scholarly journals CIC missense variants contribute to susceptibility for spina bifida

2021 ◽  
Author(s):  
Xiao Han ◽  
Xuanye Cao ◽  
Vanessa Aguiar-Pulido ◽  
Wei Yang ◽  
Menuka Karki ◽  
...  
Keyword(s):  
Spina Bifida ◽  
Cell Line ◽  
Neural Tube ◽  
Folate Receptor ◽  
Spinocerebellar Ataxia Type ◽  
Loss Of Function ◽  
Missense Variants ◽  
Increased Risk ◽  
Cell Line Hela

Neural Tube Defects (NTDs) are congenital malformations resulting from abnormal embryonic development of the brain, spine, or spinal column. The genetic etiology of human NTDs remains poorly understood despite intensive investigation. CIC, homolog of the Capicua transcription repressor, has been reported to interact with ataxin-1 (ATXN1) and participate in the pathogenesis of spinocerebellar ataxia type 1. Our previous study demonstrated that CIC loss of function (LoF) variants contributed to cerebral folate deficiency by downregulating folate receptor 1 (FOLR1) expression. Given the importance of folate transport in neural tube formation, we hypothesized that CIC variants could contribute to increased risk for NTDs by depressing embryonic folate concentrations. In this study, we examined CIC variants from whole genome sequencing (WGS) data of 140 isolated spina bifida cases and identified 8 missense variants of CIC gene. We tested the pathogenicity of the observed variants through multiple in vitro experiments. We determined that CIC variants decreased FOLR1 protein level and planar cell polarity (PCP) pathway signaling in a human cell line (HeLa). In a murine cell line (NIH3T3), CIC loss of function variants down regulated PCP signaling. Taken together, this study provides evidence supporting CIC as a risk gene for human NTD.

scholarly journals Loss-of-function and missense variants in NSD2 cause decreased methylation activity and are associated with a distinct developmental phenotype

2021 ◽  
Author(s):  
Paolo Zanoni ◽  
Katharina Steindl ◽  
Deepanwita Sengupta ◽  
Pascal Joset ◽  
Angela Bahr ◽  
...  
Keyword(s):  
Loss Of Function ◽  
Mild Phenotype ◽  
Psychological Issues ◽  
Missense Variants ◽  
Mild Developmental Delay ◽  
Pathogenic Variants ◽  
In Silico Modeling ◽  
And Function ◽  
Methylation Activity

Abstract Purpose Despite a few recent reports of patients harboring truncating variants in NSD2, a gene considered critical for the Wolf–Hirschhorn syndrome (WHS) phenotype, the clinical spectrum associated with NSD2 pathogenic variants remains poorly understood. Methods We collected a comprehensive series of 18 unpublished patients carrying heterozygous missense, elongating, or truncating NSD2 variants; compared their clinical data to the typical WHS phenotype after pooling them with ten previously described patients; and assessed the underlying molecular mechanism by structural modeling and measuring methylation activity in vitro. Results The core NSD2-associated phenotype includes mostly mild developmental delay, prenatal-onset growth retardation, low body mass index, and characteristic facial features distinct from WHS. Patients carrying missense variants were significantly taller and had more frequent behavioral/psychological issues compared with those harboring truncating variants. Structural in silico modeling suggested interference with NSD2’s folding and function for all missense variants in known structures. In vitro testing showed reduced methylation activity and failure to reconstitute H3K36me2 in NSD2 knockout cells for most missense variants. Conclusion NSD2 loss-of-function variants lead to a distinct, rather mild phenotype partially overlapping with WHS. To avoid confusion for patients, NSD2 deficiency may be named Rauch–Steindl syndrome after the delineators of this phenotype.

scholarly journals A combined in silico, in vitro and clinical approach to characterise novel pathogenic missense variants in PRPF31 in retinitis pigmentosa

2018 ◽  
Author(s):  
Gabrielle Wheway ◽  
Liliya Nazlamova ◽  
Nervine Meshad ◽  
Samantha Hunt ◽  
Nicola Jackson ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
In Silico ◽  
Autosomal Dominant ◽  
Missense Variant ◽  
Incomplete Penetrance ◽  
Clinical Approach ◽  
Loss Of Function ◽  
Autosomal Dominant Retinitis Pigmentosa ◽  
Missense Variants

AbstractAt least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localise to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood.In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T>A, p.Ile114Asn.This work demonstrates how in silico modelling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.

In vitro studies on potentiation of cytotoxic effects of anticancer drugs by interferon on a human neoplastic cell line (HeLa)

1983 ◽  
Vol 20 (2) ◽  
pp. 131-138 ◽  
Author(s):  
Shoichi Yamamoto ◽  
Hiroyoshi Tanaka ◽  
Toshinori Kanamori ◽  
Masahiro Nobuhara ◽  
Masayoshi Namba
Keyword(s):  
Cell Line ◽  
Anticancer Drugs ◽  
Neoplastic Cell ◽  
In Vitro Studies ◽  
Cytotoxic Effects ◽  
Cell Line Hela ◽  
Line Hela

GFI1 Is a Tumor Suppressor in Myeloid Progenitors

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2942-2942
Author(s):  
Aditya Chaubey ◽  
Shane Hormon ◽  
Chinavenmeni S. Velu ◽  
Tristan Bourdeau ◽  
Jinfang Zhu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Myeloid Leukemia ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Increased Risk ◽  
Myeloid Leukemias ◽  
Dose Dependent ◽  
Anterior Posterior

Abstract In severe congenital neutropenia (SCN) patients and mice with Growth factor independent-1 (Gfi1) loss of function, arrested progenitors are suspended in a hyperproliferative state while terminal granulpoiesis is blocked. SCN patients are at increased risk for the development of acute myeloid leukemia. We demonstrate that Gfi1 directly targets HoxA9, Pbx1 and Meis1 during normal myelopoiesis. Gfi1−/− progenitors exhibit elevated levels of HoxA9, Pbx1 and Meis1, exaggerated HoxA9-Pbx1-Meis1 activity, and increased persistence in vivo and in vitro. Limiting HoxA9 alleles corrects, in a dose dependent manner, in vivo and in vitro phenotypes observed with loss of Gfi1. Moreover, in a manner conserved in Drosophila anterior/posterior patterning, we demonstrate that these factors can compete for occupancy of DNA sequences encoding composite Gfi1-HoxA9-Pbx1-Meis1 binding sites. Finally, the expression of Gfi1 and HoxA9 are inverse and stratify human myeloid leukemias, suggesting a role for HoxA9- Gfi1 antagonism in human AML. In agreement with this, a myeloproliferative disorder progresses into a rapid, lethal and transplantable myeloid leukemia in a Gfi1−/− setting. We conclude that the lifespan and oncogenic transformation of hematopoietic progenitor cells is regulated through a conserved competition between Gfi1 and HoxA9-Pbx1-Meis1.

scholarly journals Genetic Analysis of Osteoblast Activity Identifies Zbtb40 as a Regulator of Osteoblast Activity and Bone Mass

2019 ◽  
Author(s):  
Madison L. Doolittle ◽  
Gina M Calabrese ◽  
Larry D. Mesner ◽  
Dana A. Godfrey ◽  
Robert D. Maynard ◽  
...  
Keyword(s):  
Bone Formation ◽  
Genetic Basis ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Loss Of Function ◽  
Mineral Density ◽  
Osteoblast Activity ◽  
Genome Wide ◽  
Increased Risk

ABSTRACTOsteoporosis is a genetic disease characterized by progressive reductions in bone mineral density (BMD) leading to an increased risk of fracture. Over the last decade, genome-wide association studies (GWASs) have identified over 1000 associations for BMD. However, as a phenotype BMD is challenging as bone is a multicellular tissue affected by both local and systemic physiology. Here, we focused on a single component of BMD, osteoblast-mediated bone formation in mice, and identified associations influencing osteoblast activity on mouse Chromosomes (Chrs) 1, 4, and 17. The locus on Chr. 4 was in an intergenic region between Wnt4 and Zbtb40, homologous to a locus for BMD in humans. We tested both Wnt4 and Zbtb40 for a role in osteoblast activity and BMD. Knockdown of Zbtb40, but not Wnt4, in osteoblasts drastically reduced mineralization. Additionally, loss-of-function mouse models for both genes exhibited reduced BMD. Our results highlight that investigating the genetic basis of in vitro osteoblast mineralization can be used to identify genes impacting bone formation and BMD.

scholarly journals Docking-designed Green Synthesis and In-Vitro Anticancer Studies of New Binuclear Se-N-Heterocyclic Carbene Adducts and their Azolium Salts

2021 ◽  
Author(s):  
Muhammad Atif ◽  
Mansoureh Nazari V ◽  
Mohamed B Khadeer Ahamed ◽  
Maryam Aslam ◽  
Aman Shah Abdul Majid ◽  
...  
Keyword(s):  
Growth Factor ◽  
Cell Line ◽  
Angiogenic Factor ◽  
Breast Adenocarcinoma ◽  
Cervical Cancer Cell Line ◽  
Synthetic Approach ◽  
Standard Drug ◽  
Cell Line Hela ◽  
Benzimidazolium Salts

Abstract Two binuclear selenium adducts (5 and 6) were designed using molecular docking approach while finding their promising interaction to four angiogenic factor-proteins including COX-1 (Cyclooxygenase-1), VEGF-A (vascular endothelial growth factor A), HIF (Hypoxia-inducible factor) and EGF (human epidermal growth factor). They were consequently synthesized using In-situ coordination approach. The green synthetic approach was employed for coordination as it was carried out in water instead of organic solvents. The synthesized adducts as well as their respective bis-benzimidazolium salts (2 and 4) were confirmed by 1H and 13C-NMR along with FT-IR spectroscopy. The both were, then, subjected to In-vitro anticancer activities against breast adenocarcinoma cell line (MCF-7), cervical cancer cell line (Hela), mouse melanoma cell line (B16F10) and retinal ganglion cell line (RGC-5) using MTT assay while comparing their activities with a commercially established standard-drug 5-Fluorouracil. However, the exceptional activities of both adducts and bis-benzimidazolium salts were explored.

An in vitro study of biological safety of condoms and their additives

2003 ◽  
Vol 22 (12) ◽  
pp. 659-664 ◽  
Author(s):  
N A Motsoane ◽  
M J Bester ◽  
E Pretorius ◽  
P J Becker
Keyword(s):  
Hela Cell ◽  
Cell Viability ◽  
Cell Line ◽  
Tumor Cell Line ◽  
Toxic Effects ◽  
Specific Cell ◽  
Epithelial Tumor ◽  
Hela Cell Lines ◽  
Cell Line Hela

The use of condoms to prevent sexually transmitted diseases, especially HIV, is widely encouraged. Condoms contain latex, nonspermicidal lubricants (such as dimethylsiliconium) and other nonspecified compounds, such as colorants and flavorings. Latex causes allergy reaction in susceptible individuals but little is known regarding the cytotoxic effects of other additives. The objective of this study was to develop a sensitive in vitrosystem to determine the toxic effects of condom material. The modified L929 FDA method and a more specific cell type, such as the cervical epithelial tumor cell line HeLa, was used. Lubricated (LC), lubricated and flavored (LFC), and lubricated, flavored and colored condoms (LFCC) were evaluated. Washings containing condom surface material were prepared by washing condom fragments in medium for different time intervals. Changes in cell number, viability and lysosome integrity in the L929 and HeLa cell lines was determined using the Crystal Violet, MTT and Neutral Red assays, respectively. The condom type affected cell viability and lysosome integrity, with LC inducing an increase in cell viability and LFC a decrease in lysosome integrity. The HeLa cell line in combination with the MTT and NR assay was the most sensitive in vitro system to determine the toxic effects of condom material.

scholarly journals Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions

2020 ◽  
Vol 23 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Xiaolei Zhang ◽  
Roddy Walsh ◽  
Nicola Whiffin ◽  
Rachel Buchan ◽  
William Midwinter ◽  
...  
Keyword(s):  
State Of The Art ◽  
Adverse Outcomes ◽  
Clinical Severity ◽  
Specific Information ◽  
Loss Of Function ◽  
Missense Variants ◽  
Pathogenicity Prediction ◽  
Increased Risk ◽  
Inherited Cardiac Conditions ◽  
Disease Specific

Abstract Purpose Accurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning variant prioritization tools are imprecise and ignore important parameters defining gene–disease relationships, e.g., distinct consequences of gain-of-function versus loss-of-function variants. We hypothesized that incorporating disease-specific information would improve tool performance. Methods We developed a disease-specific variant classifier, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias. We assessed CardioBoost’s ability to discriminate known pathogenic from benign variants, prioritize disease-associated variants, and stratify patient outcomes. Results CardioBoost has high global discrimination accuracy (precision recall area under the curve [AUC] 0.91 for cardiomyopathies; 0.96 for arrhythmias), outperforming existing tools (4–24% improvement). CardioBoost obtains excellent accuracy (cardiomyopathies 90.2%; arrhythmias 91.9%) for variants classified with >90% confidence, and increases the proportion of variants classified with high confidence more than twofold compared with existing tools. Variants classified as disease-causing are associated with both disease status and clinical severity, including a 21% increased risk (95% confidence interval [CI] 11–29%) of severe adverse outcomes by age 60 in patients with hypertrophic cardiomyopathy. Conclusions A disease-specific variant classifier outperforms state-of-the-art genome-wide tools for rare missense variants in inherited cardiac conditions (https://www.cardiodb.org/cardioboost/), highlighting broad opportunities for improved pathogenicity prediction through disease specificity.

scholarly journals The Golgi matrix protein giantin is required for normal cilia function in zebrafish

2017 ◽  
Author(s):  
Dylan J.M. Bergen ◽  
Nicola L. Stevenson ◽  
Roderick E.H. Skinner ◽  
David J. Stephens ◽  
Chrissy L. Hammond
Keyword(s):  
Neural Tube ◽  
Matrix Protein ◽  
Intraflagellar Transport ◽  
Loss Of Function ◽  
Golgi Stack ◽  
Summary Statement ◽  
Almost All ◽  
Golgi Organization ◽  
Golgi Matrix

AbstractThe Golgi is essential for glycosylation of newly synthesised proteins including almost all cell-surface and extracellular matrix proteoglycans. Giantin, encoded by the golgb1 gene, is a member of the golgin family of proteins that reside within the Golgi stack but its function remains elusive. Loss-of-function of giantin in rats causes osteochondrodysplasia; knockout mice show milder defects, notably a cleft palate. In vitro, giantin has been implicated in Golgi organization, biosynthetic trafficking, and ciliogenesis. Here we show that loss-of-function of giantin in zebrafish, using either morpholino or knockout techniques, causes defects in cilia function. Giantin morphants have fewer cilia in the neural tube and those remaining are longer. Mutants have the same number of cilia in the neural tube but these cilia are also elongated. Scanning electron microscopy shows that loss of giantin results in an accumulation of material at the ciliary tip, consistent with a loss-of-function of retrograde intraflagellar transport. Mutants show milder defects than morphants consistent with adaptation to loss of giantin.Summary statementLoss of giantin following either morpholino injection or genome editing in zebrafish results in defects in ciliogenesis.

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