Integrative Analysis Identifies Key Molecular Signatures Underlying Neurodevelopmental Deficits in Fragile X Syndrome

BACKGROUND

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by epigenetic silencing of FMR1 and loss of FMRP expression. Efforts to understand the molecular underpinnings of the disease have been largely performed in rodent or nonisogenic settings. A detailed examination of the impact of FMRP loss on cellular processes and neuronal properties in the context of isogenic human neurons remains lacking.

METHODS

Using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 to introduce indels in exon 3 of FMR1, we generated an isogenic human pluripotent stem cell model of FXS that shows complete loss of FMRP expression. We generated neuronal cultures and performed genome-wide transcriptome and proteome profiling followed by functional validation of key dysregulated processes. We further analyzed neurodevelopmental and neuronal properties, including neurite length and neuronal activity, using multielectrode arrays and patch clamp electrophysiology.

RESULTS

We showed that the transcriptome and proteome profiles of isogenic FMRP-deficient neurons demonstrate perturbations in synaptic transmission, neuron differentiation, cell proliferation and ion transmembrane transporter activity pathways, and autism spectrum disorder-associated gene sets. We uncovered key deficits in FMRP-deficient cells demonstrating abnormal neural rosette formation and neural progenitor cell proliferation. We further showed that FMRP-deficient neurons exhibit a number of additional phenotypic abnormalities, including neurite outgrowth and branching deficits and impaired electrophysiological network activity. These FMRP-deficient related impairments have also been validated in additional FXS patient-derived human-induced pluripotent stem cell neural cells.

CONCLUSIONS

Using isogenic human pluripotent stem cells as a model to investigate the pathophysiology of FXS in human neurons, we reveal key neural abnormalities arising from the loss of FMRP.

Glutaminase Deficiency Caused by Short Tandem Repeat Expansion in GLS

We report an inborn error of metabolism caused by an expansion of a GCA-repeat tract in the 5' untranslated region of the gene encoding glutaminase (GLS) that was identified through detailed clinical and biochemical phenotyping, combined with whole-genome sequencing. The expansion was observed in three unrelated patients who presented with an early-onset delay in overall development, progressive ataxia, and elevated levels of glutamine. In addition to ataxia, one patient also showed cerebellar atrophy. The expansion was associated with a relative deficiency of GLS messenger RNA transcribed from the expanded allele, which probably resulted from repeat-mediated chromatin changes upstream of the GLS repeat. Our discovery underscores the importance of careful examination of regions of the genome that are typically excluded from or poorly captured by exome sequencing.

Reversal of Phenotypic Abnormalities by CRISPR/Cas9-Mediated Gene Correction in Huntington Disease Patient-Derived Induced Pluripotent Stem Cells

Huntington disease (HD) is a dominant neurodegenerative disorder caused by a CAG repeat expansion in HTT. Here we report correction of HD human induced pluripotent stem cells (hiPSCs) using a CRISPR-Cas9 and piggyBac transposon-based approach. We show that both HD and corrected isogenic hiPSCs can be differentiated into excitable, synaptically active forebrain neurons. We further demonstrate that phenotypic abnormalities in HD hiPSC-derived neural cells, including impaired neural rosette formation, increased susceptibility to growth factor withdrawal, and deficits in mitochondrial respiration, are rescued in isogenic controls. Importantly, using genome-wide expression analysis, we show that a number of apparent gene expression differences detected between HD and non-related healthy control lines are absent between HD and corrected lines, suggesting that these differences are likely related to genetic background rather than HD-specific effects. Our study demonstrates correction of HD hiPSCs and associated phenotypic abnormalities, and the importance of isogenic controls for disease modeling using hiPSCs.

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.

In vitro genesis of subaxial cervical unilateral facet dislocations through sequential soft tissue ablation

STUDY DESIGN

In vitro anatomic study investigating the degree of soft tissue disruption required to produce a subaxial cervical unilateral facet dislocation.

OBJECTIVES

To develop an understanding of the relative contributions to stability of the subaxial cervical soft tissues and to define an anatomic threshold of injury necessary to produce a unilateral cervical facet dislocation.

SUMMARY OF BACKGROUND DATA

The literature at this time is unclear regarding the precise pathomechanics of a cervical unilateral facet dislocation and the required threshold of soft tissue injury necessary for its genesis. Published clinical reports do not make any specific reference to these factors or are unclear in their objectivity.

METHODS

Two adjacent vertebra at a time in 10 fresh-frozen subaxial cervical spine specimens (C2-C3 to C6-C7) were transfixed in the coronal plane with 3.5-mm Schanz screws. A steady unilateral vertical distraction force resulting in lateral cervical flexion was applied to these screws as the surrounding cervical soft tissue structures were sequentially ablated. Four experimental models were developed, varying the order of soft tissue disruption.

RESULTS

The physiologic coupling of subaxial cervical unilateral distraction and rotation, because of the spatial orientation or inclination of the cervical facet joints, allowed the creation of a unilateral facet dislocation without an additional flexion moment. Disruption of the ipsilateral articular capsule, ligamentum flavum, and more than half of the anulus fibrosus was necessary for the genesis of a unilateral facet dislocation. Disruption of the supraspinous and interspinous ligaments was not necessary but appeared to facilitate or lessen the force required to dislocate a unilateral facet. Disruption of the anterior and posterior longitudinal ligaments and intertransverse ligaments was not necessary to create a unilateral facet dislocation.

CONCLUSION

This anatomic study further supports the theory that discontinuity of the anterior and posterior longitudinal ligaments is not necessary for a unilateral facet dislocation to occur. The ipsilateral facet capsule, anulus fibrosus, and ligamentum flavum appear to be the physical soft tissue restraints that need to be disrupted to produce a unilateral facet dislocation.

The influence of gamma irradiation and aging on degradation mechanisms of ultra-high molecular weight polyethylene

The aging behavior of ultra-high molecular weight polyethylene (UHMWPE) has been studied following gamma irradiation in air. Accelerated aging procedures used elevated temperature (70 degrees C), pressurized oxygen (5 bar) and applied stress. Shelf and in vivo aged components have also been investigated. The variation in polymer properties with depth into the polymer was determined using density measurements, infra-red spectroscopy and differential scanning calorimetry. Accelerated aging in pressurized oxygen resulted in peaks in polymer density and degree of oxidation up to 500 microm below the polymer surface. Shelf and in vivo aging was also found to result in increased density at or below the component surfaces. Changes in density were mainly due to changes in crystallinity within the UHMWPE and, to a smaller extent, due to oxygen incorporation within the polymer. The application of stress did not appear to influence the accelerated aging of UHMWPE. A method for estimating the residual stress distribution in the UHMWPE using the measured changes in density is proposed. This study has indicated that oxidation of UHMWPE may lead to the development of tensile residual stresses, near the component surface, in the region of 1.7 MPa. These stresses may contribute to the failure mechanism of UHMWPE acetabular cups or knee tibial trays during service.

Influence of packaging conditions on the properties of gamma-irradiated UHMWPE following accelerated ageing and shelf ageing

The ageing behaviour of ultra-high molecular weight polyethylene (UHMWPE) has been studied following gamma irradiation (25 or 40 kGy) in air or in inert atmosphere (vacuum packed). Accelerated ageing procedures used elevated temperature (70 degrees C) and/or pressurised oxygen (5 bar). Shelf ageing for up to six months was also performed. The variation in polymer properties with depth into the polymer was determined using density measurements, infra-red spectroscopy and differential scanning calorimetry. Tensile properties of the irradiated polymer after accelerated ageing were also determined. Accelerated ageing in air for 20 days or pressurised oxygen for 4 days resulted in peaks in polymer density, crystallinity and degree of oxidation at the polymer surface. Accelerated ageing in pressurised oxygen for 8 days resulted in peaks in these properties 500 microns below the polymer surface. Where gamma irradiation was performed in inert atmosphere the amount of polymer degradation following accelerated ageing (in oxidising conditions) was generally lower but still significant. Differences were also observed in tensile properties between material gamma-irradiated in air and in vacuum. This study indicated that performing gamma sterilisation procedures under inert conditions can reduce the level of UHMWPE degradation when exposed to an oxidising environment.

The dependence of osteoblastic response on variations in the chemical composition and physical properties of hydroxyapatite

Two synthetic hydroxyapatite powders (A and B), supplied by different manufacturers, were physically and chemically characterized before being die pressed and sintered at 1250 degrees C. The powders were characterized using X-ray diffraction (XRD), infrared spectroscopy (IRS), X-ray fluorescence, surface area analysis (BET), particle size analysis and scanning electron microscopy (SEM). The materials were then pressed and sintered to produce hydroxyapatite discs of similar densities and grain sizes for in vitro evaluation. The ceramics were seeded with osteoblastic cells and after 15 days in culture the cell morphology was assessed using scanning electron microscopy (SEM), the ultrastructure of the cells was studied using transmission electron microscopy (TEM) with EDAX, and the rate of cell growth was assessed using biochemical techniques. The results clearly showed that the rate of cell proliferation but not the rate of alkaline phosphatase production, was highly dependent on the composition of the hydroxyapatite powders that were used to make the ceramic discs. The ultrastructural studies confirmed the relative viabilities of the cells and the nature of the ceramic interface indicating visually the marked differences in the performance of the two materials.

Blends of synthetic and natural polymers as drug delivery systems for growth hormone

In order to overcome the biological deficiencies of synthetic polymers and to enhance the mechanical characteristics of natural polymers, two synthetic polymers, poly(vinyl alcohol) (PVA) and poly(acrylic acid) (PAA) were blended, in different ratios, with two biological polymers, collagen (C) and hyaluronic acid (HA). These blends were used to prepare films, sponges and hydrogels which were loaded with growth hormone (GH) to investigate their potential use as drug delivery systems. The GH release was monitored in vitro using a specific enzyme-linked immunosorbent assay. The results show that GH can be released from HA/PAA sponges and from HA/PVA and C/PVA hydrogels. The initial GH concentration used for sample loading affected the total quantity of GH released but not the pattern of release. The rate and quantity of GH released was significantly dependent on the HA or C content of the polymers.

Inhibition of crevicular fluid neutrophil elastase by alpha 1-antitrypsin in periodontal health and disease

Gingival crevicular fluid (GCF) was collected from two healthy, two gingivitis and two periodontitis sites of two groups of individuals presenting for treatment of chronic adult periodontitis (group 1, 25 subjects; group 2, seven subjects) and from distal approximal sites of two incisors and one molar of 10 subjects with periodontal health. GCF eluates of periodontitis group 1 and controls, prepared by a technique that lysed polymorphonuclear leucocytes (PMN) in the samples, were assayed for functional neutrophil elastase (NE) and immunoreactive alpha 1-antitrypsin (alpha 1-AT) and alpha 1-antitrypsin-neutrophil elastase complex (alpha 1-AT-NE). Periodontitis group 2 GCF eluates, generated by a method that did not disrupt PMNs, were assayed for functional NE in the presence and absence of a specific NE inhibitor. A greater amount of NE (ng/5-s sample) was found in eluates of GCF from diseased sites irrespective of whether or not the eluates contained products of lysed PMNs. However, the GCF eluates prepared without disrupting PMNs contained only about one-tenth as much NE as eluates of corresponding sites that included constituents of lysed PMNs. The amount of alpha-AT in GCF was insufficient to inactivate most of the NE available for release into the gingival sulcus at either healthy or diseased sites. In addition, much of the alpha 1-AT in GCF was not complexed with NE under conditions of excess NE. More than 90% of the NE in GCF from each site category was inactivated by the NE specific inhibitor. It is concluded, because of the large quantity of NE available in PMNs compared to the amount of NE inhibitors in GCF, that at least locally transient free NE occurs, which contributes to tissue destruction in chronic adult periodontitis.