Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss

The cochlear matrisome: Importance in hearing and deafness

The extracellular matrix (ECM) consists in a complex meshwork of collagens, glycoproteins, and proteoglycans, which serves a scaffolding function and provides viscoelastic properties to the tissues. ECM acts as a biomechanical support, and actively participates in cell signaling to induce tissular changes in response to environmental forces and soluble cues. Given the remarkable complexity of the inner ear architecture, its exquisite structure-function relationship, and the importance of vibration-induced stimulation of its sensory cells, ECM is instrumental to hearing. Many factors of the matrisome are involved in cochlea development, function and maintenance, as evidenced by the variety of ECM proteins associated with hereditary deafness. This review describes the structural and functional ECM components in the auditory organ and how they are modulated over time and following injury.

Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis

Genomic variants affecting pre-messenger RNA splicing and its regulation are known to underlie many rare genetic diseases. However, common workflows for genetic diagnosis and clinical variant interpretation frequently overlook splice-altering variants. To better serve patient populations and advance biomedical knowledge, it has become increasingly important to develop and refine approaches for detecting and interpreting pathogenic splicing variants. In this review, we will summarize a few recent developments and challenges in using RNA sequencing technologies for rare disease investigation. Moreover, we will discuss how recent computational splicing prediction tools have emerged as complementary approaches for revealing disease-causing variants underlying splicing defects. We speculate that continuous improvements to sequencing technologies and predictive modeling will not only expand our understanding of splicing regulation but also bring us closer to filling the diagnostic gap for rare disease patients.

Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference

Identifying the causal interactions in gene-regulatory networks requires an accurate understanding of the time-lagged relationships between transcription factors and their target genes. Here we describe DELAY (short for Depicting Lagged Causality), a convolutional neural network for the inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. We show that combining supervised deep learning with joint probability matrices of pseudotime-lagged trajectories allows the network to overcome important limitations of ordinary Granger causality-based methods, for example, the inability to infer cyclic relationships such as feedback loops. Our network outperforms several common methods for inferring gene regulation and, when given partial ground-truth labels, predicts novel regulatory networks from single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data sets. To validate this approach, we used DELAY to identify important genes and modules in the regulatory network of auditory hair cells, as well as likely DNA-binding partners for two hair cell cofactors (Hist1h1c and Ccnd1) and a novel binding sequence for the hair cell-specific transcription factor Fiz1. We provide an easy-to-use implementation of DELAY under an open-source license at https://github.com/calebclayreagor/DELAY.

Radiologic Features in Cochlear Implant Candidates: A Prospective Study Comparing Candidates Carrying the p.Pro51Ser Mutation in Coagulation Factor C Homology With Noncarriers

BACKGROUND

DFNA9 is a form of autosomal progressive sensorineural hearing loss, caused by more than 30 variants in the COCH gene. p.Pro51Ser (p.P51S) variant is characterized by late-onset functional deterioration toward bilateral severe hearing loss and vestibulopathy. Focal sclerosis on computed tomography (CT) and T2-weighted magnetic resonance imaging (MRI) signal loss of semicircular canals are presumably radiologic biomarkers of advanced otovestibular deterioration.

OBJECTIVES

The aim of this study was to investigate whether these biomarkers are more frequent in cochlear implant candidates carrying the p.P51S mutation versus noncarriers. Second, the correlation between the hearing and vestibular function and carrier status was studied. Finally, the relationship between the presence of these radiologic features and the degree of hearing and vestibular deterioration was investigated.

METHODS

A prospective cohort study was performed on 38 candidates for cochlear implantation in a tertiary referral center. Patients underwent pure tone audiometry, videonystagmography, video head impulse tests and vestibular-evoked myogenic potentials. In addition, three dizziness questionnaires were used. All subjects were administered CT, MRI, and molecular genetic analysis.

RESULTS

Sixteen of 38 patients were carriers of the p.P51S COCH mutation. Radiologic lesions were almost exclusively observed in carriers. MRI was more sensitive in showing lesions than CT. Furthermore, p.P51S carriers showed significantly lower function on most vestibular tests, including questionnaires, than noncarriers. Patients with imaging abnormalities showed more pronounced vestibulopathy.

CONCLUSION

The present study supplements previous data that endorse the hypothesis that focal sclerosis of semicircular canals are biomarkers of advanced vestibular deterioration, especially in DFNA9.

Expanding the phenotypic spectrum of COLEC10-Related 3MC syndrome: A glimpse into COLEC10-Related 3MC syndrome in the Ashkenazi Jewish population

Bi-allelic variants in COLEC11 and MASP1 have been associated with 3MC syndrome, a clinical entity made of up four rare autosomal recessive disorders: Carnevale, Mingarelli, Malpuech, and Michels syndromes, characterized by variable expression of facial dysmorphia, cleft lip/palate, postnatal growth deficiency, hearing loss, cognitive impairment, craniosynostosis, radioulnar synostosis, and genital and vesicorenal anomalies. More recently, bi-allelic variants in COLEC10 have been described to be associated with 3MC syndrome. Syndromic features seen in 3MC syndrome are thought to be due to disruption of the chemoattractant properties that influence neural crest cell migration. We identified nine individuals from five families of Ashkenazi Jewish descent with homozygosity of the c.311G > T (p.Gly104Val) variant in COLEC10 and phenotype consistent with 3MC syndrome. Carrier frequency was calculated among 52,278 individuals of Jewish descent. Testing revealed 400 carriers out of 39,750 individuals of Ashkenazi Jewish descent, giving a carrier frequency of 1 in 99 or 1.01%. Molecular protein modeling suggested that the p.Gly104Val substitution alters local conformation. The c.311G > T (p.Gly104Val) variant likely represents a founder variant, and homozygosity is associated with features of 3MC syndrome. 3MC syndrome should be in the differential diagnosis for individuals with short stature, radioulnar synostosis, cleft lip and cleft palate.

A TP53 Related Immune Prognostic Model for the Prediction of Clinical Outcomes and Therapeutic Responses in Lung Adenocarcinoma

TP53 is the most frequently mutated gene in lung adenocarcinoma (LUAD). The tumor immune microenvironment (TIM) is considered a vital factor that influences tumor progression and survival rate. The influence of TP53 mutation on TIM in LUAD has not been fully studied. Here we systematically investigated the relationship and potential mechanisms between TP53 mutation status and immune response in LUAD. We constructed an immune prognostic model (IPM) using immune associated genes, which were expressed differentially between the TP53 mutant and wild type LUAD patients. We discovered that TP53 mutations were significantly associated with 5 immune related biological processes. Thirty-six immune genes were expressed differentially between TP53 mutant and wild type LUAD patients. An IPM was constructed using 3 immune genes to differentiate the prognostic survival in LUAD. The high-risk LUAD group displayed significantly higher proportions of dendritic cell resting, T cell CD4 memory resting and mast cell resting, and significantly low proportions of dendritic cell activated, T cell CD4 memory activated, and mast cell activated. Moreover, IPM was found to be an independent clinical feature and can be used to predict immunotherapy responses. In summary, we constructed and validated an IPM using 3 immune related genes, which provides a better understanding of the mechanism from an immunological perspectives.

Genotype-Phenotype Correlations of Pathogenic COCH Variants in DFNA9: A HuGE Systematic Review and Audiometric Meta-Analysis

Pathogenic missense variants in COCH are associated with DFNA9, an autosomal dominantly inherited type of progressive sensorineural hearing loss with or without vestibular dysfunction. This study is a comprehensive overview of genotype-phenotype correlations using the PRISMA and HuGENet guidelines. Study characteristics, risk of bias, genotyping and data on the self-reported age of onset, symptoms of vestibular dysfunction, normative test results for vestibular function, and results of audiovestibular examinations were extracted for each underlying pathogenic COCH variant. The literature search yielded 48 studies describing the audiovestibular phenotypes of 27 DFNA9-associated variants in COCH. Subsequently, meta-analysis of audiometric data was performed by constructing age-related typical audiograms and by performing non-linear regression analyses on the age of onset and progression of hearing loss. Significant differences were found between the calculated ages of onset and progression of the audiovestibular phenotypes of subjects with pathogenic variants affecting either the LCCL domain of cochlin or the vWFA2 and Ivd1 domains. We conclude that the audiovestibular phenotypes associated with DFNA9 are highly variable. Variants affecting the LCCL domain of cochlin generally lead to more progression of hearing loss when compared to variants affecting the other domains. This review serves as a reference for prospective natural history studies in anticipation of mutation-specific therapeutic interventions.

Genotype-phenotype Correlation Study in a Large Series of Patients Carrying the p.Pro51Ser (p.P51S) Variant in COCH (DFNA9): Part I-A Cross-sectional Study of Hearing Function in 111 Carriers

INTRODUCTION

DFNA9 is characterized by adult-onset progressive sensorineural hearing loss (SNHL) and vestibular impairment. More than 15 years ago, genotype-phenotype correlation studies estimated the initial age of hearing deterioration in the fourth to fifth decade (ranging from 32 to 43 years). However, these analyses were based on relatively limited numbers of mainly symptomatic carriers using markedly different methodologies. The starting point for the hearing deterioration is more correctly determined with larger numbers of carriers and with a more clearly defined starting point of the hearing deterioration.

AIM

The aim of this study was to determine milestone ages (start and maximal hearing deterioration, potential eligibility for hearing aids and cochlear implants based on pure-tone average [PTA]) in a large series of p.Pro51Ser COCH variant carriers. The degree of individual interaural asymmetry and the degree of variability (interquartile range) with which the hearing deterioration progresses across ages were also studied, and age-related typical audiograms (ARTA) were constructed.

MATERIAL AND METHODS

One hundred eleven Belgian and Dutch p.P51S variant carriers were identified and recruited for audiological investigation. Their hearing thresholds were compared with p50th, p95th, and p97.5th percentile values of presbyacusis (ISO 7029 standards). The onset and degree of hearing deterioration were defined and assessed for each frequency and with three PTAs (PTA0.5-4 [0.5, 1, 2, and 4 kHz]; PTA4-8 [4 and 8 kHz]; and PTA6-8 [6 and 8 kHz]). The milestones ages were derived from nonlinear regression model of hearing thresholds against age, for male and female carriers separately, because of different age-referenced limits. Interaural right-left asymmetry was assessed, and variability of hearing thresholds were calculated using interquartile range. ARTAs were built with both observed data and a prediction model.

RESULTS

Hearing dysfunction in p.P51S carriers begins at about 38 years of age (ranging from 28 to 43 years) on average in female and 46 years (ranging from 42 to 49 years) in male carriers (third decade: female, fifth decade: male carriers), depending on the hearing frequency and with differences in deterioration sequence between both genders. These differences, however, were mainly due to more stringent age-referenced limits for men. In contrast, predictions (ARTA) did not show any difference of phenotypic expression between genders. At about 48 to 50 years of age on average, the majority of DFNA9 patients may need conventional hearing aids (PTA ≥ 40 dB HL), whereas this is about 56 to 59 years for cochlear implants (PTA ≥ 70 dB HL). There is a high degree of individual interaural asymmetry and interindividual variability throughout all ages.

CONCLUSION

This study demonstrates that the onset of sensorineural hearing deterioration starts in the third decade and probably even earlier. Regardless of differences in estimates, DFNA9 expresses similarly in male and female carriers, but male carriers are much more difficult to identify in early stages of the disease. Comprehensive assessment of the natural course of DFNA9 is of particular interest to predict the age of onset or critical period of most significant function deterioration in individual carriers of the pathogenic variant. This will help to design studies in the search for disease-modifying therapies.

Genotype-Phenotype Correlation Study in a Large Series of Patients Carrying the p.Pro51Ser (p.P51S) Variant in COCH (DFNA9) Part II: A Prospective Cross-Sectional Study of the Vestibular Phenotype in 111 Carriers

INTRODUCTION

DFNA9 is characterized by adult-onset hearing loss and evolution toward bilateral vestibulopathy (BVP). The genotype-phenotype correlation studies were conducted 15 years ago. However, their conclusions were mainly based on symptomatic carriers and the vestibular data exclusively derived from the horizontal (lateral) semicircular canal (SCC). The last decade was marked by the emergence of new clinical diagnostic tools, such as the video head impulse test (vHIT) and vestibular-evoked myogenic evoked potentials (VEMPs), expanding our evaluation to all six SCCs and the otolith organs (saccule and utricule).

AIM

The aim of this study was to comprehensively evaluate vestibular function in the largest series presymptomatic as well as symptomatic p.P51S variant carriers, to determine which labyrinthine part shows the first signs of deterioration and which SCC function declines at first and to determine the age at which p.P51S variant carriers develop caloric areflexia on VNG and vHIT vestibulo-ocular reflex (VOR)-gain dysfunction as defined by the Barany Society criteria for BVP.

MATERIAL AND METHODS

One hundred eleven p.P51S variant carriers were included. The following vestibular function tests were applied in two different centers: ENG/VNG, vHIT, and VEMPs. The following parameters were analyzed: age (years), hearing loss (pure-tone average of 0.5-4 kHz [PTA0.5-4, dB HL]), sum of maximal peak slow-phase eye velocity obtained with bi-thermal (30°C and 44°C, water irrigation; 25°C and 44°C, air irrigation) caloric test (°/s), vHIT VOR-gain on LSCC, superior SCC and posterior SCC, C-VEMP both numerical (threshold, dB nHL) and categorical (present or absent), and O-VEMP as categorical (present or absent). The age of onset of vestibular dysfunction was determined both with categorical (onset in decades using Box & Whisker plots) and numeric approach (onset in years using regression analysis). The same method was applied for determining the age at which vestibular function declined beyond the limits of BVP, as defined by the Barany Society.

RESULTS

With the categorical approach, otolith function was declining first (3rd decade), followed by caloric response (5th decade) and vHIT VOR-gains (5th-6th decade). Estimated age of onset showed that the deterioration began with C-VEMP activity (31 years), followed by caloric responses (water irrigation) (35 years) and ended with vHIT VOR-gains (48-57 years). Hearing deterioration started earlier than vestibular deterioration in female carriers, which is different from earlier reports. BVP was predicted at about 53 years of age on average with VNG caloric gain (water irrigation) and between 47 and 57 years of age for the three SCCs. Loss of C-VEMP response was estimated at about 46 years of age.

CONCLUSION

Former hypothesis of vestibular decline preceding hearing deterioration by 9 years was confirmed by the numeric approach, but this was less obvious with the categorical approach. Wide confidence intervals of the regression models may explain deviation of the fits from true relationship. There is a typical vestibular deterioration hierarchy in p.P51S variant carriers. To further refine the present findings, a prospective longitudinal study of the auditory and vestibular phenotype may help to get even better insights in this matter.

Identification of Novel and Recurrent Variants in MYO15A in Ashkenazi Jewish Patients With Autosomal Recessive Nonsyndromic Hearing Loss

Hearing loss is a genetically and phenotypically heterogeneous disorder. The purpose of this study was to determine the genetic cause underlying hearing loss in four Ashkenazi Jewish families. We screened probands from each family using a combination of targeted mutation screening and exome sequencing to identifiy the genetic cause of hearing loss in each family. We identified four variants in MYO15A, two novel variants never previously linked to deafness (c.7212+5G>A and p.Leu2532ArgfsTer37) and two recurrent variants (p.Tyr2684His and p.Gly3287Gly). One family showed locus heterogeneity, segregrating two genetic forms of hearing loss. Mini-gene assays revealed the c.7212+5G>A variant results in abnormal splicing and is most likely a null allele. We show that families segregrating the p.Gly3287Gly variant show both inter and intra-familial phenotypic differences. These results add to the list of MYO15A deafness-causing variants, further confirm the pathogenicity of the p.Gly3287Gly variant and shed further light on the genetic etiology of hearing loss in the Ashkenazi Jewish population.