Common Polymorphisms Research Articles

Utilizing Human Genetics to Develop Chemoprevention for Cancer-Too Good an Opportunity to be Missed.

Large-scale genetic studies are reliably identifying many risk factors for disease in the general population. Several of these genetic risk factors encode potential drug targets, and genetics has already helped to introduce targeted agents for some diseases, an example being lipid-lowering drugs to reduce the incidence of cardiovascular disease. Multiple drugs have been developed to treat cancers based on somatic mutations and genomics, but in stark contrast, there seems to be a reluctance to use germline genetic data to develop drugs to prevent malignancy, despite the large numbers of people who could benefit, the potential for lowering cancer rates, and the widespread current use of non-pharmaceutical measures to reduce cancer risk factors such as tobacco, alcohol, and infectious diseases. We argue that concerted efforts for cancer prevention based on genetics, including genes influenced by common polymorphisms that modulate cancer risk, are urgently needed. There are enormous, yet underutilized, opportunities to develop novel targeted agents for chemoprevention of cancer based on human germline genetics. Such efforts are likely to require the support of a dedicated funding program by national and international agencies. See related commentary by Winham and Sherman, p. 13.

A Common Polymorphism in RNASE6 Impacts Its Antimicrobial Activity toward Uropathogenic Escherichia coli.

Human Ribonuclease (RNase) 6 is a monocyte and macrophage-derived protein with potent antimicrobial activity toward uropathogenic bacteria. The RNASE6 gene is heterogeneous in humans due to the presence of single nucleotide polymorphisms (SNPs). RNASE6 rs1045922 is the most common non-synonymous SNP, resulting in a G to A substitution that determines an arginine (R) to glutamine (Q) transversion at position 66 in the protein sequence. By structural analysis we observed that R66Q substitution significantly reduces the positive electrostatic charge at the protein surface. Here, we generated both recombinant RNase 6-R66 and -Q66 protein variants and determined their antimicrobial activity toward uropathogenic Escherichia coli (UPEC), the most common cause of UTI. We found that the R66 variant, encoded by the major SNP rs1045922 allele, exhibited superior bactericidal activity in comparison to the Q66 variant. The higher bactericidal activity of R66 variant correlated with an increase in the protein lipopolysaccharide binding and bacterial agglutination abilities, while retaining the same enzymatic efficiency. These findings encourage further work to evaluate RNASE6 SNP distribution and its impact in UTI susceptibility.

Allele-specific effect of various dietary fatty acids and ETS1 transcription factor on SCD1 expression

Overnutrition and genetic predisposition are major risk factors for various metabolic disorders. Stearoyl-CoA desaturase-1 (SCD1) plays a key role in these conditions by synthesizing unsaturated fatty acids (FAs), thereby promoting fat storage and alleviating lipotoxicity. Expression of SCD1 is influenced by various saturated and cis-unsaturated FAs, but the possible role of dietary trans FAs (TFAs) and SCD1 promoter polymorphisms in its regulations has not been addressed. Therefore, we aimed to investigate the impact of the two main TFAs, vaccenate and elaidate, and four common promoter polymorphisms (rs1054411, rs670213, rs2275657, rs2275656) on SCD1 expression in HEK293T and HepG2 cell cultures using luciferase reporter assay, qPCR and immunoblotting. We found that SCD1 protein and mRNA levels as well as SCD1 promoter activity are markedly elevated by elaidate, but not altered by vaccenate. The promoter polymorphisms did not affect the basal transcriptional activity of SCD1. However, the minor allele of rs1054411 increased SCD1 expression in the presence of various FAs. Moreover, this variant was predicted in silico and verified in vitro to reduce the binding of ETS1 transcription factor to SCD1 promoter. Although we could not confirm an association with type 2 diabetes mellitus, the FA-dependent and ETS1-mediated effect of rs1054411 polymorphism deserves further investigation as it may modulate the development of lipid metabolism-related conditions.

Association of common glutathione transferase polymorphisms with ovarian cancer risk and chemoresistance

Ovarian cancer is regarded as the most lethal gynecological cancer with a five-year survival below 45%. It represents the seventh most common cancer among women. Due to the limited availability of biomarkers and reliable screening methods for early diagnosis of ovarian cancer, much research is being conducted to explore and understand the factors that may increase the risk of developing this kind of cancer. When surgery and chemotherapy treatments have been fully utilized, the development of chemoresistance becomes a critical factor in the progression of the disease. Glutathione transferases (GSTs) are a group of enzymes that play a role in the process of detoxification. Genes that code for GSTs proteins exhibit polymorphism, which can lead to either total or partial loss of enzymatic function. Cytosolic GST activity is composed of many different isoenzymes that facilitate interactions between glutathione and hazardous chemicals, including cancerogenes, anticancer drugs, and byproducts of oxidative stress. The scope of this review is to clarify the association of common GST polymorphisms with ovarian cancer risk and chemoresistance.

Genetic architecture of anterior abdominal wall hernias

To analyze genome-wide studies devoted to polymorphisms of factors of anterior abdominal wall hernias, to study the association of the most common polymorphism In Russian population. Searching for literature data was carried out in the RSCI and PubMed databases. We enrolled national and foreign reports. The study on Russian population included 577 people. We found 5 genome-wide studies performed by foreign authors. We identified the loci responsible for genetic predisposition to inguinal hernias: WT1, EFEMP1, EBF2 and ADAMTS6. The Japanese scientists revealed an important role of loci TGFB2, RNA5SP214/VGLL2, LOC646588, HMCN2, ATP5F1CP1/CDKN3. In other studies, loci 1q41 (ZC3H11B), 2p16.1 (EFEMP1), 6p22.1 (MHC region), 7q33 (CALD1) and 11p13 (WT1) determined different hernias. The EFEMP1 gene polymorphism was among genes most associated with anterior abdominal wall hernias in all studies. Analysis of this polymorphism In Russian population revealed significant association with anterior abdominal wall hernias. The obtained data on target correction of DNA chains can significantly reduce the incidence of anterior abdominal wall hernias. In turn, this will significantly reduce the cost of surgical treatment and risk of complications with recurrences of hernias. Moreover, identifying the most associated polymorphisms may be valuable to determine the most appropriate surgical treatment.

Association of IL13 polymorphisms with susceptibility to myocardial infarction: A case-control study in Chinese population.

Inflammatory cytokines play a major role in the pathogenesis of myocardial infarction (MI). Although information on the importance of interleukin 13 (IL13) in human MI is limited, it has been well documented in the mouse model. Genetic variation in the IL13 gene has been associated with the structure and expression of the IL13. In the present study, we hypothesized that IL13 common genetic variants would be associated with a predisposition to the development of MI. The present study enrolled 305 MI patients and 310 matched healthy controls. Common genetic polymorphisms in the IL13 gene (rs20541, rs1881457, and rs1800925) were genotyped using the TaqMan SNP genotyping method. Plasma levels of IL13 were measured using an enzyme-linked immunosorbent assay (ELISA). In MI patients, minor alleles of the IL13 rs1881457 and rs1800925 polymorphisms were less common than in healthy controls [rs1881457: AC (P = 0.004, OR = 0.61), C (P = 0.001, OR = 0.66); rs1800925: CT (P = 0.006, OR = 0.59)]. Further haplotype analysis of three studied SNPs revealed a significant association with predisposition to MI. Interestingly, IL13 rs1881457 and rs1800925 were linked to plasma levels of IL13: the reference genotype had higher levels, heterozygotes were intermediate, and the alternate genotype had the lowest levels. In the Chinese population, IL13 (rs1881457 and rs180092) variants are associated with different plasma IL13 levels and offer protection against MI development. However, additional research is required to validate our findings in different populations, including descent samples.

Human Genetics of Tetralogy of Fallot and Double-Outlet Right Ventricle.

Tetralogy of Fallot (TOF) and double-outlet right ventricle (DORV) are conotruncal defects resulting from disturbances of the second heart field and the neural crest, which can occur as isolated malformations or as part of multiorgan syndromes. Their etiology is multifactorial and characterized by overlapping genetic causes. In this chapter, we present the different genetic alterations underlying the two diseases, which range from chromosomal abnormalities like aneuploidies and structural mutations to rare singlenucleotide variations affecting distinct genes. For example, mutations in the cardiac transcription factors NKX2-5, GATA4, and HAND2 have been identified in isolated TOF cases, while mutations of TBX5 and 22q11 deletion, leading to haploinsufficiency of TBX1, cause Holt-Oram and DiGeorge syndrome, respectively. Moreover, genes involved in signaling pathways, laterality determination, and epigenetic mechanisms have also been found mutated in TOF and/or DORV patients. Finally, genome-wide association studies identified common singlenucleotide polymorphisms associated with the risk for TOF.

Correlation of LaboratoryParameters Between Subgroups of "Wild Type", Mutated, Heterozygous Patients Based on the Presence of Rs231775 CTLA-4 Gene Polymorphisms in Pluriglandular Autoimmune Syndrome (PAS III)

Background: Autoimmune thyroid disease and diabetes mellitus type 1 are multifactorial diseases, in which there are several common, suspect genes, as well as environmental factors that contribute to the etiology of the disease. These genes were nominated as common susceptibility genes for PAS-III. Family and population studies have shown that PAS IIIA has a strong genetic background. Objective: In this work, gene polymorphisms were examined in 50 patients with PAS-IIIA. It is about polymorphism CTLA-4 gene polymorphism: rs231775. Rs231775, also known as + 49 A/G (or CTLA-4 A49G), is a common nonsynonymous CTLA-4 polymorphism. So far, it has been linked to several autoimmune diseases, especially autoimmune thyroiditis, as well as several other disorders. Methods: Peripheral blood of 50 patients was used as clinical material for the study. DNA was isolated from the collected peripheral blood samples using the Qiamp DNA mini kit, using the attached protocol and manufacturer's instructions. We also performed laboratory blood tests: Hba1c values as a parameter of glycoregulation in the last 3 months, fasting and 2-hour glycemia values, total cholesterol and triglyceride values, anti-TPO and anti-Tg thyroid antibodies. We were interested in the difference in laboratory tests in subgroups GWT, GM and GH. Results: Using the chi-square test, the association between the rs231775 polymorphism and PAS-III was proven. The values of GUK, HbA1C, cholesterol, triglycerides, antibodies to thyroglobulin and antibodies to thyroperoxidase were not statistically significantly different in all three subgroups of patients suffering from PAS III. Conclusion: It has been previously shown that people with a mutation in one allele of CTLA-4 are highly susceptible to autoimmunity, which raises the possibility that more subtle variations in the level of CTLA-4 in the general population can influence the response to therapy. Non-pathogenic polymorphisms in CTLA-4 that alter CTLA-4 expression may affect an individual's lifetime risk for the development of autoimmune and malignant disorders..

Structural and Functional Impact of Adrenoceptor Beta-1 Gene Polymorphism in Patients with Hypertrophic Cardiomyopathy and Response to Beta-Blocker Therapy.

Hypertrophic cardiomyopathy (HCM) is a genetically inherited cardiac disorder with diverse clinical presentations. Adrenergic activity, primarily mediated through beta-adrenoceptors, plays a central role in the clinical course of HCM. Adrenergic stimulation increases cardiac contractility and heart rate through beta-1 adrenoceptor activation. Beta-blocker drugs are recommended as the primary treatment for symptomatic HCM patients to mitigate these effects. This prospective study aimed to investigate the impact of common ADRB-1 gene polymorphisms, specifically serine-glycine at position 49 and arginine-glycine at position 389, on the clinical and structural aspects of HCM. Additionally, the study explored the association between these genetic variations and the response to beta-blocker therapy in HCM patients. A cohort of 147 HCM patients was enrolled, and comprehensive assessments were performed. The findings revealed that the Ser49Gly polymorphism significantly influenced ventricular ectopic beats, with beta-blocker therapy effectively reducing them in Ser49 homozygous patients. Moreover, natriuretic peptide levels decreased, particularly in Ser49 homozygotes, indicating improved cardiac function. Left ventricular outflow obstruction, a hallmark of HCM, was also reduced following beta-blocker treatment in all patient groups. In contrast, the Arg389Gly polymorphism did not significantly impact baseline parameters or beta-blocker response. These results emphasize the role of the Ser49Gly polymorphism in the ADRB-1 gene in shaping the clinical course and response to beta-blocker therapy in HCM patients. This insight may enable a more personalized approach to managing HCM by considering genetic factors in treatment decisions. Further research with larger populations and longer follow-up periods is needed to confirm and expand upon these findings.

Common Genetic Variants in SIRT1 Gene Promoter and Type 2 Diabetes Mellitus in Saudi Arabia.

Type 2 diabetes mellitus (T2DM) is common in Saudi Arabia and represents a major health concern. Silent information regulator of transcription-1 (SIRT1) positively influences insulin sensitivity and might contribute to the pathogenesis of T2DM. This study aimed to investigate the frequency of two common functional single nucleotide polymorphisms (SNPs) in the promoter region of SIRT1; rs12778366 (T>C) and rs3758391 (T>C) in Saudi Arabian population and examine any association with T2DM. A total of 445 volunteers were divided into 224 healthy controls and 221 patients previously diagnosed with T2DM. Genomic DNA was extracted from all samples and genotyped for SIRT1 rs12778366 and rs3758391 SNPs by TaqMan RT-PCR allelic discrimination assay. Logistic regression analysis was used to establish any relationship between these polymorphisms and T2DM. In the total study population, rs12778366 genotype frequencies were TT (89.2%), TC (10.3%), and CC (0.45%) and for the rs3758391 they were TT (16.4%), TC (44.5%), and CC (39.1%). The distribution of these genotypes, in both polymorphisms, were similar among T2DM and controls. Logistic regression analysis confirmed the lack of association between the presence of CC or CT variants and T2DM for rs12778366 and rs3758391 SNP (OR = 0.98 [CI]: 0.55 - 1.75; p = 0.999 and OR= 0.75; [CI]: 0.45 - 1.24; p = 0.313), respectively. This study revealed the frequency of SIRT1 rs12778366 and rs3758391 SNPs in our population and reported no association between these polymorphisms and the risk for T2DM. This finding might add to the growing body of literature exploring the genetics of T2DM.

Determination of Frequency of Type 2 Deiodinase Thr92Ala Polymorphism (rs225014) in 131I-treated Differentiated Thyroid Cancer Patients Undertaking L-thyroxine (L-T4) Suppression Therapy.

Type 2 deiodinase (DIO2) enzyme plays a vital role in peripheral T4 to T3 conversion and in the negative feedback regulation of pituitary thyroid-stimulating hormone (TSH) secretion. Thr92Ala polymorphism (rs225014) is a common single-nucleotide polymorphism (SNP) that lowers DIO2 activity and is associated with diverse physiological disorders. Differentiated thyroid cancer (DTC) patients are given L-T4 therapy after total thyroidectomy and 131I treatment to suppress TSH levels. The aim of the study was to determine the frequency of rs225014 in DTC patients and to investigate its effect on the thyroid function tests (TFTs) and L-T4 dose required to suppress TSH levels. The study included a DTC patient group and a control group. TFTs were estimated by RIA/IRMA kits. Genomic DNA of all the subjects was screened for rs225014 SNP by polymerase chain reaction. The frequency of Thr/Thr (wild type), Thr/Ala (heterozygous mutant), and Ala/Ala (homozygous mutant) genotypes in the DTC patients' group was 0.21, 0.52, and 0.27, respectively. T3 levels and T3/T4 ratio were significantly low in the Ala/Ala genotype in the DTC group indicating impaired DIO2 activity. L-T4 dose requirement to suppress TSH levels in the DTC patients harboring rs225014 SNP was not statistically different from the wild-type genotype. The SNP rs225014 was observed to be associated with T3 and T3/T4 ratio but not with the L-T4 dose in DTC harboring SNP suggesting the presence of a compensatory pathway to overcome DIO2 impairment. However, it is essential to study the genetic makeup of DTC patients showing reduced response to TSH suppression to enable quicker decision-making in the implementation of personalized L-T4 dose to prevent any adverse effects.

Possible effect of OAS1 and TMPRSS6 but not DPP4 and ZNF335 polymorphisms on COVID-19 severity in the Czech population.

The acute respiratory syndrome, known as COVID-19, is characterised by high morbidity and increased mortality. Genetic factors may partially explain the differences in susceptibility to and severity of COVID-19. We have analysed common functional polymorphisms within the OAS1 (rs4767027), TMPRSS6 (rs855791), DPP4 (rs3788979), and ZNF335 (rs3848719) genes in SARS-CoV-2 positive subjects (n = 521, different disease severity) and in population controls (n = 2,559 subjects, COVID-19 status unknown). Neither DPP4 nor ZNF335 were associated with disease susceptibility or severity in the Czech population in any of the models used for calculation. T allele carriers of the OAS1 polymorphism seem to be protective against symptomatic COVID-19 (p = 0.002 calculated for trend; asymptomatic, symptomatic, hospitalised). Similarly, within the TMPRSS6, minor TT homozygotes associated with lower plasma Fe concentrations were underrepresented in the overall patient group (p = 0.044; OR = 0.77, 95% CI: 0.59-0.99), and the difference was mainly driven by the severe COVID-19 subjects. In general, risky homozygotes of these two polymorphisms were less frequent than expected in the group of hospitalised COVID-19 survivors. Common variants within OAS1 (rs4767027) and TMPRSS6 (rs855791) play some role in COVID-19 pathology in the Czech Caucasian population. Whether the depletion of minor allele carriers of these two variants is associated with increased COVID-19 mortality, needs to be analysed in an external confirmatory study.

Evaluation of mutations on O6-methylguanine methyl transferase structure and its interactions: molecular dynamics simulation study

O6-methylguanine DNA methyl transferase (MGMT) is a significant vehicle for the cellular clearance of alkyl lesions, particularly the methyl group of the O-6 and O-4 positions of guanine and thymine, respectively. Many publications have studied the correlation between polymorphisms in MGMT and susceptibility to various cancers. In the present study, we investigated the consequence of L84F, common single-nucleotide polymorphism, K125E, site-specific mutagenesis, and L84F/K125E on conformation, stability, and behavior of MGMT in the free form and interaction with proliferating cell nuclear antigen (PCNA) and DNA as partners in the biochemical network by using molecular dynamics simulation method. Our results showed that all free variants of MGMT differed from the native form. However, among all free variants of MGMT, the L84F/K125E variant exhibited similar properties compared with the wild-type. In contrast, in complex modes, only amino acid residues of the L84F variant are involved in the interactions with PCNA and DNA somewhat differently relative to the wild-type. Furthermore, L84F SNP showed the highest binding free energy compared to other variants and native forms. These alterations in the amino acids and binding free energy of L84F relative to the native are the reasons for changing its region connection compared to the native form. Therefore, we propose conducting further investigations into the impact of inhibitors or chemotherapeutic agents to assess their effectiveness on MGMT variants compared to the wild-type, aiming to reduce the cost of cancer treatment that will depend on inhibiting native MGMT protein. Communicated by Ramaswamy H. Sarma

Comparative genomics of fungal mutants provides a systemic view of extreme cadmium tolerance in eukaryotic microbes

Whether eukaryotic organisms can evolve for higher heavy metal resistance in laboratory conditions remains unknown. In this study, we challenged a macrofungi, Pleurotus ostreatus, in a designed microbial evolution and growth arena (MEGA)-plate with an extreme Cd gradient. Within months, the wild-type strain developed 10 mutants, exhibiting a maximum three-fold increase in Cd tolerance and slower growth rates. Genomic sequencing and re-sequencing of the wild-type and ten mutant strains generated about 51 GB data, allowing a comprehensive comparative genomics analysis. As a result, a total of 2512 common single nucleotide polymorphisms, 70 inserts and deletes, 39 copy number variations and 21 structural variations were found in the 10 mutants. The mutant genes were primarily involved in substrate transport. In combination with transcriptome analysis, we discovered that the ten mutants had a distinct Cd-resistant mechanism compared to the wild-type strain. Genes involved in oxidation-reduction, ion transmembrane transport, and metal compartment/efflux are primarily responsible for the extreme Cd tolerance in the P. ostreatus mutants. Our findings contribute to the understanding of eukaryotic Cd resistance at the genome level and establish a foundation for developing bioremediation tools utilizing highly tolerant macrofungi.

Genotype-Phenotype Relationship among 785 Unrelated White Women with Inherited Congenital Factor VII Deficiency: A Three-Center Database Study.

Congenital factor VII (FVII) deficiency, a rare bleeding disorder resulting from mutations in the F7 gene with autosomal recessive inheritance, exhibits clinical heterogeneity that lacks a strong correlation with FVII:C levels. The objective of this study was to discern genetic defects and assess their associations with the clinical phenotype in a substantial cohort comprising 785 white women exhibiting FVII:C levels below the age-dependent cut-off percentage. Individuals with verified inherited factor VII deficiency underwent i) genotyping using the Sanger method and multiplex ligation-dependent probe amplification (MLPA) to identify F7 mutations, including common polymorphic variants. Additionally, they were ii) categorized based on clinical bleeding scores (BS). Thrombophilic variants and blood groups were also determined in the study participants. The probands in this study encompassed both asymptomatic individuals (referred for a laboratory investigation due to recurrent prolonged prothrombin time; n = 221) and patients who manifested mild, moderate, or severe bleeding episodes (n = 564). The spectrum of bleeding symptoms included epistaxis, gum bleeding, gastrointestinal bleeding, hematuria, postoperative bleeding, and gynecologic hemorrhage. The median ISTH bleeding score (BS) recorded within a two-year period prior to the work-up was 2 (0-17). Notably, this score was significantly higher in symptomatic women compared to their asymptomatic counterparts (3 versus 0; p < 0.001). The corresponding PBAC score before hormonal treatment stood at 225 (5-1200), exhibiting a positive correlation with the ISTH BS (rho = 0.38; p = 0.001). Blood group O was more prevalent in symptomatic women compared to asymptomatic individuals (58 versus 42%; p = 0.01). Among the 329 women (42%), known and novel mutations in the F7 gene, encompassing coding regions, exon/intron boundaries, and the promoter region, were identified, while common polymorphisms were detected in 647 subjects (95%). Logistic regression analysis, adjusted for clinical and laboratory data (including blood group, FVII activity, the presence of F7 gene mutations and/or polymorphisms, thrombophilia status, and additional factor deficiencies) revealed that older age at referral (increase per year) (odds/95% CI: 1.02/1.007-1.03), the presence of blood group O (odds/95% CI: 1.9/1.2-3.3), and the coexistence of further bleeding defects (odds/95% CI: 1.8/1.03-3.1) partially account for the differences in the clinical bleeding phenotype associated with FVII deficiency. The clinical phenotype in individuals with FVII deficiency is impacted by factors such as age, blood group, and the concurrent presence of other bleeding defects.

The Disease Model of Addiction: The Impact of Genetic Variability in the Oxidative Stress and Inflammation Pathways on Alcohol Dependance and Comorbid Psychosymptomatology.

Oxidative stress and neuroinflammation are involved in the pathogenesis of alcohol addiction. However, little is known regarding the effect of genetic, behavioral, psychological, and environmental sources of origin on the inflammation and oxidative stress pathways of patients with alcohol addiction. Our study aimed to evaluate the impact of selected common functional single-nucleotide polymorphisms in inflammation and oxidative stress genes on alcohol addiction, and common comorbid psychosymptomatology. Our study included 89 hospitalized alcohol-addicted patients and 93 healthy individuals, all Slovenian males. Their DNA was isolated from peripheral blood and patients were genotyped for PON1 rs705379, rs705381, rs854560, and rs662, SOD2 rs4880, GPX1 rs1050450, IL1B rs1143623, rs16944, and rs1071676, IL6 rs1800795, IL6R rs2228145, and miR146a rs2910164. Kruskal-Wallis and Mann-Whitney tests were used for the additive and dominant genetic models, respectively. Our findings suggested the involvement of IL6 rs1800795 in alcohol addiction. Moreover, our data indicated that the genetic variability of SOD2 and PON1, as well as IL1B and IL6R, may be related to comorbid psychosymptomatology, revealing a potential indirect means of association of both the oxidative stress and inflammation pathways.

Neural Network Connectivity Following Opioid Dependence is Altered by a Common Genetic Variant in the µ-Opioid Receptor, OPRM1 A118G.

Opioid use disorder is a chronic, relapsing disease associated with persistent changes in brain plasticity. A common single nucleotide polymorphism (SNP) in the µ-opioid receptor gene, OPRM1 A118G, is associated with altered vulnerability to opioid addiction. Reconfiguration of neuronal connectivity may explain dependence risk in individuals with this SNP. Mice with the equivalent Oprm1 variant, A112G, demonstrate sex-specific alterations in the rewarding properties of morphine and heroin. To determine whether this SNP influences network-level changes in neuronal activity, we compared FOS expression in male and female mice that were opioid-naive or opioid-dependent. Network analyses identified significant differences between the AA and GG Oprm1 genotypes. Based on several graph theory metrics, including small-world analysis and degree centrality, we show that GG females in the opioid-dependent state exhibit distinct patterns of connectivity compared to other groups of the same genotype. Using a network control theory approach, we identified key cortical brain regions that drive the transition between opioid-naive and opioid-dependent brain states; however, these regions are less influential in GG females leading to sixfold higher average minimum energy needed to transition from the acute to the dependent state. In addition, we found that the opioid-dependent brain state is significantly less stable in GG females compared to other groups. Collectively, our findings demonstrate sex- and genotype-specific modifications in local, mesoscale, and global properties of functional brain networks following opioid exposure and provide a framework for identifying genotype differences in specific brain regions that play a role in opioid dependence.

AKR1C1 and hormone metabolism in lipedema pathogenesis: a computational biology approach.

Lipedema is an autosomal dominant genetic disease that mainly affects women. It is characterized by excess deposition of subcutaneous adipose tissue, pain, and anxiety. The genetic and environmental etiology of lipedema is still largely unknown. Although considered a rare disease, this pathology has been suggested to be underdiagnosed or misdiagnosed as obesity or lymphedema. Steroid hormones seem to be involved in the pathogenesis of lipedema. Indeed, aldo-keto reductase family 1 member C1 (AKR1C1), a gene coding for a protein involved in steroid hormones metabolism, was the first proposed to be correlated with lipedema. In this study, we employed a molecular dynamics approach to assess the pathogenicity of AKR1C1 genetic variants found in patients with lipedema. Moreover, we combined information theory and structural bioinformatics to identify AKR1C1 polymorphisms from the gnomAD database that could predispose to the development of lipedema. Three genetic variants in AKR1C1 found in patients with lipedema were disruptive to the protein's function. Furthermore, eight AKR1C1 variants found in the general population could predispose to the development of lipedema. The results of this study provide evidence that AKR1C1 may be a key gene in lipedema pathogenesis, and that common polymorphisms could predispose to lipedema development.

Enlighten the association of Angiotensinogen gene (AGT) polymorphisms and hypertension in Jammu region of north Indian population: A case-control study

BackgroundHypertension is a common cause associated with various life-threatening disorders such as stroke, heart attack, etc. AGT, with its two common polymorphisms, i.e., rs699 and rs4762, has been associated with variation in plasma angiotensinogen concentration and linked to essential hypertension. AimIn the present study, we aimed to find the association between the two polymorphisms, namely rs699 and rs4762 of the AGT gene, with the risk of hypertension in people of the Jammu region of Jammu and Kashmir. MethodTo achieve the aim, an observational with case-control study design was utilized where the descriptive and inferential data were presented in frequency, and an Odds ratio with a 95% Confidence Interval was used for determining the risk association, respectively. Online free statistical tools were used for the statistical analysis. The pairwise linkage disequilibrium (LD) and its respective measures (D′ & r(Mills et al., 2020 (Mills et al., 2020))) for the SNPs among the hypertensive patients and controls were calculated using Haploview software. ResultA total of 180 cases and 350 controls were enrolled, where “rs699” showed an increased risk (OR: 1.72 [1.28–2.31], p-value =0.0003) for hypertension in contrast to “rs4762” which showed a protective role (OR: 0.55 [0.37–0.82], p-value <0.002) in the population of Jammu. After linkage disequilibrium analysis, the risk of disease due to haplotype was also analyzed, and it was found that CC (rs699/ rs4762) significantly (p-value <0.00001) increases the risk by 1.9-fold. ConclusionThe present study concluded that “rs699” showed an increased risk for hypertension in the population of the Jammu region in contrast to “rs4762”.

Diversity and structure assessment of the genetic resources in a germplasm collection from a vanilla breeding programme in Madagascar

AbstractA breeding programme of aromatic vanilla, dating back to 1944, was conducted in Ambohitsara, Antalaha, SAVA (Sambava, Antalaha, Vohemara, Andapa) – Madagascar. Imported, local, wild and cultivated vanillas were used as progenitors and thousands of hybrids were generated. However, this germplasm has not undergone any genetic evaluation, and it appears that these valuable genetic resources have been dispersed or lost after the end of the programme (2000). This study aims to investigate the genetic diversity and structure of rescued genotypes currently held in a local collection in Antalaha. Double digest restriction associated-site (RAD)-seq (ddRAD)-seq protocol was applied, providing 865 million read sequences from 56 accessions. The ddRAD sequences have been deposited to the SRA archive of NCBI. From the data, 23,701 filtered concordant common Single Nucleotide Polymorphisms (SNPs) were identified using the three widely used tools (Stacks, BCFtools, Genome Analysis ToolKit - GATK) for short-read library sequencing. These SNPs were used for germplasm evaluation. Clustering analysis segregated samples into five genetic groups: Vanilla planifolia, Vanilla pompona, hybrid Tsitaitra, Vanille Banane and the phenotype Tsivaky. Our analysis revealed distinct subgroups within V. pompona and Tsitaitra, emphasizing the importance of further characterization to accurately reflect the genetic diversity and facilitate better utilization of these accessions in future research and germplasm management. The presence of private alleles in all groups (from 487 to 2866) indicated that populations were diverging and represented a large gene pool that could be useful for future breeding efforts. The genetic data obtained from this study offers valuable insights into the genetic diversity and structure of the vanilla population, with potential applications in breeding and conservation efforts.