Regulatory domain or CpG site variation in SLC12A5, encoding the chloride transporter KCC2, in human autism and schizophrenia

Abstract

Many encoded gene products responsible for neurodevelopmental disorders (NDs) like autism spectrum disorders (ASD), schizophrenia (SCZ), intellectual disability (ID), and idiopathic generalized epilepsy (IGE) converge on networks controlling synaptic function. An increase in KCC2 (SLC12A5) Cl− transporter activity drives the developmental GABA excitatory-inhibitory sequence, but the role of KCC2 in human NDs is essentially unknown. Here, we report two rare, non-synonymous (NS), functionally-impairing variants in the KCC2 C-terminal regulatory domain (CTRD) in human ASD (R952H and R1049C) and SCZ (R952H) previously linked with IGE and familial febrile seizures, and another novel NS KCC2 variant in ASD (R1048W) with highly-predicted pathogenicity. Exome data from 2517 simplex families in the ASD Simon Simplex Collection (SSC) revealed significantly more KCC2 CTRD variants in ASD cases than controls, and interestingly, these were more often synonymous and predicted to disrupt or introduce a CpG site. Furthermore, full gene analysis showed ASD cases are more likely to contain rare KCC2 variants affecting CpG sites than controls. These data suggest genetically-encoded dysregulation of KCC2-dependent GABA signaling may contribute to multiple human NDs.

Contribution of Resting Conductance, GABAA-Receptor Mediated Miniature Synaptic Currents and Neurosteroid to Chloride Homeostasis in Central Neurons

“…There is, however, no generally accepted view on the resting Cl – permeability or g Cl in central neurons. A low resting permeability has been suggested by Thompson et al (1988), but a significant conductance has been described in other studies (Forsythe and Redman, 1988; Sacchi et al, 1999; Müller, 2000). …”

“…This implies that the gain in speed of recovery contributed by KCC2 is not dramatic, if a sufficiently negative resting potential can be maintained. Nevertheless, KCC2 has been shown important for nervous function, with reduced KCC2 function being associated with several types of pathology, such as neuropathic pain (Coull et al, 2003), epilepsy (Huberfeld et al, 2007), autism (Tyzio et al, 2014; Merner et al, 2015), schizophrenia (Merner et al, 2015), spasticity (Boulenguez et al, 2010), and ischemia (Jaenisch et al, 2010). There are several possibilities as to why KCC2 may be needed despite substantial conductive recovery.…”

Opioid and nondopamine reward circuitry and state‐dependent mechanisms

“…GABA can act as an excitatory neurotransmitter in immature neurons because they have higher intracellular chloride ion concentrations compared with adult neurons, leading to depolarization instead of hyperpolarization . A shift from inhibitory to excitatory GABAergic neuron function may also be involved in several neurological and psychiatric disorders, including epilepsy, chronic pain, autism, and schizophrenia …”

Bio-collections in autism research

“…Both contribute 3 and 2% to ASD risk, respectively.[63]SSCLymphoblasts386 subjectsCNV studyRecurrent and rare de novo CNVs were discovered to alter gene expression in chromosome regions 3q27, 3p13, 3p26, 2p15, 16p11.2 and 7q11.23.[129]SSCIPSCs12 subjectsDisease modellingOverexpression of FOXG1 was linked to increased head circumference and ASD severity in idiopathic autism subjects. An overabundance of inhibitory neurons in ASD cell lines was also found.[319]SSCGenomic and clinical data2478 subjectsGene-environment studyIndividuals with ASD-associated CNVs were more susceptible to effects of febrile episodes and maternal infection during pregnancy and have impact on behavioural outcomes[320]SSCBlood10118 (TOTAL)1974 (SSC)Genetic associationHigher prevalence of SLC12A5 variants containing altered CpG sites amongst ASD patients.[321]SSCDNSBBlood2418 subjects (SSC)1353 subjects (DSNB)CNV analysis17q12 deletion identified as a CNV variant that confers high risk of ASD and Schizophrenia[322]SSCAGREGenomic data49167 subjects (total)1124 subjects (SSC)1835 subjects (AGRE)CNV analysisMore significant CNVs that could infer ASD risk were identified using combined large clinical datasets of neurodevelopmental disorders than with ASD cohorts alone[323]SSCLymphoblasts5451 subjectsAssociation studyNo association was found for heterozygous mutations in CNTNAP2 and contribution to ASD risk[324]SSCBlood and lymphoblastoid cell lines593 familiesMethod descriptionA novel method was used to detect de novo and transmitted insert-deletions(Intel’s) in exomic data[325]SSCBlood1315 subjects (total)145 subjects (SSC)CNV analysisDuplication CNVs enriched in negative regulation categories, deletion CNVs enriched in positive regulation categories. Highly connected genes in network enriched in patients with a single gene CNV change[65]SSCBlood677 subjects (SSC)WESDe novo mutations paternal in origin (4:1) and positive correlation with age.…”