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Shin T, Song JHT, Kosicki M, Kenny C, Beck SG, Kelley L, Antony I, Qian X, Bonacina J, Papandile F, Gonzalez D, Scotellaro J, Bushinsky EM, Andersen RE, Maury E, Pennacchio LA, Doan RN, Walsh CA. Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk. CELL GENOMICS 2024; 4:100609. [PMID: 39019033 PMCID: PMC11406188 DOI: 10.1016/j.xgen.2024.100609] [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: 09/20/2023] [Revised: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024]
Abstract
Little is known about the role of non-coding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of non-coding regions: human accelerated regions (HARs), which show signatures of positive selection in humans; experimentally validated neural VISTA enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole-genome analysis of >16,600 samples and >4,900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly contribute, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in VEs near OTX1 and SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved non-coding regions in ASD risk and suggest potential mechanisms of how regulatory changes can modulate social behavior.
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Affiliation(s)
- Taehwan Shin
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Janet H T Song
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Samantha G Beck
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lily Kelley
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA
| | - Irene Antony
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julieta Bonacina
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA
| | - Frances Papandile
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julia Scotellaro
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Evan M Bushinsky
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Rebecca E Andersen
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
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Carvalho Silva R, Martini P, Hohoff C, Mattevi S, Bortolomasi M, Abate M, Menesello V, Gennarelli M, Baune BT, Minelli A. Unraveling epigenomic signatures and effectiveness of electroconvulsive therapy in treatment-resistant depression patients: a prospective longitudinal study. Clin Epigenetics 2024; 16:93. [PMID: 39020437 PMCID: PMC11256624 DOI: 10.1186/s13148-024-01704-z] [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: 02/14/2024] [Accepted: 07/05/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Electroconvulsive therapy (ECT) benefits patients with treatment-resistant depression (TRD), but the underlying biological processes are unclear. We conducted an epigenome-wide association study in 32 TRD patients undergoing ECT to depict ECT-associated methylation changes. Illness severity and ECT outcomes were assessed with the Montgomery-Åsberg Depression Rating Scale at baseline (T0) and 1 month after its end (T1). Methylation was profiled at T0 and T1 with the Illumina Infinium Methylation EPIC BeadChip array. RESULTS Longitudinal T0-T1 analyses showed 3 differentially methylated probes (DMPs) with nominal p values ≤ 10-5, with 2 annotated in the genes CYB5B and PVRL4. Including covariates, we found 4 DMPs for symptoms variation, annotated in FAM20C, EPB41, OTUB1 and ADARB1, and 3 DMPs for response status, with 2 annotated in IQCE and FAM20C. Regional analysis revealed 54 differentially methylated regions (DMRs) with nominal p value area ≤ 0.05, with 9 presenting adjusted p-value area ≤ 0.10, annotated in MCF2L, SLC25A24, RUNX3, MIR637, FOXK2, FAM180B, POU6F1, ALS2CL and CCRL2. Considering covariates, we found 21 DMRs for symptoms variation and 26 DMRs for response (nominal p value area ≤ 0.05), with 4 presenting adjusted p-value area ≤ 0.10 for response, annotated in SNORD34, NLRP6, GALNT2 and SFT2D3. None remained significant after false discovery rate correction. Notably, ADARB1 variants are associated with suicide attempt in patients with psychiatric disorders, and SLC25A24 relates to conduct disorder. Several DMPs and DMRs are annotated in genes associated with inflammatory/immune processes. Longitudinal analyses on females (n = 22) revealed statistically significant DMRs (adjusted p value area ≤ 0.05) and trend-significant DMRs (adjusted p value area ≤ 0.07) for symptoms variation and response status, annotated in genes related to psychiatric disorders (ZFP57, POLD4, TRIM10, GAS7, ADORA2A, TOLLIP), trauma exposure (RIPOR2) and inflammatory/immune responses (LAT, DLX4, POLD4, FAM30A, H19). Pathway analysis on females revealed enrichment for transcriptional activity, growth factors, DNA maintenance, and immune pathways including IRF7 and IRF2. CONCLUSION Although no significant results were found for the whole cohort, the study provides insights into ECT-associated methylation changes, highlighting DMPs and DMRs related to ECT outcomes. Analyses on females revealed significant DMRs and pathways related to psychiatric disorders and inflammatory/immune processes.
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Affiliation(s)
- Rosana Carvalho Silva
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | - Christa Hohoff
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Stefania Mattevi
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | | | - Maria Abate
- Psychiatric Hospital "Villa Santa Chiara", Verona, Italy
| | - Valentina Menesello
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy.
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.
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3
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Shin T, Song JH, Kosicki M, Kenny C, Beck SG, Kelley L, Qian X, Bonacina J, Papandile F, Antony I, Gonzalez D, Scotellaro J, Bushinsky EM, Andersen RE, Maury E, Pennacchio LA, Doan RN, Walsh CA. Rare variation in noncoding regions with evolutionary signatures contributes to autism spectrum disorder risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.19.23295780. [PMID: 37790480 PMCID: PMC10543033 DOI: 10.1101/2023.09.19.23295780] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally validated neural Vista Enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole genome analysis of >16,600 samples and >4900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in a VE near SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved noncoding regions in ASD risk and suggest potential mechanisms of how changes in regulatory regions can modulate social behavior.
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Affiliation(s)
- Taehwan Shin
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Janet H.T. Song
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Michael Kosicki
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Samantha G. Beck
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Lily Kelley
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Julieta Bonacina
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Frances Papandile
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Irene Antony
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Julia Scotellaro
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Evan M. Bushinsky
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Rebecca E. Andersen
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Len A. Pennacchio
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan N. Doan
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
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4
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A Nuclear Belt Fastens on Neural Cell Fate. Cells 2022; 11:cells11111761. [PMID: 35681456 PMCID: PMC9179901 DOI: 10.3390/cells11111761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/22/2022] Open
Abstract
Successful embryonic and adult neurogenesis require proliferating neural stem and progenitor cells that are intrinsically and extrinsically guided into a neuronal fate. In turn, migration of new-born neurons underlies the complex cytoarchitecture of the brain. Proliferation and migration are therefore essential for brain development, homeostasis and function in adulthood. Among several tightly regulated processes involved in brain formation and function, recent evidence points to the nuclear envelope (NE) and NE-associated components as critical new contributors. Classically, the NE was thought to merely represent a barrier mediating selective exchange between the cytoplasm and nucleoplasm. However, research over the past two decades has highlighted more sophisticated and diverse roles for NE components in progenitor fate choice and migration of their progeny by tuning gene expression via interactions with chromatin, transcription factors and epigenetic factors. Defects in NE components lead to neurodevelopmental impairments, whereas age-related changes in NE components are proposed to influence neurodegenerative diseases. Thus, understanding the roles of NE components in brain development, maintenance and aging is likely to reveal new pathophysiological mechanisms for intervention. Here, we review recent findings for the previously underrepresented contribution of the NE in neuronal commitment and migration, and envision future avenues for investigation.
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Özdaş S, Canatar İ. Targeting of nucleo‑cytoplasmic transport factor exportin 1 in malignancy (Review). MEDICINE INTERNATIONAL 2022; 2:2. [PMID: 38938904 PMCID: PMC11208992 DOI: 10.3892/mi.2021.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/03/2021] [Indexed: 06/29/2024]
Abstract
Nuclear pore complexes (NPCs) regulate the entry and exit of molecules from the cell nucleus. Small molecules pass through NPCs by diffusion while large molecules enter and exit the nucleus by karyopherins, which serve as transport factors. Exportin-1 (XPO1) is a protein that is an important member of the karyopherin family and carries macromolecules from the nucleus to the cytoplasm. XPO1 is responsible for nuclear-cytoplasmic transport of protein, ribosomal RNA and certain required mRNAs for ribosomal biogenesis. Furthermore, XPO1-mediated nuclear export is associated with various types of disease, such as cancer, inflammation and viral infection. The key role of XPO1 in carcinogenesis and its potential as a therapeutic target has been demonstrated by previous studies. Clinical use of novel developed generation-specific XPO1 inhibitors and their combination with other agents to block XPO1-mediated nuclear export are a promising new treatment strategy. The aim of the present study was to explain the working mechanism of XPO1 and inhibitors that block XPO1-mediated nuclear export.
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Affiliation(s)
- Sibel Özdaş
- Department of Bioengineering, Faculty of Engineering Sciences, Adana Alparslan Türkeş Science and Technology University, Adana 01250, Turkey
| | - İpek Canatar
- Department of Bioengineering, Faculty of Engineering Sciences, Adana Alparslan Türkeş Science and Technology University, Adana 01250, Turkey
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6
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Kim N, Kim KH, Lim WJ, Kim J, Kim SA, Yoo HJ. Whole Exome Sequencing Identifies Novel De Novo Variants Interacting with Six Gene Networks in Autism Spectrum Disorder. Genes (Basel) 2020; 12:genes12010001. [PMID: 33374967 PMCID: PMC7822011 DOI: 10.3390/genes12010001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable condition caused by a combination of environmental and genetic factors such as de novo and inherited variants, as well as rare or common variants among hundreds of related genes. Previous genome-wide association studies have identified susceptibility genes; however, most ASD-associated genes remain undiscovered. This study aimed to examine rare de novo variants to identify genetic risk factors of ASD using whole exome sequencing (WES), functional characterization, and genetic network analyses of identified variants using Korean familial dataset. We recruited children with ASD and their biological parents. The clinical best estimate diagnosis of ASD was made according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5TM), using comprehensive diagnostic instruments. The final analyses included a total of 151 individuals from 51 families. Variants were identified and filtered using the GATK Best Practices for bioinformatics analysis, followed by genome alignments and annotation to the reference genome assembly GRCh37 (liftover to GRCh38), and further annotated using dbSNP 154 build databases. To evaluate allele frequencies of de novo variants, we used the dbSNP, gnomAD exome v2.1.1, and genome v3.0. We used Ingenuity Pathway Analysis (IPA, Qiagen) software to construct networks using all identified de novo variants with known autism-related genes to find probable relationships. We identified 36 de novo variants with potential relations to ASD; 27 missense, two silent, one nonsense, one splice region, one splice site, one 5′ UTR, and one intronic SNV and two frameshift deletions. We identified six networks with functional relationships. Among the interactions between de novo variants, the IPA assay found that the NF-κB signaling pathway and its interacting genes were commonly observed at two networks. The relatively small cohort size may affect the results of novel ASD genes with de novo variants described in our findings. We did not conduct functional experiments in this study. Because of the diversity and heterogeneity of ASD, the primary purpose of this study was to investigate probable causative relationships between novel de novo variants and known autism genes. Additionally, we based functional relationships with known genes on network analysis rather than on statistical analysis. We identified new variants that may underlie genetic factors contributing to ASD in Korean families using WES and genetic network analyses. We observed novel de novo variants that might be functionally linked to ASD, of which the variants interact with six genetic networks.
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Affiliation(s)
- Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Soon Ae Kim
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon 34824, Korea
- Correspondence: (S.A.K.); (H.J.Y.); Tel.: +82-42-259-1672 (S.A.K.); +82-31-787-7436 (H.J.Y.)
| | - Hee Jeong Yoo
- Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Korea
- Department of Psychiatry, Seoul National University Bundang Hospital, Gyeonggi 13620, Korea
- Correspondence: (S.A.K.); (H.J.Y.); Tel.: +82-42-259-1672 (S.A.K.); +82-31-787-7436 (H.J.Y.)
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7
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Punjani N, Lamb DJ. Male infertility and genitourinary birth defects: there is more than meets the eye. Fertil Steril 2020; 114:209-218. [PMID: 32741459 PMCID: PMC10590568 DOI: 10.1016/j.fertnstert.2020.06.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
Male factor infertility is a significant problem present in up to 50% of infertile couples. The relationship between male infertility and systemic disease is of significant interest, and emerging evidence suggests a relationship between male infertility and male genitourinary (GU) birth defects (cryptorchidism, hypospadias, ambiguous genitalia, and congenital anomalies of the kidney and urinary tract). Many of these birth defects are treated in isolation by busy urologists without acknowledgment that these may be related to more global syndromic conditions. Conversely, geneticists and nonurologists who treat variable systemic phenotypes may overlook GU defects, which are indeed related conditions. Many of these defects are attributed to copy number variants dosage-sensitive genes due to chromosome microdeletions or microduplications. These variants are responsible for disease phenotypes seen in the general population. The copy number variants described in this review are syndromic in some cases and responsible for both GU birth defects as well as other systemic phenotypes. This review highlights the emerging evidence between these birth defects, male infertility, and other systemic conditions.
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Affiliation(s)
- Nahid Punjani
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, New York
| | - Dolores J Lamb
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York; Center for Reproductive Genomics, Weill Cornell Medical College, New York, New York.
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8
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Li X, Feng Y, Yan M, Tu X, Xie B, Ni F, Qu C, Chen JG. Inhibition of Autism-Related Crm1 Disrupts Mitosis and Induces Apoptosis of the Cortical Neural Progenitors. Cereb Cortex 2020; 30:3960-3976. [PMID: 32008040 DOI: 10.1093/cercor/bhaa011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/06/2019] [Accepted: 01/11/2020] [Indexed: 11/14/2022] Open
Abstract
De novo microdeletion of chromosome 2p15-16.1 presents clinically recognizable phenotypes that include mental retardation, autism, and microcephaly. Chromosomal maintenance 1 (CRM1) is a gene commonly missing in patients with 2p15-16.1 microdeletion and one of two genes found in the smallest deletion case. In this study, we investigate the role and mechanism of Crm1 in the developing mouse brain by inhibiting the protein or knocking down the gene in vivo. Inhibition of Crm1 reduces the proliferation and increases p53-dependent apoptosis of the cortical neural progenitors, thereby impeding the growth of embryonic cerebral cortex. Live imaging of mitosis in ex vivo embryonic brain slices reveals that inhibition of CRM1 arrests the cortical progenitors at metaphase. The arrested cells eventually slip into a pseudo-G1 phase without chromosome segregation. The mitotic slippage cells are marked by persistent expression of the spindle assembly checkpoint (SAC), repressing of which rescues the cells from apoptosis. Our study reveals that activating the SAC and inducing the mitotic slippage may lead to apoptosis of the cortical neural progenitors. The resulting cell death may well contribute to microcephaly associated with microdeletion of chromosome 2p15-16.1 involving CRM1.
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Affiliation(s)
- Xue Li
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
| | - Yue Feng
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
| | - Meifang Yan
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
| | - Xiaomeng Tu
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
| | - Bin Xie
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
| | - Fangfang Ni
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
| | - Chunsheng Qu
- Clinical Laboratory of Lishui People's Hospital, Sixth Affiliated Hospital, Wenzhou Medical University, LiShui, Zhejiang 323000, China
| | - Jie-Guang Chen
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science and Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou, Zhejiang 325027, P.R. China
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9
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Ziak J, Weissova R, Jeřábková K, Janikova M, Maimon R, Petrasek T, Pukajova B, Kleisnerova M, Wang M, Brill MS, Kasparek P, Zhou X, Alvarez-Bolado G, Sedlacek R, Misgeld T, Stuchlik A, Perlson E, Balastik M. CRMP2 mediates Sema3F-dependent axon pruning and dendritic spine remodeling. EMBO Rep 2020; 21:e48512. [PMID: 31919978 DOI: 10.15252/embr.201948512] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022] Open
Abstract
Regulation of axon guidance and pruning of inappropriate synapses by class 3 semaphorins are key to the development of neural circuits. Collapsin response mediator protein 2 (CRMP2) has been shown to regulate axon guidance by mediating semaphorin 3A (Sema3A) signaling; however, nothing is known about its role in synapse pruning. Here, using newly generated crmp2-/- mice we demonstrate that CRMP2 has a moderate effect on Sema3A-dependent axon guidance in vivo, and its deficiency leads to a mild defect in axon guidance in peripheral nerves and the corpus callosum. Surprisingly, crmp2-/- mice display prominent defects in stereotyped axon pruning in hippocampus and visual cortex and altered dendritic spine remodeling, which is consistent with impaired Sema3F signaling and with models of autism spectrum disorder (ASD). We demonstrate that CRMP2 mediates Sema3F signaling in primary neurons and that crmp2-/- mice display ASD-related social behavior changes in the early postnatal period as well as in adults. Together, we demonstrate that CRMP2 mediates Sema3F-dependent synapse pruning and its dysfunction shares histological and behavioral features of ASD.
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Affiliation(s)
- Jakub Ziak
- Department of Molecular Neurobiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Romana Weissova
- Department of Molecular Neurobiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Kateřina Jeřábková
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Janikova
- Department of Neurophysiology of the Memory, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Roy Maimon
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Tomas Petrasek
- Department of Neurophysiology of the Memory, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Barbora Pukajova
- Department of Molecular Neurobiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Marie Kleisnerova
- Department of Molecular Neurobiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mengzhe Wang
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Monika S Brill
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Petr Kasparek
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Xunlei Zhou
- Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | | | - Radislav Sedlacek
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,German Center for Neurodegenerative Diseases and Munich Cluster for Systems Neurology, Munich, Germany
| | - Ales Stuchlik
- Department of Neurophysiology of the Memory, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Martin Balastik
- Department of Molecular Neurobiology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
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10
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He X, Zhang H, Tao B, Yang M, Chen H, Lu L, Yi H, Pan H, Tang S. The A/A Genotype of XPO1 rs4430924 Is Associated With Higher Risk of Antituberculosis Drug-Induced Hepatotoxicity in Chinese Patients. J Clin Pharmacol 2019; 59:1014-1021. [PMID: 30817003 DOI: 10.1002/jcph.1398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/05/2019] [Indexed: 11/10/2022]
Abstract
Antituberculosis (anti-TB) drug-induced hepatotoxicity may be related to the excessive reactive oxygen species induced by hepatotoxic metabolites. Antioxidant activity involves the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway. The BTB domain and CNC homologue 1 (Bach1) may compete with Nrf2 for binding to transcriptional enhancers. Elimination of Bach1-mediated transcriptional repression depends on nuclear exporter exportin 1 (Xpo1). Thus, Xpo1 may indirectly affect antioxidant activity. The present study aimed to examine the role of tag single-nucleotide polymorphisms in XPO1 in Chinese anti-TB treatment patients. A 1:2 matched case-control study was conducted using 314 anti-TB drug-induced hepatotoxicity cases and 628 controls. After correcting for weight and hepatoprotectant use, conditional logistic regression analysis showed that patients carrying the AA genotype of rs4430924 in XPO1 were at higher risk of anti-TB drug-induced hepatotoxicity than those carrying the GG genotype based on the subgroup of probable cases (adjusted OR, 1.938; 95%CI, 1.035-3.628; P = .039), and marginally significant differences were also found under the recessive model (P = .048) and the additive model (P = .047). Based on this 1:2 matched case-control study, the AA genotype of rs4430924 in XPO1 may be associated with higher risk of anti-TB drug-induced hepatotoxicity in Chinese anti-TB treatment patients. Further studies in larger and more varied populations are required to validate this relationship.
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Affiliation(s)
- Xiaomin He
- Department of Infectious Disease, The People's Hospital of Taixing, Taixing, China
| | - Haiping Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bilin Tao
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Miaomiao Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbo Chen
- Department of Infectious Disease, The Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Lihuan Lu
- Department of Tuberculosis, The Second People's Hospital of Changshu, Changshu, China
| | - Honggang Yi
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongqiu Pan
- Department of Tuberculosis, The Third People's Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, China
| | - Shaowen Tang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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11
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Huang B, Li X, Tu X, Zhao W, Zhu D, Feng Y, Si X, Chen JG. OTX1 regulates cell cycle progression of neural progenitors in the developing cerebral cortex. J Biol Chem 2017; 293:2137-2148. [PMID: 29273633 DOI: 10.1074/jbc.ra117.001249] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Indexed: 01/01/2023] Open
Abstract
The progenitor cells in the cerebral cortex coordinate proliferation and mitotic exit to generate the correct number of neurons and glial cells during development. However, mechanisms for regulating the mitotic cycle of cortical progenitors are not fully understood. Otx1 is one of the homeobox-containing transcription factors frequently implicated in the development of the central nervous system. Mice bearing a targeted deletion of Otx1 exhibit brain hypoplasia and a decrease in the number of cortical neurons. We hypothesized that Otx1 might be crucial to the proliferation and differentiation of cortical progenitors. Otx1 knockdown by in utero electroporation in the mouse brain reduced the proportion of the G1 phase while increasing the S and M phases of progenitor cells. The knockdown diminished Tbr1+ neurons but increased GFAP+ astrocytes in the early postnatal cortex as revealed by lineage tracing study. Tbr2+ basal progenitors lacking Otx1 were held at the transit-amplifying stage. In contrast, overexpression of wildtype Otx1 but not an astrocytoma-related mutant Y320C inhibited proliferation of the progenitor cells in embryonic cortex. This study demonstrates that Otx1 is one of the key elements regulating cortical neurogenesis, and a loss-of-function in Otx1 may contribute to the overproduction of astrocytes in vivo.
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Affiliation(s)
- Baoshan Huang
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xue Li
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiaomeng Tu
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Wei Zhao
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Dan Zhu
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yue Feng
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiang Si
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jie-Guang Chen
- From the School of Ophthalmology and Optometry and Eye Hospital, .,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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12
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Hosseinpour M, Mashayekhi F, Bidabadi E, Salehi Z. Neuropilin-2 rs849563 gene variations and susceptibility to autism in Iranian population: A case-control study. Metab Brain Dis 2017; 32:1471-1474. [PMID: 28484884 DOI: 10.1007/s11011-017-0024-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental disruptions usually diagnosed in the first three years of child's life that characterized by some impairments in verbal and nonverbal communication, problems in social interactions and repetitive behaviors. The neuropilin-2 (NRP2) gene has been shown to both guide axons and control neuronal migration in the central nervous system (CNS). In this study the association between the NRP2 gene and autism using a cohort of 120 Iranian children (50 cases with autism and 70 control cases) was analyzed. Single nucleotide polymorphism (SNP) was genotyped by the polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) analyses. There was significant difference between the genotype and allele frequency between control and patient groups (P = 0.003 and P = 0.01, respectively). The prevalence of genotype frequencies of TT and TG in autistic children were 40% and 60%, respectively, while in controls were 68.5% and 31.5%, respectively. The heterozyote TG was associated with an increased risk of autism compared with TT genotype (OR = 3.72, 95%CI = 1.53-6.95, P = 0.02). The allele frequencies of T and G in autistic children were 78.5% and 21.4%, respectively and in controls were 84.2% and 15.7%, respectively. The NRP2 G allele conferred a 2.29-fold increased risk to autism relative to the T allele (OR = 2.29, 95%CI = 1.23-4.29, P = 0.009). The results of this study showed that there is a significant association between rs849563 polymorphism and autism in the studied population. However in order to obtain a definitive conclusion larger studies with more samples are required to confirm the results of this study.
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Affiliation(s)
| | - Farhad Mashayekhi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran.
| | - Elham Bidabadi
- Faculty of Medicine, Department of Child Neurology, Guilan University of Medical Sciences, Rasht, Iran
| | - Zivar Salehi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
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13
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Reilly J, Gallagher L, Chen JL, Leader G, Shen S. Bio-collections in autism research. Mol Autism 2017; 8:34. [PMID: 28702161 PMCID: PMC5504648 DOI: 10.1186/s13229-017-0154-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. These provide deeper insight into ASD progression during development and could generate human cell models for drug screening. Finally, we provide perspectives concerning the utilities of ASD bio-collections and limitations, and highlight considerations in setting up a new bio-collection for ASD research.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | - Louise Gallagher
- Trinity Translational Medicine Institute and Department of Psychiatry, Trinity Centre for Health Sciences, St. James Hospital Street, Dublin 8, Ireland
| | - June L. Chen
- Department of Special Education, Faculty of Education, East China Normal University, Shanghai, 200062 China
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
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14
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Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry 2017; 22:836-849. [PMID: 27240531 PMCID: PMC5508252 DOI: 10.1038/mp.2016.84] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/18/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
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15
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Mutation of genes controlling mRNA metabolism and protein synthesis predisposes to neurodevelopmental disorders. Biochem Soc Trans 2016; 43:1259-65. [PMID: 26614670 DOI: 10.1042/bst20150168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Brain development is a tightly controlled process that depends upon differentiation and function of neurons to allow for the formation of functional neural networks. Mutation of genes encoding structural proteins is well recognized as causal for neurodevelopmental disorders (NDDs). Recent studies have shown that aberrant gene expression can also lead to disorders of neural development. Here we summarize recent evidence implicating in the aetiology of NDDs mutation of factors acting at the level of mRNA splicing, mRNA nuclear export, translation and mRNA degradation. This highlights the importance of these fundamental processes for human health and affords new strategies and targets for therapeutic intervention.
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16
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Bagheri H, Badduke C, Qiao Y, Colnaghi R, Abramowicz I, Alcantara D, Dunham C, Wen J, Wildin RS, Nowaczyk MJ, Eichmeyer J, Lehman A, Maranda B, Martell S, Shan X, Lewis SM, O’Driscoll M, Gregory-Evans CY, Rajcan-Separovic E. Identifying candidate genes for 2p15p16.1 microdeletion syndrome using clinical, genomic, and functional analysis. JCI Insight 2016; 1:e85461. [PMID: 27699255 PMCID: PMC5033885 DOI: 10.1172/jci.insight.85461] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/09/2016] [Indexed: 01/14/2023] Open
Abstract
The 2p15p16.1 microdeletion syndrome has a core phenotype consisting of intellectual disability, microcephaly, hypotonia, delayed growth, common craniofacial features, and digital anomalies. So far, more than 20 cases of 2p15p16.1 microdeletion syndrome have been reported in the literature; however, the size of the deletions and their breakpoints vary, making it difficult to identify the candidate genes. Recent reports pointed to 4 genes (XPO1, USP34, BCL11A, and REL) that were included, alone or in combination, in the smallest deletions causing the syndrome. Here, we describe 8 new patients with the 2p15p16.1 deletion and review all published cases to date. We demonstrate functional deficits for the above 4 candidate genes using patients' lymphoblast cell lines (LCLs) and knockdown of their orthologs in zebrafish. All genes were dosage sensitive on the basis of reduced protein expression in LCLs. In addition, deletion of XPO1, a nuclear exporter, cosegregated with nuclear accumulation of one of its cargo molecules (rpS5) in patients' LCLs. Other pathways associated with these genes (e.g., NF-κB and Wnt signaling as well as the DNA damage response) were not impaired in patients' LCLs. Knockdown of xpo1a, rel, bcl11aa, and bcl11ab resulted in abnormal zebrafish embryonic development including microcephaly, dysmorphic body, hindered growth, and small fins as well as structural brain abnormalities. Our multifaceted analysis strongly implicates XPO1, REL, and BCL11A as candidate genes for 2p15p16.1 microdeletion syndrome.
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Affiliation(s)
- Hani Bagheri
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Chansonette Badduke
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Ying Qiao
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Diana Alcantara
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Jiadi Wen
- University of Texas at Dallas, Dallas, Texas, USA
| | | | - Malgorzata J.M. Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University Medical Centre, Hamilton, Ontario, Canada
| | | | - Anna Lehman
- Department of Medical Genetics, UBC, Vancouver, British Columbia, Canada
| | - Bruno Maranda
- Medical Genetics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sally Martell
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Xianghong Shan
- Department of Ophthalmology, UBC, Vancouver, British Columbia, Canada
| | - Suzanne M.E. Lewis
- Department of Medical Genetics, UBC, Vancouver, British Columbia, Canada
| | - Mark O’Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | | | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
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17
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Yoo H. Genetics of Autism Spectrum Disorder: Current Status and Possible Clinical Applications. Exp Neurobiol 2015; 24:257-72. [PMID: 26713075 PMCID: PMC4688327 DOI: 10.5607/en.2015.24.4.257] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 12/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is one of the most complex behavioral disorders with a strong genetic influence. The objectives of this article are to review the current status of genetic research in ASD, and to provide information regarding the potential candidate genes, mutations, and genetic loci possibly related to pathogenesis in ASD. Investigations on monogenic causes of ASD, candidate genes among common variants, rare de novo mutations, and copy number variations are reviewed. The current possible clinical applications of the genetic knowledge and their future possibilities are highlighted.
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Affiliation(s)
- Heejeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Korea
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18
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Adi A, Tawil B, Aldosari M, Shinwari J, Nester M, Aldhalaan H, Alshamrani H, Ghannam M, Meyer B, Al Tassan N. Homozygosity analysis in subjects with autistic spectrum disorder. Mol Med Rep 2015; 12:2307-12. [PMID: 25901489 DOI: 10.3892/mmr.2015.3663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 03/23/2015] [Indexed: 11/06/2022] Open
Abstract
Autistic spectrum disorder (ASD) is a complex neurodevelopmental disorder that results in social and communication impairments, as well as repetitive and stereotyped patterns. Genetically, ASD has been described as a multifactorial genetic disorder. The aim of the present study was to investigate possible susceptibility loci of ASD, utilizing the highly consanguineous and inbred nature of numerous families within the population of Saudi Arabia. A total of 13 multiplex families and 27 affected individuals were recruited and analyzed using Affymetrix GeneChip(®) Mapping 250K and 6.0 arrays as well as Axiom arrays. Numerous regions of homozygosity were identified, including regions in genes associated with synaptic function and neurotransmitters, as well as energy and mitochondria-associated genes, and developmentally-associated genes. The loci identified in the present study represent regions that may be further investigated, which could reveal novel changes and variations associated with ASD, reinforcing the complex inheritance of the disease.
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Affiliation(s)
- Ahmad Adi
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Basma Tawil
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mohammed Aldosari
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Jameela Shinwari
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Michael Nester
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Hisham Aldhalaan
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Hussain Alshamrani
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Manar Ghannam
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Brian Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Nada Al Tassan
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Yingjun X, Wen T, Yujian L, Lingling X, Huimin H, Qun F, Junhong C. Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability. Eur J Med Genet 2014; 58:116-21. [PMID: 25450604 DOI: 10.1016/j.ejmg.2014.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
Whole-genome microarray analysis is proven to be useful in the identification of submicroscopic copy number imbalances in families with intellectual disabilities. The first case of Xq25 duplication was identified using genome-wide array comparative genomic hybridization (array-CGH) in a 24-year-old patient with a syndromic intellectual disability. We report a 4-year-old boy with a de novo 591 kb duplication at Xq25. The duplication was first detected by a CytoScan HD array platform (Affymetrix, USA) and was confirmed by real-time quantitative PCR (qPCR) of the STAG2 gene, and by fluorescence in situ hybridization (FISH). The patient had clinical features partially consistent with published cases, including an intellectual disability and speech delay. The identification of this additional patient and a detailed analysis of duplications identified in other patient cohorts and absent in normal individuals support the existence of a rare pathological microduplication at Xq25 that encompasses STAG2.
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Affiliation(s)
- Xie Yingjun
- Department of Prenatal Diagnosis, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, 510080, China
| | - Tang Wen
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Liang Yujian
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xu Lingling
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Huang Huimin
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Fang Qun
- Department of Prenatal Diagnosis, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Chen Junhong
- Department of Prenatal Diagnosis, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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20
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Jorgez CJ, Rosenfeld JA, Wilken NR, Vangapandu HV, Sahin A, Pham D, Carvalho CMB, Bandholz A, Miller A, Weaver DD, Burton B, Babu D, Bamforth JS, Wilks T, Flynn DP, Roeder E, Patel A, Cheung SW, Lupski JR, Lamb DJ. Genitourinary defects associated with genomic deletions in 2p15 encompassing OTX1. PLoS One 2014; 9:e107028. [PMID: 25203062 PMCID: PMC4159299 DOI: 10.1371/journal.pone.0107028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/06/2014] [Indexed: 02/08/2023] Open
Abstract
Normal development of the genitourinary (GU) tract is a complex process that frequently goes awry. In male children the most frequent congenital GU anomalies are cryptorchidism (1-4%), hypospadias (1%) and micropenis (0.35%). Bladder exstrophy and epispadias complex (BEEC) (1∶47000) occurs less frequently but significantly impacts patients' lives. Array comparative genomic hybridization (aCGH) identified seven individuals with overlapping deletions in the 2p15 region (66.0 kb-5.6 Mb). Six of these patients have GU defects, while the remaining patient has no GU defect. These deletions encompass the transcription factor OTX1. Subjects 2-7 had large de novo CNVs (2.39-6.31 Mb) and exhibited features similar to those associated with the 2p15p16.1 and 2p15p14 microdeletion syndromes, including developmental delay, short stature, and variable GU defects. Subject-1 with BEEC had the smallest deletion (66 kb), which deleted only one copy of OTX1. Otx1-null mice have seizures, prepubescent transient growth retardation and gonadal defects. Two subjects have short stature, two have seizures, and six have GU defects, mainly affecting the external genitalia. The presence of GU defects in six patients in our cohort and eight of thirteen patients reported with deletions within 2p14p16.1 (two with deletion of OTX1) suggest that genes in 2p15 are important for GU development. Genitalia defects in these patients could result from the effect of OTX1 on pituitary hormone secretion or on the regulation of SHH signaling, which is crucial for development of the bladder and genitalia.
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Affiliation(s)
- Carolina J. Jorgez
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (CJJ); (DJL)
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Nathan R. Wilken
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hima V. Vangapandu
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aysegul Sahin
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dung Pham
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Claudia M. B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anne Bandholz
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Amanda Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - David D. Weaver
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Barbara Burton
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, United States of America
| | - Deepti Babu
- University of Alberta, Edmonton, Alberta, Canada
| | | | - Timothy Wilks
- Madigan Army Medical Center, Department of Pediatrics, Tacoma, Washington, United States of America
| | - Daniel P. Flynn
- Department of Children's Endocrinology, St. Luke's Children's Specialty Center, Boise, Idaho, United States of America
| | - Elizabeth Roeder
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dolores J. Lamb
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Scott Department of Urology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (CJJ); (DJL)
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Fannemel M, Barøy T, Holmgren A, Rødningen OK, Haugsand TM, Hansen B, Frengen E, Misceo D. Haploinsufficiency of XPO1 and USP34 by a de novo 230 kb deletion in 2p15, in a patient with mild intellectual disability and cranio-facial dysmorphisms. Eur J Med Genet 2014; 57:513-9. [PMID: 24911659 DOI: 10.1016/j.ejmg.2014.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/28/2014] [Indexed: 12/30/2022]
Abstract
2p15p16.1-deletion syndrome was first described in 2007 based on the clinical presentation of two patients. The syndrome is characterized by intellectual disability, autism spectrum disorders, microcephaly, dysmorphic facial features and a variety of congenital organ defects. The precise genotype-phenotype correlation in 2p15-deletion syndrome is not understood. However, greater insight can be obtained by thorough clinical investigation of patients carrying deletions, especially those of small size. We report a 21-year-old male patient with features overlapping the clinical spectrum of the 2p15p16.1-deletion syndrome, such as intellectual disability, dysmorphic facial features, and congenital defects. He carried a 230 kb de novo deletion (chr2:61500346-61733075 bp, hg19), which affects the genes USP34, SNORA70B and XPO1. While there is a lack of functional data on SNORA70B, the involvement of USP34 and XPO1 in the regulation of fundamental developmental processes is well known. We suggest that haploinsufficiency of one or both of these genes is likely to be responsible for the disease in our patient.
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Affiliation(s)
- Madeleine Fannemel
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Tuva Barøy
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Asbjørn Holmgren
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Olaug K Rødningen
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Trine M Haugsand
- Department for Adult Habilitation, Akershus University Hospital, Oslo, Norway.
| | - Børre Hansen
- Department for Adult Habilitation, Akershus University Hospital, Oslo, Norway.
| | - Eirik Frengen
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Doriana Misceo
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.
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Kimura M, Imamoto N. Biological significance of the importin-β family-dependent nucleocytoplasmic transport pathways. Traffic 2014; 15:727-48. [PMID: 24766099 DOI: 10.1111/tra.12174] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
Importin-β family proteins (Imp-βs) are nucleocytoplasmic transport receptors (NTRs) that import and export proteins and RNAs through the nuclear pores. The family consists of 14-20 members depending on the biological species, and each member transports a specific group of cargoes. Thus, the Imp-βs mediate multiple, parallel transport pathways that can be regulated separately. In fact, the spatiotemporally differential expressions and the functional regulations of Imp-βs have been reported. Additionally, the biological significance of each pathway has been characterized by linking the function of a member of Imp-βs to a cellular consequence. Connecting these concepts, the regulation of the transport pathways conceivably induces alterations in the cellular physiological states. However, few studies have linked the regulation of an importin-β family NTR to an induced cellular response and the corresponding cargoes, despite the significance of this linkage in comprehending the biological relevance of the transport pathways. This review of recent reports on the regulation and biological functions of the Imp-βs highlights the significance of the transport pathways in physiological contexts and points out the possibility that the identification of yet unknown specific cargoes will reinforce the importance of transport regulation.
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Affiliation(s)
- Makoto Kimura
- Cellular Dynamics Laboratory, RIKEN, Hirosawa 2-1, Wako, Saitama, 351-0198, Japan
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23
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Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disorders. Mol Autism 2014; 5:28. [PMID: 24720851 PMCID: PMC4098665 DOI: 10.1186/2040-2392-5-28] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/17/2014] [Indexed: 11/10/2022] Open
Abstract
Background Validating the potential pathogenicity of copy number variants (CNVs) identified in genome-wide studies of autism spectrum disorders (ASD) requires detailed assessment of case/control frequencies, inheritance patterns, clinical correlations, and functional impact. Here, we characterize a small recurrent duplication in the annexin A1 (ANXA1) gene, identified by the Autism Genome Project (AGP) study. Methods From the AGP CNV genomic screen in 2,147 ASD individuals, we selected for characterization an ANXA1 gene duplication that was absent in 4,964 population-based controls. We further screened the duplication in a follow-up sample including 1,496 patients and 410 controls, and evaluated clinical correlations and family segregation. Sequencing of exonic/downstream ANXA1 regions was performed in 490 ASD patients for identification of additional variants. Results The ANXA1 duplication, overlapping the last four exons and 3’UTR region, had an overall prevalence of 11/3,643 (0.30%) in unrelated ASD patients but was not identified in 5,374 controls. Duplication carriers presented no distinctive clinical phenotype. Family analysis showed neuropsychiatric deficits and ASD traits in multiple relatives carrying the duplication, suggestive of a complex genetic inheritance. Sequencing of exonic regions and the 3’UTR identified 11 novel changes, but no obvious variants with clinical significance. Conclusions We provide multilevel evidence for a role of ANXA1 in ASD etiology. Given its important role as mediator of glucocorticoid function in a wide variety of brain processes, including neuroprotection, apoptosis, and control of the neuroendocrine system, the results add ANXA1 to the growing list of rare candidate genetic etiological factors for ASD.
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Hancarova M, Simandlova M, Drabova J, Mannik K, Kurg A, Sedlacek Z. A patient with de novo 0.45 Mb deletion of 2p16.1: The role ofBCL11A,PAPOLG,REL, andFLJ16341in the 2p15-p16.1 microdeletion syndrome. Am J Med Genet A 2013; 161A:865-70. [DOI: 10.1002/ajmg.a.35783] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 10/27/2012] [Indexed: 12/25/2022]
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Florisson JMG, Mathijssen IMJ, Dumee B, Hoogeboom JAM, Poddighe PJ, Oostra BA, Frijns JP, Koster L, de Klein A, Eussen B, de Vries BBA, Swagemakers S, van der Spek PJ, Verkerk AJMH. Complex craniosynostosis is associated with the 2p15p16.1 microdeletion syndrome. Am J Med Genet A 2013; 161A:244-53. [PMID: 23303641 DOI: 10.1002/ajmg.a.35632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/28/2012] [Indexed: 12/29/2022]
Abstract
In a screening project of patients with (complex) craniosynostosis using genomic arrays, we identified two patients with craniosynostosis and microcephaly with a deletion in the 2p15p16.1 chromosomal region. This region has been associated with a new microdeletion syndrome, for which patients have various features in common, including microcephaly and intellectual disability. Deletions were identified using Affymetrix 250K SNP array and further characterized by fluorescence in situ hybridization (FISH) analysis and qPCR. The deletions in our two patients overlapped within the 2p15p16.1 microdeletion syndrome area and were 6.8 and 6.9 Mb in size, respectively. FISH and qPCR confirmed the presence of only one copy in this region. Finemapping of the breakpoints indicated precise borders in our patients and were further finemapped in two other previously reported patients. Clinical features of patients with deletions in the 2p15p16.1 region vary. Including data from our patients, now eight out of nine reported patients have microcephaly, one of the major features, and all had intellectual disability. The current reported two patients add different forms of craniosynostosis to the clinical spectrum of this recently recognized microdeletion syndrome.
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Affiliation(s)
- Joyce M G Florisson
- Department of Plastic and Reconstructive Surgery, Erasmus University Medical Centre, Rotterdam, The Netherlands
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