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Principe EL, Hagen JJ, Kempshall BW, Scammon KM. Compressed Sensing System For Scanning Probe Microscopy. Microsc Microanal 2023; 29:726-727. [PMID: 37613553 DOI: 10.1093/micmic/ozad067.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | - J J Hagen
- PanoScientific, LLC., Cocoa, FL, United States
| | | | - K M Scammon
- PanoScientific, LLC., Cocoa, FL, United States
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2
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Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG Adv 2022; 3:100107. [PMID: 35519826 PMCID: PMC9065433 DOI: 10.1016/j.xhgg.2022.100107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/06/2022] [Indexed: 11/15/2022] Open
Abstract
Esophageal atresias/tracheoesophageal fistulas (EA/TEF) are rare congenital anomalies caused by aberrant development of the foregut. Previous studies indicate that rare or de novo genetic variants significantly contribute to EA/TEF risk, and most individuals with EA/TEF do not have pathogenic genetic variants in established risk genes. To identify the genetic contributions to EA/TEF, we performed whole genome sequencing of 185 trios (probands and parents) with EA/TEF, including 59 isolated and 126 complex cases with additional congenital anomalies and/or neurodevelopmental disorders. There was a significant burden of protein-altering de novo coding variants in complex cases (p = 3.3 × 10-4), especially in genes that are intolerant of loss-of-function variants in the population. We performed simulation analysis of pathway enrichment based on background mutation rate and identified a number of pathways related to endocytosis and intracellular trafficking that as a group have a significant burden of protein-altering de novo variants. We assessed 18 variants for disease causality using CRISPR-Cas9 mutagenesis in Xenopus and confirmed 13 with tracheoesophageal phenotypes. Our results implicate disruption of endosome-mediated epithelial remodeling as a potential mechanism of foregut developmental defects. Our results suggest significant genetic heterogeneity of EA/TEF and may have implications for the mechanisms of other rare congenital anomalies.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicole A. Edwards
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Jacob J. Hagen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Christophe Faure
- Division of Pediatric Gastroenterology, CHU Sainte-Justine, Montreal, QC, Canada
| | - Qiao Lu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Kingma
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William Middlesworth
- Division of Pediatric Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie Khlevner
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Mahmoud El Fiky
- Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - David Schindel
- Division of Pediatric Surgery, UT Southwestern School of Medicine Dallas, Texas, USA
| | - Elizabeth Fialkowski
- Division of Pediatric Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Adhish Kashyap
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Sophia Forlenza
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Alan P. Kenny
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Aaron M. Zorn
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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3
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Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. Human Genetics and Genomics Advances 2022; 3:100126. [DOI: 10.1016/j.xhgg.2022.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Zhu N, Swietlik EM, Welch CL, Pauciulo MW, Hagen JJ, Zhou X, Guo Y, Karten J, Pandya D, Tilly T, Lutz KA, Martin JM, Treacy CM, Rosenzweig EB, Krishnan U, Coleman AW, Gonzaga-Jauregui C, Lawrie A, Trembath RC, Wilkins MR, Morrell NW, Shen Y, Gräf S, Nichols WC, Chung WK. Correction to: Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH. Genome Med 2021; 13:106. [PMID: 34158098 PMCID: PMC8220777 DOI: 10.1186/s13073-021-00915-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Na Zhu
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Emilia M Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jacob J Hagen
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xueya Zhou
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yicheng Guo
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tobias Tilly
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Katie A Lutz
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jennifer M Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK
| | - Carmen M Treacy
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Erika B Rosenzweig
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
| | - Usha Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
| | - Anna W Coleman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Allan Lawrie
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Richard C Trembath
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Martin R Wilkins
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | | | | | | | - Nicholas W Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK.,Addenbrooke's Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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5
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Zhu N, Swietlik EM, Welch CL, Pauciulo MW, Hagen JJ, Zhou X, Guo Y, Karten J, Pandya D, Tilly T, Lutz KA, Martin JM, Treacy CM, Rosenzweig EB, Krishnan U, Coleman AW, Gonzaga-Jauregui C, Lawrie A, Trembath RC, Wilkins MR, Morrell NW, Shen Y, Gräf S, Nichols WC, Chung WK. Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH. Genome Med 2021; 13:80. [PMID: 33971972 PMCID: PMC8112021 DOI: 10.1186/s13073-021-00891-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/19/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 (BMPR2) are the cause of most heritable cases but the vast majority of other cases are genetically undefined. METHODS To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource - Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD. RESULTS Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes (BMPR2, GDF2, and TBX4), two recently identified candidate genes (SOX17, KDR), and two new candidate genes (fibulin 2, FBLN2; platelet-derived growth factor D, PDGFD). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e-5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development. CONCLUSIONS Rare variant analysis of a large international consortium identified two new candidate genes-FBLN2 and PDGFD. The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.
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Affiliation(s)
- Na Zhu
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Emilia M Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jacob J Hagen
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xueya Zhou
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yicheng Guo
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tobias Tilly
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Katie A Lutz
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jennifer M Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK
| | - Carmen M Treacy
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Erika B Rosenzweig
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
| | - Usha Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA
| | - Anna W Coleman
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Allan Lawrie
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Richard C Trembath
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Martin R Wilkins
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | | | | | | | - Nicholas W Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK
- Addenbrooke's Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
- Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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6
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Tol MJ, van der Lienden MJC, Gabriel TL, Hagen JJ, Scheij S, Veenendaal T, Klumperman J, Donker-Koopman WE, Verhoeven AJ, Overkleeft H, Aerts JM, Argmann CA, van Eijk M. HEPES activates a MiT/TFE-dependent lysosomal-autophagic gene network in cultured cells: A call for caution. Autophagy 2018; 14:437-449. [PMID: 29455584 PMCID: PMC5915011 DOI: 10.1080/15548627.2017.1419118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In recent years, the lysosome has emerged as a highly dynamic, transcriptionally regulated organelle that is integral to nutrient-sensing and metabolic rewiring. This is coordinated by a lysosome-to-nucleus signaling nexus in which MTORC1 controls the subcellular distribution of the microphthalmia-transcription factor E (MiT/TFE) family of “master lysosomal regulators”. Yet, despite the importance of the lysosome in cellular metabolism, the impact of traditional in vitro culture media on lysosomal dynamics and/or MiT/TFE localization has not been fully appreciated. Here, we identify HEPES, a chemical buffering agent that is broadly applied in cell culture, as a potent inducer of lysosome biogenesis. Supplementation of HEPES to cell growth media is sufficient to decouple the MiT/TFE family members–TFEB, TFE3 and MITF–from regulatory mechanisms that control their cytosolic retention. Increased MiT/TFE nuclear import in turn drives the expression of a global network of lysosomal-autophagic and innate host-immune response genes, altering lysosomal dynamics, proteolytic capacity, autophagic flux, and inflammatory signaling. In addition, siRNA-mediated MiT/TFE knockdown effectively blunted HEPES-induced lysosome biogenesis and gene expression profiles. Mechanistically, we show that MiT/TFE activation in response to HEPES requires its macropinocytic ingestion and aberrant lysosomal storage/pH, but is independent of MTORC1 signaling. Altogether, our data underscore the cautionary use of chemical buffering agents in cell culture media due to their potentially confounding effects on experimental results.
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Affiliation(s)
- Marc J Tol
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands.,b Department of Pathology and Laboratory Medicine , UCLA , Los Angeles , CA , USA
| | | | - Tanit L Gabriel
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands
| | - Jacob J Hagen
- d Department of Genetics and Genomic Sciences , Icahn Institute for Genomics and Multiscale Biology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Saskia Scheij
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands
| | - Tineke Veenendaal
- e Department of Cell Biology , University Medical Centre Utrecht , The Netherlands
| | - Judith Klumperman
- e Department of Cell Biology , University Medical Centre Utrecht , The Netherlands
| | - Wilma E Donker-Koopman
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands
| | - Arthur J Verhoeven
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands
| | - Hermen Overkleeft
- c Leiden Institute of Chemistry , Leiden University , The Netherlands
| | - Johannes M Aerts
- c Leiden Institute of Chemistry , Leiden University , The Netherlands
| | - Carmen A Argmann
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands.,d Department of Genetics and Genomic Sciences , Icahn Institute for Genomics and Multiscale Biology , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Marco van Eijk
- a Department of Medical Biochemistry , University of Amsterdam , Academic Medical Centre , The Netherlands.,c Leiden Institute of Chemistry , Leiden University , The Netherlands
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Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, Naidich TP, Rodenburg RJ, Houten SM, Schadt EE. Novel, compound heterozygous, single-nucleotide variants in MARS2 associated with developmental delay, poor growth, and sensorineural hearing loss. Hum Mutat 2015; 36:587-92. [PMID: 25754315 DOI: 10.1002/humu.22781] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/24/2015] [Indexed: 11/08/2022]
Abstract
Novel, single-nucleotide mutations were identified in the mitochondrial methionyl amino-acyl tRNA synthetase gene (MARS2) via whole exome sequencing in two affected siblings with developmental delay, poor growth, and sensorineural hearing loss.We show that compound heterozygous mutations c.550C>T:p.Gln 184* and c.424C>T:p.Arg142Trp in MARS2 lead to decreased MARS2 protein levels in patient lymphoblasts. Analysis of respiratory complex enzyme activities in patient fibroblasts revealed decreased complex I and IV activities. Immunoblotting of patient fibroblast and lymphoblast samples revealed reduced protein levels of NDUFB8 and COXII, representing complex I and IV, respectively. Additionally, overexpression of wild-type MARS2 in patient fibroblasts increased NDUFB8 and COXII protein levels. These findings suggest that recessive single-nucleotide mutations in MARS2 are causative for a new mitochondrial translation deficiency disorder with a primary phenotype including developmental delay and hypotonia. Identification of additional patients with single-nucleotide mutations in MARS2 is necessary to determine if pectus carinatum is also a consistent feature of this syndrome.
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Affiliation(s)
- Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Genomics and Multi-Scale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Patricia G Wheeler
- Department of Pediatrics, Division of Genetics, Nemours Children's Clinic, Orlando, Florida
| | - Jacob J Hagen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael D Linderman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Genomics and Multi-Scale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Thomas P Naidich
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Richard J Rodenburg
- Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Genomics and Multi-Scale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Genomics and Multi-Scale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
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Abstract
Background Myosin IC is a single headed member of the myosin superfamily that localizes to the cytoplasm and the nucleus and is implicated in a variety of processes in both compartments. We recently identified a novel isoform of myosin IC and showed that the MYOIC gene in mammalian cells encodes three isoforms (isoforms A, B, and C) that differ only in the addition of short isoform-specific N-terminal peptides. The expression pattern of the isoforms and the mechanisms of expression regulation remain unknown. Results To determine the expression patterns of myosin IC isoforms, we performed a comprehensive expression analysis of the two myosin IC isoforms (isoform A and B) that contain isoform-specific sequences. By immunoblotting with isoform-specific antibodies and by qRT-PCR with isoform-specific primer we demonstrate that myosin IC isoforms A and B have distinct expression patterns in mouse tissues. Specifically, we show that myosin IC isoform A is expressed in a tissue specific pattern, while myosin IC isoform B is ubiquitously expressed at comparable levels in mouse tissues. Conclusions The differences in the expression profile of the myosin IC isoforms indicate a tissue-specific MYOIC gene regulation and further suggest that the myosin IC isoforms, despite their high sequence homology, might have tissue-specific and isoform-specific functions.
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Affiliation(s)
| | | | | | - Wilma A Hofmann
- Department of Physiology and Biophysics, University at Buffalo-State University of New York, 3435 Main Street, Buffalo, NY 14214, USA.
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9
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Hagen JJ. [Family planning and family counseling in Austria]. Sociol Diritto 2002; 7:85-95, 262. [PMID: 12339044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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10
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Rooney RD, Tuazon PT, Meek WE, Carroll EJ, Hagen JJ, Gump EL, Monnig CA, Lugo T, Traugh JA. Cleavage arrest of early frog embryos by the G protein-activated protein kinase PAK I. J Biol Chem 1996; 271:21498-504. [PMID: 8702934 DOI: 10.1074/jbc.271.35.21498] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
PAK I is a member of the PAK (p21-activated protein kinase) family and is activated by Cdc42 (Jakobi, R., Chen, C.-J., Tuazon, P. T., and Traugh, J. A. (1996) J. Biol. Chem. 271, 6206-6211). To examine the effects of PAK I on cleavage arrest, subfemtomole amounts of endogenously active (58 kDa) and inactive (60 kDa) PAK I and a tryptic peptide (37 kDa) containing the active catalytic domain were injected into one blastomere of 2-cell frog embryos. Active PAK I resulted in cleavage arrest in the injected blastomere at mitotic metaphase, whereas the uninjected blastomere progressed through mid- to late cleavage. Injection of other protein kinases at similar concentrations had no effect on cleavage. Endogenous PAK I was highly active in frog oocytes, and antibody to PAK I reacted specifically with protein of 58-60 kDa. PAK I protein was decreased at 60 min post-fertilization, with little or no PAK I protein or activity detectable at 80 min post-fertilization or in 2-cell embryos. At the 4-cell stage PAK I protein increased, but the protein kinase was present primarily as an inactive form. Rac2 and Cdc42, but not Rac 1, were identified in oocytes and throughout early embryo development. Thus, PAK I appears to be a potent cytostatic protein kinase involved in maintaining cells in a non-dividing state. PAK I activity is high in oocytes and appears to be regulated by degradation/synthesis and through autophosphorylation via binding of Cdc42. PAK I may act through regulation of the stress-activated protein kinase signaling pathway and/or by direct regulation of multiple metabolic pathways.
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Affiliation(s)
- R D Rooney
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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Hagen JJ, Washco KA, Monnig CA. Determination of retinoids by reversed-phase capillary liquid chromatography with amperometric electrochemical detection. J Chromatogr B Biomed Appl 1996; 677:225-31. [PMID: 8704925 DOI: 10.1016/0378-4347(95)00465-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A method for separating and detecting retinoids by reversed-phase capillary liquid chromatography with amperometric electrochemical detection is described. Packed columns with an inner diameter of 180 microns were employed for the separation using C18 stationary phase and a mobile phase containing acetonitrile-water methanol (65:32.5:2.5, v/v/v) with 1% tetrabutylammonium perchlorate and 0.174 M acetate buffered at pH 5. The detection cell consisted of a carbon fiber barrel electrode held at 0.9 V versus an Ag/AgCl reference. Injection volumes of 2 microliters produced detection limits of 2.73, 0.472, 0.428, and 0.267 fmol (or 410, 64.1, 60.9, and 38.2 pg ml-1) for 13-cis-retinoic acid, all-trans-retinoic acid, retinaldehyde, and retinol, respectively. This represents an improvement in detection limits of at least three orders of magnitude for similar analyses using liquid chromatography and UV absorbance detection. The detector signal was linear over two orders of magnitude of analyte concentration. Retinoid concentrations in bovine serum were determined and found to be in good agreement with previously reported values.
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Affiliation(s)
- J J Hagen
- Department of Chemistry, University of California, Riverside 92521-0403, USA
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