scholarly journals Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity

2019 ◽  
Author(s):  
Joseph Farris ◽  
Barbara Calhoun ◽  
Md Suhail Alam ◽  
Shaun Lee ◽  
Kasturi Haldar
Keyword(s):  
Disease Severity ◽  
Neurological Disease ◽  
Large Scale ◽  
Failure To Thrive ◽  
Clinical Severity ◽  
Missense Mutations ◽  
Glycine Decarboxylase ◽  
Disease States ◽  
Mutation Score ◽  
New Treatments

AbstractMonogenetic diseases provide unique opportunity for studying complex, clinical states that underlie neurological severity. Loss of glycine decarboxylase (GLDC) can severely impact neurological development as seen in non-ketotic hyperglycinemia (NKH). NKH is a neuro-metabolic disorder lacking quantitative predictors of disease states. It is characterized by elevation of glycine, seizures and failure to thrive, but glycine reduction often fails to confer neurological benefit, suggesting need for alternate tools to distinguish severe from attenuated disease. A major challenge has been that there are 255 unique disease-causing missense mutations in GLDC, of which 206 remain entirely uncharacterized. Here we report a Multiparametric Mutation Score (MMS) developed by combining in silico predictions of stability, evolutionary conservation and protein interaction models and suitable to assess 251 of 255 mutations. In addition, we created a quantitative scale of clinical disease severity comprising of four major disease domains (seizure, cognitive failure, muscular and motor control and brain-malformation) to comprehensively score patient symptoms identified in 131 clinical reports published over the last 15 years. The resulting patient Clinical Outcomes Scores (COS) were used to optimize the MMS for biological and clinical relevance and yield a patient Weighted Multiparametric Mutation Score (WMMS) that separates severe from attenuated neurological disease (p < 3.5e-5). Our study provides understanding for developing quantitative tools to predict clinical severity of neurological disease and a clinical scale that advances monitoring disease progression needed to evaluate new treatments for NKH.

scholarly journals Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity

2020 ◽  
Vol 16 (5) ◽  
pp. e1007871
Author(s):  
Joseph Farris ◽  
Barbara Calhoun ◽  
Md. Suhail Alam ◽  
Shaun Lee ◽  
Kasturi Haldar
Keyword(s):  
Disease Severity ◽  
Neurological Disease ◽  
Large Scale ◽  
Glycine Decarboxylase

scholarly journals Genomic analyses of glycine decarboxylase neurogenic mutations, yield a large scale prediction model for prenatal disease

2020 ◽  
Author(s):  
Joseph D. Farris ◽  
Md. Suhail Alam ◽  
Arpitha MysoreRajashekara ◽  
Kasturi Haldar
Keyword(s):  
Neurological Disease ◽  
Large Scale ◽  
Mitochondrial Protein ◽  
Glycine Decarboxylase ◽  
Linear Scale ◽  
Disease Outcomes ◽  
Genomic Analyses ◽  
Age Dependent ◽  
Genome Level

AbstractGlycine decarboxylase (GLDC) is a mitochondrial protein, hundreds of mutations in which cause a neurometabolic disorder Non-ketotic Hyperglycinemia (NKH), associated with elevation of plasma glycine. But why a mutation induces severe or attenuated neurological disease is poorly understood. We combined a human multiparametric mutation scale that separates severe from attenuated clinical, neurological disease, with new in silico tools to assess 238 of 255 NKH mutations in murine GLDC. We unified novel murine and human genome level-analyses across a linear scale of neurological severity, with in vivo evidence from mice engineered with a top-ranking attenuated mutation and another mutation >10 times more pathogenic and integrated the data in a model of pre- and post-natal disease outcomes, relevant for over a hundred major and minor neurogenic mutations. Our findings suggest that highly severe neurogenic mutations predict fatal, prenatal disease that can be remedied by metabolic supplementation of dams, in absence of amelioration of persistent and age-dependent elevation of plasma glycine.

scholarly journals Genomic analyses of glycine decarboxylase neurogenic mutations yield a large-scale prediction model for prenatal disease

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009307
Author(s):  
Joseph Farris ◽  
Md Suhail Alam ◽  
Arpitha Mysore Rajashekara ◽  
Kasturi Haldar
Keyword(s):  
Neurological Disease ◽  
Large Scale ◽  
Systems Approach ◽  
Single Gene ◽  
Genetic Diseases ◽  
Pathogenic Mutation ◽  
Glycine Decarboxylase ◽  
Functional Consequences ◽  
Genome Level

Hundreds of mutations in a single gene result in rare diseases, but why mutations induce severe or attenuated states remains poorly understood. Defect in glycine decarboxylase (GLDC) causes Non-ketotic Hyperglycinemia (NKH), a neurological disease associated with elevation of plasma glycine. We unified a human multiparametric NKH mutation scale that separates severe from attenuated neurological disease with new in silico tools for murine and human genome level-analyses, gathered in vivo evidence from mice engineered with top-ranking attenuated and a highly pathogenic mutation, and integrated the data in a model of pre- and post-natal disease outcomes, relevant for over a hundred major and minor neurogenic mutations. Our findings suggest that highly severe neurogenic mutations predict fatal, prenatal disease that can be remedied by metabolic supplementation of dams, without amelioration of persistent plasma glycine. The work also provides a systems approach to identify functional consequences of mutations across hundreds of genetic diseases. Our studies provide a new framework for a large scale understanding of mutation functions and the prediction that severity of a neurogenic mutation is a direct measure of pre-natal disease in neurometabolic NKH mouse models. This framework can be extended to analyses of hundreds of monogenetic rare disorders where the underlying genes are known but understanding of the vast majority of mutations and why and how they cause disease, has yet to be realized.

scholarly journals NRSF and Its Epigenetic Effectors: New Treatments for Neurological Disease

2018 ◽  
Vol 8 (12) ◽  
pp. 226 ◽  
Author(s):  
Ryan Thompson ◽  
Christina Chan
Keyword(s):  
Gene Expression ◽  
Neurological Disease ◽  
Neurological Diseases ◽  
Neuronal Cell ◽  
Basic Function ◽  
Brain Diseases ◽  
Chromatin Remodelers ◽  
Disease States ◽  
Important Player ◽  
New Treatments

The Neuron Restrictive Silencer Factor (NRSF) is the well-known master transcriptional repressor of the neuronal phenotype. Research to date has shown that it is an important player in the growth and development of the nervous system. Its role in the maturation of neural precursor cells to adult neurons has been well characterized in stem cell models. While much has been characterized from a developmental perspective, research is revealing that NRSF plays a role in various neurological diseases, ranging from neurodegenerative, neuropsychiatric, to cancer. Dysregulation of NRSF activity disrupts downstream gene expression that is responsible for neuronal cell homeostasis in several models that contribute to pathologic states. Interestingly, it is now becoming apparent that the dysregulation of NRSF contributes to neurological disease through epigenetic mechanisms. Although NRSF itself is a transcription factor, its major effectors are chromatin modifiers. At the level of epigenetics, changes in NRSF activity have been well characterized in models of neuropathic pain and epilepsy. Better understanding of the epigenetic basis of brain diseases has led to design and use of small molecules that can prevent NRSF from repressing gene expression by neutralizing its interactions with its chromatin remodelers. This review will address the basic function of NRSF and its cofactors, investigate their mechanisms, then explore how their dysfunction can cause disease states. This review will also address research on NRSF as a therapeutic target and delve into new therapeutic strategies that focus on disrupting NRSF’s ability to recruit chromatin remodelers.

scholarly journals HPV Strain Predicts Severity of Juvenile-Onset Recurrent Respiratory Papillomatosis with Implications for Disease Screening

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2556
Author(s):  
Mary C. Bedard ◽  
Alessandro de Alarcon ◽  
Yann-Fuu Kou ◽  
David Lee ◽  
Alexandra Sestito ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Severity ◽  
Disease Onset ◽  
Tissue Bank ◽  
Benign Neoplasm ◽  
Recurrent Respiratory Papillomatosis ◽  
Clinical Severity ◽  
Viral Gene ◽  
Juvenile Onset ◽  
Severity Scores

Juvenile-onset recurrent respiratory papillomatosis (JoRRP) is the most common benign neoplasm of the larynx in children, presenting with significant variation in clinical course and potential for progression to malignancy. Since JoRRP is driven by human papillomavirus (HPV), we evaluated viral factors in a prospective cohort to identify predictive factors of disease severity. Twenty children with JoRRP undergoing routine debridement of papillomas were recruited and followed for ≥1 year. Demographical features, clinical severity scores, and surgeries over time were tabulated. Biopsies were used to establish a tissue bank and primary cell cultures for HPV6 vs. HPV11 genotyping and evaluation of viral gene expression. We found that patients with HPV11+ disease had an earlier age at disease onset, higher frequency of surgeries, increased number of lifetime surgeries, and were more likely to progress to malignancy. However, the amplitude of viral E6/E7 gene expression did not account for increased disease severity in HPV11+ patients. Determination of HPV strain is not routinely performed in the standard of care for JoRRP patients; we demonstrate the utility and feasibility of HPV genotyping using RNA-ISH for screening of HPV11+ disease as a biomarker for disease severity and progression in JoRRP patients.

Periodontitis Is Related to Exercise Capacity: Two Cross-sectional Studies

2021 ◽  
pp. 002203452199542
Author(s):  
B. Holtfreter ◽  
B. Stubbe ◽  
S. Gläser ◽  
J. Trabandt ◽  
H. Völzke ◽  
...  
Keyword(s):  
Oxygen Uptake ◽  
Disease Severity ◽  
Cardiorespiratory Fitness ◽  
Large Scale ◽  
Cardiopulmonary Exercise Testing ◽  
Exercise Duration ◽  
Cross Sectional ◽  
Sample Mean ◽  
Cardiometabolic Diseases ◽  
Number Of Teeth

Although a potential link between periodontitis and cardiorespiratory fitness might provide a reasonable explanation for effects of tooth-related alterations seen on cardiometabolic diseases, evidence is currently limited. Thus, we investigated the association between clinically assessed periodontitis and cardiopulmonary exercise testing (CPET). Data from 2 independent cross-sectional population-based studies (5-y follow-up of the Study of Health in Pomerania [SHIP-1; N = 1,639] and SHIP-Trend-0 [ N = 2,439]) were analyzed. Participants received a half-mouth periodontal examination, and teeth were counted. CPET was based on symptom limited-exercise tests on a bicycle ergometer. Associations of periodontitis parameters with CPET parameters were analyzed by confounder-adjusted multivariable linear regression. In the total sample, mean pocket probing depth (PPD), mean clinical attachment levels, and number of teeth were consistently associated with peak oxygen uptake (peakVO2) and exercise duration in both studies, even after restriction to cardiorespiratory healthy participants. Statistically significant associations with oxygen uptake at anaerobic threshold (VO2@AT), slope of the efficiency of ventilation in removing carbon dioxide, and peak oxygen pulse (VÉ/VCO2 slope) occurred. Further, interactions with age were identified, such that mainly older individuals with higher levels of periodontal disease severity were associated with lower peakVO2. Restricted to never smokers, associations with mean clinical attachment levels and the number of teeth mostly diminished, while associations of mean PPD with peakVO2, VO2@AT, VÉ/VCO2 slope, and exercise duration in SHIP-1 and SHIP-Trend-0 were confirmed. In SHIP-1, mean peakVO2 was 1,895 mL/min in participants with a mean PPD of 1.6 mm and 1,809 mL/min in participants with a mean PPD of 3.7 mm. To conclude, only mean PPD reflecting current disease severity was consistently linked to cardiorespiratory fitness in 2 cross-sectional samples of the general population. If confirmed in well-designed large-scale longitudinal studies, the association between periodontitis and cardiorespiratory fitness might provide a biologically plausible mechanism linking periodontitis with cardiometabolic diseases.

scholarly journals Is Bisphosphonate-Related Osteonecrosis of the Jaw an Infection? A Histological and Microbiological Ten-Year Summary

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
A. M. Hinson ◽  
C. W. Smith ◽  
E. R. Siegel ◽  
B. C. Stack
Keyword(s):  
Systematic Review ◽  
Disease Severity ◽  
Large Scale ◽  
Clinical Signs ◽  
Signs And Symptoms ◽  
Osteonecrosis Of The Jaw ◽  
Multifactorial Disease ◽  
Clinical Signs And Symptoms ◽  
Surgical Treatments

The role of infection in the etiology of bisphosphonate-related osteonecrosis of the jaw (BRONJ) is poorly understood. Large-scale epidemiological descriptions of the histology and microbiology of BRONJ are not found in the literature. Herein, we present a systematic review of BRONJ histology and microbiology (including demographics, immunocompromised associations, clinical signs and symptoms, disease severity, antibiotic and surgical treatments, and recovery status) validating that infection should still be considered a prime component in the multifactorial disease.

Rare, Damaging DNA Variants in CORIN and Risk of Coronary Artery Disease: Insights From Functional Genomics and Large-Scale Sequencing Analyses

2021 ◽  
Author(s):  
Minxian Wang ◽  
Vivian S. Lee-Kim ◽  
Deepak S. Atri ◽  
Nadine H. Elowe ◽  
John Yu ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Association Analysis ◽  
Rare Variant ◽  
Odds Ratio ◽  
Large Scale ◽  
Missense Mutations ◽  
Rare Variant Association ◽  
Missense Variants ◽  
Artery Disease

Background: Corin is a protease expressed in cardiomyocytes that plays a key role in salt handling and intravascular volume homeostasis via activation of natriuretic peptides. It is unknown if Corin loss-of-function (LOF) is causally associated with risk of coronary artery disease (CAD). Methods: We analyzed all coding CORIN variants in an Italian case-control study of CAD. We functionally tested all 64 rare missense mutations in Western Blot and Mass Spectroscopy assays for proatrial natriuretic peptide cleavage. An expanded rare variant association analysis for Corin LOF mutations was conducted in whole exome sequencing data from 37 799 CAD cases and 212 184 controls. Results: We observed LOF variants in CORIN in 8 of 1803 (0.4%) CAD cases versus 0 of 1725 controls ( P , 0.007). Of 64 rare missense variants profiled, 21 (33%) demonstrated <30% of wild-type activity and were deemed damaging in the 2 functional assays for Corin activity. In a rare variant association study that aggregated rare LOF and functionally validated damaging missense variants from the Italian study, we observed no association with CAD—21 of 1803 CAD cases versus 12 of 1725 controls with adjusted odds ratio of 1.61 ([95% CI, 0.79–3.29]; P =0.17). In the expanded sequencing dataset, there was no relationship between rare LOF variants with CAD was also observed (odds ratio, 1.15 [95% CI, 0.89–1.49]; P =0.30). Consistent with the genetic analysis, we observed no relationship between circulating Corin concentrations with incident CAD events among 4744 participants of a prospective cohort study—sex-stratified hazard ratio per SD increment of 0.96 ([95% CI, 0.87–1.07], P =0.48). Conclusions: Functional testing of missense mutations improved the accuracy of rare variant association analysis. Despite compelling pathophysiology and a preliminary observation suggesting association, we observed no relationship between rare damaging variants in CORIN or circulating Corin concentrations with risk of CAD.

scholarly journals Regression Modeling and Meta-Analysis of Diagnostic Accuracy of SNP-Based Pathogenicity Detection Tools for UGT1A1 Gene Mutation

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Fakher Rahim ◽  
Hamid Galehdari ◽  
Javad Mohammadi-asl ◽  
Najmaldin Saki
Keyword(s):  
Meta Analysis ◽  
Genomic Variation ◽  
Missense Mutations ◽  
Suggested Model ◽  
Pathogenicity Prediction ◽  
Mutation Score ◽  
Functional Scores ◽  
Comprehensive Search ◽  
Overall Performance

Aims. This review summarized all available evidence on the accuracy of SNP-based pathogenicity detection tools and introduced regression model based on functional scores, mutation score, and genomic variation degree. Materials and Methods. A comprehensive search was performed to find all mutations related to Crigler-Najjar syndrome. The pathogenicity prediction was done using SNP-based pathogenicity detection tools including SIFT, PHD-SNP, PolyPhen2, fathmm, Provean, and Mutpred. Overall, 59 different SNPs related to missense mutations in the UGT1A1 gene, were reviewed. Results. Comparing the diagnostic OR, our model showed high detection potential (diagnostic OR: 16.71, 95% CI: 3.38–82.69). The highest MCC and ACC belonged to our suggested model (46.8% and 73.3%), followed by SIFT (34.19% and 62.71%). The AUC analysis showed a significance overall performance of our suggested model compared to the selected SNP-based pathogenicity detection tool (P=0.046). Conclusion. Our suggested model is comparable to the well-established SNP-based pathogenicity detection tools that can appropriately reflect the role of a disease-associated SNP in both local and global structures. Although the accuracy of our suggested model is not relatively high, the functional impact of the pathogenic mutations is highlighted at the protein level, which improves the understanding of the molecular basis of mutation pathogenesis.

scholarly journals Investigating structure function relationships in the NOTCH family through large-scale somatic DNA sequencing studies

2020 ◽  
Author(s):  
Michael W J Hall ◽  
David Shorthouse ◽  
Philip H Jones ◽  
Benjamin A Hall
Keyword(s):  
Dna Sequencing ◽  
Structure Function ◽  
Calcium Binding ◽  
Large Scale ◽  
Driver Mutations ◽  
Missense Mutations ◽  
Mutant Selection ◽  
Ligand Interaction ◽  
Binding Interface

AbstractThe recent development of highly sensitive DNA sequencing techniques has detected large numbers of missense mutations of genes, including NOTCH1 and 2, in ageing normal tissues. Driver mutations persist and propagate in the tissue through a selective advantage over both wild-type cells and alternative mutations. This process of selection can be considered as a large scale, in vivo screen for mutations that increase clone fitness. It follows that the specific missense mutations that are observed in individual genes may offer us insights into the structure-function relationships. Here we show that the positively selected missense mutations in NOTCH1 and NOTCH2 in human oesophageal epithelium cause inactivation predominantly through protein misfolding. Once these mutations are excluded, we further find statistically significant evidence for selection at the ligand binding interface and calcium binding sites. In this, we observe stronger evidence of selection at the ligand interface on EGF12 over EGF11, suggesting that in this tissue EGF12 may play a more important role in ligand interaction. Finally, we show how a mutation hotspot in the NOTCH1 transmembrane helix arises through the intersection of both a high mutation rate and residue conservation. Together these insights offer a route to understanding the mechanism of protein function through in vivo mutant selection.

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