1
|
Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Hwang JP, Bhamidipati SV, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. CELL GENOMICS 2024; 4:100590. [PMID: 38908378 PMCID: PMC11293582 DOI: 10.1016/j.xgen.2024.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/27/2023] [Accepted: 05/31/2024] [Indexed: 06/24/2024]
Abstract
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.
Collapse
Affiliation(s)
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Ming Yin Lun
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | | | - KyungHee Park
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Wolfram Höps
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Eva Benito
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Medhat Mahmoud
- 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
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James Paul Hwang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sravya V Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- 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
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY 10013, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics and Genomics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fritz J Sedlazeck
- 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 Computer Science, Rice University, Houston TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Neurology and Developmental Neuroscience, Department of Pediatrics, 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; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- 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
| | | |
Collapse
|
2
|
Summers J, Baribeau D, Perlman P, Hoang N, Cui S, Krakowski A, Ambrozewicz P, Ho A, Selvanayagam T, Sándor-Bajusz KA, Palad K, Patel N, McGaughey S, Gallagher L, Scherer SW, Szatmari P, Vorstman J. An integrated clinical approach to children at genetic risk for neurodevelopmental and psychiatric conditions: interdisciplinary collaboration and research infrastructure. J Neurodev Disord 2024; 16:37. [PMID: 38970057 PMCID: PMC11229023 DOI: 10.1186/s11689-024-09552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 06/04/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND A sizeable proportion of pathogenic genetic variants identified in young children tested for congenital differences are associated with neurodevelopmental psychiatric disorders (NPD). In this growing group, a genetic diagnosis often precedes the emergence of diagnosable developmental concerns. Here, we describe DAGSY (Developmental Assessment of Genetically Susceptible Youth), a novel interdisciplinary 'genetic-diagnosis-first' clinic integrating psychiatric, psychological and genetic expertise, and report our first observations and feedback from families and referring clinicians. METHODS We retrieved data on referral sources and indications, genetic and NPD diagnoses and recommendations for children seen at DAGSY between 2018 and 2022. Through a survey, we obtained feedback from twenty families and eleven referring clinicians. RESULTS 159 children (mean age 10.2 years, 57.2% males) completed an interdisciplinary (psychiatry, psychology, genetic counselling) DAGSY assessment during this period. Of these, 69.8% had a pathogenic microdeletion or microduplication, 21.5% a sequence-level variant, 4.4% a chromosomal disorder, and 4.4% a variant of unknown significance with emerging evidence of pathogenicity. One in four children did not have a prior NPD diagnosis, and referral to DAGSY was motivated by their genetic vulnerability alone. Following assessment, 76.7% received at least one new NPD diagnosis, most frequently intellectual disability (24.5%), anxiety (20.7%), autism spectrum (18.9%) and specific learning (16.4%) disorder. Both families and clinicians responding to our survey expressed satisfaction, but also highlighted some areas for potential improvement. CONCLUSIONS DAGSY addresses an unmet clinical need for children identified with genetic variants that confer increased vulnerability for NPD and provides a crucial platform for research in this area. DAGSY can serve as a model for interdisciplinary clinics integrating child psychiatry, psychology and genetics, addressing both clinical and research needs for this emerging population.
Collapse
Affiliation(s)
- Jane Summers
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Danielle Baribeau
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Polina Perlman
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ny Hoang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sunny Cui
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Aneta Krakowski
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Patricia Ambrozewicz
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ariel Ho
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Thanuja Selvanayagam
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kinga A Sándor-Bajusz
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Katrina Palad
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nishi Patel
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah McGaughey
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Louise Gallagher
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Jacob Vorstman
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada.
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada.
- Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street Room 12.9702, Toronto, ON, M5G 0A4, Canada.
| |
Collapse
|
3
|
Henis M, Rücker T, Scharrenberg R, Richter M, Baltussen L, Hong S, Meka DP, Schwanke B, Neelagandan N, Daaboul D, Murtaza N, Krisp C, Harder S, Schlüter H, Kneussel M, Hermans-Borgmeyer I, de Wit J, Singh KK, Duncan KE, de Anda FC. The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation. SCIENCE ADVANCES 2024; 10:eadf7001. [PMID: 38608030 PMCID: PMC11014455 DOI: 10.1126/sciadv.adf7001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, genetics, and translation assays in cultured cells and mouse brain to reveal altered translation mediated by loss of the kinase TAOK2 in 16p11.2 deletion models. We show that TAOK2 associates with the translational machinery and functions as a translational brake by phosphorylating eukaryotic elongation factor 2 (eEF2). Previously, all signal-mediated regulation of translation elongation via eEF2 phosphorylation was believed to be mediated by a single kinase, eEF2K. However, we show that TAOK2 can directly phosphorylate eEF2 on the same regulatory site, but functions independently of eEF2K signaling. Collectively, our results reveal an eEF2K-independent signaling pathway for control of translation elongation and suggest altered translation as a molecular component in the etiology of some forms of ASD.
Collapse
Affiliation(s)
- Melad Henis
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, New Valley University, 72511 El-Kharga, Egypt
| | - Tabitha Rücker
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Robin Scharrenberg
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Melanie Richter
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Lucas Baltussen
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Shuai Hong
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Durga Praveen Meka
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Birgit Schwanke
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Nagammal Neelagandan
- Neuronal Translational Control Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Danie Daaboul
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Nadeem Murtaza
- Krembil Research Institute, Donald K. Johnson Eye Institute, University Health Network, 60 Leonard Ave, Toronto, Ontario M5T 0S8, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario L8S 4A9, Canada
| | - Christoph Krisp
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Sönke Harder
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Matthias Kneussel
- Institute of Neurogenetics, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf (UKE), 20251 Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- Transgenic Service Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
| | - Joris de Wit
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Karun K. Singh
- Krembil Research Institute, Donald K. Johnson Eye Institute, University Health Network, 60 Leonard Ave, Toronto, Ontario M5T 0S8, Canada
- Faculty of Medicine, University of Toronto, Medical Sciences Building, 1 King's College Cir, Toronto, Ontario M5S 1 A8, Canada
| | - Kent E. Duncan
- Neuronal Translational Control Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Froylan Calderón de Anda
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| |
Collapse
|
4
|
Al-Sarraj Y, Taha RZ, Al-Dous E, Ahram D, Abbasi S, Abuazab E, Shaath H, Habbab W, Errafii K, Bejaoui Y, AlMotawa M, Khattab N, Aqel YA, Shalaby KE, Al-Ansari A, Kambouris M, Abouzohri A, Ghazal I, Tolfat M, Alshaban F, El-Shanti H, Albagha OME. The genetic landscape of autism spectrum disorder in the Middle Eastern population. Front Genet 2024; 15:1363849. [PMID: 38572415 PMCID: PMC10987745 DOI: 10.3389/fgene.2024.1363849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction: Autism spectrum disorder (ASD) is characterized by aberrations in social interaction and communication associated with repetitive behaviors and interests, with strong clinical heterogeneity. Genetic factors play an important role in ASD, but about 75% of ASD cases have an undetermined genetic risk. Methods: We extensively investigated an ASD cohort made of 102 families from the Middle Eastern population of Qatar. First, we investigated the copy number variations (CNV) contribution using genome-wide SNP arrays. Next, we employed Next Generation Sequencing (NGS) to identify de novo or inherited variants contributing to the ASD etiology and its associated comorbid conditions in families with complete trios (affected child and the parents). Results: Our analysis revealed 16 CNV regions located in genomic regions implicated in ASD. The analysis of the 88 ASD cases identified 41 genes in 39 ASD subjects with de novo (n = 24) or inherited variants (n = 22). We identified three novel de novo variants in new candidate genes for ASD (DTX4, ARMC6, and B3GNT3). Also, we have identified 15 de novo variants in genes that were previously implicated in ASD or related neurodevelopmental disorders (PHF21A, WASF1, TCF20, DEAF1, MED13, CREBBP, KDM6B, SMURF1, ADNP, CACNA1G, MYT1L, KIF13B, GRIA2, CHM, and KCNK9). Additionally, we defined eight novel recessive variants (RYR2, DNAH3, TSPYL2, UPF3B KDM5C, LYST, and WNK3), four of which were X-linked. Conclusion: Despite the ASD multifactorial etiology that hinders ASD genetic risk discovery, the number of identified novel or known putative ASD genetic variants was appreciable. Nevertheless, this study represents the first comprehensive characterization of ASD genetic risk in Qatar's Middle Eastern population.
Collapse
Affiliation(s)
- Yasser Al-Sarraj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Rowaida Z. Taha
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Eman Al-Dous
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Dina Ahram
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, United States
| | - Somayyeh Abbasi
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Eman Abuazab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Hibah Shaath
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Wesal Habbab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Khaoula Errafii
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Yosra Bejaoui
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Maryam AlMotawa
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Namat Khattab
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Yasmin Abu Aqel
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Karim E. Shalaby
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Amina Al-Ansari
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Marios Kambouris
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Pathology & Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | - Adel Abouzohri
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Iman Ghazal
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Mohammed Tolfat
- The Shafallah Center for Children with Special Needs, Doha, Qatar
| | - Fouad Alshaban
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Hatem El-Shanti
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Omar M. E. Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| |
Collapse
|
5
|
Leahy D, Marin D, Xu J, Eccles J, Treff NR. High-resolution PGT-A results in incidental identification of patients with small pathogenic copy number variants. J Assist Reprod Genet 2024; 41:121-126. [PMID: 37957533 PMCID: PMC10789684 DOI: 10.1007/s10815-023-02969-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023] Open
Abstract
PURPOSE This study aimed to evaluate whether a high-throughput high-resolution PGT-A method can detect copy number variants (CNVs) that could have clinical implications for patients and their embryos. METHODS A prospective analysis of PGT-A cases was conducted using a high-resolution SNP microarray platform with over 820,000 probes. Cases where multiple embryos possessed the same segmental imbalance were identified, and preliminary PGT-A reports were issued recommending either parental microarray or conventional karyotyping to identify CNVs or translocations. RESULTS Analysis of 6080 sequential PGT-A cases led to identification of 41 cases in which incidental findings were observed (0.7%) and parental testing was recommended. All cases, in which parental studies were completed, confirmed the original PGT-A incidental findings. In 2 of the cases, parental studies indicated a pathogenic variant with clinical implications for the associated embryos. In one of these cases, the patient was identified as a carrier of a duplication in chromosome 15q11.2:q11.2 (SNRPN + +), which is associated with autism spectrum disorder. In the second case, the patient was heterozygous positive for an interstitial deletion of 3p26.1:p26.3, which is associated with 3p deletion syndrome and had clinical implications for the patient and associated embryos. In each case, parental studies were concordant with PGT-A findings and revealed the presence of an otherwise unknown CNV. CONCLUSION High-throughput high-resolution SNP array-based PGT-A has the ability to detect previously unknown and clinically significant parental deletions, duplications, and translocations. The use of cost-effective SNP array-based PGT-A methods may improve the effectiveness of PGT by identifying and preventing previously unknown pathogenic CNVs in children born to patients seeking in vitro fertilization.
Collapse
Affiliation(s)
- Deirdre Leahy
- Genomic Prediction Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA.
| | - Diego Marin
- Genomic Prediction Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| | - Jia Xu
- Genomic Prediction Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| | - Jennifer Eccles
- Genomic Prediction Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| | - Nathan R Treff
- Genomic Prediction Inc., 671 US Highway One, North Brunswick, NJ, 08902, USA
| |
Collapse
|
6
|
Mead EC, Wang CA, Phung J, Fu JY, Williams SM, Merialdi M, Jacobsson B, Lye S, Menon R, Pennell CE. The Role of Genetics in Preterm Birth. Reprod Sci 2023; 30:3410-3427. [PMID: 37450251 PMCID: PMC10692032 DOI: 10.1007/s43032-023-01287-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Preterm birth (PTB), defined as the birth of a child before 37 completed weeks gestation, affects approximately 11% of live births and is the leading cause of death in children under 5 years. PTB is a complex disease with multiple risk factors including genetic variation. Much research has aimed to establish the biological mechanisms underlying PTB often through identification of genetic markers for PTB risk. The objective of this review is to present a comprehensive and updated summary of the published data relating to the field of PTB genetics. A literature search in PubMed was conducted and English studies related to PTB genetics were included. Genetic studies have identified genes within inflammatory, immunological, tissue remodeling, endocrine, metabolic, and vascular pathways that may be involved in PTB. However, a substantial proportion of published data have been largely inconclusive and multiple studies had limited power to detect associations. On the contrary, a few large hypothesis-free approaches have identified and replicated multiple novel variants associated with PTB in different cohorts. Overall, attempts to predict PTB using single "-omics" datasets including genomic, transcriptomic, and epigenomic biomarkers have been mostly unsuccessful and have failed to translate to the clinical setting. Integration of data from multiple "-omics" datasets has yielded the most promising results.
Collapse
Affiliation(s)
- Elyse C Mead
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
- Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
| | - Jason Phung
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
- Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, NSW, 2305, Australia
| | - Joanna Yx Fu
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mario Merialdi
- Maternal Newborn Health Innovations, Geneva, PBC, Switzerland
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynaecology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalization, Institute of Public Health, Oslo, Norway
| | - Stephen Lye
- Lunenfeld Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Ramkumar Menon
- Department of Obstetrics and Gynecology, Division of Basic Science and Translational Research, University of Texas Medical Branch, Galveston, TX, USA
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, 2308, Australia.
- Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia.
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, NSW, 2305, Australia.
| |
Collapse
|
7
|
Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, Höps W, Benito-Garagorri E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560172. [PMID: 37873367 PMCID: PMC10592851 DOI: 10.1101/2023.10.02.560172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often mediated by a pair of inverted low-copy repeats (LCR) followed by iterative template switches resulting in at least two breakpoint junctions in cis . Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved and is predicted to display at least four structural variation (SV) haplotypes. Results Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the genomic DNA of 24 patients with neurodevelopmental disorders identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted SV haplotypes. Using a combination of short-read genome sequencing (GS), long- read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. This approach refined the point of template switching between inverted LCRs in 4 samples revealing a DNA segment of ∼2.2-5.5 kb of 100% nucleotide similarity. A prediction model was developed to infer the LCR used to mediate the non-allelic homology repair. Conclusions These data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate in replication-based repair mechanisms. Such inverted repeats are particularly relevant for formation of copy-number associated inversions, including the DUP-TRP/INV-DUP structures. Moreover, this type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci .
Collapse
|
8
|
Alibutud R, Hansali S, Cao X, Zhou A, Mahaganapathy V, Azaro M, Gwin C, Wilson S, Buyske S, Bartlett CW, Flax JF, Brzustowicz LM, Xing J. Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments. Int J Mol Sci 2023; 24:13248. [PMID: 37686052 PMCID: PMC10487745 DOI: 10.3390/ijms241713248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restrictive interests and/or repetitive behaviors and deficits in social interaction and communication. ASD is a multifactorial disease with a complex polygenic genetic architecture. Its genetic contributing factors are not yet fully understood, especially large structural variations (SVs). In this study, we aimed to assess the contribution of SVs, including copy number variants (CNVs), insertions, deletions, duplications, and mobile element insertions, to ASD and related language impairments in the New Jersey Language and Autism Genetics Study (NJLAGS) cohort. Within the cohort, ~77% of the families contain SVs that followed expected segregation or de novo patterns and passed our filtering criteria. These SVs affected 344 brain-expressed genes and can potentially contribute to the genetic etiology of the disorders. Gene Ontology and protein-protein interaction network analysis suggested several clusters of genes in different functional categories, such as neuronal development and histone modification machinery. Genes and biological processes identified in this study contribute to the understanding of ASD and related neurodevelopment disorders.
Collapse
Affiliation(s)
- Rohan Alibutud
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sammy Hansali
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Vaidhyanathan Mahaganapathy
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Marco Azaro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Christine Gwin
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sherri Wilson
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Steven Buyske
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Christopher W. Bartlett
- The Steve Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Judy F. Flax
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
9
|
Zarrei M, Burton CL, Engchuan W, Higginbotham EJ, Wei J, Shaikh S, Roslin NM, MacDonald JR, Pellecchia G, Nalpathamkalam T, Lamoureux S, Manshaei R, Howe J, Trost B, Thiruvahindrapuram B, Marshall CR, Yuen RKC, Wintle RF, Strug LJ, Stavropoulos DJ, Vorstman JAS, Arnold P, Merico D, Woodbury-Smith M, Crosbie J, Schachar RJ, Scherer SW. Gene copy number variation and pediatric mental health/neurodevelopment in a general population. Hum Mol Genet 2023; 32:2411-2421. [PMID: 37154571 PMCID: PMC10360394 DOI: 10.1093/hmg/ddad074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10-3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10-2) and increased prevalence of mental health diagnoses (P = 1.9 × 10-6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P's < 0.01). There was an increased burden of rare deletions in gene-sets related to brain function or expression in brain associated with more ADHD traits. With the current mental health crisis, our data established a baseline for delineating genetic contributors in pediatric-onset conditions.
Collapse
Affiliation(s)
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Christie L Burton
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sabah Shaikh
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | | | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lisa J Strug
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Departments of Statistical Sciences, Computer Science and Biostatistics, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jacob A S Vorstman
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Paul Arnold
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB T2N 1N4, Canada
- Departments of Psychiatry & Medical Genetics, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Deep Genomics Inc., Toronto, ON M5G 1M1, Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Russell J Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
10
|
Busch SE, Simmons DH, Gama E, Du X, Longo F, Gomez CM, Klann E, Hansel C. Overexpression of the autism candidate gene Cyfip1 pathologically enhances olivo-cerebellar signaling in mice. Front Cell Neurosci 2023; 17:1219270. [PMID: 37545882 PMCID: PMC10399232 DOI: 10.3389/fncel.2023.1219270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Cyfip1, the gene encoding cytoplasmic FMR1 interacting protein 1, has been of interest as an autism candidate gene for years. A potential role in autism spectrum disorder (ASD) is suggested by its location on human chromosome 15q11-13, an instable region that gives rise to a variety of copy number variations associated with syndromic autism. In addition, the CYFIP1 protein acts as a binding partner to Fragile X Messenger Ribonucleoprotein (FMRP) in the regulation of translation initiation. Mutation of FMR1, the gene encoding FMRP, causes Fragile X syndrome, another form of syndromic autism. Here, in mice overexpressing CYFIP1, we study response properties of cerebellar Purkinje cells to activity of the climbing fiber input that originates from the inferior olive and provides an instructive signal in sensorimotor input analysis and plasticity. We find that CYFIP1 overexpression results in enhanced localization of the synaptic organizer neurexin 1 (NRXN1) at climbing fiber synaptic input sites on Purkinje cell primary dendrites and concomitant enhanced climbing fiber synaptic transmission (CF-EPSCs) measured using whole-cell patch-clamp recordings from Purkinje cells in vitro. Moreover, using two-photon measurements of GCaMP6f-encoded climbing fiber signals in Purkinje cells of intact mice, we observe enhanced responses to air puff stimuli applied to the whisker field. These findings resemble our previous phenotypic observations in a mouse model for the human 15q11-13 duplication, which does not extend to the Cyfip1 locus. Thus, our study demonstrates that CYFIP1 overexpression shares a limited set of olivo-cerebellar phenotypes as those resulting from an increased number of copies of non-overlapping genes located on chromosome 15q11-13.
Collapse
Affiliation(s)
- Silas E. Busch
- Department of Neurobiology, The University of Chicago, Chicago, IL, United States
| | - Dana H. Simmons
- Department of Neurobiology, The University of Chicago, Chicago, IL, United States
| | - Eric Gama
- Department of Neurology, The University of Chicago, Chicago, IL, United States
| | - Xiaofei Du
- Department of Neurology, The University of Chicago, Chicago, IL, United States
| | - Francesco Longo
- Center for Neural Science, New York University, New York, NY, United States
- Institute for Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | | | - Eric Klann
- Center for Neural Science, New York University, New York, NY, United States
| | - Christian Hansel
- Department of Neurobiology, The University of Chicago, Chicago, IL, United States
| |
Collapse
|
11
|
Bay H, Haghighatfard A, Karimipour M, Seyedena SY, Hashemi M. Expression alteration of Neuroligin family gene in attention deficit and hyperactivity disorder and autism spectrum disorder. RESEARCH IN DEVELOPMENTAL DISABILITIES 2023; 139:104558. [PMID: 37285744 DOI: 10.1016/j.ridd.2023.104558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex neurodevelopment disorder with social and communicational deficiency, language impairment, and ritualistic behaviors. Attention deficit hyperactivity disorder (ADHD) is a pediatric psychiatric disorder with symptoms, including attention deficit, hyperactivity, and impulsiveness. ADHD is a childhood-onset disorder that can persist into adult life. Neuroligins are post-synaptic cell-adhesion molecules that connect neurons and have an essential role in the mediation of trans-synaptic signaling and shaping the synapse and circuits and neural network functioning. AIMS Present study aimed to shed light on the role of the Neuroligin gene family in ASD and ADHD. METHODS AND PROCEDURES mRNA levels of the Neuroligin gene family (NLGN1, NLGN2, NLGN3, and NLGN4X) were studied in the peripheral blood of 450 unrelated ASD patients, 450 unrelated ADHD patients, and the normal group included 490 unrelated non-psychiatric children by quantitative PCR. Also, clinical situations were considered. OUTCOMES AND RESULTS Results showed that mRNA levels of NLGN1, NLGN2, and NLGN3 were significantly down-regulated in the ASD group vs. control subjects. In ADHD, a significant reduction of NLGN2 and NLGN3 was detected in comparison with normal children. A comparison of ASD and ADHD subjects revealed that NLGN2 was significantly down-regulated in ASD subjects. CONCLUSIONS The Neuroligin family gene may play an essential role in the etiology of ASD and ADHD and thus be a source for a better understanding of neurodevelopment disorders. IMPLICATIONS Similar patterns of deficiency of Neuroligin family genes in ASDs and ADHDs may indicate the role of these genes in functions that have been affected in both disorders.
Collapse
Affiliation(s)
- Hanie Bay
- Department of biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Arvin Haghighatfard
- Department of biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Mehrdad Hashemi
- Department of Medical genetics, Tehran medical sciences branch, Islamic Azad University, Tehran, Iran.
| |
Collapse
|
12
|
Sandhu A, Kumar A, Rawat K, Gautam V, Sharma A, Saha L. Modernising autism spectrum disorder model engineering and treatment via CRISPR-Cas9: A gene reprogramming approach. World J Clin Cases 2023; 11:3114-3127. [PMID: 37274051 PMCID: PMC10237133 DOI: 10.12998/wjcc.v11.i14.3114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/13/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
A neurological abnormality called autism spectrum disorder (ASD) affects how a person perceives and interacts with others, leading to social interaction and communication issues. Limited and recurring behavioural patterns are another feature of the illness. Multiple mutations throughout development are the source of the neurodevelopmental disorder autism. However, a well-established model and perfect treatment for this spectrum disease has not been discovered. The rising era of the clustered regularly interspaced palindromic repeats (CRISPR)-associated protein 9 (Cas9) system can streamline the complexity underlying the pathogenesis of ASD. The CRISPR-Cas9 system is a powerful genetic engineering tool used to edit the genome at the targeted site in a precise manner. The major hurdle in studying ASD is the lack of appropriate animal models presenting the complex symptoms of ASD. Therefore, CRISPR-Cas9 is being used worldwide to mimic the ASD-like pathology in various systems like in vitro cell lines, in vitro 3D organoid models and in vivo animal models. Apart from being used in establishing ASD models, CRISPR-Cas9 can also be used to treat the complexities of ASD. The aim of this review was to summarize and critically analyse the CRISPR-Cas9-mediated discoveries in the field of ASD.
Collapse
Affiliation(s)
- Arushi Sandhu
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Anil Kumar
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Kajal Rawat
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Vipasha Gautam
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Antika Sharma
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Lekha Saha
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| |
Collapse
|
13
|
López-López D, Roldán G, Fernández-Rueda JL, Bostelmann G, Carmona R, Aquino V, Perez-Florido J, Ortuño F, Pita G, Núñez-Torres R, González-Neira A, Peña-Chilet M, Dopazo J. A crowdsourcing database for the copy-number variation of the Spanish population. Hum Genomics 2023; 17:20. [PMID: 36894999 PMCID: PMC9997023 DOI: 10.1186/s40246-023-00466-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/25/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. RESULTS Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/ . CONCLUSION SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.
Collapse
Affiliation(s)
- Daniel López-López
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Gema Roldán
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Jose L Fernández-Rueda
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Gerrit Bostelmann
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Rosario Carmona
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Virginia Aquino
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain
| | - Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Francisco Ortuño
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Department of Computer Architecture and Computer Technology, University of Granada, 18071, Granada, Spain
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Rocío Núñez-Torres
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - María Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain. .,Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain. .,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain. .,FPS/ELIXIR-ES, Andalusian Public Foundation Progress and Health-FPS, 41013, Seville, Spain.
| |
Collapse
|
14
|
Wei MM, Yu CQ, Li LP, You ZH, Ren ZH, Guan YJ, Wang XF, Li YC. LPIH2V: LncRNA-protein interactions prediction using HIN2Vec based on heterogeneous networks model. Front Genet 2023; 14:1122909. [PMID: 36845392 PMCID: PMC9950107 DOI: 10.3389/fgene.2023.1122909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
LncRNA-protein interaction plays an important role in the development and treatment of many human diseases. As the experimental approaches to determine lncRNA-protein interactions are expensive and time-consuming, considering that there are few calculation methods, therefore, it is urgent to develop efficient and accurate methods to predict lncRNA-protein interactions. In this work, a model for heterogeneous network embedding based on meta-path, namely LPIH2V, is proposed. The heterogeneous network is composed of lncRNA similarity networks, protein similarity networks, and known lncRNA-protein interaction networks. The behavioral features are extracted in a heterogeneous network using the HIN2Vec method of network embedding. The results showed that LPIH2V obtains an AUC of 0.97 and ACC of 0.95 in the 5-fold cross-validation test. The model successfully showed superiority and good generalization ability. Compared to other models, LPIH2V not only extracts attribute characteristics by similarity, but also acquires behavior properties by meta-path wandering in heterogeneous networks. LPIH2V would be beneficial in forecasting interactions between lncRNA and protein.
Collapse
Affiliation(s)
- Meng-Meng Wei
- School of Information Engineering, Xijing University, Xi’an, China
| | - Chang-Qing Yu
- School of Information Engineering, Xijing University, Xi’an, China,*Correspondence: Chang-Qing Yu, ; Li-Ping Li,
| | - Li-Ping Li
- School of Information Engineering, Xijing University, Xi’an, China,College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, China,*Correspondence: Chang-Qing Yu, ; Li-Ping Li,
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi’an, China
| | - Zhong-Hao Ren
- School of Information Engineering, Xijing University, Xi’an, China
| | - Yong-Jian Guan
- School of Information Engineering, Xijing University, Xi’an, China
| | | | | |
Collapse
|
15
|
Wang Y, Tang S, Ma R, Zamit I, Wei Y, Pan Y. Multi-modal intermediate integrative methods in neuropsychiatric disorders: A review. Comput Struct Biotechnol J 2022; 20:6149-6162. [PMID: 36420153 PMCID: PMC9674886 DOI: 10.1016/j.csbj.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The etiology of neuropsychiatric disorders involves complex biological processes at different omics layers, such as genomics, transcriptomics, epigenetics, proteomics, and metabolomics. The advent of high-throughput technology, as well as the availability of large open-source datasets, has ushered in a new era in system biology, necessitating the integration of various types of omics data. The complexity of biological mechanisms, the limitations of integrative strategies, and the heterogeneity of multi-omics data have all presented significant challenges to computational scientists. In comparison to early and late integration, intermediate integration may transform each data type into appropriate intermediate representations using various data transformation techniques, allowing it to capture more complementary information contained in each omics and highlight new interactions across omics layers. Here, we reviewed multi-modal intermediate integrative techniques based on component analysis, matrix factorization, similarity network, multiple kernel learning, Bayesian network, artificial neural networks, and graph transformation, as well as their applications in neuropsychiatric domains. We depicted advancements in these approaches and compared the strengths and weaknesses of each method examined. We believe that our findings will aid researchers in their understanding of the transformation and integration of multi-omics data in neuropsychiatric disorders.
Collapse
Affiliation(s)
- Yanlin Wang
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Shi Tang
- Li Chiu Kong Family Sleep Assessment Unit, Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Ruimin Ma
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Ibrahim Zamit
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yi Pan
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| |
Collapse
|
16
|
Wang HE, Cheng CM, Bai YM, Hsu JW, Huang KL, Su TP, Tsai SJ, Li CT, Chen TJ, Leventhal BL, Chen MH. Familial coaggregation of major psychiatric disorders in first-degree relatives of individuals with autism spectrum disorder: a nationwide population-based study. Psychol Med 2022; 52:1437-1447. [PMID: 32914742 DOI: 10.1017/s0033291720003207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Family coaggregation of attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), bipolar disorder (BD), major depressive disorder (MDD) and schizophrenia have been presented in previous studies. The shared genetic and environmental factors among psychiatric disorders remain elusive. METHODS This nationwide population-based study examined familial coaggregation of major psychiatric disorders in first-degree relatives (FDRs) of individuals with ASD. Taiwan's National Health Insurance Research Database was used to identify 26 667 individuals with ASD and 67 998 FDRs of individuals with ASD. The cohort was matched in 1:4 ratio to 271 992 controls. The relative risks (RRs) and 95% confidence intervals (CI) of ADHD, ASD, BD, MDD and schizophrenia were assessed among FDRs of individuals with ASD and ASD with intellectual disability (ASD-ID). RESULTS FDRs of individuals with ASD have higher RRs of major psychiatric disorders compared with controls: ASD 17.46 (CI 15.50-19.67), ADHD 3.94 (CI 3.72-4.17), schizophrenia 3.05 (CI 2.74-3.40), BD 2.22 (CI 1.98-2.48) and MDD 1.88 (CI 1.76-2.00). Higher RRs of schizophrenia (4.47, CI 3.95-5.06) and ASD (18.54, CI 16.18-21.23) were observed in FDRs of individuals with both ASD-ID, compared with ASD only. CONCLUSIONS The risk for major psychiatric disorders was consistently elevated across all types of FDRs of individuals with ASD. FDRs of individuals with ASD-ID are at further higher risk for ASD and schizophrenia. Our results provide leads for future investigation of shared etiologic pathways of ASD, ID and major psychiatric disorders and highlight the importance of mental health care delivered to at-risk families for early diagnoses and interventions.
Collapse
Affiliation(s)
- Hohui E Wang
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Chih-Ming Cheng
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ya-Mei Bai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ju-Wei Hsu
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kai-Lin Huang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Tung-Ping Su
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Psychiatry, General Cheng Hsin Hospital, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Ta Li
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Tzeng-Ji Chen
- Department of Family Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Hospital and Health Care Administration, National Yang-Ming University, Taipei, Taiwan
| | - Bennett L Leventhal
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Mu-Hong Chen
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| |
Collapse
|
17
|
Mapelli L, Soda T, D’Angelo E, Prestori F. The Cerebellar Involvement in Autism Spectrum Disorders: From the Social Brain to Mouse Models. Int J Mol Sci 2022; 23:ijms23073894. [PMID: 35409253 PMCID: PMC8998980 DOI: 10.3390/ijms23073894] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders that include a variety of forms and clinical phenotypes. This heterogeneity complicates the clinical and experimental approaches to ASD etiology and pathophysiology. To date, a unifying theory of these diseases is still missing. Nevertheless, the intense work of researchers and clinicians in the last decades has identified some ASD hallmarks and the primary brain areas involved. Not surprisingly, the areas that are part of the so-called “social brain”, and those strictly connected to them, were found to be crucial, such as the prefrontal cortex, amygdala, hippocampus, limbic system, and dopaminergic pathways. With the recent acknowledgment of the cerebellar contribution to cognitive functions and the social brain, its involvement in ASD has become unmistakable, though its extent is still to be elucidated. In most cases, significant advances were made possible by recent technological developments in structural/functional assessment of the human brain and by using mouse models of ASD. Mouse models are an invaluable tool to get insights into the molecular and cellular counterparts of the disease, acting on the specific genetic background generating ASD-like phenotype. Given the multifaceted nature of ASD and related studies, it is often difficult to navigate the literature and limit the huge content to specific questions. This review fulfills the need for an organized, clear, and state-of-the-art perspective on cerebellar involvement in ASD, from its connections to the social brain areas (which are the primary sites of ASD impairments) to the use of monogenic mouse models.
Collapse
Affiliation(s)
- Lisa Mapelli
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (T.S.); (E.D.)
- Correspondence: (L.M.); (F.P.)
| | - Teresa Soda
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (T.S.); (E.D.)
| | - Egidio D’Angelo
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (T.S.); (E.D.)
- Brain Connectivity Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Francesca Prestori
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (T.S.); (E.D.)
- Correspondence: (L.M.); (F.P.)
| |
Collapse
|
18
|
Bukina ES, Kondratyev NV, Kozin SV, Golimbet VE, Artyuhov AS, Dashinimaev EB. SLC6A1 and Neuropsychiatric Diseases: The Role of Mutations and Prospects for Treatment with Genome Editing Systems. NEUROCHEM J+ 2021. [DOI: 10.1134/s1819712421040048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
19
|
Jiang Y, Patton MH, Zakharenko SS. A Case for Thalamic Mechanisms of Schizophrenia: Perspective From Modeling 22q11.2 Deletion Syndrome. Front Neural Circuits 2021; 15:769969. [PMID: 34955759 PMCID: PMC8693383 DOI: 10.3389/fncir.2021.769969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Schizophrenia is a severe, chronic psychiatric disorder that devastates the lives of millions of people worldwide. The disease is characterized by a constellation of symptoms, ranging from cognitive deficits, to social withdrawal, to hallucinations. Despite decades of research, our understanding of the neurobiology of the disease, specifically the neural circuits underlying schizophrenia symptoms, is still in the early stages. Consequently, the development of therapies continues to be stagnant, and overall prognosis is poor. The main obstacle to improving the treatment of schizophrenia is its multicausal, polygenic etiology, which is difficult to model. Clinical observations and the emergence of preclinical models of rare but well-defined genomic lesions that confer substantial risk of schizophrenia (e.g., 22q11.2 microdeletion) have highlighted the role of the thalamus in the disease. Here we review the literature on the molecular, cellular, and circuitry findings in schizophrenia and discuss the leading theories in the field, which point to abnormalities within the thalamus as potential pathogenic mechanisms of schizophrenia. We posit that synaptic dysfunction and oscillatory abnormalities in neural circuits involving projections from and within the thalamus, with a focus on the thalamocortical circuits, may underlie the psychotic (and possibly other) symptoms of schizophrenia.
Collapse
Affiliation(s)
| | | | - Stanislav S. Zakharenko
- Division of Neural Circuits and Behavior, Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| |
Collapse
|
20
|
Kava R, Peripolli E, Berton MP, Lemos M, Lobo RB, Stafuzza NB, Pereira AS, Baldi F. Genome-wide structural variations in Brazilian Senepol cattle, a tropically adapted taurine breed. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
21
|
Gill PS, Clothier JL, Veerapandiyan A, Dweep H, Porter-Gill PA, Schaefer GB. Molecular Dysregulation in Autism Spectrum Disorder. J Pers Med 2021; 11:848. [PMID: 34575625 PMCID: PMC8466026 DOI: 10.3390/jpm11090848] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Autism Spectrum Disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders with a strong heritable genetic component. At present, ASD is diagnosed solely by behavioral criteria. Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility. Moreover, studies show rare de novo variants, copy number variation and single nucleotide polymorphisms (SNPs) also impact neurodevelopment signaling. Exploration of rare and common variants involved in common dysregulated pathways can provide new diagnostic and therapeutic strategies for ASD. Contributions of current innovative molecular strategies to understand etiology of ASD will be explored which are focused on whole exome sequencing (WES), whole genome sequencing (WGS), microRNA, long non-coding RNAs and CRISPR/Cas9 models. Some promising areas of pharmacogenomic and endophenotype directed therapies as novel personalized treatment and prevention will be discussed.
Collapse
Affiliation(s)
- Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA;
| | - Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Aravindhan Veerapandiyan
- Pediatric Neurology, Arkansas Children’s Hospital, 1 Children’s Way, Little Rock, AR 72202, USA;
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA;
| | | | - G. Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Hospital NW, Springdale, AR 72762, USA
| |
Collapse
|
22
|
Dehghani N, Guven G, Kun-Rodrigues C, Gouveia C, Foster K, Hanagasi H, Lohmann E, Samanci B, Gurvit H, Bilgic B, Bras J, Guerreiro R. A comprehensive analysis of copy number variation in a Turkish dementia cohort. Hum Genomics 2021; 15:48. [PMID: 34321086 PMCID: PMC8317312 DOI: 10.1186/s40246-021-00346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Copy number variants (CNVs) include deletions or multiplications spanning genomic regions. These regions vary in size and may span genes known to play a role in human diseases. As examples, duplications and triplications of SNCA have been shown to cause forms of Parkinson's disease, while duplications of APP cause early onset Alzheimer's disease (AD). RESULTS Here, we performed a systematic analysis of CNVs in a Turkish dementia cohort in order to further characterize the genetic causes of dementia in this population. One hundred twenty-four Turkish individuals, either at risk of dementia due to family history, diagnosed with mild cognitive impairment, AD, or frontotemporal dementia, were whole-genome genotyped and CNVs were detected. We integrated family analysis with a comprehensive assessment of potentially disease-associated CNVs in this Turkish dementia cohort. We also utilized both dementia and non-dementia individuals from the UK Biobank in order to further elucidate the potential role of the identified CNVs in neurodegenerative diseases. We report CNVs overlapping the previously implicated genes ZNF804A, SNORA70B, USP34, XPO1, and a locus on chromosome 9 which includes a cluster of olfactory receptors and ABCA1. Additionally, we also describe novel CNVs potentially associated with dementia, overlapping the genes AFG1L, SNX3, VWDE, and BC039545. CONCLUSIONS Genotyping data from understudied populations can be utilized to identify copy number variation which may contribute to dementia.
Collapse
Affiliation(s)
- Nadia Dehghani
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Gamze Guven
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Celia Kun-Rodrigues
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Catarina Gouveia
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Kalina Foster
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
- Neuroscience Department, Michigan State University College of Natural Science, East Lansing, MI, USA
| | - Hasmet Hanagasi
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Ebba Lohmann
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Bedia Samanci
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Hakan Gurvit
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Basar Bilgic
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA.
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA.
| |
Collapse
|
23
|
Meganathan K, Prakasam R, Baldridge D, Gontarz P, Zhang B, Urano F, Bonni A, Maloney SE, Turner TN, Huettner JE, Constantino JN, Kroll KL. Altered neuronal physiology, development, and function associated with a common chromosome 15 duplication involving CHRNA7. BMC Biol 2021; 19:147. [PMID: 34320968 PMCID: PMC8317352 DOI: 10.1186/s12915-021-01080-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/30/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Copy number variants (CNVs) linked to genes involved in nervous system development or function are often associated with neuropsychiatric disease. While CNVs involving deletions generally cause severe and highly penetrant patient phenotypes, CNVs leading to duplications tend instead to exhibit widely variable and less penetrant phenotypic expressivity among affected individuals. CNVs located on chromosome 15q13.3 affecting the alpha-7 nicotinic acetylcholine receptor subunit (CHRNA7) gene contribute to multiple neuropsychiatric disorders with highly variable penetrance. However, the basis of such differential penetrance remains uncharacterized. Here, we generated induced pluripotent stem cell (iPSC) models from first-degree relatives with a 15q13.3 duplication and analyzed their cellular phenotypes to uncover a basis for the dissimilar phenotypic expressivity. RESULTS The first-degree relatives studied included a boy with autism and emotional dysregulation (the affected proband-AP) and his clinically unaffected mother (UM), with comparison to unrelated control models lacking this duplication. Potential contributors to neuropsychiatric impairment were modeled in iPSC-derived cortical excitatory and inhibitory neurons. The AP-derived model uniquely exhibited disruptions of cellular physiology and neurodevelopment not observed in either the UM or unrelated controls. These included enhanced neural progenitor proliferation but impaired neuronal differentiation, maturation, and migration, and increased endoplasmic reticulum (ER) stress. Both the neuronal migration deficit and elevated ER stress could be selectively rescued by different pharmacologic agents. Neuronal gene expression was also dysregulated in the AP, including reduced expression of genes related to behavior, psychological disorders, neuritogenesis, neuronal migration, and Wnt, axonal guidance, and GABA receptor signaling. The UM model instead exhibited upregulated expression of genes in many of these same pathways, suggesting that molecular compensation could have contributed to the lack of neurodevelopmental phenotypes in this model. However, both AP- and UM-derived neurons exhibited shared alterations of neuronal function, including increased action potential firing and elevated cholinergic activity, consistent with increased homomeric CHRNA7 channel activity. CONCLUSIONS These data define both diagnosis-associated cellular phenotypes and shared functional anomalies related to CHRNA7 duplication that may contribute to variable phenotypic penetrance in individuals with 15q13.3 duplication. The capacity for pharmacological agents to rescue some neurodevelopmental anomalies associated with diagnosis suggests avenues for intervention for carriers of this duplication and other CNVs that cause related disorders.
Collapse
Affiliation(s)
- Kesavan Meganathan
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Ramachandran Prakasam
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| | - Fumihiko Urano
- Department of Medicine, Division of Endocrinology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - James E. Huettner
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - John N. Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kristen L. Kroll
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus, Box 8103, St. Louis, MO 63110 USA
| |
Collapse
|
24
|
Liu G, Zhang J. A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 12:699510. [PMID: 34262604 PMCID: PMC8273656 DOI: 10.3389/fgene.2021.699510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The next-generation sequencing technology offers a wealth of data resources for the detection of copy number variations (CNVs) at a high resolution. However, it is still challenging to correctly detect CNVs of different lengths. It is necessary to develop new CNV detection tools to meet this demand. In this work, we propose a new CNV detection method, called CBCNV, for the detection of CNVs of different lengths from whole genome sequencing data. CBCNV uses a clustering algorithm to divide the read depth segment profile, and assigns an abnormal score to each read depth segment. Based on the abnormal score profile, Tukey's fences method is adopted in CBCNV to forecast CNVs. The performance of the proposed method is evaluated on simulated data sets, and is compared with those of several existing methods. The experimental results prove that the performance of CBCNV is better than those of several existing methods. The proposed method is further tested and verified on real data sets, and the experimental results are found to be consistent with the simulation results. Therefore, the proposed method can be expected to become a routine tool in the analysis of CNVs from tumor-normal matched samples.
Collapse
Affiliation(s)
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi’an, China
| |
Collapse
|
25
|
8p21.3 deletions are rare causes of non-syndromic autism spectrum disorder. Neurogenetics 2021; 22:207-213. [PMID: 33683518 DOI: 10.1007/s10048-021-00635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
A de novo 0.95 Mb 8p21.3 deletion had been identified in an individual with non-syndromic autism spectrum disorder (ASD) through high-resolution copy number variant analysis. Subsequent screening of in-house and publicly available databases resulted in the identification of six additional individuals with 8p21.3 deletions. Through case-based reasoning, we conclude that 8p21.3 deletions are rare causes of non-syndromic neurodevelopmental and neuropsychiatric disorders. Based on literature data, we highlight six genes within the region of minimal overlap as potential ASD genes or genes for neuropsychiatric disorders: DMTN, EGR3, FGF17, LGI3, PHYHIP, and PPP3CC.
Collapse
|
26
|
Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
Collapse
|
27
|
Vorstman J, Scherer SW. What a finding of gene copy number variation can add to the diagnosis of developmental neuropsychiatric disorders. Curr Opin Genet Dev 2021; 68:18-25. [PMID: 33454514 DOI: 10.1016/j.gde.2020.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 11/26/2022]
Abstract
Among medical disciplines, diagnosis in psychiatry depends highly upon descriptive signs and symptoms, rather than biomarkers. Clear descriptions of specific genetic etiologies have been lacking; genomic technologies, however, are rapidly changing that landscape. Notably, chromosomal microarrays-which detect gene copy number variants (CNVs)-are a recommended standard of care for neurodevelopmental disorders. As a result, an increasing number of patients now receive a clinical diagnosis based on the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) and an identified genetic etiological variant. However, psychiatric and genetic diagnoses are frequently communicated and managed as two disconnected diagnostic parameters. Here, we advocate for a transition model, allowing the integration of genetic etiological information-starting with diagnostically proven CNVs-within the DSM-5 classification framework.
Collapse
Affiliation(s)
- Jacob Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Canada.
| |
Collapse
|
28
|
Gandhi T, Lee CC. Neural Mechanisms Underlying Repetitive Behaviors in Rodent Models of Autism Spectrum Disorders. Front Cell Neurosci 2021; 14:592710. [PMID: 33519379 PMCID: PMC7840495 DOI: 10.3389/fncel.2020.592710] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) is comprised of several conditions characterized by alterations in social interaction, communication, and repetitive behaviors. Genetic and environmental factors contribute to the heterogeneous development of ASD behaviors. Several rodent models display ASD-like phenotypes, including repetitive behaviors. In this review article, we discuss the potential neural mechanisms involved in repetitive behaviors in rodent models of ASD and related neuropsychiatric disorders. We review signaling pathways, neural circuits, and anatomical alterations in rodent models that display robust stereotypic behaviors. Understanding the mechanisms and circuit alterations underlying repetitive behaviors in rodent models of ASD will inform translational research and provide useful insight into therapeutic strategies for the treatment of repetitive behaviors in ASD and other neuropsychiatric disorders.
Collapse
Affiliation(s)
- Tanya Gandhi
- Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
| | | |
Collapse
|
29
|
Targeting the RHOA pathway improves learning and memory in adult Kctd13 and 16p11.2 deletion mouse models. Mol Autism 2021; 12:1. [PMID: 33436060 PMCID: PMC7805198 DOI: 10.1186/s13229-020-00405-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/15/2020] [Indexed: 11/12/2022] Open
Abstract
Background Gene copy number variants play an important role in the occurrence of neurodevelopmental disorders. Particularly, the deletion of the 16p11.2 locus is associated with autism spectrum disorder, intellectual disability, and several other features. Earlier studies highlighted the implication of Kctd13 genetic imbalance in 16p11.2 deletion through the regulation of the RHOA pathway. Methods Here, we generated a new mouse model with a small deletion of two key exons in Kctd13. Then, we targeted the RHOA pathway to rescue the cognitive phenotypes of the Kctd13 and 16p11.2 deletion mouse models in a pure genetic background. We used a chronic administration of fasudil (HA1077), an inhibitor of the Rho-associated protein kinase, for six weeks in mouse models carrying a heterozygous inactivation of Kctd13, or the deletion of the entire 16p11.2 BP4-BP5 homologous region. Results We found that the small Kctd13 heterozygous deletion induced a cognitive phenotype similar to the whole deletion of the 16p11.2 homologous region, in the Del/+ mice. We then showed that chronic fasudil treatment can restore object recognition memory in adult heterozygous mutant mice for Kctd13 and for 16p11.2 deletion. In addition, learning and memory improvement occurred in parallel to change in the RHOA pathway. Limitations The Kcdt13 mutant line does not recapitulate all the phenotypes found in the 16p11.2 Del/+ model. In particular, the locomotor activity was not altered at 12 and 18 weeks of age and the object location memory was not defective in 18-week old mutants. Similarly, the increase in locomotor activity was not modified by the treatment in the 16p11.2 Del/+ mouse model, suggesting that other loci were involved in such defects. Rescue was observed only after four weeks of treatment but no long-term experiment has been carried out so far. Finally, we did not check the social behaviour, which requires working in another hybrid genetic background. Conclusion These findings confirm KCTD13 as one target gene causing cognitive deficits in 16p11.2 deletion patients, and the relevance of the RHOA pathway as a therapeutic path for 16p11.2 deletion. In addition, they reinforce the contribution of other gene(s) involved in cognitive defects found in the 16p11.2 models in older mice.
Collapse
|
30
|
Sarovic D. A Unifying Theory for Autism: The Pathogenetic Triad as a Theoretical Framework. Front Psychiatry 2021; 12:767075. [PMID: 34867553 PMCID: PMC8637925 DOI: 10.3389/fpsyt.2021.767075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
This paper presents a unifying theory for autism by applying the framework of a pathogenetic triad to the scientific literature. It proposes a deconstruction of autism into three contributing features (an autistic personality dimension, cognitive compensation, and neuropathological risk factors), and delineates how they interact to cause a maladaptive behavioral phenotype that may require a clinical diagnosis. The autistic personality represents a common core condition, which induces a set of behavioral issues when pronounced. These issues are compensated for by cognitive mechanisms, allowing the individual to remain adaptive and functional. Risk factors, both exogenous and endogenous ones, show pathophysiological convergence through their negative effects on neurodevelopment. This secondarily affects cognitive compensation, which disinhibits a maladaptive behavioral phenotype. The triad is operationalized and methods for quantification are presented. With respect to the breadth of findings in the literature that it can incorporate, it is the most comprehensive model yet for autism. Its main implications are that (1) it presents the broader autism phenotype as a non-pathological core personality domain, which is shared across the population and uncoupled from associated features such as low cognitive ability and immune dysfunction, (2) it proposes that common genetic variants underly the personality domain, and that rare variants act as risk factors through negative effects on neurodevelopment, (3) it outlines a common pathophysiological mechanism, through inhibition of neurodevelopment and cognitive dysfunction, by which a wide range of endogenous and exogenous risk factors lead to autism, and (4) it suggests that contributing risk factors, and findings of immune and autonomic dysfunction are clinically ascertained rather than part of the core autism construct.
Collapse
Affiliation(s)
- Darko Sarovic
- Gillberg Neuropsychiatry Centre, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Radiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,MedTech West, Gothenburg, Sweden
| |
Collapse
|
31
|
Qin X, Chen J, Zhou T. 22q11.2 deletion syndrome and schizophrenia. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1181-1190. [PMID: 33098288 DOI: 10.1093/abbs/gmaa113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
22q11.2 deletion is a common microdeletion that causes an array of developmental defects including 22q11.2 deletion syndrome (22q11DS) or DiGeorge syndrome and velocardiofacial syndrome. About 30% of patients with 22q11.2 deletion develop schizophrenia. Mice with deletion of the ortholog region in mouse chromosome 16qA13 exhibit schizophrenia-like abnormal behaviors. It is suggested that the genes deleted in 22q11DS are involved in the pathogenesis of schizophrenia. Among these genes, COMT, ZDHHC8, DGCR8, and PRODH have been identified as schizophrenia susceptibility genes. And DGCR2 is also found to be associated with schizophrenia. In this review, we focused on these five genes and reviewed their functions in the brain and the potential pathophysiological mechanisms in schizophrenia, which will give us a deeper understanding of the pathology of schizophrenia.
Collapse
Affiliation(s)
- Xianzheng Qin
- Queen Mary School of Nanchang University, Nanchang University, Nanchang 330031, China
| | - Jiang Chen
- Laboratory of Synaptic Development and Plasticity, Institute of Life Science, Nanchang University, Nanchang 330031, China
| | - Tian Zhou
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| |
Collapse
|
32
|
Arakawa H. From Multisensory Assessment to Functional Interpretation of Social Behavioral Phenotype in Transgenic Mouse Models for Autism Spectrum Disorders. Front Psychiatry 2020; 11:592408. [PMID: 33329141 PMCID: PMC7717939 DOI: 10.3389/fpsyt.2020.592408] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a common heterogeneous disorder, defined solely by the core behavioral characteristics, including impaired social interaction and restricted and repeated behavior. Although an increasing number of studies have been performed extensively, the neurobiological mechanisms underlying the core symptoms of ASD remain largely unknown. Transgenic mouse models provide a useful tool for evaluating genetic and neuronal mechanisms underlying ASD pathology, which are prerequisites for validating behavioral phenotypes that mimic the core symptoms of human ASD. The purpose of this review is to propose a better strategy for analyzing and interpreting social investigatory behaviors in transgenic mouse models of ASD. Mice are nocturnal, and employ multimodal processing mechanisms for social communicative behaviors, including those that involve olfactory and tactile senses. Most behavioral paradigms that have been developed for measuring a particular ASD-like behavior in mouse models, such as social recognition, preference, and discrimination tests, are based on the evaluation of distance-based investigatory behavior in response to social stimuli. This investigatory behavior in mice is regulated by multimodal processing involving with two different motives: first, an olfactory-based novelty assessment, and second, tactile-based social contact, in a temporally sequential manner. Accurate interpretation of investigatory behavior exhibited by test mice can be achieved by functional analysis of these multimodal, sequential behaviors, which will lead to a better understanding of the specific features of social deficits associated with ASD in transgenic mouse models, at high temporal and spatial resolutions.
Collapse
|
33
|
Glennon JM, D'Souza H, Mason L, Karmiloff-Smith A, Thomas MSC. Visuo-attentional correlates of Autism Spectrum Disorder (ASD) in children with Down syndrome: A comparative study with children with idiopathic ASD. RESEARCH IN DEVELOPMENTAL DISABILITIES 2020; 104:103678. [PMID: 32505966 PMCID: PMC7429984 DOI: 10.1016/j.ridd.2020.103678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Children with Down syndrome (DS) are at increased likelihood of Autism Spectrum Disorder (ASD) relative to the general population. To better understand the nature of this comorbidity, we examined the visuo-attentional processes associated with autistic trait expression in children with DS, focusing specifically on attentional disengagement and visual search performance. METHOD We collected eye-tracking data from children with DS (n = 15) and children with idiopathic ASD (iASD, n = 16) matched according to chronological age. Seven children with DS had a formal clinical diagnosis of ASD (DS+ASD). RESULTS In children with iASD, but not DS, higher autistic trait levels were associated with decreased temporal facilitation on a gap-overlap task, implying increased visuospatial orienting efficiency. In all cases, higher autistic trait levels were associated with improved visual search performance according to decreased target detection latency. On a visual search task, children with DS+ASD outperformed their peers with DS-ASD, mirroring the phenotypic advantage associated with iASD. We found no evidence of a relationship between attentional disengagement and visual search performance, providing preliminary evidence of a differentiation in terms of underlying visuo-attentional mechanism. CONCLUSION We illustrate the value of progressing beyond insensitive behavioural measures of phenotypic description to examine, in a more fine-grained way, the attentional features associated with ASD comorbidity in children with DS.
Collapse
Affiliation(s)
- Jennifer M Glennon
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck College, University of London, United Kingdom.
| | - Hana D'Souza
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck College, University of London, United Kingdom; Department of Psychology & Newnham College, University of Cambridge, United Kingdom
| | - Luke Mason
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck College, University of London, United Kingdom
| | - Annette Karmiloff-Smith
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck College, University of London, United Kingdom
| | - Michael S C Thomas
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck College, University of London, United Kingdom
| |
Collapse
|
34
|
Vascular contributions to 16p11.2 deletion autism syndrome modeled in mice. Nat Neurosci 2020; 23:1090-1101. [PMID: 32661394 DOI: 10.1038/s41593-020-0663-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/01/2020] [Indexed: 02/08/2023]
Abstract
While the neuronal underpinnings of autism spectrum disorder (ASD) are being unraveled, vascular contributions to ASD remain elusive. Here, we investigated postnatal cerebrovascular development in the 16p11.2df/+ mouse model of 16p11.2 deletion ASD syndrome. We discover that 16p11.2 hemizygosity leads to male-specific, endothelium-dependent structural and functional neurovascular abnormalities. In 16p11.2df/+ mice, endothelial dysfunction results in impaired cerebral angiogenesis at postnatal day 14, and in altered neurovascular coupling and cerebrovascular reactivity at postnatal day 50. Moreover, we show that there is defective angiogenesis in primary 16p11.2df/+ mouse brain endothelial cells and in induced-pluripotent-stem-cell-derived endothelial cells from human carriers of the 16p11.2 deletion. Finally, we find that mice with an endothelium-specific 16p11.2 deletion (16p11.2ΔEC) partially recapitulate some of the behavioral changes seen in 16p11.2 syndrome, specifically hyperactivity and impaired motor learning. By showing that developmental 16p11.2 haploinsufficiency from endothelial cells results in neurovascular and behavioral changes in adults, our results point to a potential role for endothelial impairment in ASD.
Collapse
|
35
|
Ward ET, Kostick KM, Lázaro-Muñoz G. Integrating Genomics into Psychiatric Practice: Ethical and Legal Challenges for Clinicians. Harv Rev Psychiatry 2020; 27:53-64. [PMID: 30614887 PMCID: PMC6326091 DOI: 10.1097/hrp.0000000000000203] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Psychiatric genomics is a rapidly growing field that holds much promise for improving risk prediction, prevention, diagnosis, treatment selection, and understanding of the pathogenesis of patients' symptoms. The field of psychiatry (i.e., professional organizations, mental health clinicians, educational institutions), however, needs to address numerous challenges to promote the responsible translation of genomic technologies and knowledge into psychiatric practice. The goal of this article is to review how clinicians currently encounter and use genomics in the clinic, to summarize the existing literature on how clinicians feel about the use of genomics in psychiatry, and to analyze foreseeable ethical and legal challenges for the responsible integration of genomics into psychiatric care at the structural and clinic levels. Structural challenges are defined as aspects of the larger system of psychiatric practice that constitute potential barriers to the responsible integration of genomics for the purposes of psychiatric care and prevention. These structural challenges exist at a level where professional groups can intervene to set standards and regulate the practice of psychiatry and genomics. Clinic-level challenges are day-to-day issues clinicians face when managing genomic tests in the clinic. We discuss the need for action to mitigate these challenges and maximize the clinical and social utility of psychiatric genomics, including the following: expanding genomics training among mental health clinicians; establishing practice guidelines that consider potential clinical, psychological, and social implications of psychiatric genomics; promoting an integrated care model for managing genomics in psychiatry; emphasizing patient engagement and informed consent when managing genomic testing in psychiatric care.
Collapse
Affiliation(s)
- Eric T Ward
- From the University of North Carolina School of Medicine (Dr. Ward); Center for Medical Ethics and Health Policy, Baylor College of Medicine (Drs. Kostick and Lázaro-Muñoz)
| | | | | |
Collapse
|
36
|
Tian T, Lei Y, Chen Y, Guo Y, Jin L, Finnell RH, Wang L, Ren A. Rare copy number variations of planar cell polarity genes are associated with human neural tube defects. Neurogenetics 2020; 21:217-225. [PMID: 32388773 DOI: 10.1007/s10048-020-00613-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Select single-nucleotide variants in planar cell polarity (PCP) genes are associated with increased risk for neural tube defects (NTDs). However, whether copy number variants (CNVs) in PCP genes contribute to NTDs is unknown. Considering that CNVs are implicated in several human developmental disorders, we hypothesized that CNVs in PCP genes may be causative factors to human NTDs. DNA from umbilical cord tissues of NTD-affected fetuses and parental venous blood samples were collected. We performed a quantitative analysis of copy numbers of all exon regions in the VANGL1, VANGL2, CELSR1, SCRIB, DVL2, DVL3, and PTK7 genes using a CNVplex assay. Quantitative real-time PCR (qPCR) was carried out to confirm the results of CNV analysis. As a result, 16 CNVs were identified among the NTDs. Of these CNVs, 5 loci were identified in 11 NTD probands with CNVs involving DVL2 (exons 1-15), VANGL1 (exons 1-7, exon 8), and VANGL2 (exons 5-8, exons 7 and 8). One CNV (DVL2 exons 1-15) was a duplication and the remaining 15 CNVs were deletions. Eleven CNVs were confirmed by qPCR. One de novo CNV in VANGL1 and one DVL2 were detected from two cases. Compared with unaffected control populations in 1000 Genome, ExAC, MARRVEL, DGV, and dbVar databases, the frequencies of de novo deletion in VANGL1 (1.14%) and de novo duplication in DVL2 (0.57%) were significantly higher in our NTD subjects (p < 0.05). This study demonstrates that de novo CNVs in PCP genes, notably deletions in VANGL1 and gains in DVL2, could contribute to the risk of NTDs.
Collapse
Affiliation(s)
- Tian Tian
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory for Reproductive Health; Department of Epidemiology & Biostatistics, School of Public Health, Peking University Health Science Center, Peking University, Beijing, 100191, China
| | - Yunping Lei
- Center for Precision Environmental Health, Departments of Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yongyan Chen
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory for Reproductive Health; Department of Epidemiology & Biostatistics, School of Public Health, Peking University Health Science Center, Peking University, Beijing, 100191, China
| | - Yinnan Guo
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory for Reproductive Health; Department of Epidemiology & Biostatistics, School of Public Health, Peking University Health Science Center, Peking University, Beijing, 100191, China
| | - Lei Jin
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory for Reproductive Health; Department of Epidemiology & Biostatistics, School of Public Health, Peking University Health Science Center, Peking University, Beijing, 100191, China
| | - Richard H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Linlin Wang
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory for Reproductive Health; Department of Epidemiology & Biostatistics, School of Public Health, Peking University Health Science Center, Peking University, Beijing, 100191, China.
| | - Aiguo Ren
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory for Reproductive Health; Department of Epidemiology & Biostatistics, School of Public Health, Peking University Health Science Center, Peking University, Beijing, 100191, China.
| |
Collapse
|
37
|
Are Steroid Hormones Dysregulated in Autistic Girls? Diseases 2020; 8:diseases8010006. [PMID: 32183287 PMCID: PMC7151154 DOI: 10.3390/diseases8010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 01/04/2023] Open
Abstract
Evidence of altered cholesterol and steroid hormones in autism is increasing. However, as boys are more often affected, evidence mainly relates to autistic males, whereas evidence for affected autistic girls is sparse. Therefore, a comprehensive gas chromatography mass spectrometry-based steroid hormone metabolite analysis was conducted from autistic girls. Results show increased levels of several steroid hormones, especially in the class of androgens in autistic girls such as testosterone or androstenediol. The increase of the majority of steroid hormones in autistic girls is probably best explained multifactorially by a higher substrate provision in line with the previously developed cholesterol hypothesis of autism.
Collapse
|
38
|
Botton MR, Lu X, Zhao G, Repnikova E, Seki Y, Gaedigk A, Schadt EE, Edelmann L, Scott SA. Structural variation at the CYP2C locus: Characterization of deletion and duplication alleles. Hum Mutat 2020; 40:e37-e51. [PMID: 31260137 DOI: 10.1002/humu.23855] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/11/2019] [Accepted: 06/25/2019] [Indexed: 12/27/2022]
Abstract
The human CYP2C locus harbors the polymorphic CYP2C18, CYP2C19, CYP2C9, and CYP2C8 genes, and of these, CYP2C19 and CYP2C9 are directly involved in the metabolism of ~15% of all medications. All variant CYP2C19 and CYP2C9 star (*) allele haplotypes currently cataloged by the Pharmacogene Variation (PharmVar) Consortium are defined by sequence variants. To determine if structural variation also occurs at the CYP2C locus, the 10q23.33 region was interrogated across deidentified clinical chromosomal microarray (CMA) data from 20,642 patients tested at two academic medical centers. Fourteen copy number variants that affected the coding region of CYP2C genes were detected in the clinical CMA cohorts, which ranged in size from 39.2 to 1,043.3 kb. Selected deletions and duplications were confirmed by MLPA or ddPCR. Analysis of the clinical CMA and an additional 78,839 cases from the Database of Genomic Variants (DGV) and ClinGen (total n = 99,481) indicated that the carrier frequency of a CYP2C structural variant is ~1 in 1,000, with ~1 in 2,000 being a CYP2C19 full gene or partial-gene deletion carrier, designated by PharmVar as CYP2C19*36 and *37, respectively. Although these structural variants are rare in the general population, their detection will likely improve metabolizer phenotype prediction when interrogated for research and/or clinical testing.
Collapse
Affiliation(s)
- Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Xingwu Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Geping Zhao
- Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Elena Repnikova
- Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, Missouri.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| |
Collapse
|
39
|
Hui K, Katayama Y, Nakayama KI, Nomura J, Sakurai T. Characterizing vulnerable brain areas and circuits in mouse models of autism: Towards understanding pathogenesis and new therapeutic approaches. Neurosci Biobehav Rev 2020; 110:77-91. [DOI: 10.1016/j.neubiorev.2018.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/30/2018] [Accepted: 08/02/2018] [Indexed: 12/19/2022]
|
40
|
Yi HC, You ZH, Wang MN, Guo ZH, Wang YB, Zhou JR. RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information. BMC Bioinformatics 2020; 21:60. [PMID: 32070279 PMCID: PMC7029608 DOI: 10.1186/s12859-020-3406-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/11/2020] [Indexed: 01/03/2023] Open
Abstract
Background The interactions between non-coding RNAs (ncRNA) and proteins play an essential role in many biological processes. Several high-throughput experimental methods have been applied to detect ncRNA-protein interactions. However, these methods are time-consuming and expensive. Accurate and efficient computational methods can assist and accelerate the study of ncRNA-protein interactions. Results In this work, we develop a stacking ensemble computational framework, RPI-SE, for effectively predicting ncRNA-protein interactions. More specifically, to fully exploit protein and RNA sequence feature, Position Weight Matrix combined with Legendre Moments is applied to obtain protein evolutionary information. Meanwhile, k-mer sparse matrix is employed to extract efficient feature of ncRNA sequences. Finally, an ensemble learning framework integrated different types of base classifier is developed to predict ncRNA-protein interactions using these discriminative features. The accuracy and robustness of RPI-SE was evaluated on three benchmark data sets under five-fold cross-validation and compared with other state-of-the-art methods. Conclusions The results demonstrate that RPI-SE is competent for ncRNA-protein interactions prediction task with high accuracy and robustness. It’s anticipated that this work can provide a computational prediction tool to advance ncRNA-protein interactions related biomedical research.
Collapse
Affiliation(s)
- Hai-Cheng Yi
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhu-Hong You
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Mei-Neng Wang
- School of Mathematics and Computer Science, Yichun University, Yichun, 336000, China
| | - Zhen-Hao Guo
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Yan-Bin Wang
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Ji-Ren Zhou
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Xinjiang Technical Institutes of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, China
| |
Collapse
|
41
|
Zhao L, Lee VHF, Ng MK, Yan H, Bijlsma MF. Molecular subtyping of cancer: current status and moving toward clinical applications. Brief Bioinform 2020; 20:572-584. [PMID: 29659698 DOI: 10.1093/bib/bby026] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/01/2018] [Indexed: 12/14/2022] Open
Abstract
Cancer is a collection of genetic diseases, with large phenotypic differences and genetic heterogeneity between different types of cancers and even within the same cancer type. Recent advances in genome-wide profiling provide an opportunity to investigate global molecular changes during the development and progression of cancer. Meanwhile, numerous statistical and machine learning algorithms have been designed for the processing and interpretation of high-throughput molecular data. Molecular subtyping studies have allowed the allocation of cancer into homogeneous groups that are considered to harbor similar molecular and clinical characteristics. Furthermore, this has helped researchers to identify both actionable targets for drug design as well as biomarkers for response prediction. In this review, we introduce five frequently applied techniques for generating molecular data, which are microarray, RNA sequencing, quantitative polymerase chain reaction, NanoString and tissue microarray. Commonly used molecular data for cancer subtyping and clinical applications are discussed. Next, we summarize a workflow for molecular subtyping of cancer, including data preprocessing, cluster analysis, supervised classification and subtype characterizations. Finally, we identify and describe four major challenges in the molecular subtyping of cancer that may preclude clinical implementation. We suggest that standardized methods should be established to help identify intrinsic subgroup signatures and build robust classifiers that pave the way toward stratified treatment of cancer patients.
Collapse
Affiliation(s)
- Lan Zhao
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong
| | - Victor H F Lee
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Michael K Ng
- Centre for Mathematical Imaging and Vision and Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Hong Yan
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Academic Medical Center, Amsterdam, The Netherlands
| |
Collapse
|
42
|
McClain L, Segreti AM, Nau S, Shaw P, Finegold DN, Pan LA, Peters DG. Chromosome 15q13.3 microduplications are associated with treatment refractory major depressive disorder. GENES BRAIN AND BEHAVIOR 2019; 19:e12628. [PMID: 31828948 DOI: 10.1111/gbb.12628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/18/2019] [Accepted: 12/02/2019] [Indexed: 12/25/2022]
Abstract
Major depressive disorder (MDD) affects approximately 15 million Americans. Approximately 2 million of these are classified as being refractory to treatment (TR-MDD). Because of the lack of available therapies for TR-MDD, and the high risk of suicide, there is interest in identifying new treatment modalities and diagnostic methods. Understanding of the impact of genomic copy number variation in the etiology of a variety of neuropsychiatric phenotypes is increasing. Low copy repeat elements at 15q13.3 facilitate non-allelic homologous recombination, resulting in recurrent copy number variants (CNVs). Numerous reports have described association between microdeletions in this region and a variety of neuropsychiatric phenotypes, with CHRNA7 implicated as a candidate gene. However, the pathogenicity of 15q13.3 duplications is less clear. As part of an ongoing study, in which we have identified a number of metabolomic anomalies in spinal fluid from TR-MDD patients, we also evaluated genomic copy number variation in patients (n = 125) and controls (n = 26) via array-based copy number genomic hybridization (CGH); the case frequency was compared with frequencies reported in a prior study as well as a larger population-sized cohort. We identified five TR-MDD patients with microduplications involving CHRNA7. CHRNA7 duplications are the most common CNVs identified by clinical CGH in this cohort. Therefore, this study provides insight into the potential involvement of CHRNA7 duplications in the etiology of TR-MDD and informs those involved with care of affected individuals.
Collapse
Affiliation(s)
- Lora McClain
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anna M Segreti
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sharon Nau
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patricia Shaw
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - David N Finegold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lisa A Pan
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David G Peters
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
43
|
Lauhasurayotin S, Cuvelier GD, Klaassen RJ, Fernandez CV, Pastore YD, Abish S, Rayar M, Steele M, Jardine L, Breakey VR, Brossard J, Sinha R, Silva M, Goodyear L, Lipton JH, Michon B, Corriveau-Bourque C, Sung L, Shabanova I, Li H, Zlateska B, Dhanraj S, Cada M, Scherer SW, Dror Y. Reanalysing genomic data by normalized coverage values uncovers CNVs in bone marrow failure gene panels. NPJ Genom Med 2019; 4:30. [PMID: 31839986 PMCID: PMC6901453 DOI: 10.1038/s41525-019-0104-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/04/2019] [Indexed: 11/09/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included RPS19, RPL11, and RPL5. A diagnosis of GATA2-related disorder was made in a patient with myelodysplastic syndrome who was found to have a heterozygous GATA2 deletion. Importantly, homozygous FANCA deletion were detected in a patient who could not be previously assigned a specific syndromic diagnosis. Lastly, we identified compound heterozygousity for deletions and pathogenic point variants in RBM8A and PARN genes. All deletions were validated by orthogonal methods. We conclude that careful analysis of normalized coverage values can detect CNVs in NGS panels and should be considered as a standard practice prior to do further investigations.
Collapse
Affiliation(s)
- Supanun Lauhasurayotin
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Geoff D Cuvelier
- 3Pediatric Hematology-Oncology-Bone Marrow Transplantation, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB Canada
| | - Robert J Klaassen
- 4Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON Canada
| | | | | | - Sharon Abish
- 7Pediatric Hematology Oncology, Montreal Children's Hospital, Montreal, QC Canada
| | - Meera Rayar
- 8Division of Hematology/Oncology, UBC & B.C. Children's Hospital, Vancouver, BC Canada
| | | | - Lawrence Jardine
- 10Children's Hospital, London Health Sciences Centre, London, ON Canada
| | - Vicky R Breakey
- 11Department of Pediatrics, McMaster University, Hamilton, ON Canada
| | - Josee Brossard
- 12Centre hospitalier universitaire, Sherbrooke, QC Canada
| | - Roona Sinha
- 13Royal University Hospital, Saskatoon, SK Canada
| | | | - Lisa Goodyear
- 15Pediatric Hematology/Oncology, Janeway Child Health Centre, St. John's, NF Canada
| | - Jeffrey H Lipton
- 16Allogeneic Blood and Marrow Transplant Program, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON Canada
| | - Bruno Michon
- 17Centre Hospitalier Universitaire de Quebec, Sainte-Foy, QC Canada
| | | | - Lillian Sung
- 19Population Health Sciences, Research Institute, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Iren Shabanova
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Hongbing Li
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Bozana Zlateska
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Santhosh Dhanraj
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,20Institute of Medical Science, University of Toronto, Toronto, ON Canada
| | - Michaela Cada
- 2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Stephen W Scherer
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,21McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Yigal Dror
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada.,20Institute of Medical Science, University of Toronto, Toronto, ON Canada
| |
Collapse
|
44
|
Jutla A, Turner JB, Green Snyder L, Chung WK, Veenstra-VanderWeele J. Psychotic symptoms in 16p11.2 copy-number variant carriers. Autism Res 2019; 13:187-198. [PMID: 31724820 DOI: 10.1002/aur.2232] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 01/26/2023]
Abstract
16p11.2 copy-number variation (CNV) is implicated in neurodevelopmental disorders, with the duplication and deletion associated with autism spectrum disorder (ASD) and the duplication associated with schizophrenia (SCZ). The 16p11.2 CNV may therefore provide insight into the relationship between ASD and SCZ, distinct disorders that co-occur at an elevated rate, and are difficult to distinguish from each other and from common co-occurring diagnoses such as obsessive compulsive disorder (OCD), itself a potential risk factor for SCZ. As psychotic symptoms are core to SCZ but distinct from ASD, we sought to examine their predictors in a population (n = 546) of 16p11.2 CNV carriers and their noncarrier siblings recruited by the Simons Variation in Individuals Project. We hypothesized that psychotic symptoms would be most common in duplication carriers followed by deletion carriers and noncarriers, that an ASD diagnosis would predict psychotic symptoms among CNV carriers, and that OCD symptoms would predict psychotic symptoms among all participants. Using data collected across multiple measures, we identified 19 participants with psychotic symptoms. Logistic regression models adjusting for biological sex, age, and IQ found that 16p11.2 duplication and ASD diagnosis predicted psychotic symptom presence. Our findings suggest that the association between 16p11.2 duplication and psychotic symptoms is independent of ASD diagnosis and that ASD diagnosis and psychotic symptoms may be associated in 16p11.2 CNV carriers. Autism Res 2020, 13: 187-198. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Either deletion or duplication at chromosome 16p11.2 raises the risk of autism spectrum disorder, and duplication, but not deletion, has been reported in schizophrenia (SCZ). In a sample of 16p11.2 deletion and duplication carriers, we found that having the duplication or having an autism diagnosis may increase the risk of psychosis, a key feature of SCZ.
Collapse
Affiliation(s)
- Amandeep Jutla
- Department of Psychiatry, Columbia University, New York, New York.,New York State Psychiatric Institute, New York, New York
| | - J Blake Turner
- Department of Psychiatry, Columbia University, New York, New York.,New York State Psychiatric Institute, New York, New York
| | | | - Wendy K Chung
- Department of Pediatrics and Department of Medicine, Columbia University, New York, New York
| | - Jeremy Veenstra-VanderWeele
- Department of Psychiatry, Columbia University, New York, New York.,New York State Psychiatric Institute, New York, New York.,Center for Autism and the Developing Brain, New York-Presbyterian Hospital, New York, New York
| |
Collapse
|
45
|
Zarrei M, Burton CL, Engchuan W, Young EJ, Higginbotham EJ, MacDonald JR, Trost B, Chan AJS, Walker S, Lamoureux S, Heung T, Mojarad BA, Kellam B, Paton T, Faheem M, Miron K, Lu C, Wang T, Samler K, Wang X, Costain G, Hoang N, Pellecchia G, Wei J, Patel RV, Thiruvahindrapuram B, Roifman M, Merico D, Goodale T, Drmic I, Speevak M, Howe JL, Yuen RKC, Buchanan JA, Vorstman JAS, Marshall CR, Wintle RF, Rosenberg DR, Hanna GL, Woodbury-Smith M, Cytrynbaum C, Zwaigenbaum L, Elsabbagh M, Flanagan J, Fernandez BA, Carter MT, Szatmari P, Roberts W, Lerch J, Liu X, Nicolson R, Georgiades S, Weksberg R, Arnold PD, Bassett AS, Crosbie J, Schachar R, Stavropoulos DJ, Anagnostou E, Scherer SW. A large data resource of genomic copy number variation across neurodevelopmental disorders. NPJ Genom Med 2019; 4:26. [PMID: 31602316 PMCID: PMC6779875 DOI: 10.1038/s41525-019-0098-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/05/2019] [Indexed: 12/29/2022] Open
Abstract
Copy number variations (CNVs) are implicated across many neurodevelopmental disorders (NDDs) and contribute to their shared genetic etiology. Multiple studies have attempted to identify shared etiology among NDDs, but this is the first genome-wide CNV analysis across autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), and obsessive-compulsive disorder (OCD) at once. Using microarray (Affymetrix CytoScan HD), we genotyped 2,691 subjects diagnosed with an NDD (204 SCZ, 1,838 ASD, 427 ADHD and 222 OCD) and 1,769 family members, mainly parents. We identified rare CNVs, defined as those found in <0.1% of 10,851 population control samples. We found clinically relevant CNVs (broadly defined) in 284 (10.5%) of total subjects, including 22 (10.8%) among subjects with SCZ, 209 (11.4%) with ASD, 40 (9.4%) with ADHD, and 13 (5.6%) with OCD. Among all NDD subjects, we identified 17 (0.63%) with aneuploidies and 115 (4.3%) with known genomic disorder variants. We searched further for genes impacted by different CNVs in multiple disorders. Examples of NDD-associated genes linked across more than one disorder (listed in order of occurrence frequency) are NRXN1, SEH1L, LDLRAD4, GNAL, GNG13, MKRN1, DCTN2, KNDC1, PCMTD2, KIF5A, SYNM, and long non-coding RNAs: AK127244 and PTCHD1-AS. We demonstrated that CNVs impacting the same genes could potentially contribute to the etiology of multiple NDDs. The CNVs identified will serve as a useful resource for both research and diagnostic laboratories for prioritization of variants.
Collapse
Affiliation(s)
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Christie L. Burton
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Edwin J. Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Edward J. Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Jeffrey R. MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Ada J. S. Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON Canada
| | - Bahareh A. Mojarad
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Barbara Kellam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Tara Paton
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Muhammad Faheem
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Karin Miron
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Chao Lu
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Ting Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Kozue Samler
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Xiaolin Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada
- Medical Genetics Residency Training Program, University of Toronto, Toronto, ON Canada
| | - Ny Hoang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Rohan V. Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | | | - Maian Roifman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON Canada
- Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Deep Genomics Inc., Toronto, ON Canada
| | - Tara Goodale
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Irene Drmic
- Hamilton Health Sciences, Ron Joyce Children’s Health Centre, Hamilton, On Canada
| | - Marsha Speevak
- Trillium Health Partners Credit Valley Site, Mississauga, Ontario Canada
| | - Jennifer L. Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Ryan K. C. Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Janet A. Buchanan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Jacob A. S. Vorstman
- Department of Psychiatry, University of Toronto, Toronto, ON Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Richard F. Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - David R. Rosenberg
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, MI USA
- The Children’s Hospital of Michigan, Detroit, MI United States
| | - Gregory L. Hanna
- Department of Psychiatry, University of Michigan, Ann Arbor, MI USA
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Cheryl Cytrynbaum
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada
- Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, Toronto, ON Canada
| | | | - Mayada Elsabbagh
- Montreal Neurological Institute, McGill University, Montreal, QC Canada
| | - Janine Flanagan
- Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Bridget A. Fernandez
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL Canada
| | - Melissa T. Carter
- Regional Genetics Program, The Children’s Hospital of Eastern Ontario, Ottawa, ON Canada
| | - Peter Szatmari
- Department of Psychiatry, University of Toronto, Toronto, ON Canada
- Centre for Addiction and Mental Health, Toronto, ON Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON Canada
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
| | - Jason Lerch
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON Canada
| | - Xudong Liu
- Department of Psychiatry, Queen’s University, Kinston, ON Canada
| | - Rob Nicolson
- Children’s Health Research Institute, London, ON Canada
- Western University, London, ON Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada
| | - Paul D. Arnold
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB Canada
- Departments of Psychiatry and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON Canada
- Department of Psychiatry, University of Toronto, Toronto, ON Canada
- The Dalglish Family 22q Clinic, Toronto General Hospital, Toronto, ON Canada
| | - Jennifer Crosbie
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada
- Department of Psychiatry, University of Toronto, Toronto, ON Canada
| | - Russell Schachar
- Neurosciences and Mental Health Program, The Hospital for Sick Children, Toronto, ON Canada
- Department of Psychiatry, University of Toronto, Toronto, ON Canada
- Institute of Medical Science, University of Toronto, Toronto, ON Canada
| | - Dimitri J. Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, University of Toronto, Toronto, ON Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON Canada
| |
Collapse
|
46
|
Lee C, Kang EY, Gandal MJ, Eskin E, Geschwind DH. Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage. Nat Neurosci 2019; 22:1521-1532. [PMID: 31455884 PMCID: PMC6750256 DOI: 10.1038/s41593-019-0461-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/09/2019] [Indexed: 12/21/2022]
Abstract
One fundamental but understudied mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expression of one allele. We leveraged RNA-sequencing data from human brain to assess ASE in autism spectrum disorder (ASD). When ASE is observed in ASD, the allele with lower population frequency (minor allele) is preferentially more highly expressed than the major allele, opposite to the canonical pattern. Importantly, genes showing ASE in ASD are enriched in those downregulated in ASD postmortem brains and in genes harboring de novo mutations in ASD. Two regions, 14q32 and 15q11, containing all known orphan C/D box small nucleolar RNAs (snoRNAs), are particularly enriched in shifts to higher minor allele expression. We demonstrate that this allele shifting enhances snoRNA-targeted splicing changes in ASD-related target genes in idiopathic ASD and 15q11-q13 duplication syndrome. Together, these results implicate allelic imbalance and dysregulation of orphan C/D box snoRNAs in ASD pathogenesis.
Collapse
Affiliation(s)
- Changhoon Lee
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eun Yong Kang
- Department of Computer Science, Henry Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, Henry Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
47
|
Keel BN, Nonneman DJ, Lindholm-Perry AK, Oliver WT, Rohrer GA. A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence. Front Genet 2019; 10:737. [PMID: 31475038 PMCID: PMC6707380 DOI: 10.3389/fgene.2019.00737] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties. In this work, we identified and characterized CNV by utilizing whole-genome sequence from 240 members of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the purebred founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Using a combination of split reads, paired-end mapping, and read depth approaches, we identified a total of 3,538 copy number variable regions (CNVRs), including 1,820 novel CNVRs not reported in previous studies. The CNVRs covered 0.94% of the porcine genome and overlapped 1,401 genes. Gene ontology analysis identified that CNV-overlapped genes were enriched for functions related to organism development. Additionally, CNVRs overlapped with many known quantitative trait loci (QTL). In particular, analysis of QTL previously identified in the USMARC herd showed that CNVRs were most overlapped with reproductive traits, such as age of puberty and ovulation rate, and CNVRs were significantly enriched for reproductive QTL.
Collapse
Affiliation(s)
- Brittney N Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | | | - William T Oliver
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Gary A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| |
Collapse
|
48
|
Bonati MT, Castronovo C, Sironi A, Zimbalatti D, Bestetti I, Crippa M, Novelli A, Loddo S, Dentici ML, Taylor J, Devillard F, Larizza L, Finelli P. 9q34.3 microduplications lead to neurodevelopmental disorders through EHMT1 overexpression. Neurogenetics 2019; 20:145-154. [PMID: 31209758 DOI: 10.1007/s10048-019-00581-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022]
Abstract
Both copy number losses and gains occur within subtelomeric 9q34 region without common breakpoints. The microdeletions cause Kleefstra syndrome (KS), whose responsible gene is EHMT1. A 9q34 duplication syndrome (9q34 DS) had been reported in literature, but it has never been characterized by a detailed molecular analysis of the gene content and endpoints. To the best of our knowledge, we report on the first patient carrying the smallest 9q34.3 duplication containing EHMT1 as the only relevant gene. We compared him with 21 reported patients described here as carrying 9q34.3 duplications encompassing the entire gene and extending within ~ 3 Mb. By surveying the available clinical and molecular cytogenetic data, we were able to discover that similar neurodevelopmental disorders (NDDs) were shared by patient carriers of even very differently sized duplications. Moreover, some facial features of the 9q34 DS were more represented than those of KS. However, an accurate in silico analysis of the genes mapped in all the duplications allowed us to support EHMT1 as being sufficient to cause a NDD phenotype. Wider patient cohorts are needed to ascertain whether the rearrangements have full causative role or simply confer the susceptibility to NDDs and possibly to identify the cognitive and behavioral profile associated with the increased dosage of EHMT1.
Collapse
Affiliation(s)
- Maria Teresa Bonati
- Istituto Auxologico Italiano, IRCCS, Clinic of Medical Genetics, Piazzale Brescia 20, 20149, Milan, Italy.
| | - Chiara Castronovo
- Research Lab of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145, Milan, Italy
| | - Alessandra Sironi
- Research Lab of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Milan, Italy
| | - Dario Zimbalatti
- Istituto Auxologico Italiano, IRCCS, Clinic of Medical Genetics, Piazzale Brescia 20, 20149, Milan, Italy
| | - Ilaria Bestetti
- Research Lab of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Milan, Italy
| | - Milena Crippa
- Research Lab of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Milan, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Juliet Taylor
- Genetic Health Service New Zealand - Northern Hub, Auckland, New Zealand
| | - Françoise Devillard
- Département de Génétique et Procréation Hôpital Couple-Enfant, CHU Grenoble Alpes, 38043, Grenoble, France
| | - Lidia Larizza
- Research Lab of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145, Milan, Italy
| | - Palma Finelli
- Research Lab of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, 20145, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Milan, Italy
| |
Collapse
|
49
|
Analysis of a Protein Network Related to Copy Number Variations in Autism Spectrum Disorder. J Mol Neurosci 2019; 69:140-149. [DOI: 10.1007/s12031-019-01343-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 05/22/2019] [Indexed: 01/17/2023]
|
50
|
Suga H, Oka T, Sugaya M, Sato Y, Ishii T, Nishida H, Ishikawa S, Fukayama M, Sato S. Keratinocyte Proline-Rich Protein Deficiency in Atopic Dermatitis Leads to Barrier Disruption. J Invest Dermatol 2019; 139:1867-1875.e7. [PMID: 30905808 DOI: 10.1016/j.jid.2019.02.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 01/03/2023]
Abstract
Atopic dermatitis is a common inflammatory skin disease caused by the interaction of genetic and environmental factors. By allelic copy number analysis at missense single-nucleotide polymorphisms on 26 genes with copy number variation, we identified a significant association between atopic dermatitis and human KPRP. Human KPRP expression, which was localized to the upper granular layer of epidermis, was significantly decreased in atopic dermatitis compared with normal skin. KPRP was histologically colocalized with loricrin and was mainly detected in cytoskeleton fractions of human keratinocytes. To further investigate the role of KPRP in skin, Kprp-knockout mice were generated. Heterozygous knockout (Kprp+/-) mice exhibited reduced KPRP expression to level a similar to that of human AD lesional skin. Kprp+/- mice showed abnormal desmosome structure and detachment of lower layers of the stratum corneum. Percutaneous inflammation by topical application of croton oil or oxazolone was enhanced, and epicutaneous immunization with ovalbumin induced a high level of IgE in Kprp+/- mice. Our study, started from allelic copy number analysis in human AD, identified the importance of KPRP, the decrease of which leads to barrier dysfunction.
Collapse
MESH Headings
- Adjuvants, Immunologic/administration & dosage
- Animals
- Case-Control Studies
- Croton Oil/immunology
- Cytoskeletal Proteins/deficiency
- Cytoskeletal Proteins/genetics
- DNA Copy Number Variations
- Dermatitis, Atopic/chemically induced
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/immunology
- Dermatitis, Atopic/pathology
- Desmosomes/pathology
- Desmosomes/ultrastructure
- Disease Models, Animal
- Epidermis/drug effects
- Epidermis/immunology
- Epidermis/pathology
- Humans
- Intracellular Signaling Peptides and Proteins/deficiency
- Intracellular Signaling Peptides and Proteins/genetics
- Keratinocytes/drug effects
- Keratinocytes/immunology
- Keratinocytes/pathology
- Mice
- Mice, Knockout
- Microscopy, Electron, Transmission
- Oxazolone/immunology
- Proteins/genetics
- Proteins/metabolism
- Water Loss, Insensible/genetics
Collapse
Affiliation(s)
- Hiraku Suga
- Department of Dermatology, the University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Tomonori Oka
- Department of Dermatology, the University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Makoto Sugaya
- Department of Dermatology, the University of Tokyo Graduate School of Medicine, Tokyo, Japan; Department of Dermatology, International University of Health and Welfare, Chiba, Japan.
| | - Yasunari Sato
- Research and Development Division, Rohto Pharmaceutical Company, Osaka, Japan
| | - Tsuyoshi Ishii
- Research and Development Division, Rohto Pharmaceutical Company, Osaka, Japan
| | - Hiroyuki Nishida
- Research and Development Division, Rohto Pharmaceutical Company, Osaka, Japan
| | - Shumpei Ishikawa
- Department of Pathology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Shinichi Sato
- Department of Dermatology, the University of Tokyo Graduate School of Medicine, Tokyo, Japan
| |
Collapse
|