1
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Lee YH. Regarding "A Call for New Theories on the Pathogenesis and Pathophysiology of Endometriosis". J Minim Invasive Gynecol 2024; 31:624. [PMID: 38648970 DOI: 10.1016/j.jmig.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Yie Hou Lee
- KK Research Centre, KK Women's and Children's Hospital, Singapore; OBGYN-Academic Medicine Programme, Duke-NUS Medical School, Singapore
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2
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Skalniak A, Trofimiuk-Müldner M, Surmiak M, Totoń-Żurańska J, Jabrocka-Hybel A, Hubalewska-Dydejczyk A. Whole-Exome Screening and Analysis of Signaling Pathways in Multiple Endocrine Neoplasia Type 1 Patients with Different Outcomes: Insights into Cellular Mechanisms and Possible Functional Implications. Int J Mol Sci 2024; 25:1065. [PMID: 38256138 PMCID: PMC10816043 DOI: 10.3390/ijms25021065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Multiple endocrine neoplasia type 1 (MEN1) is a syndrome characterized by tumors in multiple organs. Although being a dominantly inherited monogenic disease, disease phenotypes are unpredictable and differ even among members of the same family. There is growing evidence for the role of modifier genes in the alteration of the course of this disease. However, genome-wide screening data are still lacking. In our study, we addressed the different outcomes of the disease, focusing on pituitary and adrenocortical tumors. By means of exome sequencing we identified the affected signaling pathways that segregated with those symptoms. Most significantly, we identified damaging alterations in numerous structural genes responsible for cell adhesion and migration. Additionally, in the case of pituitary tumors, genes related to neuronal function, survival, and morphogenesis were repeatedly identified, while in patients with adrenocortical tumors, TLR10, which is involved in the regulation of the innate immunity, was commonly modified. Our data show that using exome screening, it is possible to find signatures which correlate with the given clinical MEN1 outcomes, providing evidence that studies addressing modifier effects in MEN1 are reasonable.
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Affiliation(s)
- Anna Skalniak
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland;
| | - Małgorzata Trofimiuk-Müldner
- Department of Endocrinology, Jagiellonian University Medical College, 30-688 Krakow, Poland; (M.T.-M.); (A.J.-H.); (A.H.-D.)
| | - Marcin Surmiak
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland;
| | - Justyna Totoń-Żurańska
- Center for Medical Genomics—OMICRON, Jagiellonian University Medical College, 31-034 Krakow, Poland;
| | - Agata Jabrocka-Hybel
- Department of Endocrinology, Jagiellonian University Medical College, 30-688 Krakow, Poland; (M.T.-M.); (A.J.-H.); (A.H.-D.)
| | - Alicja Hubalewska-Dydejczyk
- Department of Endocrinology, Jagiellonian University Medical College, 30-688 Krakow, Poland; (M.T.-M.); (A.J.-H.); (A.H.-D.)
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3
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Kim JK, Jha NN, Awano T, Caine C, Gollapalli K, Welby E, Kim SS, Fuentes-Moliz A, Wang X, Feng Z, Sera F, Takeda T, Homma S, Ko CP, Tabares L, Ebert AD, Rich MM, Monani UR. A spinal muscular atrophy modifier implicates the SMN protein in SNARE complex assembly at neuromuscular synapses. Neuron 2023; 111:1423-1439.e4. [PMID: 36863345 PMCID: PMC10164130 DOI: 10.1016/j.neuron.2023.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 03/04/2023]
Abstract
Reduced survival motor neuron (SMN) protein triggers the motor neuron disease, spinal muscular atrophy (SMA). Restoring SMN prevents disease, but it is not known how neuromuscular function is preserved. We used model mice to map and identify an Hspa8G470R synaptic chaperone variant, which suppressed SMA. Expression of the variant in the severely affected mutant mice increased lifespan >10-fold, improved motor performance, and mitigated neuromuscular pathology. Mechanistically, Hspa8G470R altered SMN2 splicing and simultaneously stimulated formation of a tripartite chaperone complex, critical for synaptic homeostasis, by augmenting its interaction with other complex members. Concomitantly, synaptic vesicular SNARE complex formation, which relies on chaperone activity for sustained neuromuscular synaptic transmission, was found perturbed in SMA mice and patient-derived motor neurons and was restored in modified mutants. Identification of the Hspa8G470R SMA modifier implicates SMN in SNARE complex assembly and casts new light on how deficiency of the ubiquitous protein causes motor neuron disease.
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Affiliation(s)
- Jeong-Ki Kim
- Department of Neurology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA
| | - Narendra N Jha
- Department of Neurology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA
| | - Tomoyuki Awano
- Department of Neurology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA
| | - Charlotte Caine
- Department of Neurology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA
| | - Kishore Gollapalli
- Department of Neurology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA
| | - Emily Welby
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Seung-Soo Kim
- Department of Obstetrics and Gynecology, New York, NY, USA
| | - Andrea Fuentes-Moliz
- Department of Medical Physiology and Biophysics, University of Seville School of Medicine, 41009, Seville, Spain
| | - Xueyong Wang
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH 45435, USA
| | - Zhihua Feng
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fusako Sera
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Taishi Takeda
- Department of Neurology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA
| | - Shunichi Homma
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chien-Ping Ko
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Lucia Tabares
- Department of Medical Physiology and Biophysics, University of Seville School of Medicine, 41009, Seville, Spain
| | - Allison D Ebert
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mark M Rich
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH 45435, USA
| | - Umrao R Monani
- Department of Neurology, New York, NY, USA; Department of Pathology & Cell Biology, New York, NY, USA; Center for Motor Neuron Biology & Disease, New York, NY, USA; Colleen Giblin Research Laboratory, Columbia University Irving Medical Center, New York, NY 10032, USA.
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4
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Zhuri D, Gurkan H, Eker D, Karal Y, Yalcintepe S, Atli E, Demir S, Atli EI. Investigation on the Effects of Modifying Genes on the Spinal Muscular Atrophy Phenotype. Glob Med Genet 2022; 9:226-236. [PMID: 36071912 PMCID: PMC9444347 DOI: 10.1055/s-0042-1751302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Introduction
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by the degeneration of motor neurons, muscle weakness, and atrophy that leads to infant's death. The duplication of exon 7/8 in the
SMN2
gene reduces the clinical severity of disease, and it is defined as modifying effect. In this study, we aim to investigate the expression of modifying genes related to the prognosis of SMA like
PLS3
,
PFN2
,
ZPR1
,
CORO1C
,
GTF2H2
,
NRN1
,
SERF1A
,
NCALD
,
NAIP
, and
TIA1. Methods
Seventeen patients, who came to Trakya University, Faculty of Medicine, Medical Genetics Department, with a preliminary diagnosis of SMA disease, and eight healthy controls were included in this study after multiplex ligation-dependent probe amplification analysis. Gene expression levels were determined by real-time reverse transcription polymerase chain reaction and delta–delta CT method by the isolation of RNA from peripheral blood of patients and controls.
Results
SERF1A
and
NAIP
genes compared between A group and B + C + D groups, and A group of healthy controls, showed statistically significant differences (
p
= 0.037,
p
= 0.001).
Discussion
PLS3, NAIP
, and
NRN1
gene expressions related to SMA disease have been reported before in the literature. In our study, the expression levels of
SERF1A
,
GTF2H2
,
NCALD
,
ZPR1
,
TIA1
,
PFN2
, and
CORO1C
genes have been studied for the first time in SMA patients.
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Affiliation(s)
- Drenushe Zhuri
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Damla Eker
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Yasemin Karal
- Department of Pediatric Neurology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Engin Atli
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Selma Demir
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Emine Ikbal Atli
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
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5
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Wang HH, Portincasa P, Liu M, Wang DQH. Genetic Analysis of ABCB4 Mutations and Variants Related to the Pathogenesis and Pathophysiology of Low Phospholipid-Associated Cholelithiasis. Genes (Basel) 2022; 13:1047. [PMID: 35741809 PMCID: PMC9222727 DOI: 10.3390/genes13061047] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 12/28/2022] Open
Abstract
Clinical studies have revealed that the ABCB4 gene encodes the phospholipid transporter on the canalicular membrane of hepatocytes, and its mutations and variants are the genetic basis of low phospholipid-associated cholelithiasis (LPAC), a rare type of gallstone disease caused by a single-gene mutation or variation. The main features of LPAC include a reduction or deficiency of phospholipids in bile, symptomatic cholelithiasis at <40 years of age, intrahepatic sludge and microlithiasis, mild chronic cholestasis, a high cholesterol/phospholipid ratio in bile, and recurrence of biliary symptoms after cholecystectomy. Needle-like cholesterol crystals, putatively “anhydrous” cholesterol crystallization at low phospholipid concentrations in model and native bile, are characterized in ABCB4 knockout mice, a unique animal model for LPAC. Gallbladder bile with only trace amounts of phospholipids in these mice is supersaturated with cholesterol, with lipid composition plotting in the left two-phase zone of the ternary phase diagram, consistent with “anhydrous” cholesterol crystallization. In this review, we summarize the molecular biology and physiological functions of ABCB4 and comprehensively discuss the latest advances in the genetic analysis of ABCB4 mutations and variations and their roles in the pathogenesis and pathophysiology of LPAC in humans, based on the results from clinical studies and mouse experiments. To date, approximately 158 distinct LPAC-causing ABCB4 mutations and variants in humans have been reported in the literature, indicating that it is a monogenic risk factor for LPAC. The elucidation of the ABCB4 function in the liver, the identification of ABCB4 mutations and variants in LPAC patients, and the exploration of gene therapy for ABCB4 deficiency in animal models can help us to better understand the cellular, molecular, and genetic mechanisms underlying the onset of the disease, and will pave the way for early diagnosis and prevention of susceptible subjects and effective intervention for LPAC in patients.
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Affiliation(s)
- Helen H. Wang
- Department of Medicine and Genetics, Division of Gastroenterology and Liver Diseases, Marion Bessin Liver Research Center, Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Piero Portincasa
- Department of Biomedical Sciences and Human Oncology, Clinica Medica “A. Murri”, University of Bari Medical School, 70124 Bari, Italy;
| | - Min Liu
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45237, USA;
| | - David Q.-H. Wang
- Department of Medicine and Genetics, Division of Gastroenterology and Liver Diseases, Marion Bessin Liver Research Center, Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
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6
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Meyers E, Werner Z, Wichman D, Mathews HL, Radcliffe RA, Nadeau JH, Stitzel JA. Genetic Modifiers of Oral Nicotine Consumption in Chrna5 Null Mutant Mice. Front Psychiatry 2021; 12:773400. [PMID: 34803779 PMCID: PMC8601376 DOI: 10.3389/fpsyt.2021.773400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
The gene CHRNA5 is strongly associated with the level of nicotine consumption in humans and manipulation of the expression or function of Chrna5 similarly alters nicotine consumption in rodents. In both humans and rodents, reduced or complete loss of function of Chrna5 leads to increased nicotine consumption. However, the mechanism through which decreased function of Chrna5 increases nicotine intake is not well-understood. Toward a better understanding of how loss of function of Chrna5 increases nicotine consumption, we have initiated efforts to identify genetic modifiers of Chrna5 deletion-dependent oral nicotine consumption in mice. For this, we introgressed the Chrna5 knockout (KO) mutation onto a panel of C57BL/6J-Chr#A/J/NAJ chromosome substitution strains (CSS) and measured oral nicotine consumption in 18 CSS and C57BL/6 (B6) mice homozygous for the Chrna5 KO allele as well as their Chrna5 wild type littermates. As expected, nicotine consumption was significantly increased in Chrna5 KO mice relative to Chrna5 wildtype mice on a B6 background. Among the CSS homozygous for the Chrna5 KO allele, several exhibited altered nicotine consumption relative to B6 Chrna5 KO mice. Sex-independent modifiers were detected in CSS possessing A/J chromosomes 5 and 11 and a male-specific modifier was found on chromosome 15. In all cases nicotine consumption was reduced in the CSS Chrna5 KO mice relative to B6 Chrna5 KO mice and consumption in the CSS KO mice was indistinguishable from their wild type littermates. Nicotine consumption was also reduced in both Chrna5 KO and wildtype CSS mice possessing A/J chromosome 1 and increased in both KO and wild type chromosome 17 CSS relative to KO and wild type B6 mice. These results demonstrate the presence of several genetic modifiers of nicotine consumption in Chrna5 KO mice as well as identify loci that may affect nicotine consumption independent of Chrna5 genotype. Identification of the genes that underlie the altered nicotine consumption may provide novel insight into the mechanism through which Chrna5 deletion increases nicotine consumption and, more generally, a better appreciation of the neurobiology of nicotine intake.
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Affiliation(s)
- Erin Meyers
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - Zachary Werner
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - David Wichman
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - Hunter L. Mathews
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
| | - Richard A. Radcliffe
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joseph H. Nadeau
- Maine Medical Center Research Institute, Scarborough, ME, United States
| | - Jerry A. Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, United States
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7
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Kovács K, Farkas Z, Bajić D, Kalapis D, Daraba A, Almási K, Kintses B, Bódi Z, Notebaart RA, Poyatos JF, Kemmeren P, Holstege FCP, Pál C, Papp B. Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations. Mol Biol Evol 2021; 38:1137-1150. [PMID: 33306797 PMCID: PMC7947755 DOI: 10.1093/molbev/msaa280] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The fitness impact of loss-of-function mutations is generally assumed to reflect the loss of specific molecular functions associated with the perturbed gene. Here, we propose that rewiring of the transcriptome upon deleterious gene inactivation is frequently nonspecific and mimics stereotypic responses to external environmental change. Consequently, transcriptional response to gene deletion could be suboptimal and incur an extra fitness cost. Analysis of the transcriptomes of ∼1,500 single-gene deletion Saccharomyces cerevisiae strains supported this scenario. First, most transcriptomic changes are not specific to the deleted gene but are rather triggered by perturbations in functionally diverse genes. Second, gene deletions that alter the expression of dosage-sensitive genes are especially harmful. Third, by elevating the expression level of downregulated genes, we could experimentally mitigate the fitness defect of gene deletions. Our work shows that rewiring of genomic expression upon gene inactivation shapes the harmful effects of mutations.
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Affiliation(s)
- Károly Kovács
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Zoltán Farkas
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Djordje Bajić
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
- Logic of Genomic Systems Laboratory, Department of Systems Biology, CNB-CSIC, Madrid, Spain
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Microbial Sciences Institute, Yale University West Campus, West Haven, CT
| | - Dorottya Kalapis
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Andreea Daraba
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Karola Almási
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Bálint Kintses
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
- HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Zoltán Bódi
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Richard A Notebaart
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, Department of Systems Biology, CNB-CSIC, Madrid, Spain
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Csaba Pál
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Synthetic and Systems Biology Unit, Institute of Biochemistry, Szeged, Hungary
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8
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Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020; 81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Genetic predisposition affects the penetrance of tumor-initiating mutations, such as APC mutations that stabilize β-catenin and cause intestinal tumors in mice and humans. However, the mechanisms involved in genetically predisposed penetrance are not well understood. Here, we analyzed tumor multiplicity and gene expression in tumor-prone Apc Min/+ mice on highly variant C57BL/6J (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 × PWD) F1 APC Min offspring mice were largely free of intestinal adenoma, and several chromosome substitution (consomic) strains carrying single PWD chromosomes on the B6 genetic background displayed reduced adenoma numbers. Multiple dosage-dependent modifier loci on PWD chromosome 5 each contributed to tumor suppression. Activation of β-catenin-driven and stem cell-specific gene expression in the presence of Apc Min or following APC loss remained moderate in intestines carrying PWD chromosome 5, suggesting that PWD variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 were predominantly cis controlled and largely reflected parental patterns, providing a genetic basis for inheritance of tumor susceptibility. Human SNP variants of several modifier candidates were depleted in colorectal cancer genomes, suggesting that similar mechanisms may also affect the penetrance of cancer driver mutations in humans. Overall, our analysis highlights the strong impact that multiple genetic variants acting in networks can exert on tumor development. SIGNIFICANCE: These findings in mice show that, in addition to accidental mutations, cancer risk is determined by networks of individual gene variants.
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Affiliation(s)
- Alexandra L Farrall
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Christina Grimm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecophysiology and Aquaculture, Berlin, Germany
| | | | - Marta Caparros
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Prague, Czech Republic
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
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9
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Lines KE, Javid M, Reed AAC, Walls GV, Stevenson M, Simon M, Kooblall KG, Piret SE, Christie PT, Newey PJ, Mallon AM, Thakker RV. Genetic background influences tumour development in heterozygous Men1 knockout mice. Endocr Connect 2020; 9:426-437. [PMID: 32348957 PMCID: PMC7274560 DOI: 10.1530/ec-20-0103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 04/28/2020] [Indexed: 01/17/2023]
Abstract
Multiple endocrine neoplasia type 1 (MEN1), an autosomal dominant disorder caused by MEN1 germline mutations, is characterised by parathyroid, pancreatic and pituitary tumours. MEN1 mutations also cause familial isolated primary hyperparathyroidism (FIHP), a milder condition causing hyperparathyroidism only. Identical mutations can cause either MEN1 or FIHP in different families, thereby implicating a role for genetic modifiers in altering phenotypic expression of tumours. We therefore investigated the effects of genetic background and potential for genetic modifiers on tumour development in adult Men1+/- mice, which develop tumours of the parathyroids, pancreatic islets, anterior pituitary, adrenal cortex and gonads, that had been backcrossed to generate C57BL/6 and 129S6/SvEv congenic strains. A total of 275 Men1+/- mice, aged 5-26 months were macroscopically studied, and this revealed that genetic background significantly influenced the development of pituitary, adrenal and ovarian tumours, which occurred in mice over 12 months of age and more frequently in C57BL/6 females, 129S6/SvEv males and 129S6/SvEv females, respectively. Moreover, pituitary and adrenal tumours developed earlier, in C57BL/6 males and 129S6/SvEv females, respectively, and pancreatic and testicular tumours developed earlier in 129S6/SvEv males. Furthermore, glucagon-positive staining pancreatic tumours occurred more frequently in 129S6/SvEv Men1+/- mice. Whole genome sequence analysis of 129S6/SvEv and C57BL/6 Men1+/- mice revealed >54,000 different variants in >300 genes. These included, Coq7, Dmpk, Ccne2, Kras, Wnt2b, Il3ra and Tnfrsf10a, and qRT-PCR analysis revealed that Kras was significantly higher in pituitaries of male 129S6/SvEv mice. Thus, our results demonstrate that Kras and other genes could represent possible genetic modifiers of Men1.
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Affiliation(s)
- Kate E Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Mahsa Javid
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Anita A C Reed
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Gerard V Walls
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Sian E Piret
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Paul T Christie
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Paul J Newey
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, Headington, Oxford, UK
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10
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Li X, Liu M, Ren X, Loncle N, Wang Q, Hemba-Waduge RUS, Yu SH, Boube M, Bourbon HMG, Ni JQ, Ji JY. The Mediator CDK8-Cyclin C complex modulates Dpp signaling in Drosophila by stimulating Mad-dependent transcription. PLoS Genet 2020; 16:e1008832. [PMID: 32463833 PMCID: PMC7282676 DOI: 10.1371/journal.pgen.1008832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/09/2020] [Accepted: 05/05/2020] [Indexed: 11/19/2022] Open
Abstract
Dysregulation of CDK8 (Cyclin-Dependent Kinase 8) and its regulatory partner CycC (Cyclin C), two subunits of the conserved Mediator (MED) complex, have been linked to diverse human diseases such as cancer. Thus, it is essential to understand the regulatory network modulating the CDK8-CycC complex in both normal development and tumorigenesis. To identify upstream regulators or downstream effectors of CDK8, we performed a dominant modifier genetic screen in Drosophila based on the defects in vein patterning caused by specific depletion or overexpression of CDK8 or CycC in developing wing imaginal discs. We identified 26 genomic loci whose haploinsufficiency can modify these CDK8- or CycC-specific phenotypes. Further analysis of two overlapping deficiency lines and mutant alleles led us to identify genetic interactions between the CDK8-CycC pair and the components of the Decapentaplegic (Dpp, the Drosophila homolog of TGFβ, or Transforming Growth Factor-β) signaling pathway. We observed that CDK8-CycC positively regulates transcription activated by Mad (Mothers against dpp), the primary transcription factor downstream of the Dpp/TGFβ signaling pathway. CDK8 can directly interact with Mad in vitro through the linker region between the DNA-binding MH1 (Mad homology 1) domain and the carboxy terminal MH2 (Mad homology 2) transactivation domain. Besides CDK8 and CycC, further analyses of other subunits of the MED complex have revealed six additional subunits that are required for Mad-dependent transcription in the wing discs: Med12, Med13, Med15, Med23, Med24, and Med31. Furthermore, our analyses confirmed the positive roles of CDK9 and Yorkie in regulating Mad-dependent gene expression in vivo. These results suggest that CDK8 and CycC, together with a few other subunits of the MED complex, may coordinate with other transcription cofactors in regulating Mad-dependent transcription during wing development in Drosophila.
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Affiliation(s)
- Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Xingjie Ren
- School of Medicine, Tsinghua University, Beijing, China
| | - Nicolas Loncle
- Centre de Biologie Intégrative, Centre de Biologie du Développement, UMR5544 du CNRS, Université de Toulouse, Toulouse, France
| | - Qun Wang
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Rajitha-Udakara-Sampath Hemba-Waduge
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Stephen H. Yu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Muriel Boube
- Centre de Biologie Intégrative, Centre de Biologie du Développement, UMR5544 du CNRS, Université de Toulouse, Toulouse, France
| | - Henri-Marc G. Bourbon
- Centre de Biologie Intégrative, Centre de Biologie du Développement, UMR5544 du CNRS, Université de Toulouse, Toulouse, France
| | - Jian-Quan Ni
- School of Medicine, Tsinghua University, Beijing, China
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas, United States of America
- Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
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A Loss-of-Function Mutation in the Integrin Alpha L ( Itgal) Gene Contributes to Susceptibility to Salmonella enterica Serovar Typhimurium Infection in Collaborative Cross Strain CC042. Infect Immun 2019; 88:IAI.00656-19. [PMID: 31636138 DOI: 10.1128/iai.00656-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/05/2019] [Indexed: 12/18/2022] Open
Abstract
Salmonella is an intracellular bacterium found in the gastrointestinal tract of mammalian, avian, and reptilian hosts. Mouse models have been extensively used to model in vivo distinct aspects of human Salmonella infections and have led to the identification of several host susceptibility genes. We have investigated the susceptibility of Collaborative Cross strains to intravenous infection with Salmonella enterica serovar Typhimurium as a model of human systemic invasive infection. In this model, strain CC042/GeniUnc (CC042) mice displayed extreme susceptibility with very high bacterial loads and mortality. CC042 mice showed lower spleen weights and decreased splenocyte numbers before and after infection, affecting mostly CD8+ T cells, B cells, and all myeloid cell populations, compared with control C57BL/6J mice. CC042 mice also had lower thymus weights with a reduced total number of thymocytes and double-negative and double-positive (CD4+, CD8+) thymocytes compared to C57BL/6J mice. Analysis of bone marrow-resident hematopoietic progenitors showed a strong bias against lymphoid-primed multipotent progenitors. An F2 cross between CC042 and C57BL/6N mice identified two loci on chromosome 7 (Stsl6 and Stsl7) associated with differences in bacterial loads. In the Stsl7 region, CC042 carried a loss-of-function variant, unique to this strain, in the integrin alpha L (Itgal) gene, the causative role of which was confirmed by a quantitative complementation test. Notably, Itgal loss of function increased the susceptibility to S. Typhimurium in a (C57BL/6J × CC042)F1 mouse background but not in a C57BL/6J mouse inbred background. These results further emphasize the utility of the Collaborative Cross to identify new host genetic variants controlling susceptibility to infections and improve our understanding of the function of the Itgal gene.
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Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice. Genetics 2017; 206:621-639. [PMID: 28592500 PMCID: PMC5499176 DOI: 10.1534/genetics.116.198051] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022] Open
Abstract
In this study, Tyler et al. analyzed the complex genetic architecture of metabolic disease-related traits using the Diversity Outbred mouse population Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice. This population contained both sexes and two dietary cohorts. Transcript data were reduced to functional gene modules with weighted gene coexpression network analysis (WGCNA), which were used as summary phenotypes representing enriched biological processes. These module phenotypes were jointly analyzed with body composition and serum biomarkers in a combined analysis of pleiotropy and epistasis (CAPE), which inferred networks of epistatic interactions between quantitative trait loci that affect one or more traits. This network frequently mapped interactions between alleles of different ancestries, providing evidence of both genetic synergy and redundancy between haplotypes. Furthermore, a number of loci interacted with sex and diet to yield sex-specific genetic effects and alleles that potentially protect individuals from the effects of a high-fat diet. Although the epistatic interactions explained small amounts of trait variance, the combination of directional interactions, allelic specificity, and high genomic resolution provided context to generate hypotheses for the roles of specific genes in complex traits. Our approach moves beyond the cataloging of single loci to infer genetic networks that map genetic etiology by simultaneously modeling all phenotypes.
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Requena T, Gallego-Martinez A, Lopez-Escamez JA. A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets. Hum Genomics 2017; 11:11. [PMID: 28532469 PMCID: PMC5441048 DOI: 10.1186/s40246-017-0107-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/11/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets. RESULTS PAVAR and VAAST were able to select the same sets of candidate variants independently of the studied disease. In contrast, Exomiser V2 and VAAST-Phevor had a variable correlation depending on the phenotypic information available for the disease on each family. Nevertheless, all the selected diseases ranked a limited number of concordant variants in the top 10 ranking, using the three systems or other combined algorithm such as CADD or FATHMM. Benchmarking analyses confirmed that the combination of systems with different approaches improves the prediction of candidate variants compared with the use of a single method. The overall efficiency of combined tools ranges between 68 and 71% in the top 10 ranked variants. CONCLUSIONS Our pipeline prioritizes a short list of heterozygous variants in exome datasets based on the top 10 concordant variants combining multiple systems.
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Affiliation(s)
- Teresa Requena
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research – Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research – Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain
| | - Jose A. Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research – Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain
- Department of Otolaryngology, Complejo Hospitalario Universidad de Granada (CHUGRA), ibs.granada, 18014 Granada, Spain
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Zaragoza MV, Fung L, Jensen E, Oh F, Cung K, McCarthy LA, Tran CK, Hoang V, Hakim SA, Grosberg A. Exome Sequencing Identifies a Novel LMNA Splice-Site Mutation and Multigenic Heterozygosity of Potential Modifiers in a Family with Sick Sinus Syndrome, Dilated Cardiomyopathy, and Sudden Cardiac Death. PLoS One 2016; 11:e0155421. [PMID: 27182706 PMCID: PMC4868298 DOI: 10.1371/journal.pone.0155421] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/28/2016] [Indexed: 11/18/2022] Open
Abstract
The goals are to understand the primary genetic mechanisms that cause Sick Sinus Syndrome and to identify potential modifiers that may result in intrafamilial variability within a multigenerational family. The proband is a 63-year-old male with a family history of individuals (>10) with sinus node dysfunction, ventricular arrhythmia, cardiomyopathy, heart failure, and sudden death. We used exome sequencing of a single individual to identify a novel LMNA mutation and demonstrated the importance of Sanger validation and family studies when evaluating candidates. After initial single-gene studies were negative, we conducted exome sequencing for the proband which produced 9 gigabases of sequencing data. Bioinformatics analysis showed 94% of the reads mapped to the reference and identified 128,563 unique variants with 108,795 (85%) located in 16,319 genes of 19,056 target genes. We discovered multiple variants in known arrhythmia, cardiomyopathy, or ion channel associated genes that may serve as potential modifiers in disease expression. To identify candidate mutations, we focused on ~2,000 variants located in 237 genes of 283 known arrhythmia, cardiomyopathy, or ion channel associated genes. We filtered the candidates to 41 variants in 33 genes using zygosity, protein impact, database searches, and clinical association. Only 21 of 41 (51%) variants were validated by Sanger sequencing. We selected nine confirmed variants with minor allele frequencies <1% for family studies. The results identified LMNA c.357-2A>G, a novel heterozygous splice-site mutation as the primary mutation with rare or novel variants in HCN4, MYBPC3, PKP4, TMPO, TTN, DMPK and KCNJ10 as potential modifiers and a mechanism consistent with haploinsufficiency.
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Affiliation(s)
- Michael V. Zaragoza
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
- * E-mail:
| | - Lianna Fung
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Ember Jensen
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Frances Oh
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Katherine Cung
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Linda A. McCarthy
- Department of Biomedical Engineering and The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California Irvine, Irvine, California, United States of America
| | - Christine K. Tran
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Van Hoang
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Simin A. Hakim
- UC Irvine Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Sciences, University of California Irvine, Irvine, California, United States of America
| | - Anna Grosberg
- Department of Biomedical Engineering and The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California Irvine, Irvine, California, United States of America
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Cartilage-specific deletion of ephrin-B2 in mice results in early developmental defects and an osteoarthritis-like phenotype during aging in vivo. Arthritis Res Ther 2016; 18:65. [PMID: 26980243 PMCID: PMC4791873 DOI: 10.1186/s13075-016-0965-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/29/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Ephrins and their related receptors have been implicated in some developmental events. We have demonstrated that ephrin-B2 (EFNB2) could play a role in knee joint pathology associated with osteoarthritis (OA). Here, we delineate the in vivo role of EFNB2 in musculoskeletal growth, development, and in OA using a cartilage-specific EFNB2 knockout (EFNB2(Col2)KO) mouse model. METHODS EFNB2(Col2)KO was generated with Col2a1-Cre transgenic mice. The skeletal development was evaluated using macroscopy, immunohistochemistry, histomorphometry, radiology, densitometry, and micro-computed tomography. Analyses were performed at P0 (birth) and on postnatal days P15, P21, and on 8-week- and 1-year-old mice. RESULTS EFNB2(Col2)KO mice exhibited significant reduction in size, weight, length, and in long bones. At P0, the growth plates of EFNB2(Col2)KO mice displayed increased type X collagen, disorganized hyphertrophic zone, and decreased mineralization. At P15, mutant mice demonstrated a significant reduction in VEGF and TRAP at the chondro-osseous junction and a delay in the secondary ossification, including a decrease in bone volume and trabecular thickness. At P21 and 8 weeks old, EFNB2(Col2)KO mice exhibited reduced bone mineral density in the total skeleton, femur and spine. One-year-old EFNB2(Col2)KO mice demonstrated OA phenotypic features in both the knee and hip. By P15, 27 % of the EFNB2(Col2)KO mice developed a hip locomotor phenotype, which further experiments demonstrated reflected the neurological midline abnormality involving the corticospinal tract. CONCLUSION This in vivo study demonstrated, for the first time, that EFNB2 is essential for normal long bone growth and development and its absence leads to a knee and hip OA phenotype in aged mice.
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16
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QTL analysis of modifiers for pigmentary disorder in rats carrying Ednrb sl mutations. Sci Rep 2016; 6:19697. [PMID: 26796131 PMCID: PMC4726237 DOI: 10.1038/srep19697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/16/2015] [Indexed: 11/09/2022] Open
Abstract
Pigmentary variation in animals has been studied because of its application in genetics, evolution, and developmental biology. The large number of known color loci provides rich resource to elucidate the functional pigmentary system. Nonetheless, more color loci remain to be identified. In our previous study, we revealed that two different strains, namely, AGH rats and LEH rats, but which had the same null mutation of the Ednrb gene (Ednrb(sl)) showed markedly different pigmented coat ratio. This result strongly suggested that the severity of pigment abnormality was modified by genetic factor(s) in each strain. To elucidate the modifier locus of pigment disorder, we carried out whole-genome scanning for quantitative trait loci (QTLs) on 149 F2 (AGH-Ednrb(sl) × LEH-Ednrb(sl)) rats. A highly significant QTL, constituting 26% of the total pigmentation phenotype variance, was identified in a region around D7Got23 on chromosome (Chr) 7. In addition, investigation on epistatic interaction revealed significant interactions between D7Got23 and D3Rat78 and between D7Got23 and D14Mit4. Results suggested that a modified locus on Chr 7 was mainly responsible for the variance of pigmentary disorder between AGH-Ednrb(sl) rats and LEH-Ednrb(sl) rats, and two modifier loci showing epistatic interaction may, in part, influence pigment phenotype.
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17
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Chow CY, Kelsey KJP, Wolfner MF, Clark AG. Candidate genetic modifiers of retinitis pigmentosa identified by exploiting natural variation in Drosophila. Hum Mol Genet 2015; 25:651-9. [PMID: 26662796 DOI: 10.1093/hmg/ddv502] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/07/2015] [Indexed: 01/10/2023] Open
Abstract
Individuals carrying the same pathogenic mutation can present with a broad range of disease outcomes. While some of this variation arises from environmental factors, it is increasingly recognized that the background genetic variation of each individual can have a profound effect on the expressivity of a pathogenic mutation. In order to understand this background effect on disease-causing mutations, studies need to be performed across a wide range of backgrounds. Recent advancements in model organism biology allow us to test mutations across genetically diverse backgrounds and identify the genes that influence the expressivity of a mutation. In this study, we used the Drosophila Genetic Reference Panel, a collection of ∼200 wild-derived strains, to test the variability of the retinal phenotype of the Rh1(G69D) Drosophila model of retinitis pigmentosa (RP). We found that the Rh1(G69D) retinal phenotype is quite a variable quantitative phenotype. To identify the genes driving this extensive phenotypic variation, we performed a genome-wide association study. We identified 106 candidate genes, including 14 high-priority candidates. Functional testing by RNAi indicates that 10/13 top candidates tested influence the expressivity of Rh1(G69D). The human orthologs of the candidate genes have not previously been implicated as RP modifiers and their functions are diverse, including roles in endoplasmic reticulum stress, apoptosis and retinal degeneration and development. This study demonstrates the utility of studying a pathogenic mutation across a wide range of genetic backgrounds. These candidate modifiers provide new avenues of inquiry that may reveal new RP disease mechanisms and therapies.
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Affiliation(s)
- Clement Y Chow
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Keegan J P Kelsey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA and
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA and
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA and
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18
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Incomplete penetrance: The role of stochasticity in developmental cell colonization. J Theor Biol 2015; 380:309-14. [DOI: 10.1016/j.jtbi.2015.05.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/23/2022]
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Buchner DA, Nadeau JH. Contrasting genetic architectures in different mouse reference populations used for studying complex traits. Genome Res 2015; 25:775-91. [PMID: 25953951 PMCID: PMC4448675 DOI: 10.1101/gr.187450.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models.
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Affiliation(s)
- David A Buchner
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph H Nadeau
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA
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Szabó NE, Haddad-Tóvolli R, Zhou X, Alvarez-Bolado G. Cadherins mediate sequential roles through a hierarchy of mechanisms in the developing mammillary body. Front Neuroanat 2015; 9:29. [PMID: 25852491 PMCID: PMC4365714 DOI: 10.3389/fnana.2015.00029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 02/25/2015] [Indexed: 11/13/2022] Open
Abstract
Expression of intricate combinations of cadherins (a family of adhesive membrane proteins) is common in the developing central nervous system. On this basis, a combinatorial cadherin code has long been proposed to underlie neuronal sorting and to be ultimately responsible for the layers, columns and nuclei of the brain. However, experimental proof of this particular function of cadherins has proven difficult to obtain and the question is still not clear. Alternatively, non-specific, non-combinatorial, purely quantitative adhesive differentials have been proposed to explain neuronal sorting in the brain. Do cadherin combinations underlie brain cytoarchitecture? We approached this question using as model a well-defined forebrain nucleus, the mammillary body (MBO), which shows strong, homogeneous expression of one single cadherin (Cdh11) and patterned, combinatorial expression of Cdh6, −8 and −10. We found that, besides the known combinatorial Cdh pattern, MBO cells are organized into a second, non-overlapping pattern grouping neurons with the same date of neurogenesis. We report that, in the Foxb1 mouse mutant, Cdh11 expression fails to be maintained during MBO development. This disrupted the combination-based as well as the birthdate-based sorting in the mutant MBO. In utero RNA interference (RNAi) experiments knocking down Cdh11 in MBO-fated migrating neurons at one specific age showed that Cdh11 expression is required for chronological entrance in the MBO. Our results suggest that neuronal sorting in the developing MBO is caused by adhesion-based, non-combinatorial mechanisms that keep neurons sorted according to birthdate information (possibly matching them to target neurons chronologically sorted in the same manner). Non-specific adhesion mechanisms would also prevent cadherin combinations from altering the birthdate-based sorting. Cadherin combinations would presumably act later to support specific synaptogenesis through specific axonal fasciculation and final target recognition.
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Affiliation(s)
- Nora-Emöke Szabó
- Department Neurobiology and Development, Neural Circuit Development Unit, IRCM Montréal, QC, Canada
| | | | - Xunlei Zhou
- Department of Neuroanatomy, University of Heidelberg Heidelberg, Germany
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21
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Huang J, Dang R, Torigoe D, Lei C, Lan X, Chen H, Sasaki N, Wang J, Agui T. Identification of genetic loci affecting the severity of symptoms of Hirschsprung disease in rats carrying Ednrbsl mutations by quantitative trait locus analysis. PLoS One 2015; 10:e0122068. [PMID: 25790447 PMCID: PMC4366197 DOI: 10.1371/journal.pone.0122068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/12/2015] [Indexed: 01/17/2023] Open
Abstract
Hirschsprung’s disease (HSCR) is a congenital disease in neonates characterized by the absence of the enteric ganglia in a variable length of the distal colon. This disease results from multiple genetic interactions that modulate the ability of enteric neural crest cells to populate developing gut. We previously reported that three rat strains with different backgrounds (susceptible AGH-Ednrbsl/sl, resistant F344-Ednrbsl/sl, and LEH-Ednrbsl/sl) but the same null mutation of Ednrb show varying severity degrees of aganglionosis. This finding suggests that strain-specific genetic factors affect the severity of HSCR. Consistent with this finding, a quantitative trait locus (QTL) for the severity of HSCR on chromosome (Chr) 2 was identified using an F2 intercross between AGH and F344 strains. In the present study, we performed QTL analysis using an F2 intercross between the susceptible AGH and resistant LEH strains to identify the modifier/resistant loci for HSCR in Ednrb-deficient rats. A significant locus affecting the severity of HSCR was also detected within the Chr 2 region. These findings strongly suggest that a modifier gene of aganglionosis exists on Chr 2. In addition, two potentially causative SNPs (or mutations) were detected upstream of a known HSCR susceptibility gene, Gdnf. These SNPs were possibly responsible for the varied length of gut affected by aganglionosis.
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Affiliation(s)
- Jieping Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (RD); (CL)
| | - Daisuke Torigoe
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (RD); (CL)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, School of Veterinary Medicine, Kitasato University, Aomori, Japan
| | - Jinxi Wang
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takashi Agui
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
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Wetzel-Smith MK, Hunkapiller J, Bhangale TR, Srinivasan K, Maloney JA, Atwal JK, Sa SM, Yaylaoglu MB, Foreman O, Ortmann W, Rathore N, Hansen DV, Tessier-Lavigne M, Mayeux R, Pericak-Vance M, Haines J, Farrer LA, Schellenberg GD, Goate A, Behrens TW, Cruchaga C, Watts RJ, Graham RR. A rare mutation in UNC5C predisposes to late-onset Alzheimer's disease and increases neuronal cell death. Nat Med 2014; 20:1452-7. [PMID: 25419706 DOI: 10.1038/nm.3736] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/23/2014] [Indexed: 12/23/2022]
Abstract
We have identified a rare coding mutation, T835M (rs137875858), in the UNC5C netrin receptor gene that segregated with disease in an autosomal dominant pattern in two families enriched for late-onset Alzheimer's disease and that was associated with disease across four large case-control cohorts (odds ratio = 2.15, Pmeta = 0.0095). T835M alters a conserved residue in the hinge region of UNC5C, and in vitro studies demonstrate that this mutation leads to increased cell death in human HEK293T cells and in rodent neurons. Furthermore, neurons expressing T835M UNC5C are more susceptible to cell death from multiple neurotoxic stimuli, including β-amyloid (Aβ), glutamate and staurosporine. On the basis of these data and the enriched hippocampal expression of UNC5C in the adult nervous system, we propose that one possible mechanism in which T835M UNC5C contributes to the risk of Alzheimer's disease is by increasing susceptibility to neuronal cell death, particularly in vulnerable regions of the Alzheimer's disease brain.
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Affiliation(s)
| | - Julie Hunkapiller
- Department of Human Genetics, Genentech, South San Francisco, California, USA
| | - Tushar R Bhangale
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, California, USA
| | | | - Janice A Maloney
- Department of Neuroscience, Genentech, South San Francisco, California, USA
| | - Jasvinder K Atwal
- Department of Neuroscience, Genentech, South San Francisco, California, USA
| | - Susan M Sa
- Department of Pathology, Genentech, South San Francisco, California, USA
| | - Murat B Yaylaoglu
- Department of Pathology, Genentech, South San Francisco, California, USA
| | - Oded Foreman
- Department of Pathology, Genentech, South San Francisco, California, USA
| | - Ward Ortmann
- Department of Human Genetics, Genentech, South San Francisco, California, USA
| | - Nisha Rathore
- Department of Human Genetics, Genentech, South San Francisco, California, USA
| | - David V Hansen
- Department of Neuroscience, Genentech, South San Francisco, California, USA
| | - Marc Tessier-Lavigne
- Laboratory of Brain Development and Repair, Rockefeller University, New York, New York, USA
| | | | - Richard Mayeux
- 1] Department of Neurology, Taub Institute on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA. [2] Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
| | - Margaret Pericak-Vance
- 1] The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA. [2] Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Jonathan Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Lindsay A Farrer
- 1] Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA. [2] Department of Neurology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA. [3] Department of Ophthalmology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA. [4] Department of Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA. [5] Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alison Goate
- 1] Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA. [3] Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Timothy W Behrens
- Department of Human Genetics, Genentech, South San Francisco, California, USA
| | - Carlos Cruchaga
- 1] Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ryan J Watts
- Department of Neuroscience, Genentech, South San Francisco, California, USA
| | - Robert R Graham
- Department of Human Genetics, Genentech, South San Francisco, California, USA
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Abstract
Clinically relevant features of monogenic diseases, including severity of symptoms and age of onset, can vary widely in response to environmental differences as well as to the presence of genetic modifiers affecting the trait’s penetrance and expressivity. While a better understanding of modifier loci could lead to treatments for Mendelian diseases, the rarity of individuals harboring both a disease-causing allele and a modifying genotype hinders their study in human populations. We examined the genetic architecture of monogenic trait modifiers using a well-characterized yeast model of the human Mendelian disease classic galactosemia. Yeast strains with loss-of-function mutations in the yeast ortholog (GAL7) of the human disease gene (GALT) fail to grow in the presence of even small amounts of galactose due to accumulation of the same toxic intermediates that poison human cells. To isolate and individually genotype large numbers of the very rare (∼0.1%) galactose-tolerant recombinant progeny from a cross between two gal7Δ parents, we developed a new method, called “FACS-QTL.” FACS-QTL improves upon the currently used approaches of bulk segregant analysis and extreme QTL mapping by requiring less genome engineering and strain manipulation as well as maintaining individual genotype information. Our results identified multiple distinct solutions by which the monogenic trait could be suppressed, including genetic and nongenetic mechanisms as well as frequent aneuploidy. Taken together, our results imply that the modifiers of monogenic traits are likely to be genetically complex and heterogeneous.
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Li Y, Konicki WS, Wright JT, Suggs C, Xue H, Kuehl MA, Kulkarni AB, Gibson CW. Mouse genetic background influences the dental phenotype. Cells Tissues Organs 2014; 198:448-56. [PMID: 24732779 DOI: 10.1159/000360157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2014] [Indexed: 11/19/2022] Open
Abstract
Dental enamel covers the crown of the vertebrate tooth and is considered to be the hardest tissue in the body. Enamel develops during secretion of an extracellular matrix by ameloblast cells in the tooth germ, prior to eruption of the tooth into the oral cavity. Secreted enamel proteins direct mineralization patterns during the maturation stage of amelogenesis as the tooth prepares to erupt. The amelogenins are the most abundant enamel proteins and are required for normal enamel development. Phenotypic differences were observed between incisors from individual Amelx (amelogenin) null mice that had a mixed 129xC57BL/6J genetic background and between inbred wild-type (WT) mice with different genetic backgrounds (C57BL/6J, C3H/HeJ, FVB/NJ). We hypothesized that this could be due to modifier genes, as human patients with a mutation in an enamel protein gene causing the enamel defect amelogenesis imperfecta (AI) can also have varied appearance of dentitions within a kindred. Enamel density measurements varied for all WT inbred strains midway during incisor development. Enamel thickness varied between some WT strains, and, unexpectedly, dentin density varied extensively between incisors and molars of all WT and Amelx null strains studied. WTFVB/NJ incisors were more similar to those of Amelx null mice than to those of the other WT strains in terms of incisor height/width ratio and pattern of enamel mineralization. Strain-specific differences led to the conclusion that modifier genes may be implicated in determining both normal development and severity of enamel appearance in AI mouse models and may in future studies be related to phenotypic heterogeneity within human AI kindreds reported in the literature.
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Affiliation(s)
- Yong Li
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pa., USA
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25
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Balistreri CR, Candore G, Lio D, Carruba G. Prostate cancer: from the pathophysiologic implications of some genetic risk factors to translation in personalized cancer treatments. Cancer Gene Ther 2014; 21:2-11. [DOI: 10.1038/cgt.2013.77] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/16/2013] [Accepted: 09/19/2013] [Indexed: 02/07/2023]
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Xu M, Da YW, Liu L, Wang F, Jia JP. Giant axonal neuropathy caused by a novel compound heterozygous mutation in the gigaxonin gene. J Child Neurol 2013; 28:1316-9. [PMID: 23248352 DOI: 10.1177/0883073812467688] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Giant axonal neuropathy is a rare autosomal recessive disorder, which typically involves both central and peripheral nervous system. Yet the phenotypic-genotypic correlation remains obscure. We report a novel compound heterozygous mutation with the c. 805C>T in exon 4(Arg545His missense mutation) and the c. 1634G>A in exon 11(Arg269Trp missense mutation) in an 11-year-old Chinese giant axonal neuropathy case. This patient had an atypical giant axonal neuropathy phenotype rather similar to Charcot-Marie-Tooth disease, without tightly curled hair and mental retardation. The patient had a slowly progressive sensory motor neuropathy since age 3 years, and she also had nystagmus, feet deformities, scoliosis, and cerebellar tonsillar protrusion. Electrophysiological studies indicated a predominantly axonal sensory-motor neuropathy. The diagnosis was confirmed by sural nerve biopsy and direct sequencing of all the 11 gigaxonin exons. The proband's parents are heterozygotes of the disease without symptoms. Our findings extend the number of gigaxonin mutations that cause giant axonal neuropathy.
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Affiliation(s)
- Min Xu
- 1Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
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27
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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Chari S, Dworkin I. The conditional nature of genetic interactions: the consequences of wild-type backgrounds on mutational interactions in a genome-wide modifier screen. PLoS Genet 2013; 9:e1003661. [PMID: 23935530 PMCID: PMC3731224 DOI: 10.1371/journal.pgen.1003661] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 06/05/2013] [Indexed: 01/15/2023] Open
Abstract
The phenotypic outcome of a mutation cannot be simply mapped onto the underlying DNA variant. Instead, the phenotype is a function of the allele, the genetic background in which it occurs and the environment where the mutational effects are expressed. While the influence of genetic background on the expressivity of individual mutations is recognized, its consequences on the interactions between genes, or the genetic network they form, is largely unknown. The description of genetic networks is essential for much of biology; yet if, and how, the topologies of such networks are influenced by background is unknown. Furthermore, a comprehensive examination of the background dependent nature of genetic interactions may lead to identification of novel modifiers of biological processes. Previous work in Drosophila melanogaster demonstrated that wild-type genetic background influences the effects of an allele of scalloped (sd), with respect to both its principal consequence on wing development and its interactions with a mutation in optomotor blind. In this study we address whether the background dependence of mutational interactions is a general property of genetic systems by performing a genome wide dominant modifier screen of the sd(E3) allele in two wild-type genetic backgrounds using molecularly defined deletions. We demonstrate that ~74% of all modifiers of the sd(E3) phenotype are background-dependent due in part to differential sensitivity to genetic perturbation. These background dependent interactions include some with qualitative differences in the phenotypic outcome, as well as instances of sign epistasis. This suggests that genetic interactions are often contingent on genetic background, with flexibility in genetic networks due to segregating variation in populations. Such background dependent effects can substantially alter conclusions about how genes influence biological processes, the potential for genetic screens in alternative wild-type backgrounds identifying new loci that contribute to trait expression, and the inferences of the topology of genetic networks.
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Affiliation(s)
- Sudarshan Chari
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
| | - Ian Dworkin
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
- Program in Genetics, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Overexpression of ALS-associated p.M337V human TDP-43 in mice worsens disease features compared to wild-type human TDP-43 mice. Mol Neurobiol 2013; 48:22-35. [PMID: 23475610 PMCID: PMC3718993 DOI: 10.1007/s12035-013-8427-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 02/05/2013] [Indexed: 12/12/2022]
Abstract
Mutations in TAR DNA-binding protein 43 (TDP-43) are associated with familial forms of amyotrophic lateral sclerosis (ALS), while wild-type TDP-43 is a pathological hallmark of patients with sporadic ALS and frontotemporal lobar degeneration (FTLD). Various in vitro and in vivo studies have also demonstrated toxicity of both mutant and wild-type TDP-43 to neuronal cells. To study the potential additional toxicity incurred by mutant TDP-43 in vivo, we generated mutant human TDP-43 (p.M337V) transgenic mouse lines driven by the Thy-1.2 promoter (Mt-TAR) and compared them in the same experimental setting to the disease phenotype observed in wild-type TDP-43 transgenic lines (Wt-TAR) expressing comparable TDP-43 levels. Overexpression of mutant TDP-43 leads to a worsened dose-dependent disease phenotype in terms of motor dysfunction, neurodegeneration, gliosis, and development of ubiquitin and phosphorylated TDP-43 pathology. Furthermore, we show that cellular aggregate formation or accumulation of TDP-43 C-terminal fragments (CTFs) are not primarily responsible for development of the observed disease phenotype in both mutant and wild-type TDP-43 mice.
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De Castro SCP, Malhas A, Leung KY, Gustavsson P, Vaux DJ, Copp AJ, Greene NDE. Lamin b1 polymorphism influences morphology of the nuclear envelope, cell cycle progression, and risk of neural tube defects in mice. PLoS Genet 2012; 8:e1003059. [PMID: 23166514 PMCID: PMC3499363 DOI: 10.1371/journal.pgen.1003059] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 09/14/2012] [Indexed: 11/18/2022] Open
Abstract
Neural tube defects (NTDs), including spina bifida and anencephaly, are common birth defects whose complex multigenic causation has hampered efforts to delineate their molecular basis. The effect of putative modifier genes in determining NTD susceptibility may be investigated in mouse models, particularly those that display partial penetrance such as curly tail, a strain in which NTDs result from a hypomorphic allele of the grainyhead-like-3 gene. Through proteomic analysis, we found that the curly tail genetic background harbours a polymorphic variant of lamin B1, lacking one of a series of nine glutamic acid residues. Lamins are intermediate filament proteins of the nuclear lamina with multiple functions that influence nuclear structure, cell cycle properties, and transcriptional regulation. Fluorescence loss in photobleaching showed that the variant lamin B1 exhibited reduced stability in the nuclear lamina. Genetic analysis demonstrated that the variant also affects neural tube closure: the frequency of spina bifida and anencephaly was reduced three-fold when wild-type lamin B1 was bred into the curly tail strain background. Cultured fibroblasts expressing variant lamin B1 show significantly increased nuclear dysmorphology and diminished proliferative capacity, as well as premature senescence, associated with reduced expression of cyclins and Smc2, and increased expression of p16. The cellular basis of spinal NTDs in curly tail embryos involves a proliferation defect localised to the hindgut epithelium, and S-phase progression was diminished in the hindgut of embryos expressing variant lamin B1. These observations indicate a mechanistic link between altered lamin B1 function, exacerbation of the Grhl3-mediated cell proliferation defect, and enhanced susceptibility to NTDs. We conclude that lamin B1 is a modifier gene of major effect for NTDs resulting from loss of Grhl3 function, a role that is likely mediated via the key function of lamin B1 in maintaining integrity of the nuclear envelope and ensuring normal cell cycle progression.
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Affiliation(s)
- Sandra C. P. De Castro
- Neural Development Unit, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Ashraf Malhas
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Kit-Yi Leung
- Neural Development Unit, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - David J. Vaux
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Andrew J. Copp
- Neural Development Unit, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Nicholas D. E. Greene
- Neural Development Unit, UCL Institute of Child Health, University College London, London, United Kingdom
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Davisson MT, Bergstrom DE, Reinholdt LG, Donahue LR. Discovery Genetics - The History and Future of Spontaneous Mutation Research. ACTA ACUST UNITED AC 2012; 2:103-118. [PMID: 25364627 DOI: 10.1002/9780470942390.mo110200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Historically, spontaneous mutations in mice have served as valuable models of heritable human diseases, contributing substantially to our understanding of both disease mechanisms and basic biological pathways. While advances in molecular technologies have improved our ability to create mouse models of human disease through targeted mutagenesis and transgenesis, spontaneous mutations continue to provide valuable research tools for discovery of novel genes and functions. In addition, the genetic defects caused by spontaneous mutations are molecularly similar to mutations in the human genome and, therefore often produce phenotypes that more closely resemble those characteristic of human disease than do genetically engineered mutations. Due to the rarity with which spontaneous mutations arise and the animal intensive nature of their genetic analysis, large-scale spontaneous mutation analysis has traditionally been limited to large mammalian genetics institutes. More recently, ENU mutagenesis and new screening methods have increased the rate of mutant strain discovery, and high-throughput DNA sequencing has enabled rapid identification of the underlying genes and their causative mutations. Here, we discuss the continued value of spontaneous mutations for biomedical research.
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Zhao D, Qiu GX, Wang YP, Zhang JG, Shen JX, Wu ZH. Association between adolescent idiopathic scoliosis with double curve and polymorphisms of calmodulin1 gene/estrogen receptor-α gene. Orthop Surg 2012; 1:222-30. [PMID: 22009847 DOI: 10.1111/j.1757-7861.2009.00038.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To investigate whether single nucleotide polymorphisms (SNP) of the calmodulin1 (CALM1) and estrogen receptor-α genes correlate with double curve in adolescent idiopathic scoliosis (AIS). METHODS A total of 67 Chinese patients with AIS with double curve and 100 healthy controls were recruited. Curve pattern and Cobb angle of each patient were recorded. The Cobb angle is at least 30°. There were 60 patients with Cobb angle ≥ 40°. According to the apical location of the major curve, there were 40 thoracic curve patients. Four polymorphic loci, including rs12885713 (-16C > T) and rs5871 in the CALM1 gene and rs2234693 (Pvu II) and rs9340799 (Xba I) in the estrogen receptor 1 (ER1) gene were analyzed by the ABI3730 genetic analyzer. RESULTS The current study indicates that: (i) there are statistical differences between patients with double curve, with Cobb angle ≥ 40° and with thoracic curve and healthy controls in the polymorphic distribution of the rs2234693 site of the ER1 gene, (P= 0.014, 0.0128, 0.0184 respectively); (ii) there is a difference between patients with double curve and controls in the polymorphic distribution of the rs12885713 site in the CALM1 gene (P= 0.034); and (iii) there is a difference between thoracic curve patients and controls in the polymorphic distribution of the rs5871 site in the CALM1 gene (P= 0.0102). CONCLUSIONS Different subtypes of AIS might be related to different SNP. A combination of CALM1 and ER1 gene polymorphisms might be related to double curve in patients with AIS. Further study is necessary to confirm these hypotheses.
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Affiliation(s)
- Dong Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Beijing, China
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Dang R, Torigoe D, Sasaki N, Agui T. QTL analysis identifies a modifier locus of aganglionosis in the rat model of Hirschsprung disease carrying Ednrb(sl) mutations. PLoS One 2011; 6:e27902. [PMID: 22132166 PMCID: PMC3222640 DOI: 10.1371/journal.pone.0027902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/27/2011] [Indexed: 01/31/2023] Open
Abstract
Hirschsprung disease (HSCR) exhibits complex genetics with incomplete penetrance and variable severity thought to result as a consequence of multiple gene interactions that modulate the ability of enteric neural crest cells to populate the developing gut. As reported previously, when the same null mutation of the Ednrb gene, Ednrbsl, was introgressed into the F344 strain, almost 60% of F344-Ednrbsl/sl pups did not show any symptoms of aganglionosis, appearing healthy and normally fertile. These findings strongly suggested that the severity of HSCR was affected by strain-specific genetic factor (s). In this study, the genetic basis of such large strain differences in the severity of aganglionosis in the rat model was studied by whole-genome scanning for quantitative trait loci (QTLs) using an intercross of (AGH-Ednrbsl×F344-Ednrbsl) F1 with the varying severity of aganglionosis. Genome linkage analysis identified one significant QTL on chromosome 2 for the severity of aganglionosis. Our QTL analyses using rat models of HSCR revealed that multiple genetic factors regulated the severity of aganglionosis. Moreover, a known HSCR susceptibility gene, Gdnf, was found in QTL that suggested a novel non-coding sequence mutation in GDNF that modifies the penetrance and severity of the aganglionosis phenotype in EDNRB-deficient rats. A further identification and analysis of responsible genes located on the identified QTL could lead to the richer understanding of the genetic basis of HSCR development.
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Affiliation(s)
- Ruihua Dang
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Daisuke Torigoe
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takashi Agui
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
- * E-mail:
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Devoto M, Specchia C, Laudenslager M, Longo L, Hakonarson H, Maris J, Mossé Y. Genome-wide linkage analysis to identify genetic modifiers of ALK mutation penetrance in familial neuroblastoma. Hum Hered 2011; 71:135-9. [PMID: 21734404 DOI: 10.1159/000324843] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is an important childhood cancer with a strong genetic component related to disease susceptibility. Approximately 1% of NB cases have a positive family history. Following a genome-wide linkage analysis and sequencing of candidate genes in the critical region, we identified ALK as the major familial NB gene. Dominant mutations in ALK are found in more than 50% of familial NB cases. However, in the families used for the linkage study, only about 50% of carriers of ALK mutations are affected by NB. METHODS To test whether genetic variation may explain the reduced penetrance of the disease phenotype, we analyzed genome-wide genotype data in ALK mutation-positive families using a model-based linkage approach with different liability classes for carriers and non-carriers of ALK mutations. RESULTS The region with the highest LOD score was located at chromosome 2p23-p24 and included the ALK locus under models of dominant and recessive inheritance. CONCLUSIONS This finding suggests that variants in the non-mutated ALK gene or another gene linked to it may affect penetrance of the ALK mutations and risk of developing NB in familial cases.
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Affiliation(s)
- Marcella Devoto
- Division of Genetics, The Children's Hospital of Philadelphia, Pa., USA. devoto @ chop.edu
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Alcaraz WA, Chen E, Valdes P, Kim E, Lo YH, Vo J, Hamilton BA. Modifier genes and non-genetic factors reshape anatomical deficits in Zfp423-deficient mice. Hum Mol Genet 2011; 20:3822-30. [PMID: 21729880 DOI: 10.1093/hmg/ddr300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Development of neural circuitry depends on the integration of signaling pathways to coordinate specification, proliferation and differentiation of cell types in the right number, in the right place, at the right time. Zinc finger protein 423 (Zfp423), a 30-zinc finger transcription factor, forms alternate complexes with components of several developmental signaling pathways, suggesting it as a point of signal integration during brain development. We previously showed that mice lacking Zfp423 have reduced proliferation of cerebellar precursor cells, resulting in complete loss of vermis and variable hypoplasia of cerebellar hemispheres. Here, we show that Zfp423(-/-) hemisphere malformations are shaped by both genetic and non-genetic factors, producing distinct phenotype distributions in different inbred genetic backgrounds. In genetic mapping studies, we identify four additive modifier loci (Amzn1-4) and seven synthetically interacting loci (Smzn1.1-3.1) that together explain approximately one-third of the phenotypic variance. Strain-specific sequence polymorphism and expression data provide a reduced list of functional variant candidate genes at each modifier locus. Environmental covariates add only modest explanatory power, suggesting an additional stochastic component. These results provide a comprehensive analysis of sources of phenotype variation in a model of hindbrain malformation.
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Affiliation(s)
- Wendy A Alcaraz
- Biomedical Sciences Graduate Program,, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0644, USA
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Justice MJ, Siracusa LD, Stewart AF. Technical approaches for mouse models of human disease. Dis Model Mech 2011; 4:305-10. [PMID: 21558063 PMCID: PMC3097452 DOI: 10.1242/dmm.000901] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The mouse is the leading organism for disease research. A rich resource of genetic variation occurs naturally in inbred and special strains owing to spontaneous mutations. However, one can also obtain desired gene mutations by using the following processes: targeted mutations that eliminate function in the whole organism or in a specific tissue; forward genetic screens using chemicals or transposons; or the introduction of exogenous transgenes as DNAs, bacterial artificial chromosomes (BACs) or reporter constructs. The mouse is the only mammal that provides such a rich resource of genetic diversity coupled with the potential for extensive genome manipulation, and is therefore a powerful application for modeling human disease. This poster review outlines the major genome manipulations available in the mouse that are used to understand human disease: natural variation, reverse genetics, forward genetics, transgenics and transposons. Each of these applications will be essential for understanding the diversity that is being discovered within the human population.
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Affiliation(s)
- Monica J Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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Libé R, Horvath A, Vezzosi D, Fratticci A, Coste J, Perlemoine K, Ragazzon B, Guillaud-Bataille M, Groussin L, Clauser E, Raffin-Sanson ML, Siegel J, Moran J, Drori-Herishanu L, Faucz FR, Lodish M, Nesterova M, Bertagna X, Bertherat J, Stratakis CA. Frequent phosphodiesterase 11A gene (PDE11A) defects in patients with Carney complex (CNC) caused by PRKAR1A mutations: PDE11A may contribute to adrenal and testicular tumors in CNC as a modifier of the phenotype. J Clin Endocrinol Metab 2011; 96:E208-14. [PMID: 21047926 PMCID: PMC3038483 DOI: 10.1210/jc.2010-1704] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Carney complex (CNC) is an autosomal dominant multiple neoplasia, caused mostly by inactivating mutations of the regulatory subunit 1A of the protein kinase A (PRKAR1A). Primary pigmented nodular adrenocortical disease (PPNAD) is the most frequent endocrine manifestation of CNC with a great inter-individual variability. Germline, protein-truncating mutations of phosphodiesterase type 11A (PDE11A) have been described to predispose to a variety of endocrine tumors, including adrenal and testicular tumors. OBJECTIVES Our objective was to investigate the role of PDE11A as a possible gene modifier of the phenotype in a series of 150 patients with CNC. RESULTS A higher frequency of PDE11A variants in patients with CNC compared with healthy controls was found (25.3 vs. 6.8%, P < 0.0001). Among CNC patients, those with PPNAD were significantly more frequently carriers of PDE11A variants compared with patients without PPNAD (30.8 vs. 13%, P = 0.025). Furthermore, men with PPNAD were significantly more frequently carriers of PDE11A sequence variants (40.7%) than women with PPNAD (27.3%) (P < 0.001). A higher frequency of PDE11A sequence variants was also found in patients with large-cell calcifying Sertoli cell tumors (LCCSCT) compared with those without LCCSCT (50 vs. 10%, P = 0.0056). PDE11A variants were significantly associated with the copresence of PPNAD and LCCSCT in men: 81 vs. 20%, P < 0.004). The simultaneous inactivation of PRKAR1A and PDE11A by small inhibitory RNA led to an increase in cAMP-regulatory element-mediated transcriptional activity under basal conditions and after stimulation by forskolin. CONCLUSIONS We demonstrate, in a large cohort of CNC patients, a high frequency of PDE11A variants, suggesting that PDE11A is a genetic modifying factor for the development of testicular and adrenal tumors in patients with germline PRKAR1A mutation.
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Affiliation(s)
- Rossella Libé
- Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Paris, France
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Davis SW, Castinetti F, Carvalho LR, Ellsworth BS, Potok MA, Lyons RH, Brinkmeier ML, Raetzman LT, Carninci P, Mortensen AH, Hayashizaki Y, Arnhold IJP, Mendonça BB, Brue T, Camper SA. Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes. Mol Cell Endocrinol 2010; 323:4-19. [PMID: 20025935 PMCID: PMC2909473 DOI: 10.1016/j.mce.2009.12.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Defects in pituitary gland organogenesis are sometimes associated with congenital anomalies that affect head development. Lesions in transcription factors and signaling pathways explain some of these developmental syndromes. Basic research studies, including the characterization of genetically engineered mice, provide a mechanistic framework for understanding how mutations create the clinical characteristics observed in patients. Defects in BMP, WNT, Notch, and FGF signaling pathways affect induction and growth of the pituitary primordium and other organ systems partly by altering the balance between signaling pathways. The PITX and LHX transcription factor families influence pituitary and head development and are clinically relevant. A few later-acting transcription factors have pituitary-specific effects, including PROP1, POU1F1 (PIT1), and TPIT (TBX19), while others, such as NeuroD1 and NR5A1 (SF1), are syndromic, influencing development of other endocrine organs. We conducted a survey of genes transcribed in developing mouse pituitary to find candidates for cases of pituitary hormone deficiency of unknown etiology. We identified numerous transcription factors that are members of gene families with roles in syndromic or non-syndromic pituitary hormone deficiency. This collection is a rich source for future basic and clinical studies.
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Affiliation(s)
- S W Davis
- University of Michigan Medical School, Ann Arbor, MI 41809-5618, USA
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Amendola E, Sanges R, Galvan A, Dathan N, Manenti G, Ferrandino G, Alvino FM, Di Palma T, Scarfò M, Zannini M, Dragani TA, De Felice M, Di Lauro R. A locus on mouse chromosome 2 is involved in susceptibility to congenital hypothyroidism and contains an essential gene expressed in thyroid. Endocrinology 2010; 151:1948-58. [PMID: 20160132 DOI: 10.1210/en.2009-1240] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We report here the mapping of a chromosomal region responsible for strain-specific development of congenital hypothyroidism in mice heterozygous for null mutations in genes encoding Nkx2-1/Titf1 and Pax8. The two strains showing a differential predisposition to congenital hypothyroidism contain several single-nucleotide polymorphisms in this locus, one of which leads to a nonsynonymous amino acid change in a highly conserved region of Dnajc17, a member of the type III heat-shock protein-40 (Hsp40) family. We demonstrate that Dnajc17 is highly expressed in the thyroid bud and had an essential function in development, suggesting an important role of this protein in organogenesis and/or function of the thyroid gland.
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Affiliation(s)
- Elena Amendola
- Stazione Zoologica Anton Dohrn, Villa Comunale I, Naples 80121, Italy
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KLINTMAN J, BERNTORP E, ASTERMARK J. Thrombin generationin vitroin the presence of by-passing agents in siblings with severe haemophilia A. Haemophilia 2010; 16:e210-5. [DOI: 10.1111/j.1365-2516.2009.02132.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jéru I, Hayrapetyan H, Duquesnoy P, Cochet E, Serre JL, Feingold J, Grateau G, Sarkisian T, Jeanpierre M, Amselem S. Involvement of the modifier gene of a human Mendelian disorder in a negative selection process. PLoS One 2009; 4:e7676. [PMID: 19888326 PMCID: PMC2765618 DOI: 10.1371/journal.pone.0007676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
Background Identification of modifier genes and characterization of their effects represent major challenges in human genetics. SAA1 is one of the few modifiers identified in humans: this gene influences the risk of renal amyloidosis (RA) in patients with familial Mediterranean fever (FMF), a Mendelian autoinflammatory disorder associated with mutations in MEFV. Indeed, the SAA1 α homozygous genotype and the p.Met694Val homozygous genotype at the MEFV locus are two main risk factors for RA. Methodology/Principal Findings Here, we investigated Armenian FMF patients and controls from two neighboring countries: Armenia, where RA is frequent (24%), and Karabakh, where RA is rare (2.5%). Sequencing of MEFV revealed similar frequencies of p.Met694Val homozygotes in the two groups of patients. However, a major deficit of SAA1 α homozygotes was found among Karabakhian patients (4%) as compared to Armenian patients (24%) (p = 5.10−5). Most importantly, we observed deviations from Hardy-Weinberg equilibrium (HWE) in the two groups of patients, and unexpectedly, in opposite directions, whereas, in the two control populations, genotype distributions at this locus were similar and complied with (HWE). Conclusions/Significance The excess of SAA1α homozygotes among Armenian patients could be explained by the recruitment of patients with severe phenotypes. In contrast, a population-based study revealed that the deficit of α/α among Karabakhian patients would result from a negative selection against carriers of this genotype. This study, which provides new insights into the role of SAA1 in the pathophysiology of FMF, represents the first example of deviations from HWE and selection involving the modifier gene of a Mendelian disorder.
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Affiliation(s)
- Isabelle Jéru
- INSERM, U933, Paris, France
- Université Pierre et Marie Curie-Paris6, UMR S_933, Paris, France
| | - Hasmik Hayrapetyan
- Center of Medical Genetics and Primary Health Care, National Academy of Sciences, Yerevan, Armenia
| | | | | | - Jean-Louis Serre
- Equipe Structure-Fonction, EA 2493, Université de Versailles-Saint Quentin en Yvelines, Versailles, France
| | | | | | - Tamara Sarkisian
- Center of Medical Genetics and Primary Health Care, National Academy of Sciences, Yerevan, Armenia
| | - Marc Jeanpierre
- Center of Medical Genetics and Primary Health Care, National Academy of Sciences, Yerevan, Armenia
| | - Serge Amselem
- INSERM, U933, Paris, France
- Université Pierre et Marie Curie-Paris6, UMR S_933, Paris, France
- * E-mail:
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Menalled L, El-Khodor BF, Patry M, Suárez-Fariñas M, Orenstein SJ, Zahasky B, Leahy C, Wheeler V, Yang XW, MacDonald M, Morton AJ, Bates G, Leeds J, Park L, Howland D, Signer E, Tobin A, Brunner D. Systematic behavioral evaluation of Huntington's disease transgenic and knock-in mouse models. Neurobiol Dis 2009; 35:319-36. [PMID: 19464370 DOI: 10.1016/j.nbd.2009.05.007] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 05/04/2009] [Accepted: 05/15/2009] [Indexed: 11/19/2022] Open
Abstract
Huntington's disease (HD) is one of the few neurodegenerative diseases with a known genetic cause, knowledge that has enabled the creation of animal models using genetic manipulations that aim to recapitulate HD pathology. The study of behavioral and neuropathological phenotypes of these HD models, however, has been plagued by inconsistent results across laboratories stemming from the lack of standardized husbandry and testing conditions, in addition to the intrinsic differences between the models. We have compared different HD models using standardized conditions to identify the most robust phenotypic differences, best suited for preclinical therapeutic efficacy studies. With a battery of tests of sensory-motor function, such as the open field and prepulse inhibition tests, we replicate previous results showing a strong and progressive behavioral deficit in the R6/2 line with an average of 129 CAG repeats in a mixed CBA/J and C57BL/6J background. We present the first behavioral characterization of a new model, an R6/2 line with an average of 248 CAG repeats in a pure C57BL/6J background, which also showed a progressive and robust phenotype. The BACHD in a FVB/N background showed robust and progressive behavioral phenotype, while the YAC128 full-length model on either an FVB/N or a C57BL/6J background generally showed milder deficits. Finally, the Hdh(Q111) knock-in mouse on a CD1 background showed very mild deficits. This first extensive standardized cross-characterization of several HD animal models under standardized conditions highlights several behavioral outcomes, such as hypoactivity, amenable to standardized preclinical therapeutic drug screening.
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Turner DJ, Keane TM, Sudbery I, Adams DJ. Next-generation sequencing of vertebrate experimental organisms. Mamm Genome 2009; 20:327-38. [PMID: 19452216 PMCID: PMC2714443 DOI: 10.1007/s00335-009-9187-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 04/21/2009] [Indexed: 12/22/2022]
Abstract
Next-generation sequencing technologies are revolutionizing biology by allowing for genome-wide transcription factor binding-site profiling, transcriptome sequencing, and more recently, whole-genome resequencing. While it is currently not possible to generate complete de novo assemblies of higher-vertebrate genomes using next-generation sequencing, improvements in sequence read lengths and throughput, coupled with new assembly algorithms for large data sets, will soon make this a reality. These developments will in turn spawn a revolution in how genomic data are used to understand genetics and how model organisms are used for disease gene discovery. This review provides an overview of the current next-generation sequencing platforms and the newest computational tools for the analysis of next-generation sequencing data. We also describe how next-generation sequencing may be applied in the context of vertebrate model organism genetics.
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Affiliation(s)
- Daniel J Turner
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
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Genomic consequences of background effects on scalloped mutant expressivity in the wing of Drosophila melanogaster. Genetics 2008; 181:1065-76. [PMID: 19064709 DOI: 10.1534/genetics.108.096453] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genetic background effects contribute to the phenotypic consequences of mutations and are pervasive across all domains of life that have been examined, yet little is known about how they modify genetic systems. In part this is due to the lack of tractable model systems that have been explicitly developed to study the genetic and evolutionary consequences of background effects. In this study we demonstrate that phenotypic expressivity of the scalloped(E3) (sd(E3)) mutation of Drosophila melanogaster is background dependent and is the result of at least one major modifier segregating between two standard lab wild-type strains. We provide evidence that at least one of the modifiers is linked to the vestigial region and demonstrate that the background effects modify the spatial distribution of known sd target genes in a genotype-dependent manner. In addition, microarrays were used to examine the consequences of genetic background effects on the global transcriptome. Expression differences between wild-type strains were found to be as large as or larger than the effects of mutations with substantial phenotypic effects, and expression differences between wild type and mutant varied significantly between genetic backgrounds. Significantly, we demonstrate that the epistatic interaction between sd(E3) and an optomotor blind mutation is background dependent. The results are discussed within the context of developing a complex but more realistic view of the consequences of genetic background effects with respect to mutational analysis and studies of epistasis and cryptic genetic variation segregating in natural populations.
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Mazzeo A, Muglia M, Rodolico C, Toscano A, Patitucci A, Quattrone A, Messina C, Vita G. Charcot-Marie-Tooth disease type 1B: marked phenotypic variation of the Ser78Leu mutation in five Italian families. Acta Neurol Scand 2008; 118:328-32. [PMID: 18422810 DOI: 10.1111/j.1600-0404.2008.01021.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To describe clinical, electrophysiological and genetic data of five unrelated Sicilian pedigrees harbouring a heterozygous Ser78Leu mutation in the myelin protein zero (MPZ) extracellular domain. MATERIALS AND METHODS Clinical, electrophysiological and genetic findings of 16 patients were reported. Polymorphic markers flanking the coding sequence of MPZ gene were also analysed. RESULTS A wide range of age at onset was observed in families 1 and 3, with a clinical heterogeneity, in terms of severity of the disease, within the same family (families 1 and 3), and among families. A markedly unsteady gait was a distinctive feature of many members of family 1. All patients in family 2 complained of severe cramps and painful paresthesia. Molecular genetic analysis showed that all affected subjects shared a common haplotype at three microsatellite loci D1S2858, D1S2624 and D1S484. CONCLUSIONS Our study provides further evidence that phenotypic features of MPZ mutations can vary within and among different families. High frequency of Ser78Leu mutation in Sicily as well as the results of haplotype analyses suggest that the mutation may have been inherited from a common ancestor.
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Affiliation(s)
- A Mazzeo
- Department of Neurosciences, Psychiatry and Anaesthesiology University of Messina, Messina, Italy.
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Chaudhry AM, Marsh-Rollo SE, Aksenov V, Rollo CD, Szechtman H. Modifier Selection by Transgenes: The Case of Growth Hormone Transgenesis and Hyperactive Circling Mice. Evol Biol 2008. [DOI: 10.1007/s11692-008-9036-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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47
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Catano G, Agan BK, Kulkarni H, Telles V, Marconi VC, Dolan MJ, Ahuja SK. Independent effects of genetic variations in mannose-binding lectin influence the course of HIV disease: the advantage of heterozygosity for coding mutations. J Infect Dis 2008; 198:72-80. [PMID: 18498240 PMCID: PMC3777826 DOI: 10.1086/588712] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The in vivo impact of mannose-binding lectin (MBL), a molecule involved in innate immunity, on the pathogenesis of human immunodeficiency virus (HIV)-1 infection and AIDS is unknown. METHODS A total of 1102 HIV-positive and 2213 HIV-negative adult subjects were screened for polymorphisms in the coding and promoter regions of MBL2, the gene that encodes MBL. RESULTS Variations in MBL2 did not influence the risk of acquiring HIV-1. Heterozygosity for coding mutations (O allele) and homozygosity for the -221 promoter polymorphism (X allele) in MBL2 were associated with a delay in and an accelerated rate of disease progression, respectively. MBL2 variations influenced the rate of progression to AIDS-defining illnesses. In a multivariate model, the effects of MBL2 variations were independent of several parameters known to influence disease progression, including steady-state viral load, baseline CD4(+) T cell counts, and delayed-type hypersensitivity skin test responses, an in vivo marker of cell-mediated immunity. The effects of MBL2 variations were most evident in those who possessed protective genotypes of CCR5 and a high copy number of CCL3L1, the most potent HIV-suppressive CCR5 ligand. CONCLUSIONS MBL2 genotypes are independent determinants of HIV disease progression and heterozygosity for MBL2 coding mutations confer disease-retarding effects. MBL-dependent immune responses may play a role in the pathogenesis of HIV infection.
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Affiliation(s)
- Gabriel Catano
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System and Department of Medicine, Texas
| | - Brian K. Agan
- Infectious Diseases Service, Texas
- Henry M. Jackson Foundation, Wilford Hall United States Air Force Medical Center, Lackland Air Force Base, Texas
- San Antonio Military Medical Center, Fort Sam Houston, San Antonio, Texas
- Infectious Diseases Clinical Research Program, Uniformed Services University, Bethesda, Maryland
| | - Hemant Kulkarni
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System and Department of Medicine, Texas
| | - Vanessa Telles
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System and Department of Medicine, Texas
| | - Vincent C. Marconi
- Infectious Diseases Service, Texas
- San Antonio Military Medical Center, Fort Sam Houston, San Antonio, Texas
- Infectious Diseases Clinical Research Program, Uniformed Services University, Bethesda, Maryland
| | - Matthew J. Dolan
- Infectious Diseases Service, Texas
- Henry M. Jackson Foundation, Wilford Hall United States Air Force Medical Center, Lackland Air Force Base, Texas
- San Antonio Military Medical Center, Fort Sam Houston, San Antonio, Texas
- Infectious Diseases Clinical Research Program, Uniformed Services University, Bethesda, Maryland
| | - Sunil K. Ahuja
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System and Department of Medicine, Texas
- Department of Microbiology, Immunology, and Biochemistry, University of Texas Health Science Center, Texas
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Zuberi AR. Strategies for assessment of botanical action on metabolic syndrome in the mouse and evidence for a genotype-specific effect of Russian tarragon in the regulation of insulin sensitivity. Metabolism 2008; 57:S10-5. [PMID: 18555848 PMCID: PMC2504519 DOI: 10.1016/j.metabol.2008.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Published reports of botanical action are often hampered by the lack of generalized systematic approaches or by the failure to explore mechanisms that could confirm and extend the reported observations. Choice of mouse or rat housing conditions (singly or group housed) and imposed stress during handling procedures are often variable and can contribute significantly to differences in baseline phenotypes measured across studies. Differences can also be observed in the role of the extract in either the treatment of the metabolic syndrome or roles in the regulation of the emergence of metabolic syndrome. The choice of diet used can also vary between the different studies, and diet-botanical interactions must be considered. This minireview highlights the strategies being pursued by the Botanical Research Center Animal Research Core to evaluate the in vivo phenotypes of several botanical extracts during long-term feeding studies. We describe a phenotyping strategy that promotes a more rigorous interpretation of botanical action and can suggest or eliminate possible mechanisms that may be involved. We discuss the importance of selecting the mouse model, as background strain can significantly alter the underlying susceptibilities to the various components of metabolic syndrome. Finally, we present data suggesting that one of the major botanical extracts being studied, an extract of Russian tarragon, may manifest a mouse strain genotype-specific insulin-sensitizing phenotype.
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Affiliation(s)
- Aamir R Zuberi
- Botanical Research Center, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA 70810, USA.
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Schlichting CD. Hidden Reaction Norms, Cryptic Genetic Variation, and Evolvability. Ann N Y Acad Sci 2008; 1133:187-203. [DOI: 10.1196/annals.1438.010] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Kariya S, Park GH, Maeno-Hikichi Y, Leykekhman O, Lutz C, Arkovitz MS, Landmesser LT, Monani UR. Reduced SMN protein impairs maturation of the neuromuscular junctions in mouse models of spinal muscular atrophy. Hum Mol Genet 2008; 17:2552-69. [PMID: 18492800 DOI: 10.1093/hmg/ddn156] [Citation(s) in RCA: 336] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a common pediatric neuromuscular disorder caused by insufficient levels of the survival of motor neuron (SMN) protein. Studies involving SMA patients and animal models expressing the human SMN2 gene have yielded relatively little information about the earliest cellular consequences of reduced SMN protein. In this study, we have used severe- and mild-SMN2 expressing mouse models of SMA as well as material from human patients to understand the initial stages of neurodegeneration in the human disease. We show that the earliest structural defects appear distally and involve the neuromuscular synapse. Insufficient SMN protein arrests the post-natal development of the neuromuscular junction (NMJ), impairing the maturation of acetylcholine receptor (AChR) clusters into 'pretzels'. Pre-synaptic defects include poor terminal arborization and intermediate filament aggregates which may serve as a useful biomarker of the disease. These defects are reflected in functional deficits at the NMJ characterized by intermittent neurotransmission failures. We suggest that SMA might best be described as a NMJ synaptopathy and that one promising means of treating it could involve maintaining function at the NMJ.
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Affiliation(s)
- Shingo Kariya
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
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