Pleiotropic effects of candidate genes on autism spectrum disorder and comorbidities: genetics, funcional studies and animal models

[eng] Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and interaction, as well as repetitive and restricted patterns of behaviour. Although growing evidence supports a main contribution of genetic factors to its neurobiology and hundreds of candidate genes have been identified in recent years, the genetic architecture of the disorder is still not fully understood. Moreover, ASD frequently co-occurs with other developmental and psychiatric disorders, and shared genetic mechanisms are hypothesized to underlie these comorbidities. In this doctoral thesis, we aimed to study the contribution of several candidate genes to ASD and comorbidities. We have focused on the 14-3-3 gene family, RBFOX1 and the BEX/TCEAL gene family, performed genetic and functional studies and further characterized the neurobiological effects of their deficiency using animal models. First, our results suggest a role for the 14-3-3 genes in ASD and schizophrenia (SCZ). Ultra-rare variants in the 14-3-3 genes are enriched in ASD and common and rare variants in the YWHAE and YWHAZ genes, respectively, are associated with SCZ. We have also reported alterations in the expression of these genes in postmortem brains of ASD or SCZ patients. Furthermore, we have demonstrated a loss-of-function effect of a damaging variant in the YWHAZ gene present in two siblings with ASD and attention deficit/hyperactivity disorder (ADHD). In addition, we have characterized ywhaz expression in zebrafish across development and in adulthood and demonstrated that ywhaz depletion causes alterations in behaviour, in neuronal activity and connectivity and in monoamine signalling. The behavioural changes included freezing and were rescued with drug treatments that target monoamine neurotransmission. Second, we have demonstrated a relevant contribution of common variants in RBFOX1 to psychiatric disorders and traits. Also, we have shown that a high number of copy number variants (CNVs) spanning RBFOX1 are reported in patients with psychiatric conditions, the vast majority in patients with ASD or SCZ, and patients with these disorders also show a decreased expression of RBFOX1 in cortex. Finally, we have used knockout animal models to understand its role in psychiatric disorders, and demonstrated that both mice and zebrafish RBFOX1- deficient models present behavioural alterations that can be related to neurodevelopmental disorders such as ASD, ADHD and SCZ. Third, we found that all BEX/TCEAL genes are downregulated in postmortem brain regions of ASD and SCZ patients and that rare CNVs spanning several BEX/TCEAL genes have been reported in patients with severe neurodevelopmental problems. Furthermore, Bex3-deficient mice show anatomical and molecular alterations in brain, an excitatory/inhibitory imbalance and behavioural alterations that can be assimilated to ASD- and SCZ-like symptoms.[spa] El trastorno del espectro autista (TEA) es un trastorno del neurodesarrollo caracterizado por problemas en la comunicación e interacción social, así como patrones restrictivos y repetitivos de comportamiento. El peso de la genética en su etiología es cada vez más evidente, aunque la compleja arquitectura genética del trastorno sigue siendo una incógnita. Además, el diagnóstico de otros trastornos comórbidos es frecuente en pacientes con TEA, por lo que se hipotetiza una base genética común. El objetivo de esta tesis doctoral es elucidar la contribución de varios genes candidatos, concretamente la familia de genes 14-3-3, el gen RBFOX1 y la familia BEX/TCEAL, al TEA y otros trastornos comórbidos, realizando estudios genéticos y funcionales, así como caracterizando los efectos neurobiológicos de su deficiencia en modelos animales. En primer lugar, nuestros resultados sugieren que variantes ultra-raras en los genes 14-3-3 contribuyen al TEA y que variantes comunes y raras en los genes YWHAE y YWHAZ, respectivamente, están asociadas a esquizofrenia (SCZ). Además, la expresión de los genes 14- 3-3 está alterada en pacientes con TEA o SCZ. Hemos demostrado que una variante patogénica en el gen YWHAZ presente en dos hermanos con TEA y trastorno de déficit de atención e hiperactividad (TDAH) provoca una pérdida de función de la proteína. Asimismo, hemos demostrado que la deleción de ywhaz produce alteraciones en la actividad y conectividad neuronal, la señalización monoaminérgica y el comportamiento, pudiéndose este último recuperar mediante fármacos. En segundo lugar, hemos demostrado que variantes comunes en RBFOX1 están asociadas a diferentes trastornos psiquiátricos y que un número elevado de variantes del número de copias (CNV) afectan a RBFOX1 en pacientes con trastornos psiquiátricos, siendo especialmente frecuentes en pacientes con TEA o SCZ que, además, presentan una disminución en la expresión de RBFOX1 en corteza cerebral. Asimismo, hemos usado modelos animales genoanulados para estudiar la implicación de RBFOX1 en trastornos psiquiátricos, demostrando que tanto el modelo murino como los de pez cebra presentan alteraciones de comportamiento relacionadas con trastornos del neurodesarrollo, como ASD, TDAH y SCZ. Por último, la expresión de los genes BEX/TCEAL está disminuida en regiones cerebrales de pacientes con TEA o SCZ y, además, se han descrito CNVs que abarcan varios genes BEX/TCEAL en pacientes con trastornos severos del neurodesarrollo. Los ratones genoanulados para Bex3 muestran alteraciones anatómicas y moleculares en cerebro, un desequilibro excitación/inhibición y alteraciones de comportamiento asimilables a síntomas de TEA y SCZ

The pleiotropic contribution of genes in dopaminergic and serotonergic pathways to addiction and related behavioral traits

Introduction: Co-occurrence of substance use disorders (SUD) and other behavioral conditions, such as stress-related, aggressive or risk-taking behaviors, in the same individual has been frequently described. As dopamine (DA) and serotonin (5-HT) have been previously identified as key neurotransmitters for some of these phenotypes, we explored the genetic contribution of these pathways to SUD and these comorbid phenotypes in order to better understand the genetic relationship between them. Methods: We tested the association of 275 dopaminergic genes and 176 serotonergic genes with these phenotypes by performing gene-based, gene-set and transcriptome-wide association studies in 11 genome-wide association studies (GWAS) datasets on SUD and related behaviors. Results: At the gene-wide level, 68 DA and 27 5-HT genes were found to be associated with at least one GWAS on SUD or related behavior. Among them, six genes had a pleiotropic effect, being associated with at least three phenotypes: ADH1C, ARNTL, CHRNA3, HPRT1, HTR1B and DRD2. Additionally, we found nominal associations between the DA gene sets and SUD, opioid use disorder, antisocial behavior, irritability and neuroticism, and between the 5-HT-core gene set and neuroticism. Predicted gene expression correlates in brain were also found for 19 DA or 5-HT genes. Discussion: Our study shows a pleiotropic contribution of dopaminergic and serotonergic genes to addiction and related behaviors such as anxiety, irritability, neuroticism and risk-taking behavior, highlighting a role for DA genes, which could explain, in part, the co-occurrence of these phenotype

Involvement of the 14-3-3 gene family in autism spectrum disorder and schizophrenia: Genetics, transcriptomics and functional analyses

The 14-3-3 protein family are molecular chaperones involved in several biological functions and neurological diseases. We previously pinpointed YWHAZ (encoding 14-3-3ζ) as a candidate gene for autism spectrum disorder (ASD) through a whole-exome sequencing study, which identified a frameshift variant within the gene (c.659-660insT, p.L220Ffs*18). Here, we explored the contribution of the seven human 14-3-3 family members in ASD and other psychiatric disorders by investigating the: (i) functional impact of the 14-3-3ζ mutation p.L220Ffs*18 by assessing solubility, target binding and dimerization; (ii) contribution of common risk variants in 14-3-3 genes to ASD and additional psychiatric disorders; (iii) burden of rare variants in ASD and schizophrenia; and iv) 14-3-3 gene expression using ASD and schizophrenia transcriptomic data. We found that the mutant 14-3-3ζ protein had decreased solubility and lost its ability to form heterodimers and bind to its target tyrosine hydroxylase. Gene-based analyses using publicly available datasets revealed that common variants in YWHAE contribute to schizophrenia (p = 6.6 × 10-7), whereas ultra-rare variants were found enriched in ASD across the 14-3-3 genes (p = 0.017) and in schizophrenia for YWHAZ (meta-p = 0.017). Furthermore, expression of 14-3-3 genes was altered in post-mortem brains of ASD and schizophrenia patients. Our study supports a role for the 14-3-3 family in ASD and schizophrenia

Behavioural and functional evidence revealing the role of RBFOX1 variation in multiple psychiatric disorders and traits

Common variation in the gene encoding the neuron-specific RNA splicing factor RNA Binding Fox-1 Homolog 1 (RBFOX1) has been identified as a risk factor for several psychiatric conditions, and rare genetic variants have been found causal for autism spectrum disorder (ASD). Here, we explored the genetic landscape of RBFOX1 more deeply, integrating evidence from existing and new human studies as well as studies in Rbfox1 knockout mice. Mining existing data from large-scale studies of human common genetic variants, we confirmed gene-based and genome-wide association of RBFOX1 with risk tolerance, major depressive disorder and schizophrenia. Data on six mental disorders revealed copy number losses and gains to be more frequent in ASD cases than in controls. Consistently, RBFOX1 expression appeared decreased in post-mortem frontal and temporal cortices of individuals with ASD and prefrontal cortex of individuals with schizophrenia. Brain-functional MRI studies demonstrated that carriers of a common RBFOX1 variant, rs6500744, displayed increased neural reactivity to emotional stimuli, reduced prefrontal processing during cognitive control, and enhanced fear expression after fear conditioning, going along with increased avoidance behaviour. Investigating Rbfox1 neuron-specific knockout mice allowed us to further specify the role of this gene in behaviour. The model was characterised by pronounced hyperactivity, stereotyped behaviour, impairments in fear acquisition and extinction, reduced social interest, and lack of aggression; it provides excellent construct and face validity as an animal model of ASD. In conclusion, convergent translational evidence shows that common variants in RBFOX1 are associated with a broad spectrum of psychiatric traits and disorders, while rare genetic variation seems to expose to early-onset neurodevelopmental psychiatric disorders with and without developmental delay like ASD, in particular. Studying the pleiotropic nature of RBFOX1 can profoundly enhance our understanding of mental disorder vulnerability

The translational genetics of ADHD and related phenotypes in model organisms

Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalent neurodevelopmental disorder resulting from the interaction between genetic and environmental risk factors. It is well known that ADHD co-occurs frequently with other psychiatric disorders due, in part, to shared genetics factors. Although many studies have contributed to delineate the genetic landscape of psychiatric disorders, their specific molecular underpinnings are still not fully understood. The use of animal models can help us to understand the role of specific genes and environmental stimuli-induced epigenetic modifications in the pathogenesis of ADHD and its comorbidities. The aim of this review is to provide an overview on the functional work performed in rodents, zebrafish and fruit fly and highlight the generated insights into the biology of ADHD, with a special focus on genetics and epigenetics. We also describe the behavioral tests that are available to study ADHD-relevant phenotypes and comorbid traits in these models. Furthermore, we have searched for new models to study ADHD and its comorbidities, which can be useful to test potential pharmacological treatments

Deficiency of the ywhaz gene, involved in neurodevelopmental disorders, alters brain activity and behaviour in zebrafish

Genetic variants in YWHAZ contribute to psychiatric disorders such as autism spectrum disorder and schizophrenia, and have been related to an impaired neurodevelopment in humans and mice. Here, we have used zebrafish to investigate the mechanisms by which YWHAZ contributes to neurodevelopmental disorders. We observed that ywhaz expression was pan-neuronal during developmental stages and restricted to Purkinje cells in the adult cerebellum, cells that are described to be reduced in number and size in autistic patients. We then performed whole-brain imaging in wild-type and ywhaz CRISPR/Cas9 knockout (KO) larvae and found altered neuronal activity and connectivity in the hindbrain. Adult ywhaz KO fish display decreased levels of monoamines in the hindbrain and freeze when exposed to novel stimuli, a phenotype that can be reversed with drugs that target monoamine neurotransmission. These findings suggest an important role for ywhaz in establishing neuronal connectivity during development and modulating both neurotransmission and behaviour in adults

Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions

Background One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood. Results Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes. Conclusions We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.Major financial support for this research was received from Spanish “Ministerio de Ciencia, Innovación y Universidades.” Grants BFU2015-68655-P and BFU2017-861152-P to J.G.F., RTI2018-100968-B-I00, 2017-SGR-738, H2020/2014-2020 under grant agreements n°667302, n°643051, and n°728018 to B.C., PGC2018-098229-B-I00 to J.L.F., BES-2016-077374 to E.A.-G., CVI-7290 Junta de Andalucía to A.R.M., SAF2016-80937-R (Ministerio de Economía y Competitividad/FEDER) to G.M., Institutional Grant MDM-2016-0687 (Maria de Maeztu Excellence Unit, Department of Gene Regulation and Morphogenesis at CABD) and BFU2017-83150-P to J.J.C, BFU2017-89780-R and P12-CTS-2257 to A.M.C. and SAF2016-76340-R and María de Maeztu Excellence Unit, Institute of Neurosciences to E.S.. E.N.P. held an FPI pre-doctoral fellowship (Spanish “Ministerio de Ciencia, Innovación y Universidades”). S.M. was first supported by a contract with the “Centro de Investigación Biomédica en Enfermedades Neurodegenerativas,” and later by “Centro de Investigación Biomédica en Red de Enfermedades Raras” (CIBERER). N.F.C. is also under contract by CIBERER. This study makes use of data generated by the DECIPHER community. A full list of centres who contributed to the generation of the data is available at http://decipher.sanger.ac.uk and via email from [email protected]. Funding for the project was provided by the Wellcome Trust.Ye