Gain-of-function GABRB3 variants identified in vigabatrin-hypersensitive epileptic encephalopathies

Variants in the GABRB3 gene encoding the b3-subunit of the c-aminobutyric acid type A ( receptor are associated with various developmental and epileptic encephalopathies. Typically, these variants cause a loss-of-function molecular phenotype whereby c-aminobutyric acid has reduced inhibitory effectiveness leading to seizures. Drugs that potentiate inhibitory GABAergic activity, such as nitrazepam, phenobarbital or vigabatrin, are expected to compensate for this and thereby reduce seizure frequency. However, vigabatrin, a drug that inhibits c-aminobutyric acid transaminase to increase tonic c-aminobutyric acid currents, has mixed success in treating seizures in patients with GABRB3 variants: some patients experience seizure cessation, but there is hypersensitivity in some patients associated with hypotonia, sedation and respiratory suppression. A GABRB3 variant that responds well to vigabatrin involves a truncation variant (p.Arg194*) resulting in a clear loss-of-function. We hypothesized that patients with a hypersensitive response to vigabatrin may exhibit a different c-aminobutyric acid A receptor phenotype. To test this hypothesis, we evaluated the phenotype of de novo variants in GABRB3 (p.Glu77Lys and p.Thr287Ile) associated with patients who are clinically hypersensitive to vigabatrin. We introduced the GABRB3 p.Glu77Lys and p.Thr287Ile variants into a concatenated synaptic and extrasynaptic caminobutyric acid A receptor construct, to resemble the c-aminobutyric acid A receptor expression by a patient heterozygous for the GABRB3 variant. The mRNA of these constructs was injected into Xenopus oocytes and activation properties of each receptor measured by two-electrode voltage clamp electrophysiology. Results showed an atypical gain-of-function molecular phenotype in the GABRB3 p.Glu77Lys and p.Thr287Ile variants characterized by increased potency of c-aminobutyric acid A without change to the estimated maximum open channel probability, deactivation kinetics or absolute currents. Modelling of the activation properties of the receptors indicated that either variant caused increased chloride flux in response to low concentrations of c-aminobutyric acid that mediate tonic currents. We therefore propose that the hypersensitivity reaction to vigabatrin is a result of GABRB3 variants that exacerbate GABAergic tonic currents and caution is required when prescribing vigabatrin. In contrast, drug strategies increasing tonic currents in loss-of-function variants are likely to be a safe and effective therapy. This study demonstrates that functional genomics can explain beneficial and adverse anti-epileptic drug effects, and propose that vigabatrin should be considered in patients with clear loss-of-function GABRB3 variants

RLIM Is a candidate dosage-sensitive gene for individuals with varying duplications of Xq13, intellectual disability, and distinct facial features

Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.Elizabeth E. Palmer, Renee Carroll, Marie Shaw, Raman Kumar, Andre E. Minoche, Melanie Leffler, Lucinda Murray, Rebecca Macintosh, Dale Wright, Chris Troedson, Fiona McKenzie, Sharron Townshend, Michelle Ward, Urwah Nawaz, Anja Ravine, Cassandra K. Runke, Erik C. Thorland, Marybeth Hummel, Nicola Foulds, Olivier Pichon, Bertrand Isidor, Cédric Le Caignec, Bénédicte Demeer, Joris Andrieux, Salam Hadah Albarazi, Ann Bye, Rani Sachdev, Edwin P. Kirk, Mark J. Cowley, Mike Field, and Jozef Gec

RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features

Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males

Geomorphology and surficial sediments of the southeast Australian continental margin

The southeast Australian continental margin stretches 1500 km north from Bass Strait to the Great Barrier Reef. This part of the Australian margin represents a distinct oceanographic, climatic and geological province. Recent initiatives by the Australian Hydrographic Office, Geoscience Australia and the Environmental Geoscience Group at the University of Newcastle have provided a new digital database of bathymetric soundings and surface-sediment distribution for the southeast Australian margin. This database is used here to provide the first detailed digital 3-D representations of the southeast Australian margin, leading to new morphological classifications and integrated sedimentation models. As a result of its tectonic history of asymmetric passive margin rifting, the continental margin as a whole is narrow, steep and sediment deficient. The shelf can be divided into an inner zone with bedrock cropping out or close to the surface, and an outer zone that represents the top of a Cenozoic sediment wedge. The continental shelf and slope can be classified into a variety of morphological units based on detailed analysis of geometry and slope. These units include a succession of shore-normal zones (shoreface, inner plain, inner and mid-slope, outer plain and continental slope) and a number of local regions (mounds, lobes, tongues, depressions, deltas and bedrock). Sediments are generally siliciclastic in composition on the inner margin and carbonate-rich on the outer margin, reflecting carbonate production at low sea-levels on the outer shelf/continental slope and terrestrial sediment input to the inner shelf. Fine-grained sediments are rare on the shelf north from Port Stephens, and occur draped across the inner and mid-slope further south. Outer shelf carbonate sediments are coarse grained with a patchy distribution related to winnowing by the East Australian Current. The East Australian Current also produces erosional depressions and southward prograding sediment tongues and lobes where it separates from the shelf off Port Stephens. The margin character varies markedly from south to north in terms of fine-sediment distribution, depth to the shelf break and width of the outer shelf. These outer shelf features reflect an inherited palaeotopography from underlying Cenozoic sediment wedges that are better developed on the southern margin

Biochemical basis of resistance to pod borer ( Helicoverpa armigera ) in Australian wild relatives of pigeonpea

The domestication of pigeonpea has severely impacted the intrinsic host-plant resistance (HPR) to pest and diseases, particularly pod borer (Helicoverpa armigera hubner). This study with 41 Australian wild Cajanus genotypes and interspecific hybrids demonstrated a high level of resistance to H. armigera in the accessions of Cajanus acutifolius, C. latisepalus, C. lanceolatus, C. pubescens, and C. reticulatus var. reticulatus. Significant variation in herbivory development and mortality (P < 0.001) was observed in the wild accessions and their hybrids in response to feeding on leaves. A strong positive relationship (R2 = 0.69, P < 0.001) between total phenolic compounds (TPC) and the HPR was observed. Australian wild genotypes demonstrated the role of TPC and the absence of certain flavonoids such as rutin and quercetin in resistant genotypes. The detached leaf bioassay technique separated the wild and domesticated accessions into wild resistant, with herbivory weight difference (HWD) (Day 7–Day 1) ranging between −27 - 104 mg, wild susceptible, with HWD ranging between 124 - 207 mg and domesticated susceptible, with HWD ranging from 208 - 300 mg. Similarly, based on TPC, accessions were also categorised into wild high TPC, with TPC ranging between 32.3 - 42.5 GAE mg/g DW, and wild low TPC had only 17.2–24.8 GAE mg/g DW. Low TPC concentrations were found in domesticated pigeonpea, with 10.7–17.6 GAE mg/g DW. The presence of very high concentrations of the flavone isoorientin, an important antioxidant implicated in the intracellular defence mechanism of cancer therapy, was identified for the first time in wild species of pigeonpea