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Spirito G, Filosi M, Domenici E, Mangoni D, Gustincich S, Sanges R. Exploratory analysis of L1 retrotransposons expression in autism. Mol Autism 2023; 14:22. [PMID: 37381037 DOI: 10.1186/s13229-023-00554-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 06/15/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a set of highly heterogeneous neurodevelopmental diseases whose genetic etiology is not completely understood. Several investigations have relied on transcriptome analysis from peripheral tissues to dissect ASD into homogenous molecular phenotypes. Recently, analysis of changes in gene expression from postmortem brain tissues has identified sets of genes that are involved in pathways previously associated with ASD etiology. In addition to protein-coding transcripts, the human transcriptome is composed by a large set of non-coding RNAs and transposable elements (TEs). Advancements in sequencing technologies have proven that TEs can be transcribed in a regulated fashion, and their dysregulation might have a role in brain diseases. METHODS We exploited published datasets comprising RNA-seq data from (1) postmortem brain of ASD subjects, (2) in vitro cell cultures where ten different ASD-relevant genes were knocked out and (3) blood of discordant siblings. We measured the expression levels of evolutionarily young full-length transposable L1 elements and characterized the genomic location of deregulated L1s assessing their potential impact on the transcription of ASD-relevant genes. We analyzed every sample independently, avoiding to pool together the disease subjects to unmask the heterogeneity of the molecular phenotypes. RESULTS We detected a strong upregulation of intronic full-length L1s in a subset of postmortem brain samples and in in vitro differentiated neurons from iPSC knocked out for ATRX. L1 upregulation correlated with an high number of deregulated genes and retained introns. In the anterior cingulate cortex of one subject, a small number of significantly upregulated L1s overlapped with ASD-relevant genes that were significantly downregulated, suggesting the possible existence of a negative effect of L1 transcription on host transcripts. LIMITATIONS Our analyses must be considered exploratory and will need to be validated in bigger cohorts. The main limitation is given by the small sample size and by the lack of replicates for postmortem brain samples. Measuring the transcription of locus-specific TEs is complicated by the repetitive nature of their sequence, which reduces the accuracy in mapping sequencing reads to the correct genomic locus. CONCLUSIONS L1 upregulation in ASD appears to be limited to a subset of subjects that are also characterized by a general deregulation of the expression of canonical genes and an increase in intron retention. In some samples from the anterior cingulate cortex, L1s upregulation seems to directly impair the expression of some ASD-relevant genes by a still unknown mechanism. L1s upregulation may therefore identify a group of ASD subjects with common molecular features and helps stratifying individuals for novel strategies of therapeutic intervention.
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Affiliation(s)
- Giovanni Spirito
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Area of Neuroscience, Via Bonomea 265, 34136, Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
- CMP3vda, Via Lavoratori Vittime del Col Du Mont 28, Aosta, Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, TN, Italy
- Eurac Research, Institute for Biomedicine, Bolzano, BZ, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, TN, Italy
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.
- CMP3vda, Via Lavoratori Vittime del Col Du Mont 28, Aosta, Italy.
| | - Remo Sanges
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Area of Neuroscience, Via Bonomea 265, 34136, Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia - IIT, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.
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Anashkina AA, Erlykina EI. Molecular Mechanisms of Aberrant Neuroplasticity in Autism Spectrum Disorders (Review). Sovrem Tekhnologii Med 2021; 13:78-91. [PMID: 34513070 PMCID: PMC8353687 DOI: 10.17691/stm2021.13.1.10] [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: 08/28/2020] [Indexed: 01/03/2023] Open
Abstract
This review presents the analysis and systematization of modern data on the molecular mechanisms of autism spectrum disorders (ASD) development. Polyetiology and the multifactorial nature of ASD have been proved. The attempt has been made to jointly review and systematize current hypotheses of ASD pathogenesis at the molecular level from the standpoint of aberrant brain plasticity. The mechanism of glutamate excitotoxicity formation, the effect of imbalance of neuroactive amino acids and their derivatives, neurotransmitters, and hormones on the ASD formation have been considered in detail. The strengths and weaknesses of the proposed hypotheses have been analyzed from the standpoint of evidence-based medicine. The conclusion has been drawn on the leading role of glutamate excitotoxicity as a biochemical mechanism of aberrant neuroplasticity accompanied by oxidative stress and mitochondrial dysfunction. The mechanism of aberrant neuroplasticity has also been traced at the critical moments of the nervous system development taking into account the influence of various factors of the internal and external environment. New approaches to searching for ASD molecular markers have been considered.
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Affiliation(s)
- A A Anashkina
- Senior Teacher, Department of Biochemistry named after G.Y. Gorodisskaya; Senior Researcher, Central Scientific Research Laboratory, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - E I Erlykina
- Professor, Head of the Department of Biochemistry named after G.Y. Gorodisskaya, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
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Popow C, Ohmann S, Plener P. Practitioner's review: medication for children and adolescents with autism spectrum disorder (ASD) and comorbid conditions. NEUROPSYCHIATRIE : KLINIK, DIAGNOSTIK, THERAPIE UND REHABILITATION : ORGAN DER GESELLSCHAFT OSTERREICHISCHER NERVENARZTE UND PSYCHIATER 2021; 35:113-134. [PMID: 34160787 PMCID: PMC8429404 DOI: 10.1007/s40211-021-00395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/15/2021] [Indexed: 11/14/2022]
Abstract
Alleviating the multiple problems of children with autism spectrum disorder (ASD) and its comorbid conditions presents major challenges for the affected children, parents, and therapists. Because of a complex psychopathology, structured therapy and parent training are not always sufficient, especially for those patients with intellectual disability (ID) and multiple comorbidities. Moreover, structured therapy is not available for a large number of patients, and pharmacological support is often needed, especially in those children with additional attention deficit/hyperactivity and oppositional defiant, conduct, and sleep disorders.
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Affiliation(s)
- Christian Popow
- Dept. Child and Adolescent Psychiatry, Medical University of Vienna, Waehringer Guertel 18–20, 1090 Vienna, Austria
| | - Susanne Ohmann
- Dept. Child and Adolescent Psychiatry, Medical University of Vienna, Waehringer Guertel 18–20, 1090 Vienna, Austria
| | - Paul Plener
- Dept. Child and Adolescent Psychiatry, Medical University of Vienna, Waehringer Guertel 18–20, 1090 Vienna, Austria
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Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet 2019; 10:258. [PMID: 31001316 PMCID: PMC6456656 DOI: 10.3389/fgene.2019.00258] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
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Affiliation(s)
- Weidi Wang
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Roser Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Guan Ning Lin
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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May T, Brignell A, Hawi Z, Brereton A, Tonge B, Bellgrove MA, Rinehart NJ. Trends in the Overlap of Autism Spectrum Disorder and Attention Deficit Hyperactivity Disorder: Prevalence, Clinical Management, Language and Genetics. CURRENT DEVELOPMENTAL DISORDERS REPORTS 2018. [DOI: 10.1007/s40474-018-0131-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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van der Weiden RMF, Helmerhorst FM, Eriksson T. Gonadotropin-releasing hormone agonist against severe aggression in autism. BMJ Case Rep 2016; 2016:bcr-2016-216378. [PMID: 27655876 DOI: 10.1136/bcr-2016-216378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Aggression in patients with autism spectrum disorder (ASD) presents an important therapeutic challenge. Conventional treatment appears to be inadequate in a number of cases. The occurrence of severe aggressive symptoms since the inception of adolescence in a male patient with ASD suggested a hormonal influence by androgens. Conventional treatment with antipsychotic and antiepileptic drugs and benzodiazepines was ineffective. A subcutaneous long-acting gonadotropin-releasing hormone agonist (GnRH agonist) injection was given on a monthly basis resulting in a substantial improvement in his aggressive behaviour and renewed socialisation.
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Affiliation(s)
| | - Frans M Helmerhorst
- Department of Obstetrics and Gynaecology, Leids Universitair Medisch Centrum, Leiden, Zuid-Holland, The Netherlands
| | - Tomas Eriksson
- The Biological Psychiatry Research Group, Department of Clinical Sciences, Lund University, Lund, Sweden
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Abstract
The high heritability, early age at onset, and reproductive disadvantages of autism spectrum disorders (ASDs) are consistent with an etiology composed of dominant-acting de novo (spontaneous) mutations. Mutation detection by microarray analysis and DNA sequencing has confirmed that de novo copy-number variants or point mutations in protein-coding regions of genes contribute to risk, and some of the underlying causal variants and genes have been identified. As our understanding of autism genes develops, the spectrum of autism is breaking up into quanta of many different genetic disorders. Given the diversity of etiologies and underlying biochemical pathways, personalized therapy for ASDs is logical, and clinical genetic testing is a prerequisite.
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Koelkebeck K, Riedel A, Ohrmann P, Biscaldi M, Tebartz van Elst L. [High-functioning autism spectrum disorders in adulthood]. DER NERVENARZT 2014; 85:891-902. [PMID: 24969950 DOI: 10.1007/s00115-014-4050-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The prevalence of autism spectrum disorders in the general population is approximately 1 %. Some individuals with high-functioning autism graduate from regular schools without autism having been diagnosed and problems only occur when the demands for social competence increase. Then patients often present with secondary psychiatric symptoms, such as depression, anxiety or interpersonal problems. At this time, typical autistic features, such as social interaction deficits, restricted interests and stereotypic behavior can be camouflaged by high compensatory skills, particularly in highly intelligent patients. Therefore, missed or wrong diagnoses are frequent. Interviews, questionnaires and neuropsychological tests might be used to support the diagnosis. In cases where there is evidence for a secondary cause of autistic symptoms, somatic disorders should be excluded. Pharmacological treatment should be symptom-oriented. Individualized psychotherapeutic approaches are becoming increasingly more available; however, pragmatic solutions often need to be deployed.
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Affiliation(s)
- K Koelkebeck
- Klinik für Psychiatrie und Psychotherapie, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A9, 48149, Münster, Deutschland,
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