TY - JOUR AU - Knaus, Lisa AU - Tarlungeanu, Dora-Clara AU - Novarino, Gaia ID - 7414 IS - Supplement 6 JF - European Neuropsychopharmacology SN - 0924-977X TI - S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly VL - 29 ER - TY - DATA AB - This dataset contains the supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition". The contained files have the following content: 'Supplementary Figures.pdf' Additional figures (as referenced in the paper). 'Supplementary Table 1. Statistics.xlsx' Details on statistical tests performed in the paper. 'Supplementary Table 2. Differentially expressed gene analysis.xlsx' Results for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples. 'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx' Results for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down). 'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx' Results for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant. 'Supplementary Table 5. Cluster identification.xlsx' Results for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories). 'Supplementary Table 6. GO term cluster analysis.xlsx' Results for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1). 'Supplementary Table 7. Setd5 mass spectrometry results.xlsx' Results showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma. 'Supplementary Table 8. PolII ChIP-seq analysis.xlsx' Results for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS. AU - Dotter, Christoph AU - Novarino, Gaia ID - 6074 TI - Supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition" ER - TY - JOUR AB - Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. AU - Novarino, Gaia ID - 456 IS - 423 JF - Science Translational Medicine TI - Zika-associated microcephaly: Reduce the stress and race for the treatment VL - 10 ER - TY - JOUR AB - Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in genomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered, the etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype- based diagnosis of individual patients has become a requisite. In this review we look at recent advancements in genomic analysis and their translation into clinical practice. AU - Tarlungeanu, Dora-Clara AU - Novarino, Gaia ID - 5888 IS - 8 JF - Experimental & Molecular Medicine SN - 2092-6413 TI - Genomics in neurodevelopmental disorders: an avenue to personalized medicine VL - 50 ER - TY - JOUR AB - The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies. AU - Sacco, Roberto AU - Cacci, Emanuele AU - Novarino, Gaia ID - 546 IS - 2 JF - Current Opinion in Neurobiology TI - Neural stem cells in neuropsychiatric disorders VL - 48 ER - TY - JOUR AB - Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain. Objective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families. Methods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease. Results: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold. Conclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function. AU - Marin Valencia, Isaac AU - Novarino, Gaia AU - Johansen, Anide AU - Rosti, Başak AU - Issa, Mahmoud AU - Musaev, Damir AU - Bhat, Gifty AU - Scott, Eric AU - Silhavy, Jennifer AU - Stanley, Valentina AU - Rosti, Rasim AU - Gleeson, Jeremy AU - Imam, Farhad AU - Zaki, Maha AU - Gleeson, Joseph ID - 691 IS - 1 JF - Journal of Medical Genetics SN - 0022-2593 TI - A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features VL - 55 ER - TY - THES AB - Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. AU - Tarlungeanu, Dora-Clara ID - 395 SN - 2663-337X TI - The branched chain amino acids in autism spectrum disorders ER - TY - JOUR AB - SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder. AU - Deliu, Elena AU - Arecco, Niccoló AU - Morandell, Jasmin AU - Dotter, Christoph AU - Contreras, Ximena AU - Girardot, Charles AU - Käsper, Eva AU - Kozlova, Alena AU - Kishi, Kasumi AU - Chiaradia, Ilaria AU - Noh, Kyung AU - Novarino, Gaia ID - 3 IS - 12 JF - Nature Neuroscience TI - Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition VL - 21 ER - TY - JOUR AB - RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host. AU - Khamina, Kseniya AU - Lercher, Alexander AU - Caldera, Michael AU - Schliehe, Christopher AU - Vilagos, Bojan AU - Sahin, Mehmet AU - Kosack, Lindsay AU - Bhattacharya, Anannya AU - Májek, Peter AU - Stukalov, Alexey AU - Sacco, Roberto AU - James, Leo AU - Pinschewer, Daniel AU - Bennett, Keiryn AU - Menche, Jörg AU - Bergthaler, Andreas ID - 540 IS - 12 JF - PLoS Pathogens SN - 15537366 TI - Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein VL - 13 ER - TY - CHAP AB - Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology. AU - Hill Yardin, Elisa AU - Mckeown, Sonja AU - Novarino, Gaia AU - Grabrucker, Andreas ED - Schmeisser, Michael ED - Boekers, Tobias ID - 623 SN - 03015556 T2 - Translational Anatomy and Cell Biology of Autism Spectrum Disorder TI - Extracerebral dysfunction in animal models of autism spectrum disorder VL - 224 ER - TY - CHAP AB - As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans. AU - Schroeder, Jan AU - Deliu, Elena AU - Novarino, Gaia AU - Schmeisser, Michael ED - Schmeisser, Michael ED - Boekers, Tobias ID - 634 T2 - Translational Anatomy and Cell Biology of Autism Spectrum Disorder TI - Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder VL - 224 ER - TY - JOUR AB - Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets. AU - Novarino, Gaia ID - 656 IS - 381 JF - Science Translational Medicine SN - 19466234 TI - Modeling Alzheimer's disease in mice with human neurons VL - 9 ER - TY - JOUR AB - Perinatal exposure to penicillin may result in longlasting gut and behavioral changes. AU - Novarino, Gaia ID - 667 IS - 387 JF - Science Translational Medicine SN - 19466234 TI - The antisocial side of antibiotics VL - 9 ER - TY - JOUR AB - Rett syndrome modeling in monkey mirrors the human disorder. AU - Novarino, Gaia ID - 689 IS - 393 JF - Science Translational Medicine SN - 19466234 TI - Rett syndrome modeling goes simian VL - 9 ER - TY - JOUR AB - Leading autism-associated mutation in mouse partially mimics human disorder. AU - Novarino, Gaia ID - 702 IS - 399 JF - Science Translational Medicine SN - 19466234 TI - The riddle of CHD8 haploinsufficiency in autism spectrum disorder VL - 9 ER - TY - JOUR AB - To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta. AU - Andergassen, Daniel AU - Dotter, Christoph AU - Wenzel, Dyniel AU - Sigl, Verena AU - Bammer, Philipp AU - Muckenhuber, Markus AU - Mayer, Daniela AU - Kulinski, Tomasz AU - Theussl, Hans AU - Penninger, Josef AU - Bock, Christoph AU - Barlow, Denise AU - Pauler, Florian AU - Hudson, Quanah ID - 713 JF - eLife SN - 2050084X TI - Mapping the mouse Allelome reveals tissue specific regulation of allelic expression VL - 6 ER - TY - JOUR AB - Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients. AU - Brailoiu, Gabriela AU - Deliu, Elena AU - Barr, Jeffrey AU - Console Bram, Linda AU - Ciuciu, Alexandra AU - Abood, Mary AU - Unterwald, Ellen AU - Brǎiloiu, Eugen ID - 714 JF - Drug and Alcohol Dependence SN - 03768716 TI - HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens VL - 178 ER - TY - JOUR AB - D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome. AU - Novarino, Gaia ID - 715 IS - 405 JF - Science Translational Medicine SN - 19466234 TI - More excitation for Rett syndrome VL - 9 ER - TY - JOUR AB - Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently. AU - Novarino, Gaia ID - 731 IS - 411 JF - Science Translational Medicine SN - 19466234 TI - The science of love in ASD and ADHD VL - 9 ER - TY - JOUR AB - Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD. AU - Sauerzopf, Ulrich AU - Sacco, Roberto AU - Novarino, Gaia AU - Niello, Marco AU - Weidenauer, Ana AU - Praschak Rieder, Nicole AU - Sitte, Harald AU - Willeit, Matthaeus ID - 1228 IS - 1 JF - European Journal of Neuroscience TI - Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence VL - 45 ER - TY - JOUR AB - Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia. AU - Brǎiloiu, Eugen AU - Mcguire, Matthew AU - Shuler, Shadaria AU - Deliu, Elena AU - Barr, Jeffrey AU - Abood, Mary AU - Brailoiu, Gabriela ID - 747 JF - Neuroscience SN - 03064522 TI - Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus VL - 365 ER - TY - JOUR AB - Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers. AU - Kornienko, Aleksandra AU - Dotter, Christoph AU - Guenzl, Philipp AU - Gisslinger, Heinz AU - Gisslinger, Bettina AU - Cleary, Ciara AU - Kralovics, Robert AU - Pauler, Florian AU - Barlow, Denise ID - 1240 IS - 1 JF - Genome Biology TI - Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans VL - 17 ER - TY - JOUR AB - Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function. AU - Tarlungeanu, Dora-Clara AU - Deliu, Elena AU - Dotter, Christoph AU - Kara, Majdi AU - Janiesch, Philipp AU - Scalise, Mariafrancesca AU - Galluccio, Michele AU - Tesulov, Mateja AU - Morelli, Emanuela AU - Sönmez, Fatma AU - Bilgüvar, Kaya AU - Ohgaki, Ryuichi AU - Kanai, Yoshikatsu AU - Johansen, Anide AU - Esharif, Seham AU - Ben Omran, Tawfeg AU - Topcu, Meral AU - Schlessinger, Avner AU - Indiveri, Cesare AU - Duncan, Kent AU - Caglayan, Ahmet AU - Günel, Murat AU - Gleeson, Joseph AU - Novarino, Gaia ID - 1183 IS - 6 JF - Cell TI - Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder VL - 167 ER - TY - JOUR AB - Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide. AU - Andergassen, Daniel AU - Dotter, Christoph AU - Kulinski, Tomasz AU - Guenzl, Philipp AU - Bammer, Philipp AU - Barlow, Denise AU - Pauler, Florian AU - Hudson, Quanah ID - 1497 IS - 21 JF - Nucleic Acids Research TI - Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data VL - 43 ER - TY - JOUR AB - Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID. AU - Kuechler, Alma AU - Zink, Alexander AU - Wieland, Thomas AU - Lüdecke, Hermann AU - Cremer, Kirsten AU - Salviati, Leonardo AU - Magini, Pamela AU - Najafi, Kimia AU - Zweier, Christiane AU - Czeschik, Johanna AU - Aretz, Stefan AU - Endele, Sabine AU - Tamburrino, Federica AU - Pinato, Claudia AU - Clementi, Maurizio AU - Gundlach, Jasmin AU - Maylahn, Carina AU - Mazzanti, Laura AU - Wohlleber, Eva AU - Schwarzmayr, Thomas AU - Kariminejad, Roxana AU - Schlessinger, Avner AU - Wieczorek, Dagmar AU - Strom, Tim AU - Novarino, Gaia AU - Engels, Hartmut ID - 1789 IS - 6 JF - European Journal of Human Genetics TI - Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome VL - 23 ER - TY - JOUR AB - Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease. AU - Novarino, Gaia AU - Fenstermaker, Ali AU - Zaki, Maha AU - Hofree, Matan AU - Silhavy, Jennifer AU - Heiberg, Andrew AU - Abdellateef, Mostafa AU - Rosti, Başak AU - Scott, Eric AU - Mansour, Lobna AU - Masri, Amira AU - Kayserili, Hülya AU - Al Aama, Jumana AU - Abdel Salam, Ghada AU - Karminejad, Ariana AU - Kara, Majdi AU - Kara, Bülent AU - Bozorgmehri, Bita AU - Ben Omran, Tawfeg AU - Mojahedi, Faezeh AU - Mahmoud, Iman AU - Bouslam, Naïma AU - Bouhouche, Ahmed AU - Benomar, Ali AU - Hanein, Sylvain AU - Raymond, Laure AU - Forlani, Sylvie AU - Mascaro, Massimo AU - Selim, Laila AU - Shehata, Nabil AU - Al Allawi, Nasir AU - Bindu, Parayil AU - Azam, Matloob AU - Günel, Murat AU - Caglayan, Ahmet AU - Bilgüvar, Kaya AU - Tolun, Aslihan AU - Issa, Mahmoud AU - Schroth, Jana AU - Spencer, Emily AU - Rosti, Rasim AU - Akizu, Naiara AU - Vaux, Keith AU - Johansen, Anide AU - Koh, Alice AU - Megahed, Hisham AU - Dürr, Alexandra AU - Brice, Alexis AU - Stévanin, Giovanni AU - Gabriel, Stacy AU - Ideker, Trey AU - Gleeson, Joseph ID - 1916 IS - 6170 JF - Science TI - Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders VL - 343 ER -