scholarly journals Insertion of the protective APP A673T mutation by CRISPR/Cas9 base editing or PRIME editing

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 669-669
Author(s):  
Jacques P Tremblay ◽  
Antoine Guyon ◽  
Joël Rousseau ◽  
Guillaume Tremblay ◽  
Francis-Gabriel Begin ◽  
...  
Keyword(s):  
Beta Amyloid ◽  
Sporadic Alzheimer’S Disease ◽  
Single Nucleotide ◽  
Amyloid Peptides ◽  
Base Editing ◽  
Beta Secretase ◽  
Human Neurons ◽  
Nucleotide Mutation ◽  
App Gene ◽  
Therapeutic Avenue

Abstract There is currently no treatment for Alzheimer disease (AD). However, the Icelandic mutation in the APP gene (A673T) has been shown to confer a protection against the onset and development of AD (Jonsson et al. Nature 2012). This single nucleotide mutation in APP exon 16 reduces the cleavage of the APP protein by the beta-secretase by 40% thus preventing the development of AD even in persons more than 95 years old. Our research group has initially shown that the presence of the A673T mutation in an APP gene reduced the secretion of beta-amyloid peptides even if there is also a FAD mutation in the gene. This is the case for 14 different FAD mutations. We have used CRISPR/Cas9 base editing and PRIME editing technologies to insert the A673T mutation in the APP gene. We have compared several different cytidine base editor complexes to achieve the most effective and accurate genome modification possible in HEK293T cells and in SH-SY5Y neuroblastomas. The insertion of the A673T mutation in cells containing the London mutation reduced the secretion of beta-amyloid peptides. We are currently using lentiviral vectors to infect neurons from a mouse model and human neurons induced from fibroblasts of a patient with the London mutation. The insertion of the protective Icelandic mutation in the APP gene using these editing technologies opens a new potential therapeutic avenue not only for Familial Alzheimer’s diseases but also for sporadic Alzheimer’s disease.

scholarly journals In Silico Analysis of Pathogenic CRB1 Single Nucleotide Variants and Their Amenability to Base Editing as a Potential Lead for Therapeutic Intervention

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1908
Author(s):  
Julia-Sophia Bellingrath ◽  
Michelle E. McClements ◽  
Maria Kaukonen ◽  
Manuel Dominik Fischer ◽  
Robert E. MacLaren
Keyword(s):  
In Silico Analysis ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Base Editing ◽  
Retinal Degenerations ◽  
Dna Base ◽  
Variation Database ◽  
Therapeutic Avenue ◽  
Selection Of ◽  
Cas Proteins

Mutations in the Crumbs homolog 1 (CRB1) gene cause both autosomal recessive retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA). Since three separate CRB1 isoforms are expressed at meaningful levels in the human retina, base editing shows promise as a therapeutic approach. This retrospective analysis aims to summarise the reported pathogenic CRB1 variants and investigate their amenability to treatment with currently available DNA base editors. Pathogenic single nucleotide variants (SNVs) were extracted from the Leiden open-source variation database (LOVD) and ClinVar database and coded by mutational consequence. They were then analyzed for their amenability to currently available DNA base editors and available PAM sites from a selection of different Cas proteins. Of a total of 1115 unique CRB1 variants, 69% were classified as pathogenic SNVs. Of these, 62% were amenable to currently available DNA BEs. Adenine base editors (ABEs) alone have the potential of targeting 34% of pathogenic SNVs; 19% were amenable to a CBE while GBEs could target an additional 9%. Of the pathogenic SNVs targetable with a DNA BE, 87% had a PAM site for a Cas protein. Of the 33 most frequently reported pathogenic SNVs, 70% were targetable with a base editor. The most common pathogenic variant was c.2843G>A, p.Cys948Arg, which is targetable with an ABE. Since 62% of pathogenic CRB1 SNVs are amenable to correction with a base editor and 87% of these mutations had a suitable PAM site, gene editing represents a promising therapeutic avenue for CRB1-associated retinal degenerations.

scholarly journals A Novel Single-Nucleotide Mutation in a CLAVATA3 Gene Homolog Controls a Multilocular Silique Trait in Brassica rapa L.

2014 ◽  
Vol 7 (12) ◽  
pp. 1788-1792 ◽  
Author(s):  
Chuchuan Fan ◽  
Yudi Wu ◽  
Qingyong Yang ◽  
Yang Yang ◽  
Qingwei Meng ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Nucleotide Mutation

In-Silico and In-vitro Analysis of Human SOS1 Protein Causing Noonan Syndrome – A Novel Approach to Explore the Molecular Pathways

2021 ◽  
Vol 22 ◽  
Author(s):  
Vinoth Sigamani ◽  
Sheeja Rajasingh ◽  
Narasimman Gurusamy ◽  
Arunima Panda ◽  
Johnson Rajasingh
Keyword(s):  
Noonan Syndrome ◽  
In Silico ◽  
Genetic Disorder ◽  
In Vitro Study ◽  
Human Skin Fibroblast ◽  
Nucleotide Polymorphisms ◽  
Gene Expressions ◽  
Single Nucleotide ◽  
Nucleotide Mutation

Aims: Noonan syndrome (NS) is an autosomal dominant genetic disorder caused by single nucleotide mutation in PTPN11, SOS1, RAF1, and KRAS genes. Background: We hypothesize that in-silico analysis of human SOS1 mutations would be a promising predictor in identifying the pathogenic effect of NS. Methods: Here, we computationally analyzed the SOS1 gene to identify the pathogenic non-synonymous single nucleotide polymorphisms (nsSNPs) to cause NS. The variant information of SOS1 was collected from the SNP database (dbSNP). The variants were further analyzed by in-silico tools I-Mutant, iPTREE-STAB, and MutPred to elucidate their structural and functional characteristics. Results: We found that 11 nsSNPs of SOS1 were more pathogenic to cause NS. The 3D modeling of the wild-type and the 11 nsSNPs were performed using I-TASSER and validated via ERRAT and RAMPAGE. SOS1 interacting proteins were analysed through STRING, which showed that SOS1 interacted with cardiac proteins GATA4, TNNT2, and ACTN2. During these interactions, GRB2 and HRAS act as an intermediate molecules between SOS1 and cardiac proteins. These in-silico analyses were validated using induced cardiomyocytes (iCMCs) derived from NS patients carrying SOS1 gene variant c.1654A>G (NS-iCMCs) and compared with control human skin fibroblast-derived iCMCs (C-iCMCs). Our in vitro data further confirmed that the SOS1, GRB2 and HRAS gene expressions as well as the activated ERK protein, were significantly decreased in NS-iCMCs compared to C-iCMCs. Conclusion: This is the first in-silico and in vitro study demonstrating that 11 nsSNPs of SOS1 were playing a deleterious pathogenic role in causing NS.

scholarly journals Beta-Amyloid Peptides Enhance the Proliferative Response of Activated CD4+CD28+ Lymphocytes from Alzheimer Disease Patients and from Healthy Elderly

PLoS ONE ◽  
2012 ◽  
Vol 7 (3) ◽  
pp. e33276 ◽  
Author(s):  
Agnieszka Jóźwik ◽  
Jerzy Landowski ◽  
Leszek Bidzan ◽  
Tamas Fülop ◽  
Ewa Bryl ◽  
...  
Keyword(s):  
Alzheimer Disease ◽  
Proliferative Response ◽  
Beta Amyloid ◽  
Amyloid Peptides ◽  
Healthy Elderly

scholarly journals Association between the c. 2495 A>G ATP7B Polymorphism and Sporadic Alzheimer's Disease

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Serena Bucossi ◽  
Stefania Mariani ◽  
Mariacarla Ventriglia ◽  
Renato Polimanti ◽  
Massimo Gennarelli ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Single Nucleotide Polymorphism ◽  
Logistic Regression ◽  
Atp7b Gene ◽  
Regression Analyses ◽  
Susceptibility Loci ◽  
Nucleotide Polymorphism ◽  
Sporadic Alzheimer’S Disease ◽  
Single Nucleotide

Nonceruloplasmin-bound copper (“free”) is reported to be elevated in Alzheimer's disease (AD). In Wilson's disease (WD) Cu-ATPase 7B protein tightly controls free copper body levels. To explore whether the ATP7B gene harbours susceptibility loci for AD, we screened 180 AD chromosomes for sequence changes in exons 2, 5, 8, 10, 14, and 16, where most of the Mediterranean WD-causing mutations lie. No WD mutation, but sequence changes corresponding to c.1216 T>G Single-Nucleotide Polymorphism (SNP) and c.2495 A>G SNP were found. Thereafter, we genotyped 190 AD patients and 164 controls for these SNPs frequencies estimation. Logistic regression analyses revealed either a trend for the c.1216 SNP (P=.074) or a higher frequency for c.2495 SNP of the GG genotype in patients, increasing the probability of AD by 74% (P=.028). Presence of the GG genotype in ATP7B c.2495 could account for copper dysfunction in AD which has been shown to raise the probability of the disease.

scholarly journals Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

2020 ◽  
Vol 10 (9) ◽  
pp. 3309-3319 ◽  
Author(s):  
Ajith V Pankajam ◽  
Suman Dash ◽  
Asma Saifudeen ◽  
Abhishek Dutta ◽  
Koodali T Nishant
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Loss Of Heterozygosity ◽  
Mutation Rates ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Genome Wide ◽  
Nucleotide Mutation ◽  
Specific Variation ◽  
Chromosomal Changes ◽  
Species Specific

Abstract A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae. The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gross chromosomal changes, and aneuploidy. Short copy number aberrations were observed in the S/R background. LOH data from the S/Y and S/R hybrids were used to construct a LOH map for S288c to identify hotspots. Further, we observe up to a sixfold difference in single nucleotide mutation rates among the S. cerevisiae S/Y and S/R genetic backgrounds. Our results demonstrate LOH is common during mitotic divisions in S. cerevisiae hybrids and also highlight genome-wide differences in LOH patterns and rates of single nucleotide mutations between commonly used S. cerevisiae hybrid genetic backgrounds.

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