-
Journal of Applied Biomedicine Dec 2021Nephrotic syndrome (NS) might be caused by a kidney disorder or it can be a secondary disease. Untreated or resistant to treatment, NS stimulates glomerular damage that...
INTRODUCTION
Nephrotic syndrome (NS) might be caused by a kidney disorder or it can be a secondary disease. Untreated or resistant to treatment, NS stimulates glomerular damage that reduces the kidney function. This reduction leads to the end stage of renal failure. Therefore, it is very important to diagnose NS early, with the aim of inhibiting or lessening its associated morbidity and mortality.
METHODS
Gene polymorphism analysis for the three genes eNOS 27 bp VNTR, GSTP1 and IL-10(1082 G/A) were checked in 98 children with NS and 101 control subjects.
RESULTS
eNOS 27 bp VNTR genotypes and alleles are significantly different in the group of 98 children with NS compared to the 101 control subjects. The frequencies of ab and bb genotypes are significantly lower in patients than in the control group (ab: 17.2% vs. 22.8%; OR: 0.19; 95% CI: 0.06-0.58; p = 0.0026 & bb: 54.7% vs. 70.3%; OR: 0.19; 95% CI: 0.07-0.5; p = 0.0004). However, neither GSTP1 nor IL-10(1082 G/A) genotypes showed any significant difference in both groups.
CONCLUSIONS
eNOS 27 bp VNTR gene might be considered as an independent risk factor in the early prediction of nephrotic syndrome incidence, which may help prevent/reduce the occurrence of other complications associated with the late diagnosis and treatment of the disease.
Topics: Alleles; Child; Egypt; Female; Genotype; Glutathione S-Transferase pi; Humans; Interleukin-10; Male; Minisatellite Repeats; Nephrotic Syndrome; Nitric Oxide Synthase Type III
PubMed: 34907742
DOI: 10.32725/jab.2021.022 -
Acta Orthopaedica Et Traumatologica... Nov 2019The aim of this meta-analysis was to clarify the role of Interleukin-1 receptor antagonist gene (IL1-RN) Variable Number of Tandem Repeats (VNTR) polymorphism on the... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVE
The aim of this meta-analysis was to clarify the role of Interleukin-1 receptor antagonist gene (IL1-RN) Variable Number of Tandem Repeats (VNTR) polymorphism on the risk of OA by means of meta-analysis.
METHODS
Eligible articles were retrieved from PubMed, Web of science and Google scholar with a total of 1187 OA cases and 2659 controls. The strength of the association between the IL1-RN VNTR polymorphism and the risk of OA was assessed by odds ratios (ORs) with the corresponding 95% confidence interval (CI) for each study.
RESULTS
The meta-analysis of seven published studies retrieved from the literature search showed a significantly increased OA risk in the recessive model analysis (22 vs 2L + LL: P = 0.18, I = 32.8, OR(95% CI) = 1.50(1.12, 2.02), P = 0.007), the additive model analysis (22 vs LL: P = 0.08, I = 46.8, OR(95% CI) = 1.56(1.15, 2.12), P = 0.004) and in the allele contrast model (2 vs L: P = 0.02, I = 58.8, OR(95% CI) = 1.20(1.05, 1.36), P = 0.007). By subgroup analysis, the IL1-RN VNTR polymorphism was found to be significantly associated with OA susceptibility in Caucasian and Hospital based case-control study (HCC) groups.
CONCLUSION
This meta-analysis showed that IL1-RN VNTR polymorphism may increase the susceptibility to OA. More studies with detailed information are needed to validate our conclusion.
LEVEL OF EVIDENCE
Level III, diagnostic study.
Topics: DNA; Genetic Predisposition to Disease; Humans; Interleukin 1 Receptor Antagonist Protein; Minisatellite Repeats; Osteoarthritis; Polymorphism, Genetic
PubMed: 31444012
DOI: 10.1016/j.aott.2019.07.004 -
Journal of Affective Disorders Dec 2020Evidences suggest that alterations in circadian rhythms trigger the development of mental disorders. Eveningness, sleep behavior, and circadian genes polymorphisms have...
BACKGROUND
Evidences suggest that alterations in circadian rhythms trigger the development of mental disorders. Eveningness, sleep behavior, and circadian genes polymorphisms have been associated with depression and anxiety symptomatology. However, the mechanism underlying these interactions is not well understood. We investigated the contribution of diurnal preference, sleep habits, and PER3 VNTR polymorphism (rs57875989) to depression and anxiety symptoms in a Northeast sample from the Brazilian population.
METHODS
Eight hundred and four young adults completed the Morningness-Eveningness (MEQ), Munich Chronotype (MCTQ), Center for Epidemiologic Studies - Depression (CES-D), and Beck Anxiety Inventory (BAI) questionnaires. All participants were genotyped and linear regression was performed to test the interactions between the genetic /behavioral variants and depression/ anxiety symptoms.
RESULTS
Eveningness and sleep behaviors (bedtime, wake-up time, sleep duration, and midpoint of sleep) were correlated with depression symptomatology, specifically in somatic factors of the CES-D questionnaire. No correlation was found between diurnal preference/sleep habits with anxiety symptoms for both BAI total score and its factors. However, women with PER3 genotype showed less interpesonal affect in depression symptomatology and more anxiety symptoms in four factors of the BAI questionnaire.
LIMITATIONS
Mainly because this study was based on self-report questionnaires and was limited to undergraduate students aging 18 to 30 years old.
CONCLUSION
These results reinforce a role for sleep and diurnal preference in depression, and PER3 VNTR polymorphism in anxiety symptomatology, particularly in women.
Topics: Adolescent; Adult; Anxiety; Brazil; Circadian Rhythm; Depression; Female; Humans; Minisatellite Repeats; Period Circadian Proteins; Polymorphism, Genetic; Sleep; Surveys and Questionnaires; Young Adult
PubMed: 32841827
DOI: 10.1016/j.jad.2020.07.138 -
The SLC6A3 gene polymorphism is related to the development of attentional functions but not to ADHD.Scientific Reports Apr 2020Neuropharmacological and human clinical studies have suggested that the brain dopaminergic system is substantively involved in normal and pathological phenotypes of... (Observational Study)
Observational Study
Neuropharmacological and human clinical studies have suggested that the brain dopaminergic system is substantively involved in normal and pathological phenotypes of attention. Dopamine transporter gene (SLC6A3) was proposed as a candidate gene for Attention-Deficit/Hyperactivity Disorder (ADHD). We investigated the effect of the SLC6A3 variants on cognitive performance in ADHD and healthy children and teenagers. Participants completed cognitive tasks measuring attentional switching, selective and sustained attention, and effectiveness of alerting, orienting and executive attention. We estimated the effects of 40 bp variable number of tandem repeat (VNTR) polymorphism located in the 3' untranslated region (3' UTR) (9-repeat vs 10-repeat allele) of the SLC6A3 gene, ADHD diagnosis, age, and their interactions as predictors of cognitive performance. ADHD children demonstrated deficits in most of the examined attention processes, persistent within the examined age range (9-16 years). No significant effects were observed for the interaction of ADHD and the SLC6A3 polymorphism, but the results revealed a significant main effect of SLC6A3 genotype in the entire research sample. Subjects carrying 9R allele performed the switching task significantly worse in comparison to children with 10R/10R or 10R/11R genotype. SLC6A3 polymorphism moderated age-related improvements in orienting and attentional switching. Results suggest that SLC6A3 genotype influence these attentional/cognitive functions which deficits are not the key symptoms in ADHD.
Topics: Adolescent; Adolescent Development; Age Factors; Alleles; Attention; Attention Deficit Disorder with Hyperactivity; Case-Control Studies; Child; Child Development; Cognition; Dopamine Plasma Membrane Transport Proteins; Female; Healthy Volunteers; Humans; Male; Minisatellite Repeats; Polymorphism, Genetic
PubMed: 32277231
DOI: 10.1038/s41598-020-63296-x -
Tropical Animal Health and Production Sep 2021This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle,... (Review)
Review
This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle, sheep, and goats in Latin America and the Caribbean? An electronic search was conducted on three platforms (i.e., OVID®, Web of Science®, SciELO) as well as on the proceedings of the International Colloquium on Paratuberculosis. Inclusion and exclusion criteria were defined a priori and conserved through the systematic process and only articles published in peer-reviewed journals were considered. A total of 26 articles met the definitive inclusion criteria. All were published in English, in 15 different journals, and between 1989 and 2020. The relevant articles reported the use of six different genotyping techniques (i.e., polymerase chain reaction-restriction endonuclease analysis, restriction fragment length polymorphism, type-specific-PCR, mycobacterial interspersed repetitive units-variable number of tandem repeats, multi-locus short sequence repeat, single nucleotide polymorphism) in isolates from seven countries. Genotypes found so far in the region using typing techniques were mainly C type. MIRU-VNTR mostly reported INMV 1, INMV 2, and INMV 11 subtypes, among others. MLSSR reported genotypes from four different countries, reporting nine different subtypes of which 7g-10g-4ggt was the most common for loci 1, 2, and 8, respectively. Regardless the high diversity of techniques used so far to genotype Latin American and Caribbean MAP isolates, the original question of this systematic review has been answered. In addition, a relative genetic similarity between MAP strains recovered from cattle, goats, and sheep unrelatedly of the matrix and geographic origin was identified.
Topics: Animals; Cattle; Genotype; Goat Diseases; Goats; Latin America; Minisatellite Repeats; Mycobacterium avium subsp. paratuberculosis; Paratuberculosis; Sheep; Sheep Diseases
PubMed: 34546430
DOI: 10.1007/s11250-021-02923-9 -
Bioinformatics (Oxford, England) Mar 2020Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in...
SUMMARY
Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in epidemiological studies for tracking tuberculosis transmission. Recent long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore Technologies can produce reads that are long enough to cover the entire repeat regions in each MIRU-VNTR locus which was previously not possible using the short reads from Illumina high-throughput sequencing technologies. We thus developed MIRUReader for MIRU-VNTR typing directly from long sequence reads.
AVAILABILITY AND IMPLEMENTATION
Source code and documentation for MIRUReader program is freely available at https://github.com/phglab/MIRUReader.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Bacterial Typing Techniques; Genotype; Interspersed Repetitive Sequences; Minisatellite Repeats; Mycobacterium tuberculosis; Polymorphism, Restriction Fragment Length
PubMed: 31603462
DOI: 10.1093/bioinformatics/btz771 -
Microbial Genomics Apr 2023Malarial parasites exhibit extensive genomic plasticity, which induces the antigen diversification and the development of antimalarial drug resistance. Only a few...
Malarial parasites exhibit extensive genomic plasticity, which induces the antigen diversification and the development of antimalarial drug resistance. Only a few studies have examined the genome maintenance mechanisms of parasites. The study aimed at elucidating the impact of a mutation in a DNA mismatch repair gene on genome stability by maintaining the mutant and wild-type parasites through serial cultures for approximately 400 days and analysing the subsequent spontaneous mutations. A P513T mutant of the DNA mismatch repair protein PfMSH2-1 from 3D7 was created. The mutation did not influence the base substitution rate but significantly increased the insertion/deletion (indel) mutation rate in short tandem repeats (STRs) and minisatellite loci. STR mutability was affected by allele size, genomic category and certain repeat motifs. In the mutants, significant telomere healing and homologous recombination at chromosomal ends caused extensive gene loss and generation of chimeric genes, resulting in large-scale chromosomal alteration. Additionally, the mutant showed increased tolerance to N-methyl-N'-nitro-N-nitrosoguanidine, suggesting that PfMSH2-1 was involved in recognizing DNA methylation damage. This work provides valuable insights into the role of PfMSH2-1 in genome stability and demonstrates that the genomic destabilization caused by its dysfunction may lead to antigen diversification.
Topics: Humans; Plasmodium falciparum; MutS Homolog 2 Protein; Mutation; Genomic Instability; Phenotype
PubMed: 37083479
DOI: 10.1099/mgen.0.001003 -
Pediatric Research May 2022Interleukin-1 receptor antagonist (IL1RN) variable number tandem repeats (VNTRs) are not fully understood in Type 1 diabetes mellitus (T1DM). It may affect IL1RN level...
BACKGROUND
Interleukin-1 receptor antagonist (IL1RN) variable number tandem repeats (VNTRs) are not fully understood in Type 1 diabetes mellitus (T1DM). It may affect IL1RN level and modify the disease risk. We aimed to study IL1RN VNTR polymorphism in Egyptian children with T1DM to clarify its potential role as a risk factor for T1DM and its effect on plasma IL1RN level.
METHODS
A case-controlled study including 200 children (120 T1DM and 80 controls) was carried on. All children were subjected to genotyping of IL1RN VNTR. Plasma IL1RN was estimated by ELISA.
RESULTS
The A1A2 and LS genotypes and A2 allele were significantly higher among cases compared to controls with increased T1DM risk (OR = 5.35, 2.56 and 3.13, respectively). The S allele was significantly elevated in cases compared to controls with 2.09-fold increased risk of having T1DM. The median plasma IL1RN significantly decreased in cases compared to controls. Within cases, IL1RN was significantly decreased in LS versus LL genotype.
CONCLUSIONS
There is a strong relationship between IL1RN VNTR and T1DM in Egyptian children. A1A1 genotype, LL genotype, A1 allele, and L allele were protective. A1A2 and LS genotypes, short (S), and A2 alleles were risk factors. IL1RN was decreased in T1DM, especially in LS genotype.
IMPACT
The relationship between IL1RN gene polymorphism and risk for T1DM among Egyptian children. Plasma IL1RN protein level in T1DM. Low IL1RN protein level in T1DM patients could be therapeutic targets for IL1RN medications in the future.
Topics: Child; Diabetes Mellitus, Type 1; Genetic Predisposition to Disease; Genotype; Humans; Interleukin 1 Receptor Antagonist Protein; Minisatellite Repeats; Polymorphism, Genetic
PubMed: 34002010
DOI: 10.1038/s41390-021-01569-5 -
PloS One 2022Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular...
Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular epidemiology of Mycobacterium tuberculosis in this country. The aim of this work was to analyze the genetic structure of drug-resistant (DR) M. tuberculosis population in the Plateau State (central Nigeria), with the results placed in the broader context of West Africa. The study sample included 67 DR M. tuberculosis isolates, recovered from as many TB patients between November 2015 and January 2016, in the Plateau State. The isolates were subjected to spoligotyping and MIRU-VNTR typing. A total of 20 distinct spoligotypes were obtained, split into 3 clusters (n = 50, 74.6%, 2-33 isolates per cluster) and 17 (25.4%) unique patterns. The Cameroon clade was the largest lineage (62.7%) followed by T (28.3%), LAM (3%), and Haarlem (3%) clades. Upon MIRU-VNTR typing, the isolates produced 31 profiles, i.e. 7 clusters (n = 43, 64.2%, 2-17 isolates per cluster) and 24 singletons. A combined spoligotyping and MIRU-VNTR typing analysis showed 20.9% of the cases clustered and estimated the recent transmission rate at 11.9%. In conclusion, two lineages, namely Cameroon, and T accounted for the majority (91%) of cases. No association was observed between the most prevalent Cameroon lineage and drug resistance, including multidrug resistant (MDR) phenotype, or any of the patient demographic characteristics.
Topics: Genotype; Humans; Minisatellite Repeats; Mycobacterium tuberculosis; Nigeria; Tuberculosis; Tuberculosis, Multidrug-Resistant
PubMed: 35609028
DOI: 10.1371/journal.pone.0266837 -
Proceedings of the National Academy of... Jun 2021Multiple independent sequence variants of the locus have been associated with telomere length and cancer risks in genome-wide association studies. Here, we identified...
Multiple independent sequence variants of the locus have been associated with telomere length and cancer risks in genome-wide association studies. Here, we identified an intronic variable number tandem repeat, VNTR2-1, as an enhancer-like element, which activated hTERT transcription in a cell in a chromatin-dependent manner. VNTR2-1, consisting of 42-bp repeats with an array of enhancer boxes, cooperated with the proximal promoter in the regulation of hTERT transcription by basic helix-loop-helix transcription factors and maintained hTERT expression during embryonic stem-cell differentiation. Genomic deletion of VNTR2-1 in MelJuSo melanoma cells markedly reduced hTERT transcription, leading to telomere shortening, cellular senescence, and impairment of xenograft tumor growth. Interestingly, VNTR2-1 lengths varied widely in human populations; alleles with shorter VNTR2-1 were underrepresented in African American centenarians, indicating its role in human aging. Therefore, this polymorphic element is likely a missing link in the telomerase regulatory network and a molecular basis for genetic diversities of telomere homeostasis and age-related disease susceptibilities.
Topics: Black or African American; Aged, 80 and over; Animals; Base Sequence; Cell Differentiation; Cell Line; Cell Proliferation; Chromosomes, Artificial, Bacterial; E-Box Elements; Genome, Human; Human Embryonic Stem Cells; Humans; Mice, Nude; Minisatellite Repeats; Neoplasms; Polymorphism, Genetic; Promoter Regions, Genetic; Protein Binding; Sequence Deletion; Telomerase; Telomere Homeostasis; Transcriptional Activation; Mice
PubMed: 34155099
DOI: 10.1073/pnas.2019043118