Sequence analysis of ADARB1 gene in patients with familial bipolar disorder

Amore, Mario; Strippoli, Pierluigi; Laterza, C.; Tagariello, P.; Vitale, Lorenza; Casadei, Raffaella; Frabetti, Flavia; Canaider, Silvia; Lenzi, Luca; D’Addabbo, Pietro; Carinci, Paolo; Torroni, Arianna; Ferrari, G.; Zannotti, Maria

doi:10.1016/j.jad.2003.08.006

Cited by 9 publications

(4 citation statements)

References 28 publications

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“…Because ADARB1 and ADAR both share some overlapping editing targets as well as have gene-specific ones [52,53], this expression pattern suggests that both ADAR genes may play complementary roles in the differential response to ZIKV infection [54]. This would be consistent with prior suggestions that ADARB1 contributes to dysregulation of RNA editing in many diseases [55][56][57][58].…”

Section: Mapping Adar Expression and Editing Landscapessupporting

confidence: 87%

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data

et al. 2020

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Background As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism—RNA editing due to post-transcriptional changes of individual nucleotides—remains under-appreciated. Both these mechanisms play an essential role in physiological and diseases processes, including cancer and neurological disorders. However, elucidation of RNA editing events at transcriptome-wide level requires increasingly complex computational tools, in turn resulting in a steep entrance barrier for labs who are interested in high-throughput variant calling applications on a large scale but lack the manpower and/or computational expertise. Results Here we present an easy-to-use, fully automated, computational pipeline (Automated Isoform Diversity Detector, AIDD) that contains open source tools for various tasks needed to map transcriptome diversity, including RNA editing events. To facilitate reproducibility and avoid system dependencies, the pipeline is contained within a pre-configured VirtualBox environment. The analytical tasks and format conversions are accomplished via a set of automated scripts that enable the user to go from a set of raw data, such as fastq files, to publication-ready results and figures in one step. A publicly available dataset of Zika virus-infected neural progenitor cells is used to illustrate AIDD’s capabilities. Conclusions AIDD pipeline offers a user-friendly interface for comprehensive and reproducible RNA-seq analyses. Among unique features of AIDD are its ability to infer RNA editing patterns, including ADAR editing, and inclusion of Guttman scale patterns for time series analysis of such editing landscapes. AIDD-based results show importance of diversity of ADAR isoforms, key RNA editing enzymes linked with the innate immune system and viral infections. These findings offer insights into the potential role of ADAR editing dysregulation in the disease mechanisms, including those of congenital Zika syndrome. Because of its automated all-inclusive features, AIDD pipeline enables even a novice user to easily explore common mechanisms of transcriptome diversity, including RNA editing landscapes.

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Section: Mapping Adar Expression and Editing Landscapessupporting

confidence: 87%

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data

et al. 2020

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“…47 The locus of ADAR2, 22q22.3, has been suggested to be associated with familial BD by the linkage studies. 59,60 Based on these findings, Amore et al examined cDNA sequences of ADAR2 cloned from patients with familial BDs, 61 and Kostyrko et al performed mutation screening analysis in BD. 62 Neither study, however, identified SNPs or mutations specific to patients with BD.…”

Section: Effect Of Genetic Variations Of Adars On Htr2c Rna Editingmentioning

confidence: 99%

Serotonin receptor 2C and mental disorders: Genetic, expression, and RNA editing studies

Iwamoto¹,

Bundo²,

Kato³

2009

RNA Biology

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“…SNPs in ADARB2 were found to be associated with longevity and these findings were replicated in three independent cohorts of different genetic backgrounds [ 27 ]. Amore et al [ 28 ] identified a common neutral SNP in three out of seven patients with bipolar disorder in the ADARB1 gene, but no other major alterations. In a separate study, Kostyrko et al [ 29 ] analysed the coding sequence of ADARB1 and its association with bipolar affective disorder and did not find any mutations except one already known transition.…”

Section: Discussionmentioning

confidence: 99%

Case-control study of ADARB1 and ADARB2 gene variants in migraine

et al. 2015

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BackgroundMigraine causes crippling attacks of severe head pain along with associated nausea, vomiting, photophobia and/or phonophobia. The aim of this study was to investigate single nucleotide polymorphisms (SNPs) in the adenosine deaminase, RNA-specific, B1 (ADARB1) and adenosine deaminase, RNA specific, B2 (ADARB2) genes in an Australian case–control Caucasian population for association with migraine. Both candidate genes are highly expressed in the central nervous system and fit criteria for migraine neuropathology. SNPs in the ADARB2 gene were previously found to be positively associated with migraine in a pedigree-based genome wide association study using the genetic isolate of Norfolk Island, Australia. The ADARB1 gene was also chosen for investigation due to its important function in editing neurotransmitter receptor transcripts.MethodsFour SNPs in ADARB1 and nine in ADARB2 were selected by inspecting blocks of linkage disequilibrium in Haploview for genotyping using either TaqMan or Sequenom assays. These SNPs were genotyped in two-hundred and ninety one patients who satisfied the International Classification of Headache Disorders-II 2004 diagnostic criteria for migraine, and three-hundred and fourteen controls, and PLINK was used for association testing.ResultsChi-square analysis found no significant association between any of the SNPs tested in the ADARB1 and ADARB2 genes in this study and the occurrence of migraine.ConclusionsIn contrast to findings that SNPs in the ADARB2 gene were positively associated with migraine in the Norfolk Island population, we find no evidence to support the involvement of RNA editing genes in migraine susceptibility in an Australian Caucasian population.

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Sequence analysis of ADARB1 gene in patients with familial bipolar disorder

Cited by 9 publications

References 28 publications

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data

Serotonin receptor 2C and mental disorders: Genetic, expression, and RNA editing studies

Case-control study of ADARB1 and ADARB2 gene variants in migraine

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