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Sheldon M, Grimwood R, Nahas SA. Letter to the Editor: Biobanks and International Initiatives Are Playing a Critical Role in Redressing Historic Inadequacies in Biosample and Data Access from Underrepresented Minority Populations. Biopreserv Biobank 2022; 20:465-466. [DOI: 10.1089/bio.2022.0059] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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2
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Moreno Traspas R, Teoh TS, Wong PM, Maier M, Chia CY, Lay K, Ali NA, Larson A, Al Mutairi F, Al-Sannaa NA, Faqeih EA, Alfadhel M, Cheema HA, Dupont J, Bézieau S, Isidor B, Low DY, Wang Y, Tan G, Lai PS, Piloquet H, Joubert M, Kayserili H, Kripps KA, Nahas SA, Wartchow EP, Warren M, Bhavani GS, Dasouki M, Sandoval R, Carvalho E, Ramos L, Porta G, Wu B, Lashkari HP, AlSaleem B, BaAbbad RM, Abreu Ferrão AN, Karageorgou V, Ordonez-Herrera N, Khan S, Bauer P, Cogne B, Bertoli-Avella AM, Vincent M, Girisha KM, Reversade B. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis. Nat Genet 2022; 54:1214-1226. [PMID: 35864190 PMCID: PMC7615854 DOI: 10.1038/s41588-022-01120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Cirrhosis is usually a late-onset and life-threatening disease characterized by fibrotic scarring and inflammation that disrupts liver architecture and function. While it is typically the result of alcoholism or hepatitis viral infection in adults, its etiology in infants is much less understood. In this study, we report 14 children from ten unrelated families presenting with a syndromic form of pediatric liver cirrhosis. By genome/exome sequencing, we found recessive variants in FOCAD segregating with the disease. Zebrafish lacking focad phenocopied the human disease, revealing a signature of altered messenger RNA (mRNA) degradation processes in the liver. Using patient's primary cells and CRISPR-Cas9-mediated inactivation in human hepatic cell lines, we found that FOCAD deficiency compromises the SKI mRNA surveillance pathway by reducing the levels of the RNA helicase SKIC2 and its cofactor SKIC3. FOCAD knockout hepatocytes exhibited lowered albumin expression and signs of persistent injury accompanied by CCL2 overproduction. Our results reveal the importance of FOCAD in maintaining liver homeostasis and disclose a possible therapeutic intervention point via inhibition of the CCL2/CCR2 signaling axis.
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Affiliation(s)
- Ricardo Moreno Traspas
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze Shin Teoh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pui-Mun Wong
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Michael Maier
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Crystal Y Chia
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kenneth Lay
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Nur Ain Ali
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Austin Larson
- Section of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Fuad Al Mutairi
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Medical Genomic Research, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Huma Arshad Cheema
- Division of Pediatric Gastroenterology-Hepatology and Nutrition, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Juliette Dupont
- Department of Pediatrics, Genetic Services, Lisbon North University Hospital Center, Lisbon, Portugal
| | - Stéphane Bézieau
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Bertrand Isidor
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Dorrain Yanwen Low
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Grace Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hugues Piloquet
- Gastropediatrics Department, Nantes University Hospital Center, Nantes, France
| | - Madeleine Joubert
- Anatomopathology Department, Nantes University Hospital Center, Nantes, France
| | - Hulya Kayserili
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey
| | - Kimberly A Kripps
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric P Wartchow
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Majed Dasouki
- Department of Pediatric Genetics, AdventHealth Medical Group, Orlando, FL, USA
| | - Renata Sandoval
- Department of Oncogenetics, Hospital Sírio-Libanês, Brasília, Brazil
| | - Elisa Carvalho
- Department of Pediatric Gastroenterology and Hepatology, Hospital da Criança de Brasília José Alencar, UniCEUB, Brasília, Brazil
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo, Brazil
| | - Gilda Porta
- Department of Pediatric Hepatology, Transplant Unit, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College, Mangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Badr AlSaleem
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Raeda M BaAbbad
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | | | | | | | - Benjamin Cogne
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | | | - Marie Vincent
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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3
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Owen MJ, Lefebvre S, Hansen C, Kunard CM, Dimmock DP, Smith LD, Scharer G, Mardach R, Willis MJ, Feigenbaum A, Niemi AK, Ding Y, Van Der Kraan L, Ellsworth K, Guidugli L, Lajoie BR, McPhail TK, Mehtalia SS, Chau KK, Kwon YH, Zhu Z, Batalov S, Chowdhury S, Rego S, Perry J, Speziale M, Nespeca M, Wright MS, Reese MG, De La Vega FM, Azure J, Frise E, Rigby CS, White S, Hobbs CA, Gilmer S, Knight G, Oriol A, Lenberg J, Nahas SA, Perofsky K, Kim K, Carroll J, Coufal NG, Sanford E, Wigby K, Weir J, Thomson VS, Fraser L, Lazare SS, Shin YH, Grunenwald H, Lee R, Jones D, Tran D, Gross A, Daigle P, Case A, Lue M, Richardson JA, Reynders J, Defay T, Hall KP, Veeraraghavan N, Kingsmore SF. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13:4057. [PMID: 35882841 PMCID: PMC9325884 DOI: 10.1038/s41467-022-31446-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.
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Affiliation(s)
- Mallory J. Owen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sebastien Lefebvre
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Christian Hansen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Chris M. Kunard
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David P. Dimmock
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Laurie D. Smith
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Gunter Scharer
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Rebecca Mardach
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mary J. Willis
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Annette Feigenbaum
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Anna-Kaisa Niemi
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Luca Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Katarzyna Ellsworth
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucia Guidugli
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Bryan R. Lajoie
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | | | - Kevin K. Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong H. Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shimul Chowdhury
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Seema Rego
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - James Perry
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Speziale
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Nespeca
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego, San Diego, CA 92093 USA
| | - Meredith S. Wright
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | | | | | - Joe Azure
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | | | - Sandy White
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Charlotte A. Hobbs
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Sheldon Gilmer
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Gail Knight
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Albert Oriol
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Jerica Lenberg
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Shareef A. Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kate Perofsky
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Kyu Kim
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jeanne Carroll
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Nicole G. Coufal
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Erica Sanford
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Kristen Wigby
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jacqueline Weir
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Vicki S. Thomson
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Louise Fraser
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Seka S. Lazare
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Yoon H. Shin
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - Richard Lee
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David Jones
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Duke Tran
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Andrew Gross
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Patrick Daigle
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Anne Case
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Marisa Lue
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - John Reynders
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Thomas Defay
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Kevin P. Hall
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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4
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Goswami C, Sheldon M, Bixby C, Keddache M, Bogdanowicz A, Wang Y, Schultz J, McDevitt J, LaPorta J, Kwon E, Buyske S, Garbolino D, Biloholowski G, Pastuszak A, Storella M, Bhalla A, Charlier-Rodriguez F, Hager R, Grimwood R, Nahas SA. Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis 2022; 22:404. [PMID: 35468749 PMCID: PMC9035976 DOI: 10.1186/s12879-022-07374-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. METHODS RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina's Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. RESULTS An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron. CONCLUSION These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Chirayu Goswami
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Michael Sheldon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Christian Bixby
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | | | - Yihe Wang
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jonathan Schultz
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jessica McDevitt
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - James LaPorta
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Elaine Kwon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Steven Buyske
- Rutgers University, 559 Hill Center, 110 Frelinghuysen Rd, Piscataway, NJ, 08854, USA
| | - Dana Garbolino
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Alex Pastuszak
- Vault Health, 115 Broadway Suite 1800, 18th Floor, Dobbs Ferry, NY, 10522, USA
| | - Mary Storella
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Amit Bhalla
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Russ Hager
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Robin Grimwood
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Shareef A Nahas
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA.
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5
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Owen MJ, Niemi AK, Dimmock DP, Speziale M, Nespeca M, Chau KK, Van Der Kraan L, Wright MS, Hansen C, Veeraraghavan N, Ding Y, Lenberg J, Chowdhury S, Hobbs CA, Batalov S, Zhu Z, Nahas SA, Gilmer S, Knight G, Lefebvre S, Reynders J, Defay T, Weir J, Thomson VS, Fraser L, Lajoie BR, McPhail TK, Mehtalia SS, Kunard CM, Hall KP, Kingsmore SF. Rapid Sequencing-Based Diagnosis of Thiamine Metabolism Dysfunction Syndrome. N Engl J Med 2021; 384:2159-2161. [PMID: 34077649 PMCID: PMC9844116 DOI: 10.1056/nejmc2100365] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | - Kevin K Chau
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Zhanyang Zhu
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA
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6
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Friedman J, Bird LM, Haas R, Robbins SL, Nahas SA, Dimmock DP, Yousefzadeh MJ, Witt MA, Niedernhofer LJ, Chowdhury S. Ending a diagnostic odyssey: Moving from exome to genome to identify cockayne syndrome. Mol Genet Genomic Med 2021; 9:e1623. [PMID: 34076366 PMCID: PMC8372079 DOI: 10.1002/mgg3.1623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 01/04/2023] Open
Abstract
Background Cockayne syndrome (CS) is a rare autosomal recessive disorder characterized by growth failure and multisystemic degeneration. Excision repair cross‐complementation group 6 (ERCC6 OMIM: *609413) is the gene most frequently mutated in CS. Methods A child with pre and postnatal growth failure and progressive neurologic deterioration with multisystem involvement, and with nondiagnostic whole‐exome sequencing, was screened for causal variants with whole‐genome sequencing (WGS). Results WGS identified biallelic ERCC6 variants, including a previously unreported intronic variant. Pathogenicity of these variants was established by demonstrating reduced levels of ERCC6 mRNA and protein expression, normal unscheduled DNA synthesis, and impaired recovery of RNA synthesis in patient fibroblasts following UV‐irradiation. Conclusion The study confirms the pathogenicity of a previously undescribed upstream intronic variant, highlighting the power of genome sequencing to identify noncoding variants. In addition, this report provides evidence for the utility of a combination approach of genome sequencing plus functional studies to provide diagnosis in a child for whom a lengthy diagnostic odyssey, including exome sequencing, was previously unrevealing.
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Affiliation(s)
- Jennifer Friedman
- Department of NeurosciencesUniversity of California San DiegoSan DiegoCAUSA
- Department of PediatricsUniversity of California San DiegoSan DiegoCAUSA
- Division of Neurology Rady Children’s HospitalSan DiegoCAUSA
- Rady Children’s Institute for Genomic MedicineSan DiegoCAUSA
| | - Lynne M. Bird
- Department of PediatricsUniversity of California San DiegoSan DiegoCAUSA
- Division of Genetics/DysmorphologyRady Children’s Hospital San DiegoSan DiegoCAUSA
| | - Richard Haas
- Department of NeurosciencesUniversity of California San DiegoSan DiegoCAUSA
- Department of PediatricsUniversity of California San DiegoSan DiegoCAUSA
- Division of Neurology Rady Children’s HospitalSan DiegoCAUSA
| | - Shira L. Robbins
- Viterbi Family Department of Ophthalmology at the Shiley Eye InstituteUniversity of California San DiegoLa JollaCAUSA
| | | | | | - Matthew J. Yousefzadeh
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
| | - Mariah A. Witt
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
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7
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Sweeney NM, Nahas SA, Chowdhury S, Batalov S, Clark M, Caylor S, Cakici J, Nigro JJ, Ding Y, Veeraraghavan N, Hobbs C, Dimmock D, Kingsmore SF. Author Correction: Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease. NPJ Genom Med 2021; 6:38. [PMID: 34039997 PMCID: PMC8155217 DOI: 10.1038/s41525-021-00205-9] [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: 11/28/2022] Open
Affiliation(s)
- Nathaly M Sweeney
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA. .,Rady Children's Hospital, San Diego, CA, USA. .,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Michelle Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Julie Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - John J Nigro
- Rady Children's Hospital, San Diego, CA, USA.,Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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8
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Sweeney NM, Nahas SA, Chowdhury S, Batalov S, Clark M, Caylor S, Cakici J, Nigro JJ, Ding Y, Veeraraghavan N, Hobbs C, Dimmock D, Kingsmore SF. Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease. NPJ Genom Med 2021; 6:29. [PMID: 33888711 PMCID: PMC8062477 DOI: 10.1038/s41525-021-00192-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 08/31/2020] [Accepted: 03/19/2021] [Indexed: 11/09/2022] Open
Abstract
Congenital heart disease (CHD) is the most common congenital anomaly and a major cause of infant morbidity and mortality. While morbidity and mortality are highest in infants with underlying genetic conditions, molecular diagnoses are ascertained in only ~20% of cases using widely adopted genetic tests. Furthermore, cost of care for children and adults with CHD has increased dramatically. Rapid whole genome sequencing (rWGS) of newborns in intensive care units with suspected genetic diseases has been associated with increased rate of diagnosis and a net reduction in cost of care. In this study, we explored whether the clinical utility of rWGS extends to critically ill infants with structural CHD through a retrospective review of rWGS study data obtained from inpatient infants < 1 year with structural CHD at a regional children's hospital. rWGS diagnosed genetic disease in 46% of the enrolled infants. Moreover, genetic disease was identified five times more frequently with rWGS than microarray ± gene panel testing in 21 of these infants (rWGS diagnosed 43% versus 10% with microarray ± gene panels, p = 0.02). Molecular diagnoses ranged from syndromes affecting multiple organ systems to disorders limited to the cardiovascular system. The average daily hospital spending was lower in the time period post blood collection for rWGS compared to prior (p = 0.003) and further decreased after rWGS results (p = 0.000). The cost was not prohibitive to rWGS implementation in the care of this cohort of infants. rWGS provided timely actionable information that impacted care and there was evidence of decreased hospital spending around rWGS implementation.
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Affiliation(s)
- Nathaly M Sweeney
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
- Rady Children's Hospital, San Diego, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Michelle Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Julie Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - John J Nigro
- Rady Children's Hospital, San Diego, CA, USA
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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9
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Rusert JM, Juarez EF, Brabetz S, Jensen J, Garancher A, Chau LQ, Tacheva-Grigorova SK, Wahab S, Udaka YT, Finlay D, Seker-Cin H, Reardon B, Gröbner S, Serrano J, Ecker J, Qi L, Kogiso M, Du Y, Baxter PA, Henderson JJ, Berens ME, Vuori K, Milde T, Cho YJ, Li XN, Olson JM, Reyes I, Snuderl M, Wong TC, Dimmock DP, Nahas SA, Malicki D, Crawford JR, Levy ML, Van Allen EM, Pfister SM, Tamayo P, Kool M, Mesirov JP, Wechsler-Reya RJ. Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer Res 2020; 80:5393-5407. [PMID: 33046443 DOI: 10.1158/0008-5472.can-20-1655] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/04/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Medulloblastoma is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most patients with medulloblastoma receive similar therapies, including surgery, radiation, and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease and survivors suffer severe long-term side effects from therapy. We hypothesize that each patient with medulloblastoma is sensitive to different therapies and that tailoring therapy based on the molecular and cellular characteristics of patients' tumors will improve outcomes. To test this, we assembled a panel of orthotopic patient-derived xenografts (PDX) and subjected them to DNA sequencing, gene expression profiling, and high-throughput drug screening. Analysis of DNA sequencing revealed that most medulloblastomas do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provided valuable information about potential therapies for every tumor. For example, drug screening demonstrated that actinomycin D, which is used for treatment of sarcoma but rarely for medulloblastoma, was active against PDXs representing Group 3 medulloblastoma, the most aggressive form of the disease. Functional analysis of tumor cells was successfully used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their specific tumor. SIGNIFICANCE: These findings show that high-throughput drug screening identifies therapies for medulloblastoma that cannot be predicted by genomic or transcriptomic analysis.
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Affiliation(s)
- Jessica M Rusert
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Edwin F Juarez
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Sebastian Brabetz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - James Jensen
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Alexandra Garancher
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Lianne Q Chau
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Silvia K Tacheva-Grigorova
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Sameerah Wahab
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Yoko T Udaka
- Rady Children's Hospital San Diego, San Diego, California
| | - Darren Finlay
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Huriye Seker-Cin
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Susanne Gröbner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lin Qi
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Mari Kogiso
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Yuchen Du
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, Illinois
| | - Patricia A Baxter
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, Illinois
| | - Jacob J Henderson
- Papé Family Pediatric Research Institute, Department of Pediatrics, and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Kristiina Vuori
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yoon-Jae Cho
- Papé Family Pediatric Research Institute, Department of Pediatrics, and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Xiao-Nan Li
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, Illinois
| | - James M Olson
- Fred Hutchinson Cancer Research Center and Seattle Children's Hospital, Seattle, Washington
| | - Iris Reyes
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York, New York
| | - Terence C Wong
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Denise Malicki
- Rady Children's Hospital, San Diego, California
- Department of Pathology, University of California San Diego, La Jolla, California
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - John R Crawford
- Rady Children's Hospital, San Diego, California
- Department of Pediatrics, University of California San Diego, La Jolla, California
- Department of Neurosciences, University of California San Diego, La Jolla, California
| | - Michael L Levy
- Rady Children's Hospital, San Diego, California
- Department of Surgery, University of California San Diego, La Jolla, California
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
- Rady Children's Institute for Genomic Medicine, San Diego, California
- Department of Pediatrics, University of California San Diego, La Jolla, California
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10
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Farnaes L, Nahas SA, Chowdhury S, Nelson J, Batalov S, Dimmock DM, Kingsmore SF. Rapid whole-genome sequencing identifies a novel GABRA1 variant associated with West syndrome. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001776. [PMID: 28864462 PMCID: PMC5593154 DOI: 10.1101/mcs.a001776] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/14/2017] [Indexed: 01/08/2023] Open
Abstract
A 9-mo-old infant was admitted with infantile spasms that improved on administration of topiramate and steroids. He also had developmental delay, esotropia, and hypsarrhythmia on interictal electroencephalogram (EEG), and normal brain magnetic resonance imaging (MRI). West syndrome is the triad of infantile spasms, interictal hypsarrhythmia, and mental retardation. Rapid trio whole-genome sequencing (WGS) revealed a novel, likely pathogenic, de novo variant in the gene encoding γ-aminobutyric acid (GABA) type A receptor, α1 polypeptide (GABRA1 c.789G>A, p.Met263Ile) in the proband. GABRA1 mutations have been associated with early infantile epileptic encephalopathy type 19 (EIEE19). We suggest that GABRA1 p.Met263Ile is associated with a distinct West syndrome phenotype.
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Affiliation(s)
- Lauge Farnaes
- Rady Children's Institute of Genomic Medicine (RCIGM), San Diego, California 92123, USA
| | - Shareef A Nahas
- Rady Children's Institute of Genomic Medicine (RCIGM), San Diego, California 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute of Genomic Medicine (RCIGM), San Diego, California 92123, USA
| | - James Nelson
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093, USA
| | - Serge Batalov
- Rady Children's Institute of Genomic Medicine (RCIGM), San Diego, California 92123, USA
| | - David M Dimmock
- Rady Children's Institute of Genomic Medicine (RCIGM), San Diego, California 92123, USA
| | - Stephen F Kingsmore
- Rady Children's Institute of Genomic Medicine (RCIGM), San Diego, California 92123, USA
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11
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Martin NT, Nakamura K, Davies R, Nahas SA, Brown C, Tunuguntla R, Gatti RA, Hu H. ATM-dependent MiR-335 targets CtIP and modulates the DNA damage response. PLoS Genet 2013; 9:e1003505. [PMID: 23696749 PMCID: PMC3656122 DOI: 10.1371/journal.pgen.1003505] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 03/26/2013] [Indexed: 01/28/2023] Open
Abstract
ATM plays a critical role in cellular responses to DNA double-strand breaks (DSBs). We describe a new ATM–mediated DSB–induced DNA damage response pathway involving microRNA (miRNA): irradiation (IR)-induced DSBs activate ATM, which leads to the downregulation of miR-335, a miRNA that targets CtIP, which is an important trigger of DNA end resection in homologous recombination repair (HRR). We demonstrate that CREB is responsible for a large portion of miR-335 expression by binding to the promoter region of miR-335. CREB binding is greatly reduced after IR, corroborating with previous studies that IR-activated ATM phosphorylates CREB to reduce its transcription activity. Overexpression of miR-335 in HeLa cells resulted in reduced CtIP levels and post-IR colony survival and BRCA1 foci formation. Further, in two patient-derived lymphoblastoid cell lines with decreased post-IR colony survival, a “radiosensitive” phenotype, we demonstrated elevated miR-335 expression, reduced CtIP levels, and reduced BRCA1 foci formation. Colony survival, BRCA1 foci, and CtIP levels were partially rescued by miRNA antisense AMO-miR-335 treatment. Taken together, these findings strongly suggest that an ATM–dependent CREB–miR-335–CtIP axis influences the selection of HRR for repair of certain DSB lesions. ATM (Ataxia-Telangiectasia Mutated) serine/threonine kinase plays a critical role in coordinating the cellular response to DNA double-strand breaks (DSBs), such as cell cycle checkpoint, DNA repair, and apoptosis. miRNAs have been reported to be involved in many cellular processes, and their role in DSB–triggered DNA damage response (DDR) is just being elucidated. Here we describe a novel DSB response mechanism whereby ATM–dependent miR-335 downregulates CtIP. CtIP is a multifunctional protein that is crucial for DNA homologous recombination repair; and we show, for the first time, that this protein is subject to miRNA downregulation. CtIP downregulation was verified in cell lines from radiosensitive patients, and we demonstrate that this pathway contributes to radiosensitization and DNA repair defects in BRCA1 foci formation and cell cycle checkpoint. Given that miR-335 is also a tumor metastasis suppressor, our finding suggests that miR-335 overexpression could not only increase tumor sensitivity to radiation or chemical therapy but also inhibit tumor metastasis or re-initiation of tumor growth.
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Affiliation(s)
- Nathan T Martin
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
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12
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Davies RC, Pettijohn K, Fike F, Wang J, Nahas SA, Tunuguntla R, Hu H, Gatti RA, McCurdy D. Defective DNA double-strand break repair in pediatric systemic lupus erythematosus. ACTA ACUST UNITED AC 2012; 64:568-78. [PMID: 21905016 DOI: 10.1002/art.33334] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Previous reports of cells from patients with systemic lupus erythematosus (SLE) note that repair of single-strand breaks is delayed, and these lesions may be converted to double-strand breaks (DSBs) at DNA replication forks. We undertook this study to assess the integrity of DSB recognition, signaling, and repair mechanisms in B lymphoblastoid cell lines derived from patients with pediatric SLE. METHODS Nine assays were used to interrogate DSB repair and recognition in lymphoblastoid cell lines from patients with pediatric SLE, including the neutral comet assay (NCA), colony survival assay (CSA), irradiation-induced foci formation for γ-H2AX and 53BP1 proteins, kinetics of phosphorylation of structural maintenance of chromosomes protein 1 (SMC1), postirradiation bromodeoxyuridine incorporation to evaluate S phase checkpoint integrity, monoubiquitination of Fanconi protein D2, ATM protein expression, and non-homologous DNA end joining protein expression and function. RESULTS Three of the 9 assays revealed abnormal patterns of response to irradiation-induced DNA damage. The NCA and CSA yielded aberrant results in the majority of SLE lymphoblastoid cell lines. Abnormal prolongation of SMC1 phosphorylation was also noted in 2 of 16 SLE lymphoblastoid cell lines. CONCLUSION Our data suggest that DSB repair is defective in some lymphoblastoid cell lines from pediatric patients with SLE, especially when assessed by both NCA and CSA. Since these studies are nonspecific, further studies of DNA repair and kinetics are indicated to further delineate the underlying pathogenesis of SLE and possibly identify therapeutic targets.
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Affiliation(s)
- Robert C Davies
- David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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13
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Li X, Zhou J, Nahas SA, Wan H, Hu H, Gatti RA. Common copy number variations in fifty radiosensitive cell lines. Genomics 2012; 99:96-100. [DOI: 10.1016/j.ygeno.2011.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 01/15/2023]
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14
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Nahas SA, Davies R, Fike F, Nakamura K, Du L, Kayali R, Martin NT, Concannon P, Gatti RA. Comprehensive profiling of radiosensitive human cell lines with DNA damage response assays identifies the neutral comet assay as a potential surrogate for clonogenic survival. Radiat Res 2012; 177:176-86. [PMID: 21962002 PMCID: PMC4316198 DOI: 10.1667/rr2580.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In an effort to explore the possible causes of human radiosensitivity and identify more rapid assays for cellular radiosensitivity, we interrogated a set of assays that evaluate cellular functions involved in recognition and repair of DNA double-strand breaks: (1) neutral comet assay, (2) radiation-induced γ-H2AX focus formation, (3) the temporal kinetics of structural maintenance of chromosomes 1 phosphorylation, (4) intra-S-phase checkpoint integrity, and (5) mitochondrial respiration. We characterized a unique panel of 19 "radiosensitive" human lymphoblastoid cell lines from individuals with undiagnosed diseases suggestive of a DNA repair disorder. Radiosensitivity was defined by reduced cellular survival using a clonogenic survival assay. Each assay identified cell lines with defects in DNA damage response functions. The highest concordance rate observed, 89% (17/19), was between an abnormal neutral comet assay and reduced survival by the colony survival assay. Our data also suggested that the neutral comet assay would be a more rapid surrogate for analyzing DNA repair/processing disorders.
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Affiliation(s)
- Shareef A Nahas
- UCLA School of Medicine, Department of Pathology and Laboratory Medicine, Los Angeles, California 90095, USA.
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Martin NT, Nahas SA, Tunuguntla R, Fike F, Gatti RA. Assessing 'radiosensitivity' with kinetic profiles of γ-H2AX, 53BP1 and BRCA1 foci. Radiother Oncol 2011; 101:35-8. [PMID: 21722985 DOI: 10.1016/j.radonc.2011.05.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [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: 04/30/2011] [Revised: 05/24/2011] [Accepted: 05/26/2011] [Indexed: 01/09/2023]
Abstract
BACKGROUND AND PURPOSE DNA repair assays to identify radiosensitive patients have had limited clinical implementation due to long turn-around times or limited specificity. This study evaluates γ-H2AX-Irradiation Induced Foci (IRIF) kinetics as a more rapid surrogate for the 'gold standard' colony survival assay (CSA) using several known DNA repair disorders as reference models. MATERIALS AND METHODS Radiosensitive cells of known and unknown etiology were studied. γ-H2AX-IRIFs were quantified over 24 h, and the curves were fitted by combining logarithmic growth and exponential decay functions. Fitted values that differed from radionormal controls were considered aberrant and compared to CSA results. RESULTS We observed 87% agreement of IRIF data with the CSA for the 14 samples tested. Analysis of γ-H2AX-IRIF kinetics for known repair disorders indicated similarities between an RNF168(-/-) cell line and an RS cell of unknown etiology. These cell lines were further characterized by a reduction in BRCA1-IRIF formation and G2/M checkpoint activation. CONCLUSIONS γ-H2AX-IRIF kinetics showed high concordance with the CSA in RS populations demonstrating its potential as a more rapid surrogate assay. This method provides a means to globally identify defective DNA repair pathways in RS cells of unknown etiology through comparison with known DNA repair defects.
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Affiliation(s)
- Nathan T Martin
- UCLA School of Medicine, Department of Pathology and Laboratory Medicine, Los Angeles, CA 90095-1732, USA.
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16
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Abstract
PURPOSE OF REVIEW It is important to assess 'radiosensitivity' in patients suspected of immunodeficiency because underlying DNA double strand break (DSB) repair defects have considerable impact on V(D)J recombination, class switching and lymphocyte maturation, leading to increased infections and cancer risk. In addition, the phenotype of 'radiosensitivity' may identify patients with increased toxicity to radiation and chemotherapeutic agents and could impact upon their preparation for stem cell transplantation. To date, the gold standard for evaluating 'radiosensitivity' has been the colony-survival assay (CSA), which reflects the efficiency of DNA repair of DSBs as it impacts upon replication and cell survival. Other methods measure other aspects of DNA repair; however, their limited specificity often leads to false negatives for predicting 'radiosensitivity', especially clinical radiosensitivity. Lastly, clinical awareness of an overarching syndrome of DSB repair disorders, XCIND, could help to raise diagnostic levels of suspicion and, thereby, identify additional patients with new forms of immunodeficiency, cancer susceptibility and radiosensitivity. RECENT FINDINGS Within the past year, three new radiosensitivity disorders of DSB repair have been described, involving deficiencies of RNF168, RAD50, and DNA-PKcs. These are truly translational advances because they validate laboratory models and allow new patients to be identified. SUMMARY Recognizing compromised genome stability is important but difficult. We review the evidence for correlations between DSB repair, abnormal colony formation, clinical radiosensitivity and other laboratory methods.
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Mitui M, Nahas SA, Du LT, Yang Z, Lai CH, Nakamura K, Arroyo S, Scott S, Purayidom A, Concannon P, Lavin M, Gatti RA. Functional and computational assessment of missense variants in the ataxia-telangiectasia mutated (ATM) gene: mutations with increased cancer risk. Hum Mutat 2009; 30:12-21. [PMID: 18634022 DOI: 10.1002/humu.20805] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The functional consequences of missense variants are often difficult to predict. This becomes especially relevant when DNA sequence changes are used to determine a diagnosis or prognosis. To analyze the consequences of 12 missense variants in patients with mild forms of ataxia-telangiectasia (A-T), we employed site-directed mutagenesis of ataxia-telangiectasia mutated (ATM) cDNA followed by stable transfections into a single A-T cell line to isolate the effects of each allele on the cellular phenotype. After induction of the transfected cells with CdCl2, we monitored for successful ATM transcription and subsequently assessed: 1) intracellular ATM protein levels; 2) ionizing radiation (IR)-induced ATM kinase activity; and 3) cellular radiosensitivity. We then calculated SIFT and PolyPhen scores for the missense changes. Nine variants produced little or no correction of the A-T cellular phenotype and were interpreted to be ATM mutations; SIFT/PolyPhen scores supported this. Three variants corrected the cellular phenotype, suggesting that they represented benign variants or polymorphisms. SIFT and PolyPhen scores supported the functional analyses for one of these variants (c.1709T>C); the other two were predicted to be "not tolerated" (c.6188G>A and c.6325T>G) and were classified as "operationally neutral." Genotype/phenotype relationships were compared: three deleterious missense variants were associated with an increased risk of cancer (c.6679C>T, c.7271T>G, and c.8494C>T). In situ mutagenesis represents an effective experimental approach for distinguishing deleterious missense mutations from benign or operationally neutral missense variants.
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Affiliation(s)
- M Mitui
- Department of Pathology and Laboratory Medicine, The David Geffen School of Medicine at the University of California, Los Angeles (UCLA), Los Angeles, California 90095-1732, USA
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Nahas SA, Butch AW, Du L, Gatti RA. Rapid flow cytometry-based structural maintenance of chromosomes 1 (SMC1) phosphorylation assay for identification of ataxia-telangiectasia homozygotes and heterozygotes. Clin Chem 2009; 55:463-72. [PMID: 19147735 PMCID: PMC2980758 DOI: 10.1373/clinchem.2008.107128] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [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: 12/18/2022]
Abstract
BACKGROUND No rapid reliable method exists for identifying ataxia-telangiectasia (A-T) homozygotes or heterozygotes. Heterozygotes are at an increased risk of cancer and are more sensitive to the effects of ionizing radiation (IR) than the general population. We report a rapid flow cytometry (FC)-based ataxia-telangiectasia mutated (ATM) kinase assay that measures ATM- dependent phosphorylation of structural maintenance of chromosomes 1 (SMC1) following DNA damage (FC-pSMC1 assay). METHODS After optimizing conditions with lymphoblastoid cell lines (LCLs), we studied peripheral blood mononuclear cells (PBMCs) isolated from 16 healthy donors (unknowns), 10 obligate A-T heterozygotes, and 6 unrelated A-T patients. One hour after DNA damage (by either IR or bleomycin), the cells were fixed and incubated with a primary antibody to SMC1pSer966. We analyzed the stained cells by FC to determine the difference in geometric mean fluorescence intensity (DeltaGMFI) of untreated and treated cells; this difference was expressed as a percentage of daily experimental controls. RESULTS The FC-pSMC1 assay reliably distinguished ATM heterozygotes and homozygotes from controls. Average DeltaGMFI percentages (SD) of daily controls were, for unknowns, 106.1 (37.6); for A-T heterozygotes, 37.0 (18.7); and for A-T homozygotes; -8.73 (16.2). Values for heterozygotes and homozygotes were significantly different from those of controls (P < 0.0001). CONCLUSIONS The FC-pSMC1 assay shortens the turnaround time for diagnosing A-T homozygotes from approximately 3 months to approximately 3 h. It also identifies A-T heterozygotes and can be used for prenatal counseling or for screening individuals in large study cohorts for potential ATM heterozygosity, which can then be confirmed by sequencing.
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Affiliation(s)
- Shareef A. Nahas
- Molecular Toxicology Interdepartmental Doctoral Program, UCLA School of Medicine and School of Public Health, Los Angeles, CA
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, CA
| | - Anthony W. Butch
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, CA
| | - Liutao Du
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, CA
| | - Richard A. Gatti
- Molecular Toxicology Interdepartmental Doctoral Program, UCLA School of Medicine and School of Public Health, Los Angeles, CA
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, CA
- Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA
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Ehlayel M, de Beaucoudrey L, Fike F, Nahas SA, Feinberg J, Casanova JL, Gatti RA. Simultaneous presentation of 2 rare hereditary immunodeficiencies: IL-12 receptor β1 deficiency and ataxia-telangiectasia. J Allergy Clin Immunol 2008; 122:1217-9. [DOI: 10.1016/j.jaci.2008.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 05/26/2008] [Accepted: 07/01/2008] [Indexed: 02/01/2023]
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Nahas SA, Duquette A, Roddier K, Gatti RA, Brais B. Ataxia-oculomotor apraxia 2 patients show no increased sensitivity to ionizing radiation. Neuromuscul Disord 2007; 17:968-9. [PMID: 17720498 DOI: 10.1016/j.nmd.2007.06.464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 06/01/2007] [Accepted: 06/22/2007] [Indexed: 10/22/2022]
Abstract
Mutations in senataxin have been described recently in 24 cases of French-Canadian descent with ataxia-oculomotor apraxia 2. This recessive ataxia is associated with an elevation in alpha-fetoprotein as in ataxia-telangiectasia. Because ataxia-telangiectasia cells are highly radiosensitive, we used a colony survival assay to measure the radiosensitivity of lymphoblastoid cell lines derived from five French-Canadian patients with ataxia-oculomotor apraxia 2. Two were homozygous for the common French-Canadian L1976R SETX missense mutation; the three others were compound heterozygotes for the common mutation and three different missense mutations. Overall, lymphoblastoid cell lines derived from these cases did not show significant variation from a normal response to 1 Gray of ionizing radiation but the two patients who were homozygous for the common L1976R mutation fell in the intermediate or non-diagnostic range.
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Affiliation(s)
- S A Nahas
- UCLA School of Medicine, Department of Pathology & Laboratory Medicine, Macdonald Research Laboratories, Los Angeles, CA, USA
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Landmark H, Nahas SA, Aarøe J, Gatti R, Børresen-Dale AL, Rødningen OK. Transcriptional response to ionizing radiation in human radiation sensitive cell lines. Radiother Oncol 2007; 83:256-60. [PMID: 17512073 DOI: 10.1016/j.radonc.2007.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 04/28/2007] [Accepted: 04/29/2007] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND PURPOSE Radiation is a common treatment of cancer, but some patients show severe side effects when exposed to small doses of radiation. The aim of this study was to explore the underlying cause of radiation sensitivity in a group of radiation sensitive patients. MATERIALS AND METHODS Lymphoblastoid cell lines from 5 normal individuals, 4 Ataxia Telangiectasia (AT), and 12 non-AT radiation sensitive (RS) patients were irradiated. RNA was isolated before and after radiation and hybridized to 15k cDNA microarrays and gene expression was recorded. RESULTS AND CONCLUSION The RS cell lines showed an expression phenotype different from both the AT and normal cell lines. Six of the RS cell lines had a distinct expression profile before radiation. This implies that the RS patients are a heterogeneous group, but that six of the patients may have a common cause of radiation sensitivity.
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Affiliation(s)
- H Landmark
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Norway.
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Nahas SA, Lai CH, Gatti RA. Post-irradiation phosphorylation of structural maintenance chromosome 1 (SMC1) is independent of the Fanconi protein pathway. Int J Radiat Oncol Biol Phys 2005; 61:1167-72. [PMID: 15752898 DOI: 10.1016/j.ijrobp.2004.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 06/23/2004] [Revised: 11/04/2004] [Accepted: 11/09/2004] [Indexed: 10/25/2022]
Abstract
PURPOSE To confirm the sensitivity of cells from patients with Fanconi anemia (FA) to ionizing radiation, and to determine whether the phosphorylation of structural maintenance chromosome 1 (SMC1) was associated with radiosensitivity, as it is in other DNA repair disorders. METHODS AND MATERIALS Using lymphoblastoid cell lines from FA patients before and after exposure to ionizing radiation, the colony survival assay, radioresistant DNA synthesis, and SMC1 phosphorylation were measured. FA lymphoblastoid cell lines that had been transfected with the wild-type FANC gene were used as controls. RESULTS Cells from FA patients of six complementation groups were radiosensitive. Despite this, SMC1 phosphorylation was normal in each case; radioresistant DNA synthesis, a measure of S phase checkpoint integrity, was defective in FANCD2 lymphoblastoid cell lines and was corrected in FANCD2 + D2 cells. CONCLUSIONS The data indicate that the FANC pathway proteins play a major role in the cellular responses to ionizing radiation, but not in SMC1 phosphorylation or in the S phase checkpoint of FANCD2-deficient cells. Thus, SMC1 activation is not a common denominator of radiosensitivity, as has been suggested by radiation responses of cells from ataxia-telangiectasia, Nijmegen breakage syndrome, or Mre11 deficiency patients.
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Affiliation(s)
- Shareef A Nahas
- Department of Pathology, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, CA 90095-1732, USA
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Lai CH, Chun HH, Nahas SA, Mitui M, Gamo KM, Du L, Gatti RA. Correction of ATM gene function by aminoglycoside-induced read-through of premature termination codons. Proc Natl Acad Sci U S A 2004; 101:15676-81. [PMID: 15498871 PMCID: PMC524838 DOI: 10.1073/pnas.0405155101] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 09/23/2004] [Indexed: 11/18/2022] Open
Abstract
Approximately 14% of genetic mutations in patients with ataxia-telangiectsia (A-T) are single-nucleotide changes that result in primary premature termination codons (PTCs), either UAA, UAG, or UGA. The purpose of this study was to explore a potential therapeutic approach for this subset of patients by using aminoglycosides to induce PTC read-through, thereby restoring levels of full-length ATM (A-T mutated) protein. In experiments using a modified in vitro cDNA coupled transcription/translation protein truncation test, 13 A-T cell lines carrying PTC mutations in different contexts exhibited read-through expression of ATM fragments, with three of four aminoglycosides tested. In ex vivo experiments with lymphoblastoid cell lines, we used radiosensitivity, radioresistant DNA synthesis, and irradiation-induced autophosphorylation of ATM Ser-1981 to show that the aminoglycoside-induced full-length ATM protein was functional and corrected, to various extents, the phenotype of A-T cells. These results encourage further testing of other compounds in this class, as well as follow up animal studies. Because some A-T patients with 5-20% of normal levels of ATM protein show slower neurological progression, A-T may prove to be a good model for aminoglycoside-induced read-through therapy.
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Affiliation(s)
- Chih-Hung Lai
- Department of Pathology and Laboratory Medicine, The David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1732, USA
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Abstract
BACKGROUND Ataxia-telangiectasia (A-T) is a neurologic disorder caused by mutations in the ataxia-telangiectasia mutated (ATM) gene. A clinical diagnosis of A-T is confirmed by radiosensitivity testing and immunoblotting for ATM protein. Because both of these tests have long turnaround times (> or =3 months), we developed a rapid immunoassay to measure ATM protein and determined its sensitivity and specificity for diagnosing A-T. METHODS Recombinant ATM protein was used for standardization. Lysates of lymphoblastoid cell lines (LCLs) and peripheral blood mononuclear cells (PBMCs) from A-T patients, controls, and A-T heterozygotes were tested for ATM protein by immunoassay. RESULTS Between-run imprecision (CV) was < or =13%. Nuclear lysates from control LCLs and PBMCs had ATM protein concentrations of 49-610 microg/L and 48-943 microg/L, respectively. ATM protein was not detectable in LCL nuclear lysates from 18 of 21 A-T patients. The three remaining A-T patients had trace amounts of ATM protein, which was confirmed on immuoblots. ATM protein was also detectable in whole-cell lysates from 4 x 10(6) cells at concentrations of 64-463 microg/L and 42-444 microg/L for control LCLs and PBMCs, respectively. A-T heterozygotes had ATM protein concentrations of 52-98 microg/L. ATM protein was stable in PBMCs stored for 1 month at -70 degrees C, but rapidly decreased after 1 day in unprocessed blood. CONCLUSIONS This ATM protein immunoassay can be used to confirm a diagnosis of A-T in 2 days on small numbers of PBMCs and can potentially identify A-T carriers and individuals at increased risk for cancer.
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Affiliation(s)
- Anthony W Butch
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA 90095, USA.
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Chun HH, Sun X, Nahas SA, Teraoka S, Lai CH, Concannon P, Gatti RA. Improved diagnostic testing for ataxia-telangiectasia by immunoblotting of nuclear lysates for ATM protein expression. Mol Genet Metab 2003; 80:437-43. [PMID: 14654357 DOI: 10.1016/j.ymgme.2003.09.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The laboratory diagnosis of ataxia-telangiectasia (A-T) currently relies upon measurement of serum alphafetoprotein (AFP) and cellular sensitivity to ionizing radiation. A previous report suggests that immunoblotting of whole cell lysates from lymphoblastoid cell lines (LCLs) might be informative for diagnosis. To further evaluate this possibility, and improve sensitivity, we performed immunoblotting for ATM protein on nuclear lysates of 71 consecutive radiosensitive LCLs that were established from patients with clinical features suggestive of A-T. Fifty-two LCLs (73%) contained no detectable ATM protein, with a representative sample (N=25) testing negative for ATM kinase activity, having at least one ATM mutation, and having elevated AFP levels; these results confirmed the diagnosis. Seventeen LCLs (24%) expressed intermediate or normal levels of ATM protein and exhibited normal ATM kinase activity; follow-up studies failed to detect ATM mutations and AFP levels were normal in all but three. Of the remaining two radiosensitive LCLs, one had 35% of normal protein with normal kinase activity and no ATM mutations. The other LCL had 9% of normal protein, with intermediate levels of kinase activity, a homozygous missense ATM mutation, and elevated AFP. Our data suggest that it is very uncommon to encounter bonafide A-T patients with more than trace amounts of ATM protein. We conclude that immunoblotting for ATM protein is of higher specificity for diagnosing A-T than radiosensitivity testing. In addition, we have documented in vitro radiosensitivity in other patients who share some clinical features with A-T.
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Affiliation(s)
- Helen H Chun
- Department of Pathology, The David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1732, USA
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