Influence Of Single Nucleotide Polymorphisms Research Articles

Tenascin-C-Matrix Metalloproteinase-3 Phenotype and the Risk of Tendinopathy in High-Performance Athletes: A Case–Control Study

Background/Objectives: Tendon structure is predominantly composed of the extracellular matrix (ECM), and genetic variants in non-collagenous ECM components may influence susceptibility to tendinopathy. We investigated the potential influence of single nucleotide polymorphisms (SNPs) in fibrillin-2 (FBN2), tenascin-C (TNC), and matrix metalloproteinase-3 (MMP3) on the tendon regeneration failure phenotype and impact on the susceptibility to tendinopathy in Brazilian high-performance athletes. Methods: This case–control study was conducted with 397 high-performance athletes from different sports modalities (197 tendinopathy cases and 200 controls), and they were analyzed by validated TaqManTM SNP genotyping assays of the SNPs FBN2 (rs331079), TNC (rs2104772), and MMP3 (rs591058). Results: Out of the 197 tendinopathy cases, 63% suffered from chronic tendon pain and 22% experienced more than three episodes of disease manifestation. The TNC-rs2104772-A allele was significantly associated with tendinopathy (OR: 1.4; 95% CI: 1.1–1.8), while athletes carrying the MMP3-rs591058-T allele were linked to an increased risk of more episodes of disease manifestation (OR: 1.7; 95% CI: 1.1–2.8). The TNC-MMP3 tendon regeneration failure phenotype (TNC-A/MMP3-T) was associated with an increased risk of tendinopathy (OR: 1.4; 95% CI: 1.1–2.0) and episodes of disease manifestation (OR: 2.0; 95% CI: 1.2–3.5). Athletes with tendinopathy who had the TNC-A/MMP3-T interaction were more prone to experiencing more than three disease exacerbations (OR: 4.3; 95% CI: 1.8–10.5) compared to TNC-A/TNC-C. Conclusions: This study suggests that rs2104772 and rs591058 SNPs could be involved in the tendon regeneration failure phenotype and may influence the molecular mechanism related to the regulation of the tendon ECM during training workload.

Genomic insight into COVID-19 severity in MAFLD patients: a single-center prospective cohort study.

This study investigated the influence of single nucleotide polymorphisms (SNPs) in genes associated with the interferon pathway (IFNAR2 rs2236757), antiviral response (OAS1 rs10774671, OAS3 rs10735079), and viral entry (ACE2 rs2074192) on COVID-19 severity and their association with nonalcoholic fatty liver disease (MAFLD). We did not observe a significant association between the investigated SNPs and COVID-19 severity. While the IFNAR2 rs2236757 A allele was correlated with higher creatinine levels upon admission and the G allele was correlated with lower band neutrophils upon discharge, these findings require further investigation. The distribution of OAS gene polymorphisms (rs10774671 and rs10735079) did not differ between MAFLD patients and non-MAFLD patients. Our study population's distribution of ACE2 rs2074192 genotypes and alleles differed from that of the European reference population. Overall, our findings suggest that these specific SNPs may not be major contributors to COVID-19 severity in our patient population, highlighting the potential role of other genetic factors and environmental influences.

Influence of Single Nucleotide Polymorphisms on CRS Outcomes: A Preliminary Observational Study.

To conduct a preliminary investigation into the relationship between specific SNP variants, type II inflammation, and the effectiveness of dupilumab therapy and surgery in patients with CRS. In this prospective study, 48 subjects were enrolled, comprising 32 CRS patients and 16 healthy controls. The CRS patients were subjected to either dupilumab therapy or endoscopic surgery according to EPOS guidelines. SNP variants were identified using the TaqMan SNP genotyping technique. The identified SNP profiles were compared between the control group and CRS patients, and their potential influence on treatment outcomes was evaluated. Treatment responses were assessed based on symptom scores, such as SS-I, SNOT-22, disease progression using the NPS findings, and SNP profiles at a 6-month follow-up. The primary measures included the Nasal Polyp Score, Smell Identification Test (SIT) score, and SNOT-22 outcomes. Dupilumab therapy and surgery significantly decreased NPS, with the last showing superior results. However, dupilumab therapy resulted in a significantly improved SIT score. Significant differences were observed in SNP profiles, particularly with rs1800629 (TNFA), rs2856838 (IL1a), rs17561 (IL1a), and rs1805011 (IL4R). In particular, the expression of rs2856838 and rs1805011 variants in the dupilumab group was associated with significantly better SIT and SNOT-22 outcomes than non-expressors. Also, the surgery group patients expressing the rs2856838 variant reported significant improvements in SNOT-22 scores. These preliminary findings suggest that SNP genotypes may guide personalized treatment strategies for CRS. Further larger prospective studies are required to confirm these initial observations. 2 Laryngoscope, 2024.

Genotyping the BCL11A Single Nucleotide Polymorphism and Associated Levels of Fetal Hemoglobin in Mauritanian Sickle Cell Patients.

Sickle cell disease (SCD) is a major heritable genetic disease in sub-Saharan Africa, including Mauritania. Fetal hemoglobin (HbF) can affect the pathophysiology, moderate the clinical course, and offer prospects for curative treatment of SCD. This study aimed to investigate the influence of single nucleotide polymorphisms (SNPs) in the BCL11A gene on the levels of HbF and hematological parameters in Mauritanian sickle cell (HbSS) patients. Complete blood count was assessed in 565 patients suspected to have SCD. Polymerase chain reaction (PCR)-restriction fragment length polymorphism was performed to identify the HbSS, and sequencing was used for genotyping three SNPs: rs4671393 (A>G) and rs11886868 (C>T) in the intron 2 and rs1052520 (G>A) in the 3'UTR regions of the BCL11A gene in 50 sickle cell patients. The prevalence of HbSS among the study population was 8.8% (50/565), and the mean (± standard deviation) of HbF level was 15.0% (± 6.0%). Sequencing showed the presence of three genotypes: AA (13.6%), AG (46.6%), GG (39.6%) in rs4671393; CC (17.6%), CT (48.7%), and TT (33.6%) in rs11886868. All samples from HbSS individuals displayed a wild-type genotype in the rs1052520 allele. The prevalence of minor alleles A (rs4671393) and C (rs11886868) were 37% and 39%, respectively. There was a statistically significant association (p = 0.034) between rs4671393 SNP and elevated HbF (mean 12.72 ± 6.26%). The study of three SNPs in the BCL11A locus in Mauritanian patients with SCD showed a significant association of rs4671393 allele with the HbF level. Further research is needed to explore additional SNPs in the BCL11A locus and investigate other genetic markers reported to modulate HbF levels, such as HBS1L-MYB and Xmn1-HBG2, to improve the management of this potentially life-threatening condition in Mauritania.

DNA Methylation in the Anti-Mullerian Hormone Gene and the Risk of Disease Activity in Multiple Sclerosis.

Multiple sclerosis (MS) has a complex pathobiology, with genetic and environmental factors being crucial players. Understanding the mechanisms underlying heterogeneity in disease activity is crucial for tailored treatment. We explored the impact of DNA methylation, a key mechanism in the genetics-environment interplay, on disease activity in MS. Peripheral immune methylome profiling using Illumina Infinium MethylationEPIC BeadChips was conducted on 249 untreated relapsing-remitting MS patients, sampled at the start of disease-modifying treatment (DMT). A differential methylation analysis compared patients with evidence of disease activity (EDA) to those with no evidence of disease activity (NEDA) over 2 years from DMT start. Utilizing causal inference testing (CIT) and Mendelian randomization (MR), we sought to elucidate the relationships between DNA methylation, gene expression, genetic variation, and disease activity. Four differentially methylated regions (DMRs) were identified between EDA and NEDA. Examining the influence of single nucleotide polymorphisms (SNPs), 923 variants were found to account for the observed differences in the 4 DMRs. Importantly, 3 out of the 923 SNPs, affecting DNA methylation in a DMR linked to the anti-Mullerian hormone (AMH) gene, were associated with disease activity risk in an independent cohort of 1,408 MS patients. CIT and MR demonstrated that DNA methylation in AMH acts as a mediator for the genetic risk of disease activity. This study uncovered a novel molecular pathway implicating the interaction between DNA methylation and genetic variation in the risk of disease activity in MS, emphasizing the role of sex hormones, particularly the AMH, in MS pathobiology. ANN NEUROL 2024;96:289-301.

Influence of single nucleotide polymorphism on position-607 in IL18 gene on disease development in Bulgarian patients with rheumatoid arthritis

Influence of single nucleotide polymorphism on position-607 in IL18 gene on disease development in Bulgarian patients with rheumatoid arthritis

The Impact of ABCC2 -24C>T Gene Polymorphism on Graft Survival in Kidney Transplant Recipients.

Personalized medicine in kidney transplantation has the potential to improve outcomes and reduce complications. The aim of this study was to investigate the influence of single nucleotide polymorphisms in genes encoding metabolizing enzymes (CYP3A5) and transporters (ABCC2) on clinical outcomes (acute graft failure and/or acute tubular necrosis (ATN)) in kidney transplant recipients (KTR). This was a multicenter, retrospective cohort study where adult KTR who had undergone kidney transplantation between 2020 and 2021 and received tacrolimus-mycophenolate treatment were enrolled in the study. DNA was extracted from collected blood samples using a commercially available kit. CYP3A5*3, ABCC2 -24C>T and ABCC2 3972C>T SNP were determined by polymerase chain reaction. Of the total 39 patients included, nine (23.1%) KTR had an incidence of acute graft failure and/or ATN. A multiple logistic regression showed wildtype ABCC2 -24C>T C allele had a higher risk of developing acute graft rejection and/or ATN compared to the variant allele carriers (adjusted Odd Ratios [aOR]: 27.675, p = 0.038). Recipients who had delayed graft function (aOR: 49.214, p = 0.012) and a history of CMV infection (aOR: 18.097, p = 0.009) were at 49.2 and 18.1-times increased risk for acute graft failure and/or ATN, respectively. The large aOR was inevitable due to the small sample size and required cautious interpretation. This is the first study to determine the effect of the ABCC2 -24C>T genetic polymorphism on clinical outcomes in Malaysian KTR and forms the basis for further work on ABCC2 -24C>T effects in long-term KTR.

Impact of Genetic Polymorphisms in NF-ĸB2 and TRAF3 Genes on Response to Bortezomib-Based Therapy in Multiple Myeloma Patients.

Multiple myeloma (MM), being the second most common hematological malignancy, has garnered significant attention. The ubiquitin proteasomal pathway (UPP), crucial for normal cell function, plays a pivotal role in myeloma pathophysiology, especially with the advent of bortezomib (BTZ). Dysregulation of the UPP has implications ranging from developmental abnormalities to cancer. This study aimed to delineate the clinical characteristics of newly diagnosed multiple myeloma patients and investigate the influence of single nucleotide polymorphisms (SNPs) in NF-ĸB2 and TRAF3 genes on the risk and treatment response to bortezomib-based chemotherapy. Conducted at JIPMER, Pondicherry, this prospective study enrolled 184 participants, comprising cases and controls. DNA extraction from peripheral blood samples was followed by SNP analysis through Real-time Polymerase Chain Reaction. Patients were categorized into Good and Poor responders, and SNP associations with treatment response, response rates, and survival outcomes were assessed using chi-square and Kaplan-Meier analyses. The median age of participants was 55 years, with backache being the most prevalent symptom (66.3%). Hypercalcemia (22%), renal failure (8.7%), and bone fractures (45.7%) were also observed, alongside high prevalence of anemia. Notably, the frequency of the TRAF3 rs12147254 A allele was lower in cases compared to controls (31% vs. 49%, P-value=0.002). Poor responders exhibited higher frequencies of the GA+AA genotypes in TRAF3 rs12147254 (OR-3.882(1.629-9.251), P-value-0.002) and NFKB2 rs1056890 (OR-3.308(1.366-8.012), P-value-0.008) when compared to good responders. The GA+AA genotype in TRAF3 rs11160707 SNP correlated with improved progression-free survival. The study findings underscore a significant association between genetic polymorphisms and treatment response outcomes, suggesting their utility in prognostic determinations and clinical outcomes prediction in multiple myeloma patients.

Uticaj pojedinačnih nukleotidnih polimorfizama na terapijsku efikasnost antiretrovirusnih lekova

The availability of combined antiretroviral therapy (cART) has significantly improved the prognosis of HIV infection. To control the infection, patients chronically take different groups of antiretroviral drugs, which can lead to numerous unwanted and toxic effects, as well as potential interactions with other co-administered medications and food. Most available antiretroviral drugs are metabolized by cytochrome P450 enzymes and excreted through various transport proteins, which can undergo multiple genetic changes. Single nucleotide polymorphisms (SNPs) have been research subjects in various fields, including HIV infection. Variations in the genetic makeup of metabolic enzymes and transporters are particularly noteworthy. Objective: This research aimed to provide a review and analysis of the most common gene polymorphisms encoding metabolic enzymes and transporters that are essential for the pharmacokinetics of antiretroviral drugs. Methodology: A literature review was conducted by searching the PubMed and Medline databases from 1998 to 2022. The search was performed using appropriate keywords such as "cytochrome", "antiretroviral", "genotype", "polymorphism", "pharmacogenetic", "pharmacogenomic", "pharmacokinetic", "variant", and "single nucleotide polymorphism" in combination with "human immunodeficiency virus" and "acquired immunodeficiency syndrome". The identified literature was then reviewed and analyzed. Results: The clinically most relevant polymorphisms affecting the therapeutic efficacy of antiretroviral drugs include HLA-B5701, CYP2B6 polymorphisms corelated with high plasma concentrations of efavirenz, and UGT1A1*6 and *28 responsible for individual variations in the pharmacokinetics of dolutegravir. Conclusion: Genetic variations, including variations in individual nucleotides, as well as other factors such as gender, coexisting medical conditions, and patient-related factors, play a significant role in therapeutic response. Understanding these factors is of crucial importance for personalized approaches to the treatment of HIV infection and the optimization of therapeutic outcomes.

Host genetic variants associated with susceptibility and severity of pneumococcal pneumonia in adult patients

BackgroundPneumococcal community-acquired pneumonia (P-CAP) is a major cause of morbidity and hospitalization. Several host genetics factors influencing risk of pneumococcal disease have been identified, with less information about its association with P-CAP. The aim of the study was to assess the influence of single nucleotide polymorphisms (SNP) within key genes involved in the innate immune response on the susceptibility to P-CAP and to study whether these polymorphic variants were associated with the severity and outcome of the episodes in a cohort of adult Caucasian patients.MethodsSeventeen SNPs from 7 genes (IL-R1, IL-4, IL-10, IL-12B, NFKBIA, NFKBIE, NFKBIZ) were analyzed. For susceptibility, a case-control study including a cohort of 57 adult with P-CAP, and 280 ethnically matched controls was performed. Genetic influence on clinical severity and outcome was evaluated in a prospective observational study including all consecutive adult P-CAP patients from November 2015 to May 2017.ResultsThe NFKBIA polymorphism rs696 and a haplotype combination were associated with susceptibility to P-CAP (OR = 0.62, p = 0.005 and OR = 0.63, p = 0.008, respectively). The SNP IL4 rs2227284 was associated with severe P-CAP (OR = 2.17, p = 0.04). IL-R1 (rs3917267) and IL-10 (rs3024509) variants were related with respiratory failure (OR = 3.31, p = 0.001 and OR = 0.18, p = 0.003, respectively) as well as several haplotype combinations in NFKBIA, NFKBIZ, IL-R1 and IL-10 (p = 0,02, p = 0,01, p = 0,001, p = 0,03, respectively). CURB-65 values were associated with the IL-10 rs3024509 variant (beta = − 0.4, p = 0.04), and with haplotype combinations of NFKBIZ and IL-10 (p = 0.05, p = 0.04, respectively). Genetic variants in IL-10 (rs3024509) and in IL-12B (rs730691) were associated with PSI values (beta = − 0.54, p = 0.01, and beta = − 0.28, p = 0.04, respectively), as were allelic combinations in IL-R1 (p = 0.02) and IL-10 (p = 0.01). Finally, several polymorphisms in the IL-R1 gene (rs13020778, rs2160227, & rs3917267) were associated with the time elapsed until clinical stability (beta = − 0.83, p = 0.03; beta = − 1, p = 0.02 and beta = 1.07, p = 0.008, respectively).ConclusionsA genetic variant in NFKBIA was associated with susceptibility to P-CAP in adult Caucasian patients and genetic variants from key cytokines of the innate immune response (Il-4, IL-10, IL-R1 and IL-12B) and NF-κB inhibitors were associated with different phenotypes of severe P-CAP. If validated, these SNPs may help to identify people at risk of P-CAP or severe P-CAP on which preventive measures could be applied.

Computing Acceleration to Genome-Wide Association Study Based on CPU/FPGA Heterogeneous System

Genome Wide Association Study (GWAS) reveals the influence of single nucleotide polymorphisms (SNP) and other genetic markers on the complex genetic disease traits, making a significant contribution to the prevention and treatment of genetic diseases. Since GWAS needs to calculate large numbers of pairwise tests, it is highly time-consuming and this limits its widespread promotion in many medical applications. To solve the above problem, many studies deploy GWAS on the CPU/GPU platform. By taking advantages of GPUs' high parallelism, the completion time of GWAS can be significantly decreased. However, GPUs have high energy consumption, which increases GWAS's operating cost. Considering FPGA has low power, high parallelism and programmability, this article aims to use FPGA to design a hardware accelerator dedicated to GWAS for the purpose of optimizing both completion time and energy cost of GWAS. First, the CPU/FPGA heterogenous computing system is built, and the computationally-intensive GWAS tasks such as the contingency table creation (CTC) and Kirkwood Superposition Approximation (KSA) screening are offloaded to run on FPGA. Then, a specific FPGA architectures dedicated to CTC and KSA tasks of GWAS are implemented by using a set of architectural design technologies such as hardware and software co-optimization, systolic array, loop unrolling, pipeline and parallelism. To evaluate the performance of FPGA, we compare its completion time, energy cost and performance per Watt with those of CPU and GPU. The results show the FPGA and GPU can respectively achieve 105--fold and 148--fold speedup compared with CPU. Although FPGA's computing performance is a bit lower than that of GPU, it has higher energy efficiency and its performance per Watt is 1.4 times that of GPU.

135 Gene Variants in Bola-Dmb, DECR1, Fasn and SREBF1 Associated with Conceptus Death on Day 16 of Pregnancy in Holstein Cows

Abstract Investigating the influences of single nucleotide polymorphisms (SNP) associated with conceptus death (CD) on day 16 of pregnancy could distinguish cows who have inferior value for fertility traits. We hypothesized that CD is associated with SNP genotypes that disrupt maternal recognition and lead to early pregnancy loss. RNA sequences from Holstein cow pregnancies (n = 15) with normal conceptuses (Norm) or CD were subjected to SNP discovery via Qiagen CLC Genomics Workbench. Selected SNP were based on previous fertility studies, differentially expressed genes within pregnancy development analyses and proximity to SNP associated with fertility traits in the Cattle QTL Database. A second cohort of Holstein cows (n = 500) was used to conduct a validation and genotype to phenotype analysis of candidate SNP (cSNP) via DNA from blood samples and farm records. PLINK software was used to remove cows (n = 34) missing more than >20% cSNP and remove cSNP with monomorphic alleles, minor allele frequency (MAF) < 10% and not in Hardy-Weinberg Equilibrium (>1e-15). The GLM-one way ANOVA was used for all statistical models in SAS. Statistically significant models (P <0.05) were further analyzed for LSMEANS, Bonferroni adjustment of P-values, additive allele effect and predicted effect of amino acid (aa) change on protein function via SIFT analyses tool in the Ensembl variant table (scoring 0-1.0; < 0.05 being significant). Previously, we identified 69 cSNP on the RNA sequences of Norm or CD pregnancies from the initial group of Holstein cows and in proximity to >1 SNP associated with fertility traits from the Cattle QTL database. Quality control measures in PLINK reduced the number of Holstein cows in the second cohort to 466 and identified 4 cSNP associated with non-binary reproductive traits. Herein, we report an additional 4 cSNP discovered and validated with binary reproductive traits. The cSNP within genes were associated with the following roles: BOLA-DMB (antigen loading in the immune system), DECR1 (lipid metabolism), FASN (reconstitution of body reserves during pregnancy) and SREBF1 (synthesis of fatty acids). Cows with T allele, in BOLA-DMB and SREBF1, were less likely (P < 0.05) to become pregnant <150 days in milk (DIM). For DECR1 and FASN, cows were less likely (P < 0.05) to become pregnant at 1st artificial insemination with C or A allele, respectively. Only the cSNP in SREBF1 had both an additive allele effect and a predicted effect of aa change on protein function. When cows had C allele, in the SREBF1 cSNP, there was 6% greater (P < 0.01) probability of becoming pregnant <150 DIM. While SIFT revealed the cSNP in SREBF1 have a predicted significant effect with a score of 0.03 for the aa change of proline/leucine. The reported cSNP, specifically those influenced by CD, add valuable information for the development of improved genetic tools for the dairy industry. USDA-NIFA#2019-07133.

Tetra-ARMS PCR analysis of angiotensinogen AGT T174M (rs4762) genetic polymorphism in diabetic patients: a comprehensive study.

Hypertension (HTN) is a multifactorial chronic disease that poses a significant global health burden and is associated with increased mortality rates. It often coexists with other conditions, such as cardiovascular, liver, and renal diseases, and has a strong association with diabetes mellitus. Insulin resistance and endothelial dysfunction commonly occur in individuals with both HTN and type 2 diabetes mellitus (T2DM). Genetic factors, along with environmental and pathological factors, play a role in the development of HTN. Recent studies have revealed the influence of single nucleotide polymorphisms (SNPs) in various genes on HTN. In this study, we aimed to investigate the genetic polymorphism of angiotensinogen (AGT) T174M (rs4762) and its association with HTN in diabetic patients. A total of 300 participants were enrolled in this study and divided into three groups: control, hypertensive, and hypertensive diabetic. Blood samples were collected, and predetermined biochemical parameters were assessed. Genotyping of the AGT T174M (rs4762) gene was conducted using Tetra ARMS PCR with specific primers. The study findings revealed a significant association between AGT T174M (rs4762) genotype and HTN in diabetic patients within the Pakistani population. The C/T genotype of AGT T174M (rs4762) was found to be significant in both the hypertensive and hypertensive diabetic participants compared to the control group. This genotype was identified as a risk factor for developing HTN in both the hypertensive and hypertensive diabetic participants. This study demonstrates a significant association between AGT T174M (rs4762) genetic polymorphism and HTN in diabetic patients. The C/T genotype of AGT T174M (rs4762) may serve as a potential marker for identifying individuals at risk of developing HTN, specifically in the hypertensive and hypertensive diabetic populations. Further research is warranted to elucidate the underlying mechanisms and validate these findings in larger cohorts.

The Influence of Single Nucleotide Polymorphisms on Vitamin D Receptor Protein Levels and Function in Chronic Liver Disease.

Single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene have been associated with chronic liver disease. We investigated the role of VDR SNPs on VDR protein levels and function in patients with chronic liver disease. VDR expression levels were determined in peripheral T lymphocytes (CD3+VDR+), monocytes (CD14+VDR+), and plasma from patients (n = 66) and healthy controls (n = 38). Genotyping of SNPs and the determination of expression of VDR/vitamin D-related genes were performed by using qPCR. The effect of FokI SNP on vitamin D-binding to VDR was investigated by molecular dynamics simulations. CD14+VDR+ cells were correlated with the MELD score. The ApaI SNP was associated with decreased CD3+VDR+ levels in cirrhotic patients and with higher liver stiffness in HCV patients. The BsmI and TaqI SNPs were associated with increased VDR plasma concentrations in cirrhotic patients and decreased CD14+VDR+ levels in HCV patients. The FokI SNP was associated with increased CD3+VDR+ levels in cirrhotic patients and controls. VDR polymorphisms were significantly related to the expression of genes critical for normal hepatocyte function and immune homeostasis. VDR expression levels were related to the clinical severity of liver disease. VDR SNPs may be related to the progression of chronic liver disease by affecting VDR expression levels.

The Influence of Single Nucleotide Polymorphisms On Body Weight Trajectory After Bariatric Surgery: A Systematic Review.

To conduct a systematic review to summarize the results of studies on this subject and to identify whether single nucleotide polymorphisms (SNPs) are good prognostic markers for body weight trajectory after bariatric surgery. A considerable number of events can influence the body weight trajectory after bariatric surgery, and in the post-genomic era, genetic factors have been explored. This study is registered with PROSPERO (CRD42021240903). SNPs positively associated with poor weight loss after bariatric surgery were rs17702901, rs9939609, rs1360780, rs1126535, rs1137101, rs17782313, rs490683, and rs659366. Alternatively, SNPs rs2229616, rs5282087, rs490683, rs9819506, rs4771122, rs9939609, rs4846567, rs9930506, rs3813929, rs738409, rs696217, rs660339, rs659366, rs6265, rs1801260, and rs2419621 predicted a higher weight loss after bariatric surgery. Six studies performed with a genetic risk score (GRS) model presented significant associations between GRS and outcomes following bariatric surgery. This systematic review shows that, different SNPs and genetic models could be good predictors for body weight trajectory after bariatric surgery. Based on the results of the selected studies for this Systematic Review is possible to select SNPs and metabolic pathways of interest for the GRS construction to predict the outcome of bariatric surgery to be applied in future studies.

Influence of Single-Nucleotide Polymorphisms on Clinical Outcomes of Capecitabine-Based Chemotherapy in Colorectal Cancer Patients: A Systematic Review.

The aim of this systematic review was to provide a comprehensive overview of the literature published in the last decade on the association of single-nucleotide polymorphisms in genes involved in the pharmacodynamic and pharmacokinetic pathways of capecitabine with treatment outcomes among colorectal cancer patients. A systematic search of the literature published in the last 10 years was carried out in two databases (Medline and Scopus) using keywords related to the objective. Quality assessment of the studies included was performed using an assessment tool derived from the Strengthening the Reporting of Genetic Association (STREGA) statement. Thirteen studies were included in this systematic review. Genes involved in bioactivation, metabolism, transport, mechanism of action of capecitabine, DNA repair, and folate cycle were associated with toxicity. Meanwhile, genes related to DNA repair were associated with therapy effectiveness. This systematic review reveals that several SNPs other than the four DPYD variants that are screened in clinical practice could have an impact on treatment outcomes. These findings suggest the identification of future predictive biomarkers of effectiveness and toxicity in colorectal cancer patients treated with capecitabine. However, the evidence is sparse and requires further validation.

Genetic impacts on nigral iron deposition in Parkinson's disease: A preliminary quantitative susceptibility mapping study.

Dysfunction of iron metabolism, especially in substantia nigra (SN), is widely acknowledged in Parkinson's disease (PD), but the genetic influence on iron deposition remains largely unknown. Thus, in this study, we aimed to investigate potential genetic impacts on iron deposition in PD. Seventy-four subjects, including 38 patients with PD and 36 age-matched normal controls, participated in this study. Imaging genetic association analysis was used to identify the specific influence of single nucleotide polymorphism (SNP) on iron-related quantitative traits (QT). Genetic effects on iron deposition at the disease level, SNP level, and their interactive effect were highlighted. Four strong SNP-QT associations were detected: rs602201-susceptibility of bilateral SN, rs198440-susceptibility of left SN, and rs7895403-susceptibility of left caudate head. Detailed analyses showed that: (1) significant iron deposition was exclusively found in bilateral SN in PD; (2) altered polymorphisms of the A allele/A- genotype of rs602201 and G allele/G- genotype of rs198440 and rs7895403 were more frequently observed in PD; (3) for rs602201, among all subjects, A- genotype carriers showed significantly increased iron content than TT genotype in bilateral SN; for rs198440 and rs7895403, G- carriers showed increased iron content than AA genotype in left SN and left caudate head, respectively; and (4) rs602201 exhibited significant SNP-by-disease interaction in bilateral SN. This study shows that rs602201 and rs198440 have a stimulative impact on nigral iron deposition in PD, which provides improved understanding of iron-related pathogenesis in PD, and specifically, that vulnerability to iron deposition in SN is genetic-based.

Evaluation of Systemic Genotoxic/Oxidative and Proinflammatory Effects in Workers of a Titanium Dioxide Production Plant.

This study is aimed at evaluating whether the occupational exposure to TiO2 during the industrial production process is able to induce genotoxic, oxidative, and inflammatory effects on blood, biomonitoring the same workers that showed micronucleus induction in the exfoliated buccal cells, as previous published. The final aim was to find sensitive and suitable biomarkers to evaluate potential early toxicity of occupational exposure to TiO2. On the same 40 workers involved in the manufacture of TiO2 pigment, 5 office workers, and 18 controls previously studied, we used formamidopyrimidine glycosylase- (Fpg-) comet assay on lymphocytes to evaluate genotoxic/oxidative effects and detected cytokine (IL-6, IL-8, and TNFα) release by ELISA to evaluate proinflammation. Moreover, we studied the possible influence of single nucleotide polymorphisms of XRCC1 and hOGG1 DNA repair genes and of GST metabolism-related genes (GSTT1 and GSTM1) on the evaluated effects. We did not find statistically significant differences in the mean values of the analysed Fpg-comet assay parameters; only the percentage of DNA damaged cells appearing in the test as comets (% comets) resulted higher in the exposed workers compared to controls. Also, the data analysed taking into account the specific task (bagging, industrial cleaning, mobile operations, maintaining, and production) showed differences only for % comets which resulted higher in industrial cleaners compared to controls. We found variations of IL-6 and IL-8 levels in the exposed workers with concentrations that were lower for IL-6 and higher for IL-8 compared to the control group. XRCC1, hOGG1, and GSTT1 polymorphisms did not influence neither comet parameters nor cytokine release. These findings demonstrate that TiO2 production process is able to induce slight proinflammatory effects in terms of IL-8 increased release but not significant genotoxic/oxidative effects on lymphocytes, which do not seem to be a target of TiO2, prevalently inhalable particles, generated in the studied production site.

Influence of Single-Nucleotide Polymorphisms on Vitamin D Receptor Expression in Periodontal Ligament Fibroblasts as a Response to Orthodontic Compression.

This study aimed to evaluate if single-nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene are associated with gene expression in human periodontal ligament (hPDL) fibroblasts under simulated orthodontic compressive force. hPDL samples from 57 patients were used. A physiological compressive strain was performed to simulate orthodontic tooth movement in pressure areas under cell culture conditions. The RNA from hPDL fibroblasts was isolated to determine the relative gene expression (mRNA) of the VDR. The DNA was also isolated for the genotyping analysis of five SNPs in the VDR gene: BglI (rs739837, G/T), BsmI (rs1544410, T/C), ApaI (rs7975232, A/C), FokI (rs2228570, A/G), and TaqI (rs731236, A/G). Real-time polymerase chain reaction was used for both analyses. Kruskal-Wallis tests were used to compare VDR expression among genotypes of each SNP. A linear regression analysis was performed to evaluate SNP-SNP interaction. An established alpha of 5% was used. The relative mRNA VDR expression according to the genotypes in the SNPs BglI, BsmI, ApaI, FokI, and TaqI was not statistically significantly different (p > 0.05). The SNP-SNP interaction evaluated by regression analysis did not demonstrate any statistically significant association. No association was observed (p > 0.05). In conclusion, the SNPs BglI (rs739837), BsmI (rs1544410), ApaI (rs7975232), FokI (rs2228570), and TaqI (rs731236) did not show an impact on VDR gene expression in hPDL fibroblasts under simulated orthodontic compressive force.

Influence of single nucleotide polymorphism in the IGF-1 gene on performance and conformation traits in Munjal sheep.

Genetic polymorphism research in livestock species aims to assess genetic differences within and among breeds, primarily for conservation and development objectives. The aim of the present study was to determine the point mutation in the IGF-1 gene (g.855G>C and g.857G>A) and its association with performance traits in Munjal sheep. In total, 50 Munjal sheep were selected and the genomic DNA was isolated using the Automated Maxell RSC DNA/RNA purification system and the Maxwell RSC whole blood DNA kit. A reported set of primers was used to amplify the 294-bp fragment encompassing the targeted region, i.e. the 5' flanking region of the IGF-1 gene. The polymerase chain reaction product of 294-bp size harbouring the g.857G>A mutation in the 5' flanking region of the IGF-1 gene was digested with HaeII enzyme. Three possible genotypes were defined by distinct banding patterns, i.e. GG (194, 100 bp), GA (294, 194, 100 bp) and AA (294 bp) in the studied population of Munjal sheep. The genotypic and allelic frequencies of g.857G>A single nucleotide polymorphism of the IGF-1 gene indicated that the frequency of the A allele was higher in the studied population, i.e. 0.59 and the GA genotype was found to be the predominant genotype (0.66). Allele A of the IGF-1 gene was found to be associated with higher body weights and can be used in selection criteria for improving the performance of Munjal sheep. The positive effect of the IGF-1 gene on several conformational traits as observed in this study suggests that this area of the ovine IGF-I gene is particularly important and warrants further investigation on a larger population size.