1
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Neri P, Barwick BG, Jung D, Patton JC, Maity R, Tagoug I, Stein CK, Tilmont R, Leblay N, Ahn S, Lee H, Welsh SJ, Riggs DL, Stong N, Flynt E, Thakurta A, Keats JJ, Lonial S, Bergsagel PL, Boise LH, Bahlis NJ. ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma. Blood Cancer Discov 2024; 5:56-73. [PMID: 37934799 PMCID: PMC10772538 DOI: 10.1158/2643-3230.bcd-23-0061] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
Immunomodulatory drugs (IMiD) are a backbone therapy for multiple myeloma (MM). Despite their efficacy, most patients develop resistance, and the mechanisms are not fully defined. Here, we show that IMiD responses are directed by IMiD-dependent degradation of IKZF1 and IKZF3 that bind to enhancers necessary to sustain the expression of MYC and other myeloma oncogenes. IMiD treatment universally depleted chromatin-bound IKZF1, but eviction of P300 and BRD4 coactivators only occurred in IMiD-sensitive cells. IKZF1-bound enhancers overlapped other transcription factor binding motifs, including ETV4. Chromatin immunoprecipitation sequencing showed that ETV4 bound to the same enhancers as IKZF1, and ETV4 CRISPR/Cas9-mediated ablation resulted in sensitization of IMiD-resistant MM. ETV4 expression is associated with IMiD resistance in cell lines, poor prognosis in patients, and is upregulated at relapse. These data indicate that ETV4 alleviates IKZF1 and IKZF3 dependency in MM by maintaining oncogenic enhancer activity and identify transcriptional plasticity as a previously unrecognized mechanism of IMiD resistance. SIGNIFICANCE We show that IKZF1-bound enhancers are critical for IMiD efficacy and that the factor ETV4 can bind the same enhancers and substitute for IKZF1 and mediate IMiD resistance by maintaining MYC and other oncogenes. These data implicate transcription factor redundancy as a previously unrecognized mode of IMiD resistance in MM. See related article by Welsh, Barwick, et al., p. 34. See related commentary by Yun and Cleveland, p. 5. This article is featured in Selected Articles from This Issue, p. 4.
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Affiliation(s)
- Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - David Jung
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Jonathan C. Patton
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Ranjan Maity
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Ines Tagoug
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Caleb K. Stein
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Remi Tilmont
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Noemie Leblay
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Sungwoo Ahn
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Holly Lee
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Seth J. Welsh
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Daniel L. Riggs
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Nicholas Stong
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Erin Flynt
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey
| | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - P. Leif Bergsagel
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona
| | - Lawrence H. Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Nizar J. Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
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2
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Sullivan JA, Spillmann RC, Schoch K, Walley N, Alkelai A, Stong N, Shea PR, Petrovski S, Jobanputra V, McConkie-Rosell A, Shashi V. The best of both worlds: Blending cutting-edge research with clinical processes for a productive exome clinic. Clin Genet 2024; 105:62-71. [PMID: 37853563 DOI: 10.1111/cge.14437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting.
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Affiliation(s)
- Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Genomics and Bioinformatics Analysis Resource, Columbia University, New York, New York, USA
| | - Slavè Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
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3
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Wenzl K, Stokes M, Novak JP, Bock AM, Khan S, Hopper MA, Krull JE, Dropik AR, Walker JS, Sarangi V, Mwangi R, Ortiz M, Stong N, Huang CC, Maurer MJ, Rimsza L, Link BK, Slager SL, Asmann Y, Mondello P, Morin R, Ansell SM, Habermann TM, Feldman AL, King RL, Nowakowski G, Cerhan JR, Gandhi AK, Novak AJ. Multiomic Analysis Identifies a High-Risk Metabolic and TME Depleted Signature that Predicts Early Clinical Failure in DLBCL. medRxiv 2023:2023.06.07.23290748. [PMID: 37333387 PMCID: PMC10274962 DOI: 10.1101/2023.06.07.23290748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
PURPOSE 60-70% of newly diagnosed diffuse large B-cell lymphoma (DLBCL) patients avoid events within 24 months of diagnosis (EFS24) and the remainder have poor outcomes. Recent genetic and molecular classification of DLBCL has advanced our knowledge of disease biology, yet were not designed to predict early events and guide anticipatory selection of novel therapies. To address this unmet need, we used an integrative multiomic approach to identify a signature at diagnosis that will identify DLBCL at high risk of early clinical failure. PATIENTS AND METHODS Tumor biopsies from 444 newly diagnosed DLBCL were analyzed by WES and RNAseq. A combination of weighted gene correlation network analysis and differential gene expression analysis followed by integration with clinical and genomic data was used to identify a multiomic signature associated with high risk of early clinical failure. RESULTS Current DLBCL classifiers are unable to discriminate cases who fail EFS24. We identified a high risk RNA signature that had a hazard ratio (HR, 18.46 [95% CI 6.51-52.31] P < .001) in a univariate model, which did not attenuate after adjustment for age, IPI and COO (HR, 20.8 [95% CI, 7.14-61.09] P < .001). Further analysis revealed the signature was associated with metabolic reprogramming and a depleted immune microenvironment. Finally, WES data was integrated into the signature and we found that inclusion of ARID1A mutations resulted in identification of 45% of cases with an early clinical failure which was validated in external DLBCL cohorts. CONCLUSION This novel and integrative approach is the first to identify a signature at diagnosis that will identify DLBCL at high risk for early clinical failure and may have significant implications for design of therapeutic options.
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4
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Ansari-Pour N, Samur M, Flynt E, Gooding S, Towfic F, Stong N, Estevez MO, Mavrommatis K, Walker B, Morgan G, Munshi N, Avet-Loiseau H, Thakurta A. Whole-genome analysis identifies novel drivers and high-risk double-hit events in relapsed/refractory myeloma. Blood 2023; 141:620-633. [PMID: 36223594 PMCID: PMC10163277 DOI: 10.1182/blood.2022017010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Large-scale analyses of genomic data from patients with newly diagnosed multiple myeloma (ndMM) have been undertaken, however, large-scale analysis of relapsed/refractory MM (rrMM) has not been performed. We hypothesize that somatic variants chronicle the therapeutic exposures and clonal structure of myeloma from ndMM to rrMM stages. We generated whole-genome sequencing (WGS) data from 418 tumors (386 patients) derived from 6 rrMM clinical trials and compared them with WGS from 198 unrelated patients with ndMM in a population-based case-control fashion. We identified significantly enriched events at the rrMM stage, including drivers (DUOX2, EZH2, TP53), biallelic inactivation (TP53), noncoding mutations in bona fide drivers (TP53BP1, BLM), copy number aberrations (CNAs; 1qGain, 17pLOH), and double-hit events (Amp1q-ISS3, 1qGain-17p loss-of-heterozygosity). Mutational signature analysis identified a subclonal defective mismatch repair signature enriched in rrMM and highly active in high mutation burden tumors, a likely feature of therapy-associated expanding subclones. Further analysis focused on the association of genomic aberrations enriched at different stages of resistance to immunomodulatory agent (IMiD)-based therapy. This analysis revealed that TP53, DUOX2, 1qGain, and 17p loss-of-heterozygosity increased in prevalence from ndMM to lenalidomide resistant (LENR) to pomalidomide resistant (POMR) stages, whereas enrichment of MAML3 along with immunoglobulin lambda (IGL) and MYC translocations distinguished POM from the LEN subgroup. Genomic drivers associated with rrMM are those that confer clonal selective advantage under therapeutic pressure. Their role in therapy evasion should be further evaluated in longitudinal patient samples, to confirm these associations with the evolution of clinical resistance and to identify molecular subsets of rrMM for the development of targeted therapies.
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Affiliation(s)
- Naser Ansari-Pour
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mehmet Samur
- Dana-Farber Cancer Institute, Boston, MA
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | - Sarah Gooding
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | | | | | - Maria Ortiz Estevez
- Predictive Sciences, BMS Center for Innovation and Translational Research Europe, A Bristol Myers Squibb Company, Sevilla, Spain
| | | | - Brian Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN
| | - Gareth Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY
| | - Nikhil Munshi
- Dana-Farber Cancer Institute, Boston, MA
- VA Boston Healthcare System, West Roxbury, MA
- Harvard Medical School, Boston, MA
| | | | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Bristol Myers Squibb, Summit, NJ
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Disease, University of Oxford, Oxford, United Kingdom
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5
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Barish S, Senturk M, Schoch K, Minogue AL, Lopergolo D, Fallerini C, Harland J, Seemann JH, Stong N, Kranz PG, Kansagra S, Mikati MA, Jasien J, El-Dairi M, Galluzzi P, Ariani F, Renieri A, Mari F, Wangler MF, Arur S, Jiang YH, Yamamoto S, Shashi V, Bellen HJ. The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder. Hum Mol Genet 2022; 31:2934-2950. [PMID: 35405010 PMCID: PMC9433733 DOI: 10.1093/hmg/ddac085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 11/15/2022] Open
Abstract
DROSHA encodes a ribonuclease that is a subunit of the Microprocessor complex and is involved in the first step of microRNA (miRNA) biogenesis. To date, DROSHA has not yet been associated with a Mendelian disease. Here, we describe two individuals with profound intellectual disability, epilepsy, white matter atrophy, microcephaly and dysmorphic features, who carry damaging de novo heterozygous variants in DROSHA. DROSHA is constrained for missense variants and moderately intolerant to loss-of-function (o/e = 0.24). The loss of the fruit fly ortholog drosha causes developmental arrest and death in third instar larvae, a severe reduction in brain size and loss of imaginal discs in the larva. Loss of drosha in eye clones causes small and rough eyes in adult flies. One of the identified DROSHA variants (p.Asp1219Gly) behaves as a strong loss-of-function allele in flies, while another variant (p.Arg1342Trp) is less damaging in our assays. In worms, a knock-in that mimics the p.Asp1219Gly variant at a worm equivalent residue causes loss of miRNA expression and heterochronicity, a phenotype characteristic of the loss of miRNA. Together, our data show that the DROSHA variants found in the individuals presented here are damaging based on functional studies in model organisms and likely underlie the severe phenotype involving the nervous system.
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Affiliation(s)
- Scott Barish
- 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
| | - Mumine Senturk
- 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
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda L Minogue
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diego Lopergolo
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
| | - Jake Harland
- 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
| | - Jacob H Seemann
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke Health, Durham, NC 27710, USA
| | - Paolo Galluzzi
- Department of Medical Genetics, NeuroImaging and NeuroInterventional Unit, Azienda Ospedaliera e Universitaria, Senese, Siena 53100, Italy
| | - Francesca Ariani
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Francesca Mari
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Michael F Wangler
- 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
| | - Swathi Arur
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
- Yale School of Medicine, New Haven, CT 06510, 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
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, 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
- Howard Hughes Medical Institute, BCM, 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
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6
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Ritter AL, Gold J, Hayashi H, Ackermann AM, Hanke S, Skraban C, Cuddapah S, Bhoj E, Li D, Kuroda Y, Wen J, Takeda R, Bibb A, El Chehadeh S, Piton A, Ohl J, Kukolich MK, Nagasaki K, Kato K, Ogi T, Bhatti T, Russo P, Krock B, Murrell JR, Sullivan JA, Shashi V, Stong N, Hakonarson H, Sawano K, Torti E, Willaert R, Si Y, Wilcox WR, Wirgenes KV, Thomassen K, Carlotti K, Erwin A, Lazier J, Marquardt T, He M, Edmondson AC, Izumi K. Expanding the phenotypic spectrum of ARCN1-related syndrome. Genet Med 2022; 24:1227-1237. [PMID: 35300924 PMCID: PMC9923403 DOI: 10.1016/j.gim.2022.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/18/2023] Open
Abstract
PURPOSE This study aimed to describe the phenotypic and molecular characteristics of ARCN1-related syndrome. METHODS Patients with ARCN1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. RESULTS In total, we identified 14 cases of ARCN1-related syndrome, (9 pediatrics, and 5 fetal cases from 3 families). The clinical features these newly identified cases were compared to 6 previously reported cases for a total of 20 cases. Intrauterine growth restriction, micrognathia, and short stature were present in all patients. Other common features included prematurity (11/15, 73.3%), developmental delay (10/14, 71.4%), genitourinary malformations in males (6/8, 75%), and microcephaly (12/15, 80%). Novel features of ARCN1-related syndrome included transient liver dysfunction and specific glycosylation abnormalities during illness, giant cell hepatitis, hepatoblastoma, cataracts, and lethal skeletal manifestations. Developmental delay was seen in 73% of patients, but only 3 patients had intellectual disability, which is less common than previously reported. CONCLUSION ARCN1-related syndrome presents with a wide clinical spectrum ranging from a severe embryonic lethal syndrome to a mild syndrome with intrauterine growth restriction, micrognathia, and short stature without intellectual disability. Patients with ARCN1-related syndrome should be monitored for liver dysfunction during illness, cataracts, and hepatoblastoma. Additional research to further define the phenotypic spectrum and possible genotype-phenotype correlations are required.
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Affiliation(s)
- Alyssa L Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jessica Gold
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hiroshi Hayashi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amanda M Ackermann
- Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Stephanie Hanke
- Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Cara Skraban
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sanmati Cuddapah
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth Bhoj
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jessica Wen
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ryojun Takeda
- Division of Genetics, Nagano Children's Hospital, Nagano, Japan
| | - Audrey Bibb
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Laboratoire de Génétique Médicale, UMR_S1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | - Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institut Génétique Biologie Moléculaire Cellulaire, IGBMC - CNRS UMR 7104 - Inserm U 1258, Illkirch, France; Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jeanine Ohl
- Service d'assistance Médicale à la Procréation, Centre médico-chirurgical et obstétrical (CMCO), Schiltigheim, France
| | - Mary K Kukolich
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX
| | - Keisuke Nagasaki
- Department of Pediatrics, Niigata University Medical & Dental Hospital, Niigata, Japan
| | - Kohji Kato
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tricia Bhatti
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pierre Russo
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bryan Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kentaro Sawano
- Department of Pediatrics, Niigata University Medical & Dental Hospital, Niigata, Japan
| | | | | | | | - William Ross Wilcox
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Katrine Verena Wirgenes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristian Thomassen
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Angelika Erwin
- Genomic Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Joanna Lazier
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Thorsten Marquardt
- Department of Pediatrics, University Hospital of Muenster, Muenster, Germany
| | - Miao He
- Metabolic and Advanced Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew C Edmondson
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA.
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7
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Hayeck TJ, Stong N, Baugh E, Dhindsa R, Turner TN, Malakar A, Mosbruger TL, Shaw GTW, Duan Y, Ionita-Laza I, Goldstein D, Allen AS. Ancestry adjustment improves genome-wide estimates of regional intolerance. Genetics 2022; 221:iyac050. [PMID: 35385101 PMCID: PMC9157129 DOI: 10.1093/genetics/iyac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/24/2022] [Indexed: 11/12/2022] Open
Abstract
Genomic regions subject to purifying selection are more likely to carry disease-causing mutations than regions not under selection. Cross species conservation is often used to identify such regions but with limited resolution to detect selection on short evolutionary timescales such as that occurring in only one species. In contrast, genetic intolerance looks for depletion of variation relative to expectation within a species, allowing species-specific features to be identified. When estimating the intolerance of noncoding sequence, methods strongly leverage variant frequency distributions. As the expected distributions depend on ancestry, if not properly controlled for, ancestral population source may obfuscate signals of selection. We demonstrate that properly incorporating ancestry in intolerance estimation greatly improved variant classification. We provide a genome-wide intolerance map that is conditional on ancestry and likely to be particularly valuable for variant prioritization.
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Affiliation(s)
- Tristan J Hayeck
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Evan Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Ryan Dhindsa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Tychele N Turner
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ayan Malakar
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Timothy L Mosbruger
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Grace Tzun-Wen Shaw
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yuncheng Duan
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA
| | | | - David Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA
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8
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Ortiz-Estévez M, Towfic F, Flynt E, Stong N, Jang IS, Wang K, Trotter MWB, Thakurta A. Integrative multi-omics identifies high risk multiple myeloma subgroup associated with significant DNA loss and dysregulated DNA repair and cell cycle pathways. BMC Med Genomics 2021; 14:295. [PMID: 34922559 PMCID: PMC8684160 DOI: 10.1186/s12920-021-01140-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Background Despite significant therapeutic advances in improving lives of multiple myeloma (MM) patients, it remains mostly incurable, with patients ultimately becoming refractory to therapies. MM is a genetically heterogeneous disease and therapeutic resistance is driven by a complex interplay of disease pathobiology and mechanisms of drug resistance. We applied a multi-omics strategy using tumor-derived gene expression, single nucleotide variant, copy number variant, and structural variant profiles to investigate molecular subgroups in 514 newly diagnosed MM (NDMM) samples and identified 12 molecularly defined MM subgroups (MDMS1-12) with distinct genomic and transcriptomic features. Results Our integrative approach let us identify NDMM subgroups with transversal profiles to previously described ones, based on single data types, which shows the impact of this approach for disease stratification. One key novel subgroup is our MDMS8, associated with poor clinical outcome [median overall survival, 38 months (global log-rank p-value < 1 × 10−6)], which uniquely presents a broad genomic loss (> 9% of entire genome, t-test p value < 1e−5) driving dysregulation of various transcriptional programs affecting DNA repair and cell cycle/mitotic processes. This subgroup was validated on multiple independent datasets, and a master regulator analyses identified transcription factors controlling MDMS8 transcriptomic profile, including CKS1B and PRKDC among others, which are regulators of the DNA repair and cell cycle pathways. Conclusion Using multi-omics unsupervised clustering we were able to discover a new high-risk multiple myeloma patient segment. This high-risk group presents diverse previously known genetic markers, but also a new characteristic defined by accumulation of genomic loss which seems to drive transcriptional dysregulation of cell cycle, DNA repair and DNA damage. Finally, our work identified various master regulators, including E2F2 and CKS1B as the genes controlling these key biological pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01140-5.
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Affiliation(s)
- María Ortiz-Estévez
- BMS Center for Innovation and Translational Research Europe (CITRE), A Bristol Myers Squibb Company, Sevilla, Spain
| | | | - Erin Flynt
- Bristol Myers Squibb, 181 Passaic Ave, Summit, NJ, 07901, USA
| | - Nicholas Stong
- Bristol Myers Squibb, 181 Passaic Ave, Summit, NJ, 07901, USA
| | | | - Kai Wang
- Bristol Myers Squibb, San Diego, CA, USA
| | - Matthew W B Trotter
- BMS Center for Innovation and Translational Research Europe (CITRE), A Bristol Myers Squibb Company, Sevilla, Spain
| | - Anjan Thakurta
- Bristol Myers Squibb, 181 Passaic Ave, Summit, NJ, 07901, USA.
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9
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Luo X, Schoch K, Jangam SV, Bhavana VH, Graves HK, Kansagra S, Jasien JM, Stong N, Keren B, Mignot C, Ravelli C, Bellen HJ, Wangler MF, Shashi V, Yamamoto S. Rare deleterious de novo missense variants in Rnf2/Ring2 are associated with a neurodevelopmental disorder with unique clinical features. Hum Mol Genet 2021; 30:1283-1292. [PMID: 33864376 PMCID: PMC8255132 DOI: 10.1093/hmg/ddab110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 01/16/2023] Open
Abstract
The Polycomb group (PcG) gene RNF2 (RING2) encodes a catalytic subunit of the Polycomb repressive complex 1 (PRC1), an evolutionarily conserved machinery that post-translationally modifies chromatin to maintain epigenetic transcriptional repressive states of target genes including Hox genes. Here, we describe two individuals, each with rare de novo missense variants in RNF2. Their phenotypes include intrauterine growth retardation, severe intellectual disabilities, behavioral problems, seizures, feeding difficulties and dysmorphic features. Population genomics data suggest that RNF2 is highly constrained for loss-of-function (LoF) and missense variants, and both p.R70H and p.S82R variants have not been reported to date. Structural analyses of the two alleles indicate that these changes likely impact the interaction between RNF2 and BMI1, another PRC1 subunit or its substrate Histone H2A, respectively. Finally, we provide functional data in Drosophila that these two missense variants behave as LoF alleles in vivo. The evidence provide support for deleterious alleles in RNF2 being associated with a new and recognizable genetic disorder. This tentative gene-disease association in addition to the 12 previously identified disorders caused by PcG genes attests to the importance of these chromatin regulators in Mendelian disorders.
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Affiliation(s)
- Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Sharayu V Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Venkata Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan M Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Boris Keren
- Département de Génétique, Hospitalier Pitié-Salpêtrière, APHP, Paris 75013, France
- Sorbonne Université, Paris 75006, France
| | - Cyril Mignot
- Sorbonne Université, Paris 75006, France
- APHP, Sorbonne Université, Département de Génétique et Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière et Hôpital Trousseau, Paris 75013, France
| | - Claudia Ravelli
- Sorbonne Université, Paris 75006, France
- Département de Neuropédiatrie, Hôpital Armand Trousseau, APHP, Paris 75012, France
| | | | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
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10
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Bowles B, Ferrer A, Nishimura CJ, Pinto E Vairo F, Rey T, Leheup B, Sullivan J, Schoch K, Stong N, Agolini E, Cocciadiferro D, Williams A, Cummings A, Loddo S, Genovese S, Roadhouse C, McWalter K, Wentzensen IM, Li C, Babovic-Vuksanovic D, Lanpher BC, Dentici ML, Ankala A, Hamm JA, Dallapiccola B, Radio FC, Shashi V, Gérard B, Bloch-Zupan A, Smith RJ, Klee EW. TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. Am J Med Genet A 2021; 185:2417-2433. [PMID: 34042254 PMCID: PMC8361973 DOI: 10.1002/ajmg.a.62347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/21/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022]
Abstract
Biallelic loss‐of‐function variants in the thrombospondin‐type laminin G domain and epilepsy‐associated repeats (TSPEAR) gene have recently been associated with ectodermal dysplasia and hearing loss. The first reports describing a TSPEAR disease association identified this gene is a cause of nonsyndromic hearing loss, but subsequent reports involving additional affected families have questioned this evidence and suggested a stronger association with ectodermal dysplasia. To clarify genotype–phenotype associations for TSPEAR variants, we characterized 13 individuals with biallelic TSPEAR variants. Individuals underwent either exome sequencing or panel‐based genetic testing. Nearly all of these newly reported individuals (11/13) have phenotypes that include tooth agenesis or ectodermal dysplasia, while three newly reported individuals have hearing loss. Of the individuals displaying hearing loss, all have additional variants in other hearing‐loss‐associated genes, specifically TMPRSS3, GJB2, and GJB6, that present competing candidates for their hearing loss phenotype. When presented alongside previous reports, the overall evidence supports the association of TSPEAR variants with ectodermal dysplasia and tooth agenesis features but creates significant doubt as to whether TSPEAR variants are a monogenic cause of hearing loss. Further functional evidence is needed to evaluate this phenotypic association.
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Affiliation(s)
- Bradley Bowles
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tristan Rey
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Bruno Leheup
- Département de Médecine Infantile, CHRU de Nancy, Nancy, France
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Brystol Myers Squibb, New York, New York, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Abigail Williams
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Alex Cummings
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA.,University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, USA
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chelsea Roadhouse
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | | | | | - Chumei Li
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arun Ankala
- EGL Genetics LLC, Tucker, Georgia, USA.,Emory University School of Medicine, Atlanta, Georgia, USA
| | - J Austin Hamm
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Benedicte Gérard
- Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Agnes Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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11
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Ernst ME, Baugh EH, Thomas A, Bier L, Lippa N, Stong N, Mulhern MS, Kushary S, Akman CI, Heinzen EL, Yeh R, Bi W, Hanchard NA, Burrage LC, Leduc MS, Chong JSC, Bend R, Lyons MJ, Lee JA, Suwannarat P, Brilstra E, Simon M, Koopmans M, van Binsbergen E, Groepper D, Fleischer J, Nava C, Keren B, Mignot C, Mathieu S, Mancini GMS, Madan-Khetarpal S, Infante EM, Bluvstein J, Seeley A, Bachman K, Klee EW, Schultz-Rogers LE, Hasadsri L, Barnett S, Ellingson MS, Ferber MJ, Narayanan V, Ramsey K, Rauch A, Joset P, Steindl K, Sheehan T, Poduri A, Vasquez A, Ruivenkamp C, White SM, Pais L, Monaghan KG, Goldstein DB, Sands TT, Aggarwal V. CSNK2B: A broad spectrum of neurodevelopmental disability and epilepsy severity. Epilepsia 2021; 62:e103-e109. [PMID: 34041744 DOI: 10.1111/epi.16931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 11/29/2022]
Abstract
CSNK2B has recently been implicated as a disease gene for neurodevelopmental disability (NDD) and epilepsy. Information about developmental outcomes has been limited by the young age and short follow-up for many of the previously reported cases, and further delineation of the spectrum of associated phenotypes is needed. We present 25 new patients with variants in CSNK2B and refine the associated NDD and epilepsy phenotypes. CSNK2B variants were identified by research or clinical exome sequencing, and investigators from different centers were connected via GeneMatcher. Most individuals had developmental delay and generalized epilepsy with onset in the first 2 years. However, we found a broad spectrum of phenotypic severity, ranging from early normal development with pharmacoresponsive seizures to profound intellectual disability with intractable epilepsy and recurrent refractory status epilepticus. These findings suggest that CSNK2B should be considered in the diagnostic evaluation of patients with a broad range of NDD with treatable or intractable seizures.
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Affiliation(s)
- Michelle E Ernst
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Amanda Thomas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Maureen S Mulhern
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sulagna Kushary
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Cigdem I Akman
- Department of Neurology, The Neurological Institute of New York, Columbia University Irving Medical Center, New York, NY, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Raymond Yeh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Magalie S Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Josephine S C Chong
- Joint CUHK-Baylor Center of Medical Genetics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC, USA
| | | | | | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, MD, USA
| | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marleen Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Caroline Nava
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France.,Reference Center for Intellectual Disabilities of Rare Causes, Paris, France
| | - Sophie Mathieu
- Department of Neuropediatrics, APHP Sorbonne University, Trousseau Hospital, Paris, France
| | - Grazia M S Mancini
- Department of Clinical Genetics, ErasmusMC University Medical Center, Rotterdam, The Netherlands
| | | | - Elena M Infante
- Department of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marissa S Ellingson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Clinical Genome Sequencing Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Schlieren, Zürich, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zürich, Schlieren, Zürich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zürich, Schlieren, Zürich, Switzerland
| | - Theodore Sheehan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Alejandra Vasquez
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA.,Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tristan T Sands
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Neurology, The Neurological Institute of New York, Columbia University Irving Medical Center, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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12
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Dias C, Pfundt R, Kleefstra T, Shuurs-Hoeijmakers J, Boon EMJ, van Hagen JM, Zwijnenburg P, Weiss MM, Keren B, Mignot C, Isapof A, Weiss K, Hershkovitz T, Iascone M, Maitz S, Feichtinger RG, Kotzot D, Mayr JA, Ben-Omran T, Mahmoud L, Pais LS, Walsh CA, Shashi V, Sullivan JA, Stong N, Lecoquierre F, Guerrot AM, Charollais A, Rodan LH. De novo variants in TCF7L2 are associated with a syndromic neurodevelopmental disorder. Am J Med Genet A 2021; 185:2384-2390. [PMID: 34003604 DOI: 10.1002/ajmg.a.62254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/25/2021] [Accepted: 04/24/2021] [Indexed: 01/21/2023]
Abstract
TCF7L2 encodes transcription factor 7-like 2 (OMIM 602228), a key mediator of the evolutionary conserved canonical Wnt signaling pathway. Although several large-scale sequencing studies have implicated TCF7L2 in intellectual disability and autism, both the genetic mechanism and clinical phenotype have remained incompletely characterized. We present here a comprehensive genetic and phenotypic description of 11 individuals who have been identified to carry de novo variants in TCF7L2, both truncating and missense. Missense variation is clustered in or near a high mobility group box domain, involving this region in these variants' pathogenicity. All affected individuals present with developmental delays in childhood, but most ultimately achieved normal intelligence or had only mild intellectual disability. Myopia was present in approximately half of the individuals, and some individuals also possessed dysmorphic craniofacial features, orthopedic abnormalities, or neuropsychiatric comorbidities including autism and attention-deficit/hyperactivity disorder (ADHD). We thus present an initial clinical and genotypic spectrum associated with variation in TCF7L2, which will be important in informing both medical management and future research.
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Affiliation(s)
- Caroline Dias
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rolph Pfundt
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | | | - Elles M J Boon
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Petra Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marjan M Weiss
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Boris Keren
- Département de Génétique, hôpital Pitié-Salpêtrière, APHP.Sorbonne Université, Paris, France
| | - Cyril Mignot
- Département de Génétique, hôpital Pitié-Salpêtrière, APHP.Sorbonne Université, Paris, France
| | - Arnaud Isapof
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tova Hershkovitz
- Genetics Institute, Rambam Health Care Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetic Unit, Pediatric Clinic, Fondazione MBBM, San Gerardo Hospital, Monza, Italy
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Dieter Kotzot
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Tawfeg Ben-Omran
- Department of Pediatrics, Sidra Medicine, Department of Medical Genetics, Hamad Medical Corporation, Weill Cornell Medical College, Doha, Qatar
| | - Laila Mahmoud
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Francois Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France
| | - Aude Charollais
- Reference Centre for Learning Disorders, Rouen University Hospital, F-76031 Rouen Cedex, Rouen, France.,Department of Neonatology and Paediatric Intensive Care, Rouen University Hospital, F-76031 Cedex, Rouen, France
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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13
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Schoch K, Esteves C, Bican A, Spillmann R, Cope H, McConkie-Rosell A, Walley N, Fernandez L, Kohler JN, Bonner D, Reuter C, Stong N, Mulvihill JJ, Novacic D, Wolfe L, Abdelbaki A, Toro C, Tifft C, Malicdan M, Gahl W, Liu P, Newman J, Goldstein DB, Hom J, Sampson J, Wheeler MT, Cogan J, Bernstein JA, Adams DR, McCray AT, Shashi V. Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. Genet Med 2021; 23:259-271. [PMID: 33093671 PMCID: PMC7867619 DOI: 10.1038/s41436-020-00984-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices. METHODS We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods. RESULTS Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling. CONCLUSION Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.
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Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Anna Bican
- Vanderbilt Center for Undiagnosed Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Division of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Liliana Fernandez
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - John J Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Donna Novacic
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Lynne Wolfe
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Ayat Abdelbaki
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Cyndi Tifft
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Office of the Clinical Director, NHGRI, NIH, Bethesda, MD, USA
| | - May Malicdan
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - William Gahl
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - John Newman
- Vanderbilt Center for Undiagnosed Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Jason Hom
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Jacinda Sampson
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Neurology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joy Cogan
- Vanderbilt Center for Undiagnosed Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Division of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - David R Adams
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Office of the Clinical Director, NHGRI, NIH, Bethesda, MD, USA
| | - Alexa T McCray
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
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14
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Klöckner C, Sticht H, Zacher P, Popp B, Babcock HE, Bakker DP, Barwick K, Bonfert MV, Bönnemann CG, Brilstra EH, Chung WK, Clarke AJ, Devine P, Donkervoort S, Fraser JL, Friedman J, Gates A, Ghoumid J, Hobson E, Horvath G, Keller-Ramey J, Keren B, Kurian MA, Lee V, Leppig KA, Lundgren J, McDonald MT, McLaughlin HM, McTague A, Mefford HC, Mignot C, Mikati MA, Nava C, Raymond FL, Sampson JR, Sanchis-Juan A, Shashi V, Shieh JTC, Shinawi M, Slavotinek A, Stödberg T, Stong N, Sullivan JA, Taylor AC, Toler TL, van den Boogaard MJ, van der Crabben SN, van Gassen KLI, van Jaarsveld RH, Van Ziffle J, Wadley AF, Wagner M, Wigby K, Wortmann SB, Zarate YA, Møller RS, Lemke JR, Platzer K. De novo variants in SNAP25 cause an early-onset developmental and epileptic encephalopathy. Genet Med 2020; 23:653-660. [PMID: 33299146 DOI: 10.1038/s41436-020-01020-w] [Citation(s) in RCA: 8] [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: 05/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This study aims to provide a comprehensive description of the phenotypic and genotypic spectrum of SNAP25 developmental and epileptic encephalopathy (SNAP25-DEE) by reviewing newly identified and previously reported individuals. METHODS Individuals harboring heterozygous missense or loss-of-function variants in SNAP25 were assembled through collaboration with international colleagues, matchmaking platforms, and literature review. For each individual, detailed phenotyping, classification, and structural modeling of the identified variant were performed. RESULTS The cohort comprises 23 individuals with pathogenic or likely pathogenic de novo variants in SNAP25. Intellectual disability and early-onset epilepsy were identified as the core symptoms of SNAP25-DEE, with recurrent findings of movement disorders, cerebral visual impairment, and brain atrophy. Structural modeling for all variants predicted possible functional defects concerning SNAP25 or impaired interaction with other components of the SNARE complex. CONCLUSION We provide a comprehensive description of SNAP25-DEE with intellectual disability and early-onset epilepsy mostly occurring before the age of two years. These core symptoms and additional recurrent phenotypes show an overlap to genes encoding other components or associated proteins of the SNARE complex such as STX1B, STXBP1, or VAMP2. Thus, these findings advance the concept of a group of neurodevelopmental disorders that may be termed "SNAREopathies."
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Affiliation(s)
- Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Holly E Babcock
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Dewi P Bakker
- Department of Child Neurology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Katy Barwick
- Institute of Child Health, University Collge London, London, UK
| | - Michaela V Bonfert
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU - University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Angus J Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jamie L Fraser
- Rare Disease Institute, Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego and Division of Neurology, Rady Children's Hospital, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Alyssa Gates
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Jamal Ghoumid
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - Emma Hobson
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Gabriella Horvath
- Department of Pediatrics, Division of Biochemical Diseases, University of British Columbia, Vancouver, Canada
| | | | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Manju A Kurian
- Institute of Child Health, University Collge London, London, UK
| | - Virgina Lee
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen A Leppig
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Johan Lundgren
- Institute of Clinical Sciences, Skane University Hospital, Lund, Sweden
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Amy McTague
- Institute of Child Health, University Collge London, London, UK
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Caroline Nava
- Sorbonne University, Paris Brain Institute, Inserm U1127, CNRS UMR 7225, AP-HP, Pitié Salpêtrière Hospital, Department of Genetics, Paris, France
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Julian R Sampson
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Joseph T C Shieh
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Slavotinek
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tommy Stödberg
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Ashley C Taylor
- Section of Genetics, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Tomi L Toler
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Saskia N van der Crabben
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Matias Wagner
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Kristen Wigby
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, CA, USA
| | - Saskia B Wortmann
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands.,University Childrens Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rikke S Møller
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark.,Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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15
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Del Dotto V, Ullah F, Di Meo I, Magini P, Gusic M, Maresca A, Caporali L, Palombo F, Tagliavini F, Baugh EH, Macao B, Szilagyi Z, Peron C, Gustafson MA, Khan K, La Morgia C, Barboni P, Carbonelli M, Valentino ML, Liguori R, Shashi V, Sullivan J, Nagaraj S, El-Dairi M, Iannaccone A, Cutcutache I, Bertini E, Carrozzo R, Emma F, Diomedi-Camassei F, Zanna C, Armstrong M, Page M, Stong N, Boesch S, Kopajtich R, Wortmann S, Sperl W, Davis EE, Copeland WC, Seri M, Falkenberg M, Prokisch H, Katsanis N, Tiranti V, Pippucci T, Carelli V. SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder. J Clin Invest 2020; 130:108-125. [PMID: 31550240 DOI: 10.1172/jci128514] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/19/2019] [Indexed: 01/07/2023] Open
Abstract
Inherited optic neuropathies include complex phenotypes, mostly driven by mitochondrial dysfunction. We report an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions. By whole-exome sequencing, we identified mutations affecting the mitochondrial single-strand binding protein (SSBP1) in 4 families with dominant and 1 with recessive inheritance. We show that SSBP1 mutations in patient-derived fibroblasts variably affect the amount of SSBP1 protein and alter multimer formation, but not the binding to ssDNA. SSBP1 mutations impaired mtDNA, nucleoids, and 7S-DNA amounts as well as mtDNA replication, affecting replisome machinery. The variable mtDNA depletion in cells was reflected in severity of mitochondrial dysfunction, including respiratory efficiency, OXPHOS subunits, and complex amount and assembly. mtDNA depletion and cytochrome c oxidase-negative cells were found ex vivo in biopsies of affected tissues, such as kidney and skeletal muscle. Reduced efficiency of mtDNA replication was also reproduced in vitro, confirming the pathogenic mechanism. Furthermore, ssbp1 suppression in zebrafish induced signs of nephropathy and reduced optic nerve size, the latter phenotype complemented by WT mRNA but not by SSBP1 mutant transcripts. This previously unrecognized disease of mtDNA maintenance implicates SSBP1 mutations as a cause of human pathology.
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Affiliation(s)
- Valentina Del Dotto
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Ivano Di Meo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Pamela Magini
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Francesca Tagliavini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Evan Harris Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Zsolt Szilagyi
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Camille Peron
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Margaret A Gustafson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Chiara La Morgia
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Piero Barboni
- Department of Ophthalmology, Studio Oculistico d'Azeglio, Bologna, Italy
| | - Michele Carbonelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Maria Lucia Valentino
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Rocco Liguori
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | | | | | - Shashi Nagaraj
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Alessandro Iannaccone
- Center for Retinal Degenerations and Ophthalmic Genetic Diseases and Visual Function Diagnostic Laboratory, Duke Eye Center, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Diseases, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Diseases, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco Emma
- Division of Nephrology, Department of Pediatric Subspecialties, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | | | - Matthew Page
- Translational Medicine, UCB Pharma, Slough, United Kingdom
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Sylvia Boesch
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Saskia Wortmann
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany.,Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Wolfgang Sperl
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Marco Seri
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Departments of Pediatrics and Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Valeria Tiranti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valerio Carelli
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
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16
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Sullivan JA, Stong N, Baugh EH, McDonald MT, Takeuchi A, Shashi V. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Am J Med Genet A 2020; 182:1947-1951. [PMID: 32445275 DOI: 10.1002/ajmg.a.61630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Schinzel-Giedion syndrome (SGS; OMIM 269150) is an ultra-rare genetic disorder associated with a distinctive facial gestalt, congenital malformations, severe intellectual disability, and a progressive neurological course. The prognosis for SGS is poor, with survival beyond the first decade rare. Germline, de novo heterozygous variants in the SETBP1 gene cause SGS with the pathogenic variants associated with the SGS phenotype missense and confined to exon 4 of the gene, clustered in a four amino acid (12 bp) hotspot in the SKI homologous region of the SETBP1 protein. We report a patient with a de novo I871S variant within the SKI homologous region, which has been associated with the severe phenotype previously; but our patient has fewer features of SGS and a milder course. This is the first report of a forme-fruste phenotype in a patient with a pathogenic variant within the SGS hotspot on the SETBP1 gene and it highlights the importance of considering atypical clinical presentations in the context of severe ultra-rare genetic disorders.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Akihito Takeuchi
- Department of Neonatology, Okayama Medical Center, National Hospital Organization, Okayama, Japan
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
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17
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Schoch K, Tan QKG, Stong N, Deak KL, McConkie-Rosell A, McDonald MT, Goldstein DB, Jiang YH, Shashi V. Alternative transcripts in variant interpretation: the potential for missed diagnoses and misdiagnoses. Genet Med 2020; 22:1269-1275. [PMID: 32366967 PMCID: PMC7335342 DOI: 10.1038/s41436-020-0781-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Guidelines by professional organizations for assessing variant pathogenicity include the recommendation to utilize biologically relevant transcripts; however, there is variability in transcript selection by laboratories. METHODS We describe three patients whose genomic results were incorrect, because alternative transcripts and tissue expression patterns were not considered by the commercial laboratories. RESULTS In individual 1, a pathogenic coding variant in a brain-expressed isoform of CKDL5 was missed twice on sequencing, because the variant was intronic in the transcripts considered in analysis. In individual 2, a microdeletion affecting KMT2C was not reported on microarray, since deletions of proximal exons in this gene are seen in healthy individuals; however, this individual had a more distal deletion involving the brain-expressed KMT2C isoform, giving her a diagnosis of Kleefstra syndrome. Individual 3 was reported to have a pathogenic variant in exon 10 of OFD1 on exome, but had no typical features of the OFD1-related disorders. Since exon 10 is spliced from the more biologically relevant transcripts of OFD1, it was determined that he did not have an OFD1 disorder. CONCLUSION These examples illustrate the importance of considering alternative transcripts as a potential confounder when genetic results are negative or discordant with the phenotype.
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Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Kristen L Deak
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
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18
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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.
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19
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Lee W, Paavo M, Zernant J, Stong N, Laurente Z, Bearelly S, Nagasaki T, Tsang SH, Goldstein DB, Allikmets R. Modification of the PROM1 disease phenotype by a mutation in ABCA4. Ophthalmic Genet 2019; 40:369-375. [PMID: 31576780 DOI: 10.1080/13816810.2019.1660382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background: The extensive phenotypic heterogeneity of monogenic diseases can be largely traced to intragenic variation; however, recent advances in clinical detection and gene sequencing have uncovered the emerging role of non-allelic variation (i.e. genetic trans-modifiers) in shaping disease phenotypes. Identifying these associations are not only of significant diagnostic value, but also provides scientific insight into the expanded molecular etiology of rare diseases. This reports describes the discordant clinical manifestation of a family segregating mutations in ABCA4 and PROM1. Methods: Three patients across a two generation family underwent multimodal imaging and functional testing of the retina including color photography, fundus autofluorescence (AF), spectral domain-optical coherence tomography (SD-OCT) and full-field electroretinography (ffERG). Genetic characterization was carried out by direct Sanger and whole exome sequencing. Results: Clinical examination revealed similar retinal degenerative phenotypes in the proband and her mother. Despite being younger, the proband's phenotype was more advanced and exhibited additional features related to Stargardt disease not found in the mother. Whole exome sequencing identified a pathogenic missense variant in PROM1, c.400C > T, p.(Arg134Cys), as the underlying cause of retinal disease in both the proband and mother. Sequencing of the ABCA4 locus uncovered a single disease-causing variant, c.5714 + 5G > A in the daughter segregating from the father who, surprisingly, also exhibited very subtle disease changes associated with STGD1 despite being a heterozygous carrier. Conclusions: Harboring an additional heterozygous ABCA4 mutation increases severity and confers STGD1-like features in patients with PROM1 disease which provides supporting evidence for their shared pathophysiology and potential treatment prospects.
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Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University , New York , New York , USA
| | - Maarjaliis Paavo
- Department of Ophthalmology, Columbia University , New York , New York , USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University , New York , New York , USA
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University , New York , New York , USA
| | - Zachary Laurente
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Northwestern University , Chicago , Illinois , USA
| | - Srilaxmi Bearelly
- Department of Ophthalmology, Columbia University , New York , New York , USA
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University , New York , New York , USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University , New York , New York , USA.,Department of Pathology & Cell Biology, Columbia University , New York , New York , USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University , New York , New York , USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University , New York , New York , USA.,Department of Pathology & Cell Biology, Columbia University , New York , New York , USA
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20
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Shashi V, Geist J, Lee Y, Yoo Y, Shin U, Schoch K, Sullivan J, Stong N, Smith E, Jasien J, Kranz P, Lee Y, Shin YB, Wright NT, Choi M, Kontrogianni-Konstantopoulos A. Heterozygous variants in MYBPC1 are associated with an expanded neuromuscular phenotype beyond arthrogryposis. Hum Mutat 2019; 40:1115-1126. [PMID: 31264822 PMCID: PMC6688907 DOI: 10.1002/humu.23760] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 11/28/2018] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/22/2023]
Abstract
Encoding the slow skeletal muscle isoform of myosin binding protein-C, MYBPC1 is associated with autosomal dominant and recessive forms of arthrogryposis. The authors describe a novel association for MYBPC1 in four patients from three independent families with skeletal muscle weakness, myogenic tremors, and hypotonia with gradual clinical improvement. The patients carried one of two de novo heterozygous variants in MYBPC1, with the p.Leu263Arg variant seen in three individuals and the p.Leu259Pro variant in one individual. Both variants are absent from controls, well conserved across vertebrate species, predicted to be damaging, and located in the M-motif. Protein modeling studies suggested that the p.Leu263Arg variant affects the stability of the M-motif, whereas the p.Leu259Pro variant alters its structure. In vitro biochemical and kinetic studies demonstrated that the p.Leu263Arg variant results in decreased binding of the M-motif to myosin, which likely impairs the formation of actomyosin cross-bridges during muscle contraction. Collectively, our data substantiate that damaging variants in MYBPC1 are associated with a new form of an early-onset myopathy with tremor, which is a defining and consistent characteristic in all affected individuals, with no contractures. Recognition of this expanded myopathic phenotype can enable identification of individuals with MYBPC1 variants without arthrogryposis.
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Affiliation(s)
- Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Janelle Geist
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yongjin Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Jennifer Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York
| | - Edward Smith
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, North Carolina
| | - Peter Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, North Carolina
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Yong Beom Shin
- Department of Rehabilitation Medicine, Pusan National University College of Medicine, Pusan, Republic of Korea
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
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21
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Sands TT, Miceli F, Lesca G, Beck AE, Sadleir LG, Arrington DK, Schönewolf-Greulich B, Moutton S, Lauritano A, Nappi P, Soldovieri MV, Scheffer IE, Mefford HC, Stong N, Heinzen EL, Goldstein DB, Perez AG, Kossoff EH, Stocco A, Sullivan JA, Shashi V, Gerard B, Francannet C, Bisgaard AM, Tümer Z, Willems M, Rivier F, Vitobello A, Thakkar K, Rajan DS, Barkovich AJ, Weckhuysen S, Cooper EC, Taglialatela M, Cilio MR. Autism and developmental disability caused by KCNQ3 gain-of-function variants. Ann Neurol 2019; 86:181-192. [PMID: 31177578 DOI: 10.1002/ana.25522] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Recent reports have described single individuals with neurodevelopmental disability (NDD) harboring heterozygous KCNQ3 de novo variants (DNVs). We sought to assess whether pathogenic variants in KCNQ3 cause NDD and to elucidate the associated phenotype and molecular mechanisms. METHODS Patients with NDD and KCNQ3 DNVs were identified through an international collaboration. Phenotypes were characterized by clinical assessment, review of charts, electroencephalographic (EEG) recordings, and parental interview. Functional consequences of variants were analyzed in vitro by patch-clamp recording. RESULTS Eleven patients were assessed. They had recurrent heterozygous DNVs in KCNQ3 affecting residues R230 (R230C, R230H, R230S) and R227 (R227Q). All patients exhibited global developmental delay within the first 2 years of life. Most (8/11, 73%) were nonverbal or had a few words only. All patients had autistic features, and autism spectrum disorder (ASD) was diagnosed in 5 of 11 (45%). EEGs performed before 10 years of age revealed frequent sleep-activated multifocal epileptiform discharges in 8 of 11 (73%). For 6 of 9 (67%) recorded between 1.5 and 6 years of age, spikes became near-continuous during sleep. Interestingly, most patients (9/11, 82%) did not have seizures, and no patient had seizures in the neonatal period. Voltage-clamp recordings of the mutant KCNQ3 channels revealed gain-of-function (GoF) effects. INTERPRETATION Specific GoF variants in KCNQ3 cause NDD, ASD, and abundant sleep-activated spikes. This new phenotype contrasts both with self-limited neonatal epilepsy due to KCNQ3 partial loss of function, and with the neonatal or infantile onset epileptic encephalopathies due to KCNQ2 GoF. ANN NEUROL 2019;86:181-192.
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Affiliation(s)
- Tristan T Sands
- Department of Neurology, Columbia University Medical Center, New York, NY.,Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Francesco Miceli
- Section of Pharmacology, Department of Neuroscience, University of Naples "Federico II,", Naples, Italy
| | - Gaetan Lesca
- Department of Medical Genetics, Reference Center for Developmental Anomalies, Civil Hospices of Lyon, Lyon, France.,French Institute of Health and Medical Research U1028, French National Center for Scientific Research UMR5292, Center for Research in Neuroscience in Lyon, Genetics of Neurodevelopment Team, Claude Bernard University Lyon 1, Lyon, France.,Claude Bernard University Lyon 1, Lyon, France
| | - Anita E Beck
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA.,Seattle Children's Hospital, Seattle, WA
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | | | - Bitten Schönewolf-Greulich
- Center for Rett Syndrome, Department of Pediatrics and Adolescent Medicine, National Hospital, Copenhagen, Denmark.,Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sébastien Moutton
- French Institute of Health and Medical Research U1231, Laboratory of Cognitive Neuroscience UMR1231, Genetics of Developmental Anomalies, Burgundy University, F-21000, Dijon, France
| | - Anna Lauritano
- Section of Pharmacology, Department of Neuroscience, University of Naples "Federico II,", Naples, Italy
| | - Piera Nappi
- Section of Pharmacology, Department of Neuroscience, University of Naples "Federico II,", Naples, Italy
| | - Maria Virginia Soldovieri
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Ingrid E Scheffer
- University of Melbourne, Austin Health, Royal Children's Hospital, Florey and Murdoch Institutes, Melbourne, Victoria, Australia
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Ana Grijalvo Perez
- Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Eric H Kossoff
- Departments of Pediatrics and Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Amber Stocco
- Pediatric Neurology, INTEGRIS Baptist Medical Center, Oklahoma City, OK
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC
| | - Benedicte Gerard
- Molecular Genetic Unit, Strasbourg University Hospital, Strasbourg, France
| | - Christine Francannet
- Genetics Department, Reference Center for Developmental Anomalies, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Anne-Marie Bisgaard
- Center for Rett Syndrome, Department of Pediatrics and Adolescent Medicine, National Hospital, Copenhagen, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marjolaine Willems
- Reference Center for Developmental Disorders, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier University Hospital, Montpellier, France
| | - François Rivier
- Department of Pediatric Neurology, University Hospital of Montpellier, and Physiology and Experimental Medicine of Heart and Muscle Unit, University of Montpellier, National Institute for Health and Medical Research, French National Center for Scientific Research, Montpellier, France
| | - Antonio Vitobello
- Functional Unit 12, Innovation in Genomic Diagnosis of Rare Diseases, University Hospital Dijon-Bourgogne, Dijon, France
| | - Kavita Thakkar
- Division of Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Deepa S Rajan
- Division of Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - A James Barkovich
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA
| | - Sarah Weckhuysen
- Neurogenetics Group, University of Antwerp, Antwerp, Belgium.,Neurology Department, University Hospital Antwerp, Antwerp, Belgium
| | - Edward C Cooper
- Departments of Neurology, Neuroscience, and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Maurizio Taglialatela
- Section of Pharmacology, Department of Neuroscience, University of Naples "Federico II,", Naples, Italy
| | - M Roberta Cilio
- Department of Neurology, University of California, San Francisco, San Francisco, CA.,Departments of Pediatrics and Institute of Experimental and Clinical Research, University of Louvain, Brussels, Belgium
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22
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Ma CJ, Lee W, Stong N, Zernant J, Chang S, Goldstein D, Nagasaki T, Allikmets R. Late-onset pattern macular dystrophy mimicking ABCA4 and PRPH2 disease is caused by a homozygous frameshift mutation in ROM1. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003624. [PMID: 30630813 PMCID: PMC6549556 DOI: 10.1101/mcs.a003624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 11/07/2018] [Accepted: 12/27/2018] [Indexed: 12/31/2022] Open
Abstract
ROM1 (retinal outer segment membrane protein 1) is a 351-amino acid integral membrane protein on Chromosome 11q, with high structural similarity to PRPH2/RDS. Localized at the rims of photoreceptor outer segments (OSs), it is required for the maintenance of OS structure. Here, we describe a case with a phenotypic manifestation of a homozygous single-base pair deletion, c.712delC (p.Leu238Cysfs*78) in the ROM1 gene, resulting in early termination at exon 2. The variant was detected by whole-exome sequencing (WES) in a 63-yr-old Caucasian woman with late-onset pattern macular dystrophy. Notably, although the phenotype resembles those caused by pathogenic variants in ABCA4 or RDS/PRPH2, no pathogenic variants in these, or any other plausible candidate genes, were identified by WES. Clinical features include the presence of hyperautofluorescent flecks, relative sparing of the central macula, and preserved visual acuity. Reduced visual sensitivity was detected among flecked regions in the retina; however, full-field electroretinogram testing revealed no generalized cone dysfunction. The described first case of the complete loss of ROM1 protein function in the retina suggests its sufficiency for late-onset macular dystrophy. ROM1 and PRPH2 pattern macular dystrophies exhibit phenotype overlap, which may be attributable to their shared role in maintenance of the photoreceptor outer segment structure.
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Affiliation(s)
- Chu Jian Ma
- Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Winston Lee
- Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Jana Zernant
- Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Stanley Chang
- Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - David Goldstein
- Institute of Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Takayuki Nagasaki
- Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
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23
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Cogné B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR, Sanders SJ, Uguen K, Harris J, Cohen JS, Blyth M, Lehman A, Berg J, Li MH, Kini U, Joss S, von der Lippe C, Gordon CT, Humberson JB, Robak L, Scott DA, Sutton VR, Skraban CM, Johnston JJ, Poduri A, Nordenskjöld M, Shashi V, Gerkes EH, Bongers EM, Gilissen C, Zarate YA, Kvarnung M, Lally KP, Kulch PA, Daniels B, Hernandez-Garcia A, Stong N, McGaughran J, Retterer K, Tveten K, Sullivan J, Geisheker MR, Stray-Pedersen A, Tarpinian JM, Klee EW, Sapp JC, Zyskind J, Holla ØL, Bedoukian E, Filippini F, Guimier A, Picard A, Busk ØL, Punetha J, Pfundt R, Lindstrand A, Nordgren A, Kalb F, Desai M, Ebanks AH, Jhangiani SN, Dewan T, Coban Akdemir ZH, Telegrafi A, Zackai EH, Begtrup A, Song X, Toutain A, Wentzensen IM, Odent S, Bonneau D, Latypova X, Deb W, Redon S, Bilan F, Legendre M, Troyer C, Whitlock K, Caluseriu O, Murphree MI, Pichurin PN, Agre K, Gavrilova R, Rinne T, Park M, Shain C, Heinzen EL, Xiao R, Amiel J, Lyonnet S, Isidor B, Biesecker LG, Lowenstein D, Posey JE, Denommé-Pichon AS, Férec C, Yang XJ, Rosenfeld JA, Gilbert-Dussardier B, Audebert-Bellanger S, Redon R, Stessman HA, Nellaker C, Yang Y, Lupski JR, Goldstein DB, Eichler EE, Bolduc F, Bézieau S, Küry S, Campeau PM, Küry S, Campeau PM. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. Am J Hum Genet 2019; 104:530-541. [PMID: 30827496 DOI: 10.1016/j.ajhg.2019.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sébastien Küry
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France; INSERM, CNRS, UNIV Nantes, l'institut du thorax, 44007 Nantes, France.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T1J4, Canada.
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24
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Petrovski S, Aggarwal V, Giordano JL, Stosic M, Wou K, Bier L, Spiegel E, Brennan K, Stong N, Jobanputra V, Ren Z, Zhu X, Mebane C, Nahum O, Wang Q, Kamalakaran S, Malone C, Anyane-Yeboa K, Miller R, Levy B, Goldstein DB, Wapner RJ. Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study. Lancet 2019; 393:758-767. [PMID: 30712878 DOI: 10.1016/s0140-6736(18)32042-7] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/14/2018] [Accepted: 08/28/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Identification of chromosomal aneuploidies and copy number variants that are associated with fetal structural anomalies has substantial value. Although whole-exome sequencing (WES) has been applied to case series of a few selected prenatal cases, its value in routine clinical settings has not been prospectively assessed in a large unselected cohort of fetuses with structural anomalies. We therefore aimed to determine the incremental diagnostic yield (ie, the added value) of WES following uninformative results of standard investigations with karyotype testing and chromosomal microarray in an unselected cohort of sequential pregnancies showing fetal structural anomalies. METHODS In this prospective cohort study, the parents of fetuses who were found to have a structural anomaly in a prenatal ultrasound were screened for possible participation in the study. These participants were predominantly identified in or were referred to the Columbia University Carmen and John Thain Center for Prenatal Pediatrics (New York, NY, USA). Fetuses with confirmed aneuploidy or a causal pathogenic copy number variant were excluded from WES analyses. By use of WES of the fetuses and parents (parent-fetus trios), we identified genetic variants that indicated an underlying cause (diagnostic genetic variants) and genetic variants that met the criteria of bioinformatic signatures that had previously been described to be significantly enriched among diagnostic genetic variants. FINDINGS Between April 24, 2015, and April 19, 2017, 517 sequentially identified pregnant women found to have fetuses with a structural anomaly were screened for their eligibility for inclusion in our study. 71 (14%) couples declined testing, 87 (17%) trios were missing at least one DNA sample (from either parent or the fetus), 69 (13%) trios had a clinically relevant abnormal karyotype or chromosomal microarray finding, 51 (10%) couples did not consent to WES or withdrew consent, and five (1%) samples were not of good enough quality for analysis. DNA samples from 234 (45%) eligible trios were therefore used for analysis of the primary outcome. By use of trio sequence data, we identified diagnostic genetic variants in 24 (10%) families. Mutations with bioinformatic signatures that were indicative of pathogenicity but with insufficient evidence to be considered diagnostic were also evaluated; 46 (20%) of the 234 fetuses assessed were found to have such signatures. INTERPRETATION Our analysis of WES data in a prospective cohort of unselected fetuses with structural anomalies shows the value added by WES following the use of routine genetic tests. Our findings suggest that, in cases of fetal anomalies in which assessment with karyotype testing and chromosomal microarray fail to determine the underlying cause of a structural anomaly, WES can add clinically relevant information that could assist current management of a pregnancy. The unique challenges of WES-based prenatal diagnostics require analysis by a multidisciplinary team of perinatal practitioners and laboratory specialists. FUNDING Institute for Genomic Medicine (Columbia University Irving Medical Center).
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Affiliation(s)
- Slavé Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jessica L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Melissa Stosic
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Karen Wou
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Erica Spiegel
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Kelly Brennan
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Vaidehi Jobanputra
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Caroline Mebane
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Odelia Nahum
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Quanli Wang
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Colin Malone
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Russell Miller
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Brynn Levy
- Laboratory of Personalized Genomic Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Ronald J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA.
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25
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Hall D, Stong N, Lippa N, Pitman MJ, Pullman SL, Levy OA. Spasmodic Dysphonia in Hereditary Spastic Paraplegia Type 7. Mov Disord Clin Pract 2019; 5:221-222. [PMID: 30746405 DOI: 10.1002/mdc3.12580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- Devin Hall
- Department of Neurology Columbia University Medical Center New York NY
| | - Nicholas Stong
- Institute of Genomic Medicine Columbia University Medical Center New York NY
| | - Natalie Lippa
- Institute of Genomic Medicine Columbia University Medical Center New York NY
| | - Michael J Pitman
- Department of Otolaryngology Columbia University Medical Center New York NY
| | - Seth L Pullman
- Department of Neurology Columbia University Medical Center New York NY
| | - Oren A Levy
- Department of Neurology Columbia University Medical Center New York NY
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26
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Hayeck TJ, Stong N, Wolock CJ, Copeland B, Kamalakaran S, Goldstein DB, Allen AS. Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance. Am J Hum Genet 2019; 104:299-309. [PMID: 30686509 DOI: 10.1016/j.ajhg.2018.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/21/2018] [Indexed: 02/04/2023] Open
Abstract
Different parts of a gene can be of differential importance to development and health. This regional heterogeneity is also apparent in the distribution of disease-associated mutations, which often cluster in particular regions of disease-associated genes. The ability to precisely estimate functionally important sub-regions of genes will be key in correctly deciphering relationships between genetic variation and disease. Previous methods have had some success using standing human variation to characterize this variability in importance by measuring sub-regional intolerance, i.e., the depletion in functional variation from expectation within a given region of a gene. However, the ability to precisely estimate local intolerance was restricted by the fact that only information within a given sub-region is used, leading to instability in local estimates, especially for small regions. We show that borrowing information across regions using a Bayesian hierarchical model stabilizes estimates, leading to lower variability and improved predictive utility. Specifically, our approach more effectively identifies regions enriched for ClinVar pathogenic variants. We also identify significant correlations between sub-region intolerance and the distribution of pathogenic variation in disease-associated genes, with AUCs for classifying de novo missense variants in Online Mendelian Inheritance in Man (OMIM) genes of up to 0.86 using exonic sub-regions and 0.91 using sub-regions defined by protein domains. This result immediately suggests that considering the intolerance of regions in which variants are found may improve diagnostic interpretation. We also illustrate the utility of integrating regional intolerance into gene-level disease association tests with a study of known disease-associated genes for epileptic encephalopathy.
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27
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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.
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Shashi V, Schoch K, Spillmann R, Cope H, Tan QKG, Walley N, Pena L, McConkie-Rosell A, Jiang YH, Stong N, Need AC, Goldstein DB. A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative. Genet Med 2019; 21:161-172. [PMID: 29907797 PMCID: PMC6295275 DOI: 10.1038/s41436-018-0044-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES reanalysis resolving 10-15% of the ES negatives, further approaches are necessary to maximize diagnoses in these individuals. METHODS In 38 ES negative patients an individualized genomic-phenotypic approach was employed utilizing (1) phenotyping; (2) reanalyses of FASTQ files, with innovative bioinformatics; (3) targeted molecular testing; (4) genome sequencing (GS); and (5) conferring of clinical diagnoses when pathognomonic clinical findings occurred. RESULTS Certain and highly likely diagnoses were made in 18/38 (47%) individuals, including identifying two new developmental disorders. The majority of diagnoses (>70%) were due to our bioinformatics, phenotyping, and targeted testing identifying variants that were undetected or not prioritized on prior ES. GS diagnosed 3/18 individuals with structural variants not amenable to ES. Additionally, tentative diagnoses were made in 3 (8%), and in 5 individuals (13%) candidate genes were identified. Overall, diagnoses/potential leads were identified in 26/38 (68%). CONCLUSIONS Our comprehensive approach to ES negatives maximizes the ES and clinical data for both diagnoses and candidate gene identification, without GS in the majority. This iterative approach is cost-effective and is pertinent to the current conundrum of ES negatives.
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Affiliation(s)
- Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA.
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Queenie K-G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Loren Pena
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
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29
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Shashi V, Magiera MM, Klein D, Zaki M, Schoch K, Rudnik-Schöneborn S, Norman A, Lopes Abath Neto O, Dusl M, Yuan X, Bartesaghi L, De Marco P, Alfares AA, Marom R, Arold ST, Guzmán-Vega FJ, Pena LD, Smith EC, Steinlin M, Babiker MO, Mohassel P, Foley AR, Donkervoort S, Kaur R, Ghosh PS, Stanley V, Musaev D, Nava C, Mignot C, Keren B, Scala M, Tassano E, Picco P, Doneda P, Fiorillo C, Issa MY, Alassiri A, Alahmad A, Gerard A, Liu P, Yang Y, Ertl-Wagner B, Kranz PG, Wentzensen IM, Stucka R, Stong N, Allen AS, Goldstein DB, Schoser B, Rösler KM, Alfadhel M, Capra V, Chrast R, Strom TM, Kamsteeg EJ, Bönnemann CG, Gleeson JG, Martini R, Janke C, Senderek J. Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration. EMBO J 2018; 37:e100540. [PMID: 30420557 PMCID: PMC6276871 DOI: 10.15252/embj.2018100540] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [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: 08/22/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 11/09/2022] Open
Abstract
A set of glutamylases and deglutamylases controls levels of tubulin polyglutamylation, a prominent post-translational modification of neuronal microtubules. Defective tubulin polyglutamylation was first linked to neurodegeneration in the Purkinje cell degeneration (pcd) mouse, which lacks deglutamylase CCP1, displays massive cerebellar atrophy, and accumulates abnormally glutamylated tubulin in degenerating neurons. We found biallelic rare and damaging variants in the gene encoding CCP1 in 13 individuals with infantile-onset neurodegeneration and confirmed the absence of functional CCP1 along with dysregulated tubulin polyglutamylation. The human disease mainly affected the cerebellum, spinal motor neurons, and peripheral nerves. We also demonstrate previously unrecognized peripheral nerve and spinal motor neuron degeneration in pcd mice, which thus recapitulated key features of the human disease. Our findings link human neurodegeneration to tubulin polyglutamylation, entailing this post-translational modification as a potential target for drug development for neurodegenerative disorders.
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Affiliation(s)
- Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Maria M Magiera
- Institut Curie, CNRS UMR3348, PSL Research University, Orsay, France
- CNRS UMR3348, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Dennis Klein
- Department of Neurology, Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Maha Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Andrew Norman
- Department of Clinical Genetics, St. Michael's Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Osorio Lopes Abath Neto
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Marina Dusl
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
| | - Xidi Yuan
- Department of Neurology, Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Luca Bartesaghi
- Department of Neuroscience and Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Ahmed A Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francisco J Guzmán-Vega
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Loren Dm 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
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Maja Steinlin
- Division of Neuropaediatrics, Development and Rehabilitation, University Children's Hospital, Inselspital, University of Bern, Bern, Switzerland
| | | | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Rupleen Kaur
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Partha S Ghosh
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Damir Musaev
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Caroline Nava
- Department of Genetics, Assistance Publique des Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Universités, Inserm U1127, CNRS, UMR 7225, UPMC Univ Paris 06, Paris, France
| | - Cyril Mignot
- Department of Genetics, Assistance Publique des Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Universités, Inserm U1127, CNRS, UMR 7225, UPMC Univ Paris 06, Paris, France
| | - Boris Keren
- Department of Genetics, Assistance Publique des Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Universités, Inserm U1127, CNRS, UMR 7225, UPMC Univ Paris 06, Paris, France
| | | | | | - Paolo Picco
- IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Paola Doneda
- Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Chiara Fiorillo
- IRCCS Istituto Giannina Gaslini, Genova, Italy
- Università degli Studi di Genova, Genova, Italy
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ali Alassiri
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Alahmad
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Birgit Ertl-Wagner
- Department of Diagnostic Imaging, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | | | - Rolf Stucka
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Andrew S Allen
- Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Benedikt Schoser
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
| | - Kai M Rösler
- Neuromuscular Centre, University Department of Neurology, Inselspital, Bern, Switzerland
| | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | - Roman Chrast
- Department of Neuroscience and Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Donders Centre for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Rudolf Martini
- Department of Neurology, Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Carsten Janke
- Institut Curie, CNRS UMR3348, PSL Research University, Orsay, France
- CNRS UMR3348, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Jan Senderek
- Friedrich Baur Institute at the Department of Neurology, Friedrich Baur Institute, University Hospital, LMU Munich, Munich, Germany
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30
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Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM. De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLoS Genet 2018; 14:e1007671. [PMID: 30500825 PMCID: PMC6291162 DOI: 10.1371/journal.pgen.1007671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/12/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases. While many causes of developmental disabilities have been identified, a large number of affected children cannot be diagnosed despite extensive medical testing. Previously unknown genetic factors are likely to be the culprits in many of these cases. Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA. The affected individuals all have similar symptoms, including intellectual disability, speech delay (or no speech), and problems with motor skills like walking. In nearly all of these cases (10 of 11), the genetic change found in the child was not inherited from either parent. The locations and biological properties of these changes suggest that they are likely to disrupt the normal functions of RALA. Functional experiments also show that the genetic changes found in these individuals alter two key functions of RALA. Together, we have provided evidence that genetic changes in RALA can cause developmental disabilities. These results will allow doctors and researchers to identify additional children with the same condition, providing a clinical diagnosis to these families and leading to new research opportunities.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Matthew B. Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States of America
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Prchal
- Laboratory of NMR Spectroscopy, University of Chemistry and Technology, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent Medicine, Diagnostic and Research Unit for Rare Diseases, Charles University 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Dwight K. C. Yim
- Kaiser Permanente-Hawaii, Honolulu, HI, United States of America
| | - Zöe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Groupe de Recherche Clinique UPMC "Déficience Intellectuelle et Autisme", Paris, France
| | - Marlene Rio
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Assistance Publique-Hôpitaux de Paris, service de Génétique, Hôpital Necker-Enfants-Malades, Paris, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Alejandro D. Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America
| | | | | | | | - Patricia G. Wheeler
- Arnold Palmer Hospital, Division of Genetics, Orlando, FL, United States of America
| | - Lauren Brick
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Mariya Kozenko
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - James W. Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Memphis, TN, United States of America
- Le Bonheur Children’s Hospital, Memphis, TN, United States of America
| | - Yves Lacassie
- Division of Clinical Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States of America
- Department of Genetics, Children's Hospital, New Orleans, LA, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail:
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Mulhern MS, Stumpel C, Stong N, Brunner HG, Bier L, Lippa N, Riviello J, Rouhl RPW, Kempers M, Pfundt R, Stegmann APA, Kukolich MK, Telegrafi A, Lehman A, Lopez-Rangel E, Houcinat N, Barth M, den Hollander N, Hoffer MJV, Weckhuysen S, Roovers J, Djemie T, Barca D, Ceulemans B, Craiu D, Lemke JR, Korff C, Mefford HC, Meyers CT, Siegler Z, Hiatt SM, Cooper GM, Bebin EM, Snijders Blok L, Veenstra-Knol HE, Baugh EH, Brilstra EH, Volker-Touw CML, van Binsbergen E, Revah-Politi A, Pereira E, McBrian D, Pacault M, Isidor B, Le Caignec C, Gilbert-Dussardier B, Bilan F, Heinzen EL, Goldstein DB, Stevens SJC, Sands TT. NBEA: Developmental disease gene with early generalized epilepsy phenotypes. Ann Neurol 2018; 84:788-795. [PMID: 30269351 DOI: 10.1002/ana.25350] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/27/2018] [Accepted: 09/23/2018] [Indexed: 12/14/2022]
Abstract
NBEA is a candidate gene for autism, and de novo variants have been reported in neurodevelopmental disease (NDD) cohorts. However, NBEA has not been rigorously evaluated as a disease gene, and associated phenotypes have not been delineated. We identified 24 de novo NBEA variants in patients with NDD, establishing NBEA as an NDD gene. Most patients had epilepsy with onset in the first few years of life, often characterized by generalized seizure types, including myoclonic and atonic seizures. Our data show a broader phenotypic spectrum than previously described, including a myoclonic-astatic epilepsy-like phenotype in a subset of patients. Ann Neurol 2018;84:796-803.
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Affiliation(s)
- Maureen S Mulhern
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - Constance Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Nicholas Stong
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - Han G Brunner
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands.,Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Louise Bier
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - Natalie Lippa
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - James Riviello
- Department of Neurology, Columbia University Department of Neurology, New York, NY
| | - Rob P W Rouhl
- Department of Neurology, Maastricht University Medical Center, Maastricht, the Netherlands.,Academic Center for Epileptology, Kempenhaeghe/Maastricht University Medical Center, Maastricht, the Netherlands.,School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Marlies Kempers
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | | | | | - Anna Lehman
- Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elena Lopez-Rangel
- Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nada Houcinat
- University of Burgundy-Franche-Comté, UMR1231 GAD, INSERM, Dijon, France.,Dijon Bourgogne University Hospital Center, Rare Diseases Reference Center "Developmental Anomalies and Informational Syndromes," Genetic Center, FHU-TRANSLAD, Dijon, France
| | - Magalie Barth
- Department of Biochemistry and Genetics, Angers University Hospital Center, Angers, France
| | | | - Mariette J V Hoffer
- Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sarah Weckhuysen
- Center for Molecular Neurology, VIB, Neurogenetics Group, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | | | - Jolien Roovers
- Center for Molecular Neurology, VIB, Neurogenetics Group, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Tania Djemie
- Center for Molecular Neurology, VIB, Neurogenetics Group, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Diana Barca
- Pediatric Neurology Clinic, Al Obregia Hospital, Carol Davila University of Medicine, Bucharest, Romania
| | - Berten Ceulemans
- Department of Pediatric Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Dana Craiu
- Pediatric Neurology Clinic, Al Obregia Hospital, Carol Davila University of Medicine, Bucharest, Romania
| | - Johannes R Lemke
- Institute for Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Christian Korff
- Pediatric Neurology Unit, Child and Adolescent Department, University Hospitals, Geneva, Switzerland
| | | | | | - Zsuzsanna Siegler
- Bethesda Children's Hospital, Department of Neurology, Budapest, Hungary
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL
| | - Lot Snijders Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Evan H Baugh
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - Eva H Brilstra
- University Medical Center Utrecht, Department of Genetics, Utrecht, the Netherlands
| | | | - Ellen van Binsbergen
- University Medical Center Utrecht, Department of Genetics, Utrecht, the Netherlands
| | - Anya Revah-Politi
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - Elaine Pereira
- Division of Clinical Genetics, Department of Pediatrics, New York-Presbyterian Morgan Stanley Children's Hospital, Columbia University Medical Center, New York, NY
| | - Danielle McBrian
- Department of Neurology, Columbia University Department of Neurology, New York, NY
| | - Mathilde Pacault
- Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Bertrand Isidor
- Genetics Service, Nantes University Hospital Center, Nantes, France
| | | | - Brigitte Gilbert-Dussardier
- Genetics Service, Poitiers University Hospital Center, Poitiers, France.,University of Poitiers, EA3808 NEUVACOD, Poitiers, France
| | - Frederic Bilan
- Genetics Service, Poitiers University Hospital Center, Poitiers, France.,University of Poitiers, EA3808 NEUVACOD, Poitiers, France
| | - Erin L Heinzen
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
| | - David B Goldstein
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY
| | - Servi J C Stevens
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Tristan T Sands
- Columbia University Medical Center, Institute for Genomic Medicine, New York, NY.,Department of Neurology, Columbia University Department of Neurology, New York, NY
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32
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Tan QKG, Cope H, Spillmann RC, Stong N, Jiang YH, McDonald MT, Rothman JA, Butler MW, Frush DP, Lachman RS, Lee B, Bacino CA, Bonner MJ, McCall CM, Pendse AA, Walley N, Shashi V, Pena LDM. Further evidence for the involvement of EFL1 in a Shwachman-Diamond-like syndrome and expansion of the phenotypic features. Cold Spring Harb Mol Case Stud 2018; 4:a003046. [PMID: 29970384 PMCID: PMC6169826 DOI: 10.1101/mcs.a003046] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 03/24/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Recent evidence has implicated EFL1 in a phenotype overlapping Shwachman-Diamond syndrome (SDS), with the functional interplay between EFL1 and the previously known causative gene SBDS accounting for the similarity in clinical features. Relatively little is known about the phenotypes associated with pathogenic variants in the EFL1 gene, but the initial indication was that phenotypes may be more severe, when compared with SDS. We report a pediatric patient who presented with a metaphyseal dysplasia and was found to have biallelic variants in EFL1 on reanalysis of trio whole-exome sequencing data. The variant had not been initially reported because of the research laboratory's focus on de novo variants. Subsequent phenotyping revealed variability in her manifestations. Although her metaphyseal abnormalities were more severe than in the original reported cohort with EFL1 variants, the bone marrow abnormalities were generally mild, and there was equivocal evidence for pancreatic insufficiency. Despite the limited number of reported patients, variants in EFL1 appear to cause a broader spectrum of symptoms that overlap with those seen in SDS. Our report adds to the evidence of EFL1 being associated with an SDS-like phenotype and provides information adding to our understanding of the phenotypic variability of this disorder. Our report also highlights the value of exome data reanalysis when a diagnosis is not initially apparent.
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Affiliation(s)
- Queenie K-G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jennifer A Rothman
- Department of Pediatrics, Division of Hematology-Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Megan W Butler
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Donald P Frush
- Department of Radiology, Division of Pediatric Radiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Ralph S Lachman
- Cedars-Sinai Medical Center, International Skeletal Dysplasia Registry, Los Angeles, California 90048, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Melanie J Bonner
- Department of Psychiatry and Behavioral Sciences, Division of Child and Family Mental Health and Developmental Neuroscience, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chad M McCall
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Avani A Pendse
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Loren D M Pena
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
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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
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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 LDM. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:245-260. [PMID: 30057031 PMCID: PMC6081494 DOI: 10.1016/j.ajhg.2018.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 05/15/2018] [Accepted: 07/02/2018] [Indexed: 12/23/2022] Open
Abstract
Interferon regulatory factor 2 binding protein-like (IRF2BPL) encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals who carry damaging heterozygous variants in IRF2BPL and are affected with neurological symptoms. Five individuals who carry IRF2BPL nonsense variants resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The IRF2BPL bioinformatics signature based on population genomics is consistent with a gene that is intolerant to variation. We show that the fruit-fly IRF2BPL ortholog, called pits (protein interacting with Ttk69 and Sin3A), is broadly detected, including in the nervous system. Complete loss of pits is lethal early in development, whereas partial knockdown with RNA interference in neurons leads to neurodegeneration, revealing a requirement for this gene in proper neuronal function and maintenance. The identified IRF2BPL nonsense variants behave as severe loss-of-function alleles in this model organism, and ectopic expression of the missense variants leads to a range of phenotypes. Taken together, our results show that IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary Kay Koenig
- Division of Child & Adolescent Neurology, Department of Pediatrics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Julián A Martínez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Child and Adolescent Psychiatry, Resnick Neuropsychiatric Hospital, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew Herzog
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Agnes H Chen
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Patricia I Dickson
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Henry J Lin
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Moin U Vera
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Noriko Salamon
- Department of Radiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John M Graham
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Damara Ortiz
- Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Elena Infante
- Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Wouter Steyaert
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bart Dermaut
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bruce Poppe
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gail Spiridigliozzi
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Lark
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kacie Riley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dwight D Koeberl
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, 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
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, 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; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Loren D M Pena
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.
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Wattacheril J, Shea PR, Mohammad S, Behling C, Aggarwal V, Wilson LA, Yates KP, Ito J, Fishbein M, Stong N, Lavine JE, Goldstein DB. Exome sequencing of an adolescent with nonalcoholic fatty liver disease identifies a clinically actionable case of Wilson disease. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003087. [PMID: 30026388 PMCID: PMC6169823 DOI: 10.1101/mcs.a003087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/06/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022] Open
Abstract
Diagnostic whole-exome sequencing has proven highly successful in a range of rare diseases, particularly early-onset genetic conditions. In more common conditions, however, exome sequencing for diagnostic purposes remains the exception. Here we describe a patient initially diagnosed with a common, complex liver disease, nonalcoholic fatty liver disease (NAFLD), who was determined to have Wilson disease (WD) upon research-related exome sequencing. The patient presented as a 14.5-yr-old adolescent with chronically elevated aminotransferases, normal ceruloplasmin, and histologic examination consistent with NAFLD with advanced fibrosis. He was enrolled in a large longitudinal study of patients with NAFLD and was found to have WD by exome sequencing performed 4 yr later. This new diagnosis, confirmed clinically by 24 h urine copper quantification, led to a change in the therapy from lifestyle counseling to directed treatment with d-penicillamine, a copper chelating agent. In this case, the likelihood of making the correct diagnosis and thereby choosing the appropriate treatment was increased by exome sequencing and careful interpretation. This example illustrates the utility of exome sequencing diagnostically in more common conditions not currently considered as targets for genome-wide evaluation and adds to a growing body of evidence that patients diagnosed with more common conditions often in fact have rarer genetically determined syndromes that have escaped clinical detection.
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Affiliation(s)
- Julia Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, New York 10032, USA
| | - Patrick R Shea
- Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Saeed Mohammad
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Cynthia Behling
- Department of Pathology, University of California, San Diego, La Jolla, California 90293, USA
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Laura A Wilson
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Katherine P Yates
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joy Ito
- Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Mark Fishbein
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann and Robert Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Joel E Lavine
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, Children's Hospital of New York, New York, New York 10032, USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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Liu N, Schoch K, Luo X, Pena LDM, Bhavana VH, Kukolich MK, Stringer S, Powis Z, Radtke K, Mroske C, Deak KL, McDonald MT, McConkie-Rosell A, Markert ML, Kranz PG, Stong N, Need AC, Bick D, Amaral MD, Worthey EA, Levy S, Wangler MF, Bellen HJ, Shashi V, Yamamoto S. Functional variants in TBX2 are associated with a syndromic cardiovascular and skeletal developmental disorder. Hum Mol Genet 2018; 27:2454-2465. [PMID: 29726930 PMCID: PMC6030957 DOI: 10.1093/hmg/ddy146] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/07/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
The 17 genes of the T-box family are transcriptional regulators that are involved in all stages of embryonic development, including craniofacial, brain, heart, skeleton and immune system. Malformation syndromes have been linked to many of the T-box genes. For example, haploinsufficiency of TBX1 is responsible for many structural malformations in DiGeorge syndrome caused by a chromosome 22q11.2 deletion. We report four individuals with an overlapping spectrum of craniofacial dysmorphisms, cardiac anomalies, skeletal malformations, immune deficiency, endocrine abnormalities and developmental impairments, reminiscent of DiGeorge syndrome, who are heterozygotes for TBX2 variants. The p.R20Q variant is shared by three affected family members in an autosomal dominant manner; the fourth unrelated individual has a de novo p.R305H mutation. Bioinformatics analyses indicate that these variants are rare and predict them to be damaging. In vitro transcriptional assays in cultured cells show that both variants result in reduced transcriptional repressor activity of TBX2. We also show that the variants result in reduced protein levels of TBX2. Heterologous over-expression studies in Drosophila demonstrate that both p.R20Q and p.R305H function as partial loss-of-function alleles. Hence, these and other data suggest that TBX2 is a novel candidate gene for a new multisystem malformation disorder.
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Affiliation(s)
- Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Loren D M Pena
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | | | - Mary K Kukolich
- Department of Genetics, Cook Children’s Hospital, Fort Worth, TX, USA
| | - Sarah Stringer
- Department of Genetics, Cook Children’s Hospital, Fort Worth, TX, USA
| | - Zöe Powis
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Kelly Radtke
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Kristen L Deak
- Department of Pathology, Duke University, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - M Louise Markert
- Division of Allergy and Immunology, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Houston, TX, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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Pena LDM, Jiang YH, Schoch K, Spillmann RC, Walley N, Stong N, Horn SR, Sullivan JA, McConkie-Rosell A, Kansagra S, Smith EC, El-Dairi M, Bellet J, Ann Keels M, Jasien J, Kranz PG, Noel R, Nagaraj SK, Lark RK, Wechsler DSG, del Gaudio D, Leung ML, Hendon LG, Parker CC, Jones KL, Goldstein DB, Shashi V. Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. Genet Med 2018; 20:464-469. [PMID: 28914269 PMCID: PMC5851806 DOI: 10.1038/gim.2017.128] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 05/16/2017] [Accepted: 06/16/2017] [Indexed: 12/01/2022] Open
Abstract
PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the noncoding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity, and magnetic resonance image changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, probably missed owing to failure of alignment.ConclusionThese cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses.
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Affiliation(s)
- Loren DM Pena
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Rebecca C. Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University, New York, N.Y
| | | | - Jennifer A. Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
| | - Sujay Kansagra
- Division of Neurology, Department of Pediatrics, Duke University Medical Center
| | - Edward C. Smith
- Division of Neurology, Department of Pediatrics, Duke University Medical Center
| | - Mays El-Dairi
- Department of Ophthalmology, Duke University Medical Center
| | - Jane Bellet
- Departments of Dermatology and Pediatrics, Duke University Medical Center
| | - Martha Ann Keels
- Departments of Pediatrics and Surgery, Duke University Medical Center
| | - Joan Jasien
- Division of Neurology, Department of Pediatrics, Duke University Medical Center
| | - Peter G. Kranz
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center
| | - Richard Noel
- Division of Gastroenterology, Department of Pediatrics, Duke University Medical Center
| | - Shashi K. Nagaraj
- Division of Pediatric Nephrology, Department of Pediatrics, Duke University Medical Center
| | - Robert K. Lark
- Department of Orthopedic Surgery, Duke University Medical Center
| | - Daniel SG Wechsler
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Duke University Medical Center
| | | | - Marco L. Leung
- Department of Human Genetics, University of Chicago, Chicago Ill
| | - Laura G. Hendon
- Division of Maternal Fetal Medicine, University of Mississippi Medical Center, Jackson, Miss
| | - Collette C. Parker
- Division of Child Neurology, Department of Pediatrics, University of Mississippi Medical Center
| | - Kelly L. Jones
- Division of Medical Genetics, Department of Pediatrics, University of Mississippi Medical Center
| | | | | | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center
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Rotemberg V, Garzon M, Lauren C, Iglesias A, Brachio SS, Aggarwal V, Stong N, Goldstein DB, Diacovo T. A Novel Mutation in Junctional Plakoglobin Causing Lethal Congenital Epidermolysis Bullosa. J Pediatr 2017; 191:266-269.e1. [PMID: 29173316 DOI: 10.1016/j.jpeds.2017.08.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/20/2017] [Accepted: 08/14/2017] [Indexed: 01/14/2023]
Abstract
We report a case of neonatal generalized erythema and epidermolysis resulting from a novel mutation in the junctional plakoglobin gene causing truncation of the plakoglobin protein. Expedited genetic testing enabled diagnosis while the patient was in the neonatal intensive care unit, providing valuable information for the clinicians and family.
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Affiliation(s)
| | - Maria Garzon
- Department of Dermatology, Columbia University, New York, NY; Department of Pediatrics, Columbia University, New York, NY
| | - Christine Lauren
- Department of Dermatology, Columbia University, New York, NY; Department of Pediatrics, Columbia University, New York, NY
| | - Alejandro Iglesias
- Department of Pediatrics, Columbia University, New York, NY; Department of Clinical Genetics, Columbia University, New York, NY
| | | | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY
| | - David B Goldstein
- Department of Genetics and Development, Columbia University, New York, NY
| | - Thomas Diacovo
- Department of Pediatrics, Columbia University, New York, NY; Department of Pathology and Cell Biology, Columbia University, New York, NY
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39
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Myers CT, Stong N, Mountier EI, Helbig KL, Freytag S, Sullivan JE, Ben Zeev B, Nissenkorn A, Tzadok M, Heimer G, Shinde DN, Rezazadeh A, Regan BM, Oliver KL, Ernst ME, Lippa NC, Mulhern MS, Ren Z, Poduri A, Andrade DM, Bird LM, Bahlo M, Berkovic SF, Lowenstein DH, Scheffer IE, Sadleir LG, Goldstein DB, Mefford HC, Heinzen EL. De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures. Am J Hum Genet 2017; 101:516-524. [PMID: 28942967 DOI: 10.1016/j.ajhg.2017.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 06/21/2017] [Accepted: 08/10/2017] [Indexed: 12/30/2022] Open
Abstract
Exome sequencing has readily enabled the discovery of the genetic mutations responsible for a wide range of diseases. This success has been particularly remarkable in the severe epilepsies and other neurodevelopmental diseases for which rare, often de novo, mutations play a significant role in disease risk. Despite significant progress, the high genetic heterogeneity of these disorders often requires large sample sizes to identify a critical mass of individuals with disease-causing mutations in a single gene. By pooling genetic findings across multiple studies, we have identified six individuals with severe developmental delay (6/6), refractory seizures (5/6), and similar dysmorphic features (3/6), each harboring a de novo mutation in PPP3CA. PPP3CA encodes the alpha isoform of a subunit of calcineurin. Calcineurin encodes a calcium- and calmodulin-dependent serine/threonine protein phosphatase that plays a role in a wide range of biological processes, including being a key regulator of synaptic vesicle recycling at nerve terminals. Five individuals with de novo PPP3CA mutations were identified among 4,760 trio probands with neurodevelopmental diseases; this is highly unlikely to occur by chance (p = 1.2 × 10-8) given the size and mutability of the gene. Additionally, a sixth individual with a de novo mutation in PPP3CA was connected to this study through GeneMatcher. Based on these findings, we securely implicate PPP3CA in early-onset refractory epilepsy and further support the emerging role for synaptic dysregulation in epilepsy.
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Affiliation(s)
- Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Emily I Mountier
- Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand
| | | | - Saskia Freytag
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Joseph E Sullivan
- Department of Neurology & Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bruria Ben Zeev
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Andreea Nissenkorn
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michal Tzadok
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gali Heimer
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Arezoo Rezazadeh
- Division of Neurology, Epilepsy Genetics Research Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Brigid M Regan
- Division of Neurology, Epilepsy Genetics Research Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Karen L Oliver
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Michelle E Ernst
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Natalie C Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Maureen S Mulhern
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Danielle M Andrade
- Division of Neurology, Epilepsy Genetics Research Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA; Rady Children's Hospital, San Diego, CA 92037, USA
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Daniel H Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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Schoch K, Meng L, Szelinger S, Bearden DR, Stray-Pedersen A, Busk OL, Stong N, Liston E, Cohn RD, Scaglia F, Rosenfeld JA, Tarpinian J, Skraban CM, Deardorff MA, Friedman JN, Akdemir ZC, Walley N, Mikati MA, Kranz PG, Jasien J, McConkie-Rosell A, McDonald M, Wechsler SB, Freemark M, Kansagra S, Freedman S, Bali D, Millan F, Bale S, Nelson SF, Lee H, Dorrani N, Goldstein DB, Xiao R, Yang Y, Posey JE, Martinez-Agosto JA, Lupski JR, Wangler MF, Shashi V. A Recurrent De Novo Variant in NACC1 Causes a Syndrome Characterized by Infantile Epilepsy, Cataracts, and Profound Developmental Delay. Am J Hum Genet 2017; 100:343-351. [PMID: 28132692 PMCID: PMC5294886 DOI: 10.1016/j.ajhg.2016.12.013] [Citation(s) in RCA: 30] [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: 11/15/2016] [Accepted: 12/22/2016] [Indexed: 02/08/2023] Open
Abstract
Whole-exome sequencing (WES) has increasingly enabled new pathogenic gene variant identification for undiagnosed neurodevelopmental disorders and provided insights into both gene function and disease biology. Here, we describe seven children with a neurodevelopmental disorder characterized by microcephaly, profound developmental delays and/or intellectual disability, cataracts, severe epilepsy including infantile spasms, irritability, failure to thrive, and stereotypic hand movements. Brain imaging in these individuals reveals delay in myelination and cerebral atrophy. We observe an identical recurrent de novo heterozygous c.892C>T (p.Arg298Trp) variant in the nucleus accumbens associated 1 (NACC1) gene in seven affected individuals. One of the seven individuals is mosaic for this variant. NACC1 encodes a transcriptional repressor implicated in gene expression and has not previously been associated with germline disorders. The probability of finding the same missense NACC1 variant by chance in 7 out of 17,228 individuals who underwent WES for diagnoses of neurodevelopmental phenotypes is extremely small and achieves genome-wide significance (p = 1.25 × 10-14). Selective constraint against missense variants in NACC1 makes this excess of an identical missense variant in all seven individuals more remarkable. Our findings are consistent with a germline recurrent mutational hotspot associated with an allele-specific neurodevelopmental phenotype in NACC1.
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Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Szabolcs Szelinger
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David R Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY 14627, USA
| | - Asbjorg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Oslo University Hospital, 0424 Oslo, Norway
| | - Oyvind L Busk
- Section of Medical Genetics, Department of Laboratory Medicine, Telemark Hospital, 3710 Skien, Norway
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Eriskay Liston
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ronald D Cohn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Tarpinian
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeremy N Friedman
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Zeynep Coban Akdemir
- Norwegian National Unit for Newborn Screening, Oslo University Hospital, 0424 Oslo, Norway
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Stephanie Burns Wechsler
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA; Division of Cardiology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Michael Freemark
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | | | - Deeksha Bali
- Department of Pathology, Duke Health, Durham, NC 27710, USA
| | | | | | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Naghmeh Dorrani
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julian A Martinez-Agosto
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA.
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Shashi V, Pena LDM, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin HM, Cho M, Stong N, Hickey SE, Shuss CM, Freemark MS, Bellet JS, Keels MA, Bonner MJ, El-Dairi M, Butler M, Kranz PG, Stumpel CTRM, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki MI, Hoischen A, Need AC, Goldstein DB, Kortüm F. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet 2017; 100:179. [PMID: 28061364 DOI: 10.1016/j.ajhg.2016.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG, Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MCV, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernstein JA, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brush M, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Mashid AS, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, 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, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Rodan LH, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tift CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Worthe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet 2017; 100:128-137. [PMID: 28017372 PMCID: PMC5223093 DOI: 10.1016/j.ajhg.2016.11.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [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: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.
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Shashi V, Pena LD, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin HM, Cho M, Stong N, Hickey SE, Shuss CM, Freemark MS, Bellet JS, Keels MA, Bonner MJ, El-Dairi M, Butler M, Kranz PG, Stumpel CT, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki MI, Hoischen A, Need AC, Goldstein DB, Kortüm F, Bacino A, Lee BH, Balasubramanyam A, Burrage LC, Clark GD, Craigen WJ, Dhar SU, Emrick LT, Graham BH, Jain M, Lalani SR, Lewis RA, Moretti PM, Nicholas SK, Orange JS, Posey JE, Potocki L, Rosenfeld JA, Scott DA, Hanchard NA, Alyssa TA, Mercedes AE, Mashid AS, Bellen HJ, Yamamoto S, Wangler MF, Westerfield M, Postlethwait JH, Eng CM, Yang Y, Muzny DM, Ward PA, Ramoni RB, McCray AT, Kohane IS, Holm IA, Might M, Mazur P, Splinter K, Esteves C, Shashi V, Jiang YH, Pena LD, McConkie-Rosell A, Schoch K, Spillmann RC, Sullivan JA, Walley NM, Goldstein DB, Stong N, Beggs AH, Loscalzo J, MacRae CA, Silverman EK, Stoler JM, Sweetser DA, Maas RL, Krier JB, Rodan LH, Walsh CA, Cooper CM, Pallais JC, Donnell-Fink LA, Krieg EL, Lincoln SA, Briere LC, Jacob HJ, Worthey EA, Lazar J, Strong KA, Handley LH, Newberry JS, Bick DP, Schroeder MC, Brown DM, Birch CL, Levy SE, Boone BE, Dorset DC, Jones AL, Manolio TA, Mulvihill JJ, Wise AL, Dayal JG, Eckstein DJ, Krasnewich DM, Loomis CR, Mamounas LA, Iglesias B, Martin C, Koeller DM, Metz TO, Ashley EA, Fisher PG, Bernstein JA, Wheeler MT, Zornio PA, Waggott DM, Dries AM, Kohler JN, Dipple KM, Nelson SF, Palmer CG, Vilain E, Allard P, Dell Angelica EC, Lee H, Sinsheimer JS, Papp JC, Dorrani N, Herzog MR, Barseghyan H, Adams DR, Adams CJ, Burke EA, Chao KR, Davids M, Draper DD, Estwick T, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Gordon MG, Groden CA, Gropman AL, Hackbarth ME, Hardee I, Johnston JM, Koehler AE, Latham L, Latour YL, Lau CYC, Lee PR, Levy DJ, Liebendorder AP, Macnamara EF, Maduro VV, Malicdan MV, Markello TC, McCarty AJ, Murphy JL, Nehrebecky ME, Novacic D, Pusey BN, Sadozai S, Schaffer KE, Sharma P, Soldatos AG, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Valivullah ZM, Wahl CE, Warburton M, Weech AA, Wolfe LA, Yu G, Hamid R, Newman JH, Phillips JA, Cogan JD. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet 2016; 99:991-999. [PMID: 27693232 PMCID: PMC5065681 DOI: 10.1016/j.ajhg.2016.08.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [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: 05/02/2016] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The ASXL genes (ASXL1, ASXL2, and ASXL3) participate in body patterning during embryogenesis and encode proteins involved in epigenetic regulation and assembly of transcription factors to specific genomic loci. Germline de novo truncating variants in ASXL1 and ASXL3 have been respectively implicated in causing Bohring-Opitz and Bainbridge-Ropers syndromes, which result in overlapping features of severe intellectual disability and dysmorphic features. ASXL2 has not yet been associated with a human Mendelian disorder. In this study, we performed whole-exome sequencing in six unrelated probands with developmental delay, macrocephaly, and dysmorphic features. All six had de novo truncating variants in ASXL2. A careful review enabled the recognition of a specific phenotype consisting of macrocephaly, prominent eyes, arched eyebrows, hypertelorism, a glabellar nevus flammeus, neonatal feeding difficulties, hypotonia, and developmental disabilities. Although overlapping features with Bohring-Opitz and Bainbridge-Ropers syndromes exist, features that distinguish the ASXL2-associated condition from ASXL1- and ASXL3-related disorders are macrocephaly, absence of growth retardation, and more variability in the degree of intellectual disabilities. We were also able to demonstrate with mRNA studies that these variants are likely to exert a dominant-negative effect, given that both alleles are expressed in blood and the mutated ASXL2 transcripts escape nonsense-mediated decay. In conclusion, de novo truncating variants in ASXL2 underlie a neurodevelopmental syndrome with a clinically recognizable phenotype. This report expands the germline disorders that are linked to the ASXL genes.
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Nelson DM, Jaber-Hijazi F, Cole JJ, Robertson NA, Pawlikowski JS, Norris KT, Criscione SW, Pchelintsev NA, Piscitello D, Stong N, Rai TS, McBryan T, Otte GL, Nixon C, Clark W, Riethman H, Wu H, Schotta G, Garcia BA, Neretti N, Baird DM, Berger SL, Adams PD. Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biol 2016; 17:158. [PMID: 27457071 PMCID: PMC4960804 DOI: 10.1186/s13059-016-1017-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 04/06/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although H4K20me3 abundance increases during cellular senescence, a stable proliferation arrest and tumor suppressor process, triggered by diverse molecular cues, including activated oncogenes. Here, we investigate the function of H4K20me3 in senescence and tumor suppression. RESULTS Using immunofluorescence and ChIP-seq we determine the distribution of H4K20me3 in proliferating and senescent human cells. Altered H4K20me3 in senescence is coupled to H4K16ac and DNA methylation changes in senescence. In senescent cells, H4K20me3 is especially enriched at DNA sequences contained within specialized domains of senescence-associated heterochromatin foci (SAHF), as well as specific families of non-genic and genic repeats. Altered H4K20me3 does not correlate strongly with changes in gene expression between proliferating and senescent cells; however, in senescent cells, but not proliferating cells, H4K20me3 enrichment at gene bodies correlates inversely with gene expression, reflecting de novo accumulation of H4K20me3 at repressed genes in senescent cells, including at genes also repressed in proliferating cells. Although elevated SUV420H2 upregulates H4K20me3, this does not accelerate senescence of primary human cells. However, elevated SUV420H2/H4K20me3 reinforces oncogene-induced senescence-associated proliferation arrest and slows tumorigenesis in vivo. CONCLUSIONS These results corroborate a role for chromatin in underpinning the senescence phenotype but do not support a major role for H4K20me3 in initiation of senescence. Rather, we speculate that H4K20me3 plays a role in heterochromatinization and stabilization of the epigenome and genome of pre-malignant, oncogene-expressing senescent cells, thereby suppressing epigenetic and genetic instability and contributing to long-term senescence-mediated tumor suppression.
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Affiliation(s)
- David M. Nelson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Farah Jaber-Hijazi
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - John J. Cole
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Neil A. Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Jeffrey S. Pawlikowski
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Kevin T. Norris
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903 USA
| | - Nikolay A. Pchelintsev
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Desiree Piscitello
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | | | - Taranjit Singh Rai
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, PA1 2BE UK
| | - Tony McBryan
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Gabriel L. Otte
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Colin Nixon
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - William Clark
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | | | - Hong Wu
- Fox Chase Cancer Center, Philadelphia, PA 19111 USA
| | - Gunnar Schotta
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried, Germany
| | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903 USA
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Shelley L. Berger
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Peter D. Adams
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
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45
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Tutton S, Azzam GA, Stong N, Vladimirova O, Wiedmer A, Monteith JA, Beishline K, Wang Z, Deng Z, Riethman H, McMahon SB, Murphy M, Lieberman PM. Subtelomeric p53 binding prevents accumulation of DNA damage at human telomeres. EMBO J 2015; 35:193-207. [PMID: 26658110 DOI: 10.15252/embj.201490880] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 11/11/2015] [Indexed: 11/09/2022] Open
Abstract
Telomeres and tumor suppressor protein TP53 (p53) function in genome protection, but a direct role of p53 at telomeres has not yet been described. Here, we have identified non-canonical p53-binding sites within the human subtelomeres that suppress the accumulation of DNA damage at telomeric repeat DNA. These non-canonical subtelomeric p53-binding sites conferred transcription enhancer-like functions that include an increase in local histone H3K9 and H3K27 acetylation and stimulation of subtelomeric transcripts, including telomere repeat-containing RNA (TERRA). p53 suppressed formation of telomere-associated γH2AX and prevented telomere DNA degradation in response to DNA damage stress. Our findings indicate that p53 provides a direct chromatin-associated protection to human telomeres, as well as other fragile genomic sites. We propose that p53-associated chromatin modifications enhance local DNA repair or protection to provide a previously unrecognized tumor suppressor function of p53.
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Affiliation(s)
| | | | | | | | | | - Jessica A Monteith
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Zhuo Wang
- The Wistar Institute, Philadelphia, PA, USA
| | - Zhong Deng
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Steven B McMahon
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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46
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Stong N, Deng Z, Gupta R, Hu S, Paul S, Weiner AK, Eichler EE, Graves T, Fronick CC, Courtney L, Wilson RK, Lieberman PM, Davuluri RV, Riethman H. Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res 2014; 24:1039-50. [PMID: 24676094 PMCID: PMC4032850 DOI: 10.1101/gr.166983.113] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/26/2014] [Indexed: 12/25/2022]
Abstract
Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling telomere-adjacent gaps using clone-based resources. A bioinformatic pipeline incorporating multiread mapping for annotation of the updated assemblies using short-read data sets was developed and implemented. Annotation of subtelomeric sequence features as well as mapping of CTCF and cohesin binding sites using ChIP-seq data sets from multiple human cell types confirmed that CTCF and cohesin bind within 3 kb of the start of terminal repeat tracts at many, but not all, subtelomeres. CTCF and cohesin co-occupancy were also enriched near internal telomere-like sequence (ITS) islands and the nonterminal boundaries of subtelomere repeat elements (SREs) in transformed lymphoblastoid cell lines (LCLs) and human embryonic stem cell (ES) lines, but were not significantly enriched in the primary fibroblast IMR90 cell line. Subtelomeric CTCF and cohesin sites predicted by ChIP-seq using our bioinformatics pipeline (but not predicted when only uniquely mapping reads were considered) were consistently validated by ChIP-qPCR. The colocalized CTCF and cohesin sites in SRE regions are candidates for mediating long-range chromatin interactions in the transcript-rich SRE region. A public browser for the integrated display of short-read sequence-based annotations relative to key subtelomere features such as the start of each terminal repeat tract, SRE identity and organization, and subtelomeric gene models was established.
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Affiliation(s)
- Nicholas Stong
- Graduate Group in Genomics and Computational Biology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Zhong Deng
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Ravi Gupta
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Sufen Hu
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Shiela Paul
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Laura Courtney
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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