scholarly journals Phenotyping Zebrafish Mutant Models to Assess Candidate Genes Associated with Aortic Aneurysm

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 123
Author(s):  
Andrew Prendergast ◽  
Bulat A. Ziganshin ◽  
Dimitra Papanikolaou ◽  
Mohammad A. Zafar ◽  
Stefania Nicoli ◽  
...  
Keyword(s):  
Aortic Aneurysm ◽  
Candidate Genes ◽  
Low Cost ◽  
Positive Control ◽  
Experimental Models ◽  
Loss Of Function ◽  
Skeletal Abnormalities ◽  
Cell Counts ◽  
Uncertain Significance ◽  
Models Of Disease

(1) Background: Whole Exome Sequencing of patients with thoracic aortic aneurysm often identifies “Variants of Uncertain Significance” (VUS), leading to uncertainty in clinical management. We assess a novel mechanism for potential routine assessment of these genes in TAA patients. Zebrafish are increasingly used as experimental models of disease. Advantages include low cost, rapid maturation, and physical transparency, permitting direct microscopic assessment. (2) Methods: Zebrafish loss of function mutations were generated using a CRISPRC/CAS9 approach for EMILIN1 and MIB1 genes similar to VUSs identified in clinical testing. Additionally, “positive control” mutants were constructed for known deleterious variants in FBN1 (Marfan’s) and COL1A2, COL5A1, COL5A2 (Ehlers-Danlos). Zebrafish embryos were followed to six days post-fertilization. Embryos were studied by brightfield and confocal microscopy to ascertain any vascular, cardiac, and skeletal abnormalities. (3) Results: A dramatic pattern of cardiac, cerebral, aortic, and skeletal abnormalities was identified for the known pathogenic FBN1 and COL1A2, COL5A1, and COL5A2 mutants, as well as for the EMILIN1 and MIB1 mutants of prior unknown significance. Visualized abnormalities included hemorrhage (peri-aortic and cranial), cardiomegaly, reduced diameter of the aorta and intersegmental vessels, lower aortic cell counts, and scoliosis (often extremely severe). (4) Conclusion: This pilot study suggests that candidate genes arising in clinical practice may be rapidly assessed via zebrafish mutants—thus permitting evidence-based decisions about pathogenicity. Thus, years-long delays to clinically demonstrate pathogenicity may be obviated. Zebrafish data would represent only one segment of analysis, which would also include frequency of the variant in the general population, in silico genetic analysis, and degree of preservation in phylogeny.

Translational and Functional Oncogenomics. From Cancer-Oriented Genomic Screenings to New Diagnostic Tools and Improved Cancer Treatment

2008 ◽  
Vol 94 (2) ◽  
pp. 172-178
Author(s):  
Enzo Medico ◽  
Keyword(s):  
Candidate Genes ◽  
Cancer Progression ◽  
Human Cancer ◽  
Function Analysis ◽  
Functional Characterization ◽  
Experimental Models ◽  
Diagnostic Tools ◽  
Cancer Genes ◽  
Loss Of Function ◽  
Diagnostic Potential

We present here an experimental pipeline for the systematic identification and functional characterization of genes with high potential diagnostic and therapeutic value in human cancer. Complementary competences and resources have been brought together in the TRANSFOG Consortium to reach the following integrated research objectives: 1) execution of cancer-oriented genomic screenings on tumor tissues and experimental models and merging of the results to generate a prioritized panel of candidate genes involved in cancer progression and metastasis; 2) setup of systems for high-throughput delivery of full-length cDNAs, for gain-of-function analysis of the prioritized candidate genes; 3) collection of vectors and oligonucleotides for systematic, RNA interference-mediated down-regulation of the candidate genes; 4) adaptation of existing cell-based and model organism assays to a systematic analysis of gain and loss of function of the candidate genes, for identification and preliminary validation of novel potential therapeutic targets; 5) proteomic analysis of signal transduction and protein-protein interaction for better dissection of aberrant cancer signaling pathways; 6) validation of the diagnostic potential of the identified cancer genes towards the clinical use of diagnostic molecular signatures; 7) generation of a shared informatics platform for data handling and gene functional annotation. The results of the first three years of activity of the TRANSFOG Consortium are also briefly presented and discussed.

scholarly journals Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Na Li ◽  
Belle W. X. Lim ◽  
Ella R. Thompson ◽  
Simone McInerny ◽  
Magnus Zethoven ◽  
...  
Keyword(s):  
Breast Cancer ◽  
High Risk ◽  
Candidate Genes ◽  
Familial Aggregation ◽  
Loss Of Function ◽  
Cancer Data ◽  
Pathogenic Variants ◽  
New Genes ◽  
Predisposing Genes ◽  
Predisposition Genes

AbstractBreast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. The coding regions and exon–intron boundaries of all candidate genes and 14 previously proposed BC genes were sequenced using custom designed sequencing panels. Pedigree and pathology data were analysed to identify genotype-specific associations. The contribution of ATM, PALB2 and CHEK2 to BC predisposition was confirmed, but not RAD50 and NBN. An overall excess of loss-of-function (LoF) (OR 1.27, p = 9.05 × 10−9) and missense (OR 1.27, p = 3.96 × 10−73) variants was observed in the cases for the 145 candidate genes. Leading candidates harbored LoF variants with observed ORs of 2–4 and individually accounted for no more than 0.79% of the cases. New genes proposed by this study include NTHL1, WRN, PARP2, CTH and CDK9. The new candidate BC predisposition genes identified in BEACCON indicate that much of the remaining genetic causes of high-risk BC families are due to genes in which pathogenic variants are both very rare and convey only low to moderate risk.

Stereoscopically Observed Deformations of a Compliant Abdominal Aortic Aneurysm Model

2011 ◽  
Vol 133 (11) ◽  
Author(s):  
Clark A. Meyer ◽  
Eric Bertrand ◽  
Olivier Boiron ◽  
Valérie Deplano
Keyword(s):  
Abdominal Aortic Aneurysm ◽  
Aortic Aneurysm ◽  
Computational Models ◽  
Imaging System ◽  
Strain Differences ◽  
Cyclic Strain ◽  
Experimental Models ◽  
Body Motion ◽  
Abdominal Aortic ◽  
The Impact

A new experimental setup has been implemented to precisely measure the deformations of an entire model abdominal aortic aneurysm (AAA). This setup addresses a gap between the computational and experimental models of AAA that have aimed at improving the limited understanding of aneurysm development and rupture. The experimental validation of the deformations from computational approaches has been limited by a lack of consideration of the large and varied deformations that AAAs undergo in response to physiologic flow and pressure. To address the issue of experimentally validating these calculated deformations, a stereoscopic imaging system utilizing two cameras was constructed to measure model aneurysm displacement in response to pressurization. The three model shapes, consisting of a healthy aorta, an AAA with bifurcation, and an AAA without bifurcation, were also evaluated with computational solid mechanical modeling using finite elements to assess the impact of differences between material properties and for comparison against the experimental inflations. The device demonstrated adequate accuracy (surface points were located to within 0.07 mm) for capturing local variation while allowing the full length of the aneurysm sac to be observed at once. The experimental model AAA demonstrated realistic aneurysm behavior by having cyclic strains consistent with reported clinical observations between pressures 80 and 120 mm Hg. These strains are 1–2%, and the local spatial variations in experimental strain were less than predicted by the computational models. The three different models demonstrated that the asymmetric bifurcation creates displacement differences but not cyclic strain differences within the aneurysm sac. The technique and device captured regional variations of strain that are unobservable with diameter measures alone. It also allowed the calculation of local strain and removed rigid body motion effects on the strain calculation. The results of the computations show that an asymmetric aortic bifurcation created displacement differences but not cyclic strain differences within the aneurysm sac.

Genetic analysis of Pycr1 and Pycr2 in mice

Genetics ◽  
2021 ◽  
Author(s):  
Morgane G Stum ◽  
Abigail L D Tadenev ◽  
Kevin L Seburn ◽  
Kathy E Miers ◽  
Pak P Poon ◽  
...  
Keyword(s):  
Neuromuscular Disorders ◽  
Subcutaneous Fat ◽  
Mutant Mice ◽  
Loss Of Function ◽  
Proline Biosynthesis ◽  
Cell Counts ◽  
Chemically Induced ◽  
White Blood Cell Counts ◽  
Redundant Functions ◽  
Altered Lipid

Abstract The final step in proline biosynthesis is catalyzed by three pyrroline-5-carboxylate reductases, PYCR1, PYCR2, and PYCR3, which convert pyrroline-5-carboxylate (P5C) to proline. Mutations in human PYCR1 and ALDH18A1 (P5C Synthetase) cause Cutis Laxa (CL), whereas mutations in PYCR2 cause hypomyelinating leukodystrophy 10 (HLD10). Here, we investigated the genetics of Pycr1 and Pycr2 in mice. A null allele of Pycr1 did not show integument or CL-related phenotypes. We also studied a novel chemically-induced mutation in Pycr2. Mice with recessive loss-of-function mutations in Pycr2 showed phenotypes consistent with neurological and neuromuscular disorders, including weight loss, kyphosis, and hind-limb clasping. The peripheral nervous system was largely unaffected, with only mild axonal atrophy in peripheral nerves. A severe loss of subcutaneous fat in Pycr2 mutant mice is reminiscent of a CL-like phenotype, but primary features such as elastin abnormalities were not observed. Aged Pycr2 mutant mice had reduced white blood cell counts and altered lipid metabolism, suggesting a generalized metabolic disorder. PYCR1 and -2 have similar enzymatic and cellular activities, and consistent with previous studies, both were localized in the mitochondria in fibroblasts. Both PYCR1 and -2 were able to complement the loss of Pro3, the yeast enzyme that converts P5C to proline, confirming their activity as P5C reductases. In mice, Pycr1; Pycr2 double mutants were sub-viable and unhealthy compared to either single mutant, indicating the genes are largely functionally redundant. Proline levels were not reduced, and precursors were not increased in serum from Pycr2 mutant mice or in lysates from skin fibroblast cultures, but placing Pycr2 mutant mice on a proline-free diet worsened the phenotype. Thus, Pycr1 and -2 have redundant functions in proline biosynthesis, and their loss makes proline a semi-essential amino acid. These findings have implications for understanding the genetics of CL and HLD10, and for modeling these disorders in mice.

20 Effect of Adding Bioactive Peptide in Combination of Pharmaceutical Zinc Oxide or Organic Acids on Growth Performance, Hematology Profile, and Nutrient Digestibility in Nursery Pigs

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 22-23
Author(s):  
Richard A Mudarra ◽  
Tsung Cheng Cheng Tsai ◽  
Kristopher Bottoms ◽  
Thomas S Shieh ◽  
Casey Bradly ◽  
...  
Keyword(s):  
Growth Performance ◽  
Phase 1 ◽  
Random Effect ◽  
Positive Control ◽  
Negative Control ◽  
Nutrient Digestibility ◽  
Bioactive Peptide ◽  
Nursery Pigs ◽  
Cell Counts ◽  
High Zinc

Abstract To evaluate the effect of bioactive peptide (P) in combination with high level of zinc (HZ) or acidifiers on growth performance, complete blood cell counts (CBC) and nutrient digestibility in nursery pigs, a total of 288 weaned pigs (PIC1050xDNA600) were stratified by initial BW within gender and allotted to 1of 7 treatments. Treatments for phase 1&2 were: 1) nutrient adequate positive control with HZ (PC), 2) nutrient deficient negative control with HZ (NC, -0.13% SID Lysine by reducing fish meal), 3) NC+0.25% peptide (0.25PZ), 4) NC+0.5% peptide (0.5PZ), 5) NC+0.25% peptide with standard zinc (0.25P), 6) NC+0.5% peptide with standard zinc (0.5P), 7) as 5 + 0.1% sodium butyrate and 0.5% benzoic acid (PSB). All pigs were fed a common low Zn diet (197 ppm) during phase 3. The whole blood was obtained from a close-to-average pen-BW pig repeatedly at weaning, and at the end of phase 2 and 3 to determine CBC. Titanium dioxide was used as an indigestible marker to determine nutrient digestibility. Data were analyzed using the Mixed procedures of SAS as a RCBD with treatment as fixed effect, and BW block as random effect. In overall phase 1&2, pigs fed PSB had similar ADG and BW when compared to pigs fed 0.25PZ and both were greater than NC pigs (Table 1). With the same inclusion rate of peptide, pigs fed a high zinc diet had greater BW and ADG than pigs fed a standard zinc diet. PSB pigs had the greatest G:F ratio and nitrogen digestibility among treatments. Increasing peptide in high zinc diets gradually decreased Neutrophil-to-lymphocyte ratio. This study indicates that the improvement in growth performance from pigs fed peptide is pharmaceutical zinc dependent and acidifiers can be an alternative to replace ZnO without affecting growth performance.

scholarly journals Muscle-tendon weakness contributes to chronic fatigue syndrome in Gaucher’s disease

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Mercedes Roca-Espiau ◽  
Marcio Andrade-Campos ◽  
Jorge J. Cebolla ◽  
Laura López de Frutos ◽  
Blanca Medrano-Engay ◽  
...  
Keyword(s):  
Low Cost ◽  
Chronic Fatigue ◽  
Strain Elastography ◽  
Fatigue Syndrome ◽  
Cell Counts ◽  
Enzymatic Replacement Therapy ◽  
Quality Of Life Scale ◽  
Life Scale ◽  
Persistent Fatigue ◽  
Type 3

Abstract Background Chronic fatigue (CFg) is a prevalent symptom in Gaucher disease (GD) at diagnosis (79%) and remains in a quarter of patients after years of therapy. Bone abnormalities are present in over 70% and peripheral neuropathy in about 11% of the patients, which contributes to the disabling and debilitating complications. Our hypothesis is that other factors such as muscle-tendinous weakness could have influence in the development of CFg. Methods We have evaluated the fiber structure and elasticity of muscle-tendinous unit by strain-elastography (S-ELA) and analyzed their influence in the CFg. S-ELA study was performed in Achilles tendon in 25 type 1 and two type 3 GD patients, all of them with fatigue and were on enzymatic replacement therapy for mean 13 years; simultaneously, bone marrow burden by MRI and calcaneus ultrasound densitometry were evaluated. Blood cell counts, plasma biomarkers, GBA1 genotyping, and SF36 quality of life scale (QoL) were also performed. Statistical analysis: descriptive and comparative test. Results All patients showed a normal Achilles tendinous structure. Abnormal stiff grade 2–3 was found in 17/27 (62.9%); in 11/27 (40.7%) of patients, the alteration was bilateral. There were no correlations between the S-ELA results to other variables; nevertheless, a significant correlation between the degree of tendon hardness and the low score on the QoL scales (p = 0.0035) was found. The S-ELA is a sensitive painless, fast, and low cost method to detect muscle-tendinous subclinical dysfunction that could contribute to CFg in GD. The identification of subclinical tendon alteration would be a sign of alarm, focused on the risk of development of bone complications. Conclusion Intratendinous alteration in strain-elastography is an independent variable in GD patients with persistent fatigue.

A transcriptional and post-transcriptional dysregulation of Dishevelled 1 and 2 underlies the Wnt signaling impairment in type I Gaucher disease experimental models

2019 ◽  
Vol 29 (2) ◽  
pp. 274-285 ◽  
Author(s):  
Roberto Costa ◽  
Stefania Bellesso ◽  
Susanna Lualdi ◽  
Rosa Manzoli ◽  
Valeria Pistorio ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Gaucher Disease ◽  
Wnt Pathway ◽  
Experimental Models ◽  
Type I ◽  
Loss Of Function ◽  
Single Nucleotide Variants ◽  
Bone Differentiation

Abstract Bone differentiation defects have been recently tied to Wnt signaling alterations occurring in vitro and in vivo Gaucher disease (GD) models. In this work, we provide evidence that the Wnt signaling multi-domain intracellular transducers Dishevelled 1 and 2 (DVL1 and DVL2) may be potential upstream targets of impaired beta glucosidase (GBA1) activity by showing their misexpression in different type 1 GD in vitro models. We also show that in Gba mutant fish a miR-221 upregulation is associated with reduced dvl2 expression levels and that in type I Gaucher patients single-nucleotide variants in the DVL2 3′ untranslated region are related to variable canonical Wnt pathway activity. Thus, we strengthen the recently outlined relation between bone differentiation defects and Wnt/β-catenin dysregulation in type I GD and further propose novel mechanistic insights of the Wnt pathway impairment caused by glucocerebrosidase loss of function.

The Applications of Natural Zeolites for Cadmium Removal from Sample Water: Models on Laboratory Scale

2011 ◽  
Vol 347-353 ◽  
pp. 1930-1933 ◽  
Author(s):  
Usa Onthong ◽  
Pornpan Pungpo ◽  
Wikanda Thongnueakhaeng
Keyword(s):  
Removal Efficiency ◽  
Low Cost ◽  
Experimental Models ◽  
Laboratory Scale ◽  
Natural Zeolites ◽  
Cadmium Removal ◽  
Adsorption Parameters ◽  
Effective Removal ◽  
Sample Water ◽  
Preliminary Study

The removal of the cadmium ion from aqueous solution was studied in batch experiments using five natural zeolites were obtained from South of Thailnd, Clinoptiolite, Mordenite, Willhensonite, Offretite and Ferrierite, on the basis of experimental models on laboratory scale. Clinoptiolite was used for preliminary study of the adsorption parameters. An hour contact time and 40 g/L of the ratio of zeolite per water sample are optimum adsorption parameters with an average cadmium removal efficiency of 91.68 %. The optimum adsorption conditions were then used for other four natural zeolites. The results show that the effective removal sequence can be listed as Offretite  Clinoptiolite > Willhensonite > Mordenite > Ferrierite. Clinoptiolite, Offretite and Willhensonite are successfully used to reduce significantly cadmium from sample water with removal efficiency ranging from of 87-92%, respectively. Accordingly, the natural zeolites are recommendable adsorbents for highly cadmium removal of industrial wastewater with low cost of wastewater treatments and environmentally friendly chemical processes.

Sequencing candidate genes in African American and Hispanic/ Latino probands with early-onset Atrial Fibrillation

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
B Chalazan ◽  
D Mol ◽  
A Sridhar ◽  
A Ornelas-Loredo ◽  
F Darbar ◽  
...  
Keyword(s):  
African American ◽  
Candidate Genes ◽  
Ethnic Minorities ◽  
Early Onset ◽  
Heart Association ◽  
Read Depth ◽  
Funding Source ◽  
Loss Of Function ◽  
Hispanic Latinos ◽  
Family Based

Abstract Introduction Mutations in cardiac ion channels, structural proteins and signaling molecules have been identified in European whites with early-onset AF (EOAF). However, it remains unclear if genetic variation also contributes to the etiology of EOAF in ethnic minorities. Purpose To determine the prevalence of disease causing variants in candidate AF genes in African American and Hispanic/Latino probands with EOAF. Method In this family-based study, probands of African and Hispanic descent with EOAF (defined as AF ≤65 years) were prospectively enrolled in a clinical-DNA biorepository and underwent targeted sequencing for 60 AF candidate genes. Variants were filtered at 20X read depth and clinically evaluated with American College of Medical Genetics and Genomics and Association for Molecular Pathology (ACMG/AMP) as well as the Association for Clinical Genomic Science (ACGS) criteria for disease-causing mutations. Results Among 227 EOAF probands with mean (SD) age of AF 51.0 (9.9) years, 132 (58.0%) were men and 148 (65.0%) African American and 79 (35.0%) Hispanic/Latino. Sequencing 60 candidate AF genes revealed 90 variants that met filtering criteria and underwent clinical evaluation. We identified 16 (7.0%) EOAF probands with a likely pathogenic or pathogenic variant with the majority being loss of function (62.5%) and located in the TTN gene (50.0%). We confirmed a family history of AF in 24 probands (10.6%) and 6 families with >1 affected member a variant of unknown significance (VUS) in genes encoding for a sodium channel (SCN10A), potassium channel (KCNE5), sarcomeric proteins (MYH6, TTN) and atrial natriuretic peptide (NPPA) co-segregated with AF. Conclusion Gene sequencing in African American and Hispanic/Latinos probands with EOAF identified a small percentage of disease causing variants in patients with EOAF. Our findings not only represent important progress toward molecular phenotyping of EOAF, but also provides insight into the underlying pathophysiology toward targeted mechanism-based therapies for AF in ethnic minorities. Funding Acknowledgement Type of funding source: Private grant(s) and/or Sponsorship. Main funding source(s): American Heart Association

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