Genomic Analysis of Human Spinal Deformity and Characterization of a Zebrafish Disease Model

Scoliosis is characterized by a lateral curvature of the spine that requires long-term bracing and invasive spinal surgery in cases with progressive deformity. Some individuals develop scoliosis secondary to congenital malformations or syndromic disorders, but most scoliosis is considered idiopathic and has no known cause. Adolescent idiopathic scoliosis (AIS) onsets in late childhood and causes spinal deformity in approximately 3% of the pediatric population. Despite a strong genetic basis, genetic risk factors for AIS are unknown and the pathogenesis remains poorly understood, which has been further hindered by the lack of a relevant animal model. Therefore, we used multiple approaches to better understand the genetic and molecular etiology of AIS using human and animal-based studies. First, we performed copy number variation analysis on 143 patients with isolated scoliosis using the Affymetrix Genome-wide Human SNP Array 6.0. We identified a duplication of chromosome 1q21.1 in 2.1% (N=3/143) of AIS patients, which was enriched compared to 0.09% (N=1/1079) of controls (P=0.0057) and 0.07% (N=6/8329) of published controls (P=0.0004). Other notable findings include trisomy X, which was identified in 1.8% (N=2/114) of female AIS patients, and rearrangements of chromosome 15q11.2 and 16p11.2 that may be relevant to scoliosis susceptibility. We also report rare CNVs that will be of use to future studies investigating candidate genes for AIS. Second, we performed a genome-wide rare variant burden analysis using exome sequence data and identified FBN1 (fibrillin-1) as the most significantly associated gene with AIS. Mutations in FBN1 are most frequently association with Marfan syndrome, a syndromic condition that causes scoliosis in 60% of patients. Based on these results, FBN1 and a related gene, FBN2 (fibrillin-2), were sequenced in a total of 852 AIS cases and 669 controls. In individuals of European ancestry, rare variants in FBN1 and FBN2 were enriched in severely affected AIS cases (7.6%) compared to in-house controls (2.4%) (OR=3.5, P=5.46×10-4) and Exome Sequencing Project controls (2.3%) (OR=3.5, P=1.48×10-6). Scoliosis severity in AIS cases was associated with FBN1 and FBN2 rare variants (P=0.0012) and replicated in an independent Han Chinese cohort (P=0.0376), suggesting that rare variants have utility as predictors of curve progression. Clinical evaluations revealed that the majority of AIS cases with rare FBN1 variants do not meet diagnostic criteria for Marfan syndrome, though variants are associated with tall stature (P=0.0035) and upregulation of the TGF-β pathway. Finally, we characterized a recessive zebrafish mutant, called skolios, which develops a spinal deformity phenotype that parallels many features of human AIS, including an isolated lateral curvature of the spine that arises independent of congenital vertebral malformations. Skolios was identified in a mutagenesis screen and previously mapped to a 2.7 Mb region on chromosome 17. Because skolios may be an informative model of scoliosis, we sought to identify its genetic basis. We performed low coverage whole genome sequencing on a skolios mutant and identified a single nonsense mutation in the mapped region, which caused a premature stop in kinesin family member 6 (kif6), a poorly characterized kinesin of unknown function. To determine if the loss of kif6 is responsible for the skolios phenotype, we used TALENs to create additional mutant alleles. We isolated three new TALEN-induced mutations that caused frameshift mutations in kif6. All zebrafish homozygous or compound heterozygous for kif6 frameshift mutations developed body axis curvature that was indistinguishable from skolios mutants, verifying kif6 as the causative gene. Preliminary investigation into the mechanism of spinal deformity revealed no association with vertebral malformations or cilia defects in skolios mutants. Overall, these results identify important genetic risk factors for AIS, including clinically relevant copy number variants and rare genetic variation in FBN1 and FBN2. Moreover, we have identified an animal model with scoliosis and demonstrated a novel role for kif6 in the developing spine. These findings have significant impact on our understanding of the genetic basis of AIS and reveal new strategies to identify and treat AIS

Polygenic threshold model with sex dimorphism in adolescent idiopathic scoliosis: The Carter effect

Background: Idiopathic clubfoot is approximately twice as common in males than in females. The reason for this discrepancy is unclear butmay represent an inherent difference in the susceptibility to thedeformity. If this difference is due to genetic factors it is predicted that in order to inherit clubfoot, females need to have a greater number of susceptibility genes than males. Females would also be more likely to transmit the disease to their children and have siblings with clubfoot. This phenomenon is known as the Carter effect, and the presence of such an effect supports a multifactorial threshold model of inheritance. Methods: Ninety-seven multiplex families with more than one individual with idiopathic clubfoot were studied. The study included1093 individuals: 291with clubfoot and802unaffected relatives. Ratesof transmissionby the thirty-seven affected fathers and twenty-six affected mothers were calculated, and the prevalence among siblings was determined in the nuclear families of affected persons

Kinesin family member 6 (kif6) is necessary for spine development in zebrafish

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Developmental Dynamics 243 (2014): 1646–1657, doi:10.1002/dvdy.24208.Idiopathic scoliosis is a form of spinal deformity that affects 2–3% of children and results in curvature of the spine without structural defects of the vertebral units. The pathogenesis of idiopathic scoliosis remains poorly understood, in part due to the lack of a relevant animal model. We performed a forward mutagenesis screen in zebrafish to identify new models for idiopathic scoliosis. We isolated a recessive zebrafish mutant, called skolios, which develops isolated spinal curvature that arises independent of vertebral malformations. Using meiotic mapping and whole genome sequencing, we identified a nonsense mutation in kinesin family member 6 (kif6gw326) unique to skolios mutants. Three additional kif6 frameshift alleles (gw327, gw328, gw329) were generated with transcription activator-like effector nucleases (TALENs). Zebrafish homozygous or compound heterozygous for kif6 frameshift mutations developed a scoliosis phenotype indistinguishable from skolios mutants, confirming that skolios is caused by the loss of kif6. Although kif6 may play a role in cilia, no evidence for cilia dysfunction was seen in kif6gw326 mutants. Overall, these findings demonstrate a novel role for kif6 in spinal development and identify a new candidate gene for human idiopathic scoliosis.2015-11-1

De novo variants in ATXN7L3 lead to developmental delay, hypotonia and distinctive facial features

Deubiquitination is critical for the proper functioning of numerous biological pathways such as DNA repair, cell cycle progression, transcription, signal transduction, and autophagy. Accordingly, pathogenic variants in deubiquitinating enzymes (DUBs) have been implicated in neurodevelopmental disorders (ND) and congenital abnormalities. ATXN7L3 is a component of the DUB module of the SAGA complex, and two other related DUB modules, and serves as an obligate adaptor protein of 3 ubiquitin-specific proteases (USP22, USP27X or USP51). Through exome sequencing and GeneMatching, we identified nine individuals with heterozygous variants in ATXN7L3. The core phenotype included global motor and language developmental delay, hypotonia, and distinctive facial characteristics including hypertelorism, epicanthal folds, blepharoptosis, a small nose and mouth, and low-set posteriorly rotated ears. In order to assess pathogenicity, we investigated the effects of a recurrent nonsense variant [c.340C>T; p.(Arg114Ter)] in fibroblasts of an affected individual. ATXN7L3 protein levels were reduced, and deubiquitylation was impaired, as indicated by an increase in histone H2Bub1 levels. This is consistent with the previous observation of increased H2Bub1 levels in Atxn7l3-null mouse embryos, which have developmental delay and embryonic lethality. In conclusion, we present clinical information and biochemical characterization supporting ATXN7L3 variants in the pathogenesis of a rare syndromic ND

The role of supportive supervision on immunization program outcome - a randomized field trial from Georgia

<p>Abstract</p> <p>Background</p> <p>One of the most common barriers to improving immunization coverage rates is human resources and its management. In the Republic of Georgia, a country where widespread health care reforms have taken place over the last decade, an intervention was recently implemented to strengthen performance of immunization programs. A range of measures were taken to ensure that immunization managers carry out their activities effectively through direct, personal contact on a regular basis to guide, support and assist designated health care facility staff to become more competent in their immunization work. The aim of this study was to document the effects of "supportive" supervision on the performance of the immunization program at the district(s) level in Georgia.</p> <p>Methods</p> <p>A pre-post experimental research design is used for the quantitative evaluation. Data come from baseline and follow-up surveys of health care providers and immunization managers in 15 intervention and 15 control districts. These data were supplemented by focus group discussions amongst Centre of Public Health and health facility staff.</p> <p>Results</p> <p>The results of the study suggest that the intervention package resulted in a number of expected improvements. Among immunization managers, the intervention independently contributed to improved knowledge of supportive supervision, and helped remove self-perceived barriers to supportive supervision such as availability of resources to supervisors, lack of a clear format for providing supportive supervision, and lack of recognition among providers of the importance of supportive supervision. The intervention independently contributed to relative improvements in district-level service delivery outcomes such as vaccine wastage factors and the DPT-3 immunization coverage rate. The clear positive improvement in all service delivery outcomes across both the intervention and control districts can be attributed to an overall improvement in the Georgian population's access to health care.</p> <p>Conclusion</p> <p>Provider-based interventions such as supportive supervision can have independent positive effects on immunization program indicators. Thus, it is recommended to implement supportive supervision within the framework of national immunization programs in Georgia and other countries in transition with similar institutional arrangements for health services organization.</p> <p>Abstract in Russian</p> <p>See the full article online for a translation of this abstract in Russian.</p

Adaptation and validation of the ACMG/AMP variant classification framework for MYH7-associated inherited cardiomyopathies: recommendations by ClinGen’s Inherited Cardiomyopathy Expert Panel

Purpose Integrating genomic sequencing in clinical care requires standardization of variant interpretation practices. The Clinical Genome Resource has established expert panels to adapt the American College of Medical Genetics and Genomics/Association for Molecular Pathology classification framework for specific genes and diseases. The Cardiomyopathy Expert Panel selected MYH7, a key contributor to inherited cardiomyopathies, as a pilot gene to develop a broadly applicable approach. Methods: Expert revisions were tested with 60 variants using a structured double review by pairs of clinical and diagnostic laboratory experts. Final consensus rules were established via iterative discussions. Results: Adjustments represented disease-/gene-informed specifications (12) or strength adjustments of existing rules (5). Nine rules were deemed not applicable. Key specifications included quantitative frameworks for minor allele frequency thresholds, the use of segregation data, and a semiquantitative approach to counting multiple independent variant occurrences where fully controlled case-control studies are lacking. Initial inter-expert classification concordance was 93%. Internal data from participating diagnostic laboratories changed the classification of 20% of the variants (n = 12), highlighting the critical importance of data sharing. Conclusion: These adapted rules provide increased specificity for use in MYH7-associated disorders in combination with expert review and clinical judgment and serve as a stepping stone for genes and disorders with similar genetic and clinical characteristics

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Adding 6 months of androgen deprivation therapy to postoperative radiotherapy for prostate cancer: a comparison of short-course versus no androgen deprivation therapy in the RADICALS-HD randomised controlled trial

Background Previous evidence indicates that adjuvant, short-course androgen deprivation therapy (ADT) improves metastasis-free survival when given with primary radiotherapy for intermediate-risk and high-risk localised prostate cancer. However, the value of ADT with postoperative radiotherapy after radical prostatectomy is unclear. Methods RADICALS-HD was an international randomised controlled trial to test the efficacy of ADT used in combination with postoperative radiotherapy for prostate cancer. Key eligibility criteria were indication for radiotherapy after radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to radiotherapy alone (no ADT) or radiotherapy with 6 months of ADT (short-course ADT), using monthly subcutaneous gonadotropin-releasing hormone analogue injections, daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as distant metastasis arising from prostate cancer or death from any cause. Standard survival analysis methods were used, accounting for randomisation stratification factors. The trial had 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 80% to 86% (hazard ratio [HR] 0·67). Analyses followed the intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov, NCT00541047. Findings Between Nov 22, 2007, and June 29, 2015, 1480 patients (median age 66 years [IQR 61–69]) were randomly assigned to receive no ADT (n=737) or short-course ADT (n=743) in addition to postoperative radiotherapy at 121 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 9·0 years (IQR 7·1–10·1), metastasis-free survival events were reported for 268 participants (142 in the no ADT group and 126 in the short-course ADT group; HR 0·886 [95% CI 0·688–1·140], p=0·35). 10-year metastasis-free survival was 79·2% (95% CI 75·4–82·5) in the no ADT group and 80·4% (76·6–83·6) in the short-course ADT group. Toxicity of grade 3 or higher was reported for 121 (17%) of 737 participants in the no ADT group and 100 (14%) of 743 in the short-course ADT group (p=0·15), with no treatment-related deaths. Interpretation Metastatic disease is uncommon following postoperative bed radiotherapy after radical prostatectomy. Adding 6 months of ADT to this radiotherapy did not improve metastasis-free survival compared with no ADT. These findings do not support the use of short-course ADT with postoperative radiotherapy in this patient population