Host Defense and Parasite Evasion
Eric S. Loker, Bruce V. Hofkin in Parasitology, 2023
The CRISPR system, in addition to being a fascinating and effective means of protection of bacteria from their pathogens, is also worthy of mention for its exploitation by biologists as a powerful and specific gene-editing tool, including for host–parasite studies. The 2020 Nobel prize in chemistry was awarded to Dr. Jennifer Doudna and Dr. Emmanuelle Charpentier for their ground-breaking discoveries with CRISPR gene editing. Applications of CRISPR technology relevant to parasitology are mentioned elsewhere in the book (e.g. Chapters 8 p. 411, and 9 p. 436). Basically, we have learned to make various DNA constructs bearing sequences encoding Cas enzymes and to introduce them into cells of many kinds, including human cells. Also included in the constructs are sequences that specifically match those of target genes we wish to modify or disable. Depending on the specific approach taken, the target gene can be disabled by addition or deletion of incorrect bases (an indel mutation), or modified to have a different function or altered expression (Figure 4.3). Here it must be stressed that this powerful technology has the potential to have “off-target” effects and alter genes other than those intended. Also, genomes of targeted cells may devise ways to protect themselves from such modifications. Many more sophisticated variations on this common theme are constantly being developed by the bioengineering community to effect precise and efficient gene-editing changes.
A Novel Complex Indel Mutation in the Fibrinogen Aα Chain Gene in an Asian Child with Systemic Amyloidosis
Gilles Grateau, Robert A. Kyle, Martha Skinner in Amyloid and Amyloidosis, 2004
Systemic amyloidosis in early childhood is extremely rare, and is usually of AA type complicating JIA and other chronic inflammatory diseases. We report the molecular basis of amyloidosis that presented with asymptomatic proteinuria in an otherwise healthy Korean girl aged 7 years, who progressed to end-stage renal failure associated with amyloid hepatomegaly within 2 years. A renal biopsy showed enlarged glomeruli virtually replaced by amyloid, but no interstitial or vascular involvement, an appearance identical to that seen in more than 40 Caucasian patients we have evaluated with hereditary fibrinogen A α chain Glu526Val amyloidosis. The amyloid deposits in fixed sections stained specifically with antibodies to fibrinogen, and we identified a frameshift deletion-insertion (indel) mutation in one allele of her fibrinogen A (chain gene (FGA NM_000508.2, c.1636_1650del, 1649_1650insCA). This encodes a partly novel peptide and a premature stop signal (517_522delinsQSfsX548), similar to the two previously reported amyloidogenic point deletions at positions 522 and 524. The mutation was absent in samples verified to be from her parents, indicating that it had occurred de novo. No mutations were identified in the other genes known to be associated with hereditary renal amyloid. This is the first case of AFib characterized in an Asian individual, and the distinctive renal histology offered a strong clue to the diagnosis. The disease is potentially curable by combined hepatorenal transplantation.
Clinical Manifestation of Mitochondrial Disorders in Childhood
Shamim I. Ahmad in Handbook of Mitochondrial Dysfunction, 2019
Mitochondrial disorders were previously considered as rare; however, despite the fact that the precise prevalence of mitochondria disorders is difficult to find, current epidemiological studies suggest otherwise. The minimum disease prevalence in adults is established to about 12.5 per 100,000 in adults and 4.7 per 100,000 in children (Skladal et al., 2003; Thorburn, 2004; Schaefer et al., 2008; Bannwarth et al., 2013; Gorman et al., 2015). The research team of Patrick Chinnery in the United Kingdom estimated population prevalence even of one in 200 for mtDNA point mutations (including small indel mutations) (Chinnery et al., 2012). The most frequent primary mtDNA disorders are caused by point mutations and large-scale mtDNA deletions. Whereas point mtDNA mutations are usually maternally inherited, large-scale mtDNA deletions typically arise de novo during embryonic development (Alston et al., 2017). Genetic and biochemical causes of mitochondrial disorders summarizes Table 1.
Molecular-genetic diagnostics of von Hippel-Lindau syndrome (VHL) in Bulgaria: first complex mutation event in the VHL gene
Published in International Journal of Neuroscience, 2018
Maria Glushkova, Petia Dimova, Iglika Yordanova, Tihomir Todorov, Ivan Tourtourikov, Vanyo Mitev, Albena Todorova
We report here five genetically confirmed Bulgarian patients with suspected VHL. One of the mutations is novel and consists of a complex mutation event combining duplication and an indel. It is obvious that in our country, the clinical diagnosis of the VHL disease is difficult not only because of the heterogeneous manifestation of the condition, but probably also because of the insufficient knowledge on the established diagnostic criteria, which are necessary as a good platform for doing genetic testing for VHL. Nevertheless, we believe that our results confirm the role of the molecular genetic testing in proving or revising the diagnosis, but mainly in affected patients and their family members, in whom it has to be strongly recommended as important for improving the early diagnosis, the intensive carrier supervision and the appropriate treatment of the malignancies.
Targeted next-generation DNA sequencing identifies Notch signaling pathway mutation as a predictor of radiation response
Published in International Journal of Radiation Biology, 2019
Seung Hyuck Jeon, Eui Kyu Chie, Yi-Jun Kim, Kyung-Hun Lee, Hyun-Seob Lee, Min Jung Kim, Seock-Ah Im, Jong-Il Kim, Tae-You Kim
Single nucleotide variants (SNVs) were detected using MuTect (version 1.1.7) and mpileup in SAMtools. SNVs with at least 100× coverage and 15% of allele frequency were filtered because mutations with lower frequencies may not have significant effects on tumor biology and the filtering process could help to remove variations derived from formalin fixation artifacts (Wong et al. 2014). The followings were filtered for indel mutations: mutations with allele depth ≥3 with total depth ≥10 for hotspot mutations and ≥50 for non-hotspot mutations and allele frequency ≥5% for hotspot mutation and ≥10% for non-hotspot mutation. Somatic variants (a) with a minor allele frequency >1% in 1000 genome alleles (East Asian), Exome Variant Server 6500, Exome Aggregation Consortium (East Asian), and 1303 Korean whole exomes (Kwak et al. 2017), (b) segmental duplications of human genome not reported in The Cancer Genome Atlas data, (c) observed in this study >1% and average allele fraction <10%, and (d) in the repeat region of AR were filtered out. Additionally, phred-scaled Combined Annotation Dependent Depletion (CADD) score (Kircher et al. 2014) was calculated for detected SNVs. Variants with a CADD score ≥10, corresponding to the top 10% deleterious variants, were considered pathogenic and those with a score <10 were considered nonpathogenic. Nonpathogenic SNVs were filtered out from the analysis.
Analysis of polymorphisms in genes associated with the FA/BRCA pathway in three patients with multiple primary malignant neoplasms
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2019
Le Wang, Hao Wang, Ting Wang, Jinhui Liu, Wei Chen, Yamin Wang, Chao Chen, Hongli Zhu, Penggao Dai
We implement below steps to obtain the candidate genes based on SNP and INDEL mutation across three patients.1. Filtering out dbSNP_nonflagged (including minor allele frequency (MAF) ≥1% and clinically irrelevant mutation loci). This step retained mutation loci that were not in dbSNP_nonflagged. 2. Filtering mutation loci from the 1000 Genomes Project database [7] (frequency >0.005 in the human population) to obtain rare mutations that can cause disease. This step retained mutation loci in the 1000 G with a frequency <0.005. 3. Screening of mutations in exons or splice sites (10 base pairs upstream and downstream). 4. Exclusion of synonymous mutations (do not change encoded amino acids) to obtain mutations affecting gene expression products. 5. Obtaining non-synonymous mutation loci affecting protein function based on SIFT [8] prediction. A mutation locus with an SIFT value <0.05 was considered to have large effects on gene function. 6. According to the target of gene polymorphisms conferring genetic susceptibility, databases were selected for alignment and screening to obtain mutated genes and loci.
Related Knowledge Centers
- Bloom Syndrome
- Coding Region
- Frameshift Mutation
- Genome
- Nucleobase
- Nucleotide
- Insertion
- Deletion
- Structural Variation
- Point Mutation