Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome

Abstract

BackgroundCommon genetic variation and rare mutations in genes encoding calcium channel subunits have pleiotropic effects on risk for multiple neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia. To gain further mechanistic insights by extending previous gene expression data, we constructed co-expression networks in Timothy syndrome (TS), a monogenic condition with high penetrance for ASD, caused by mutations in the L-type calcium channel, Cav1.2.MethodsTo identify patient-specific alterations in transcriptome organization, we conducted a genome-wide weighted co-expression network analysis (WGCNA) on neural progenitors and neurons from multiple lines of induced pluripotent stem cells (iPSC) derived from normal and TS (G406R in CACNA1C) individuals. We employed transcription factor binding site enrichment analysis to assess whether TS associated co-expression changes reflect calcium-dependent co-regulation.ResultsWe identified reproducible developmental and activity-dependent gene co-expression modules conserved in patient and control cell lines. By comparing cell lines from case and control subjects, we also identified co-expression modules reflecting distinct aspects of TS, including intellectual disability and ASD-related phenotypes. Moreover, by integrating co-expression with transcription factor binding analysis, we showed the TS-associated transcriptional changes were predicted to be co-regulated by calcium-dependent transcriptional regulators, including NFAT, MEF2, CREB, and FOXO, thus providing a mechanism by which altered Ca2+ signaling in TS patients leads to the observed molecular dysregulation.ConclusionsWe applied WGCNA to construct co-expression networks related to neural development and depolarization in iPSC-derived neural cells from TS and control individuals for the first time. These analyses illustrate how a systems biology approach based on gene networks can yield insights into the molecular mechanisms of neural development and function, and provide clues as to the functional impact of the downstream effects of Ca2+ signaling dysregulation on transcription.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-014-0075-5) contains supplementary material, which is available to authorized users.

Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops

“…Abnormalities were observed in neuronal precursors derived from individuals with Timothy syndrome; the expression of >200 genes were altered, many of them CREB-dependent (Pasca et al, 2011). When subjected to an unbiased systems biology analysis (Tian et al, 2014), the pattern of differences in gene expression was compatible with involvement of known Ca 2+ -dependent transcriptional regulators, including CREB, NFAT, MEF2, and FOXO. The analysis uncovered Ca 2+ -dependent co-expression modules that reflect distinct aspects of TS, including intellectual disability and ASD-related phenotypes.…”

“…In turn, this organization spurs us to offer some fresh perspective to multiple themes in ASD research. With respect to signaling from synapse to nucleus (Ebert and Greenberg, 2013), we reopen the question of how cascades of ASD-related proteins (Ma et al, 2014) may control the expression of other ASD-related genes (Tian et al, 2014). Regarding synaptic plasticity by local regulation of protein synthesis (Aguilar-Valles et al, 2015; Fernandez et al, 2013; Kelleher and Bear, 2008; Kelleher et al, 2004; Niere et al, 2012), we meld the concept of coordination amongst neighboring dendritic synapses (Bourne and Harris, 2012; Rabinowitch and Segev, 2008) with ideas about ASD as dysfunctional homeostasis (Huguet et al, 2013; Ramocki and Zoghbi, 2008; Toro et al, 2010).…”

The Emerging Roles of the Calcineurin-Nuclear Factor of Activated T-Lymphocytes Pathway in Nervous System Functions and Diseases

“…A more recent genome-wide weighted coexpression network analysis on neural progenitors and neurons from individuals with Timothy syndrome, an autism spectrum disorder resulting from mutations in the gene encoding L-type CaV1.2 Ca 2+ channels, suggested that the disease may be caused by disturbances in transcriptional activities of Ca 2+ -dependent signaling molecules like FOX proteins, MEF2, CREB, and NFATs [247]. …”

Human induced pluripotent stem cells for modelling neurodevelopmental disorders

“…HiPSCs derived from these patients had abnormal differentiation tendencies and differentiated neurons had reduced expression of genes marking lower cortical layers and callosal projection neurons. The same group later used a bioinformatics approach, integrating co-expression network analysis and transcription factor binding analysis, to provide mechanisms by which altered calcium signaling generates altered level of calcium-dependent transcriptional regulators leading to the transcriptional network changes observed in TS patient-derived neurons 113 . Another group reported that hiPSC-derived neurons from individuals with Timothy syndrome have activity-dependent dendrite retraction 114 .…”