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Tian Y, Wu X, Luo S, Xiong D, Liu R, Hu L, Yuan Y, Shi G, Yao J, Huang Z, Fu F, Yang X, Tang Z, Zhang J, Hu K. A multi-omic single-cell landscape of cellular diversification in the developing human cerebral cortex. Comput Struct Biotechnol J 2024; 23:2173-2189. [PMID: 38827229 PMCID: PMC11141146 DOI: 10.1016/j.csbj.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell. We computationally reconstructed the differentiation trajectories of excitatory projection neurons of cortical origin and inferred the regulatory logic governing lineage bifurcation decisions for neuronal diversification. We demonstrated that neuronal diversity arises from progenitor cell lineage specificity and postmitotic differentiation at distinct stages. Our data paves the way for understanding the primarily coordinated regulatory logic for neuronal diversification in the neocortex.
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Affiliation(s)
- Yuhan Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Songhao Luo
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Rong Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Lanqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Guowei Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiwei Huang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Fang Fu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Xin Yang
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Kunhua Hu
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Public Platform Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
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Park M, Shin JE, Yee J, Ahn YM, Joo EJ. Gene-gene interaction analysis for age at onset of bipolar disorder in a Korean population. J Affect Disord 2024; 361:97-103. [PMID: 38834091 DOI: 10.1016/j.jad.2024.05.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Multiple genes might interact to determine the age at onset of bipolar disorder. We investigated gene-gene interactions related to age at onset of bipolar disorder in the Korean population, using genome-wide association study (GWAS) data. METHODS The study population consisted of 303 patients with bipolar disorder. First, the top 1000 significant single-nucleotide polymorphisms (SNPs) associated with age at onset of bipolar disorder were selected through single SNP analysis by simple linear regression. Subsequently, the QMDR method was used to find gene-gene interactions. RESULTS The best 10 SNPs from simple regression were located in chromosome 1, 2, 3, 10, 11, 14, 19, and 21. Only five SNPs were found in several genes, such as FOXN3, KIAA1217, OPCML, CAMSAP2, and PTPRS. On QMDR analyses, five pairs of SNPs showed significant interactions with a CVC exceeding 1/5 in a two-locus model. The best interaction was found for the pair of rs60830549 and rs12952733 (CVC = 1/5, P < 1E-07). In three-locus models, four combinations of SNPs showed significant associations with age at onset, with a CVC of >1/5. The best three-locus combination was rs60830549, rs12952733, and rs12952733 (CVC = 2/5, P < 1E-6). The SNPs showing significant interactions were located in the KIAA1217, RBFOX3, SDK2, CYP19A1, NTM, SMYD3, and RBFOX1 genes. CONCLUSIONS Our analysis confirmed genetic interactions influencing the age of onset for bipolar disorder and identified several potential candidate genes. Further exploration of the functions of these promising genes, which may have multiple roles within the neuronal network, is necessary.
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Affiliation(s)
- Mira Park
- Department of Preventive Medicine, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Ji-Eun Shin
- Department of Biomedical Informatics, School of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Jaeyong Yee
- Department of Physiology and Biophysics, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Yong Min Ahn
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun-Jeong Joo
- Department of Psychiatry, Uijeongbu Eulji Medical Center, Eulji University, Gyeonggi, Republic of Korea; Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon, Republic of Korea.
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Yotova AY, Li LL, O'Leary A, Tegeder I, Reif A, Courtney MJ, Slattery DA, Freudenberg F. Synaptic proteome perturbations after maternal immune activation: Identification of embryonic and adult hippocampal changes. Brain Behav Immun 2024; 121:351-364. [PMID: 39089536 DOI: 10.1016/j.bbi.2024.07.040] [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] [Received: 03/19/2024] [Revised: 07/10/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Maternal immune activation (MIA) triggers neurobiological changes in offspring, potentially reshaping the molecular synaptic landscape, with the hippocampus being particularly vulnerable. However, critical details regarding developmental timing of these changes and whether they differ between males and females remain unclear. METHODS We induced MIA in C57BL/6J mice on gestational day nine using the viral mimetic poly(I:C) and performed mass spectrometry-based proteomic analyses on hippocampal synaptoneurosomes of embryonic (E18) and adult (20 ± 1 weeks) MIA offspring. RESULTS In the embryonic synaptoneurosomes, MIA led to lipid, polysaccharide, and glycoprotein metabolism pathway disruptions. In the adult synaptic proteome, we observed a dynamic shift toward transmembrane trafficking, intracellular signalling cascades, including cell death and growth, and cytoskeletal organisation. In adults, many associated pathways overlapped between males and females. However, we found distinct sex-specific enrichment of dopaminergic and glutamatergic pathways. We identified 50 proteins altered by MIA in both embryonic and adult samples (28 with the same directionality), mainly involved in presynaptic structure and synaptic vesicle function. We probed human phenome-wide association study data in the cognitive and psychiatric domains, and 49 of the 50 genes encoding these proteins were significantly associated with the investigated phenotypes. CONCLUSIONS Our data emphasise the dynamic effects of viral-like MIA on developing and mature hippocampi and provide novel targets for study following prenatal immune challenges. The 22 proteins that changed directionality from the embryonic to adult hippocampus, suggestive of compensatory over-adaptions, are particularly attractive for future investigations.
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Affiliation(s)
- Anna Y Yotova
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany; Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Cell Biology and Neuroscience, Frankfurt, Germany
| | - Li-Li Li
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Turku Brain and Mind Center, University of Turku and Åbo Akademi University, 20014 Turku, Finland
| | - Aet O'Leary
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany; Department of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Irmgard Tegeder
- Goethe University Frankfurt, Faculty of Medicine, Institute of Clinical Pharmacology, Frankfurt, Germany
| | - Andreas Reif
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Michael J Courtney
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Turku Brain and Mind Center, University of Turku and Åbo Akademi University, 20014 Turku, Finland
| | - David A Slattery
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany
| | - Florian Freudenberg
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany; Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Cell Biology and Neuroscience, Frankfurt, Germany.
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Pal A, Noble MA, Morales M, Pal R, Baumgartner M, Yang JW, Yim KM, Uebbing S, Noonan JP. Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600691. [PMID: 39091792 PMCID: PMC11291010 DOI: 10.1101/2024.06.25.600691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.
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Chung Y, Dienel SJ, Belch MJ, Fish KN, Ermentrout GB, Lewis DA, Chung DW. Altered Rbfox1-Vamp1 pathway and prefrontal cortical dysfunction in schizophrenia. Mol Psychiatry 2024; 29:1382-1391. [PMID: 38273110 PMCID: PMC11273323 DOI: 10.1038/s41380-024-02417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/27/2024]
Abstract
Deficient gamma oscillations in prefrontal cortex (PFC) of individuals with schizophrenia appear to involve impaired inhibitory drive from parvalbumin-expressing interneurons (PVIs). Inhibitory drive from PVIs is regulated, in part, by RNA binding fox-1 homolog 1 (Rbfox1). Rbfox1 is spliced into nuclear or cytoplasmic isoforms, which regulate alternative splicing or stability of their target transcripts, respectively. One major target of cytoplasmic Rbfox1 is vesicle associated membrane protein 1 (Vamp1). Vamp1 mediates GABA release probability from PVIs, and the loss of Rbfox1 reduces Vamp1 levels which in turn impairs cortical inhibition. In this study, we investigated if the Rbfox1-Vamp1 pathway is altered in PVIs in PFC of individuals with schizophrenia by utilizing a novel strategy that combines multi-label in situ hybridization and immunohistochemistry. In the PFC of 20 matched pairs of schizophrenia and comparison subjects, cytoplasmic Rbfox1 protein levels were significantly lower in PVIs in schizophrenia and this deficit was not attributable to potential methodological confounds or schizophrenia-associated co-occurring factors. In a subset of this cohort, Vamp1 mRNA levels in PVIs were also significantly lower in schizophrenia and were predicted by lower cytoplasmic Rbfox1 protein levels across individual PVIs. To investigate the functional impact of Rbfox1-Vamp1 alterations in schizophrenia, we simulated the effect of lower GABA release probability from PVIs on gamma power in a computational model network of pyramidal neurons and PVIs. Our simulations showed that lower GABA release probability reduces gamma power by disrupting network synchrony while minimally affecting network activity. Finally, lower GABA release probability synergistically interacted with lower strength of inhibition from PVIs in schizophrenia to reduce gamma power non-linearly. Together, our findings suggest that the Rbfox1-Vamp1 pathway in PVIs is impaired in schizophrenia and that this alteration likely contributes to deficient PFC gamma power in the illness.
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Affiliation(s)
- Youjin Chung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samuel J Dienel
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew J Belch
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kenneth N Fish
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - G Bard Ermentrout
- Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel W Chung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
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6
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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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Moroz LL. Evolutionary neurogenomics: Lengthy resolutions for complex brains. Curr Biol 2024; 34:R315-R318. [PMID: 38653198 PMCID: PMC11173357 DOI: 10.1016/j.cub.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Genomic blueprints underlying unique neuronal organization are enigmatic. A new study reveals the recruitment of ancient, larger genes for synaptic machinery, providing evolutionary constraints and flexibility, with increasing gene sizes being found in animal lineages that led to cephalopods and vertebrates.
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Affiliation(s)
- Leonid L Moroz
- Department of Neuroscience, College of Medicine and the Whitney Laboratory for Marine Biosciences, University of Florida, FL 32080, USA.
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8
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Polakkattil BK, Vellichirammal NN, Nair IV, Nair CM, Banerjee M. Methylome-wide and meQTL analysis helps to distinguish treatment response from non-response and pathogenesis markers in schizophrenia. Front Psychiatry 2024; 15:1297760. [PMID: 38516266 PMCID: PMC10954811 DOI: 10.3389/fpsyt.2024.1297760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
Schizophrenia is a complex condition with entwined genetic and epigenetic risk factors, posing a challenge to disentangle the intermixed pathological and therapeutic epigenetic signatures. To resolve this, we performed 850K methylome-wide and 700K genome-wide studies on the same set of schizophrenia patients by stratifying them into responders, non-responders, and drug-naïve patients. The key genes that signified the response were followed up using real-time gene expression studies to understand the effect of antipsychotics at the gene transcription level. The study primarily implicates hypermethylation in therapeutic response and hypomethylation in the drug-non-responsive state. Several differentially methylated sites and regions colocalized with the schizophrenia genome-wide association study (GWAS) risk genes and variants, supporting the convoluted gene-environment association. Gene ontology and protein-protein interaction (PPI) network analyses revealed distinct patterns that differentiated the treatment response from drug resistance. The study highlights the strong involvement of several processes related to nervous system development, cell adhesion, and signaling in the antipsychotic response. The ability of antipsychotic medications to alter the pathology by modulating gene expression or methylation patterns is evident from the general increase in the gene expression of response markers and histone modifiers and the decrease in class II human leukocyte antigen (HLA) genes following treatment with varying concentrations of medications like clozapine, olanzapine, risperidone, and haloperidol. The study indicates a directional overlap of methylation markers between pathogenesis and therapeutic response, thereby suggesting a careful distinction of methylation markers of pathogenesis from treatment response. In addition, there is a need to understand the trade-off between genetic and epigenetic observations. It is suggested that methylomic changes brought about by drugs need careful evaluation for their positive effects on pathogenesis, course of disease progression, symptom severity, side effects, and refractoriness.
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Affiliation(s)
- Binithamol K. Polakkattil
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- Research Center, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Neetha N. Vellichirammal
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Indu V. Nair
- Mental Health Centre, Thiruvananthapuram, Kerala, India
| | | | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Antón-Galindo E, Adel MR, García-González J, Leggieri A, López-Blanch L, Irimia M, Norton WHJ, Brennan CH, Fernàndez-Castillo N, Cormand B. Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in two zebrafish models. Transl Psychiatry 2024; 14:99. [PMID: 38374212 PMCID: PMC10876957 DOI: 10.1038/s41398-024-02801-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
RBFOX1 is a highly pleiotropic gene that contributes to several psychiatric and neurodevelopmental disorders. Both rare and common variants in RBFOX1 have been associated with several psychiatric conditions, but the mechanisms underlying the pleiotropic effects of RBFOX1 are not yet understood. Here we found that, in zebrafish, rbfox1 is expressed in spinal cord, mid- and hindbrain during developmental stages. In adults, expression is restricted to specific areas of the brain, including telencephalic and diencephalic regions with an important role in receiving and processing sensory information and in directing behaviour. To investigate the contribution of rbfox1 to behaviour, we used rbfox1sa15940, a zebrafish mutant line with TL background. We found that rbfox1sa15940 mutants present hyperactivity, thigmotaxis, decreased freezing behaviour and altered social behaviour. We repeated these behavioural tests in a second rbfox1 mutant line with a different genetic background (TU), rbfox1del19, and found that rbfox1 deficiency affects behaviour similarly in this line, although there were some differences. rbfox1del19 mutants present similar thigmotaxis, but stronger alterations in social behaviour and lower levels of hyperactivity than rbfox1sa15940 fish. Taken together, these results suggest that mutations in rbfox1 lead to multiple behavioural changes in zebrafish that might be modulated by environmental, epigenetic and genetic background effects, and that resemble phenotypic alterations present in Rbfox1-deficient mice and in patients with different psychiatric conditions. Our study, thus, highlights the evolutionary conservation of rbfox1 function in behaviour and paves the way to further investigate the mechanisms underlying rbfox1 pleiotropy on the onset of neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalunya, Spain
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalunya, Spain
| | - Maja R Adel
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Judit García-González
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, NYC 10029, USA
| | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Laura López-Blanch
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalunya, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalunya, Spain
- Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
- ICREA, Barcelona, Catalunya, Spain
| | - William H J Norton
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalunya, Spain.
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalunya, Spain.
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalunya, Spain.
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalunya, Spain.
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10
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Adel MR, Antón-Galindo E, Gago-Garcia E, Arias-Dimas A, Arenas C, Artuch R, Cormand B, Fernàndez-Castillo N. Decreased Brain Serotonin in rbfox1 Mutant Zebrafish and Partial Reversion of Behavioural Alterations by the SSRI Fluoxetine. Pharmaceuticals (Basel) 2024; 17:254. [PMID: 38399469 PMCID: PMC10891829 DOI: 10.3390/ph17020254] [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: 11/15/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
RBFOX1 functions as a master regulator of thousands of genes, exerting a pleiotropic effect on numerous neurodevelopmental and psychiatric disorders. A potential mechanism by which RBFOX1 may impact these disorders is through its modulation of serotonergic neurotransmission, a common target for pharmacological intervention in psychiatric conditions linked to RBFOX1. However, the precise effects of RBFOX1 on the serotonergic system remain largely unexplored. Here we show that homozygous rbfox1sa15940 zebrafish, which express a shorter, aberrant rbfox1 mRNA, have significantly reduced serotonin levels in telencephalon and diencephalon. We observed that the acute administration of fluoxetine partially reverses the associated behavioural alterations. The hyperactive phenotype and altered shoaling behaviour of the rbfox1sa15940/sa15940 zebrafish could be reversed with acute fluoxetine exposure in the Open Field and the Shoaling test, respectively. However, in the other paradigms, hyperactivity was not diminished, suggesting a distinct intrinsic motivation for locomotion in the different paradigms. Acute fluoxetine exposure did not reverse the alterations observed in the aggression and social novelty tests, suggesting the involvement of other neurological mechanisms in these behaviours. These findings underscore the importance of investigating the intricate working mechanisms of RBFOX1 in neurodevelopmental and psychiatric disorders to gain a better understanding of the associated disorders along with their pharmacological treatment.
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Affiliation(s)
- Maja R. Adel
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Edurne Gago-Garcia
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Angela Arias-Dimas
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Rafael Artuch
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
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11
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Ajayi T, Thomas A, Nikolic M, Henderson L, Zaheri A, Dwyer DS. Evolutionary conservation of putative suicidality-related risk genes that produce diminished motivation corrected by clozapine, lithium and antidepressants. Front Psychiatry 2024; 15:1341735. [PMID: 38362034 PMCID: PMC10867104 DOI: 10.3389/fpsyt.2024.1341735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Background Genome wide association studies (GWAS) and candidate gene analyses have identified genetic variants and genes that may increase the risk for suicidal thoughts and behaviors (STBs). Important unresolved issues surround these tentative risk variants such as the characteristics of the associated genes and how they might elicit STBs. Methods Putative suicidality-related risk genes (PSRGs) were identified by comprehensive literature search and were characterized with respect to evolutionary conservation, participation in gene interaction networks and associated phenotypes. Evolutionary conservation was established with database searches and BLASTP queries, whereas gene-gene interactions were ascertained with GeneMANIA. We then examined whether mutations in risk-gene counterparts in C. elegans produced a diminished motivation phenotype previously connected to suicide risk factors. Results and conclusions From the analysis, 105 risk-gene candidates were identified and found to be: 1) highly conserved during evolution, 2) enriched for essential genes, 3) involved in significant gene-gene interactions, and 4) associated with psychiatric disorders, metabolic disturbances and asthma/allergy. Evaluation of 17 mutant strains with loss-of-function/deletion mutations in PSRG orthologs revealed that 11 mutants showed significant evidence of diminished motivation that manifested as immobility in a foraging assay. Immobility was corrected in some or all of the mutants with clozapine, lithium and tricyclic antidepressant drugs. In addition, 5-HT2 receptor and muscarinic receptor antagonists restored goal-directed behavior in most or all of the mutants. These studies increase confidence in the validity of the PSRGs and provide initial clues about possible mechanisms that mediate STBs.
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Affiliation(s)
- Titilade Ajayi
- Department of Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, United States
| | - Alicia Thomas
- Department of Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, United States
| | - Marko Nikolic
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
| | - Lauryn Henderson
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
| | - Alexa Zaheri
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
| | - Donard S. Dwyer
- Department of Pharmacology, Toxicology and Neuroscience, LSU Health Shreveport, Shreveport, LA, United States
- Department of Psychiatry and Behavioral Medicine, LSU Health Shreveport, Shreveport, LA, United States
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12
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Antón-Galindo E, Adel M, García-Gonzalez J, Leggieri A, López-Blanch L, Irimia M, Norton WHJ, Brennan CH, Fernàndez-Castillo N, Cormand B. Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in a zebrafish model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529711. [PMID: 36865197 PMCID: PMC9980121 DOI: 10.1101/2023.02.23.529711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
RBFOX1 is a highly pleiotropic gene that contributes to several psychiatric and neurodevelopmental disorders. Both rare and common variants in RBFOX1 have been associated with several psychiatric conditions, but the mechanisms underlying the pleiotropic effects of RBFOX1 are not yet understood. Here we found that, in zebrafish, rbfox1 is expressed in spinal cord, mid- and hindbrain during developmental stages. In adults, expression is restricted to specific areas of the brain, including telencephalic and diencephalic regions with an important role in receiving and processing sensory information and in directing behaviour. To investigate the effect of rbfox1 deficiency on behaviour, we used rbfox1sa15940, a rbfox1 loss-of-function line. We found that rbfox1sa15940 mutants present hyperactivity, thigmotaxis, decreased freezing behaviour and altered social behaviour. We repeated these behavioural tests in a second rbfox1 loss-of-function line with a different genetic background, rbfox1del19, and found that rbfox1 deficiency affects behaviour similarly in this line, although there were some differences. rbfox1del19 mutants present similar thigmotaxis, but stronger alterations in social behaviour and lower levels of hyperactivity than rbfox1sa15940 fish. Taken together, these results suggest that rbfox1 deficiency leads to multiple behavioural changes in zebrafish that might be modulated by environmental, epigenetic and genetic background effects, and that resemble phenotypic alterations present in Rbfox1-deficient mice and in patients with different psychiatric conditions. Our study thus highlights the evolutionary conservation of rbfox1 function in behaviour and paves the way to further investigate the mechanisms underlying rbfox1 pleiotropy on the onset of neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER), Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Institut de recerca Sant Joan de Déu, Espluges de Llobregat, Catalunya, 08950, Spain
| | - Maja Adel
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Judit García-Gonzalez
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
- Icahn School of Medicine, Mount Sinai, NYC 10029, USA
| | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Laura López-Blanch
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - William HJ Norton
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER), Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Institut de recerca Sant Joan de Déu, Espluges de Llobregat, Catalunya, 08950, Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER), Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Institut de recerca Sant Joan de Déu, Espluges de Llobregat, Catalunya, 08950, Spain
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13
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Karimi M, Mendez-Pineda S, Blanché H, Boland A, Besse C, Deleuze JF, Meng XY, Sirab N, Groussard K, Lebret T, Bonastre J, Allory Y, Radvanyi F, Benhamou S, Michiels S. A Case-Only Genome-Wide Interaction Study of Smoking and Bladder Cancer Risk: Results from the COBLAnCE Cohort. Cancers (Basel) 2023; 15:4218. [PMID: 37686494 PMCID: PMC10487226 DOI: 10.3390/cancers15174218] [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: 07/06/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 09/10/2023] Open
Abstract
Bladder cancer (BC) is the 6th most common cancer worldwide, with tobacco smoking considered as its main risk factor. Accumulating evidence has found associations between genetic variants and the risk of BC. Candidate gene-environment interaction studies have suggested interactions between cigarette smoking and NAT2/GSTM1 gene variants. Our objective was to perform a genome-wide association case-only study using the French national prospective COBLAnCE cohort (COhort to study BLAdder CancEr), focusing on smoking behavior. The COBLAnCE cohort comprises 1800 BC patients enrolled between 2012 and 2018. Peripheral blood samples collected at enrolment were genotyped using the Illumina Global Screening Array with a Multi-Disease drop-in panel. Genotyping data (9,719,614 single nucleotide polymorphisms (SNP)) of 1674, 1283, and 1342 patients were analyzed for smoking status, average tobacco consumption, and age at smoking initiation, respectively. A genome-wide association study (GWAS) was conducted adjusting for gender, age, and genetic principal components. The results suggest new candidate loci (4q22.1, 12p13.1, 16p13.3) interacting with smoking behavior for the risk of BC. Our results need to be validated in other case-control or cohort studies.
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Affiliation(s)
- Maryam Karimi
- Oncostat U1018 Inserm, Équipe Labellisée Ligue Contre le Cancer, Université Paris-Saclay, 94805 Villejuif, France
- Bureau de Biostatistique et d’Épidémiologie, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Sebastian Mendez-Pineda
- Oncostat U1018 Inserm, Équipe Labellisée Ligue Contre le Cancer, Université Paris-Saclay, 94805 Villejuif, France
| | - Hélène Blanché
- CEPH-Biobank, Fondation Jean Dausset-CEPH, 75010 Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057 Evry, France
| | - Céline Besse
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057 Evry, France
| | - Jean-François Deleuze
- CEPH-Biobank, Fondation Jean Dausset-CEPH, 75010 Paris, France
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057 Evry, France
| | | | - Nanor Sirab
- Curie Institute, CNRS, UMR144, Molecular Oncology Team, PSL Research University, 75005 Paris, France
| | - Karine Groussard
- Oncostat U1018 Inserm, Équipe Labellisée Ligue Contre le Cancer, Université Paris-Saclay, 94805 Villejuif, France
| | | | - Julia Bonastre
- Oncostat U1018 Inserm, Équipe Labellisée Ligue Contre le Cancer, Université Paris-Saclay, 94805 Villejuif, France
- Bureau de Biostatistique et d’Épidémiologie, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Yves Allory
- CNRS UMR144, Curie Institute, 75005 Paris, France
- UVSQ, Curie Institute, Department of Pathology, Université Paris-Saclay, 92210 Saint-Cloud, France
| | | | - Simone Benhamou
- Oncostat U1018 Inserm, Équipe Labellisée Ligue Contre le Cancer, Université Paris-Saclay, 94805 Villejuif, France
| | - Stefan Michiels
- Oncostat U1018 Inserm, Équipe Labellisée Ligue Contre le Cancer, Université Paris-Saclay, 94805 Villejuif, France
- Bureau de Biostatistique et d’Épidémiologie, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
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14
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Veneruso I, Ranieri A, Falcone N, Tripodi L, Scarano C, La Monica I, Pastore L, Lombardo B, D’Argenio V. The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data. Genes (Basel) 2023; 14:1651. [PMID: 37628702 PMCID: PMC10454493 DOI: 10.3390/genes14081651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual's carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale analyses. Here, we report the case of a couple who underwent ECS for a case of autism spectrum disorder in the male partner family. aCGH and whole-exome sequencing (WES) were performed in the couple. aCGH analysis identified in the female partner two deletions involving genes associated to behavioral and neurodevelopment disorders. No clinically relevant alterations were identified in the husband. Interestingly, WES analysis identified in the male partner a pathogenic variant in the LPL gene that is emerging as a novel candidate gene for autism. This case shows that ECS may be useful in clinical contexts, especially when both the partners are analyzed before conception, thus allowing the estimation of their risk to transmit an inherited condition. On the other side, there are several concerns related to possible incidental findings and difficult-to-interpret results. Once these limits are defined by the establishment of specific guidelines, ECS may have a greater diffusion.
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Affiliation(s)
- Iolanda Veneruso
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Annaluisa Ranieri
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Noemi Falcone
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Carmela Scarano
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Ilaria La Monica
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Barbara Lombardo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, via di Val Cannuta 247, 00166 Rome, Italy
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15
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Sagar R, Azoidis I, Zivko C, Xydia A, Oh ES, Rosenberg PB, Lyketsos CG, Mahairaki V, Avramopoulos D. Excitatory Neurons Derived from Human-Induced Pluripotent Stem Cells Show Transcriptomic Differences in Alzheimer's Patients from Controls. Cells 2023; 12:1990. [PMID: 37566069 PMCID: PMC10417412 DOI: 10.3390/cells12151990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
The recent advances in creating pluripotent stem cells from somatic cells and differentiating them into a variety of cell types is allowing us to study them without the caveats associated with disease-related changes. We generated induced Pluripotent Stem Cells (iPSCs) from eight Alzheimer's disease (AD) patients and six controls and used lentiviral delivery to differentiate them into excitatory glutamatergic neurons. We then performed RNA sequencing on these neurons and compared the Alzheimer's and control transcriptomes. We found that 621 genes show differences in expression levels at adjusted p < 0.05 between the case and control derived neurons. These genes show significant overlap and directional concordance with genes reported from a single-cell transcriptome study of AD patients; they include five genes implicated in AD from genome-wide association studies and they appear to be part of a larger functional network as indicated by an excess of interactions between them observed in the protein-protein interaction database STRING. Exploratory analysis with Uniform Manifold Approximation and Projection (UMAP) suggests distinct clusters of patients, based on gene expression, who may be clinically different. Our research outcomes will enable the precise identification of distinct biological subtypes among individuals with Alzheimer's disease, facilitating the implementation of tailored precision medicine strategies.
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Affiliation(s)
- Ram Sagar
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ioannis Azoidis
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Cristina Zivko
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ariadni Xydia
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Esther S. Oh
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Paul B. Rosenberg
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Constantine G. Lyketsos
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vasiliki Mahairaki
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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16
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Yotova AY, Li LL, O’Leary A, Tegeder I, Reif A, Courtney MJ, Slattery DA, Freudenberg F. Embryonic and adult synaptic proteome perturbations after maternal immune activation: Identification of persistent changes relevant for early intervention. RESEARCH SQUARE 2023:rs.3.rs-3100753. [PMID: 37461513 PMCID: PMC10350178 DOI: 10.21203/rs.3.rs-3100753/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Maternal infections during pregnancy pose an increased risk for neurodevelopmental psychiatric disorders (NPDs) in the offspring. Here, we examined age- and sex-dependent dynamic changes of the hippocampal synaptic proteome after maternal immune activation (MIA) in embryonic and adult mice. Adult male and female MIA offspring exhibited social deficits and sex-specific depression-like behaviours, among others, validating the model. Furthermore, we observed dose-, age-, and sex-dependent synaptic proteome differences. Analysis of the embryonic synaptic proteome implicates sphingolipid and ketoacid metabolism pathway disruptions during neurodevelopment for NPD-pertinent sequelae. In the embryonic hippocampus, prenatal immune activation also led to changes in neuronal guidance, glycosphingolipid metabolism important for signalling and myelination, and post-translational modification of proteins that regulate intercellular interaction and developmental timing. In adulthood, the observed changes in synaptoneurosomes revealed a dynamic shift toward transmembrane trafficking, intracellular signalling cascades, and hormone-mediated metabolism. Importantly, 68 of the proteins with differential abundance in the embryonic brains of MIA offspring were also altered in adulthood, 75% of which retained their directionality. These proteins are involved in synaptic organisation, neurotransmitter receptor regulation, and the vesicle cycle. A cluster of persistently upregulated proteins, including AKT3, PAK1/3, PPP3CA, formed a functional network enriched in the embryonic brain that is involved in cellular responses to environmental stimuli. To infer a link between the overlapping protein alterations and cognitive and psychiatric traits, we probed human phenome-wise association study data for cognitive and psychiatric phenotypes and all, but PORCN were significantly associated with the investigated domains. Our data provide insights into the dynamic effects of an early prenatal immune activation on developing and mature hippocampi and highlights targets for early intervention in individuals exposed to such immune challenges.
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Affiliation(s)
- Anna Y. Yotova
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Cell Biology and Neuroscience, Frankfurt, Germany
| | - Li-Li Li
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Turku Brain and Mind Center, University of Turku and Åbo Akademi University, 20014, Turku, Finland
| | - Aet O’Leary
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany
- Department of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Irmgard Tegeder
- Goethe University Frankfurt, Faculty of Medicine, Institute of Clinical Pharmacology, Frankfurt, Germany
| | - Andreas Reif
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany
| | - Michael J Courtney
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Turku Brain and Mind Center, University of Turku and Åbo Akademi University, 20014, Turku, Finland
| | - David A. Slattery
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany
| | - Florian Freudenberg
- Goethe University Frankfurt, University Hospital, Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Cell Biology and Neuroscience, Frankfurt, Germany
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Chung Y, Dienel S, Belch M, Fish K, Ermentrout G, Lewis D, Chung D. Altered Rbfox1-Vamp1 pathway and prefrontal cortical dysfunction in schizophrenia. RESEARCH SQUARE 2023:rs.3.rs-2944372. [PMID: 37398467 PMCID: PMC10312957 DOI: 10.21203/rs.3.rs-2944372/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Deficient gamma oscillations in prefrontal cortex (PFC) of individuals with schizophrenia appear to involve impaired inhibitory drive from parvalbumin-expressing interneurons (PVIs). Inhibitory drive from PVIs is regulated, in part, by RNA binding fox-1 homolog 1 (Rbfox1). Rbfox1 is spliced into nuclear or cytoplasmic isoforms, which regulate alternative splicing or stability of their target transcripts, respectively. One major target of cytoplasmic Rbfox1 is vesicle associated membrane protein 1 (Vamp1). Vamp1 mediates GABA release probability from PVIs, and the loss of Rbfox1 reduces Vamp1 levels which in turn impairs cortical inhibition. In this study, we investigated if the Rbfox1-Vamp1 pathway is altered in PVIs in PFC of individuals with schizophrenia by utilizing a novel strategy that combines multi-label in situ hybridization and immunohistochemistry. In the PFC of 20 matched pairs of schizophrenia and comparison subjects, cytoplasmic Rbfox1 protein levels were significantly lower in PVIs in schizophrenia and this deficit was not attributable to potential methodological confounds or schizophrenia-associated co-occurring factors. In a subset of this cohort, Vamp1 mRNA levels in PVIs were also significantly lower in schizophrenia and were predicted by lower cytoplasmic Rbfox1 protein levels across individual PVIs. To investigate the functional impact of Rbfox1-Vamp1 alterations in schizophrenia, we simulated the effect of lower GABA release probability from PVIs on gamma power in a computational model network of pyramidal neurons and PVIs. Our simulations showed that lower GABA release probability reduces gamma power by disrupting network synchrony while minimally affecting network activity. Finally, lower GABA release probability synergistically interacted with lower strength of inhibition from PVIs in schizophrenia to reduce gamma power non-linearly. Together, our findings suggest that the Rbfox1-Vamp1 pathway in PVIs is impaired in schizophrenia and that this alteration likely contributes to deficient PFC gamma power in the illness.
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18
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Koskinen MK, Hovatta I. Genetic insights into the neurobiology of anxiety. Trends Neurosci 2023; 46:318-331. [PMID: 36828693 DOI: 10.1016/j.tins.2023.01.007] [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: 09/15/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Anxiety and fear are evolutionarily conserved emotions that increase the likelihood of an organism surviving threatening situations. Anxiety and vigilance states are regulated by neural networks involving multiple brain regions. In anxiety disorders, this intricate regulatory system is disturbed, leading to excessive or prolonged anxiety or fear. Anxiety disorders have both genetic and environmental risk factors. Genetic research has the potential to identify specific genetic variants causally associated with specific phenotypes. In recent decades, genome-wide association studies (GWASs) have revealed variants predisposing to neuropsychiatric disorders, suggesting novel neurobiological pathways in the etiology of these disorders. Here, we review recent human GWASs of anxiety disorders, and genetic studies of anxiety-like behavior in rodent models. These studies are paving the way for a better understanding of the neurobiological mechanisms underlying anxiety disorders.
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Affiliation(s)
- Maija-Kreetta Koskinen
- SleepWell Research Program and Department of Psychology and Logopedics, Faculty of Medicine, PO Box 21, 00014, University of Helsinki, Helsinki, Finland
| | - Iiris Hovatta
- SleepWell Research Program and Department of Psychology and Logopedics, Faculty of Medicine, PO Box 21, 00014, University of Helsinki, Helsinki, Finland.
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Current Status of Oligonucleotide-Based Protein Degraders. Pharmaceutics 2023; 15:pharmaceutics15030765. [PMID: 36986626 PMCID: PMC10055846 DOI: 10.3390/pharmaceutics15030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Transcription factors (TFs) and RNA-binding proteins (RBPs) have long been considered undruggable, mainly because they lack ligand-binding sites and are equipped with flat and narrow protein surfaces. Protein-specific oligonucleotides have been harnessed to target these proteins with some satisfactory preclinical results. The emerging proteolysis-targeting chimera (PROTAC) technology is no exception, utilizing protein-specific oligonucleotides as warheads to target TFs and RBPs. In addition, proteolysis by proteases is another type of protein degradation. In this review article, we discuss the current status of oligonucleotide-based protein degraders that are dependent either on the ubiquitin–proteasome system or a protease, providing a reference for the future development of degraders.
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Kamran M, Laighneach A, Bibi F, Donohoe G, Ahmed N, Rehman AU, Morris DW. Independent Associated SNPs at SORCS3 and Its Protein Interactors for Multiple Brain-Related Disorders and Traits. Genes (Basel) 2023; 14:482. [PMID: 36833409 PMCID: PMC9956385 DOI: 10.3390/genes14020482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Sortilin-related vacuolar protein sorting 10 (VPS10) domain containing receptor 3 (SORCS3) is a neuron-specific transmembrane protein involved in the trafficking of proteins between intracellular vesicles and the plasma membrane. Genetic variation at SORCS3 is associated with multiple neuropsychiatric disorders and behavioural phenotypes. Here, we undertake a systematic search of published genome-wide association studies to identify and catalogue associations between SORCS3 and brain-related disorders and traits. We also generate a SORCS3 gene-set based on protein-protein interactions and investigate the contribution of this gene-set to the heritability of these phenotypes and its overlap with synaptic biology. Analysis of association signals at SORSC3 showed individual SNPs to be associated with multiple neuropsychiatric and neurodevelopmental brain-related disorders and traits that have an impact on the experience of feeling, emotion or mood or cognitive function, while multiple LD-independent SNPs were associated with the same phenotypes. Across these SNPs, alleles associated with the more favourable outcomes for each phenotype (e.g., decreased risk of neuropsychiatric illness) were associated with increased expression of the SORCS3 gene. The SORCS3 gene-set was enriched for heritability contributing to schizophrenia (SCZ), bipolar disorder (BPD), intelligence (IQ) and education attainment (EA). Eleven genes from the SORCS3 gene-set were associated with more than one of these phenotypes at the genome-wide level, with RBFOX1 associated with SCZ, IQ and EA. Functional annotation revealed that the SORCS3 gene-set is enriched for multiple ontologies related to the structure and function of synapses. Overall, we find many independent association signals at SORCS3 with brain-related disorders and traits, with the effect possibly mediated by reduced gene expression, resulting in a negative impact on synaptic function.
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Affiliation(s)
- Muhammad Kamran
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
| | - Farhana Bibi
- Department of Biosciences, Grand Asian University, Sialkot 51040, Pakistan
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
| | - Naveed Ahmed
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Asim Ur Rehman
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Derek W. Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
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