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Ritter AL, Gold J, Hayashi H, Ackermann AM, Hanke S, Skraban C, Cuddapah S, Bhoj E, Li D, Kuroda Y, Wen J, Takeda R, Bibb A, El Chehadeh S, Piton A, Ohl J, Kukolich MK, Nagasaki K, Kato K, Ogi T, Bhatti T, Russo P, Krock B, Murrell JR, Sullivan JA, Shashi V, Stong N, Hakonarson H, Sawano K, Torti E, Willaert R, Si Y, Wilcox WR, Wirgenes KV, Thomassen K, Carlotti K, Erwin A, Lazier J, Marquardt T, He M, Edmondson AC, Izumi K. Expanding the phenotypic spectrum of ARCN1-related syndrome. Genet Med 2022; 24:1227-1237. [PMID: 35300924 PMCID: PMC9923403 DOI: 10.1016/j.gim.2022.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/18/2023] Open
Abstract
PURPOSE This study aimed to describe the phenotypic and molecular characteristics of ARCN1-related syndrome. METHODS Patients with ARCN1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. RESULTS In total, we identified 14 cases of ARCN1-related syndrome, (9 pediatrics, and 5 fetal cases from 3 families). The clinical features these newly identified cases were compared to 6 previously reported cases for a total of 20 cases. Intrauterine growth restriction, micrognathia, and short stature were present in all patients. Other common features included prematurity (11/15, 73.3%), developmental delay (10/14, 71.4%), genitourinary malformations in males (6/8, 75%), and microcephaly (12/15, 80%). Novel features of ARCN1-related syndrome included transient liver dysfunction and specific glycosylation abnormalities during illness, giant cell hepatitis, hepatoblastoma, cataracts, and lethal skeletal manifestations. Developmental delay was seen in 73% of patients, but only 3 patients had intellectual disability, which is less common than previously reported. CONCLUSION ARCN1-related syndrome presents with a wide clinical spectrum ranging from a severe embryonic lethal syndrome to a mild syndrome with intrauterine growth restriction, micrognathia, and short stature without intellectual disability. Patients with ARCN1-related syndrome should be monitored for liver dysfunction during illness, cataracts, and hepatoblastoma. Additional research to further define the phenotypic spectrum and possible genotype-phenotype correlations are required.
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Affiliation(s)
- Alyssa L Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jessica Gold
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hiroshi Hayashi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amanda M Ackermann
- Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Stephanie Hanke
- Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Cara Skraban
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sanmati Cuddapah
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth Bhoj
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jessica Wen
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ryojun Takeda
- Division of Genetics, Nagano Children's Hospital, Nagano, Japan
| | - Audrey Bibb
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Laboratoire de Génétique Médicale, UMR_S1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | - Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institut Génétique Biologie Moléculaire Cellulaire, IGBMC - CNRS UMR 7104 - Inserm U 1258, Illkirch, France; Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jeanine Ohl
- Service d'assistance Médicale à la Procréation, Centre médico-chirurgical et obstétrical (CMCO), Schiltigheim, France
| | - Mary K Kukolich
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX
| | - Keisuke Nagasaki
- Department of Pediatrics, Niigata University Medical & Dental Hospital, Niigata, Japan
| | - Kohji Kato
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tricia Bhatti
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pierre Russo
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bryan Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kentaro Sawano
- Department of Pediatrics, Niigata University Medical & Dental Hospital, Niigata, Japan
| | | | | | | | - William Ross Wilcox
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Katrine Verena Wirgenes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristian Thomassen
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Angelika Erwin
- Genomic Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Joanna Lazier
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Thorsten Marquardt
- Department of Pediatrics, University Hospital of Muenster, Muenster, Germany
| | - Miao He
- Metabolic and Advanced Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew C Edmondson
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA.
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2
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Argyropoulos KV, Lin LH, Moreira A, Krock B, Simsir A, Brandler TC. Cytologic features of NUT-carcinoma harboring an NSD3-NUTM1 fusion. Cytopathology 2022; 33:540-543. [PMID: 35325484 DOI: 10.1111/cyt.13120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/21/2022] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kimon V Argyropoulos
- Division of Cytopathology, Department of Pathology, New York University, School of Medicine, New York
| | - Lawrence Hsu Lin
- Division of Cytopathology, Department of Pathology, New York University, School of Medicine, New York
| | - Andre Moreira
- Division of Thoracic Pathology, Department of Pathology, New York University, School of Medicine, New York
| | | | - Aylin Simsir
- Division of Cytopathology, Department of Pathology, New York University, School of Medicine, New York
| | - Tamar C Brandler
- Division of Cytopathology, Department of Pathology, New York University, School of Medicine, New York
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Abstract
The genetic basis for pediatric acute myeloid leukemia (AML) is highly heterogeneous, often involving the cooperative action of characteristic chromosomal rearrangements and somatic mutations in progrowth and antidifferentiation pathways that drive oncogenesis. Although some driver mutations are shared with adult AML, many genetic lesions are unique to pediatric patients, and their appropriate identification is essential for patient care. The increased understanding of these malignancies through broad genomic studies has begun to risk-stratify patients based on their combinations of genomic alterations, a trend that will enable precision medicine in this population.
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Affiliation(s)
- Bryan Krock
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ, USA
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4
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Pitcher GC, Cembella AD, Krock B, Macey BM, Mansfield L. Do toxic Pseudo-nitzschia species pose a threat to aquaculture in the southern Benguela eastern boundary upwelling system? Harmful Algae 2020; 99:101919. [PMID: 33218444 DOI: 10.1016/j.hal.2020.101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/17/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
The productive but highly exposed coastline of the southern Benguela eastern boundary upwelling system offers limited natural environment for aquaculture. Saldanha Bay located on the west coast of South Africa is one of the few embayments on the coastline that provides a productive and relatively sheltered environment suitable for the cultivation of shellfish. Consequently, bivalve culture in South Africa is centered in Saldanha Bay and is presently targeted for expansion. Pseudo-nitzschia blooms including toxin-producing species are shown to contribute significantly to the phytoplankton of Saldanha Bay specifically in spring and summer. Their dominance at this time of the year, when upwelling is strongest, fits the ecological profile of Pseudo-nitzschia occurring during periods of high turbulence and nutrients. Multiple Pseudo-nitzschia blooms were sampled under varying environmental conditions and the strength of the relationship between Pseudo-nitzschia cell abundance and particulate domoic acid (pDA) content, reflecting bloom toxicity, varied greatly. This variability is the result of the combined influence of species and strain composition of the Pseudo-nitzschia assemblage and the effect of environmental conditions on toxin production. Elevated levels of pDA were associated with higher concentrations of cells of the P. seriata complex differentiated by frustule width (>3 µm). P. australis was identified as a toxin-producing species and a prominent member of the P. seriata complex. Low DA levels in shellfish in Saldanha Bay are considered a function of low cellular domoic acid (cDA). Silicate limitation has emerged as an important factor inducing DA production in Pseudo-nitzschia species. The high ratio of silicate to nitrate in Saldanha Bay provides a plausible explanation for the low toxin content of Pseudo-nitzschia blooms in the bay and the consequent low risk posed by these blooms to the aquaculture sector.
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Affiliation(s)
- G C Pitcher
- Department of Forestry, Fisheries and the Environment, Cape Town, South Africa; Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa.
| | - A D Cembella
- Alfred-Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, South Africa
| | - B Krock
- Alfred-Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, South Africa
| | - B M Macey
- Department of Forestry, Fisheries and the Environment, Cape Town, South Africa
| | - L Mansfield
- Department of Forestry, Fisheries and the Environment, Cape Town, South Africa
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5
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Schmidt JL, Pizzino A, Nicholl J, Foley A, Wang Y, Rosenfeld JA, Mighion L, Bean L, da Silva C, Cho MT, Truty R, Garcia J, Speare V, Blanco K, Powis Z, Hobson GM, Kirwin S, Krock B, Lee H, Deignan JL, Westemeyer MA, Subaran RL, Thiffault I, Tsai EA, Fang T, Helman G, Vanderver A. Estimating the relative frequency of leukodystrophies and recommendations for carrier screening in the era of next-generation sequencing. Am J Med Genet A 2020; 182:1906-1912. [PMID: 32573057 DOI: 10.1002/ajmg.a.61641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/25/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 11/09/2022]
Abstract
Leukodystrophies are a heterogeneous group of heritable disorders characterized by abnormal brain white matter signal on magnetic resonance imaging (MRI) and primary involvement of the cellular components of myelin. Previous estimates suggest the incidence of leukodystrophies as a whole to be 1 in 7,000 individuals, however the frequency of specific diagnoses relative to others has not been described. Next generation sequencing approaches offer the opportunity to redefine our understanding of the relative frequency of different leukodystrophies. We assessed the relative frequency of all 30 leukodystrophies (associated with 55 genes) in more than 49,000 exomes. We identified a relatively high frequency of disorders previously thought of as very rare, including Aicardi Goutières Syndrome, TUBB4A-related leukodystrophy, Peroxisomal biogenesis disorders, POLR3-related Leukodystrophy, Vanishing White Matter, and Pelizaeus-Merzbacher Disease. Despite the relative frequency of these conditions, carrier-screening laboratories regularly test only 20 of the 55 leukodystrophy-related genes, and do not test at all, or test only one or a few, genes for some of the higher frequency disorders. Relative frequency of leukodystrophies previously considered very rare suggests these disorders may benefit from expanded carrier screening.
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Affiliation(s)
- Johanna L Schmidt
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Amy Pizzino
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Allison Foley
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yue Wang
- Department of Molecular & Human Genetics, Baylor College of Medicine, and Baylor Genetics Laboratories, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, and Baylor Genetics Laboratories, Houston, Texas, USA
| | | | | | | | | | | | | | | | | | - Zoe Powis
- Ambry Genetics, Aliso Viejo, California, USA
| | - Grace M Hobson
- Nemours/Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Susan Kirwin
- Nemours/Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | | | | | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | | | | | - Guy Helman
- Murdoch Children' Research Institute, The Royal Children's Hospital, Parkville, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Adeline Vanderver
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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6
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Pritchard AB, Kanai SM, Krock B, Schindewolf E, Oliver-Krasinski J, Khalek N, Okashah N, Lambert NA, Tavares ALP, Zackai E, Clouthier DE. Loss-of-function of Endothelin receptor type A results in Oro-Oto-Cardiac syndrome. Am J Med Genet A 2020; 182:1104-1116. [PMID: 32133772 DOI: 10.1002/ajmg.a.61531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/27/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 01/14/2023]
Abstract
Craniofacial morphogenesis is regulated in part by signaling from the Endothelin receptor type A (EDNRA). Pathogenic variants in EDNRA signaling pathway components EDNRA, GNAI3, PCLB4, and EDN1 cause Mandibulofacial Dysostosis with Alopecia (MFDA), Auriculocondylar syndrome (ARCND) 1, 2, and 3, respectively. However, cardiovascular development is normal in MFDA and ARCND individuals, unlike Ednra knockout mice. One explanation may be that partial EDNRA signaling remains in MFDA and ARCND, as mice with reduced, but not absent, EDNRA signaling also lack a cardiovascular phenotype. Here we report an individual with craniofacial and cardiovascular malformations mimicking the Ednra -/- mouse phenotype, including a distinctive micrognathia with microstomia and a hypoplastic aortic arch. Exome sequencing found a novel homozygous missense variant in EDNRA (c.1142A>C; p.Q381P). Bioluminescence resonance energy transfer assays revealed that this amino acid substitution in helix 8 of EDNRA prevents recruitment of G proteins to the receptor, abrogating subsequent receptor activation by its ligand, Endothelin-1. This homozygous variant is thus the first reported loss-of-function EDNRA allele, resulting in a syndrome we have named Oro-Oto-Cardiac Syndrome. Further, our results illustrate that EDNRA signaling is required for both normal human craniofacial and cardiovascular development, and that limited EDNRA signaling is likely retained in ARCND and MFDA individuals. This work illustrates a straightforward approach to identifying the functional consequence of novel genetic variants in signaling molecules associated with malformation syndromes.
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Affiliation(s)
- Amanda Barone Pritchard
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley M Kanai
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Nahla Khalek
- Center for Fetal Diagnosis and Treatment, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Najeah Okashah
- Department of Pharmacology and Toxicology, Medical College of Georgia-Augusta University, Augusta, Georgia, USA
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia-Augusta University, Augusta, Georgia, USA
| | - Andre L P Tavares
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elaine Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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7
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Gallardo-Rodríguez J, Astuya-Villalón A, Avello V, Llanos-Rivera A, Krock B, Agurto-Muñoz C, Sánchez-Mirón A, García-Camacho F. Production of extracts with anaesthetic activity from the culture of Heterosigma akashiwo in pilot-scale photobioreactors. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Weiss K, Lazar HP, Kurolap A, Martinez AF, Paperna T, Cohen L, Smeland MF, Whalen S, Heide S, Keren B, Terhal P, Irving M, Takaku M, Roberts JD, Petrovich RM, Vergano SAS, Kenney A, Hove H, DeChene E, Quinonez SC, Colin E, Ziegler A, Rumple M, Jain M, Monteil D, Roeder ER, Nugent K, van Haeringen A, Gambello M, Santani A, Medne L, Krock B, Skraban CM, Zackai EH, Dubbs HA, Smol T, Ghoumid J, Parker MJ, Wright M, Turnpenny P, Clayton-Smith J, Metcalfe K, Kurumizaka H, Gelb BD, Feldman HB, Campeau PM, Muenke M, Wade PA, Lachlan K. Correction: The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype–phenotype correlations, and molecular basis. Genet Med 2019; 22:669. [DOI: 10.1038/s41436-019-0727-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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9
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Weiss K, Lazar HP, Kurolap A, Martinez AF, Paperna T, Cohen L, Smeland MF, Whalen S, Heide S, Keren B, Terhal P, Irving M, Takaku M, Roberts JD, Petrovich RM, Schrier Vergano SA, Kenney A, Hove H, DeChene E, Quinonez SC, Colin E, Ziegler A, Rumple M, Jain M, Monteil D, Roeder ER, Nugent K, van Haeringen A, Gambello M, Santani A, Medne L, Krock B, Skraban CM, Zackai EH, Dubbs HA, Smol T, Ghoumid J, Parker MJ, Wright M, Turnpenny P, Clayton-Smith J, Metcalfe K, Kurumizaka H, Gelb BD, Baris Feldman H, Campeau PM, Muenke M, Wade PA, Lachlan K. The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype-phenotype correlations, and molecular basis. Genet Med 2019; 22:389-397. [PMID: 31388190 DOI: 10.1038/s41436-019-0612-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Sifrim-Hitz-Weiss syndrome (SIHIWES) is a recently described multisystemic neurodevelopmental disorder caused by de novo variants inCHD4. In this study, we investigated the clinical spectrum of the disorder, genotype-phenotype correlations, and the effect of different missense variants on CHD4 function. METHODS We collected clinical and molecular data from 32 individuals with mostly de novo variants in CHD4, identified through next-generation sequencing. We performed adenosine triphosphate (ATP) hydrolysis and nucleosome remodeling assays on variants from five different CHD4 domains. RESULTS The majority of participants had global developmental delay, mild to moderate intellectual disability, brain anomalies, congenital heart defects, and dysmorphic features. Macrocephaly was a frequent but not universal finding. Additional common abnormalities included hypogonadism in males, skeletal and limb anomalies, hearing impairment, and ophthalmic abnormalities. The majority of variants were nontruncating and affected the SNF2-like region of the protein. We did not identify genotype-phenotype correlations based on the type or location of variants. Alterations in ATP hydrolysis and chromatin remodeling activities were observed in variants from different domains. CONCLUSION The CHD4-related syndrome is a multisystemic neurodevelopmental disorder. Missense substitutions in different protein domains alter CHD4 function in a variant-specific manner, but result in a similar phenotype in humans.
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Affiliation(s)
- Karin Weiss
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.
| | - Hayley P Lazar
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Alina Kurolap
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ariel F Martinez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Lior Cohen
- Genetics Institute, Schneider Children's Medical Center, Petah Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marie F Smeland
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | - Sandra Whalen
- UF de génétique clinique, Centre de Référence Maladies Rares des Anomalies du développement et syndromes malformatifs, APHP, Hôpital Trousseau, Paris, France
| | - Solveig Heide
- AP-HP, Département de Génétique, Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs" Hôpital de la Pitié Salpêtrière, Paris, France
| | - Boris Keren
- AP-HP, Département de Génétique, Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs" Hôpital de la Pitié Salpêtrière, Paris, France
| | - Pauline Terhal
- Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Melita Irving
- Department of Clinical Genetics, Guy's Hospital, London, UK
| | - Motoki Takaku
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John D Roberts
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Robert M Petrovich
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Amy Kenney
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Hanne Hove
- Centre for Rare Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elizabeth DeChene
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shane C Quinonez
- Department of Pediatrics, Division of Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Estelle Colin
- Department of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | | | - Mahim Jain
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.,Bone and Osteogenesis Imperfecta Department, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Danielle Monteil
- Department of Pediatrics, Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Elizabeth R Roeder
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, USA
| | - Kimberly Nugent
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, USA
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michael Gambello
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Līvija Medne
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thomas Smol
- Department of Clinical Genetics, Lille University Hospital, CHU Lille, Lille, France.,EA7364 RADEME (Research Team on Rare Developmental and Metabolic Diseases), Lille 2 University, Lille, France
| | - Jamal Ghoumid
- Department of Clinical Genetics, Lille University Hospital, CHU Lille, Lille, France.,EA7364 RADEME (Research Team on Rare Developmental and Metabolic Diseases), Lille 2 University, Lille, France
| | - Michael J Parker
- Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne, UK
| | - Peter Turnpenny
- University of Exeter Medical School, Clinical Genetics Royal Devon & Exeter Hospital, Exeter, UK
| | - Jill Clayton-Smith
- Institute of Evolution, Systems and Genomics, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Kay Metcalfe
- Institute of Evolution, Systems and Genomics, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hagit Baris Feldman
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal and CHU Sainte-Justine, Montreal, QC, Canada
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust. Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK
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10
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Loges NT, Antony D, Maver A, Deardorff MA, Güleç EY, Gezdirici A, Nöthe-Menchen T, Höben IM, Jelten L, Frank D, Werner C, Tebbe J, Wu K, Goldmuntz E, Čuturilo G, Krock B, Ritter A, Hjeij R, Bakey Z, Pennekamp P, Dworniczak B, Brunner H, Peterlin B, Tanidir C, Olbrich H, Omran H, Schmidts M. Recessive DNAH9 Loss-of-Function Mutations Cause Laterality Defects and Subtle Respiratory Ciliary-Beating Defects. Am J Hum Genet 2018; 103:995-1008. [PMID: 30471718 PMCID: PMC6288205 DOI: 10.1016/j.ajhg.2018.10.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/23/2018] [Indexed: 11/29/2022] Open
Abstract
Dysfunction of motile monocilia, altering the leftward flow at the embryonic node essential for determination of left-right body asymmetry, is a major cause of laterality defects. Laterality defects are also often associated with reduced mucociliary clearance caused by defective multiple motile cilia of the airway and are responsible for destructive airway disease. Outer dynein arms (ODAs) are essential for ciliary beat generation, and human respiratory cilia contain different ODA heavy chains (HCs): the panaxonemally distributed γ-HC DNAH5, proximally located β-HC DNAH11 (defining ODA type 1), and the distally localized β-HC DNAH9 (defining ODA type 2). Here we report loss-of-function mutations in DNAH9 in five independent families causing situs abnormalities associated with subtle respiratory ciliary dysfunction. Consistent with the observed subtle respiratory phenotype, high-speed video microscopy demonstrates distally impaired ciliary bending in DNAH9 mutant respiratory cilia. DNAH9-deficient cilia also lack other ODA components such as DNAH5, DNAI1, and DNAI2 from the distal axonemal compartment, demonstrating an essential role of DNAH9 for distal axonemal assembly of ODAs type 2. Yeast two-hybrid and co-immunoprecipitation analyses indicate interaction of DNAH9 with the ODA components DNAH5 and DNAI2 as well as the ODA-docking complex component CCDC114. We further show that during ciliogenesis of respiratory cilia, first proximally located DNAH11 and then distally located DNAH9 is assembled in the axoneme. We propose that the β-HC paralogs DNAH9 and DNAH11 achieved specific functional roles for the distinct axonemal compartments during evolution with human DNAH9 function matching that of ancient β-HCs such as that of the unicellular Chlamydomonas reinhardtii.
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11
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Margraf RL, Durtschi J, Krock B, Newcomb TM, Bonkowsky JL, Voelkerding KV, Bayrak-Toydemir P, Lutz RE, Swoboda KJ. Novel PLP1 Mutations Identified With Next-Generation Sequencing Expand the Spectrum of PLP1-Associated Leukodystrophy Clinical Phenotypes. Child Neurol Open 2018; 5:2329048X18789282. [PMID: 30046645 PMCID: PMC6056774 DOI: 10.1177/2329048x18789282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022] Open
Abstract
Next-generation sequencing was performed for 2 families with an undiagnosed neurologic disease. Analysis revealed X-linked mutations in the proteolipid protein 1 (PLP1) gene, which is associated with X-linked Pelizaeus-Merzbacher disease and Spastic Paraplegia type 2. In family A, the novel PLP1 missense mutation c.617T>A (p.M206K) was hemizygous in the 2 affected male children and heterozygous in the mother. In family B, the novel de novoPLP1 frameshift mutation c.359_369del (p.G120fs) was hemizygous in the affected male child. Although PLP1 mutations have been reported to cause an increasingly wide range of phenotypes inclusive of the dystonia, spastic paraparesis, motor neuronopathy, and leukodystrophy observed in our patients, atypical features included the cerebrospinal fluid deficiency of neurotransmitter and pterin metabolites and the delayed appearance of myelin abnormalities on neuroimaging studies. Next-generation sequencing studies provided a diagnosis for these families with complex leukodystrophy disease phenotypes, which expanded the spectrum of PLP1-associated leukodystrophy clinical phenotypes.
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Affiliation(s)
- Rebecca L Margraf
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT, USA
| | - Jacob Durtschi
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT, USA
| | - Bryan Krock
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Tara M Newcomb
- Pediatric Motor Disorders Research Program, Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Joshua L Bonkowsky
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Karl V Voelkerding
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Pinar Bayrak-Toydemir
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard E Lutz
- Department of Endocrinology, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kathryn J Swoboda
- Pediatric Motor Disorders Research Program, Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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12
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Vajravelu ME, Chai J, Krock B, Baker S, Langdon D, Alter C, De León DD. Congenital Hyperinsulinism and Hypopituitarism Attributable to a Mutation in FOXA2. J Clin Endocrinol Metab 2018; 103:1042-1047. [PMID: 29329447 PMCID: PMC6276717 DOI: 10.1210/jc.2017-02157] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/05/2018] [Indexed: 12/14/2022]
Abstract
CONTEXT Persistent hypoglycemia in the newborn period most commonly occurs as a result of hyperinsulinism. The phenotype of hypoketotic hypoglycemia can also result from pituitary hormone deficiencies, including growth hormone and adrenocorticotropic hormone deficiency. Forkhead box A2 (Foxa2) is a transcription factor shown in mouse models to influence insulin secretion by pancreatic β cells. In addition, Foxa2 is involved in regulation of pituitary development, and deletions of FOXA2 have been linked to panhypopituitarism. OBJECTIVE To describe an infant with congenital hyperinsulinism and hypopituitarism as a result of a mutation in FOXA2 and to determine the functional impact of the identified mutation. MAIN OUTCOME MEASURE Difference in wild-type (WT) vs mutant Foxa2 transactivation of target genes that are critical for β cell function (ABCC8, KNCJ11, HADH) and pituitary development (GLI2, NKX2-2, SHH). RESULTS Transactivation by mutant Foxa2 of all genes studied was substantially decreased compared with WT. CONCLUSIONS We report a mutation in FOXA2 leading to congenital hyperinsulinism and hypopituitarism and provide functional evidence of the molecular mechanism responsible for this phenotype.
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Affiliation(s)
- Mary Ellen Vajravelu
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Jinghua Chai
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Bryan Krock
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Samuel Baker
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - David Langdon
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Craig Alter
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Diva D De León
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Correspondence and Reprint Requests: Diva D. De León, MD, Division of Endocrinology and Diabetes, Children’s Hospital
of Philadelphia, 3615 Civic Center Boulevard, Ambramson Research Center, Room 802A,
Philadelphia, Pennsylvania 19104. E-mail:
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13
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Gade TPF, Tucker E, Nakazawa MS, Hunt SJ, Wong W, Krock B, Weber CN, Nadolski GJ, Clark TWI, Soulen MC, Furth EE, Winkler JD, Amaravadi RK, Simon MC. Ischemia Induces Quiescence and Autophagy Dependence in Hepatocellular Carcinoma. Radiology 2017; 283:702-710. [PMID: 28253108 DOI: 10.1148/radiol.2017160728] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Purpose To characterize hepatocellular carcinoma (HCC) cells surviving ischemia with respect to cell cycle kinetics, chemosensitivity, and molecular dependencies that may be exploited to potentiate treatment with transarterial embolization (TAE). Materials and Methods Animal studies were performed according to institutionally approved protocols. The growth kinetics of HCC cells were studied in standard and ischemic conditions. Viability and cell cycle kinetics were measured by using flow cytometry. Cytotoxicity profiling was performed by using a colorimetric cell proliferation assay. Analyses of the Cancer Genome Atlas HCC RNA-sequencing data were performed by using Ingenuity Pathway Analysis software. Activation of molecular mediators of autophagy was measured with Western blot analysis and fluorescence microscopy. In vivo TAE was performed in a rat model of HCC with (n = 5) and without (n = 5) the autophagy inhibitor Lys05. Statistical analyses were performed by using GraphPad software. Results HCC cells survived ischemia with an up to 43% increase in the fraction of quiescent cells as compared with cells grown in standard conditions (P < .004). Neither doxorubicin nor mitomycin C potentiated the cytotoxic effects of ischemia. Gene-set analysis revealed an increase in mRNA expression of the mediators of autophagy (eg, CDKN2A, PPP2R2C, and TRAF2) in HCC as compared with normal liver. Cells surviving ischemia were autophagy dependent. Combination therapy coupling autophagy inhibition and TAE in a rat model of HCC resulted in a 21% increase in tumor necrosis compared with TAE alone (P = .044). Conclusion Ischemia induces quiescence in surviving HCC cells, resulting in a dependence on autophagy, providing a potential therapeutic target for combination therapy with TAE. © RSNA, 2017 Online supplemental material is available for this article.
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Affiliation(s)
- Terence P F Gade
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Elizabeth Tucker
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Michael S Nakazawa
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Stephen J Hunt
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Waihay Wong
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Bryan Krock
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Charles N Weber
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Gregory J Nadolski
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Timothy W I Clark
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Michael C Soulen
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Emma E Furth
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Jeffrey D Winkler
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - Ravi K Amaravadi
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
| | - M Celeste Simon
- From the Penn Image-Guided Interventions Laboratory (T.P.F.G., S.J.H., C.N.W., G.J.N.), Department of Radiology (T.P.F.G., S.J.H., C.N.W., G.J.N., T.W.I.C., M.C. Soulen), and Department of Pathology (E.E.F.), Hospital of the University of Pennsylvania, Philadelphia, Pa; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Blvd, 456 BRB II/III, Philadelphia, PA 19104 (E.T., M.S.N., W.W., B.K., M.C. Simon); Abramson Family Cancer Center (B.K., R.K.A.) and Department of Chemistry (J.D.W.), University of Pennsylvania, Philadelphia, Pa
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Abstract
INTRODUCTION The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert commentary: NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics.
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Affiliation(s)
- Ahmad N Abou Tayoun
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Bryan Krock
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Nancy B Spinner
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
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15
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Suh E, Lee EB, Neal D, Wood EM, Toledo JB, Rennert L, Irwin DJ, McMillan CT, Krock B, Elman LB, McCluskey LF, Grossman M, Xie SX, Trojanowski JQ, Van Deerlin VM. Semi-automated quantification of C9orf72 expansion size reveals inverse correlation between hexanucleotide repeat number and disease duration in frontotemporal degeneration. Acta Neuropathol 2015; 130:363-72. [PMID: 26022924 DOI: 10.1007/s00401-015-1445-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/11/2022]
Abstract
We investigated whether chromosome 9 open reading frame 72 hexanucleotide repeat expansion (C9orf72 expansion) size in peripheral DNA was associated with clinical differences in frontotemporal degeneration (FTD) and amyotrophic lateral sclerosis (ALS) linked to C9orf72 repeat expansion mutations. A novel quantification workflow was developed to measure C9orf72 expansion size by Southern blot densitometry in a cross-sectional cohort of C9orf72 expansion carriers with FTD (n = 39), ALS (n = 33), both (n = 35), or who are unaffected (n = 21). Multivariate linear regressions were performed to assess whether C9orf72 expansion size from peripheral DNA was associated with clinical phenotype, age of disease onset, disease duration and age at death. Mode values of C9orf72 expansion size were significantly shorter in FTD compared to ALS (p = 0.0001) but were not associated with age at onset in either FTD or ALS. A multivariate regression model correcting for patient's age at DNA collection and disease phenotype revealed that C9orf72 expansion size is significantly associated with shorter disease duration (p = 0.0107) for individuals with FTD, but not with ALS. Despite considerable somatic instability of the C9orf72 expansion, semi-automated expansion size measurements demonstrated an inverse relationship between C9orf72 expansion size and disease duration in patients with FTD. Our finding suggests that C9orf72 repeat size may be a molecular disease modifier in FTD linked to hexanucleotide repeat expansion.
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Affiliation(s)
- EunRan Suh
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA, 19104-4283, USA,
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16
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Gade T, Tucker E, Hunt S, Nakazawa M, Krock B, Wong W, Nadolski G, Clark T, Furth E, Schnall M, Soulen M, Simon C. Targeting the metabolic stress response in hepatocellular carcinoma to potentiate TACE-induced ischemia. J Vasc Interv Radiol 2015. [DOI: 10.1016/j.jvir.2014.12.053] [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: 10/24/2022] Open
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Trefault N, Krock B, Delherbe N, Cembella A, Vásquez M. Latitudinal transects in the southeastern Pacific Ocean reveal a diverse but patchy distribution of phycotoxins. Toxicon 2011; 58:389-97. [DOI: 10.1016/j.toxicon.2011.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/20/2011] [Accepted: 07/12/2011] [Indexed: 11/16/2022]
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Krock B, Vetter W, Luckas B. PCB/toxaphene group separation on silica prior to congener specific determination of toxaphene residues in fish and other samples by GC/ECD. Chemosphere 1997; 35:1519-1530. [PMID: 9314190 DOI: 10.1016/s0045-6535(97)00222-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A precise quantification of toxaphene residues of environmental samples by gas chromatography/ electron capture detection (GC/ECD) requires the separation of the bulk of the polychlorinated biphenyls (PCBs) from the compounds of technical toxaphene (CTT) fraction. For this reason, a PCB/CTT group separation on silica was developed. B8-1413 (Parlar #26) and B7-515 (Parlar #32) eluted as first and last out of ten important CTT standards, and can be used to determine the elution volume of the CTT fraction on silica. GC/ECD quantification of CTTs was possible after separation of PCBs on 8.0 g activated silica eluted with 48 mL n-hexane followed by quantitative elution of CTTs with n-hexane/toluene (65:35; v/v). This method is a compromise between separation efficiency and consumption of material. Finally, eight CTTs were quantified in cod liver samples from Iceland and the Baltic Sea.
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Affiliation(s)
- B Krock
- Institut für Ernährung und Umwelt, Friedrich-Schiller-Universität Jena, Germany
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