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Zong W, Wang J, Zhao R, Niu N, Su Y, Hu Z, Liu X, Hou X, Wang L, Wang L, Zhang L. Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs. J Anim Sci Biotechnol 2023; 14:136. [PMID: 37805653 PMCID: PMC10559557 DOI: 10.1186/s40104-023-00929-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/03/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted. RESULTS Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. CONCLUSIONS: We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanfang Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ziping Hu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Chen WX, Liu B, Zhou L, Xiong X, Fu J, Huang ZF, Tan T, Tang M, Wang J, Tang YP. De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability. Hum Genomics 2022; 16:52. [PMID: 36320054 PMCID: PMC9623983 DOI: 10.1186/s40246-022-00427-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo altering genes and relative pathways which were associated with ID phenotype were analyzed. The connection nodes (genes) of above pathways were selected, and the diagnostic value of these selected genes for ID phenotype in the study population was also evaluated. RESULTS We identified 89 de novo mutant genes, of which 34 genes were previously reported to be associated with ASD, including double hits in the EGF repeats of NOTCH1 gene (p.V999M and p.S1027L). Interestingly, of these 34 genes, 22 may directly affect intelligence quotient (IQ). Further analyses revealed that these IQ-related genes were enriched in protein synthesis, energy metabolism, and amino acid metabolism, and at least 9 genes (CACNA1A, ALG9, PALM2, MGAT4A, PCK2, PLEKHA1, PSME3, ADI1, and TLE3) were involved in all these three pathways. Seven patients who harbored these gene mutations showed a high prevalence of a low IQ score (< 70), a non-verbal language, and an early diagnostic age (< 4 years). Furthermore, our panel of these 9 genes reached a 10.2% diagnostic rate (5/49) in early diagnostic patients with a low IQ score and also reached a 10% diagnostic yield in those with both a low IQ score and non-verbal language (4/40). CONCLUSION We found some new genetic disposition for ASD accompanied with intellectual disability in this study. Our results may be helpful for etiologic research and early diagnoses of intellectual disability in ASD. Larger population studies and further mechanism studies are warranted.
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Affiliation(s)
- Wen-Xiong Chen
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Bin Liu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.258164.c0000 0004 1790 3548Department of Biobank, Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, Shenzhen, 518102 Guangdong China
| | - Lijie Zhou
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaoli Xiong
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Jie Fu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Zhi-Fang Huang
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Ting Tan
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Mingxi Tang
- grid.488387.8Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Jun Wang
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ya-Ping Tang
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
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Colijn MA, Hrynchak M, Hrazdil CT, Willaeys V, White RF, Stowe RM. A 1p31.3 deletion encompassing the nuclear factor 1A gene presenting as possible temporal lobe epilepsy in association with schizoaffective disorder. Neurocase 2022; 28:382-387. [PMID: 36209511 DOI: 10.1080/13554794.2022.2132869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Chromosome 1p32-p31 deletion syndrome, which is characterized by a variety of neurodevelopmental abnormalities, is thought to occur as a result of nuclear factor 1A (NFIA) haploinsufficiency. We present a case of a right-handed 40-year-old female with a 1p31.3 deletion, who exhibited numerous common features of this syndrome, in addition to treatment resistant schizoaffective disorder and possible temporal lobe epilepsy, making her presentation unique. While neither psychosis nor temporal lobe epilepsy has been described in this syndrome previously, these conditions likely occurred in our patient as a result of NFIA haploinsufficiency.
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Affiliation(s)
- Mark A Colijn
- Department of Psychiatry, The University of Calgary, Calgary, AB, Canada
| | - Monica Hrynchak
- Molecular Cytogenetic Laboratory, Royal Columbian Hospital, The University of British Columbia, New Westminster, BC, Canada
| | - Chantelle T Hrazdil
- Division of Neurology, Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Veerle Willaeys
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada
| | - Randall F White
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada.,Department of Psychiatry, The University of British Columbia, Vancouver, BC, Canada
| | - Robert M Stowe
- BC Neuropsychiatry Program, Departments of Psychiatry and Neurology (Medicine), and Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC, Canada
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Musfee FI, Oluwafemi OO, Agopian A, Hakonarson H, Goldmuntz E, Mitchell LE. Maternal Effect Genes as Risk Factors for Congenital Heart Defects. HGG ADVANCES 2022; 3:100098. [PMID: 35345810 PMCID: PMC8957044 DOI: 10.1016/j.xhgg.2022.100098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal effect genes (MEGs) encode factors (e.g., RNA) in the oocyte that control embryonic development prior to activation of the embryonic genome. Over 80 mammalian MEGs have been identified, including several that have been associated with phenotypes in humans. Maternal variation in MEGs is associated with a range of adverse outcomes, which, in humans, include hydatidiform moles, zygotic cleavage failure, and offspring with multi-locus imprinting disorders. In addition, data from both animal models and humans suggest that the MEGs may be associated with structural birth defects such as congenital heart defects (CHDs). To further investigate the association between MEGs and CHDs, we conducted gene-level and gene-set analyses of known mammalian MEGs (n = 82) and two common groups of CHDs: conotruncal heart defects and left ventricular outflow tract defects. We identified 14 candidate CHD-related MEGs. These 14 MEGs include three (CDC20, KHDC3L, and TRIP13) of the 11 known human MEGs, as well as one (DNMT3A) of the eight MEGs that have been associated with structural birth defects in animal models. Our analyses add to the growing evidence that MEGs are associated with structural birth defects, in particular CHDs. Given the large proportion of individuals with structural birth defects for whom etiology of their condition is unknown, further investigations of MEGs as potential risk factors for structural birth defects are strongly warranted.
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EWAS of Monozygotic Twins Implicate a Role of mTOR Pathway in Pathogenesis of Tic Spectrum Disorder. Genes (Basel) 2021; 12:genes12101510. [PMID: 34680906 PMCID: PMC8535383 DOI: 10.3390/genes12101510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Tic spectrum disorder (TSD) is an umbrella term which includes Gilles de la Tourette syndrome (GTS) and chronic tic disorder (CTD). They are considered highly heritable, yet the genetic components remain largely unknown. In this study we aimed to investigate disease-associated DNA methylation differences to identify genes and pathways which may be implicated in TSD aetiology. For this purpose, we performed an exploratory analysis of the genome-wide DNA methylation patterns in whole blood samples of 16 monozygotic twin pairs, of which eight were discordant and six concordant for TSD, while two pairs were asymptomatic. Although no sites reached genome-wide significance, we identified several sites and regions with a suggestive significance, which were located within or in the vicinity of genes with biological functions associated with neuropsychiatric disorders. The two top genes identified (TSC1 and CRYZ/TYW3) and the enriched pathways and components (phosphoinosides and PTEN pathways, and insulin receptor substrate binding) are related to, or have been associated with, the PI3K/AKT/mTOR pathway. Genes in this pathway have previously been associated with GTS, and mTOR signalling has been implicated in a range of neuropsychiatric disorders. It is thus possible that altered mTOR signalling plays a role in the complex pathogenesis of TSD.
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Alnak A, Kuşcu Özücer İ, Okay Çağlayan A, Coşkun M. Peripheral Expression of MACROD2 Gene Is Reduced Among a Sample of Turkish Children with Autism Spectrum Disorder. PSYCHIAT CLIN PSYCH 2021; 31:261-268. [PMID: 38765943 PMCID: PMC11079661 DOI: 10.5152/pcp.2021.21144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/18/2021] [Indexed: 05/22/2024] Open
Abstract
Background Genomic variations in mono-ADP ribosylhydrolase 2 (MACROD2) have been associated with autism spectrum disorder (ASD) in recent genome-wide studies and case reports. In this study, we aimed to evaluate the MACROD2 expression profile in patients with ASD. Methods The study group included 100 children with a DSM-5 diagnosis of ASD, and the control group consisted of 105 healthy controls. Blood samples were obtained from all participants in this study, and the gene expression level was determined using quantitative reverse transcription PCR (RT-qPCR). Statistical analysis was performed with R 3.4.0 and Statistical Program for Social Sciences (SPSS for Windows, 21.0). Results The mean ages of the participants in the study and control groups were 9.22 ± 3.62 and 9.27 ± 3.86 years, respectively. There was no significant difference concerning gender (P = .944) and age (P = .914) between the 2 groups. MACROD2 gene expression was found to be decreased in the study group compared to the control group (study group = 5.73, control group = 89.56; fold change =-3.967; P < .001). While the level of MACROD2 expression was not correlated with the ASD severity, it was associated with the severity of the hyperactivity/impulsivity symptoms (P = .008). Conclusions This is the first study in the literature investigating the peripheral expression of the MACROD2 gene. We showed that the expression level of MACROD2 was decreased in patients with ASD when compared to the control group. As the relationship between the MACROD2 gene expression profile and ASD remains to be further investigated, this study may provide an insight for further studies.
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Affiliation(s)
- Alper Alnak
- Department of Child and Adolescent Psychiatry, Istanbul University School of Medicine, Istanbul, Turkey
| | - İpek Kuşcu Özücer
- Department of Child and Adolescent Psychiatry, Istanbul University School of Medicine, Istanbul, Turkey
| | - Ahmet Okay Çağlayan
- Department of Medical Genetics, Dokuz Eylul University School of Medicine, Izmir, Turkey
| | - Murat Coşkun
- Department of Child and Adolescent Psychiatry, Istanbul University School of Medicine, Istanbul, Turkey
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Jaini R, Wolf MR, Yu Q, King AT, Frazier TW, Eng C. Maternal genetics influences fetal neurodevelopment and postnatal autism spectrum disorder-like phenotype by modulating in-utero immunosuppression. Transl Psychiatry 2021; 11:348. [PMID: 34091589 PMCID: PMC8179926 DOI: 10.1038/s41398-021-01472-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/06/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic studies in ASD have mostly focused on the proband, with no clear understanding of parental genetic contributions to fetal neurodevelopment. Among parental etiological factors, perinatal maternal inflammation secondary to autoimmunity, infections, and toxins is associated with ASD. However, the inherent impact of maternal genetics on in-utero inflammation and fetal neurodevelopment in the absence of strong external inflammatory exposures is not known. We used the PtenWT/m3m4 mouse model for ASD to demonstrate the impact of maternal genetics on the penetrance of ASD-like phenotypes in the offspring. PtenWT/m3m4 (Momm3m4) or PtenWT/WT (MomWT) females, their offspring, and placental interface were analyzed for inflammatory markers, gene expression, and cellular phenotypes at E17.5. Postnatal behavior was tested by comparing pups from Momm3m4 vs. MomWT. Mothers of the PtenWT/m3m4 genotype (Momm3m4) showed inadequate induction of IL-10 mediated immunosuppression during pregnancy. Low IL-10 in the mother was directly correlated with decreased complement expression in the fetal liver. Fetuses from Momm3m4 had increased breakdown of the blood-brain-barrier, neuronal loss, and lack of glial cell maturation during in-utero stages. This impact of maternal genotype translated to a postnatal increase in the risk of newborn mortality, visible macrocephaly and ASD-like repetitive and social behaviors. Depending on maternal genotype, non-predisposed (wildtype) offspring showed ASD-like phenotypes, and phenotypic penetrance was decreased in predisposed pups from MomWT. Our study introduces the concept that maternal genetics alone, without any added external inflammatory insults, can modulate fetal neurodevelopment and ASD-related phenotypes in the offspring via alteration of IL-10 mediated materno-fetal immunosuppression.
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Affiliation(s)
- Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Matthew R Wolf
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Qi Yu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Alexander T King
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Thomas W Frazier
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Psychology, John Carroll University, University Heights, Cleveland, OH, 44118, USA
- Autism Speaks, Cleveland, OH, 44131, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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Lyall K, Ames JL, Pearl M, Traglia M, Weiss LA, Windham GC, Kharrazi M, Yoshida CK, Yolken R, Volk HE, Ashwood P, Van de Water J, Croen LA. A profile and review of findings from the Early Markers for Autism study: unique contributions from a population-based case-control study in California. Mol Autism 2021; 12:24. [PMID: 33736683 PMCID: PMC7977191 DOI: 10.1186/s13229-021-00429-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/23/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Early Markers for Autism (EMA) study is a population-based case-control study designed to learn more about early biologic processes involved in ASD. METHODS Participants were drawn from Southern California births from 2000 to 2003 with archived prenatal and neonatal screening specimens. Across two phases, children with ASD (n = 629) and intellectual disability without ASD (ID, n = 230) were ascertained from the California Department of Developmental Services (DDS), with diagnoses confirmed according to DSM-IV-TR criteria based on expert clinical review of abstracted records. General population controls (GP, n = 599) were randomly sampled from birth certificate files and matched to ASD cases by sex, birth month and year after excluding individuals with DDS records. EMA has published over 20 papers examining immune markers, endogenous hormones, environmental chemicals, and genetic factors in association with ASD and ID. This review summarizes the results across these studies, as well as the EMA study design and future directions. RESULTS EMA enabled several key contributions to the literature, including the examination of biomarker levels in biospecimens prospectively collected during critical windows of neurodevelopment. Key findings from EMA include demonstration of elevated cytokine and chemokine levels in maternal mid-pregnancy serum samples in association with ASD, as well as aberrations in other immune marker levels; suggestions of increased odds of ASD with prenatal exposure to certain endocrine disrupting chemicals, though not in mixture analyses; and demonstration of maternal and fetal genetic influence on prenatal chemical, and maternal and neonatal immune marker and vitamin D levels. We also observed an overall lack of association with ASD and measured maternal and neonatal vitamin D, mercury, and brain-derived neurotrophic factor (BDNF) levels. LIMITATIONS Covariate and outcome data were limited to information in Vital Statistics and DDS records. As a study based in Southern California, generalizability for certain environmental exposures may be reduced. CONCLUSIONS Results across EMA studies support the importance of the prenatal and neonatal periods in ASD etiology, and provide evidence for the role of the maternal immune response during pregnancy. Future directions for EMA, and the field of ASD in general, include interrogation of mechanistic pathways and examination of combined effects of exposures.
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Affiliation(s)
- Kristen Lyall
- A.J. Drexel Autism Institute, Drexel University, Suite 560, 3020 Market St, Philadelphia, PA, 19104, USA.
| | - Jennifer L Ames
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Michelle Pearl
- Environmental Health Investigations Branch, California Department of Public Health, Richmond, CA, USA
| | - Michela Traglia
- University of California, San Francisco, San Francisco, CA, USA
| | - Lauren A Weiss
- University of California, San Francisco, San Francisco, CA, USA
| | - Gayle C Windham
- Environmental Health Investigations Branch, California Department of Public Health, Richmond, CA, USA
| | - Martin Kharrazi
- Environmental Health Investigations Branch, California Department of Public Health, Richmond, CA, USA
| | - Cathleen K Yoshida
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Robert Yolken
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Heather E Volk
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
| | - Paul Ashwood
- UC Davis MIND Institute, University of California, Davis, Davis, CA, USA
| | - Judy Van de Water
- UC Davis MIND Institute, University of California, Davis, Davis, CA, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
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Ünsel Bolat G, Bolat H. The Role of Copy Number Variations and FHIT Gene on Phenotypic Characteristics of Cases Diagnosed with Autism Spectrum Disorder. Mol Syndromol 2020; 12:12-19. [PMID: 33776622 DOI: 10.1159/000512171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/08/2020] [Indexed: 11/19/2022] Open
Abstract
Copy number variations (CNVs) have been implied in the etiology of autism spectrum disorder (ASD), and microarray-based techniques are performed as a first-step genetic test. Our aim was to present clinical features and CNV profiles of patients with ASD and their parents. Array-CGH was applied to detect CNVs. Previously as likely pathogenic reported duplications were detected at 16p13.11 and 11p15.2p15.1. Other variants were found in 16p11.2p11.1, 3p14.2, 15q11.2, 10q11.22, 3p26.3, 4q13.3, 22q13.32q13.33, and 1q44 and were classified as variants of unknown significance. Deletion of the FHIT gene was associated with the regression of language and social skills without mental impairment. Paternal inheritance of difficulty in social skills and the FHIT gene was documented. In addition, varying olfactory receptor family genes were implicated in de novo and hereditary CNVs. In this study, we aimed to present the clinical characteristics of the cases and parents in more detail, especially in pathogenic CNV cases, which enables us to increase our knowledge on inherited CNVs and genotype-phenotype correlation. We suggest that both genetic and psychiatric evaluation of the parents of the cases is important for better understanding the clinical relevance of the CNV results.
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Affiliation(s)
- Gül Ünsel Bolat
- Department of Child and Adolescent Psychiatry, Balıkesir University School of Medicine, Balıkesir, Turkey
| | - Hilmi Bolat
- Department of Medical Genetics, Balıkesir Atatürk City Hospital, Balıkesir, Turkey
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Abstract
Many of the immunoglobulin superfamily (IgSF) molecules play pivotal roles in cell communication. The Sidekick (Sdk) gene, first described in Drosophila, encodes the single-pass transmembrane protein, Sdk, which is one of the largest among IgSF membrane proteins. Sdk first appeared in multicellular animals during the Precambrian age and later evolved to Sdk1 and Sdk2 in vertebrates by gene duplication. In flies, a single Sdk is involved in positioning photoreceptor neurons and their axons in the visual system and is responsible for dynamically rearranging cell shapes by strictly populating tricellular adherens junctions in epithelia. In vertebrates, Sdk1 and Sdk2 are expressed by unique sets of cell types and distinctively participate in the formation and/or maintenance of neural circuits in the retina, indicating that they are determinants of synaptic specificity. These functions are mediated by specific homophilic binding of their ectodomains and by intracellular association with PDZ scaffold proteins. Recent human genetic studies as well as animal experiments implicate that Sdk genes may influence various neurodevelopmental and psychiatric disorders, such as autism spectrum disorders, attention-deficit hyperactivity disorder, addiction, and depression. The gigantic Sdk1 gene is susceptible to erratic gene rearrangements or mutations in both somatic and germ-line cells, potentially contributing to neurological disorders and some types of cancers. This review summarizes what is known about the structure and roles of Sdks.
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Affiliation(s)
- Masahito Yamagata
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, United States
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Saxena R, Babadi M, Namvarhaghighi H, Roullet FI. Role of environmental factors and epigenetics in autism spectrum disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 173:35-60. [PMID: 32711816 DOI: 10.1016/bs.pmbts.2020.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder thought to be caused by predisposing high-risk genes that may be altered during the early development by environmental factors. The impact of maternal challenges during pregnancy on the prevalence of ASD has been widely studied in clinical and animal studies. Here, we review some clinical and pre-clinical evidence that links environmental factors (i.e., infection, air pollution, pesticides, valproic acid and folic acid) and the risk of ASD. Additionally, certain prenatal environmental challenges such as the valproate and folate prenatal exposures allow us to study mechanisms possibly linked to the etiology of ASD, for instance the epigenetic processes. These mechanistic pathways are also presented and discussed in this chapter.
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Affiliation(s)
- Roheeni Saxena
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Melika Babadi
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | | | - Florence I Roullet
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.
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12
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Traglia M, Windham GC, Pearl M, Poon V, Eyles D, Jones KL, Lyall K, Kharrazi M, Croen LA, Weiss LA. Genetic Contributions to Maternal and Neonatal Vitamin D Levels. Genetics 2020; 214:1091-1102. [PMID: 32047095 PMCID: PMC7153928 DOI: 10.1534/genetics.119.302792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 02/05/2020] [Indexed: 02/08/2023] Open
Abstract
Vitamin D is essential for several physiological functions and biological processes. Increasing levels of maternal vitamin D are required throughout pregnancy as a unique source of vitamin D for the fetus, and consequently maternal vitamin D deficiency may result in several adverse outcomes in newborns. However, the genetic regulation of vitamin D in pregnancy and at birth is not yet well understood. We performed genome-wide association studies of maternal midgestational serum-derived and neonatal blood-spot-derived total 25-hydroxyvitamin D from a case-control study of autism spectrum disorder (ASD). We identified one fetal locus (rs4588) significantly associated with neonatal vitamin D levels in the GC gene, encoding the binding protein for the transport and function of vitamin D. We also found suggestive cross-associated loci for neonatal and maternal vitamin D near immune genes, such as CXCL6-IL8 and ACKR1 We found no interactions with ASD. However, when including a set of cases with intellectual disability but not ASD (N = 179), we observed a suggestive interaction between decreased levels of neonatal vitamin D and a specific maternal genotype near the PKN2 gene. Our results suggest that genetic variation influences total vitamin D levels during pregnancy and at birth via proteins in the vitamin D pathway, but also potentially via distinct mechanisms involving loci with known roles in immune function that might be involved in vitamin D pathophysiology in pregnancy.
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Affiliation(s)
- Michela Traglia
- Department of Psychiatry, Institute for Human Genetics, University of California, San Francisco, California 94143
| | - Gayle C Windham
- California Department of Public Health, Environmental Health Investigations Branch, Richmond, California 94804
| | - Michelle Pearl
- California Department of Public Health, Environmental Health Investigations Branch, Richmond, California 94804
| | - Victor Poon
- Sequoia Foundation, La Jolla, California 92037
| | - Darryl Eyles
- Queensland Brain Institute, University of Queensland, Brisbane, 4072, Australia
| | - Karen L Jones
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, California 95616
| | - Kristen Lyall
- A.J. Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania 191044
| | - Martin Kharrazi
- California Department of Public Health, Environmental Health Investigations Branch, Richmond, California 94804
| | - Lisa A Croen
- Autism Research Program, Division of Research, Kaiser Permanente, Oakland, California 94612
| | - Lauren A Weiss
- Department of Psychiatry, Institute for Human Genetics, University of California, San Francisco, California 94143
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13
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Wang T, Lv X, Jiang S, Han S, Wang Y. Expression of ADAM29 and FAM135B in the pathological evolution from normal esophageal epithelium to esophageal cancer: Their differences and clinical significance. Oncol Lett 2020; 19:1727-1734. [PMID: 32194665 PMCID: PMC7039107 DOI: 10.3892/ol.2020.11272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 11/17/2019] [Indexed: 12/24/2022] Open
Abstract
A Disintegrin And Metalloprotease Domain 29 (ADAM29) and Family with sequence similarity 135 member B (FAM135B) genes have been reported to be associated with a carcinogenic risk of esophageal squamous cell carcinoma (ESCC). However, to the best of our knowledge, the expression of ADAM29 and FAM135B in the pathological evolution from normal esophageal epithelial cells to ESCC has not yet been investigated. The present study aimed to investigate the expression of ADAM29 and FAM135B in normal esophageal mucosal epithelium, low-grade and high-grade esophageal intraepithelial neoplasia, and ESCC. Furthermore, the present study aimed to investigate the role of ADAM29 and FAM135B in the development of esophageal lesions. Immunohistochemistry was performed in order to detect the expression levels of ADAM29 and FAM135B proteins in normal esophageal mucosa samples (40 cases), low-grade intraepithelial neoplasia samples (20 cases), high-grade intraepithelial neoplasia samples (20 cases) and ESCC samples (40 cases). The results of the present study demonstrated that the positive rates of ADAM29 and FAM135B proteins increased gradually from normal esophageal mucosal epithelium and esophageal intraepithelial neoplasia, to ESCC (P<0.05). Furthermore, the expression levels of ADAM29 and FAM135B proteins in ESCC were not associated with age and the tumor size (P>0.05); however, the protein levels were associated with the pathological stage, clinical stage and lymph node metastasis of ESCC (P<0.05). In addition, there was a significant association between the expression levels of ADAM29 protein and FAM135B protein (χ2=60.071; P<0.001). The results of the present study demonstrated that the expression levels of ADAM29 and FAM135B were associated with the tumor behavior characteristics and the progression of esophageal cancer, the expression of which could be used for the diagnosis of early esophageal cancer, and provide the basis for guiding individualized treatment.
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Affiliation(s)
- Tingting Wang
- Department of Radiation Oncology, PLA 960th Hospital, Jinan, Shandong 250031, P.R. China
| | - Xiaoyan Lv
- Department of Radiation Oncology, PLA 960th Hospital, Jinan, Shandong 250031, P.R. China
| | - Shen Jiang
- Department of Emergency Internal Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 201203, P.R. China
| | - Shaorong Han
- Department of Radiation Oncology, PLA 960th Hospital, Jinan, Shandong 250031, P.R. China
| | - Yanming Wang
- Department of Radiation Oncology, PLA 960th Hospital, Jinan, Shandong 250031, P.R. China
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14
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High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability. J Neural Transm (Vienna) 2019; 127:81-94. [PMID: 31838600 DOI: 10.1007/s00702-019-02114-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Copy-number variants (CNVs), in particular rare, small and large ones (< 1% frequency) and those encompassing brain-related genes, have been shown to be associated with neurodevelopmental disorders like autism spectrum disorders (ASDs), attention deficit hyperactivity disorder (ADHD), and intellectual disability (ID). However, the vast majority of CNV findings lack specificity with respect to autistic or developmental-delay phenotypes. Therefore, the aim of the study was to investigate the size and frequency of CNVs in high-functioning ASD (HFA) without ID compared with a random population sample and with published findings in ASD and ID. To investigate the role of CNVs for the "core symptoms" of high-functioning autism, we included in the present exploratory study only patients with HFA without ID. The aim was to test whether HFA have similar large rare (> 1 Mb) CNVs as reported in ASD and ID. We performed high-resolution chromosomal microarray analysis in 108 children and adolescents with HFA without ID. There was no significant difference in the overall number of rare CNVs compared to 124 random population samples. However, patients with HFA carried significantly more frequently CNVs containing brain-related genes. Surprisingly, six HFA patients carried very large CNVs known to be typically present in ID. Our findings provide new evidence that not only small, but also large CNVs affecting several key genes contribute to the genetic etiology/risk of HFA without affecting their intellectual ability.
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15
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Ames JL, Windham GC, Lyall K, Pearl M, Kharrazi M, Yoshida CK, Van de Water J, Ashwood P, Croen LA. Neonatal Thyroid Stimulating Hormone and Subsequent Diagnosis of Autism Spectrum Disorders and Intellectual Disability. Autism Res 2019; 13:444-455. [DOI: 10.1002/aur.2247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/26/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Gayle C. Windham
- Environmental Health Investigations BranchCalifornia Department of Public Health Richmond California
| | - Kristen Lyall
- A.J. Drexel Autism InstituteDrexel University Philadelphia Pennsylvania
| | - Michelle Pearl
- Environmental Health Investigations BranchCalifornia Department of Public Health Richmond California
| | - Martin Kharrazi
- Environmental Health Investigations BranchCalifornia Department of Public Health Richmond California
| | | | - Judy Van de Water
- Department of Public Health Sciences, Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California Davis California
- MIND (Medical Investigations of Neurodevelopmental Disorders) InstituteUniversity of California Davis California
| | - Paul Ashwood
- MIND (Medical Investigations of Neurodevelopmental Disorders) InstituteUniversity of California Davis California
- Department of Medical Microbiology and ImmunologyUniversity of California Davis California
| | - Lisa A. Croen
- Kaiser Permanente Division of Research Oakland California
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16
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11th International Congress on Psychopharmacology & 7th International Symposium on Child and Adolescent Psychopharmacology. PSYCHIAT CLIN PSYCH 2019. [DOI: 10.1080/24750573.2019.1608692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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17
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Ong ML, Tuan TA, Poh J, Teh AL, Chen L, Pan H, MacIsaac JL, Kobor MS, Chong YS, Kwek K, Saw SM, Godfrey KM, Gluckman PD, Fortier MV, Karnani N, Meaney MJ, Qiu A, Holbrook JD. Neonatal amygdalae and hippocampi are influenced by genotype and prenatal environment, and reflected in the neonatal DNA methylome. GENES BRAIN AND BEHAVIOR 2019; 18:e12576. [PMID: 31020763 DOI: 10.1111/gbb.12576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/01/2019] [Accepted: 04/13/2019] [Indexed: 12/28/2022]
Abstract
The amygdala and hippocampus undergo rapid development in early life. The relative contribution of genetic and environmental factors to the establishment of their developmental trajectories has yet to be examined. We performed imaging on neonates and examined how the observed variation in volume and microstructure of the amygdala and hippocampus varied by genotype, and compared with prenatal maternal mental health and socioeconomic status. Gene × Environment models outcompeted models containing genotype or environment only to best explain the majority of measures but some, especially of the amygdaloid microstructure, were best explained by genotype only. Models including DNA methylation measured in the neonate umbilical cords outcompeted the Gene and Gene × Environment models for the majority of amygdaloid measures and minority of hippocampal measures. This study identified brain region-specific gene networks associated with individual differences in fetal brain development. In particular, genetic and epigenetic variation within CUX1 was highlighted.
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Affiliation(s)
- Mei-Lyn Ong
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Ta A Tuan
- Department of Biomedical Engineering, Clinical Imaging research Centre, National University of Singapore, Singapore
| | - Joann Poh
- Department of Biomedical Engineering, Clinical Imaging research Centre, National University of Singapore, Singapore
| | - Ai L Teh
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Li Chen
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Hong Pan
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,School of Computer Engineering, Nanyang Technological University (NTU), Singapore
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yap S Chong
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Kenneth Kwek
- KK Women's and Children's Hospital, Duke National University of Singapore, Singapore
| | - Seang M Saw
- Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Peter D Gluckman
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,Centre for Human Evolution, Adaptation and disease, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Marielle V Fortier
- KK Women's and Children's Hospital, Duke National University of Singapore, Singapore
| | - Neerja Karnani
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Michael J Meaney
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,Ludmer Centre for Neuroinformatics and Mental Health, Sackler Program for Epigenetics & Psychobiology at McGill University, Douglas University Mental Health Institute, McGill University, Montreal, Canada
| | - Anqi Qiu
- Department of Biomedical Engineering, Clinical Imaging research Centre, National University of Singapore, Singapore.,Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Joanna D Holbrook
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
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18
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Palazzo L, Mikolčević P, Mikoč A, Ahel I. ADP-ribosylation signalling and human disease. Open Biol 2019; 9:190041. [PMID: 30991935 PMCID: PMC6501648 DOI: 10.1098/rsob.190041] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
ADP-ribosylation (ADPr) is a reversible post-translational modification of proteins, which controls major cellular and biological processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress and immune responses. In order to maintain the cellular homeostasis, diverse ADP-ribosyl transferases and hydrolases are involved in the fine-tuning of ADPr systems. The control of ADPr network is vital, and dysregulation of enzymes involved in the regulation of ADPr signalling has been linked to a number of inherited and acquired human diseases, such as several neurological disorders and in cancer. Conversely, the therapeutic manipulation of ADPr has been shown to ameliorate several disorders in both human and animal models. These include cardiovascular, inflammatory, autoimmune and neurological disorders. Herein, we summarize the recent findings in the field of ADPr, which support the impact of this modification in human pathophysiology and highlight the curative potential of targeting ADPr for translational and molecular medicine.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
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19
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Leppäaho E, Renvall H, Salmela E, Kere J, Salmelin R, Kaski S. Discovering heritable modes of MEG spectral power. Hum Brain Mapp 2019; 40:1391-1402. [PMID: 30600573 PMCID: PMC6590382 DOI: 10.1002/hbm.24454] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/27/2018] [Accepted: 10/19/2018] [Indexed: 12/14/2022] Open
Abstract
Brain structure and many brain functions are known to be genetically controlled, but direct links between neuroimaging measures and their underlying cellular-level determinants remain largely undiscovered. Here, we adopt a novel computational method for examining potential similarities in high-dimensional brain imaging data between siblings. We examine oscillatory brain activity measured with magnetoencephalography (MEG) in 201 healthy siblings and apply Bayesian reduced-rank regression to extract a low-dimensional representation of familial features in the participants' spectral power structure. Our results show that the structure of the overall spectral power at 1-90 Hz is a highly conspicuous feature that not only relates siblings to each other but also has very high consistency within participants' own data, irrespective of the exact experimental state of the participant. The analysis is extended by seeking genetic associations for low-dimensional descriptions of the oscillatory brain activity. The observed variability in the MEG spectral power structure was associated with SDK1 (sidekick cell adhesion molecule 1) and suggestively with several other genes that function, for example, in brain development. The current results highlight the potential of sophisticated computational methods in combining molecular and neuroimaging levels for exploring brain functions, even for high-dimensional data limited to a few hundred participants.
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Affiliation(s)
- Eemeli Leppäaho
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Helsinki, Finland
| | - Hanna Renvall
- Department of Neuroscience and Biomedical Engineering, Aalto University, Helsinki, Finland.,Aalto NeuroImaging, Aalto University, Helsinki, Finland
| | - Elina Salmela
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Molecular Neurology Research Program, University of Helsinki, Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Riitta Salmelin
- Department of Neuroscience and Biomedical Engineering, Aalto University, Helsinki, Finland.,Aalto NeuroImaging, Aalto University, Helsinki, Finland
| | - Samuel Kaski
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Helsinki, Finland
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20
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Lo Re O, Mazza T, Vinciguerra M. Mono-ADP-Ribosylhydrolase MACROD2 Is Dispensable for Murine Responses to Metabolic and Genotoxic Insults. Front Genet 2018; 9:654. [PMID: 30619475 PMCID: PMC6305994 DOI: 10.3389/fgene.2018.00654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is an important post-translational protein modification that regulates diverse biological processes, controlled by dedicated transferases, and hydrolases. Disruption in the gene encoding for MACROD2, a mono-ADP-ribosylhydrolase, has been associated to the Kabuki syndrome, a pediatric congenital disorder characterized by facial anomalies, and mental retardation. Non-coding and structural mutations/variations in MACROD2 have been associated to psychiatric disorders, to obesity, and to cancer. Mechanistically, it has been recently shown that frequent deletions of the MACROD2 alter DNA repair and sensitivity to DNA damage, resulting in chromosome instability, and colorectal tumorigenesis. Whether MACROD2 deletion sensitizes the organism to metabolic and tumorigenic stressors, in absence of other genetic drivers, is unclear. As MACROD2 is ubiquitously expressed in mice, here we generated constitutively whole-body knock-out mice for MACROD2, starting from mouse embryonic stem (ES) cells deleted for the gene using the VelociGene® technology, belonging to the Knockout Mouse Project (KOMP) repository, a NIH initiative. MACROD2 knock-out mice were viable and healthy, indistinguishable from wild type littermates. High-fat diet administration induced obesity, and glucose/insulin intolerance in mice independent of MACROD2 gene deletion. Moreover, sub-lethal irradiation did not indicate a survival or lethality bias in MACROD2 knock-out mice compared to wild type littermates. Altogether, our data point against a sufficient role of MACROD2 deletion in aggravating high-fat induced obesity and DNA damage-associated lethality, in absence of other genetic drivers.
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Affiliation(s)
- Oriana Lo Re
- International Clinical Research Center, St Anne's University Hospital, Brno, Czechia.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Tommaso Mazza
- Bioinformatics Unit, Casa Sollievo della Sofferenza (IRCCS), San Giovanni Rotondo, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St Anne's University Hospital, Brno, Czechia.,Institute for Liver and Digestive Health, Division of Medicine, University College London, London, United Kingdom
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21
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Traglia M, Croen LA, Jones KL, Heuer LS, Yolken R, Kharrazi M, DeLorenze GN, Ashwood P, Van de Water J, Weiss LA. Cross-genetic determination of maternal and neonatal immune mediators during pregnancy. Genome Med 2018; 10:67. [PMID: 30134952 PMCID: PMC6106874 DOI: 10.1186/s13073-018-0576-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The immune system plays a fundamental role in development during pregnancy and early life. Alterations in circulating maternal and neonatal immune mediators have been associated with pregnancy complications as well as susceptibility to autoimmune and neurodevelopmental conditions in later life. Evidence suggests that the immune system in adults not only responds to environmental stimulation but is also under strong genetic control. METHODS This is the first genetic study of > 700 mother-infant pairs to analyse the circulating levels of 22 maternal mid-gestational serum-derived and 42 neonatal bloodspot-derived immune mediators (cytokines/chemokines) in the context of maternal and fetal genotype. We first estimated the maternal and fetal genome-wide SNP-based heritability (h2g) for each immune molecule and then performed genome-wide association studies (GWAS) to identify specific loci contributing to individual immune mediators. Finally, we assessed the relationship between genetic immune determinants and ASD outcome. RESULTS We show maternal and neonatal cytokines/chemokines displaying genetic regulation using independent methodologies. We demonstrate that novel fetal loci for immune function independently affect the physiological levels of maternal immune mediators and vice versa. The cross-associated loci are in distinct genomic regions compared with individual-specific immune mediator loci. Finally, we observed an interaction between increased IL-8 levels at birth, autism spectrum disorder (ASD) status, and a specific maternal genotype. CONCLUSIONS Our results suggest that maternal and fetal genetic variation influences the immune system during pregnancy and at birth via distinct mechanisms and that a better understanding of immune factor determinants in early development may shed light on risk factors for developmental disorders.
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Affiliation(s)
- Michela Traglia
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Lisa A Croen
- Divison of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Karen L Jones
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California Davis, Davis, CA, USA
- MIND Institute, University of California Davis, Davis, CA, USA
| | - Luke S Heuer
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California Davis, Davis, CA, USA
- MIND Institute, University of California Davis, Davis, CA, USA
| | - Robert Yolken
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin Kharrazi
- Division of Environmental and Occupational Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Gerald N DeLorenze
- Divison of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Paul Ashwood
- MIND Institute, University of California Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Judy Van de Water
- Department of Internal Medicine, Division of Rheumatology, Allergy, and Clinical Immunology, University of California Davis, Davis, CA, USA
- MIND Institute, University of California Davis, Davis, CA, USA
| | - Lauren A Weiss
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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22
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Robichaux WG, Cheng X. Intracellular cAMP Sensor EPAC: Physiology, Pathophysiology, and Therapeutics Development. Physiol Rev 2018; 98:919-1053. [PMID: 29537337 PMCID: PMC6050347 DOI: 10.1152/physrev.00025.2017] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
This review focuses on one family of the known cAMP receptors, the exchange proteins directly activated by cAMP (EPACs), also known as the cAMP-regulated guanine nucleotide exchange factors (cAMP-GEFs). Although EPAC proteins are fairly new additions to the growing list of cAMP effectors, and relatively "young" in the cAMP discovery timeline, the significance of an EPAC presence in different cell systems is extraordinary. The study of EPACs has considerably expanded the diversity and adaptive nature of cAMP signaling associated with numerous physiological and pathophysiological responses. This review comprehensively covers EPAC protein functions at the molecular, cellular, physiological, and pathophysiological levels; and in turn, the applications of employing EPAC-based biosensors as detection tools for dissecting cAMP signaling and the implications for targeting EPAC proteins for therapeutic development are also discussed.
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Affiliation(s)
- William G Robichaux
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center , Houston, Texas
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center , Houston, Texas
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23
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刘 江, 朱 君, 张 亚, 白 杨. [Expression pattern of FAM135B and K (lysine) acetyltransferase 5 in esophageal squamous cell carcinoma in Uygur patients]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:224-228. [PMID: 29502064 PMCID: PMC6743880 DOI: 10.3969/j.issn.1673-4254.2018.02.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To explore the expression of the family with sequence similarity 135 member B (FAM135B) and K(lysine) acetyltransferase 5 (KAT5) in esophageal squamous cell carcinoma (ESCC) in Uygur patients. METHODS The expression of FAM135B and KAT5 in ESCC tissues and paired adjacent tissues from 40 Uygur patients were detected using Roche Benchmark XT. The correlation of FAM135B and KAT5 and their correlation with the clinicopathological characteristics of the patients were analyzed. RESULTS The positivity rates of FAM135B and KAT5 in ESCC tissues were 92.50% (37/40) and 15.00%(6/40) in these patients, respectively. The ESCC tissues showed a significantly higher rate of strong FAM135B expression than the adjacent tissues [45.00% (18/40) vs 22.50% (9/40); Χ2=4.528, P=0.033], but the rates of negative KAT5 expression was similar between ESCC and adjacent tissues [85.00% (34/40) vs 87.50% (35/40); Χ2=0.105, P=0.745]. Strong expressions of FAM135B in ESCC tissues and the paired adjacent tissues were well correlated (Kendall's coefficient = 0.707, P<0.001). In ESCC tissues, a strong expression of FAM135B showed a significant negative correlation with KAT5 expression (Kendall's coefficient=-0.946, P<0.001). Neither FAM135B nor KAT5 expression was associated with the patients' gender, age, tumor site, tumor differentiation, invasion, lymph node metastasis and clinical stage (all P>0.05). CONCLUSION A strong expression of FAM135B may be an important molecular basis for the occurrence of ESCC in Uygur patients and plays its role by negatively regulating the expression of KAT5.
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Affiliation(s)
- 江 刘
- 南方医科大学南方医院 消化内科,广东 广州 510515Department of Gastroenterology, Nanfang hospital, Southern Medical University, Guangzhou 510515, China
| | - 君玲 朱
- 新疆喀什地区第一人民医院病理科,新疆 喀什 844000Dpartment of Pathology, Kashi First People's Hospital, Kashi 84400, China
| | - 亚历 张
- 南方医科大学南方医院 消化内科,广东 广州 510515Department of Gastroenterology, Nanfang hospital, Southern Medical University, Guangzhou 510515, China
| | - 杨 白
- 南方医科大学南方医院 消化内科,广东 广州 510515Department of Gastroenterology, Nanfang hospital, Southern Medical University, Guangzhou 510515, China
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24
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Direk N, Williams S, Smith JA, Ripke S, Air T, Amare AT, Amin N, Baune BT, Bennett DA, Blackwood DH, Boomsma D, Breen G, Buttenschøn HN, Byrne EM, Børglum AD, Castelao E, Cichon S, Clarke TK, Cornelis MC, Dannlowski U, De Jager PL, Demirkan A, Domenici E, van Duijn CM, Dunn EC, Eriksson JG, Esko T, Faul JD, Ferrucci L, Fornage M, de Geus E, Gill M, Gordon SD, Jörgen Grabe H, van Grootheest G, Hamilton SP, Hartman CA, Heath AC, Hek K, Hofman A, Homuth G, Horn C, Hottenga JJ, Kardia SL, Kloiber S, Koenen K, Kutalik Z, Ladwig KH, Lahti J, Levinson DF, Lewis CM, Lewis G, Li QS, Llewellyn DJ, Lucae S, Lunetta KL, MacIntyre DJ, Madden P, Martin NG, McIntosh AM, Metspalu A, Milaneschi Y, Montgomery GW, Mors O, Mosley TH, Murabito JM, Müller-Myhsok B, Nöthen MM, Nyholt DR, O’Donovan MC, Penninx BW, Pergadia ML, Perlis R, Potash JB, Preisig M, Purcell SM, Quiroz JA, Räikkönen K, Rice JP, Rietschel M, Rivera M, Schulze TG, Shi J, Shyn S, Sinnamon GC, Smit JH, Smoller JW, Snieder H, Tanaka T, Tansey KE, Teumer A, Uher R, Umbricht D, Van der Auwera S, Ware EB, Weir DR, Weissman MM, Willemsen G, Yang J, Zhao W, Tiemeier H, Sullivan PF. An Analysis of Two Genome-wide Association Meta-analyses Identifies a New Locus for Broad Depression Phenotype. Biol Psychiatry 2017; 82:322-329. [PMID: 28049566 PMCID: PMC5462867 DOI: 10.1016/j.biopsych.2016.11.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND The genetics of depression has been explored in genome-wide association studies that focused on either major depressive disorder or depressive symptoms with mostly negative findings. A broad depression phenotype including both phenotypes has not been tested previously using a genome-wide association approach. We aimed to identify genetic polymorphisms significantly associated with a broad phenotype from depressive symptoms to major depressive disorder. METHODS We analyzed two prior studies of 70,017 participants of European ancestry from general and clinical populations in the discovery stage. We performed a replication meta-analysis of 28,328 participants. Single nucleotide polymorphism (SNP)-based heritability and genetic correlations were calculated using linkage disequilibrium score regression. Discovery and replication analyses were performed using a p-value-based meta-analysis. Lifetime major depressive disorder and depressive symptom scores were used as the outcome measures. RESULTS The SNP-based heritability of major depressive disorder was 0.21 (SE = 0.02), the SNP-based heritability of depressive symptoms was 0.04 (SE = 0.01), and their genetic correlation was 1.001 (SE = 0.2). We found one genome-wide significant locus related to the broad depression phenotype (rs9825823, chromosome 3: 61,082,153, p = 8.2 × 10-9) located in an intron of the FHIT gene. We replicated this SNP in independent samples (p = .02) and the overall meta-analysis of the discovery and replication cohorts (1.0 × 10-9). CONCLUSIONS This large study identified a new locus for depression. Our results support a continuum between depressive symptoms and major depressive disorder. A phenotypically more inclusive approach may help to achieve the large sample sizes needed to detect susceptibility loci for depression.
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Affiliation(s)
- Nese Direk
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Psychiatry, Dokuz Eylul University, Izmir, Turkey
| | - Stephanie Williams
- Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Jennifer A. Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Stephan Ripke
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, Berlin, Germany
| | - Tracy Air
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Azmeraw T. Amare
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bernhard T. Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - David A. Bennett
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | | | - Dorret Boomsma
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Gerome Breen
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Henriette N. Buttenschøn
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
| | - Enda M. Byrne
- The University of Queensland, Queensland Brain Institute, St. Lucia, Queensland, Australia
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark,Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Denmark
| | - Enrique Castelao
- Departement of Psychiatry, Lausanne University Hospital, Switzerland
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany,Department of Genomics, Life & Brain Center, Bonn, Germany,Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany,Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Marilyn C. Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago IL, USA
| | - Udo Dannlowski
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Philip L. De Jager
- Department of Neurology, Program in Translational NeuroPsychiatric Genomics, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA,Harvard Medical School, Boston, Massachusetts, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ayse Demirkan
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Enrico Domenici
- Centre for Integrative Biology, University of Trento, Trento, Italy,Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erin C. Dunn
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Johan G. Eriksson
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Helsinki, Finland,Department of General Practice and Primary Health Care, University of Helsinki, Finland,Unit of General Practice, Helsinki University Central Hospital, Finland,Folkhalsan Research Centre, Helsinki, Finland,Vasa Central Hospital, Vasa, Finland
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia,Division of Endocrinology, Boston Children's Hospital, Cambridge, MA, USA,Program in Medical and Populational Genetics, Broad Institute, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jessica D. Faul
- Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eco de Geus
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Michael Gill
- Department of Psychiatry, Trinity Centre for Health Science, Dublin, Ireland
| | - Scott D. Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Hans Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, Germany,Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany,German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Germany
| | - Gerard van Grootheest
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Steven P. Hamilton
- Department of Psychiatry, Kaiser Permanente San Francisco Medical Center, CA, USA
| | - Catharina A. Hartman
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Andrew C. Heath
- Department of Psychiatry, Washington University St. Louis, Missouri, USA
| | - Karin Hek
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Germany
| | - Carsten Horn
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | | | | | - Karestan Koenen
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Karl-Heinz Ladwig
- Institute of Epidemiology II, Mental Health Research Unit, Helmholtz Zentrum München, German Research Center for Environmental Health, Germany,Department of Psychosomatic Medicine and Psychotherapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jari Lahti
- Folkhalsan Research Centre, Helsinki, Finland,Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Douglas F. Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Cathryn M. Lewis
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Glyn Lewis
- Division of Psychiatry, University College London, London, UK
| | | | | | | | - Kathryn L. Lunetta
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA,Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA
| | | | - Pamela Madden
- Department of Psychiatry, Washington University St. Louis, Missouri, USA
| | | | | | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark,Research Department P, Aarhus University Hospital, Risskov, Denmark
| | - Thomas H. Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne M. Murabito
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA,Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA, USA
| | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany,University of Liverpool, Institute of Translational Medicine, Liverpool, L69 3BX, UK,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany,Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Dale R. Nyholt
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Michael C. O’Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Brenda W. Penninx
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Michele L. Pergadia
- Department of Psychiatry, Washington University St. Louis, Missouri, USA,Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Roy Perlis
- Center for Experimental Drugs and Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - James B. Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Martin Preisig
- Departement of Psychiatry, Lausanne University Hospital, Switzerland
| | - Shaun M. Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jorge A. Quiroz
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland,Solid GT, Boston, MA, USA
| | - Katri Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - John P. Rice
- Department of Psychiatry, Washington University St. Louis, Missouri, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Margarita Rivera
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK,CIBERSAM-Universidad de Granada, Granada, Spain,Instituto de Investigación Biosanitaria ibs.GRANADA. Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - Thomas G. Schulze
- Department of Psychiatry and Psychotherapy, University of Göttingen, Göttingen, Germany,Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University, Munich, 80336 Munich, Germany
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Grant C. Sinnamon
- Department of Psychiatry and Psychiatric Neuroscience, School of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Johannes H. Smit
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Jordan W. Smoller
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Harold Snieder
- Unit of Genetic Epidemiology & Bioinformatics, Department of Epidemiology, University Medical Center Groningen, Groningen, the Netherlands
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Katherine E. Tansey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Rudolf Uher
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK,Dalhousie University, 6299 South St, Halifax, Nova Scotia B3H 4R2, Canada
| | - Daniel Umbricht
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany,German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Germany
| | - Erin B. Ware
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA,Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - David R. Weir
- Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Myrna M. Weissman
- College of Physicians and Surgeons and the Mailman School of Public Health, Columbia University and New York State Psychiatric Institute, New York, NY, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Jingyun Yang
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam; Department of Psychiatry, Erasmus University Medical Center, Rotterdam.
| | - Patrick F. Sullivan
- Center for Psychiatric Genomics, Department of Genetics, Genomic Medicine, University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
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25
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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: 2.3] [Reference Citation Analysis] [Abstract] [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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26
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Guerini FR, Bolognesi E, Chiappedi M, Ghezzo A, Manca S, Zanette M, Sotgiu S, Mensi MM, Zanzottera M, Agliardi C, Costa AS, Balottin U, Clerici M. HLA-G∗14bp Insertion and the KIR2DS1-HLAC2 Complex Impact on Behavioral Impairment in Children with Autism Spectrum Disorders. Neuroscience 2017. [PMID: 28627421 DOI: 10.1016/j.neuroscience.2017.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Activating KIR-HLA-C ligand complexes and HLA-G∗14bp insertion/deletion (+/-) polymorphism were associated to Autism Spectrum Disorders (ASD) and were suggested to correlate with inflammation during fetal development. We evaluated whether HLA-G∗14bp(+/-) and KIR-HLA-C complexes are associated with cognitive and behavioral scores and EEG profile in 119 ASD children (58 from Sardinia, 61 from Peninsular Italy). KIR2DS1-C2; KIR2DS2-C1; KIR2DL1-C2; KIR2DL2-C1; KIR2DL3-C1 and HLA-G∗14bp(+/-) were molecularly genotyped by Single Specific Primer PCR and gel electrophoresis. Univariate linear model analysis adjusted for age, gender and provenience showed statistically higher scores of Childhood Autism Rating Scale (CARS) and Autistic Core Behavior in KIR2DS1-C2+/HLA-G∗14bp+ASD children (43.7±1.5, p=0.03; 3.3±0.1, p=0.03, respectively). These results suggested a synergistic polygenic association of KIR2DS1-HLAC2+/HLA-G∗14bp+ pattern with behavioral impairment in ASD children.
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Affiliation(s)
| | | | - Matteo Chiappedi
- Child Neurology and Psychiatry Unit, C. Mondino National Neurological Institute, Pavia, Italy
| | - Alessandro Ghezzo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and Associazione Nazionale Famiglie di Persone con Disabilitá Intellettiva e/o Relazionale (ANFFAS), Macerata, Italy
| | - Salvatorica Manca
- Unità Operativa Neuropsichiatria Infanzia e Adolescenza (UONPIA), ASL n. 1, Sassari, Italy
| | | | - Stefano Sotgiu
- Section of Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Sassari, Italy
| | - Maria Martina Mensi
- Child Neurology and Psychiatry Unit, C. Mondino National Neurological Institute, Pavia, Italy
| | | | | | | | - Umberto Balottin
- Child Neurology and Psychiatry Unit, C. Mondino National Neurological Institute, Pavia, Italy; Department of Brain and Behavioral Sciences University of Pavia, Pavia, Italy
| | - Mario Clerici
- Don C. Gnocchi Foundation IRCCS, Milano, Italy; Department of Pathophysiology and Transplantation, University of Milano, Milano, Italy
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27
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GABA A receptor subunit gene polymorphisms predict symptom-based and developmental deficits in Chinese Han children and adolescents with autistic spectrum disorders. Sci Rep 2017; 7:3290. [PMID: 28607477 PMCID: PMC5468250 DOI: 10.1038/s41598-017-03666-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/02/2017] [Indexed: 12/29/2022] Open
Abstract
GABAA receptor subunit genes GABRB3, GABRA5, and GABRG3 located on chromosome 15q11-q13 have been implicated in the etiology of autistic spectrum disorders (ASD). This study intended to investigate the possible role of single-nucleotide polymorphisms (SNPs) present in GABRB3 (rs2081648 and rs1426217), GABRA5 (rs35586628), and GABRG3 (rs208129) genes in ASD susceptibility and symptom-based and developmental phenotypes of ASD in Chinese Han children and adolescents. 99 ASD patients and 231 age- and gender- frequency-matched typical developing (TD) controls were tested by TaqMan® genotyping assay. Symptom-based phenotypes were evaluated by Childhood Autism Rating Scale (CARS) and Autism Behavior Checklist (ABC), and developmental phenotypes were assessed by Early Childhood Development Questionnaire (ECDQ) in ASD patients. Three haplotypes and global χ 2 test of all SNPs demonstrated significant associations between ASD and TD groups. Besides, GABRB3 rs2081648, GABRA5 rs35586628, and GABRG3 rs208129 polymorphisms were associated with symptom-based deficits in social interaction, sensorimotor and somatosensory coordination, visual response, imitation, activity level, language expression and adaptability. Developmental abnormalities in late emergences of social interaction and fine motor were detected in GABRB3 rs2081648 polymorphism. Overall results indicated that gene synergy may participate in ASD pathogenesis, and GABAA receptor gene polymorphisms can predict symptom-based and developmental deficits in ASD individuals.
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28
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Independent Maternal and Fetal Genetic Effects on Midgestational Circulating Levels of Environmental Pollutants. G3-GENES GENOMES GENETICS 2017; 7:1287-1299. [PMID: 28235828 PMCID: PMC5386877 DOI: 10.1534/g3.117.039784] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Maternal exposure to environmental pollutants could affect fetal brain development and increase autism spectrum disorder (ASD) risk in conjunction with differential genetic susceptibility. Organohalogen congeners measured in maternal midpregnancy blood samples have recently shown significant, but negative associations with offspring ASD outcome. We report the first large-scale maternal and fetal genetic study of the midpregnancy serum levels of a set of 21 organohalogens in a subset of 790 genotyped women and 764 children collected in California by the Early Markers for Autism (EMA) Project. Levels of PCB (polychlorinated biphenyl) and PBDE (polybrominated diphenyl ether) congeners showed high maternal and fetal estimated SNP-based heritability (h2g) accounting for 39–99% of the total variance. Genome-wide association analyses identified significant maternal loci for p,p′-DDE (P = 7.8 × 10−11) in the CYP2B6 gene and for BDE-28 (P = 3.2 × 10−8) near the SH3GL2 gene, both involved in xenobiotic and lipid metabolism. Fetal genetic loci contributed to the levels of BDE-100 (P = 4.6 × 10−8) and PCB187 (P = 2.8 × 10−8), near the potential metabolic genes LOXHD1 and PTPRD, previously implicated in neurodevelopment. Negative associations were observed for BDE-100, BDE153, and the sum of PBDEs with ASD, partly explained by genome-wide additive genetic effects that predicted PBDE levels. Our results support genetic control of midgestational biomarkers for environmental exposures by nonoverlapping maternal and fetal genetic determinants, suggesting that future studies of environmental risk factors should take genetic variation into consideration. The independent influence of fetal genetics supports previous hypotheses that fetal genotypes expressed in placenta can influence maternal physiology and the transplacental transfer of organohalogens.
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29
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Chen KS, Harris L, Lim JWC, Harvey TJ, Piper M, Gronostajski RM, Richards LJ, Bunt J. Differential neuronal and glial expression of nuclear factor I proteins in the cerebral cortex of adult mice. J Comp Neurol 2017; 525:2465-2483. [PMID: 28295292 DOI: 10.1002/cne.24206] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 12/31/2022]
Abstract
The nuclear factor I (NFI) family of transcription factors plays an important role in the development of the cerebral cortex in humans and mice. Disruption of nuclear factor IA (NFIA), nuclear factor IB (NFIB), or nuclear factor IX (NFIX) results in abnormal development of the corpus callosum, lateral ventricles, and hippocampus. However, the expression or function of these genes has not been examined in detail in the adult brain, and the cell type-specific expression of NFIA, NFIB, and NFIX is currently unknown. Here, we demonstrate that the expression of each NFI protein shows a distinct laminar pattern in the adult mouse neocortex and that their cell type-specific expression differs depending on the family member. NFIA expression was more frequently observed in astrocytes and oligodendroglia, whereas NFIB expression was predominantly localized to astrocytes and neurons. NFIX expression was most commonly observed in neurons. The NFI proteins were equally distributed within microglia, and the ependymal cells lining the ventricles of the brain expressed all three proteins. In the hippocampus, the NFI proteins were expressed during all stages of neural stem cell differentiation in the dentate gyrus, with higher expression intensity in neuroblast cells as compared to quiescent stem cells and mature granule neurons. These findings suggest that the NFI proteins may play distinct roles in cell lineage specification or maintenance, and establish the basis for further investigation of their function in the adult brain and their emerging role in disease.
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Affiliation(s)
- Kok-Siong Chen
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jonathan W C Lim
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Piper
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Linda J Richards
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jens Bunt
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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30
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Connolly S, Anney R, Gallagher L, Heron EA. A genome-wide investigation into parent-of-origin effects in autism spectrum disorder identifies previously associated genes including SHANK3. Eur J Hum Genet 2017; 25:234-239. [PMID: 27876814 PMCID: PMC5255953 DOI: 10.1038/ejhg.2016.153] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 09/28/2016] [Accepted: 10/07/2016] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is known to be a heritable neurodevelopmental disorder affecting more than 1% of the population but in the majority of ASD cases, the genetic cause has not been identified. Parent-of-origin effects have been highlighted as an important mechanism in the pathology of neurodevelopmental disorders such as Prader-Willi and Angelman syndrome, with individuals with these syndromes often exhibiting ASD symptoms. Consequently, systematic investigation of these effects in ASD is clearly an important line of investigation in elucidating the underlying genetic mechanisms. Using estimation of maternal, imprinting and interaction effects using multinomial modelling (EMIM), we simultaneously investigated imprinting, maternal genetic effects and associations in the Autism Genome Project and Simons Simplex Consortium genome-wide association data sets. To avoid using the overly stringent genome-wide association study significance level, we used a Bayesian threshold that takes into account the sample size, allele frequency and any available prior knowledge. Between the two data sets, we identified a total of 18 imprinting effects and 68 maternal genetic effects that met this Bayesian threshold criteria, but none met the threshold in both data sets. We identified imprinting and maternal genetic effects for regions that have previously shown evidence for parent-of-origin effects in ASD. Together with these findings, we have identified maternal genetic effects not previously identified in ASD at a locus in SHANK3 on chromosome 22 and a locus in WBSCR17 on chromosome 7 (associated with Williams syndrome). Both genes have previously been associated with ASD.
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Affiliation(s)
- Siobhan Connolly
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Trinity Centre for Health Sciences, Dublin, Ireland
| | - Richard Anney
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Trinity Centre for Health Sciences, Dublin, Ireland
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Hadyn Ellis Building, Cathays, Cardiff, UK
| | - Louise Gallagher
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Trinity Centre for Health Sciences, Dublin, Ireland
| | - Elizabeth A Heron
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Trinity Centre for Health Sciences, Dublin, Ireland
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31
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Golia B, Moeller GK, Jankevicius G, Schmidt A, Hegele A, Preißer J, Tran ML, Imhof A, Timinszky G. ATM induces MacroD2 nuclear export upon DNA damage. Nucleic Acids Res 2017; 45:244-254. [PMID: 28069995 PMCID: PMC5224513 DOI: 10.1093/nar/gkw904] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/08/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022] Open
Abstract
ADP-ribosylation is a dynamic post-translation modification that regulates the early phase of various DNA repair pathways by recruiting repair factors to chromatin. ADP-ribosylation levels are defined by the activities of specific transferases and hydrolases. However, except for the transferase PARP1/ARDT1 little is known about regulation of these enzymes. We found that MacroD2, a mono-ADP-ribosylhydrolase, is exported from the nucleus upon DNA damage, and that this nuclear export is induced by ATM activity. We show that the export is dependent on the phosphorylation of two SQ/TQ motifs, suggesting a novel direct interaction between ATM and ADP-ribosylation. Lastly, we show that MacroD2 nuclear export temporally restricts its recruitment to DNA lesions, which may decrease the net ADP-ribosylhydrolase activity at the site of DNA damage. Together, our results identify a novel feedback regulation between two crucial DNA damage-induced signaling pathways: ADP-ribosylation and ATM activation.
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Affiliation(s)
- Barbara Golia
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Giuliana Katharina Moeller
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Gytis Jankevicius
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Andreas Schmidt
- Zentrallabor für Proteinanalytik (Protein Analysis Unit), Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Anna Hegele
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Julia Preißer
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Mai Ly Tran
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik (Protein Analysis Unit), Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
| | - Gyula Timinszky
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany
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32
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Mitra I, Lavillaureix A, Yeh E, Traglia M, Tsang K, Bearden CE, Rauen KA, Weiss LA. Reverse Pathway Genetic Approach Identifies Epistasis in Autism Spectrum Disorders. PLoS Genet 2017; 13:e1006516. [PMID: 28076348 PMCID: PMC5226683 DOI: 10.1371/journal.pgen.1006516] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/01/2016] [Indexed: 02/08/2023] Open
Abstract
Although gene-gene interaction, or epistasis, plays a large role in complex traits in model organisms, genome-wide by genome-wide searches for two-way interaction have limited power in human studies. We thus used knowledge of a biological pathway in order to identify a contribution of epistasis to autism spectrum disorders (ASDs) in humans, a reverse-pathway genetic approach. Based on previous observation of increased ASD symptoms in Mendelian disorders of the Ras/MAPK pathway (RASopathies), we showed that common SNPs in RASopathy genes show enrichment for association signal in GWAS (P = 0.02). We then screened genome-wide for interactors with RASopathy gene SNPs and showed strong enrichment in ASD-affected individuals (P < 2.2 x 10-16), with a number of pairwise interactions meeting genome-wide criteria for significance. Finally, we utilized quantitative measures of ASD symptoms in RASopathy-affected individuals to perform modifier mapping via GWAS. One top region overlapped between these independent approaches, and we showed dysregulation of a gene in this region, GPR141, in a RASopathy neural cell line. We thus used orthogonal approaches to provide strong evidence for a contribution of epistasis to ASDs, confirm a role for the Ras/MAPK pathway in idiopathic ASDs, and to identify a convergent candidate gene that may interact with the Ras/MAPK pathway.
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Affiliation(s)
- Ileena Mitra
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Alinoë Lavillaureix
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Université Paris Descartes, Sorbonne Paris Cité, Faculty of Medicine, Paris, France
| | - Erika Yeh
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Michela Traglia
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Kathryn Tsang
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Carrie E. Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Psychology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Katherine A. Rauen
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Lauren A. Weiss
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
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33
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Peter S, De Zeeuw CI, Boeckers TM, Schmeisser MJ. Cerebellar and Striatal Pathologies in Mouse Models of Autism Spectrum Disorder. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 224:103-119. [PMID: 28551753 DOI: 10.1007/978-3-319-52498-6_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component. To date, several hundred different genetic mutations have been identified to play a role in its aetiology. The heterogeneity of genetic abnormalities combined with the different brain regions where aberrations are found makes the search for causative mechanisms a daunting task. Even within a limited number of brain regions, a myriad of different neural circuit dysfunctions may lead to ASD. Here, we review mouse models that incorporate mutations of ASD risk genes causing pathologies in the cerebellum and striatum and highlight the vulnerability of related circuit dysfunctions within these brain regions in ASD pathophysiology.
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Affiliation(s)
- Saša Peter
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands. .,Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Chris I De Zeeuw
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.,Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tobias M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Michael J Schmeisser
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany. .,Division of Neuroanatomy, Institute of Anatomy, Otto-von-Guericke University, Magdeburg, Germany. .,Leibniz Institute for Neurobiology, Magdeburg, Germany.
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34
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Muller CL, Anacker AMJ, Rogers TD, Goeden N, Keller EH, Forsberg CG, Kerr TM, Wender CLA, Anderson GM, Stanwood GD, Blakely RD, Bonnin A, Veenstra-VanderWeele J. Impact of Maternal Serotonin Transporter Genotype on Placental Serotonin, Fetal Forebrain Serotonin, and Neurodevelopment. Neuropsychopharmacology 2017; 42:427-436. [PMID: 27550733 PMCID: PMC5399236 DOI: 10.1038/npp.2016.166] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/16/2016] [Accepted: 08/04/2016] [Indexed: 12/29/2022]
Abstract
Biomarker, neuroimaging, and genetic findings implicate the serotonin transporter (SERT) in autism spectrum disorder (ASD). Previously, we found that adult male mice expressing the autism-associated SERT Ala56 variant have altered central serotonin (5-HT) system function, as well as elevated peripheral blood 5-HT levels. Early in gestation, before midbrain 5-HT projections have reached the cortex, peripheral sources supply 5-HT to the forebrain, suggesting that altered maternal or placenta 5-HT system function could impact the developing embryo. We therefore used different combinations of maternal and embryo SERT Ala56 genotypes to examine effects on blood, placenta and embryo serotonin levels and neurodevelopment at embryonic day E14.5, when peripheral sources of 5-HT predominate, and E18.5, when midbrain 5-HT projections have reached the forebrain. Maternal SERT Ala56 genotype was associated with decreased placenta and embryonic forebrain 5-HT levels at E14.5. Low 5-HT in the placenta persisted, but forebrain levels normalized by E18.5. Maternal SERT Ala56 genotype effects on forebrain 5-HT levels were accompanied by a broadening of 5-HT-sensitive thalamocortical axon projections. In contrast, no effect of embryo genotype was seen in concepti from heterozygous dams. Blood 5-HT levels were dynamic across pregnancy and were increased in SERT Ala56 dams at E14.5. Placenta RNA sequencing data at E14.5 indicated substantial impact of maternal SERT Ala56 genotype, with alterations in immune and metabolic-related pathways. Collectively, these findings indicate that maternal SERT function impacts offspring placental 5-HT levels, forebrain 5-HT levels, and neurodevelopment.
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Affiliation(s)
| | - Allison MJ Anacker
- Department of Psychiatry, Columbia University Medical School, New York, NY, USA
| | - Tiffany D Rogers
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nick Goeden
- Department of Cell and Neurobiology and Zilkha Neurogenetic Institute, University of Southern California School of Medicine, Los Angeles, CA, USA
| | - Elizabeth H Keller
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - C Gunnar Forsberg
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Travis M Kerr
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Carly LA Wender
- Department of Psychiatry, Columbia University Medical School, New York, NY, USA
| | - George M Anderson
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Gregg D Stanwood
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Randy D Blakely
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexandre Bonnin
- Department of Cell and Neurobiology and Zilkha Neurogenetic Institute, University of Southern California School of Medicine, Los Angeles, CA, USA
| | - Jeremy Veenstra-VanderWeele
- Department of Psychiatry, Columbia University Medical School, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
- Center for Autism and the Developing Brain, New York Presbyterian Hospital, New York, NY, USA
- Sackler Institute for Developmental Psychobiology, Columbia University, New York, NY, USA
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35
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Mitra I, Tsang K, Ladd-Acosta C, Croen LA, Aldinger KA, Hendren RL, Traglia M, Lavillaureix A, Zaitlen N, Oldham MC, Levitt P, Nelson S, Amaral DG, Herz-Picciotto I, Fallin MD, Weiss LA. Pleiotropic Mechanisms Indicated for Sex Differences in Autism. PLoS Genet 2016; 12:e1006425. [PMID: 27846226 PMCID: PMC5147776 DOI: 10.1371/journal.pgen.1006425] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/12/2016] [Indexed: 02/07/2023] Open
Abstract
Sexual dimorphism in common disease is pervasive, including a dramatic male preponderance in autism spectrum disorders (ASDs). Potential genetic explanations include a liability threshold model requiring increased polymorphism risk in females, sex-limited X-chromosome contribution, gene-environment interaction driven by differences in hormonal milieu, risk influenced by genes sex-differentially expressed in early brain development, or contribution from general mechanisms of sexual dimorphism shared with secondary sex characteristics. Utilizing a large single nucleotide polymorphism (SNP) dataset, we identify distinct sex-specific genome-wide significant loci. We investigate genetic hypotheses and find no evidence for increased genetic risk load in females, but evidence for sex heterogeneity on the X chromosome, and contribution of sex-heterogeneous SNPs for anthropometric traits to ASD risk. Thus, our results support pleiotropy between secondary sex characteristic determination and ASDs, providing a biological basis for sex differences in ASDs and implicating non brain-limited mechanisms.
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Affiliation(s)
- Ileena Mitra
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Kathryn Tsang
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Lisa A. Croen
- Division of Research, Kaiser Permanente Northern California, California, United States of America
| | - Kimberly A. Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Robert L. Hendren
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Michela Traglia
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Alinoë Lavillaureix
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, California, United States of America
- Université Paris Descartes, Sorbonne Paris Cité, Faculty of Medicine, France
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Pat Levitt
- Program in Developmental Neurogenetics, Institute for the Developing Mind, Children’s Hospital Los Angeles and Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Stanley Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - David G. Amaral
- Department of Psychiatry and Behavioral Sciences, Medicine and Medical Investigation of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California, Davis School of Medicine, Sacramento, California, United States of America
| | - Irva Herz-Picciotto
- Department of Public Health Sciences and Medicine and Medical Investigation of Neurodevelopmental Disorders (M.I.N.D.) Institute, University of California, Davis School of Medicine, Sacramento, California, United States of America
| | - M. Daniele Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Lauren A. Weiss
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, California, United States of America
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36
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A Novel Relationship for Schizophrenia, Bipolar, and Major Depressive Disorder. Part 8: a Hint from Chromosome 8 High Density Association Screen. Mol Neurobiol 2016; 54:5868-5882. [DOI: 10.1007/s12035-016-0102-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
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37
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Maternal mid-pregnancy C-reactive protein and risk of autism spectrum disorders: the early markers for autism study. Transl Psychiatry 2016; 6:e783. [PMID: 27093065 PMCID: PMC4872404 DOI: 10.1038/tp.2016.46] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 01/28/2016] [Accepted: 01/31/2016] [Indexed: 12/31/2022] Open
Abstract
Maternal pregnancy levels of the inflammatory marker C-reactive protein (CRP) has been previously associated with autism spectrum disorder (ASD) in the offspring. We conducted a population-based nested case-control study with 500 children with ASD, 235 with developmental delay (DD) and 580 general population (GP) controls to further investigate whether elevated CRP during pregnancy increases the risk of ASD. Maternal CRP concentration was measured in archived serum collected during 15-19 weeks of pregnancy and genome-wide single-nucleotide polymorphism (SNP) data were generated. The levels of CRP were compared between ASD vs GP and DD vs GP. The genetic associations with CRP were assessed via linear regression. Maternal CRP levels in mid-pregnancy were lower in mothers of ASD compared with controls. The maternal CRP levels in the upper third and fourth quartiles were associated with a 45 and 44% decreased risk of ASD, respectively. Two SNPs at the CRP locus showed strong association with CRP levels but they were not associated with ASD. No difference was found between maternal CRP levels of DD and controls. The reasons for the lower levels of CRP in mothers of ASD are not known with certainty but may be related to alterations in the immune response to infectious agents. The biological mechanisms underlying this association remain to be clarified.
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38
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Whitney O, Voyles T, Hara E, Chen Q, White SA, Wright TF. Differential FoxP2 and FoxP1 expression in a vocal learning nucleus of the developing budgerigar. Dev Neurobiol 2015; 75:778-90. [PMID: 25407828 PMCID: PMC4437895 DOI: 10.1002/dneu.22247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 11/12/2014] [Accepted: 11/17/2014] [Indexed: 12/19/2022]
Abstract
The forkhead domain FOXP2 and FOXP1 transcription factors are implicated in several cognitive disorders with language deficits, notably autism, and thus play a central role in learned vocal motor behavior in humans. Although a similar role for FoxP2 and FoxP1 is proposed for other vertebrate species, including songbirds, the neurodevelopmental expression of these genes are unknown in a species with lifelong vocal learning abilities. Like humans, budgerigars (Melopsittacus undulatus) learn new vocalizations throughout their entire lifetime. Like songbirds, budgerigars have distinct brain nuclei for vocal learning, which include the magnocellular nucleus of the medial striatum (MMSt), a basal ganglia region that is considered developmentally and functionally analogous to Area X in songbirds. Here, we used in situ hybridization and immunohistochemistry to investigate FoxP2 and FoxP1 expression in the MMSt of juvenile and adult budgerigars. We found FoxP2 mRNA and protein expression levels in the MMSt that were lower than the surrounding striatum throughout development and adulthood. In contrast, FoxP1 mRNA and protein had an elevated MMSt/striatum expression ratio as birds matured, regardless of their sex. These results show that life-long vocal plasticity in budgerigars is associated with persistent low-level FoxP2 expression in the budgerigar MMSt, and suggests the possibility that FoxP1 plays an organizational role in the neurodevelopment of vocal motor circuitry. Thus, developmental regulation of the FoxP2 and FoxP1 genes in the basal ganglia appears essential for vocal mimicry in a range of species that possess this relatively rare trait.
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Affiliation(s)
- Osceola Whitney
- New Mexico State University, Department of Biology, Las Cruces, NM 88003
| | - Tawni Voyles
- New Mexico State University, Department of Biology, Las Cruces, NM 88003
| | - Erina Hara
- New Mexico State University, Department of Biology, Las Cruces, NM 88003
| | - Qianqian Chen
- Interdepartmental Program of Molecular, Cellular, and Integrative Physiology, UCLA, Los Angeles, CA 90095
| | - Stephanie A. White
- Interdepartmental Program of Molecular, Cellular, and Integrative Physiology, UCLA, Los Angeles, CA 90095
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095
| | - Timothy F. Wright
- New Mexico State University, Department of Biology, Las Cruces, NM 88003
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Hu VW, Sarachana T, Sherrard RM, Kocher KM. Investigation of sex differences in the expression of RORA and its transcriptional targets in the brain as a potential contributor to the sex bias in autism. Mol Autism 2015; 6:7. [PMID: 26056561 PMCID: PMC4459681 DOI: 10.1186/2040-2392-6-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/05/2015] [Indexed: 12/21/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by significant impairment in reciprocal social interactions and communication coupled with stereotyped, repetitive behaviors and restricted interests. Although genomic and functional studies are beginning to reveal some of the genetic complexity and underlying pathobiology of ASD, the consistently reported male bias of ASD remains an enigma. We have recently proposed that retinoic acid-related orphan receptor alpha (RORA), which is reduced in the brain and lymphoblastoid cell lines of multiple cohorts of individuals with ASD and oppositely regulated by male and female hormones, might contribute to the sex bias in autism by differentially regulating target genes, including CYP19A1 (aromatase), in a sex-dependent manner that can also lead to elevated testosterone levels, a proposed risk factor for autism. Methods In this study, we examine sex differences in RORA and aromatase protein levels in cortical tissues of unaffected and affected males and females by re-analyzing pre-existing confocal immunofluorescence data from our laboratory. We further investigated the expression of RORA and its correlation with several of its validated transcriptional targets in the orbital frontal cortex and cerebellum as a function of development using RNAseq data from the BrainSpan Atlas of the Developing Human Brain. In a pilot study, we also analyzed the expression of Rora and the same transcriptional targets in the cortex and cerebellum of adult wild-type male and female C57BL/6 mice. Results Our findings suggest that Rora/RORA and several of its transcriptional targets may exhibit sexually dimorphic expression in certain regions of the brain of both mice and humans. Interestingly, the correlation coefficients between Rora expression and that of its targets are much higher in the cortex of male mice relative to that of female mice. A strong positive correlation between the levels of RORA and aromatase proteins is also seen in the cortex of control human males and females as well as ASD males, but not ASD females. Conclusions Based on these studies, we suggest that disruption of Rora/RORA expression may have a greater impact on males, since sex differences in the correlation of RORA and target gene expression indicate that RORA-deficient males may experience greater dysregulation of genes relevant to ASD in certain brain regions during development. Electronic supplementary material The online version of this article (doi:10.1186/2040-2392-6-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valerie W Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 Eye St. NW, Washington, DC 20037 USA
| | - Tewarit Sarachana
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 Eye St. NW, Washington, DC 20037 USA ; Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Rachel M Sherrard
- Institut de Biologie Paris Seine, Sorbonne Universités, UPMC Univ Paris 06 & CNRS, UMR 8256 Biological Adaptation and Ageing, F-75005 Paris, France
| | - Kristen M Kocher
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 Eye St. NW, Washington, DC 20037 USA
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40
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Desachy G, Croen LA, Torres AR, Kharrazi M, Delorenze GN, Windham GC, Yoshida CK, Weiss LA. Increased female autosomal burden of rare copy number variants in human populations and in autism families. Mol Psychiatry 2015; 20:170-5. [PMID: 25582617 DOI: 10.1038/mp.2014.179] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/28/2014] [Accepted: 11/13/2014] [Indexed: 01/24/2023]
Abstract
Autosomal genetic variation is presumed equivalent in males and females and makes a major contribution to disease risk. We set out to identify whether maternal copy number variants (CNVs) contribute to autism spectrum disorders (ASDs). Surprisingly, we observed a higher autosomal burden of large, rare CNVs in females in the population, reflected in, but not unique to, ASD families. Meta-analysis across control data sets confirms female excess in CNV number (P=2.1 × 10(-5)) and gene content (P=4.1 × 10(-3)). We additionally observed CNV enrichment in ASD mothers compared with control mothers (P=0.03). We speculate that tolerance for CNV burden contributes to decreased female fetal loss in the population and that ASD-specific maternal CNV burden may contribute to high sibling recurrence. These data emphasize the need for study of familial CNV risk factors in ASDs and the requirement of sex-matched comparisons.
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Affiliation(s)
- G Desachy
- Department of Psychiatry and Institute for Human Genetics, UCSF, San Francisco, CA, USA
| | - L A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - A R Torres
- Center for Persons with Disabilities, Utah State University, Logan, UT, USA
| | - M Kharrazi
- Genetic Disease Screening Program, California Department of Public Health, Richmond, CA, USA
| | - G N Delorenze
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - G C Windham
- Division of Environmental and Occupational Disease Control, California Department of Public Health, Richmond, CA, USA
| | - C K Yoshida
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - L A Weiss
- Department of Psychiatry and Institute for Human Genetics, UCSF, San Francisco, CA, USA
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Ogawa LM, Vallender EJ. Evolutionary conservation in genes underlying human psychiatric disorders. Front Hum Neurosci 2014; 8:283. [PMID: 24834046 PMCID: PMC4018557 DOI: 10.3389/fnhum.2014.00283] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/16/2014] [Indexed: 01/07/2023] Open
Abstract
Many psychiatric diseases observed in humans have tenuous or absent analogs in other species. Most notable among these are schizophrenia and autism. One hypothesis has posited that these diseases have arisen as a consequence of human brain evolution, for example, that the same processes that led to advances in cognition, language, and executive function also resulted in novel diseases in humans when dysfunctional. Here, the molecular evolution of the protein-coding regions of genes associated with these and other psychiatric disorders are compared among species. Genes associated with psychiatric disorders are drawn from the literature and orthologous sequences are collected from eleven primate species (human, chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, baboon, marmoset, squirrel monkey, and galago) and 34 non-primate mammalian species. Evolutionary parameters, including dN/dS, are calculated for each gene and compared between disease classes and among species, focusing on humans and primates compared to other mammals, and on large-brained taxa (cetaceans, rhinoceros, walrus, bear, and elephant) compared to their small-brained sister species. Evidence of differential selection in humans to the exclusion of non-human primates was absent, however elevated dN/dS was detected in catarrhines as a whole, as well as in cetaceans, possibly as part of a more general trend. Although this may suggest that protein changes associated with schizophrenia and autism are not a cost of the higher brain function found in humans, it may also point to insufficiencies in the study of these diseases including incomplete or inaccurate gene association lists and/or a greater role of regulatory changes or copy number variation. Through this work a better understanding of the molecular evolution of the human brain, the pathophysiology of disease, and the genetic basis of human psychiatric disease is gained.
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Affiliation(s)
- Lisa M Ogawa
- Division of Neuroscience, New England Primate Research Center, Harvard Medical School Southborough, MA, USA
| | - Eric J Vallender
- Division of Neuroscience, New England Primate Research Center, Harvard Medical School Southborough, MA, USA
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