Neuronal impact of patient-specific aberrant NRXN1α splicing

Abstract

NRXN1 undergoes extensive alternative splicing, and non-recurrent heterozygous deletions in NRXN1 are strongly associated with neuropsychiatric disorders. We establish that human induced pluripotent stem cell (hiPSC)-derived neurons represent well the diversity of NRXN1α alternative splicing observed in the human brain, cataloguing 123 high-confidence in-frame human NRXN1α isoforms. Patient-derived NRXN1 +/− hiPSC-neurons show greater than two-fold reduction of half of the wild-type NRXN1α isoforms and express dozens of novel isoforms expressed from the mutant allele. Reduced neuronal activity in patient-derived NRXN1 +/− hiPSC-neurons is ameliorated by overexpression of individual control isoforms in a genotype-dependent manner, whereas individual mutant isoforms decrease neuronal activity levels in control hiPSC-neurons. In a genotype-dependent manner, the phenotypic impact of patient-specific NRXN1 +/− mutations can occur through a reduction in wild-type NRXN1α isoform levels as well as the presence of mutant NRXN1α isoforms.

Human in vitro models for understanding mechanisms of autism spectrum disorder

“…Two kinds of genetic modeling have been performed using cells either from individuals whose genetic contributions are unknown or undefined, so called idiopathic [59,60,[112][113][114][115][116][117][118][119][120], or from individuals harboring major effect mutations that are presumed causal or which have been engineered to carry these mutations. These mutations include ASD-associated CNVs such as 15q11q13 deletion (Angelman syndrome) [121] and duplication (Dup15q syndrome) [122], 22q11.2 deletion (DiGeorge syndrome) [123,124], 16p11.2 deletion and duplication [125], and 15q13.3 deletion [126], as well as single-gene mutations including SHANK3 [127][128][129][130], CHD8 [131,132], NRXN1 [133][134][135][136][137], NLGN4 [138], EHMT1 (Kleefstra syndrome) [139], PTCHD1-AS [140], UBE3A (Angelman's syndrome) [141], and CACNA1C (Timothy syndrome) [142] (summarized in Table 1). In this review, we will not discuss fragile X syndrome, Rett's syndrome, and tuberous sclerosis-related autism as they have all been extensively reviewed previously [148][149][150][151][152][153][154].…”

“…Several genetic forms of ASD show a decrease in the number of neurons and synapses, including Timothy syndrome-in which there was a decrease in the fraction of neurons expressing lower layer markers [142] and 22q11.2 deletion, which showed a reduced number of neurons accompanied by an increase in the number of astrocytes [124]. Three studies on NRXN1 mutations also found evidence for a decrease in neuronal maturation [134,135,137], a finding which was not replicated in a different study [136]. Similar results (downregulation of neuronal processes) were indirectly observed using transcriptomic analysis from neurons in which CHD8 was either knocked down [132] or heterozygously deleted [131].…”

“…Dysregulation in neuronal differentiation and synaptic and dendritic deficits may underlie the decreased spontaneous activity and decreased excitability found in many studies. These are often observed in neurons derived from individuals with idiopathic forms of ASD [112,116,167], as well as from individuals with genetically defined forms of ASD such as SHANK3 [127,130], 16p11.2 deletion and duplication [125], Angelman syndrome [121], Dup15q syndrome [122], NRXN1 mutations [133,135,137], and PTCHD1-AS [140]. Decreases in spontaneous neuronal activity were also found in five out of ten genes associated with ASD when mutations were introduced into neurons derived from typically developing individuals (ATRX, AFF2, KCNQ2, SCN2A, and ASTN2; see Table 1 for the full list of genes tested) [147].…”

Focus on Causality in ESC/iPSC-Based Modeling of Psychiatric Disorders

“…This process occurs in a partly cell type-dependent manner, raising the prospect that the resultant protein isoforms may distinguish between post-synaptic binding partners to regulate specific synaptic function [47]. To explore whether this process contributes to neuropathology in carriers of heterozygous intragenic NRXN1 deletions, Flaherty et al [45] established iPSCs from four carriers with major psychiatric disorders, three with early onset, and three healthy controls. Advanced sequencing methods were applied to integrate targeted long-and short-read sequencing data, and to establish NRXN1a isoform catalogues in human postmortem brain and across iPSC-derived isogenic glutamatergic or GABAergic (γ-aminobutyric acid) iNs.…”

KRSA: Network-based Prediction of Differential Kinase Activity from Kinome Array Data

“…This method has been applied to multiple datasets and predictions have been experimentally validated in our laboratory through individual kinase activity assays and inhibitor studies (Bentea et al, 2019;Bentea et al, 2020;Dorsett et al, 2017;Flaherty et al, 2019;McGuire et al, 2017;Schrode et al, 2019). An early version of KRSA, containing only the random sampling algorithm, identified altered phosphorylation of peptides and subsequently perturbed kinase activity in the anterior cingulate cortex (ACC) between schizophrenia and control subjects (McGuire et al, 2017).…”