1
|
Pisan E, De Luca C, Brancati F, Sanchez Russo R, Li D, Bhoj E, Wenger T, Marwaha A, Johnson N, Beneteau C, Brischoux-Boucher E, Houge G, Paulsen J, Hammer TB, Ek J, Schweitzer D, Russell BE, Dutra-Clarke M, Nelson S, Douine ED, Corona RI, Dudding T, Thomson H, Low K, Belnap N, Iascone M, Priolo M, Carli D, Mussa A, Bijlsma EK, Kopp N, Jais JP, Amiel J, Gordon CT. The spectrum of heart defects in the TRAF7-related multiple congenital anomalies-intellectual disability syndrome. Proc Natl Acad Sci U S A 2024; 121:e2317601121. [PMID: 38466850 DOI: 10.1073/pnas.2317601121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Affiliation(s)
- Elise Pisan
- Laboratory of embryology and genetics of human malformations, INSERM Unité Mixte de Recherche 1163, Institut Imagine and Université Paris Cité, Paris 75015, France
| | - Chiara De Luca
- Human Genetics, Department of Life, Health and Environmental Sciences, University of L'Aquila, Coppito 67100, L'Aquila, Italy
| | - Francesco Brancati
- Human Genetics, Department of Life, Health and Environmental Sciences, University of L'Aquila, Coppito 67100, L'Aquila, Italy
- Human Functional Genomics Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Roma, Rome 00163, Italy
| | - Rossana Sanchez Russo
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Elizabeth Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Tara Wenger
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA 98105
| | - Ashish Marwaha
- Alberta Children's Hospital, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nicole Johnson
- Alberta Children's Hospital, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Claire Beneteau
- Service de Génétique Médicale, Centre Hospitalo-Universitaire de Bordeaux, Bordeaux F-33000, France
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, Centre Hospitalo-Universitaire de Besançon, Besançon 25000, France
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Julie Paulsen
- Department of Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, Trondheim 7006, Norway
| | - Trine Bjørg Hammer
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Genetics, Rigshospitalet, Copenhagen 2100, Denmark
| | - Jakob Ek
- Department of Genetics, Rigshospitalet, Copenhagen 2100, Denmark
| | - Daniela Schweitzer
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095
| | - Bianca E Russell
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095
| | - Marina Dutra-Clarke
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095
| | - Stanley Nelson
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095
| | - Rosario I Corona
- Department of Human Genetics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095
| | - Tracy Dudding
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Hannah Thomson
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Karen Low
- Department of Clinical Genetics, St. Michaels Hospital, University Hospitals Bristol and Weston National Health Service Trust, Bristol BS2 8EJ, United Kingdom
| | - Newell Belnap
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85012
| | - Maria Iascone
- Medical Genetics Laboratory, Azienda Sociosanitaria Territoriale Papa Giovanni XXIII, Bergamo 24127, Italy
| | - Manuela Priolo
- Unit of Medical Genetics, Azienda Ospedaliera di Rilievo Nazionale Cardarelli, Naples 80131, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Torino, Torino 10124, Italy
- Immunogenetics and Transplant Biology Unit, Città della Salute e della Scienza University Hospital, Torino 10126, Italy
| | - Alessandro Mussa
- Pediatric Clinical Genetics Unit, Ospedale Infantile Regina Margherita, Department of Public Health and Pediatric Sciences, University of Torino, Torino 10126, Italy
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, 2300 RC Leiden, the Netherlands
| | - Nathan Kopp
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53223
| | - Jean-Philippe Jais
- Biostatistics Unit, Université Paris Cité, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris 75015, France
| | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, INSERM Unité Mixte de Recherche 1163, Institut Imagine and Université Paris Cité, Paris 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris 75015, France
| | - Christopher T Gordon
- Laboratory of embryology and genetics of human malformations, INSERM Unité Mixte de Recherche 1163, Institut Imagine and Université Paris Cité, Paris 75015, France
| |
Collapse
|
2
|
Scala M, Bradley CA, Howe JL, Trost B, Salazar NB, Shum C, Reuter MS, MacDonald JR, Ko SY, Frankland PW, Granger L, Anadiotis G, Pullano V, Brusco A, Keller R, Parisotto S, Pedro HF, Lusk L, McDonnell PP, Helbig I, Mullegama SV, Douine ED, Russell BE, Nelson SF, Zara F, Scherer SW. Genetic variants in DDX53 contribute to Autism Spectrum Disorder associated with the Xp22.11 locus. medRxiv 2023:2023.12.21.23300383. [PMID: 38234782 PMCID: PMC10793518 DOI: 10.1101/2023.12.21.23300383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Autism Spectrum Disorder (ASD) exhibits an ~4:1 male-to-female sex bias and is characterized by early-onset impairment of social/communication skills, restricted interests, and stereotyped behaviors. Disruption of the Xp22.11 locus has been associated with ASD in males. This locus includes the three-exon PTCHD1 gene, an adjacent multi-isoform long noncoding RNA (lncRNA) named PTCHD1-AS (spanning ~1Mb), and a poorly characterized single-exon RNA helicase named DDX53 that is intronic to PTCHD1-AS. While the relationship between PTCHD1/PTCHD1-AS and ASD is being studied, the role of DDX53 has not been examined, in part because there is no apparent functional murine orthologue. Through clinical testing, here, we identified 6 males and 1 female with ASD from 6 unrelated families carrying rare, predicted-damaging or loss-of-function variants in DDX53. Then, we examined databases, including the Autism Speaks MSSNG and Simons Foundation Autism Research Initiative, as well as population controls. We identified 24 additional individuals with ASD harboring rare, damaging DDX53 variations, including the same variants detected in two families from the original clinical analysis. In this extended cohort of 31 participants with ASD (28 male, 3 female), we identified 25 mostly maternally-inherited variations in DDX53, including 18 missense changes, 2 truncating variants, 2 in-frame variants, 2 deletions in the 3' UTR and 1 copy number deletion. Our findings in humans support a direct link between DDX53 and ASD, which will be important in clinical genetic testing. These same autism-related findings, coupled with the observation that a functional orthologous gene is not found in mouse, may also influence the design and interpretation of murine-modelling of ASD.
Collapse
Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Clarrisa A. Bradley
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer L. Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nelson Bautista Salazar
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Carole Shum
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S. Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R. MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sangyoon Y. Ko
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Paul W. Frankland
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Leslie Granger
- Department of Genetics and Metabolism, Randall Children’s Hospital, Portland, OR 97227, USA
| | - George Anadiotis
- Department of Genetics and Metabolism, Randall Children’s Hospital, Portland, OR 97227, USA
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Roberto Keller
- Adult Autism Centre DSM ASL Città di Torino, 10138 Turin, Italy
| | - Sarah Parisotto
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Helio F. Pedro
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Laina Lusk
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pamela Pojomovsky McDonnell
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ingo Helbig
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Bianca E. Russell
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- McLaughlin Centre, Toronto, ON M5G 0A4, Canada
| |
Collapse
|
3
|
Nieves-Rodriguez S, Barthélémy F, Woods JD, Douine ED, Wang RT, Scripture-Adams DD, Chesmore KN, Galasso F, Miceli MC, Nelson SF. Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD. Front Genet 2023; 14:1216066. [PMID: 37576554 PMCID: PMC10415210 DOI: 10.3389/fgene.2023.1216066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.
Collapse
Affiliation(s)
- Shirley Nieves-Rodriguez
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeremy D. Woods
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Emilie D. Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Richard T. Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Deirdre D. Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin N. Chesmore
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Francesca Galasso
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - M. Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
4
|
Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
Collapse
Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
| | | |
Collapse
|
5
|
Ringman JM, Dorrani N, Fernández SG, Signer R, Martinez-Agosto J, Lee H, Douine ED, Qiao Y, Shi Y, D’Orazio L, Pawar S, Robbie L, Kashani AH, Singer M, Byers JT, Magaki S, Guzman S, Sagare A, Zlokovic B, Cederbaum S, Nelson S, Sheikh-Bahaei N, Chui HC, Chávez-Gutiérrez L, Vinters HV. Characterization of spastic paraplegia in a family with a novel PSEN1 mutation. Brain Commun 2023; 5:fcad030. [PMID: 36895955 PMCID: PMC9991506 DOI: 10.1093/braincomms/fcad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 09/09/2022] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Spastic paraparesis has been described to occur in 13.7% of PSEN1 mutations and can be the presenting feature in 7.5%. In this paper, we describe a family with a particularly young onset of spastic paraparesis due to a novel mutation in PSEN1 (F388S). Three affected brothers underwent comprehensive imaging protocols, two underwent ophthalmological evaluations and one underwent neuropathological examination after his death at age 29. Age of onset was consistently at age 23 with spastic paraparesis, dysarthria and bradyphrenia. Pseudobulbar affect followed with progressive gait problems leading to loss of ambulation in the late 20s. Cerebrospinal fluid levels of amyloid-β, tau and phosphorylated tau and florbetaben PET were consistent with Alzheimer's disease. Flortaucipir PET showed an uptake pattern atypical for Alzheimer's disease, with disproportionate signal in posterior brain areas. Diffusion tensor imaging showed decreased mean diffusivity in widespread areas of white matter but particularly in areas underlying the peri-Rolandic cortex and in the corticospinal tracts. These changes were more severe than those found in carriers of another PSEN1 mutation, which can cause spastic paraparesis at a later age (A431E), which were in turn more severe than among persons carrying autosomal dominant Alzheimer's disease mutations not causing spastic paraparesis. Neuropathological examination confirmed the presence of cotton wool plaques previously described in association with spastic parapresis and pallor and microgliosis in the corticospinal tract with severe amyloid-β pathology in motor cortex but without unequivocal disproportionate neuronal loss or tau pathology. In vitro modelling of the effects of the mutation demonstrated increased production of longer length amyloid-β peptides relative to shorter that predicted the young age of onset. In this paper, we provide imaging and neuropathological characterization of an extreme form of spastic paraparesis occurring in association with autosomal dominant Alzheimer's disease, demonstrating robust diffusion and pathological abnormalities in white matter. That the amyloid-β profiles produced predicted the young age of onset suggests an amyloid-driven aetiology though the link between this and the white matter pathology remains undefined.
Collapse
Affiliation(s)
- John M Ringman
- Department of Neurology, Keck School of Medicine at University of Southern California, Los Angeles, CA 90033, USA
| | | | - Sara Gutiérrez Fernández
- Department of Neurosciences, VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Rebecca Signer
- Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA
| | | | - Hane Lee
- Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Emilie D Douine
- Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Yuchuan Qiao
- Department of Neurology, USC Stevens Neuroimaging and Informatics Institute, Los Angeles, CA 90033, USA
| | - Yonggang Shi
- Department of Neurology, USC Stevens Neuroimaging and Informatics Institute, Los Angeles, CA 90033, USA
| | - Lina D’Orazio
- Department of Neurology, Keck School of Medicine at University of Southern California, Los Angeles, CA 90033, USA
| | - Sanjay Pawar
- Department of Neurology, Keck School of Medicine at University of Southern California, Los Angeles, CA 90033, USA
| | - Leah Robbie
- Department of Neurology, Keck School of Medicine at University of Southern California, Los Angeles, CA 90033, USA
| | - Amir H Kashani
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Maxwell Singer
- Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Joshua T Byers
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Shino Magaki
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Sam Guzman
- Department of Pathology, Keck School of Medicine at USC, Los Angeles, CA 90033, USA
| | - Abhay Sagare
- Zilkha Neurogenetics Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Berislav Zlokovic
- Zilkha Neurogenetics Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen Cederbaum
- Department of Pediatrics, UCLA, Los Angeles, CA 90095, USA
- Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Stanley Nelson
- Department of Pediatrics, UCLA, Los Angeles, CA 90095, USA
- Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nasim Sheikh-Bahaei
- Department of Radiology, University of Southern California, Los Angeles, CA 90033, USA
| | - Helena C Chui
- Department of Neurology, Keck School of Medicine at University of Southern California, Los Angeles, CA 90033, USA
| | - Lucía Chávez-Gutiérrez
- Department of Neurosciences, VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven 3000, Belgium
| | - Harry V Vinters
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
6
|
Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
Collapse
Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Miller IM, Yashar BM, Macnamara EF, Adams DR, Agrawal PB, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fernandez L, Ferreira C, Fieg EL, Findley LC, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Godfrey RA, Golden-Grant K, Goldrich MP, Goldstein DB, Grajewski A, Groden CA, Gutierrez I, Hahn S, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang Y, Huang A, Huryn L, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Krier JB, Lalani SR, Lam B, Lam C, LaMoure GL, Lanpher BC, Lanza IR, Latham L, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacDowall J, Macnamara EF, MacRae CA, Maduro VV, Mahoney R, Mak BC, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martfnez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti PM, Moretti P, Mosbrook-Davis D, Mulvihill JJ, Nakano-Okuno M, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Power B, Pusey BN, Quinlan A, Raja AN, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Signer RH, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Thurm A, Tifft CJ, Toro C, Tran AA, Tucker BM, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Walsh CA, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Perry KW, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Woods JD, Worley K, Yamamoto S, Yang J, Yousef M, Zastrow DB, Zein W, Zhang Z, Zhao C, Zuchner S, Macnamara EF. Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis 2023; 18:6. [PMID: 36624503 PMCID: PMC9830697 DOI: 10.1186/s13023-022-02598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.
Collapse
Affiliation(s)
- Ilana M. Miller
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, Rare Disease Institute, 7125 13th Place NW, DC 20012 Washington, USA ,grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | - Beverly M. Yashar
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | | | - Ellen F. Macnamara
- grid.453125.40000 0004 0533 8641National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Scripture-Adams DD, Chesmore KN, Barthélémy F, Wang RT, Nieves-Rodriguez S, Wang DW, Mokhonova EI, Douine ED, Wan J, Little I, Rabichow LN, Nelson SF, Miceli MC. Single nuclei transcriptomics of muscle reveals intra-muscular cell dynamics linked to dystrophin loss and rescue. Commun Biol 2022; 5:989. [PMID: 36123393 PMCID: PMC9485160 DOI: 10.1038/s42003-022-03938-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 05/20/2022] [Accepted: 09/01/2022] [Indexed: 02/05/2023] Open
Abstract
In Duchenne muscular dystrophy, dystrophin loss leads to chronic muscle damage, dysregulation of repair, fibro-fatty replacement, and weakness. We develop methodology to efficiently isolate individual nuclei from minute quantities of frozen skeletal muscle, allowing single nuclei sequencing of irreplaceable archival samples and from very small samples. We apply this method to identify cell and gene expression dynamics within human DMD and mdx mouse muscle, characterizing effects of dystrophin rescue by exon skipping therapy at single nuclei resolution. DMD exon 23 skipping events are directly observed and increased in myonuclei from treated mice. We describe partial rescue of type IIa and IIx myofibers, expansion of an MDSC-like myeloid population, recovery of repair/remodeling M2-macrophage, and repression of inflammatory POSTN1 + fibroblasts in response to exon skipping and partial dystrophin restoration. Use of this method enables exploration of cellular and transcriptomic mechanisms of dystrophin loss and repair within an intact muscle environment. Our initial findings will scaffold our future work to more directly examine muscular dystrophies and putative recovery pathways.
Collapse
Affiliation(s)
- Deirdre D Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kevin N Chesmore
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard T Wang
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shirley Nieves-Rodriguez
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Derek W Wang
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Amgen, Thousand Oaks, CA, USA
| | - Ekaterina I Mokhonova
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jijun Wan
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Isaiah Little
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura N Rabichow
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
9
|
Marcogliese PC, Dutta D, Ray SS, Dang NDP, Zuo Z, Wang Y, Lu D, Fazal F, Ravenscroft TA, Chung H, Kanca O, Wan J, Douine ED, Network UD, Pena LDM, Yamamoto S, Nelson SF, Might M, Meyer KC, Yeo NC, Bellen HJ. Loss of IRF2BPL impairs neuronal maintenance through excess Wnt signaling. Sci Adv 2022; 8:eabl5613. [PMID: 35044823 PMCID: PMC8769555 DOI: 10.1126/sciadv.abl5613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 05/12/2023]
Abstract
De novo truncations in Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) lead to severe childhood-onset neurodegenerative disorders. To determine how loss of IRF2BPL causes neural dysfunction, we examined its function in Drosophila and zebrafish. Overexpression of either IRF2BPL or Pits, the Drosophila ortholog, represses Wnt transcription in flies. In contrast, neuronal depletion of Pits leads to increased wingless (wg) levels in the brain and is associated with axonal loss, whereas inhibition of Wg signaling is neuroprotective. Moreover, increased neuronal expression of wg in flies is sufficient to cause age-dependent axonal loss, similar to reduction of Pits. Loss of irf2bpl in zebrafish also causes neurological defects with an associated increase in wnt1 transcription and downstream signaling. WNT1 is also increased in patient-derived astrocytes, and pharmacological inhibition of Wnt suppresses the neurological phenotypes. Last, IRF2BPL and the Wnt antagonist, CKIα, physically and genetically interact, showing that IRF2BPL and CkIα antagonize Wnt transcription and signaling.
Collapse
Affiliation(s)
- Paul C. Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shrestha Sinha Ray
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Nghi D. P. Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Yuchun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Di Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Fatima Fazal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Thomas A. Ravenscroft
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - JiJun Wan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Undiagnosed Diseases Network
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Loren D. M. Pena
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Matthew Might
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Kathrin C. Meyer
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
10
|
Barthelemy F, Woods JD, Nieves‐Rodriguez S, Douine ED, Wang R, Wanagat J, Miceli MC, Nelson SF. A well-tolerated core needle muscle biopsy process suitable for children and adults. Muscle Nerve 2020; 62:688-698. [PMID: 32820569 PMCID: PMC7756388 DOI: 10.1002/mus.27041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Serial muscle biopsies within clinical trials for Duchenne muscular dystrophy (DMD) are critical to document therapeutic responses. Less invasive means of sampling muscle are needed. We analyzed a retrospective consecutive case-series cohort of vacuum-assisted core needle muscle biopsy procedures performed on healthy and dystrophic individuals at a single institution assessing for safety and reliability of obtaining sufficient high-quality biopsy tissue for histologic assessment in adult and pediatric subjects. Of 471 muscle cores from 128 biopsy procedures, 377-550 mg of total muscle tissue was obtained per procedure with mean core weight of 129 mg (SD, 25.1 mg). All biopsies were adequate for histological assessment. There were no significant adverse events. This core needle biopsy approach, when combined with improved sample processing, provides a safe means to consistently obtain muscle samples for diagnostic and clinical trial applications.
Collapse
Affiliation(s)
- Florian Barthelemy
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and SciencesUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Jeremy D. Woods
- Department of PediatricsUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Shirley Nieves‐Rodriguez
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Richard Wang
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Jonathan Wanagat
- Department of MedicineDavid Geffen School of Medicine at UCLALos AngelesCaliforniaUSA
| | - M. Carrie Miceli
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and SciencesUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| |
Collapse
|
11
|
Tsai M, Thauland TJ, Huang AY, Bun C, Fitzwater S, Krogstad P, Douine ED, Nelson SF, Lee H, Garcia-Lloret MI, Butte MJ. Disseminated Coccidioidomycosis Treated with Interferon-γ and Dupilumab. N Engl J Med 2020; 382:2337-2343. [PMID: 32521134 PMCID: PMC7333509 DOI: 10.1056/nejmoa2000024] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe a case of life-threatening disseminated coccidioidomycosis in a previously healthy child. Like most patients with disseminated coccidioidomycosis, this child had no genomic evidence of any known, rare immune disease. However, comprehensive immunologic testing showed exaggerated production of interleukin-4 and reduced production of interferon-γ. Supplementation of antifungal agents with interferon-γ treatment slowed disease progression, and the addition of interleukin-4 and interleukin-13 blockade with dupilumab resulted in rapid resolution of the patient's clinical symptoms. This report shows that blocking of type 2 immune responses can treat infection. This immunomodulatory approach could be used to enhance immune clearance of refractory fungal, mycobacterial, and viral infections. (Supported by the Jeffrey Modell Foundation and the National Institutes of Health.).
Collapse
Affiliation(s)
- Monica Tsai
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Timothy J Thauland
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Alden Y Huang
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Chantana Bun
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Sean Fitzwater
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Paul Krogstad
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Emilie D Douine
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Stanley F Nelson
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Hane Lee
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Maria I Garcia-Lloret
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Manish J Butte
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| |
Collapse
|
12
|
Shieh C, Jones N, Vanle B, Au M, Huang AY, Silva APG, Lee H, Douine ED, Otero MG, Choi A, Grand K, Taff IP, Delgado MR, Hajianpour MJ, Seeley A, Rohena L, Vernon H, Gripp KW, Vergano SA, Mahida S, Naidu S, Sousa AB, Wain KE, Challman TD, Beek G, Basel D, Ranells J, Smith R, Yusupov R, Freckmann ML, Ohden L, Davis-Keppen L, Chitayat D, Dowling JJ, Finkel R, Dauber A, Spillmann R, Pena LDM, Metcalfe K, Splitt M, Lachlan K, McKee SA, Hurst J, Fitzpatrick DR, Morton JEV, Cox H, Venkateswaran S, Young JI, Marsh ED, Nelson SF, Martinez JA, Graham JM, Kini U, Mackay JP, Pierson TM. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. Genet Med 2020; 22:878-888. [PMID: 31949314 PMCID: PMC7920571 DOI: 10.1038/s41436-019-0747-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Determination of genotypic/phenotypic features of GATAD2B-associated neurodevelopmental disorder (GAND). METHODS Fifty GAND subjects were evaluated to determine consistent genotypic/phenotypic features. Immunoprecipitation assays utilizing in vitro transcription-translation products were used to evaluate GATAD2B missense variants' ability to interact with binding partners within the nucleosome remodeling and deacetylase (NuRD) complex. RESULTS Subjects had clinical findings that included macrocephaly, hypotonia, intellectual disability, neonatal feeding issues, polyhydramnios, apraxia of speech, epilepsy, and bicuspid aortic valves. Forty-one novelGATAD2B variants were identified with multiple variant types (nonsense, truncating frameshift, splice-site variants, deletions, and missense). Seven subjects were identified with missense variants that localized within two conserved region domains (CR1 or CR2) of the GATAD2B protein. Immunoprecipitation assays revealed several of these missense variants disrupted GATAD2B interactions with its NuRD complex binding partners. CONCLUSIONS A consistent GAND phenotype was caused by a range of genetic variants in GATAD2B that include loss-of-function and missense subtypes. Missense variants were present in conserved region domains that disrupted assembly of NuRD complex proteins. GAND's clinical phenotype had substantial clinical overlap with other disorders associated with the NuRD complex that involve CHD3 and CHD4, with clinical features of hypotonia, intellectual disability, cardiac defects, childhood apraxia of speech, and macrocephaly.
Collapse
Affiliation(s)
- Christine Shieh
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Brigitte Vanle
- Department of Psychiatry & Behavioral Neurosciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Medical College of Wisconsin-Central Wisconsin, Wausau, WI, USA
| | - Margaret Au
- Department of Pediatrics Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Hane Lee
- Department of Human Genetics and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Maria G Otero
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Choi
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ingrid P Taff
- Department of Neurology, Hofstra School of Medicine, Great Neck, NY, USA
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center and Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics, East Tennessee State University, Quillen College of Medicine, Mountain Home, TN, USA
| | | | - Luis Rohena
- Division of Genetics, Department of Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX, USA
- Department of Pediatrics, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Hilary Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Balitmore, MD, USA
| | - Karen W Gripp
- Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE, USA
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Sonal Mahida
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Sakkubai Naidu
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Ana Berta Sousa
- Serviço de Genética Médica, Hospital Santa Maria, CHULN, Lisboa, Portugal and Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Geoffrey Beek
- Children's Hospitals and Clinics of Minnesota Department of Genetics, Minneapolis, MN, USA
| | - Donald Basel
- Department of Pediatrics, Division of Genetics; Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Judith Ranells
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, USA
| | - Roman Yusupov
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FlL, USA
| | | | - Lisa Ohden
- Department of Genetic Counseling, Sanford Children's Specialty Clinic, Sioux Falls, SD, USA
| | - Laura Davis-Keppen
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, USA
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - James J Dowling
- Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Richard Finkel
- Division of Pediatric Neurology, Department of Pediatrics, Nemours Children's Hospital, Orlando, FL, USA
| | - Andrew Dauber
- Division of Endocrinology, Children's National Health System, Washington, DC, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Manchester University NHS FT, Manchester, UK
| | - Miranda Splitt
- Institute of Genetic Medicine, Northern Genetics Service, Newcastle upon Tyne Hospitals Trust, Newcastle, UK
| | - Katherine Lachlan
- Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health Division, Wessex Clinical Genetics Service, University Hospitals of Southampton NHS Trust, Southampton, UK
| | - Shane A McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jane Hurst
- Department of Clinical Genetics, NE Thames Genetics Service, Great Ormond Street Hospital, London, UK
| | - David R Fitzpatrick
- Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Juan I Young
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eric D Marsh
- Division of Neurology, Children's Hospital of Philadelphia and Department of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| |
Collapse
|
13
|
Mao D, Reuter CM, Ruzhnikov MR, Beck AE, Farrow EG, Emrick LT, Rosenfeld JA, Mackenzie KM, Robak L, Wheeler MT, Burrage LC, Jain M, Liu P, Calame D, Küry S, Sillesen M, Schmitz-Abe K, Tonduti D, Spaccini L, Iascone M, Genetti CA, Koenig MK, Graf M, Tran A, Alejandro M, Lee BH, Thiffault I, Agrawal PB, Bernstein JA, Bellen HJ, Chao HT, Acosta MT, Adam M, Adams DR, Agrawal PB, Alejandro ME, Allard P, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beck A, Beggs AH, Bejerano G, Bellen HJ, Bennet J, Berg-Rood B, Bernier R, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Briere LC, Brokamp E, Burke EA, Burrage LC, Butte MJ, Byers P, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Cunningham M, D’Souza P, Dai H, Dasari S, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple K, Doherty D, Dorrani N, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Glass I, Godfrey RA, Golden-Grant K, Goldman AM, Goldstein DB, Grajewski A, Groden CA, Gropman AL, Hahn S, Hamid R, Hanchard NA, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Huang Y, Isasi R, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jiang YH, Johnston JM, Karaviti L, Kelley EG, Kiley D, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, Lau CC, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Mefford H, Merritt JL, Might M, Mirzaa G, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raskind W, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Scott CR, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Wallace S, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Wener M, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet 2020; 106:570-583. [PMID: 32197074 PMCID: PMC7118694 DOI: 10.1016/j.ajhg.2020.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023] Open
Abstract
EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
Collapse
|
14
|
Shieh C, Jones N, Vanle B, Au M, Huang AY, Silva APG, Lee H, Douine ED, Otero MG, Choi A, Grand K, Taff IP, Delgado MR, Hajianpour MJ, Seeley A, Rohena L, Vernon H, Gripp KW, Vergano SA, Mahida S, Naidu S, Sousa AB, Wain KE, Challman TD, Beek G, Basel D, Ranells J, Smith R, Yusupov R, Freckmann ML, Ohden L, Davis-Keppen L, Chitayat D, Dowling JJ, Finkel R, Dauber A, Spillmann R, Pena LDM, Metcalfe K, Splitt M, Lachlan K, McKee SA, Hurst J, Fitzpatrick DR, Morton JEV, Cox H, Venkateswaran S, Young JI, Marsh ED, Nelson SF, Martinez JA, Graham JM, Kini U, Mackay JP, Pierson TM. Correction: GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. Genet Med 2020; 22:822. [PMID: 32047287 PMCID: PMC11000750 DOI: 10.1038/s41436-020-0760-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- Christine Shieh
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Brigitte Vanle
- Department of Psychiatry & Behavioral Neurosciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Medical College of Wisconsin-Central Wisconsin, Wausau, WI, USA
| | - Margaret Au
- Department of Pediatrics Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Hane Lee
- Department of Human Genetics and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Maria G Otero
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Choi
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ingrid P Taff
- Department of Neurology, Hofstra School of Medicine, Great Neck, NY, USA
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center and Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics, East Tennessee State University, Quillen College of Medicine, Mountain Home, TN, USA
| | | | - Luis Rohena
- Division of Genetics, Department of Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX, USA
- Department of Pediatrics, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Hilary Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Balitmore, MD, USA
| | - Karen W Gripp
- Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE, USA
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Sonal Mahida
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Sakkubai Naidu
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Ana Berta Sousa
- Serviço de Genética Médica, Hospital Santa Maria, CHULN, Lisboa, Portugal and Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Geoffrey Beek
- Children's Hospitals and Clinics of Minnesota Department of Genetics, Minneapolis, MN, USA
| | - Donald Basel
- Department of Pediatrics, Division of Genetics, Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Judith Ranells
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, USA
| | - Roman Yusupov
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FlL, USA
| | | | - Lisa Ohden
- Department of Genetic Counseling, Sanford Children's Specialty Clinic, Sioux Falls, SD, USA
| | - Laura Davis-Keppen
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, USA
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - James J Dowling
- Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Richard Finkel
- Division of Pediatric Neurology, Department of Pediatrics, Nemours Children's Hospital, Orlando, FL, USA
| | - Andrew Dauber
- Division of Endocrinology, Children's National Health System, Washington, DC, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Manchester University NHS FT, Manchester, UK
| | - Miranda Splitt
- Institute of Genetic Medicine, Northern Genetics Service, Newcastle upon Tyne Hospitals Trust, Newcastle, UK
| | - Katherine Lachlan
- Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health Division, Wessex Clinical Genetics Service, University Hospitals of Southampton NHS Trust, Southampton, UK
| | - Shane A McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jane Hurst
- Department of Clinical Genetics, NE Thames Genetics Service, Great Ormond Street Hospital, London, UK
| | - David R Fitzpatrick
- Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Juan I Young
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eric D Marsh
- Division of Neurology, Children's Hospital of Philadelphia and Department of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| |
Collapse
|
15
|
Gibbs EM, Barthélémy F, Douine ED, Hardiman NC, Shieh PB, Khanlou N, Crosbie RH, Nelson SF, Miceli MC. Large in-frame 5' deletions in DMD associated with mild Duchenne muscular dystrophy: Two case reports and a review of the literature. Neuromuscul Disord 2019; 29:863-873. [PMID: 31672265 PMCID: PMC7092699 DOI: 10.1016/j.nmd.2019.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/24/2019] [Revised: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
Duchenne muscular dystrophy is caused by mutations in the dystrophin-encoding DMD gene. While Duchenne is most commonly caused by large intragenic deletions that cause frameshift and complete loss of dystrophin expression, in-frame deletions in DMD can result in the expression of internally truncated dystrophin proteins and may be associated with a milder phenotype. In this study, we describe two individuals with large in-frame 5' deletions (exon 3-23 and exon 3-28) that remove the majority of the N-terminal region, including part of the actin binding and central rod domains. Both patients had progressive muscle weakness during childhood but are observed to have a relatively mild disease course compared to typical Duchenne. We show that in muscle biopsies from both patients, truncated dystrophin is expressed at the sarcolemma. We have additionally developed a patient-specific fibroblast-derived cell model, which can be inducibly reprogrammed to form myotubes that largely recapitulate biopsy findings for the patient with the exon 3-23 deletion, providing a culture model for future investigation of this unusual case. We discuss these mutations in the context of previously reported 5' in-frame DMD deletions and relevant animal models, and review the spectrum of phenotypes associated with these deletions.
Collapse
Affiliation(s)
- Elizabeth M Gibbs
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Natalie C Hardiman
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Perry B Shieh
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
| | - Negar Khanlou
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Rachelle H Crosbie
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
16
|
Barthélémy F, Wang RT, Hsu C, Douine ED, Marcantonio EE, Nelson SF, Miceli MC. Targeting RyR Activity Boosts Antisense Exon 44 and 45 Skipping in Human DMD Skeletal or Cardiac Muscle Culture Models. Mol Ther Nucleic Acids 2019; 18:580-589. [PMID: 31678734 PMCID: PMC6838898 DOI: 10.1016/j.omtn.2019.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/15/2019] [Accepted: 09/12/2019] [Indexed: 12/23/2022]
Abstract
Systemic delivery of antisense oligonucleotides (AO) for DMD exon skipping has proven effective for reframing DMD mRNA, rescuing dystrophin expression, and slowing disease progression in animal models. In humans with Duchenne muscular dystrophy treated with AOs, low levels of dystrophin have been induced, and modest slowing of disease progression has been observed, highlighting the need for improved efficiency of human skipping drugs. Here, we demonstrate that dantrolene and Rycals S107 and ARM210 potentiate AO-mediated exon skipping of exon 44 or exon 45 in patient-derived myotube cultures with appropriate mutations. Further, dantrolene is shown to boost AO-mediated exon skipping in patient-derived, induced cardiomyocyte cultures. Our findings further validate the ryanodine receptors (RyR) as the likely target responsible for exon skip boosting and demonstrate potential applicability beyond exon 51 skipping. These data provide preclinical support of dantrolene trial as an adjuvant to AO-mediated exon-skipping therapy in humans and identify a novel Rycal, ARM210, for development as a potential exon-skipping booster. Further, they highlight the value of mutation-specific DMD culture models for basic discovery, preclinical drug screening and translation of personalized genetic medicines.
Collapse
Affiliation(s)
- Florian Barthélémy
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard T Wang
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Hsu
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Carrie Miceli
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
17
|
Kennedy J, Goudie D, Blair E, Chandler K, Joss S, McKay V, Green A, Armstrong R, Lees M, Kamien B, Hopper B, Tan TY, Yap P, Stark Z, Okamoto N, Miyake N, Matsumoto N, Macnamara E, Murphy JL, McCormick E, Hakonarson H, Falk MJ, Li D, Blackburn P, Klee E, Babovic-Vuksanovic D, Schelley S, Hudgins L, Kant S, Isidor B, Cogne B, Bradbury K, Williams M, Patel C, Heussler H, Duff-Farrier C, Lakeman P, Scurr I, Kini U, Elting M, Reijnders M, Schuurs-Hoeijmakers J, Wafik M, Blomhoff A, Ruivenkamp CAL, Nibbeling E, Dingemans AJM, Douine ED, Nelson SF, Hempel M, Bierhals T, Lessel D, Johannsen J, Arboleda VA, Newbury-Ecob R. KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants. Genet Med 2019; 21:850-860. [PMID: 30245513 PMCID: PMC6634310 DOI: 10.1038/s41436-018-0259-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 03/09/2018] [Accepted: 07/26/2018] [Indexed: 01/27/2023] Open
Abstract
PURPOSE Pathogenic variants in KAT6A have recently been identified as a cause of syndromic developmental delay. Within 2 years, the number of patients identified with pathogenic KAT6A variants has rapidly expanded and the full extent and variability of the clinical phenotype has not been reported. METHODS We obtained data for patients with KAT6A pathogenic variants through three sources: treating clinicians, an online family survey distributed through social media, and a literature review. RESULTS We identified 52 unreported cases, bringing the total number of published cases to 76. Our results expand the genotypic spectrum of pathogenic variants to include missense and splicing mutations. We functionally validated a pathogenic splice-site variant and identified a likely hotspot location for de novo missense variants. The majority of clinical features in KAT6A syndrome have highly variable penetrance. For core features such as intellectual disability, speech delay, microcephaly, cardiac anomalies, and gastrointestinal complications, genotype- phenotype correlations show that late-truncating pathogenic variants (exons 16-17) are significantly more prevalent. We highlight novel associations, including an increased risk of gastrointestinal obstruction. CONCLUSION Our data expand the genotypic and phenotypic spectrum for individuals with genetic pathogenic variants in KAT6A and we outline appropriate clinical management.
Collapse
Affiliation(s)
- Joanna Kennedy
- Clinical Genetics, University Hospitals Bristol, Southwell St, Bristol, UK
- University of Bristol, Bristol, UK
| | - David Goudie
- Clinical Genetics, Ninewells Hospital & Medical School, Dundee, UK
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Clinical Genetics, Churchill Hospital, Headington, Oxford, UK
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester Foundation NHS Trust, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Shelagh Joss
- West of Scotland Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | - Victoria McKay
- Cheshire & Merseyside Regional Genetics Service, Liverpool Women's NHS Foundation Trust, Crown Street, Liverpool, UK
| | - Andrew Green
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Melissa Lees
- Clinical Genetics, Great Ormond Street Hospital NHS Trust, London, UK
| | | | | | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Patrick Yap
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Genetic Health Service New Zealand, Auckland, New Zealand
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center, Osaka, Japan
- Research Institute for Maternal and Child Health, Osaka Medical Center, Osaka, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ellen Macnamara
- National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | | | - Elizabeth McCormick
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marni J Falk
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Eric Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Susan Schelley
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Sarina Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Kimberley Bradbury
- Clinical Genetics Guys and St Thomas' NHS Foundation Trust, Guys Hospital, London, UK
| | - Mark Williams
- Molecular Diagnostics, Mater Group, South Brisbane, Queensland, Australia
| | - Chirag Patel
- Genetic Health Queensland, Herston, Brisbane, Queensland, Australia
| | - Helen Heussler
- Child Development Service, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | | | - Phillis Lakeman
- Academic Medical Center, Department of Clinical Genetics, Amsterdam, The Netherlands
| | - Ingrid Scurr
- Clinical Genetics, University Hospitals Bristol, Southwell St, Bristol, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Clinical Genetics, Churchill Hospital, Headington, Oxford, UK
| | - Mariet Elting
- Klinisch Geneticus, VU Medisch centrum, Amsterdam, The Netherlands
| | - Margot Reijnders
- Radboud University Medical Center, Department of Human Genetics, Nijmegen, The Netherlands
| | | | - Mohamed Wafik
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Clinical Genetics, Churchill Hospital, Headington, Oxford, UK
| | - Anne Blomhoff
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Esther Nibbeling
- Department of Genetics, University of Groningen, Groningen, The Netherlands
| | | | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Ruth Newbury-Ecob
- Clinical Genetics, University Hospitals Bristol, Southwell St, Bristol, UK.
- University of Bristol, Bristol, UK.
| |
Collapse
|
18
|
Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
Collapse
|
19
|
Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LD, Callens S, Coucke P, Dermaut B, Hemelsoet D, Poppe B, Steyaert W, Terryn W, Van Coster R, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:456. [PMID: 30193138 PMCID: PMC6128320 DOI: 10.1016/j.ajhg.2018.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
20
|
Wang RT, Barthelemy F, Martin AS, Douine ED, Eskin A, Lucas A, Lavigne J, Peay H, Khanlou N, Sweeney L, Cantor RM, Miceli MC, Nelson SF. Cover Image, Volume 39, Issue 9. Hum Mutat 2018. [DOI: 10.1002/humu.23600] [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: 11/06/2022]
|
21
|
Wang RT, Barthelemy F, Martin AS, Douine ED, Eskin A, Lucas A, Lavigne J, Peay H, Khanlou N, Sweeney L, Cantor RM, Miceli MC, Nelson SF. DMD genotype correlations from the Duchenne Registry: Endogenous exon skipping is a factor in prolonged ambulation for individuals with a defined mutation subtype. Hum Mutat 2018; 39:1193-1202. [PMID: 29907980 PMCID: PMC6175390 DOI: 10.1002/humu.23561] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/10/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023]
Abstract
Antisense oligonucleotide (AON)‐mediated exon skipping is an emerging therapeutic for individuals with Duchenne muscular dystrophy (DMD). Skipping of exons adjacent to common exon deletions in DMD using AONs can produce in‐frame transcripts and functional protein. Targeted skipping of DMD exons 8, 44, 45, 50, 51, 52, 53, and 55 is predicted to benefit 47% of affected individuals. We observed a correlation between mutation subgroups and age at loss of ambulation in the Duchenne Registry, a large database of phenotypic and genetic data for DMD (N = 765). Males amenable to exon 44 (N = 74) and exon 8 skipping (N = 18) showed prolonged ambulation compared to other exon skip groups and nonsense mutations (P = 0.035 and P < 0.01, respectively). In particular, exon 45 deletions were associated with prolonged age at loss of ambulation relative to the rest of the exon 44 skip amenable cohort and other DMD mutations. Exon 3–7 deletions also showed prolonged ambulation relative to all other exon 8 skippable mutations. Cultured myotubes from DMD patients with deletions of exons 3–7 or exon 45 showed higher endogenous skipping than other mutations, providing a potential biological rationale for our observations. These results highlight the utility of aggregating phenotypic and genotypic data for rare pediatric diseases to reveal progression differences, identify potentially confounding factors, and probe molecular mechanisms that may affect disease severity.
Collapse
Affiliation(s)
- Richard T Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California ,Los Angeles, California.,Center for Duchenne Muscular Dystrophy, University of California, Los Angeles,Los Angeles, California
| | - Florian Barthelemy
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles,Los Angeles, California.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, California
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Hackensack, New Jersey
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, University of California ,Los Angeles, California.,Center for Duchenne Muscular Dystrophy, University of California, Los Angeles,Los Angeles, California
| | - Ascia Eskin
- Department of Human Genetics, David Geffen School of Medicine, University of California ,Los Angeles, California.,Center for Duchenne Muscular Dystrophy, University of California, Los Angeles,Los Angeles, California
| | - Ann Lucas
- Parent Project Muscular Dystrophy, Hackensack, New Jersey
| | | | - Holly Peay
- Parent Project Muscular Dystrophy, Hackensack, New Jersey.,RTI International, Research Triangle Park, North Carolina
| | - Negar Khanlou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Lee Sweeney
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida
| | - Rita M Cantor
- Department of Human Genetics, David Geffen School of Medicine, University of California ,Los Angeles, California
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles,Los Angeles, California.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, California.,Molecular Biology Institute, University of California, Los Angeles, California, Los Angeles
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California ,Los Angeles, California.,Center for Duchenne Muscular Dystrophy, University of California, Los Angeles,Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| |
Collapse
|
22
|
Barseghyan H, Tang W, Wang RT, Almalvez M, Segura E, Bramble MS, Lipson A, Douine ED, Lee H, Délot EC, Nelson SF, Vilain E. Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis. Genome Med 2017; 9:90. [PMID: 29070057 PMCID: PMC5655859 DOI: 10.1186/s13073-017-0479-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [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: 03/21/2017] [Accepted: 10/10/2017] [Indexed: 11/13/2022] Open
Abstract
Background Massively parallel DNA sequencing, such as exome sequencing, has become a routine clinical procedure to identify pathogenic variants responsible for a patient’s phenotype. Exome sequencing has the capability of reliably identifying inherited and de novo single-nucleotide variants, small insertions, and deletions. However, due to the use of 100–300-bp fragment reads, this platform is not well powered to sensitively identify moderate to large structural variants (SV), such as insertions, deletions, inversions, and translocations. Methods To overcome these limitations, we used next-generation mapping (NGM) to image high molecular weight double-stranded DNA molecules (megabase size) with fluorescent tags in nanochannel arrays for de novo genome assembly. We investigated the capacity of this NGM platform to identify pathogenic SV in a series of patients diagnosed with Duchenne muscular dystrophy (DMD), due to large deletions, insertion, and inversion involving the DMD gene. Results We identified deletion, duplication, and inversion breakpoints within DMD. The sizes of deletions were in the range of 45–250 Kbp, whereas the one identified insertion was approximately 13 Kbp in size. This method refined the location of the break points within introns for cases with deletions compared to current polymerase chain reaction (PCR)-based clinical techniques. Heterozygous SV were detected in the known carrier mothers of the DMD patients, demonstrating the ability of the method to ascertain carrier status for large SV. The method was also able to identify a 5.1-Mbp inversion involving the DMD gene, previously identified by RNA sequencing. Conclusions We showed the ability of NGM technology to detect pathogenic structural variants otherwise missed by PCR-based techniques or chromosomal microarrays. NGM is poised to become a new tool in the clinical genetic diagnostic strategy and research due to its ability to sensitively identify large genomic variations. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0479-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hayk Barseghyan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC, 20010, USA
| | - Wilson Tang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Richard T Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Miguel Almalvez
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC, 20010, USA
| | - Eva Segura
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matthew S Bramble
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC, 20010, USA
| | - Allen Lipson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Emmanuèle C Délot
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC, 20010, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Eric Vilain
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. .,Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. .,Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC, 20010, USA.
| |
Collapse
|