Wild Allele Research Articles

RISK CONFERRED BY POLYMORPHIC VARIANTS OF VITAMIN D RECEPTOR (VDR) AND ANGIOTENSIN II TYPE 1 RECEPTOR (AGTR1) GENES FOR ESSENTIAL HYPERTENSION

Objective: The aim of this study was to establish the role of 1166A>C polymorphism of the AGTR1 gene (rs5186) and A/G polymorphism of the VDR gene (rs2228570) in risk prediction of essential hypertension (EH). Design and method: The study included patients with EH and hypertensive-mediated organs damage (2nd stage), moderate, high/very high cardiovascular risk. 100 subjects were involved in the case-control study. There were 70.84% females, 29.16% males among them, the mean age was 57.86±7.81 yo. Age- and gender-matched controls (n = 60) whose blood pressure measurements were in normal range and without any apparent diseases were randomly selected to compare with the patient data. In order to detect AGTR1 (rs5186) and VDR (rs2228570) gene polymorphism the qualitative real-time polymerase chain reaction was done. AGTR1 gene genotyping was performed for 72 patients and 48 healthy individuals and VDR gene – for 100 patients and 60 healthy subjects. Results: The distribution of genotypes and alleles AGTR1 (rs5186) and VDR (rs2228570) in the study and control groups did not differ significantly (p>0.05). C-allele of AGTR1 gene (rs5186) increases the risk of EAH more than 2 times [OR–2.31; 95% CI OR:1.19–4.47; p = 0.011], as well as AC- and the combination of AC- + CC-genotypes [OR–2.09; 95% CI OR:1.03–4.25; p = 0.038 and OR–2.30; 95% CI OR:1.14–4.64; p = 0.017]. The epidemiological analysis showed that polymorphic variants VDR (rs2228570) genes are not the risk factors of EH in the observed. Although, the combination of wild alleles of both genes in the homozygous state (AAAGTR1/AAVDR) makes a protective effect [OR = 0,42; OR 95%CI:0,18-1,0; ⇙2 = 3,74; p = 0,05], the combination of minor alleles (C-allele AGTR1 /AAVDR+C-allele AGTR1/AGVDR) increases the risk of EH more than threefold [OR = 3,36; OR 95%CI:1,24-9,09; ⇙2 = 5,88; p = 0,015]. Conclusions: Genotypes and alleles of VDR (rs2228570) gene are not associated with the risk of developing EH in the examined. C-allele of AGTR1 gene (rs5186) increases the risk of hypertension more than 2 times [OR–2.31; p = 0.011]. Combination of minor C-allele of AGTR1 gene and A-allele of VDR gene (C-allele AGTR1 /AAVDR+C-allele AGTR1/AGVDR) escalates the risk of EH more than 3 times [OR = 3,36; p = 0,015].

An Overview of Mapping Quantitative Trait Loci in Peanut (Arachis hypogaea L.).

Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change.

Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.).

Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.

A novel F8 variant in a Chinese hemophilia A family and involvement of X-chromosome inactivation: A case report.

Hemophilia A (HA) is an X-linked recessive bleeding disorder, which shows factor VIII (FVIII) deficiency caused by genetic variant in F8 gene. Males with F8 variants are affected, whereas female carriers with a wide range of FVIII levels are usually asymptomatic, it is possible that different X-chromosome inactivation (XCI) may effect the FVIII activity. We identified a novel variant F8: c.6193T > G in a Chinese HA proband, it was inherited from the mother and grandmother with different FVIII levels. We performed Androgen receptor gene (AR) assays and RT-PCR. AR assays revealed that the X chromosome with the F8 variant was severely skewed inactivated in the grandmother with higher FVIII levels, but not in the mother with lower FVIII levels. Further, RT-PCR of mRNA confirmed that only the wild allele of F8 was expressed in the grandmother, with lower expression in the wild allele of the mother. Our findings suggest that F8: c.6193T > G could be the cause of HA and that XCI affected the FVIII plasma levels in female carriers.

Expression Dynamics of lpa1 Gene and Accumulation Pattern of Phytate in Maize Genotypes Possessing opaque2 and crtRB1 Genes at Different Stages of Kernel Development.

Phytic acid (PA) acts as a storehouse for the majority of the mineral phosphorous (P) in maize; ~80% of the total P stored as phytate P is not available to monogastric animals and thereby causes eutrophication. In addition, phytic acid chelates positively charged minerals making them unavailable in the diet. The mutant lpa1-1 allele reduces PA more than the wild-type LPA1 allele. Further, mutant gene opaque2 (o2) enhances lysine and tryptophan and crtRB1 enhances provitamin-A (proA) more than wild-type O2 and CRTRB1 alleles, respectively. So far, the expression pattern of the mutant lpa1-1 allele has not been analysed in maize genotypes rich in lysine, tryptophan and proA. Here, we analysed the expression pattern of wild and mutant alleles of LPA1, O2 and CRTRB1 genes in inbreds with (i) mutant lpa1-1, o2 and crtRB1 alleles, (ii) wild-type LPA1 allele and mutant o2 and crtRB1 alleles and (iii) wild-type LPA1, O2 and CRTRB1 alleles at 15, 30 and 45 days after pollination (DAP). The average reduction of PA/total phosphorous (TP) in lpa1-1 mutant inbreds was 29.30% over wild-type LPA1 allele. The o2 and crtRB1-based inbreds possessed ~two-fold higher amounts of lysine and tryptophan, and four-fold higher amounts of proA compared to wild-type alleles. The transcript levels of lpa1-1, o2 and crtRB1 genes in lpa1-1-based inbreds were significantly lower than their wild-type versions across kernel development. The lpa1-1, o2 and crtRB1 genes reached their highest peak at 15 DAP. The correlation of transcript levels of lpa1-1 was positive for PA/TP (r = 0.980), whereas it was negative with inorganic phosphorous (iP) (r = -0.950). The o2 and crtRB1 transcripts showed negative correlations with lysine (r = -0.887) and tryptophan (r = -0.893), and proA (r = -0.940), respectively. This is the first comprehensive study on lpa1-1 expression in the maize inbreds during different kernel development stages. The information generated here offers great potential for comprehending the dynamics of phytic acid regulation in maize.

Analysis of intronic SNP (rs4147358) and expression of SMAD3 gene in Atopic Dermatitis: A case-control study

BackgroundAtopic Dermatitis (AD) is a multifactorial cutaneous disorder associated with chronic inflammation of the skin. Growing evidence points to TGF-β/SMAD signaling as a key player in mediating inflammation and the subsequent tissue remodeling, often resulting in fibrosis. This study investigates the role of a core transcription factor involved in TGF-β signaling i.e., SMAD3 genetic variants (rs4147358) in AD predisposition and its association with SMAD3 mRNA expression, serum IgE levels, and sensitization to various allergens in AD patients. MethodsA total of 246 subjects including 134 AD cases and 112 matched healthy controls were genotyped for SMAD3 intronic SNP by PCR-RFLP. mRNA expression of SMAD3 was determined by quantitative Real-Time PCR (qRT-PCR), Vitamin-D levels by chemiluminescence, and total serum IgE levels by ELISA. In-vivo allergy testing was performed for the evaluation of allergic reactions to house dust mites (HDM) and food allergens. ResultsA significantly higher frequency of mutant genotype AA (cases: 19.4% vs controls: 8.9%) (OR = 2.8, CI = 1.2 – 6.7, p = 0.01) was observed in AD cases. The mutant allele ‘A’ also showed a 1.9-fold higher risk for AD compared to the wild allele ‘C’ indicating that the carriers of the A allele have a higher risk for AD predisposition (OR-1.9, CI = 1.3–2.8, p < 0.001). In addition, quantitative analysis of SMAD3 mRNA in peripheral blood showed 2.8-fold increased expression in AD cases as compared to healthy controls. Stratification analysis revealed the association of the mutant AA genotype with deficient serum Vitamin D levels (p = 0.02) and SMAD3 mRNA overexpression with HDM sensitization (p = 0.03). Furthermore, no significant association of genotypes with SMAD3 mRNA expression was observed. ConclusionOur study indicates that SMAD3 intronic SNP bears a significant risk of AD development. Moreover, overexpression of SMAD3 mRNA and its association with HDM sensitization highlights the possible role of this gene in AD pathogenesis.

Mapping of QTLs Associated with Biological Nitrogen Fixation Traits in Peanuts (Arachis hypogaea L.) Using an Interspecific Population Derived from the Cross between the Cultivated Species and Its Wild Ancestors.

Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift up soil without synthetic fertilizers. We used a subset of 83 chromosome segment substitution lines (CSSLs) derived from the cross between a wild synthetic tetraploid AiAd (Arachis ipaensis × Arachis duranensis)4× and the cultivated variety Fleur11, and evaluated them for traits related to BNF under shade-house conditions. Three treatments were tested: without nitrogen; with nitrogen; and without nitrogen, but with added0 Bradyrhizobium vignae strain ISRA400. The leaf chlorophyll content and total biomass were used as surrogate traits for BNF. We found significant variations for both traits specially linked to BNF, and four QTLs (quantitative trait loci) were consistently mapped. At all QTLs, the wild alleles decreased the value of the trait, indicating a negative effect on BNF. A detailed characterization of the lines carrying those QTLs in controlled conditions showed that the QTLs affected the nitrogen fixation efficiency, nodule colonization, and development. Our results provide new insights into peanut nodulation mechanisms and could be used to target BNF traits in peanut breeding programs.

Seed germination variability: Why do genetically identical seeds not germinate at the same moment?

For survival in the wild environment, plants prefer a bet-hedging strategy where individual variation is high and also produce a range of phenotypes. When faced with unpredictable environmental conditions, fluctuation in seed behaviour is a beneficial trait that allows the survival of plants, particularly if seedlings from early germinated seeds don't survive. However, this is not a desired trait when agriculture is concerned, where a set of uniformly grown seedlings are required. Even though variability in seed behaviour is unavoidable, over the centuries, humans might have selected seeds with minimum variability for agricultural use. In the model plant Arabidopsis, non-stratified seeds even in the same silique germinate variably. How this variability is manifested from genes to a physiological outcome and what molecular mechanism of bet-hedging facilitates this diversity remains elusive. Will the reintroduction of valuable wild alleles in domesticated crops contribute to this variability between individual seeds by promotion of bet-hedging? Recent advances have shed light on possible molecular pathways of germination that are impacted at the level of single seeds and single cells. Here, we review the hormonal, molecular and cellular mechanisms that may impact the germination outcome of individual genetically identical seeds.

EWSR1 prevents the induction of aneuploidy through direct regulation of Aurora B.

EWSR1 (Ewing sarcoma breakpoint region 1) was originally identified as a part of an aberrant EWSR1/FLI1 fusion gene in Ewing sarcoma, the second most common pediatric bone cancer. Due to formation of the EWSR1/FLI1 fusion gene in the tumor genome, the cell loses one wild type EWSR1 allele. Our previous study demonstrated that the loss of ewsr1a (homologue of human EWSR1) in zebrafish leads to the high incidence of mitotic dysfunction, of aneuploidy, and of tumorigenesis in the tp53 mutant background. To dissect the molecular function of EWSR1, we successfully established a stable DLD-1 cell line that enables a conditional knockdown of EWSR1 using an Auxin Inducible Degron (AID) system. When both EWSR1 genes of DLD-1 cell were tagged with mini-AID at its 5'-end using a CRISPR/Cas9 system, treatment of the (AID-EWSR1/AID-EWSR1) DLD-1 cells with a plant-based Auxin (AUX) led to the significant levels of degradation of AID-EWSR1 proteins. During anaphase, the EWSR1 knockdown (AUX+) cells displayed higher incidence of lagging chromosomes compared to the control (AUX-) cells. This defect was proceeded by a lower incidence of the localization of Aurora B at inner centromeres, and by a higher incidence of the protein at Kinetochore proximal centromere compared to the control cells during pro/metaphase. Despite these defects, the EWSR1 knockdown cells did not undergo mitotic arrest, suggesting that the cell lacks the error correction mechanism. Significantly, the EWSR1 knockdown (AUX+) cells induced higher incidence of aneuploidy compared to the control (AUX-) cells. Since our previous study demonstrated that EWSR1 interacts with the key mitotic kinase, Aurora B, we generated replacement lines of EWSR1-mCherry and EWSR1:R565A-mCherry (a mutant that has low affinity for Aurora B) in the (AID-EWSR1/AID-EWSR1) DLD-1 cells. The EWSR1-mCherry rescued the high incidence of aneuploidy of EWSR1 knockdown cells, whereas EWSR1-mCherry:R565A failed to rescue the phenotype. Together, we demonstrate that EWSR1 prevents the induction of lagging chromosomes, and of aneuploidy through the interaction with Aurora B.

Effects of changes in myosin biomechanics on canonical and non-canonical signaling and HCM phenotypes.

Myosin heavy chain 7 (MYH7) mutations are among the most commonly found in patients with hypertrophic cardiomyopathy (HCM). To address cellular responses to biomechanical alternations due to mutations in MYH7, we employed human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as an in vitro model and deeply phenotyped the transcriptional changes in these cells using single cell RNA sequencing (scRNAseq). We profiled hiPSC-CMs carrying heterozygous G265E mutant and control wild type MYH7 alleles at 30 and 60 day after differentiation and found potential disruption in hypertrophic gene expression as well as genes regulating mitochondrial metabolism. Intriguingly, the gene expression phenotype in these mutant lines appear somewhat subtle and vary considerably from line to line and differentiation batch to batch. To assess whether the mutant cells are more susceptible to physiological stress, we treated day 30 hiPSC-CMs with isoproterenol and observed an increased in their metabolic gene defect that was corroborated using a Seahorse metabolic assay. Given the more subtle phenotype of MYH7 G256E heterozygous mutant line, we considered whether a homozygous mutant would provide a more robust phenotype manifestation at the transcriptional level. To address this, we profiled day 30 hiPSC-CM from a MYH R369Q homozygous mutant line and found a significantly greater consistency in transcriptional phenotype among different lines and batches of differentiation. In summary, our work revealed the power of MYH7 mutation-specific hiPSC-CMs as an in vitro model of HCM and the ability of scRNAseq to deeply phenotype these cells to reveal their aberrant cellular signaling and metabolic response. When combined with a comprehensive understanding of MYH7 mutation effects at the single molecular and whole tissue level, we hope to enable future development of novel therapy against HCM.

Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection.

Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.

Inheritance of Early and Late Ascochyta Blight Resistance in Wide Crosses of Chickpea.

Chickpea (Cicer arietinum) is a globally important food legume but its yield is negatively impacted by the fungal pathogen Ascochyta blight (Ascochyta rabiei) causing necrotic lesions leading to plant death. Past studies have found that Ascochyta resistance is polygenic. It is important to find new resistance genes from the wider genepool of chickpeas. This study reports the inheritance of Ascochyta blight resistance of two wide crosses between the cultivar Gokce and wild chickpea accessions of C. reticulatum and C. echinospermum under field conditions in Southern Turkey. Following inoculation, infection damage was scored weekly for six weeks. The families were genotyped for 60 SNPs mapped to the reference genome for quantitative locus (QTL) mapping of resistance. Family lines showed broad resistance score distributions. A late responding QTL on chromosome 7 was identified in the C. reticulatum family and three early responding QTLs on chromosomes 2, 3, and 6 in the C. echinospermum family. Wild alleles mostly showed reduced disease severity, while heterozygous genotypes were most diseased. Interrogation of 200k bp genomic regions of the reference CDC Frontier genome surrounding QTLs identified nine gene candidates involved in disease resistance and cell wall remodeling. This study identifies new candidate chickpea Ascochyta blight resistance QTLs of breeding potential.

Analysis of Domestication Loci in Wild Rice Populations.

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication.

High GLI-1 Expression is a Reliable Indicator of Bad Prognosis in Newly Diagnosed Acute Leukemia Patients

Purpose: To explore the expression and prognostic significance of Hedgehog signaling transcription factor GLI-1 in newly diagnosed acute myeloid leukemia (AML) patients. Methods: Clinical specimens were obtained from 46 recently diagnosed AML patients. Real-time qPCR was used to measure the GLI-1 mRNA expression in bone marrow mononuclear cells.Also, the relationship between GLI-1 mRNA levels and clinical variables and prognostic variables was assessed. Results: GLI-1 was overexpressed in the bone marrow samples of our patients. GLI-1mRNA expression did not differ significantly across different age groups, between both sexes, or between different FAB subtypes (P = 0.882, P = 0.246, and P = 0.890, respectively). GLI-1 expression varied significantly in different risk categories, with the greatest levels observed in 11 patients with poor risk (24.6 versus 22.7) compared to intermediate risk (5.2 versus 3.9; P = 0.006) and favorable risk (4.2 versus 3; P = 0.001). Comparing patients with the wild FLT3 allele to those with the mutant one, GLI-1 gene levels were considerably greater in those with the mutant allele of FLT3.Following induction chemotherapy, the levels of GLI-1 mRNA were significantly higher in 22 patients who did not experience complete remission (CR) diagnosed with de novo non-acute promyelocytic leukemia (APL) compared to 17 patients who did (P = 0.017). Significantly greater levels of expression were observed in each category of the patients with favorable risk; wild FLT3 allele (P = 0.033) and CR failure P = 0.005). Conclusion: GLI-1 overexpression is a risk factor for poor prognosis and could be a novel therapeutic target for AML.

Wild and cultivated allele effects on rice phenotypic traits in reciprocal backcross populations between Oryza rufipogon and two cultivars, O. sativa Nipponbare and IR36.

A total of four populations of reciprocal backcross recombinant inbred lines were produced from a cross between a wild accession of Oryza rufipogon W630 and two major cultivars, O. sativa Japonica Nipponbare and Indica IR36. Using these populations, quantitative trait locus (QTL) analysis for eight morphological traits (culm length, panicle length, days to heading, panicle shape, pericarp color, hull color, seed shattering and seed awning) was carried out, and the putative QTL regions were compared among the populations. The QTLs with strong allele effects were commonly detected for culm length, panicle shape, pericarp color and hull color in all four populations, and their peak locations were close to the major genes of sd1, Spr3, Rc and Bh4, respectively. For panicle length and days to heading, some QTL regions overlapped between two or three populations. In the case of seed shattering and seed awning, strong wild allele effects at major loci were observed only in the populations with cultivated backgrounds. Since the wild and cultivated alleles have never been evaluated in the reciprocal genetic backgrounds, the present results provide new information on gene effects in breeding and domestication studies.

The Investigation of the Association Between the Bcl-2 3’-UTR rs1564483 Polymorphism and miR-296-3p in the Development of Breast and Gastric Cancers

Background: B-cell leukemia/lymphoma 2 ( Bcl-2) gene regulates carcinogenesis by inhibiting apoptosis. This study evaluated the association of Bcl-2 3′-untranslated regions (3′ UTR) rs1564483 polymorphism and miR-296-3p with the development of breast and gastric cancers. Methods: A microarray analysis was performed on the Genomic Spatial Event (GSE)29431 and GSE161533 datasets for breast and gastric cancers. Blood samples were taken from 222 (111 patients and 111 controls) and 210 (84 patients and 126 controls) individuals for breast and gastric cancers, respectively. Genomic DNA was extracted from the blood samples and genotyping was performed using real-time polymerase chain reaction (RT-PCR), followed by examining the high-temperature melting curve. Statistical analysis was conducted to examine the potential correlation between the rs1564483 polymorphism and the risk of breast and gastric cancers concerning pathological characteristics. Results: The results of the microarray showed that the Bcl-2 gene was up-regulated in gastric cancer (logFC [log fold change]: 0.65, adjusted P &lt; .05). Clinical outcome showed no notable relationship between the rs1564483 polymorphism and breast cancer risk; however, for gastric cancer, it identified a large difference between healthy controls and patients for an allelic frequency of rs1564483 ( P ⩽ .001). Moreover, an assay of different models (dominant, recessive, and co-dominant) showed a significant association between the AG genotype between control and gastric cases (Pearson chi-square test, P = .046). In addition, the prevalence of the AG genotype was greater in persons under the age of 45 and in patients with H. pylori infection ( P ⩽ .001). The AG genotype was not related to smoking, although the AA genotype was associated with increased cancer incidence in smokers ( P ⩽ .001). Conclusions: In silico studies and calculations of the ΔG binding of micro ribonucleic acid (miRNA) hsa-miR-296-3p to the mutant and wild alleles of the rs15644833 single nucleotide polymorphism (SNP) have revealed that Bcl-2 mRNA expression in gastric cancer decreases, thus confirming the tumor suppressor role of the Bcl-2 gene.

ASSOCIATION OF SOLUTE CARRIER ORGANIC ANION TRANSPORTER 1B1 GENE POLYMORPHISM WITH RESPONSE TO ATORVASTATIN AND ASSOCIATED MYOPATHY IN IRAQI DYSLIPIDEMIA PATIENTS.

Aim: The study aims to investigate the effect of solute carriers organic anions transporters 1B1 (SLCO1B1) gene polymorphisms rs4149056, rs2306283, rs55901008, and rs729559745 in a sample of patients with dyslipidemia, and relate it to atorvastatin response and associated myopathy. Materials and Methods: A cross sectional enrolled 200 patients both males and females of Arabic race, Iraqi nationality aged between 30-65 years. The patients were divided into two groups: Group 1 (Atorvastatin responders and tolerant), Group 2 (Atorvastatin non responder and intolerant). Blood samples collected from the patients for biochemical studies and analyzed statistically by Student T-test and Chi-square, and DNA extracted for polymerase chains reactions (PCR). Results: The results showed insignificant association P≥0.05 between the demographic characteristics of the study population with different genotypes, and significant difference P<0.05 in the biochemical parameters regarding (T-cholesterol, triglycerides, low density lipoproteins, and Creatine kinase-MM) when comparing the two groups. Odds ratio (OR) with confidence intervals CI (95%) used to evaluate the risk association to develop myopathy and poor response to atorvastatin therapy show relevant association for CC and CT genotype of rs4149056, while rs2306283 GG genotype show low association, also rs55901008 show low association for CC genotype, and moderate association for rs72559745 genotypes GG, AG. Conclusions: The mutant allele's genotypes of rs4149056, rs55901008, and rs72559745, and the wild allele genotype of rs2306283 show significant association with the development of poor response to atorvastatin and elevated the level of CK-MM plasma concentration.

Correlation between CYP2C19 Polymorphisms and recurrent risk in Patients with Ischemic Stroke treated with Clopidogrel in Kurdistan region-Iraq

Clopidogrel is a prodrug that must be transformed into an active metabolite by hepatic cytochrome P450 (CYP) isoenzymes to prevent platelet clotting. Polymorphisms of the CYP2C19 gene can cause a reduction or complete loss of CYP2C19 enzyme activity resulting in inhibiting clopidogrel metabolism, effectiveness and increase stroke recurrence risk in ischemic stroke patients. This study aims to investigate the correlation between genetic polymorphisms in CYP2C19*2 and*3 and recurrent risk in patients with ischemic stroke taking clopidogrel 75mg in Kurdistan region –Iraq. This retrospective case-control study was carried out at Kurdistan, Erbil, Medicina medical center, and Rizgary general hospital from January 2021 to August 2021. The blood sample was taken from the participants and tested for genotyping. The collection of data was taken from patients' medical charts in the hospital and patients’ electronic medical records from the neurology clinic. Sixty patients participated, (34) were male and (26) were female, with age range (38-96) years, diagnosed from not more than two years with ischemic stroke and taking 75 mg clopidogrel maintenance dose. Genotyping analysis showed 61.7 % were homozygotes for wild allele *1, the heterozygotes divided into 26.7% (*1/*2) and 6.7 % (*1/*3) genotype, while the homozygotes for mutant alleles CYP2C19*2,*3 distributed in 3.3 %(*2/*2) and 1.7 %(*3/*3). The (*2/*3) was not detected in the study population. A significant relation was found between risk of stroke recurrence with carrying the variant allele CYP2C19 *2, reduced CYP2C19 enzyme metabolic activity, and ACEIs/ARBs usage (P = 0.024, P = 0.039, P=0.24 respectively). On the other hand, there was no significant relationship between the risk of stroke recurrence and carrying the variant allele CYP2C19 *3 (P = 1.000). Ischemic stroke patients treated with clopidogrel and carrying a CYP2C19*2 allele had a higher risk of recurrent stroke as it is associated with reduced the metabolic activity of CYP2C19 enzyme leading to reduction of clopidogrel effect.

The role of ACTN3 R/X and ACE I/D in the development of endurance in athletes

Annotation. Endurance – one of the most important sports components, which allows you to overcome the workload for a given time without significant losses in strength and speed. It is most manifested in such sports as swimming, skiing, marathon, cycling, gymnastics. Since the endurance development is mostly influenced not only by epigenomic factors, but also by the genotype of the athlete, so the purpose of this review article is to study the effects of ACTN3 and ACE genes on this physical component. In order to do so, we used basic databases to process information that is known to date on the effects of these genes and their variations. The search was conducted up to and including January 2022 in accordance with PRISMA recommendations. Genes under our study affects endurance in different ways, for example, ACTN3 R577X polymorphism increases the number of slow muscle fibers, and the presence of wild allele “I” of the ACE gene slows down the bradykinin decomposition which mitigates the workload impact on the cardiovascular system, thereby facilitating its adaptation, although there is evidence of an increased risk of injury. The purpose of the review results is to help each athlete in selection of training tactics, which could help him in sports achievements.

Gene polymorphisms of interleukin 10 (− 819 C/T and − 1082 G/A) in women with ovarian cancer

BackgroundOvarian cancer (OC) is the leading cause of death associated with gynecologic cancer. IL-10 plays an important role in tumorigenesis. We investigated IL-10 gene polymorphisms in OC patients. The current case–control study screened forty-eight women with OC and forty-eight healthy women who did not have OC. The genotyping of SNPs (− 1082 G > A; rs1800896 and − 819 C > T; rs1800871) of the IL-10 gene was done by tetra primers sequence-specific primer polymerase chain reaction (SSP-PCR) technique. The plasma levels of IL-10 were measured using an enzyme-linked immunosorbent assay (ELISA).ResultsFor IL-10 (− 1082 G/A) polymorphism, the G (wild allele) was significantly associated with increasing the risk of OC (OR = 2.054 with CI = 1.154–3.657; P < 0.05), while the A (variant allele) and AA genotype was significantly associated with decreasing the risk of OC (OR = 0.487 with CI = 0.273–0.867; P < 0.05) and (OR = 0.15; 95% CI = 0.04–0.63; P < 0.05), respectively. For IL-10 (− 819C/T) polymorphisms, the T allele (variant allele) and (TT, CT genotypes) were significantly associated with increasing the risk of OC (OR = 2.800 with 95% CI = 1.577–5.037; P < 0.05), (OR = 18.33 with 95% CI = 3.46–97.20; P < 0.001), and (OR = 9.44 with 95% CI = 2.52–35.40; P < 0.001), respectively, while the C (wild allele) was significantly associated with decreasing the risk of OC (OR = 0.357 with 95% CI = 0.199–0.642; P < 0.05). The haplotype analysis for (− 1082 G > A and − 819 C > T shows the GT haplotype was significantly associated with increasing the risk of OC (OR = 50.09 with CI = 6.34–395.92; P < 0.001). OC was substantially correlated with IL-10 level (r = 0.457; p < 0.001). There is no linkage disequilibrium (LD) between IL 10 − 1082 G/A and IL 10 − 819 C/T (D′ = 0.1315, r2 = 0.016; P = NS). A statistically significant positive relationship existed between IL-10 and CA125 and ALT (P < 0.05). IL-10 and albumin showed a strong negative association (P < 0.05), whereas the correlation of IL10 plasma level with BUN, AST, T. Bil., TLC, PLT, Cr., and HB has not any significant value (P > 0.05).ConclusionsOverall, this study supports an association of IL-10 (− 1082 G/A and − 819C/T) polymorphisms with the risk of ovarian cancer.