Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production

A critical step in preserving protein homeostasis is the recognition, binding, unfolding, and translocation of protein substrates by six AAA-ATPase proteasome subunits (ATPase-associated with various cellular activities) termed PSMC1-6, which are required for degradation of proteins by 26S proteasomes. Here, we identified 15 de novo missense variants in the PSMC3 gene encoding the AAA-ATPase proteasome subunit PSMC3/Rpt5 in 23 unrelated heterozygous patients with an autosomal dominant form of neurodevelopmental delay and intellectual disability. Expression of PSMC3 variants in mouse neuronal cultures led to altered dendrite development, and deletion of the PSMC3 fly ortholog Rpt5 impaired reversal learning capabilities in fruit flies. Structural modeling as well as proteomic and transcriptomic analyses of T cells derived from patients with PSMC3 variants implicated the PSMC3 variants in proteasome dysfunction through disruption of substrate translocation, induction of proteotoxic stress, and alterations in proteins controlling developmental and innate immune programs. The proteostatic perturbations in T cells from patients with PSMC3 variants correlated with a dysregulation in type I interferon (IFN) signaling in these T cells, which could be blocked by inhibition of the intracellular stress sensor protein kinase R (PKR). These results suggest that proteotoxic stress activated PKR in patient-derived T cells, resulting in a type I IFN response. The potential relationship among proteosome dysfunction, type I IFN production, and neurodevelopment suggests new directions in our understanding of pathogenesis in some neurodevelopmental disorders.

Cascade testing after exome sequencing: Retrospective analysis of linked family data at 2 US laboratories

PURPOSE

Cascade testing, the process of testing a proband's at-risk relatives, is integral to realizing the full value of genomic sequencing. However, there is little empirical evidence on the uptake of cascade testing after a positive exome sequencing (ES) result in a population of probands with diverse clinical indications.

METHODS

We retrospectively reviewed administrative data from 2 US clinical laboratories that perform ES. For each proband with a positive ES result, we used linked family data to describe the frequency of relatives' cascade testing performed at the same laboratory, variant detection yield of cascade tests, and characteristics of probands and relatives categorized on the basis of cascade testing completion.

RESULTS

Among the 3723 positive ES results across both laboratories, 426 relatives of 282 probands completed cascade testing (uptake = 7.6%). An average of 1.5 relatives (SD = 0.9) were tested per proband. Of the 426 relatives tested, 200 had a variant of interest detected (variant detection yield = 47.0%).

CONCLUSION

In our real-world data analysis, a small proportion of probands with a positive ES result subsequently had relatives complete cascade testing at the same laboratory. However, approximately half of the tested relatives received a clinically significant result that could have implications for clinical management or reproductive planning. Additional research on ways to increase cascade testing uptake is warranted.

Abstract 554: The Association Of Multiple Variants In The TNXB Gene With Vascular Aneurysms And Dissections

Pathogenic variants in the Tenascin-XB (TNXB) gene are associated with autosomal recessive Ehlers Danlos Syndrome (classical-like). Here, we report the association of two or more TNXB variants with aneurysms and/or dissections in different arterial beds. We compared case and control data from exome sequencing (ES) or multigene panel testing (MGPT). Statistical analysis was performed by Fisher’s exact test. From 350 cases of vascular aneurysm and/or dissection referred for genetic testing by ES, we identified 5 individuals with two or more rare missense variants in the TNXB gene (1.4%) versus 16 individuals with two or more TNXB variants from 10, 968 matched controls (0.14%, p<.0.01). In a replication cohort of 1844 individuals undergoing multigene panel testing (MGPT) for connective tissue disorders including aneurysms and dissections, we identified 27 individuals with two or more TNXB variants (1.5%, p<0.01); 19 of these individuals (70.3%, n= 19/27) had a personal history of aneurysm and/or dissection and had no other identifiable pathogenic or likely pathogenic variants. Interestingly, 3 (15.7%, n=3/19) had a diagnosis of bicuspid aortic valve (BAV), a 10-fold higher prevalence compared to the general population incidence of BAV. An additional 158 individuals with BAV who underwent ES also showed a higher prevalence of multiple TNXB variants compared to controls (1.8% vs 0.14%, p<0.01). This data strongly supports an association between multiple TNXB variants and vascular aneurysms and dissections.

Clinical characteristics of patients with hereditary transthyretin mutations primarily associated with cardiomyopathy and other rare transthyretin mutations: insights from a genetic testing programme

Background/Introduction

Hereditary transthyretin amyloidosis (hATTR; ATTRv) is a progressive, fatal disease caused by mutations in the transthyretin gene (TTR) that results in deposition of amyloid throughout the body, including in the heart. The p.V142I and p.T80A mutations typically manifest with a cardiomyopathy (CM) phenotype. Early diagnosis, which can be facilitated by genetic testing, is key to achieving optimal patient outcomes.

Purpose

To characterise the clinical profile and symptom burden of patients with hereditary transthyretin mutations associated primarily with a CM phenotype and rare hereditary transthyretin mutations.

Methods

This analysis used data from hATTR Compass, a genetic testing programme in the United States and Canada for patients suspected of having hATTR with polyneuropathy (PN) and patients with a family history of hATTR. Sequencing was performed using a TTR single-gene test, a gene panel of inherited cardiovascular disorders (CardioNext), or a gene panel of inherited neuromuscular disorders (NeuropathySelect). Akcea is aware of isolated data quality issues. Importantly, these do not affect the conclusions of this analysis.

Results

Cardiology specialists referred 466 patients with p.V142I, 15 with p.T80A, and 28 with rare TTR mutations to this programme. Of patients who reported sex, 57%, 53%, and 52% with p.V142I, p.T80A, and rare mutations, respectively, were male. Of patients who reported ethnicity, most with p.V142I were African American (94%), whereas the majority of patients with p.T80A and rare TTR mutations were Caucasian (100% and 69%, respectively). 24%, 60%, and 50%, of patients with p.V142I, p.T80A, and rare TTR mutations, respectively, had a family history of hATTR. The majority of patients with p.V142I (74%), p.T80A (53%), and rare TTR (54%) mutations were 65 years of age or older. Although most patients with p.V142I, p.T80A, and rare TTR mutations experienced symptoms/manifestations of heart disease (94% vs 100% vs 85%), many also presented with bilateral carpal tunnel syndrome (23% vs 44% vs 30%) and with sensory (27% vs 44% vs 65%), motor (15% vs 11% vs 25%), and autonomic (19% vs 11% vs 30%) dysfunction.

Conclusion

Most patients with the p.V142I mutation were African American, whereas many with p.T80A and other rare TTR mutations were Caucasian. Family history of hATTR was more common among patients with p.T80A and other rare TTR mutations than among patients with p.V142I. Regardless of the underlying mutation variant, many hATTR patients can present with various symptoms/manifestations aside from CM, such as PN and bilateral carpal tunnel syndrome. Recognising the neurological symptoms that can occur alongside CM and performing subsequent genetic testing facilitates diagnosis of hATTR. Early diagnosis is critical in hATTR because it is progressive and fatal, and early initiation of disease-modifying therapy is essential to optimising patient outcomes.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): This study was sponsored by Akcea Therapeutics, an affiliate of Ionis Pharmaceuticals, Inc.

When moments matter: Finding answers with rapid exome sequencing

Background

When time is of the essence in critical care cases, a fast molecular diagnosis is often necessary to help health care providers quickly determine best next steps for treatments, prognosis, and counseling of their patients. In this paper, we present the diagnostic rates and improved quality of life for patients undergoing clinical rapid exome sequencing.

Methods

The clinical histories and results of 41 patients undergoing rapid exome sequencing were retrospectively reviewed.

Results

Clinical rapid exome sequencing identified a definitive diagnosis in 13/41 (31.7%) and other relevant findings in 17 of the patients (41.5%). The average time to verbal report was 7 days; to written report was 11 days.

Conclusions

Our observations demonstrate the utility and effectiveness of rapid family‐based diagnostic exome sequencing in improving patients care.

Hyperammonemia as a Presenting Feature in Two Siblings with FBXL4 Variants

Early-onset mitochondrial encephalomyopathy is a rare disorder that presents in the neonatal period with lactic acidosis, hypotonia, and developmental delay. Sequence variants in the nuclear-encoded gene FBXL4 have been previously demonstrated to be a cause of early-onset mitochondrial encephalomyopathy in several unrelated families. We have identified a pair of siblings with mutations in FBXL4 who each presented in the neonatal period with hyperammonemia, low plasma levels of aspartate, low urine levels of tricarboxylic acid cycle intermediates suggesting a defect in anaplerosis, and cerebellar hypoplasia in addition to lactic acidosis and other classic signs of mitochondrial encephalomyopathy. After initial clinical stabilization, both subjects continued to have episodic exacerbations characterized by lactic acidosis and hyperammonemia. Previously reported cases of FBXL4 mutations are reviewed and compared with these affected siblings. These two new cases add to the spectrum of disease caused by mutations in FBLX4 and suggest possible benefit from anaplerotic therapies.

Mutations in the substrate binding glycine-rich loop of the mitochondrial processing peptidase-α protein (PMPCA) cause a severe mitochondrial disease

We describe a large Lebanese family with two affected members, a young female proband and her male cousin, who had multisystem involvement including profound global developmental delay, severe hypotonia and weakness, respiratory insufficiency, blindness, and lactic acidemia—findings consistent with an underlying mitochondrial disorder. Whole-exome sequencing was performed on DNA from the proband and both parents. The proband and her cousin carried compound heterozygous mutations in the PMPCA gene that encodes for α-mitochondrial processing peptidase (α-MPP), a protein likely involved in the processing of mitochondrial proteins. The variants were located close to and postulated to affect the substrate binding glycine-rich loop of the α-MPP protein. Functional assays including immunofluorescence and western blot analysis on patient's fibroblasts revealed that these variants reduced α-MPP levels and impaired frataxin production and processing. We further determined that those defects could be rescued through the expression of exogenous wild-type PMPCA cDNA. Our findings link defective α-MPP protein to a severe mitochondrial disease.

Emerging Genetic Counselor Roles within the Biotechnology and Pharmaceutical Industries: as Industry Interest Grows in Rare Genetic Disorders, How are Genetic Counselors Joining the Discussion?

Traditionally, the biotechnology and pharmaceutical industry (BPI) has focused drug development at the mass-market level targeting common medical issues. However, a recent trend is the development of therapies for orphan or rare disorders, including many genetic disorders. Developing treatments for genetic disorders requires an understanding of the needs of the community and translating genomic information to clinical and non-clinical audiences. The core skills of genetic counselors (GCs) include a deep knowledge of genetics and ability to communicate complex information to a broad audience, making GCs a choice fit for this shift in drug development. To date there is limited data defining the roles GCs hold within this industry. This exploratory study aimed to define the roles and motivation of GCs working in BPI, assess job satisfaction, and identify translatable skills and current gaps in GC training programs. The authors surveyed 26 GCs working in BPI in the United States; 79 % work for companies focused on rare disorders. GC positions in BPI are growing, with 57 % of respondents being the first GC in their role. GCs in BPI continue to utilize core genetic counseling competencies, though 72 % felt their training did not fully prepare them for BPI. These data suggest opportunities for exposure to BPI in GC training to better prepare future generations of GCs for these career opportunities. GC satisfaction was high in BPI, notably in areas traditionally reported as less satisfying on the National Society for Genetic Counselors Professional Status Survey: salary and advancement opportunities. BPI's growing interest in rare disorders represents a career opportunity for GCs, addressing both historic areas of dissatisfaction for GCs and BPI's genomic communication needs.

NPHP3 mutations are associated with neonatal onset multiorgan polycystic disease in two siblings

Two siblings with a severe multiorgan polycystic disease presenting in the neonatal period were identified. Their genetic testing identified compound heterozygous NPHP3 gene mutations, parents being heterozygous carriers. The mutations included a splice-site (c.958-2A>G) and a missense mutation (c.2342G>A; p.G781D), both being extremely rare. NPHP3 encodes for nephrocystin 3 present on the cilia-centrosome complex. We hypothesize that these mutations lead to defective cilia-based signaling, required for normal development of the renal, pancreatic, biliary and portal system. This report outlines a rare neonatal ciliopathy presentation of NPHP3 mutations leading to severe multiorgan failure in two siblings.