genetic analyses. The requirement for three homeobox genes, Lbx3, Lbx4 and Titf1, during early organogenesis was proven by gene targeting. Spontaneous mouse mutations revealed two additional homeobox genes, Pit1 and Prop1, that are critical for specialization and proliferation of subsets of the five differentiated cell types. Analysis of patients with pituitary insufficiency has demonstrated the importance of these two genes in human pituitary function. Recently, several other homeobox genes have been identified and implicated in pituitary organogenesis. Genetic manipulations of these genes will undoubtedly add to the emerging genetic hierarchy regulating the ontogeny of this major hormone-producing gland.
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Affiliation(s)
- D E Watkins-Chow
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor 48109-0638, USA
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Watkins-Chow DE, Douglas KR, Buckwalter MS, Probst FJ, Camper SA. Construction of a 3-Mb contig and partial transcript map of the central region of mouse chromosome 11. Genomics 1997; 45:147-57. [PMID: 9339371 DOI: 10.1006/geno.1997.4931] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report the establishment of a high-resolution genetic map, a physical map, and a partial transcript map of the Ames dwarf critical region on mouse chromosome 11. A contig of 24 YACs and 13 P1 clones has been assembled and spans approximately 3 Mb from Flt4 to Tcf7. A library of approximately 1000 putative transcript clones from the region was prepared using exon amplification and pituitary cDNA selection. Ten novel transcripts were partially characterized, including a member of the olfactory receptor family, an alpha-tubulin-related sequence, and a novel member of the cdc2/CDC28-like kinase family, Clk4. The location of Prop1, the gene responsible for Ames dwarfism, has been localized within the contig. This contig spans a region of mouse chromosome 11 that exhibits linkage conservation with human chromosome 5q23-q35. The strength of the genetic map and genomic resources for this region suggest that comparative DNA sequencing of this region could reveal the genes responsible for other mouse mutants and human genetic diseases.
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Affiliation(s)
- D E Watkins-Chow
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor 48109, USA
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Watkins-Chow DE, Buckwalter MS, Newhouse MM, Lossie AC, Brinkmeier ML, Camper SA. Genetic mapping of 21 genes on mouse chromosome 11 reveals disruptions in linkage conservation with human chromosome 5. Genomics 1997; 40:114-22. [PMID: 9070927 DOI: 10.1006/geno.1996.4532] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report a high-resolution genetic map of 21 genes on the central region of mouse Chr 11. These genes were mapped by segregation analysis of more than 1650 meioses from three interspecific backcrosses. The order of these genes in mouse was compared to the previously established gene order in human. Eighteen of the 21 genes map to human Chr 5, and 2 of the genes define a proximal border for the region of homology between mouse Chr 11 and human Chr 17. Our results indicate a minimum of four rearrangements within the 10-cM region of synteny homology between mouse Chr 11 and human Chr 5. In addition, the linkage conservation is disrupted by groups of genes that map to mouse Chrs 13 and 18. These data demonstrate that large regions of conserved linkage can contain numerous chromosomal microrearrangements that have occurred since the divergence of mouse and human ancestors. Comparison of the mouse and human maps with data for other species provides an emerging picture of mammalian chromosome evolution.
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Affiliation(s)
- D E Watkins-Chow
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor 48109, USA
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