1
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Massier M, Doco-Fenzy M, Egloff M, Le Guillou X, Le Guyader G, Redon S, Benech C, Le Millier K, Uguen K, Ropars J, Sacaze E, Audebert-Bellanger S, Apetrei A, Molin A, Gruchy N, Vincent-Devulder A, Spodenkiewicz M, Jacquin C, Loron G, Thibaud M, Delplancq G, Brisset S, Lesieur-Sebellin M, Malan V, Romana S, Rio M, Marlin S, Amiel J, Marquet V, Dauriat B, Moradkhani K, Mercier S, Isidor B, Arpin S, Pujalte M, Jedraszak G, Pebrel-Richard C, Salaun G, Laffargue F, Boudjarane J, Missirian C, Chelloug N, Toutain A, Chiesa J, Keren B, Mignot C, Gouy E, Jaillard S, Landais E, Poirsier C. 3q29 duplications: A cohort of 46 patients and a literature review. Am J Med Genet A 2024; 194:e63531. [PMID: 38421086 DOI: 10.1002/ajmg.a.63531] [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: 09/20/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024]
Abstract
Duplications of the 3q29 cytoband are rare chromosomal copy number variations (CNVs) (overlapping or recurrent ~1.6 Mb 3q29 duplications). They have been associated with highly variable neurodevelopmental disorders (NDDs) with various associated features or reported as a susceptibility factor to the development of learning disabilities and neuropsychiatric disorders. The smallest region of overlap and the phenotype of 3q29 duplications remain uncertain. We here report a French cohort of 31 families with a 3q29 duplication identified by chromosomal microarray analysis (CMA), including 14 recurrent 1.6 Mb duplications, eight overlapping duplications (>1 Mb), and nine small duplications (<1 Mb). Additional genetic findings that may be involved in the phenotype were identified in 11 patients. Focusing on apparently isolated 3q29 duplications, patients present mainly mild NDD as suggested by a high rate of learning disabilities in contrast to a low proportion of patients with intellectual disabilities. Although some are de novo, most of the 3q29 duplications are inherited from a parent with a similar mild phenotype. Besides, the study of small 3q29 duplications does not provide evidence for any critical region. Our data suggest that the overlapping and recurrent 3q29 duplications seem to lead to mild NDD and that a severe or syndromic clinical presentation should warrant further genetic analyses.
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Affiliation(s)
- Marie Massier
- Department of Genetics, Reims University Hospital, Reims, France
| | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Matthieu Egloff
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, INSERM, LNEC, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | - Xavier Le Guillou
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, CNRS, LMA, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | | | - Sylvia Redon
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Caroline Benech
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Kevin Uguen
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Juliette Ropars
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Elise Sacaze
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Andreea Apetrei
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Arnaud Molin
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Nicolas Gruchy
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Aline Vincent-Devulder
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | - Gauthier Loron
- Department of Neonatal Medicine and Pediatric Intensive Care, University of Reims Champagne-Ardenne, CReSTIC, Reims University Hospital, Reims, France
| | - Marie Thibaud
- Department of Pediatrics, American Memorial Hospital, Reims, France
| | | | - Sophie Brisset
- Constitutional Genetics Unit, Versailles Hospital, Le Chesnay, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valérie Malan
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Serge Romana
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Sandrine Marlin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valentine Marquet
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | | | - Sandra Mercier
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Stéphanie Arpin
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | | | - Guillaume Jedraszak
- Constitutional Genetic Laboratory, University Hospital of Amiens & UR4666 HEMATIM, University of Picardie Jules Verne, Amiens, France
| | - Céline Pebrel-Richard
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Gaëlle Salaun
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fanny Laffargue
- Department of Medical Genetics, UIC ADDIR (GRIUC ADERGEN), Constitutive Reference Center CLAD South-East: Developmental anomalies and malformative syndromes, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - John Boudjarane
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Chantal Missirian
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Nora Chelloug
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Jean Chiesa
- Department of Genetics, Nimes, University Hospital, Nimes University Hospital, Nimes, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Evan Gouy
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Jaillard
- Department of Cytogenetics and Cell Biology, Rennes university hospital, Rennes, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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2
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Sefik E, Duan K, Li Y, Sholar B, Evans L, Pincus J, Ammar Z, Murphy MM, Klaiman C, Saulnier CA, Pulver SL, Goldman-Yassen AE, Guo Y, Walker EF, Li L, Mulle JG, Shultz S. Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome. Mol Psychiatry 2024:10.1038/s41380-024-02584-8. [PMID: 38744992 DOI: 10.1038/s41380-024-02584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
High-impact genetic variants associated with neurodevelopmental disorders provide biologically-defined entry points for mechanistic investigation. The 3q29 deletion (3q29Del) is one such variant, conferring a 40-100-fold increased risk for schizophrenia, as well as high risk for autism and intellectual disability. However, the mechanisms leading to neurodevelopmental disability remain largely unknown. Here, we report the first in vivo quantitative neuroimaging study in individuals with 3q29Del (N = 24) and neurotypical controls (N = 1608) using structural MRI. Given prior radiology reports of posterior fossa abnormalities in 3q29Del, we focused our investigation on the cerebellum and its tissue-types and lobules. Additionally, we compared the prevalence of cystic/cyst-like malformations of the posterior fossa between 3q29Del and controls and examined the association between neuroanatomical findings and quantitative traits to probe gene-brain-behavior relationships. 3q29Del participants had smaller cerebellar cortex volumes than controls, before and after correction for intracranial volume (ICV). An anterior-posterior gradient emerged in finer grained lobule-based and voxel-wise analyses. 3q29Del participants also had larger cerebellar white matter volumes than controls following ICV-correction and displayed elevated rates of posterior fossa arachnoid cysts and mega cisterna magna findings independent of cerebellar volume. Cerebellar white matter and subregional gray matter volumes were associated with visual-perception and visual-motor integration skills as well as IQ, while cystic/cyst-like malformations yielded no behavioral link. In summary, we find that abnormal development of cerebellar structures may represent neuroimaging-based biomarkers of cognitive and sensorimotor function in 3q29Del, adding to the growing evidence identifying cerebellar pathology as an intersection point between syndromic and idiopathic forms of neurodevelopmental disabilities.
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Affiliation(s)
- Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Kuaikuai Duan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Yiheng Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brittney Sholar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsey Evans
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jordan Pincus
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Zeena Ammar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa M Murphy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheryl Klaiman
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Celine A Saulnier
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Neurodevelopmental Assessment & Consulting Services, Atlanta, GA, USA
| | - Stormi L Pulver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Adam E Goldman-Yassen
- Department of Radiology, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Ying Guo
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elaine F Walker
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Longchuan Li
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA.
| | - Sarah Shultz
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA.
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3
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Mori D, Ikeda R, Sawahata M, Yamaguchi S, Kodama A, Hirao T, Arioka Y, Okumura H, Inami C, Suzuki T, Hayashi Y, Kato H, Nawa Y, Miyata S, Kimura H, Kushima I, Aleksic B, Mizoguchi H, Nagai T, Nakazawa T, Hashimoto R, Kaibuchi K, Kume K, Yamada K, Ozaki N. Phenotypes for general behavior, activity, and body temperature in 3q29 deletion model mice. Transl Psychiatry 2024; 14:138. [PMID: 38453903 PMCID: PMC10920862 DOI: 10.1038/s41398-023-02679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 03/09/2024] Open
Abstract
Whole genome analysis has identified rare copy number variations (CNV) that are strongly involved in the pathogenesis of psychiatric disorders, and 3q29 deletion has been found to have the largest effect size. The 3q29 deletion mice model (3q29-del mice) has been established as a good pathological model for schizophrenia based on phenotypic analysis; however, circadian rhythm and sleep, which are also closely related to neuropsychiatric disorders, have not been investigated. In this study, our aims were to reevaluate the pathogenesis of 3q29-del by recreating model mice and analyzing their behavior and to identify novel new insights into the temporal activity and temperature fluctuations of the mouse model using a recently developed small implantable accelerometer chip, Nano-tag. We generated 3q29-del mice using genome editing technology and reevaluated common behavioral phenotypes. We next implanted Nano-tag in the abdominal cavity of mice for continuous measurements of long-time activity and body temperature. Our model mice exhibited weight loss similar to that of other mice reported previously. A general behavioral battery test in the model mice revealed phenotypes similar to those observed in mouse models of schizophrenia, including increased rearing frequency. Intraperitoneal implantation of Nano-tag, a miniature acceleration sensor, resulted in hypersensitive and rapid increases in the activity and body temperature of 3q29-del mice upon switching to lights-off condition. Similar to the 3q29-del mice reported previously, these mice are a promising model animals for schizophrenia. Successive quantitative analysis may provide results that could help in treating sleep disorders closely associated with neuropsychiatric disorders.
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Affiliation(s)
- Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Brain and Mind Research Center, Nagoya University, Nagoya, Japan.
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Ryosuke Ikeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahito Sawahata
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Japan
- Department of Applied Pharmacology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Sho Yamaguchi
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Akiko Kodama
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Hirao
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuko Arioka
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Hiroki Okumura
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Japan
| | - Chihiro Inami
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Japan
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Toshiaki Suzuki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yu Hayashi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiro Nawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seiko Miyata
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Mizoguchi
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Japan
| | - Taku Nagai
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Japan
- Division of Behavioral Neuropharmacology, International Center for Brain Science (ICBS), Fujita Health University, Toyoake, Japan
| | - Takanobu Nakazawa
- Laboratory of Molecular Biology, Department of Bioscience, Graduate School of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Kozo Kaibuchi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, 1-98 Dengakugakubo, Kusukake-cho, Toyoake, Aichi, Japan
| | - Kazuhiko Kume
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Kiyofumi Yamada
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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4
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Pollak RM, Mortillo M, Murphy MM, Mulle JG. Behavioral Phenotypes and Comorbidity in 3q29 Deletion Syndrome: Results from the 3q29 Registry. J Autism Dev Disord 2024:10.1007/s10803-023-06218-w. [PMID: 38216835 DOI: 10.1007/s10803-023-06218-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
3q29 deletion syndrome (3q29del) is associated with a significantly increased risk for neurodevelopmental and neuropsychiatric disorders. However, the full spectrum of behavioral phenotypes associated with 3q29del is still evolving. Individuals with 3q29del (n = 96, 60.42% male) or their guardian completed the Achenbach Child or Adult Behavior Checklist (CBCL/ABCL) via the online 3q29 registry (3q29deletion.org). Typically developing controls (n = 57, 49.12% male) were ascertained as a comparison group. We analyzed mean performance on the CBCL/ABCL for individuals with 3q29del and controls across composite, DSM-keyed, and developmental scales; and the relationship between CBCL/ABCL performance and clinical and developmental phenotypes for individuals with 3q29del. Individuals with 3q29del showed significantly elevated behavioral and developmental impairment relative to controls across CBCL/ABCL domains. A substantial proportion of study participants with 3q29del scored in the Borderline or Clinical range for composite and DSM-keyed scales, indicating significant behavioral problems that may require clinical evaluation. We found that the preschool CBCL DSM-keyed autism spectrum problems scale is a potential screening tool for autism spectrum disorder (ASD) for individuals with 3q29del; CBCL/ABCL DSM-keyed scales were not accurate screeners for anxiety disorders or attention-deficit/hyperactivity disorder (ADHD) in our study sample. We identified a high degree of psychiatric comorbidity in individuals with 3q29del, with 60.42% (n = 58) of individuals with 3q29del scoring in the Borderline or Clinical range on two or more DSM-keyed CBCL/ABCL scales. Finally, we found that the degree of developmental delay in participants with 3q29del does not explain the increased behavioral problems observed on the CBCL/ABCL. The CBCL/ABCL can be used as screening tools in populations such as 3q29del, even in the presence of substantial psychiatric comorbidity. These results expand our understanding of the phenotypic spectrum of 3q29del and demonstrate an effective method for recruiting and phenotyping a large sample of individuals with a rare genetic disorder.
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Affiliation(s)
- Rebecca M Pollak
- Department of Psychiatry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Ln W, Piscataway, NJ, 08854, USA
| | - Michael Mortillo
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Melissa M Murphy
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Psychiatry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Ln W, Piscataway, NJ, 08854, USA.
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA.
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5
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Purcell RH, Sefik E, Werner E, King AT, Mosley TJ, Merritt-Garza ME, Chopra P, McEachin ZT, Karne S, Raj N, Vaglio BJ, Sullivan D, Firestein BL, Tilahun K, Robinette MI, Warren ST, Wen Z, Faundez V, Sloan SA, Bassell GJ, Mulle JG. Cross-species analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion. SCIENCE ADVANCES 2023; 9:eadh0558. [PMID: 37585521 PMCID: PMC10431714 DOI: 10.1126/sciadv.adh0558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/12/2023] [Indexed: 08/18/2023]
Abstract
The 1.6-megabase deletion at chromosome 3q29 (3q29Del) is the strongest identified genetic risk factor for schizophrenia, but the effects of this variant on neurodevelopment are not well understood. We interrogated the developing neural transcriptome in two experimental model systems with complementary advantages: isogenic human cortical organoids and isocortex from the 3q29Del mouse model. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 and 12 months, as well as perinatal mouse isocortex, all at single-cell resolution. Systematic pathway analysis implicated dysregulation of mitochondrial function and energy metabolism. These molecular signatures were supported by analysis of oxidative phosphorylation protein complex expression in mouse brain and assays of mitochondrial function in engineered cell lines, which revealed a lack of metabolic flexibility and a contribution of the 3q29 gene PAK2. Together, these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species.
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Affiliation(s)
- Ryan H. Purcell
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Erica Werner
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexia T. King
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Trenell J. Mosley
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Zachary T. McEachin
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sridhar Karne
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nisha Raj
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Brandon J. Vaglio
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Dylan Sullivan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Bonnie L. Firestein
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Maxine I. Robinette
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhexing Wen
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Victor Faundez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Steven A. Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J. Bassell
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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6
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Purcell RH, Sefik E, Werner E, King AT, Mosley TJ, Merritt-Garza ME, Chopra P, McEachin ZT, Karne S, Raj N, Vaglio BJ, Sullivan D, Firestein BL, Tilahun K, Robinette MI, Warren ST, Wen Z, Faundez V, Sloan SA, Bassell GJ, Mulle JG. Cross-species transcriptomic analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525748. [PMID: 36747819 PMCID: PMC9901184 DOI: 10.1101/2023.01.27.525748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in the genetics of schizophrenia (SCZ) have identified rare variants that confer high disease risk, including a 1.6 Mb deletion at chromosome 3q29 with a staggeringly large effect size (O.R. > 40). Understanding the impact of the 3q29 deletion (3q29Del) on the developing CNS may therefore lead to insights about the pathobiology of schizophrenia. To gain clues about the molecular and cellular perturbations caused by the 3q29 deletion, we interrogated transcriptomic effects in two experimental model systems with complementary advantages: isogenic human forebrain cortical organoids and isocortex from the 3q29Del mouse model. We first created isogenic lines by engineering the full 3q29Del into an induced pluripotent stem cell line from a neurotypical individual. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 months and 12 months, as well as day p7 perinatal mouse isocortex, all at single cell resolution. Differential expression analysis by genotype in each cell-type cluster revealed that more than half of the differentially expressed genes identified in mouse cortex were also differentially expressed in human cortical organoids, and strong correlations were observed in mouse-human differential gene expression across most major cell-types. We systematically filtered differentially expressed genes to identify changes occurring in both model systems. Pathway analysis on this filtered gene set implicated dysregulation of mitochondrial function and energy metabolism, although the direction of the effect was dependent on developmental timepoint. Transcriptomic changes were validated at the protein level by analysis of oxidative phosphorylation protein complexes in mouse brain tissue. Assays of mitochondrial function in human heterologous cells further confirmed robust mitochondrial dysregulation in 3q29Del cells, and these effects are partially recapitulated by ablation of the 3q29Del gene PAK2 . Taken together these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species. These results converge with data from other rare SCZ-associated variants as well as idiopathic schizophrenia, suggesting that mitochondrial dysfunction may be a significant but overlooked contributing factor to the development of psychotic disorders. This cross-species scRNA-seq analysis of the SCZ-associated 3q29 deletion reveals that this copy number variant may produce early and persistent changes in cellular metabolism that are relevant to human neurodevelopment.
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7
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Miyahara K, Hino M, Shishido R, Nagaoka A, Izumi R, Hayashi H, Kakita A, Yabe H, Tomita H, Kunii Y. Identification of schizophrenia symptom-related gene modules by postmortem brain transcriptome analysis. Transl Psychiatry 2023; 13:144. [PMID: 37142572 PMCID: PMC10160042 DOI: 10.1038/s41398-023-02449-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Schizophrenia is a multifactorial disorder, the genetic architecture of which remains unclear. Although many studies have examined the etiology of schizophrenia, the gene sets that contribute to its symptoms have not been fully investigated. In this study, we aimed to identify each gene set associated with corresponding symptoms of schizophrenia using the postmortem brains of 26 patients with schizophrenia and 51 controls. We classified genes expressed in the prefrontal cortex (analyzed by RNA-seq) into several modules by weighted gene co-expression network analysis (WGCNA) and examined the correlation between module expression and clinical characteristics. In addition, we calculated the polygenic risk score (PRS) for schizophrenia from Japanese genome-wide association studies, and investigated the association between the identified gene modules and PRS to evaluate whether genetic background affected gene expression. Finally, we conducted pathway analysis and upstream analysis using Ingenuity Pathway Analysis to clarify the functions and upstream regulators of symptom-related gene modules. As a result, three gene modules generated by WGCNA were significantly correlated with clinical characteristics, and one of these showed a significant association with PRS. Genes belonging to the transcriptional module associated with PRS significantly overlapped with signaling pathways of multiple sclerosis, neuroinflammation, and opioid use, suggesting that these pathways may also be profoundly implicated in schizophrenia. Upstream analysis indicated that genes in the detected module were profoundly regulated by lipopolysaccharides and CREB. This study identified schizophrenia symptom-related gene sets and their upstream regulators, revealing aspects of the pathophysiology of schizophrenia and identifying potential therapeutic targets.
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Affiliation(s)
- Kazusa Miyahara
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Mizuki Hino
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Risa Shishido
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Ryuta Izumi
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hideki Hayashi
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Tohoku University Hospital, Miyagi, Japan
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan.
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8
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Buttermore E, Chamberlain S, Cody J, Costain G, Dang L, DeWoody A, DeWoody Y, Dies K, Eichler E, Girirajan S, Gramm M, Halladay A, Lal D, Lalli M, Levy T, Logsdon G, Lowenstein D, Mefford H, Mulle J, Muotri A, Murphy M, Perez Palma E, Pinter S, Pollak R, Purcell R, Samaco R, Shah B, Singh K, So J, Sundberg M, Veeraragavan S, Vogel-Farley V, Wynshaw-Boris A. Neurodevelopmental copy-number variants: A roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact. Am J Hum Genet 2022; 109:1353-1365. [PMID: 35931048 PMCID: PMC9388383 DOI: 10.1016/j.ajhg.2022.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Copy-number variants and structural variants (CNVs/SVs) drive many neurodevelopmental-related disorders. While many neurodevelopmental-related CNVs/SVs give rise to complex phenotypes, the overlap in phenotypic presentation between independent CNVs can be extensive and provides a motivation for shared approaches. This confluence at the level of clinical phenotype implies convergence in at least some aspects of the underlying genomic mechanisms. With this perspective, our Commission on Novel Technologies for Neurodevelopmental CNVs asserts that the time has arrived to approach neurodevelopmental-related CNVs/SVs as a class of disorders that can be identified, investigated, and treated on the basis of shared mechanisms and/or pathways (e.g., molecular, neurological, or developmental). To identify common etiologic mechanisms among uncommon neurodevelopmental-related disorders and to potentially identify common therapies, it is paramount for teams of scientists, clinicians, and patients to unite their efforts. We bring forward novel, collaborative, and integrative strategies to translational CNV/SV research that engages diverse stakeholders to help expedite therapeutic outcomes. We articulate a clear vision for piloted roadmap strategies to reduce patient/caregiver burden and redundancies, increase efficiency, avoid siloed data, and accelerate translational discovery across CNV/SV-based syndromes.
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Takemoto T, Baba M, Yokoyama K, Kitagawa K, Nagayasu K, Ago Y, Seiriki K, Hayata-Takano A, Kasai A, Mori D, Ozaki N, Takuma K, Hashimoto R, Hashimoto H, Nakazawa T. Molecular brain (micro report) oxytocin ameliorates impaired social behavior in a mouse model of 3q29 deletion syndrome. Mol Brain 2022; 15:26. [PMID: 35346312 PMCID: PMC8962454 DOI: 10.1186/s13041-022-00915-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by specific social symptoms, restricted interests, stereotyped repetitive behaviors, and delayed language development. The 3q29 microdeletion (3q29del), a recurrent copy number variant, confers a high risk for ASD and schizophrenia, and serves as an important pathological model for investigating the molecular pathogenesis of a large number of neurodevelopmental and psychiatric conditions. Recently, mouse models carrying a deletion of the chromosomal region corresponding to the human 3q29 region (Df/+ mice) were generated and demonstrated neurodevelopmental and psychiatric conditions associated behavioral abnormalities, pointing to the relevance of Df/+ mice as a model for these conditions with high construct and face validity. Currently, the molecular pathogenesis of these behavioral phenotypes in Df/+ mice remains unclear. The oxytocin (OXT) system plays a central role in social behavior across species and has a potential role in ASD. In this study, to elucidate the molecular mechanisms behind impaired social behavior in Df/+ mice, we investigated the possible involvement of OXT signaling in impaired social behavior in Df/+ mice. We demonstrated that OXT administration restored the impaired social behavior in Df/+ mice. We also demonstrated that the number of OXT-positive cells in the paraventricular nucleus (PVN) was significantly lower in Df/+ mice than in wild-type (WT) littermates. Consistent with this, the level of OXT peptide in the cerebral cortex of Df/+ mice was lower than in WT littermates. Our study may provide important insights into the molecular pathophysiological basis of neurodevelopmental and psychiatric conditions, including ASD.
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Affiliation(s)
- Tomoya Takemoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masayuki Baba
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazumasa Yokoyama
- Discovery Accelerator, Astellas Pharma Inc., Tsukuba-shi, Ibaraki, 305-8585, Japan
| | - Kohei Kitagawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuki Nagayasu
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.,Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami-ku, Hiroshima, 734-8553, Japan
| | - Kaoru Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.,Interdisciplinary Program for Biomedical Sciences, Institute for Transdisciplinary Graduate Degree Programs, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Atsuko Hayata-Takano
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.,United Graduate School of Child Development, Molecular Research Center for Children's Mental Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kasai
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, 466-8550, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, 466-8550, Japan
| | - Kazuhiro Takuma
- United Graduate School of Child Development, Molecular Research Center for Children's Mental Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan.,Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8553, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan. .,United Graduate School of Child Development, Molecular Research Center for Children's Mental Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka, 565-0871, Japan. .,Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8553, Japan. .,Division of Bioscience, Institute for Datability Science, Osaka University, Suita, Osaka, 565-0871, Japan. .,Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan. .,Department of Molecular Pharmaceutical Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Takanobu Nakazawa
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan. .,Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8553, Japan. .,Laboratory of Molecular Biology, Department of Bioscience, Graduate School of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.
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Metabolic effects of the schizophrenia-associated 3q29 deletion. Transl Psychiatry 2022; 12:66. [PMID: 35177588 PMCID: PMC8854723 DOI: 10.1038/s41398-022-01824-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 01/14/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
The 1.6 Mb 3q29 deletion is associated with developmental and psychiatric phenotypes, including a 40-fold increased risk for schizophrenia. Reduced birth weight and a high prevalence of feeding disorders in patients suggest underlying metabolic dysregulation. We investigated 3q29 deletion-induced metabolic changes using our previously generated heterozygous B6.Del16+/Bdh1-Tfrc mouse model. Animals were provided either standard chow (STD) or high-fat diet (HFD). Growth curves were performed on HFD mice to assess weight change (n = 30-50/group). Indirect calorimetry and untargeted metabolomics were performed on STD and HFD mice to evaluate metabolic phenotypes (n = 8-14/group). A behavioral battery was performed on STD and HFD mice to assess behavior change after the HFD challenge (n = 5-13/group). We found that B6.Del16+/Bdh1-Tfrc animals preferentially use dietary lipids as an energy source. Untargeted metabolomics of liver tissue showed a strong sex-dependent effect of the 3q29 deletion on fat metabolism. A HFD partially rescued the 3q29 deletion-associated weight deficit in females, but not males. Untargeted metabolomics of liver tissue after HFD revealed persistent fat metabolism alterations in females. The HFD did not affect B6.Del16+/Bdh1-Tfrc behavioral phenotypes, suggesting that 3q29 deletion-associated metabolic and behavioral outcomes are uncoupled. Our data suggest that dietary interventions to improve weight phenotypes in 3q29 deletion syndrome patients are unlikely to exacerbate behavioral manifestations. Our study also highlights the importance of assessing sex in metabolic studies and suggests that mechanisms underlying 3q29 deletion-associated metabolic phenotypes are sex-specific.
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11
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Mubarak G, Zahir FR. Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine. J Pers Med 2022; 12:199. [PMID: 35207687 PMCID: PMC8877836 DOI: 10.3390/jpm12020199] [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: 12/21/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/07/2022] Open
Abstract
With the advent of genome-wide screening methods-beginning with microarray technologies and moving onto next generation sequencing methods-the era of precision and personalized medicine was born. Genomics led the way, and its contributions are well recognized. However, "other-omics" fields have rapidly emerged and are becoming as important toward defining disease causes and exploring therapeutic benefits. In this review, we focus on the impacts of transcriptomics, and its extension-epitranscriptomics-on personalized and precision medicine efforts. There has been an explosion of transcriptomic studies particularly in the last decade, along with a growing number of recent epitranscriptomic studies in several disease areas. Here, we summarize and overview major efforts for cancer, cardiovascular disease, and neurodevelopmental disorders (including autism spectrum disorder and intellectual disability) for transcriptomics/epitranscriptomics in precision and personalized medicine. We show that leading advances are being made in both diagnostics, and in investigative and landscaping disease pathophysiological studies. As transcriptomics/epitranscriptomics screens become more widespread, it is certain that they will yield vital and transformative precision and personalized medicine contributions in ways that will significantly further genomics gains.
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Affiliation(s)
| | - Farah R. Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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