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Guedes JR, Ferreira PA, Costa J, Laranjo M, Pinto MJ, Reis T, Cardoso AM, Lebre C, Casquinha M, Gomes M, Shkatova V, Pereira M, Beltrão N, Hanuscheck N, Greenhalgh AD, Vogelaar CF, Carvalho AL, Zipp F, Cardoso AL, Peça J. IL-4 shapes microglia-dependent pruning of the cerebellum during postnatal development. Neuron 2023; 111:3435-3449.e8. [PMID: 37918358 DOI: 10.1016/j.neuron.2023.09.031] [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: 11/09/2022] [Revised: 06/26/2023] [Accepted: 09/22/2023] [Indexed: 11/04/2023]
Abstract
Interleukin-4 (IL-4) is a type 2 cytokine with pleiotropic functions in adaptive immunity, allergies, and cognitive processes. Here, we show that low levels of IL-4 in the early postnatal stage delineate a critical period in which microglia extensively prune cerebellar neurons. Elevating the levels of this cytokine via peripheral injection, or using a mouse model of allergic asthma, leads to defective pruning, permanent increase in cerebellar granule cells, and circuit alterations. These animals also show a hyperkinetic and impulsive-like phenotype, reminiscent of attention-deficit hyperactivity disorder (ADHD). These alterations are blocked in Il4rαfl/fl::Cx3cr1-CreER mice, which are deficient in IL-4 receptor signaling in microglia. These findings demonstrate a previously unknown role for IL-4 during a neuroimmune critical period of cerebellar maturation and provide a first putative mechanism for the comorbidity between allergic disease and ADHD observed in humans.
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Affiliation(s)
- Joana R Guedes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Pedro A Ferreira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; Doctoral Program in Biosciences, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Jéssica Costa
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; PDBEB-Doctoral Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mariana Laranjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; PDBEB-Doctoral Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Maria J Pinto
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Tiago Reis
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; PDBEB-Doctoral Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Ana Maria Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Carolina Lebre
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Maria Casquinha
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Marcos Gomes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; PDBEB-Doctoral Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Viktoriya Shkatova
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Marta Pereira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Nuno Beltrão
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; PDBEB-Doctoral Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Nicholas Hanuscheck
- University Medical Center of the Johannes Gutenberg University Mainz, Department of Neurology, 06131 Mainz, Germany
| | - Andrew D Greenhalgh
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Christina Francisca Vogelaar
- University Medical Center of the Johannes Gutenberg University Mainz, Department of Neurology, 06131 Mainz, Germany
| | - Ana Luísa Carvalho
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Frauke Zipp
- University Medical Center of the Johannes Gutenberg University Mainz, Department of Neurology, 06131 Mainz, Germany.
| | - Ana Luísa Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal.
| | - João Peça
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
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Tarchi L, Damiani S, Fantoni T, Pisano T, Castellini G, Politi P, Ricca V. Centrality and interhemispheric coordination are related to different clinical/behavioral factors in attention deficit/hyperactivity disorder: a resting-state fMRI study. Brain Imaging Behav 2022; 16:2526-2542. [PMID: 35859076 DOI: 10.1007/s11682-022-00708-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2022] [Indexed: 11/26/2022]
Abstract
Eigenvector-Centrality (EC) has shown promising results in the field of Psychiatry, with early results also pertaining to ADHD. Parallel efforts have focused on the description of aberrant interhemispheric coordination in ADHD, as measured by Voxel-Mirrored-Homotopic-Connectivity (VMHC), with early evidence of altered Resting-State fMRI. A sample was collected from the ADHD200-NYU initiative: 86 neurotypicals and 89 participants with ADHD between 7 and 18 years old were included after quality control for motion. After preprocessing, voxel-wise EC and VMHC values between diagnostic groups were compared, and network-level values from 15 functional networks extracted. Age, ADHD severity (Connor's Parent Rating-Scale), IQ (Wechsler-Abbreviated-Scale), and right-hand dominance were correlated with EC/VMHC values in the whole sample and within groups, both at the voxel-wise and network-level. Motion was controlled by censoring time-points with Framewise-Displacement > 0.5 mm, as well as controlling for group differences in mean Framewise-Displacement values. EC was significantly higher in ADHD compared to neurotypicals in the left inferior Frontal lobe, Lingual gyri, Peri-Calcarine cortex, superior and middle Occipital lobes, right inferior Occipital lobe, right middle Temporal gyrus, Fusiform gyri, bilateral Cuneus, right Precuneus, and Cerebellum (FDR-corrected-p = 0.05). No differences were observed between groups in voxel-wise VMHC. EC was positively correlated with ADHD severity scores at the network level (at p-value < 0.01, Inattentive: Cerebellum rho = 0.273; Hyper/Impulsive: High-Visual Network rho = 0.242, Cerebellum rho = 0.273; Global Index Severity: High-Visual Network rho = 0.241, Cerebellum rho = 0.293). No differences were observed between groups for motion (p = 0.443). While EC was more related to ADHD psychopathology, VMHC was consistently and negatively correlated with age across all networks.
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Affiliation(s)
- Livio Tarchi
- Psychiatry Unit, Department of Health Sciences, University of Florence, Florence, FI, Italy.
| | - Stefano Damiani
- Department of Brain and Behavioral Science, University of Pavia, 27100, Pavia, Italy
| | - Teresa Fantoni
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Tiziana Pisano
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Giovanni Castellini
- Psychiatry Unit, Department of Health Sciences, University of Florence, Florence, FI, Italy
| | - Pierluigi Politi
- Department of Brain and Behavioral Science, University of Pavia, 27100, Pavia, Italy
| | - Valdo Ricca
- Psychiatry Unit, Department of Health Sciences, University of Florence, Florence, FI, Italy
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3
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Li Z, Wang D, Liao H, Zhang S, Guo W, Chen L, Lu L, Huang T, Cai YD. Exploring the Genomic Patterns in Human and Mouse Cerebellums Via Single-Cell Sequencing and Machine Learning Method. Front Genet 2022; 13:857851. [PMID: 35309141 PMCID: PMC8930846 DOI: 10.3389/fgene.2022.857851] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022] Open
Abstract
In mammals, the cerebellum plays an important role in movement control. Cellular research reveals that the cerebellum involves a variety of sub-cell types, including Golgi, granule, interneuron, and unipolar brush cells. The functional characteristics of cerebellar cells exhibit considerable differences among diverse mammalian species, reflecting a potential development and evolution of nervous system. In this study, we aimed to recognize the transcriptional differences between human and mouse cerebellum in four cerebellar sub-cell types by using single-cell sequencing data and machine learning methods. A total of 321,387 single-cell sequencing data were used. The 321,387 cells included 4 cell types, i.e., Golgi (5,048, 1.57%), granule (250,307, 77.88%), interneuron (60,526, 18.83%), and unipolar brush (5,506, 1.72%) cells. Our results showed that by using gene expression profiles as features, the optimal classification model could achieve very high even perfect performance for Golgi, granule, interneuron, and unipolar brush cells, respectively, suggesting a remarkable difference between the genomic profiles of human and mouse. Furthermore, a group of related genes and rules contributing to the classification was identified, which might provide helpful information for deepening the understanding of cerebellar cell heterogeneity and evolution.
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Affiliation(s)
- ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - HuiPing Liao
- Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - ShiQi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
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Liu Y, Chang X, Qu HQ, Tian L, Glessner J, Qu J, Li D, Qiu H, Sleiman P, Hakonarson H. Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry. Genes (Basel) 2021; 12:310. [PMID: 33671795 PMCID: PMC7927037 DOI: 10.3390/genes12020310] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with poorly understood molecular mechanisms that results in significant impairment in children. In this study, we sought to assess the role of rare recurrent variants in non-European populations and outside of coding regions. We generated whole genome sequence (WGS) data on 875 individuals, including 205 ADHD cases and 670 non-ADHD controls. The cases included 116 African Americans (AA) and 89 European Americans (EA), and the controls included 408 AA and 262 EA. Multiple novel rare recurrent variants were identified in exonic regions, functionally classified as stop-gains and frameshifts for known ADHD genes. Deletion in introns of the protocadherins families and the ncRNA HGB8P were identified in two independent EA ADHD patients. A meta-analysis of the two ethnicities for differential ADHD recurrent variants compared to controls shows a small number of overlaps. These results suggest that rare recurrent variants in noncoding regions may be involved in the pathogenesis of ADHD in children of both AA and EA ancestry; thus, WGS could be a powerful discovery tool for studying the molecular mechanisms of ADHD.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Xiao Chang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Hui-Qi Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Lifeng Tian
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Joseph Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Jingchun Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Haijun Qiu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
| | - Patrick Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (X.C.); (H.-Q.Q.); (L.T.); (J.G.); (J.Q.); (D.L.); (H.Q.); (P.S.)
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Non-coding structural variation differentially impacts attention-deficit hyperactivity disorder (ADHD) gene networks in African American vs Caucasian children. Sci Rep 2020; 10:15252. [PMID: 32943653 PMCID: PMC7499198 DOI: 10.1038/s41598-020-71307-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
Previous studies of attention-deficit hyperactivity disorder (ADHD) have suggested that structural variants (SVs) play an important role but these were mainly studied in subjects of European ancestry and focused on coding regions. In this study, we sought to address the role of SVs in non-European populations and outside of coding regions. To that end, we generated whole genome sequence (WGS) data on 875 individuals, including 205 ADHD cases and 670 non-ADHD controls. The ADHD cases included 116 African Americans (AA) and 89 of European Ancestry (EA) with SVs in comparison with 408 AA and 262 controls, respectively. Multiple SVs and target genes that associated with ADHD from previous studies were identified or replicated, and novel recurrent ADHD-associated SV loci were discovered. We identified clustering of non-coding SVs around neuroactive ligand-receptor interaction pathways, which are involved in neuronal brain function, and highly relevant to ADHD pathogenesis and regulation of gene expression related to specific ADHD phenotypes. There was little overlap (around 6%) in the genes impacted by SVs between AA and EA. These results suggest that SVs within non-coding regions may play an important role in ADHD development and that WGS could be a powerful discovery tool for studying the molecular mechanisms of ADHD
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Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout. G3-GENES GENOMES GENETICS 2019; 9:2887-2896. [PMID: 31289024 PMCID: PMC6723140 DOI: 10.1534/g3.119.400369] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.
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Shook D, Brouwer R, de Zeeuw P, Oranje B, Durston S. XKR4 Gene Effects on Cerebellar Development Are Not Specific to ADHD. Front Cell Neurosci 2018; 11:396. [PMID: 29311829 PMCID: PMC5732973 DOI: 10.3389/fncel.2017.00396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/28/2017] [Indexed: 11/17/2022] Open
Abstract
A single-nucleotide polymorphism (SNP) of the XKR4 gene has been linked to Attention-Deficit/Hyperactivity Disorder (ADHD). This gene is preferentially expressed in cerebellum, a brain structure implicated in this disorder. This study investigated the effects of this SNP on cerebellar development in children with and without ADHD. We collected 279 longitudinal T1-weighted structural images and DNA from 58 children with ADHD and 64 typically developing (TD) children matched for age, IQ, and gender. Groups were divided by the XKR4 rs2939678 SNP into A-allele carriers versus subjects homozygous for the G-allele. Cerebellar lobular volumes were segmented into 35 regions of interest using MAGeTBrain, an automated multi-atlas segmentation pipeline for anatomical MRI, and statistically analyzed using linear mixed models. We found decreased gray matter (GM) volumes in ADHD compared to TD children in bilateral lobules VIIIA, left VIIIB, right VIIB, and vermis VI. Furthermore, we found a linear age by gene interaction in left lobule VIIB where subjects homozygous for the G-allele showed a decrease in volume over time compared to A-allele carriers. We further found quadratic age × gene and age × diagnosis interactions in left lobule IV. Subjects homozygous for the G-allele (the genotype overtransmitted in ADHD) showed more suppressed, almost flat quadratic growth curves compared to A-allele carriers, similar to individuals with ADHD compared to controls. However, there was no interaction between genotype and diagnosis, suggesting that any effects of this SNP on cerebellar development are not specific to the disorder.
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Affiliation(s)
- Devon Shook
- NICHE Laboratory, Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rachel Brouwer
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Patrick de Zeeuw
- NICHE Laboratory, Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Bob Oranje
- NICHE Laboratory, Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Sarah Durston
- NICHE Laboratory, Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
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8
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Takada L, Barbero MMD, Oliveira HN, de Camargo GMF, Fernandes Júnior GA, Aspilcueta-Borquis RR, Souza FRP, Boligon AA, Melo TP, Regatieri IC, Feitosa FLB, Fonseca LFS, Magalhães AFB, Costa RB, Albuquerque LG. Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction. PLoS One 2018; 13:e0190197. [PMID: 29293544 PMCID: PMC5749767 DOI: 10.1371/journal.pone.0190197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
Reproductive traits are of the utmost importance for any livestock farming, but are difficult to measure and to interpret since they are influenced by various factors. The objective of this study was to detect associations between known polymorphisms in candidate genes related to sexual precocity in Nellore heifers, which could be used in breeding programs. Records of 1,689 precocious and non-precocious heifers from farms participating in the Conexão Delta G breeding program were analyzed. A subset of single nucleotide polymorphisms (SNP) located in the region of the candidate genes at a distance of up to 5 kb from the boundaries of each gene, were selected from the panel of 777,000 SNPs of the High-Density Bovine SNP BeadChip. Linear mixed models were used for statistical analysis of early heifer pregnancy, relating the trait with isolated SNPs or with haplotype groups. The model included the contemporary group (year and month of birth) as fixed effect and parent of the animal (sire effect) as random effect. The fastPHASE® and GenomeStudio® were used for reconstruction of the haplotypes and for analysis of linkage disequilibrium based on r2 statistics. A total of 125 candidate genes and 2,024 SNPs forming haplotypes were analyzed. Statistical analysis after Bonferroni correction showed that nine haplotypes exerted a significant effect (p<0.05) on sexual precocity. Four of these haplotypes were located in the Pregnancy-associated plasma protein-A2 gene (PAPP-A2), two in the Estrogen-related receptor gamma gene (ESRRG), and one each in the Pregnancy-associated plasma protein-A gene (PAPP-A), Kell blood group complex subunit-related family (XKR4) and mannose-binding lectin genes (MBL-1) genes. Although the present results indicate that the PAPP-A2, PAPP-A, XKR4, MBL-1 and ESRRG genes influence sexual precocity in Nellore heifers, further studies are needed to evaluate their possible use in breeding programs.
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Affiliation(s)
- Luciana Takada
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Marina M D Barbero
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Henrique N Oliveira
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | | | | | | | - Fabio R P Souza
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Arione A Boligon
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Thaise P Melo
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Inaê C Regatieri
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Fabieli L B Feitosa
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Larissa F S Fonseca
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Ana F B Magalhães
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Raphael B Costa
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
| | - Lucia G Albuquerque
- Departamento de Zootecnia-São Paulo State University-UNESP, Jaboticabal, São Paulo, Brazil
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Polimanti R, Zhao H, Farrer LA, Kranzler HR, Gelernter J. Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors. Am J Med Genet B Neuropsychiatr Genet 2017; 174:846-853. [PMID: 28990359 PMCID: PMC5861711 DOI: 10.1002/ajmg.b.32604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/07/2017] [Accepted: 09/18/2017] [Indexed: 01/26/2023]
Abstract
We previously mapped loci for the genome-wide association studies (GWAS) and genome-wide gene-by-alcohol dependence interaction (GW-GxAD) analyses of risky sexual behaviors (RSB). This study extends those findings by analyzing the ancestry- and sex-specific AD-stratified effects on RSB. We examined the concordance of findings for the AD-stratified GWAS and the GW-GxAD analysis of RSB, with concordance defined as genome-wide significance in one analysis and at least nominal significance in the second analysis. A total of 2,173 African-American (AA) and 1,751 European-American (EA) subjects were investigated. Information regarding RSB (lifetime experiences of unprotected sex and multiple sexual partners) and DSM-IV diagnosis of lifetime AD were derived from the Semi-Structured Assessment for Drug Dependence and Alcoholism (SSADDA). In our ancestry- and sex-specific analyses, we identified four independent genome-wide significant (GWS) loci (p < 5*10-8 ) and one suggestive locus (p < 6*10-8 ). In men, we observed a GWS signal in FAM162A (rs2002594, p = 4.96*10-8 ). In women, there was a suggestive locus in PLGRKT (rs3824435, p = 5.52*10-8 ). In AAs, there was a GWS signal in GRK5 (rs1316543, p = 1.25*10-9 ). In AA men, we observed an intergenic GWS signal (rs12898370, p = 4.49*10-8 ) near LINGO1. In EA men, there was a GWS signal in CCSER1 (rs62313897; p = 7.93*10-10 ). The loci identified in this GWAS implicate molecular mechanisms related to psychiatric illness and personality features, suggesting that the interplay between AD and RSB is mediated by alleles associated with behavioral traits.
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Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania School of Medicine and VISN 4 MIRECC, Philadelphia VAMC, Philadelphia, PA, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
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10
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Vilor-Tejedor N, Cáceres A, Pujol J, Sunyer J, González JR. Imaging genetics in attention-deficit/hyperactivity disorder and related neurodevelopmental domains: state of the art. Brain Imaging Behav 2016; 11:1922-1931. [DOI: 10.1007/s11682-016-9663-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Lima LDA, Feio-dos-Santos AC, Belangero SI, Gadelha A, Bressan RA, Salum GA, Pan PM, Moriyama TS, Graeff-Martins AS, Tamanaha AC, Alvarenga P, Krieger FV, Fleitlich-Bilyk B, Jackowski AP, Brietzke E, Sato JR, Polanczyk GV, Mari JDJ, Manfro GG, do Rosário MC, Miguel EC, Puga RD, Tahira AC, Souza VN, Chile T, Gouveia GR, Simões SN, Chang X, Pellegrino R, Tian L, Glessner JT, Hashimoto RF, Rohde LA, Sleiman PMA, Hakonarson H, Brentani H. An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder. Sci Rep 2016; 6:22851. [PMID: 26947246 PMCID: PMC4780010 DOI: 10.1038/srep22851] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
Many studies have attempted to investigate the genetic susceptibility of Attention-Deficit/Hyperactivity Disorder (ADHD), but without much success. The present study aimed to analyze both single-nucleotide and copy-number variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios with sporadic ADHD. We also analyzed a Brazilian sample of 503 children/adolescent controls from a High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of five CNV studies and one GWAS meta-analysis of ADHD involving children/adolescents. The results from the Brazilian trios showed that cases with de novo SNVs tend not to have de novo CNVs and vice-versa. Although the sample size is small, we could also see that various comorbidities are more frequent in cases with only inherited variants. Moreover, using only genes expressed in brain, we constructed two "in silico" protein-protein interaction networks, one with genes from any analysis, and other with genes with hits in two analyses. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.
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Affiliation(s)
- Leandro de Araújo Lima
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Sintia Iole Belangero
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Ary Gadelha
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Rodrigo Affonseca Bressan
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Giovanni Abrahão Salum
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Hospital de Clínicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Pedro Mario Pan
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Tais Silveira Moriyama
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Ana Soledade Graeff-Martins
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Ana Carina Tamanaha
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Pedro Alvarenga
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Fernanda Valle Krieger
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Bacy Fleitlich-Bilyk
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Andrea Parolin Jackowski
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Elisa Brietzke
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - João Ricardo Sato
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Center of Mathematics, Computation and Cognition. Universidade Federal do ABC, Santo André, Brazil
| | - Guilherme Vanoni Polanczyk
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Jair de Jesus Mari
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Gisele Gus Manfro
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Hospital de Clínicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Conceição do Rosário
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Eurípedes Constantino Miguel
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Renato David Puga
- Hospital Israelita Albert Einstein, Clinical Research, São Paulo, SP, Brazil
| | - Ana Carolina Tahira
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Viviane Neri Souza
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Thais Chile
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Gisele Rodrigues Gouveia
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Sérgio Nery Simões
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Federal Institute of Espírito Santo, Serra, ES, Brazil
| | - Xiao Chang
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Renata Pellegrino
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ronaldo Fumio Hashimoto
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Mathematics &Statistics Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Luis Augusto Rohde
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Hospital de Clínicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Patrick M A Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Helena Brentani
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
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12
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Functional properties of rare missense variants of human CDH13 found in adult attention deficit/hyperactivity disorder (ADHD) patients. PLoS One 2013; 8:e71445. [PMID: 23936508 PMCID: PMC3731280 DOI: 10.1371/journal.pone.0071445] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 07/01/2013] [Indexed: 12/31/2022] Open
Abstract
The CDH13 gene codes for T-cadherin, a GPI-anchored protein with cell adhesion properties that is highly expressed in the brain and cardiovascular system. Previous studies have suggested that CDH13 may be a promising candidate gene for Attention Deficit/Hyperactivity Disorder (ADHD). The aims of this study were to identify, functionally characterize, and estimate the frequency of coding CDH13 variants in adult ADHD patients and controls. We performed sequencing of the CDH13 gene in 169 Norwegian adult ADHD patients and 63 controls and genotyping of the identified variants in 641 patients and 668 controls. Native and green fluorescent protein tagged wild type and variant CDH13 proteins were expressed and studied in CHO and HEK293 cells, respectively. Sequencing identified seven rare missense CDH13 variants, one of which was novel. By genotyping, we found a cumulative frequency of these rare variants of 2.9% in controls and 3.2% in ADHD patients, implying that much larger samples are needed to obtain adequate power to study the genetic association between ADHD and rare CDH13 variants. Protein expression and localization studies in CHO cells and HEK293 cells showed that the wild type and mutant proteins were processed according to the canonical processing of GPI-anchored proteins. Although some of the mutations were predicted to severely affect protein secondary structure and stability, no significant differences were observed between the expression levels and distribution of the wild type and mutant proteins in either HEK293 or CHO cells. This is the first study where the frequency of coding CDH13 variants in patients and controls is reported and also where the functional properties of these variants are examined. Further investigations are needed to conclude whether CDH13 is involved in the pathogenesis of ADHD or other conditions.
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Patel K, Scrimieri F, Ghosh S, Zhong J, Kim MS, Ren YR, Morgan RA, Iacobuzio-Donahue CA, Pandey A, Kern SE. FAM190A deficiency creates a cell division defect. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:296-303. [PMID: 23665203 DOI: 10.1016/j.ajpath.2013.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/13/2013] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
Like the p16, SMAD4, and RB1 genes, FAM190A (alias CCSER1) lies at a consensus site of homogeneous genomic deletions in human cancer. FAM190A transcripts in 40% of cancers also contain in-frame deletions of evolutionarily conserved exons. Its gene function was unknown. We found an internal deletion of the FAM190A gene in a pancreatic cancer having prominent focal multinuclearity. The experimental knockdown of FAM190A expression by shRNA caused focal cytokinesis defects, multipolar mitosis, and multinuclearity as observed in time-lapse microscopy. FAM190A was localized to the γ-tubulin ring complex of early mitosis and to the midbody in late cytokinesis by immunofluorescence assay and was present in the nuclear fraction of unsynchronized cells by immunoblot. FAM190A interacted with EXOC1 and Ndel1, which function in cytoskeletal organization and the cell division cycle. Levels of FAM190A protein peaked 12 hours after release from thymidine block, corresponding to M-phase. Slower-migrating phosphorylated forms accumulated toward M-phase and disappeared after release from a mitotic block and before cytokinesis. Studies of FAM190A alterations may provide mechanistic insights into mitotic dysregulation and multinuclearity in cancer. We propose that FAM190A is a regulator or structural component required for normal mitosis and that both the rare truncating mutations and common in-frame deletion alteration of FAM190A may contribute to the chromosomal instability of cancer.
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Affiliation(s)
- Kalpesh Patel
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, USA
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14
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Imaging gene and environmental effects on cerebellum in Attention-Deficit/Hyperactivity Disorder and typical development. NEUROIMAGE-CLINICAL 2012; 2:103-10. [PMID: 24179763 PMCID: PMC3777835 DOI: 10.1016/j.nicl.2012.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 10/31/2012] [Accepted: 11/20/2012] [Indexed: 11/21/2022]
Abstract
This study investigates the effects of XKR4, a recently identified candidate gene for Attention-Deficit/Hyperactivity Disorder (ADHD), birth weight, and their interaction on brain volume in ADHD. XKR4 is expressed in cerebellum and low birth weight has been associated both with changes in cerebellum and with ADHD, probably due to its relation with prenatal adversity. Anatomical MRI scans were acquired in 58 children with ADHD and 64 typically developing controls and processed to obtain volumes of cerebrum, cerebellum and gray and white matter in each structure. DNA was collected from saliva. Analyses including data on birth weight were conducted in a subset of 37 children with ADHD and 51 controls where these data were retrospectively collected using questionnaires. There was an interaction between genotype and birth weight for cerebellum gray matter volume (p = .020). The combination of homozygosity for the G-allele (the allele previously found to be overtransmitted in ADHD) and higher birth weight was associated with smaller volume. Furthermore, birth weight was positively associated with cerebellar white matter volume in controls, but not ADHD (interaction: p = .021). The interaction of genotype with birth weight affecting cerebellum gray matter is consistent with models that emphasize increased influence of genetic risk-factors in an otherwise favorable prenatal environment. The absence of an association between birth weight and cerebellum white matter volume in ADHD suggests that other genetic or environmental effects may be at play, unrelated to XKR4. These results underscore the importance of considering environmental effects in imaging genetics studies.
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Torgerson DG, Gignoux CR, Galanter JM, Drake KA, Roth LA, Eng C, Huntsman S, Torres R, Avila PC, Chapela R, Ford JG, Rodríguez-Santana JR, Rodríguez-Cintrón W, Hernandez RD, Burchard EG. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. J Allergy Clin Immunol 2012; 130:76-82.e12. [PMID: 22502797 PMCID: PMC3593143 DOI: 10.1016/j.jaci.2012.02.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Revised: 12/20/2011] [Accepted: 02/02/2012] [Indexed: 12/22/2022]
Abstract
BACKGROUND Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. OBJECTIVE We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. METHODS We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. RESULTS Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10(-3) that were significantly enriched for previously identified asthma-associated genes (P= .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. CONCLUSION Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility.
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Affiliation(s)
- Dara G Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.
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Studies of genomic copy number changes in human cancers reveal signatures of DNA replication stress. Mol Oncol 2011; 5:308-14. [PMID: 21641882 DOI: 10.1016/j.molonc.2011.05.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 05/02/2011] [Accepted: 05/11/2011] [Indexed: 11/23/2022] Open
Abstract
Human cancers are characterized by the presence of genomic instability. Recently, two studies have catalogued the presence of a specific class of genomic aberrations, large deletions and insertions, in a few thousand human cancers and reported that most of the prevalent recurrent focal deletions targeted common fragile sites and large genes. In various experimental systems, deletions in common fragile sites and large genes have been linked to the presence of DNA replication stress. Thus, taken together, these results suggest the presence of DNA replication stress in human cancers, consistent with the recently proposed oncogene-induced DNA damage model for cancer development.
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