Exome Sequencing and the Identification of New Genes and Shared Mechanisms in Polymicrogyria

Importance

Polymicrogyria is the most commonly diagnosed cortical malformation and is associated with neurodevelopmental sequelae including epilepsy, motor abnormalities, and cognitive deficits. Polymicrogyria frequently co-occurs with other brain malformations or as part of syndromic diseases. Past studies of polymicrogyria have defined heterogeneous genetic and nongenetic causes but have explained only a small fraction of cases.

Objective

To survey germline genetic causes of polymicrogyria in a large cohort and to consider novel polymicrogyria gene associations.

Design, Setting, and Participants

This genetic association study analyzed panel sequencing and exome sequencing of accrued DNA samples from a retrospective cohort of families with members with polymicrogyria. Samples were accrued over more than 20 years (1994 to 2020), and sequencing occurred in 2 stages: panel sequencing (June 2015 to January 2016) and whole-exome sequencing (September 2019 to March 2020). Individuals seen at multiple clinical sites for neurological complaints found to have polymicrogyria on neuroimaging, then referred to the research team by evaluating clinicians, were included in the study. Targeted next-generation sequencing and/or exome sequencing were performed on probands (and available parents and siblings) from 284 families with individuals who had isolated polymicrogyria or polymicrogyria as part of a clinical syndrome and no genetic diagnosis at time of referral from clinic, with sequencing from 275 families passing quality control.

Main Outcomes and Measures

The number of families in whom genetic sequencing yielded a molecular diagnosis that explained the polymicrogyria in the family. Secondarily, the relative frequency of different genetic causes of polymicrogyria and whether specific genetic causes were associated with co-occurring head size changes were also analyzed.

Results

In 32.7% (90 of 275) of polymicrogyria-affected families, genetic variants were identified that provided satisfactory molecular explanations. Known genes most frequently implicated by polymicrogyria-associated variants in this cohort were PIK3R2, TUBB2B, COL4A1, and SCN3A. Six candidate novel polymicrogyria genes were identified or confirmed: de novo missense variants in PANX1, QRICH1, and SCN2A and compound heterozygous variants in TMEM161B, KIF26A, and MAN2C1, each with consistent genotype-phenotype relationships in multiple families.

Conclusions and Relevance

This study's findings reveal a higher than previously recognized rate of identifiable genetic causes, specifically of channelopathies, in individuals with polymicrogyria and support the utility of exome sequencing for families affected with polymicrogyria.

Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements

Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.

Fingertip Skin Wrinkling – the Effect of Varying Tonicity

Fingertip skin wrinkling after prolonged immersion in water is a well-recognized phenomenon, whereas a denervated digit does not exhibit normal skin wrinkling while a finger with a regenerated or repaired nerve shows at least partial reappearance of wrinkling. This is the basis for the bedside immersion-wrinkling test of autonomic digital nerve function. The exact mechanism of fingertip skin wrinkling is still subject to controversy. The purpose of this study was to investigate the relationship between the tonicity of a solution and the time elapsed to skin wrinkling. Fourteen healthy volunteers (28 hands) were recruited for investigation. We submerged all 28 hands in solutions of varying tonicity while maintaining all other parameters constant. We found that increased tonicity significantly slowed the time to wrinkling (TTW). Hypotonic solutions such as water should be used when performing clinical bedside testing for autonomic digital nerve function.

The potential of cinnamon to reduce blood glucose levels in patients with type 2 diabetes and insulin resistance

AIM

Cinnamon has a long history as an antidiabetic spice, but trials involving cinnamon supplementation have produced contrasting results. The aim of this review was to examine the results of randomized controlled clinical trials of cinnamon and evaluate the therapeutic potential amongst patients with diabetes and insulin-resistant patients, particularly the ability to reduce blood glucose levels and inhibit protein glycation.

METHODS

A systematic electronic literature search using the medical subject headings 'cinnamon' and 'blood glucose' was carried out to include randomized, placebo-controlled in vivo clinical trials using Cinnamomum verum or Cinnamomum cassia conducted between January 2003 and July 2008.

RESULTS

Five type 2 diabetic and three non-diabetic studies (total N = 311) were eligible. Two of the diabetic studies illustrated significant fasting blood glucose (FBG) reductions of 18-29% and 10.3% (p < 0.05), supported by one non-diabetic trial reporting an 8.4% FBG reduction (p < 0.01) vs. placebo, and another illustrating significant reductions in glucose response using oral glucose tolerance tests (p < 0.05). Three diabetic studies reported no significant results.

CONCLUSIONS

Whilst definitive conclusions cannot be drawn regarding the use of cinnamon as an antidiabetic therapy, it does possess antihyperglycaemic properties and potential to reduce postprandial blood glucose levels. Further research is required to confirm a possible correlation between baseline FBG and blood glucose reduction and to assess the potential to reduce pathogenic diabetic complications with cinnamon supplementation.

Interaction between mycobacteria and mucus on a human respiratory tissue organ culture model with an air interface

Mycobacteria adhere specifically to extracellular matrix (ECM) and mucus with a fibrous, but not globular, appearance, in organ cultures of human respiratory mucosa examined by scanning electron microscopy. Previously, light microscopy sections made of tissue infected for 7 days demonstrated mycobacteria associated with mucus on the organ culture surface, and within submucosal glands in areas of damaged epithelium. The authors have now investigated the interactions between Mycobacterium avium complex (MAC), Mycobacterium tuberculosis (MTB), and Mycobacterium smegmatis (MS) and mucus by preincubating bacteria with purified mucins MUC5AC and MUC5B prior to inoculation onto the organ culture mucosal surface. They have also measured mucin production by the organ culture after mycobacterial infection. Mucus did not cause clumping of mycobacteria. There was a significant (P=.03) increase in the amount of fibrous mucus, but not globular mucus, observed on tissue inoculated with mucins compared to controls. The number of bacteria adhering to ECM was markedly reduced after incubation with mucins, which could indicate a protective effect. Mycobacterial infection did not increase mucin production by the organ culture. Mycobacterial adherence to mucins may play a role in the pathogenicity of mycobacteria in diseases such as cystic fibrosis, bronchiectasis, and chronic obstructive pulmonary disease (COPD), in which there are changes in mucus composition and clearance.

Regulation of MUC5AC mucin secretion and airway surface liquid metabolism by IL-1beta in human bronchial epithelia

Mucociliary transport in the airways significantly depends on the liquid and mucin components of the airway surface liquid (ASL). The regulation of ASL water and mucin content during pathological conditions is not well understood. We hypothesized that airway epithelial mucin production and liquid transport are regulated in response to inflammatory stimuli and tested this hypothesis by investigating the effects of the pleiotropic, early-response cytokine, IL-1beta, on cultured primary human bronchial epithelial and second-passage, normal human tracheo-bronchial epithelial (NHTBE) cell cultures. Fully differentiated NHTBE cultures secreted two major airway mucins, MUC5AC and MUC5B. IL-1beta, in a dose- and time-dependent manner, increased the secretion of MUC5AC, but not MUC5B. MUC5AC mRNA levels were only transiently increased at 1 and 4 h after the start of IL-1beta treatment and returned to control levels thereafter, even though MUC5AC mucin production remained elevated for at least 72 h. Synchronous with elevated MUC5AC secretion, ASL volume increased, its percentage of solid was reduced, and the pH/[HCO(3)(-)] of the ASL was elevated. ASL volume changes reflected altered ion transport, including an upregulation of Cl(-) secretory currents (via CFTR and Ca(2+)-activated Cl(-) conductance) and an inhibition of epithelial sodium channel (ENaC)-mediated absorptive Na(+) currents. IL-1beta increased CFTR mRNA levels without affecting those for ENaC subunits. The synchronous regulation of ASL mucin and liquid metabolism triggered by IL-1beta may be an important defense mechanism of the airway epithelium to enhance mucociliary clearance during airway inflammation.

Identification of a nonmucin glycoprotein (gp-340) from a purified respiratory mucin preparation: evidence for an association involving the MUC5B mucin

Rate-zonal centrifugation of a reduced and alkylated respiratory mucin preparation identified a protein-rich fraction. This was subjected to trypsin treatment and one of the many liberated peptides was purified and its N-terminal sequence determined. The peptide was identical to a 14 amino acid sequence from the scavenger receptor cysteine-rich domain containing glycoprotein gp-340. A polyclonal antiserum, raised against the peptide, stained the serous cells in the submucosal glands of human tracheal tissue. The glycoprotein was purified from respiratory mucus by density-gradient centrifugation, gel chromatography, and anion exchange chromatography. The molecule exhibited a heterogeneous distribution of buoyant density (1.28-1.46 g/ml) that overlapped with the gel-forming mucins, was included on Sepharose CL-2B and was quite highly anionic. SDS-PAGE indicated a mass greater than 208 kDa and measurements performed across the molecular size distribution indicated an average M(r) of 5 x 10(5) with a range of M(r) from 2 x 10(5) to 1 x 10(6). Gel chromatography of respiratory mucus extracts ("associative" and "dissociative") indicated that this glycoprotein forms complexes that may involve the large gel-forming mucins MUC5AC and MUC5B. Rate zonal centrifugation suggested such complexes are more likely to involve MUC5B rather than MUC5AC mucins.

Physical characterization of the MUC5AC mucin: a highly oligomeric glycoprotein whether isolated from cell culture or in vivo from respiratory mucous secretions

We have isolated the high-M(r) mucins from growth medium of the early stage of an HT-29 cell culture by gel chromatography and isopycnic density gradient centrifugation. The mucins (buoyant density 1.34-1.44 g/ml) were reactive with an anti-peptide antiserum (MAN-5ACI) raised against a sequence from within the MUC5AC mucin. Similar antisera raised against the MUC2 and MUC5B mucins were not reactive. The MUC5AC reduced-mucin subunits exhibited a homogeneous charge distribution on anion-exchange chromatography, but appeared as two bands, one major and one more minor, after agarose gel electrophoresis. The unreduced mucins had an average M(r) in excess of 40 MDa and were visualized in the electron microscope as large, fine filamentous threads (many microns in length) that after reduction were greatly reduced in size (number average length 570 nm). Agarose gel electrophoresis of unreduced MUC5AC mucins identified a major band just entering the gel with evidence of a 'ladder' of faster-migrating minor bands. Partial reduction of the mucins increased the proportion of the faster bands and at least 16 could be discriminated. M(r) measurements showed that these bands differed by single monomer units. The mucins behaved as very stiff extended structures in solution and this characteristic might explain the poor separation of different-sized oligomers in sedimentation-rate experiments. The cell-culture mucin preparation had similar characteristics of charge and buoyant density to MUC5AC mucins from respiratory secretions in vivo. In addition the MUC5AC mucin from respiratory tract secretions exhibited similar behaviour, reduced and unreduced on agarose gel electrophoresis, indicating that the mucin has a similar molecular phenotype in vivo and in vitro.

The effect of atrial natriuretic peptides on ion transport by muscle-stripped and full-thickness preparations of rat colon

The effects of three atrial natriuretic peptides (ANPs) have been tested for their ability to increase ion transport in muscle-stripped and intact preparations of rat colon. Anaritide (fragment 4-28 of human ANP), human ANP and rat atriopeptin III had no effect on short-circuit current in muscle-stripped preparations. Such insensitivity could not be explained by desensitisation, enzymic destruction or non-specific absorption. Short-circuit current was increased by 8-Br-cGMP and NaNP. The pharmacological activity of anaritide was demonstrated by abolition of phenylephrine-induced tone in rat aortic smooth muscle. In contrast to muscle-stripped colon, intact preparations responded with a tetrodotoxin-sensitive increase in short-circuit current to anaritide even though such preparations were less sensitive to acetylcholine and substance P. These results imply that selective neural damage or the lack of certain nerve pathways, caused by complete muscle stripping, will prevent the pro-secretory effects of anaritide in rat colon.