Distinct pathogenic genes causing intellectual disability and autism exhibit overlapping effects on neuronal network development

Abstract

An intriguing question in medical biology is how mutations in functionally distinct genes can lead to similar clinical phenotypes. For example, patients with mutations in distinct epigenetic regulators EHMT1, MBD5, MLL3 or SMARCB1 share the core clinical features of intellectual disability (ID), autism spectrum disorder (ASD) and facial dysmorphisms. To elucidate how these phenotypic similarities are reflected by convergence at the molecular, cellular and neuronal network level, we directly compared the effects of their loss of function in neurons. Interestingly, knockdown of each gene resulted in hyperactive neuronal networks with altered patterns of synchronized activity. At the single-cell level, we found genotype-specific changes in intrinsic excitability and excitatory-inhibitory balance, but in all cases leading to increased excitability. Congruent with our physiological findings, we identified dysregulated genes that converge on biological and cellular pathways related to neuronal excitability and synaptic function, including genes previously implicated in ID/ASD. Yet, our data suggests that the common cellular phenotypes depend on the ensemble of dysregulated genes engaged in neuronal excitability rather than the direction of transcriptional changes of individual genes. The demonstration of increasing convergence from molecular pathways to neuronal networks may be a paradigm for other types of ID/ASD.

The role of histone methyltransferases in neurocognitive disorders associated with brain size abnormalities

“…Therefore, convergent downstream mechanisms modulated by MLL1, MLL2, and MLL4 could lead to a reduced brain size. In contrast, knockdown of MLL3 in rat cortical neurons showed increased hyperactive neuronal networks which correlated with decreased inhibitory and excitatory synaptic puncta (Frega et al, 2020). However, MLL3 is widely expressed in developing human fetal brain which suggests that it could have additional important functions during human neuronal development (Nagase et al, 2000;Johnson et al, 2009).…”

“…H3K4me and H3K4me2 have been identified at enhancer regions leading to transcriptional activation (Hu et al, 2013). Pathogenic mutations in MLL3 are associated with Kleefstra syndrome, ID, behavioral problems, and epileptic seizures as its core features, while in some cases microcephaly is present (Kleefstra et al, 2012;Frega et al, 2020). Pathogenic variants in MLL3 were identified in large whole exon sequencing studies in patients with ASD (De Rubeis et al, 2014;Iossifov et al, 2014), and have been associated with an ID/ASD related syndrome that presents microcephaly in 50% of the cases reported (Koemans et al, 2017).…”

“…Introduction of frameshift mutations in MLL3/KMT2C by CRISPR/CAS9 genome editing in iPSC-derived neural stem cells render them unable to generate neurons (Cederquist et al, 2020). Work in other species suggests that MLL3/KMT2C might have additional roles outside of the control of neurogenesis, as knockdown of MLL3/KMT2C in rat primary neurons led to a hyperactive state of mature neuronal networks compared to control neurons (Frega et al, 2020). In Drosophila, knockdown of the MLL3/KMT2C homologue in the adult nervous system led to reduced short-term memory, but no effect on cell fate decisions or increase in cell death was observed (Koemans et al, 2017).…”

Comprehensive mapping of the AOP-Wiki database: identifying biological and disease gaps

“…ADHD was, on the other hand, associated with impaired synaptogenesis (KE ID 385) (Dark et al, 2018;Halperin et al, 2021). At last, the downstream KE 386 of the decreased neural network function is a hallmark of many cognitive disorders including fetal alcohol syndrome, ASD or intellectual disability amongst others (Uhlhaas and Singer, 2006;Frega et al, 2020;Adams et al, 2022;McCready et al, 2022). Mapping neurodevelopmental KE from AOPs to human NDD will increase certainty for their regulatory application.…”

Brunner syndrome associated MAOA dysfunction in human dopaminergic neurons results in NMDAR hyperfunction and increased network activity

“…Next to AMPAR mediated currents, NMDAR-mediated currents are an important component of balanced network activity both in vitro and in vivo, and changes in NMDAR function have been shown to affect network function in hiPSC-derived neuronal cultures (33,48). We therefore hypothesized that aberrant NMDAR function could be responsible for the hyperactive network phenotypes in the Brunner syndrome DA neurons.…”