Descripción de polimorfismos genéticos en CYP3A5 y MDR-1 y su impacto en el rechazo agudo clínico de pacientes trasplantados de hígado del Hospital San Vicente Fundación Rionegro / Description of genetic polymorphisms in CYP3A5 and MDR-1 and their impact on clinical acute rejection in liver transplant patients at Hospital San Vicente Fundación Rionegro

Introducción. El tacrolimus es un medicamento inmunosupresor ampliamente usado en trasplante hepático, que presenta una gran variabilidad interindividual la cual se considera asociada a la frecuencia de polimorfismos de CYP3A5 y MDR-1. El objetivo de este estudio fue evaluar la frecuencia de los polimorfismos rs776746, rs2032582 y rs1045642 y su asociación con rechazo clínico y toxicidad farmacológica. Métodos. Se incluyeron pacientes inmunosuprimidos con tacrolimus a quienes se les realizó trasplante hepático en el Hospital San Vicente Fundación Rionegro entre 2020 y 2022, con supervivencia mayor a un mes. Se evaluaron las variables clínicas, rechazo agudo y toxicidad farmacológica. Se secuenciaron los genes de estudio mediante PCR, comparando la expresión o no en cada uno de los pacientes. Resultados. Se identificaron 17 pacientes. El 43 % de los pacientes se clasificaron como CYP3A5*1/*1 y CYP3A5*1/*3, entre los cuales se encontró asociación con aumento en la tasa de rechazo agudo clínico, al comparar con los pacientes no expresivos (100 % vs. 44 %, p=0,05); no hubo diferencias en cuanto a la toxicidad farmacológica u otros desenlaces. Se encontró el polimorfismo rs2032582 en un 50 % y el rs1045642 en un 23,5 % de los pacientes, sin embargo, no se identificó asociación con rechazo u otros eventos clínicos. Conclusiones. Se encontró una asociación entre el genotipo CYP3A5*1/*1 y CYP3A5*1/*3 y la tasa de rechazo clínico. Sin embargo, se requiere una muestra más amplia para validar estos datos y plantear modelos de medicina personalizada.

Introduction. Tacrolimus is an immunosuppressive drug widely used in liver transplantation, which presents great interindividual variability which is considered associated with the frequency of CYP3A5 and MDR-1 polymorphisms. The objective of this study was to evaluate the frequency of the rs776746, rs2032582 and rs1045642 polymorphisms and their association with clinical rejection and drug toxicity. Methods. Immunosuppressed patients with tacrolimus who underwent a liver transplant at the Hospital San Vicente Fundación Rionegro between 2020 and 2022 were included, with survival of more than one month. Clinical variables, acute rejection and pharmacological toxicity were evaluated. The study genes were sequenced by PCR, comparing their expression or not in each of the patients. Results. Seventeen patients were identified. 43% of the patients were classified as CYP3A5*1/*1 and CYP3A5*1/*3, among which an association was found with increased rates of clinical acute rejection when compared with non-expressive patients (100% vs. 44%, p=0.05). There were no differences in drug toxicity or other outcomes. The rs2032582 polymorphism was found in 50% and rs1045642 in 23.5% of patients; however, no association with rejection or other clinical events was identified. Conclusions. An association was found between the CYP3A5*1/*1 and CYP3A5*1/*3 genotype and the clinical rejection rate. However, a larger sample is required to validate these data and propose models of personalized medicine.

Bioinformatic identification of Single Nucleotide Polymorphisms (SNPs) in keratin-associated protein genes in alpacas (Vicugna pacos) / Identificación bioinformática de Polimorfismos de Nucleótido Simple (PNSs) en genes de proteínas asociadas a queratinas en alpacas (Vicugna pacos)

Abstract This study aims to identify single nucleotide polymorphisms (SNPs) within KRTAP genes in alpacas (Vicugna pacos), which play a fundamental role in defining their physico-mechanical properties and potentially the quality of alpaca fiber, the primary product of their breeding. Thirty-four KRTAP genes, as annotated in the reference genome VicPac3.1, were investigated. Utilizing the reference genome, along with nine additional genomes and reads from 300 reduced representation DNA libraries of alpacas, SNPs were identified. Minor allele frequency (MAF) and genotyping rates were computed using PLINK software, while Illumina Scores were determined for each SNP using Illumina Design Studio software. Markers meeting the criteria of MAF ≥ 0.05, genotyping rate > 45%, and Illumina Score ≥ 0.6 per SNP were selected. A total of 67 SNPs were identified within intronic, exonic, and untranslated regions of KRTAP genes. Among these, 35 SNPs were incorporated into the 76K Alpaca SNP microarray, with 32 SNPs subsequently validated in a population of 936 alpacas. In conclusion, our findings delineate SNPs within KRTAPs that hold potential utility in genome-wide association studies, thereby facilitating the integration of modern breeding technologies into alpaca breeding programs.

Resumen Este estudio tiene como objetivo identificar polimorfismos de nucleótido simple (PNSs) dentro de los genes KRTAP en alpacas (Vicugna pacos), que juegan un papel fundamental en la definición de sus propiedades físico-mecánicas y la calidad de la fibra de alpaca, producto principal de su crianza. Se investigaron treinta y cuatro genes KRTAP, tal como están anotados en el genoma de referencia VicPac3.1. Utilizando el genoma de referencia, junto con nueve genomas adicionales y lecturas de 300 bibliotecas de representación reducida de ADN de alpacas, se identificaron los PNSs. La frecuencia de los alelos menores (MAF) y las tasas de genotipificación se calcularon utilizando el software PLINK, mientras que los Illumina Score se determinaron para cada PNS utilizando el software Illumina Design Studio. Se seleccionaron marcadores que cumplían con los criterios de MAF ≥ 0.05, tasa de genotipado > 45% e Illumina Score ≥ 0.6 por PNS. Se identificaron un total de 67 PNSs dentro de regiones intrónicas, exónicas y/o no traducidas de genes KRTAP. Entre estos, se incorporaron 35 PNSs al microarray 76K Alpaca SNP, y posteriormente se validaron 32 PNSs en una población de 936 alpacas. En conclusión, nuestros hallazgos identificaron los PNSs dentro de los KRTAP que tienen una utilidad potencial en estudios de asociación de todo el genoma, facilitando así la integración de tecnologías de reproducción modernas en los programas de reproducción de alpacas.

Correlation of FSHR gene polymorphism,BMI and sex hormone six with the risk of polycystic ovary syndrome / 解放军医学杂志

Objective To investigate the association between body mass index(BMI),sex hormone and single nucleotide polymorphisms(SNPs)of follicle-stimulating hormone receptor(FSHR)gene rs2268361 and rs2349415 and its correlation with the risk of polycystic ovary syndrome(PCOS).Methods Peripheral blood was collected from 213 PCOS patients and 207 healthy controls,attending the Department of Reproductive Medicine at the First Hospital of Shanxi Medical University,and 32 follicular fluids were randomly collected from each of the PCOS and control groups from March to August 2021.Calculation of BMI of the PCOS and control groups;The levels of follicle-stimulating hormone(FSH),luteinizing hormone(LH),estradiol(E2),testosterone(T),progesterone(P)and prolactin(PRL)in peripheral blood of the two groups were detected by immunochemiluminescence method.Polymerase chain reaction(PCR)and high-resolution melting curve(HRM)were used to analyze the polymorphisms of rs2268361 and rs2349415 in FSHR of the two groups.Quantitative real-time PCR was used to detect the expression of FSHR gene mRNA in peripheral blood and ovarian granulosa cells.Results There was a strong positive correlation between LH and LH/FSH(r=0.88,P<0.05);The levels of BMI,E2,LH,LH/FSH and T in PCOS group were significantly higher than those in control group(P<0.05);FSH level was significantly lower than that of control group(P<0.001).HRM analysis showed the frequencies of CC,CT and TT genotypes at rs2349415 were 55.9%,34.3%and 9.8%in PCOS group and 68.6%,23.2%and 8.2%in control group,respectively.The frequencies of C and T alleles were 73.0%and 27.0%in PCOS group and 80.2%and 19.8%in control group,respectively.There were significant differences in genotype frequencies and allele frequencies between the two groups(P<0.05);The expression level of FSHR mRNA was higher in ovarian granulosa cells in PCOS group than in control group(P=0.004),the expression level of FSHR mRNA in rs2349415 TT genotype was higher than that in CC(P=0.002)and CT(P=0.035)genotype.Conclusion High levels of BMI, LH, E2 and T allele of rs2349415 increased the risk of PCOS.

Association between ELL2 polymorphism and susceptibility to pleomorphic adenoma of salivary gland / 解放军医学杂志

Objective To analyze the correlation between the ELL2 gene 1119 T>C polymorphism and the susceptibility to pleomorphic adenoma of the salivary gland.Methods The pedigree of the pleomorphic adenoma family of salivary gland was drawn.The exons of ELL2 gene in 5 members of salivary pleomorphic adenoma family were sequenced.A case-control study was conducted.One hundred and twelve patients with pleomorphic adenoma of the salivary gland who visited the Department of Oral and Maxillofacial Surgery of Shanxi Bethune Hospital from January 2016 to July 2020 were taken as case group,and 176 healthy examinees from January 2019 to January 2020 were taken as control group with age and sex as matching conditions.The 1119 T>C polymorphism of ELL2 genes in the two groups were detected with high resolution melting(HRM)curve.Chi-square test was adopted to analyze the correlation between gene polymorphism and the occurrence of pleomorphic adenoma of the salivary gland,stratified analysis was performed to evaluate the synergistic effect of smoking and genotype,and real time quantitative reverse transcription polymerase chain reaction(RT-PCR)was used to detect the expression level of ELL2 in individuals with different genotypes.Results The 1119 T>C polymorphism site existed in the exon 8 of ELL2 gene in a family with pleomorphic adenoma of salivary gland.The results of case-control study showed that the genotype frequency of homozygous CC was significantly higher in patients with pleomorphic adenoma of salivary gland than that in the controls(24.1%vs.11.9%,P=0.002).Homozygous CC was associated with increased risk for developing pleomorphic adenoma of salivary gland(OR=3.059,95%CI 1.494-6.263)in this cohort.Stratification analysis showed that smoking and 1119C allele cooperated to increase the risk of pleomorphic adenoma of salivary gland(OR=3.200,95%CI 1.460-7.014).The expression level of ELL2 mRNA in CC genotype was significantly higher than that in individuals with CT or TT genotype(P<0.05).Conclusion The genetic variation of ELL2 may play an important role in the occurrence of pleomorphic adenoma of salivary gland,and smoking combined with the 1119C allele increased the risk of this disease.

Correlation of KRAS Gene 3'UTR Polymorphisms with Cervical Cancer and Cervical Intraepithelial Neoplasia in Chinese Han Population in Yunnan Province / 昆明医科大学学报

Objective To investigate the correlation between rs712 and rs7973450 located at the 3'UTR region of the KRAS gene and the risk of cervical cancer(CC)and cervical intraepithelial neoplasia(CIN)in Chinese Han population in Yunnan province.Methods A total of 2405 individuals(461 subjects with CIN,961 subjects with CC and 983 healthy controls)were enrolled.The SNPs were genotyped used TaqMan assay and the correlation of these SNPs with CIN and CC was analyzed.Results The A allele of rs7973450 might be a protective factor for the occurrence of CIN(P = 0.004,OR= 0.651,95%CI 0.487～0.871)and CC(P = 7.00×10-4,OR= 0.667,95%CI 0.529～0.844).There was no significant difference in allelic and genotypic distribution of rs712 among CIN,CC and Control groups(P>0.017).The haplotype assay showed thatrs712A-rs7973450G was associated with increased risk of CIN(P = 4.00×10-4;OR= 1.714,95%CI 1.269～2.314)and CC(P = 3.84×10-5,OR= 1.667,95%CI 1.305～2.131).While haplotype rs712A-rs7973450A was associated with a lower risk of CC(P = 0.012,OR= 0.790,95%CI 0.658～0.950).Conclusion The A allele of rs7973450 in 3'UTR of KRAS gene might be the protective factor for the occurrence of CIN and CC in a Chinese Han population in Yunnan province.

Mendelian randomization study on the association between rheumatoid arthritis and osteoporosis and bone mineral density / 中国组织工程研究

BACKGROUND:Many clinical research observations have indicated a close association between rheumatoid arthritis and osteoporosis as well as bone mineral density(BMD).However,it remains unclear whether there is a causal genetic relationship between rheumatoid arthritis and the development of osteoporosis and alterations of BMD. OBJECTIVE:To assess the potential causal relationship between rheumatoid arthritis and osteoporosis as well as BMD using a two-sample Mendelian randomization approach,provide meaningful insights from a genetic perspective into the underlying mechanisms and offer a reference for early prevention of osteoporosis and improvement in the progression of the disease. METHODS:We conducted a study using data from publicly available genome-wide association studies databases to identify single nucleotide polymorphisms associated with rheumatoid arthritis as instrumental variables(P＜5×10-8).The main outcomes of the study included osteoporosis and BMD at five different sites,including total body BMD,lumbar spine BMD,femoral neck BMD,heel BMD,and forearm BMD.The inverse variance-weighted method was used as the primary analysis method to evaluate causal effects.Weighted median,simple median,weighted mode and MR-Egger regression were used as supplementary analyses.Causal relationships between rheumatoid arthritis and the risk of osteoporosis and BMD were assessed using odds ratios(OR)and 95%confidence intervals(CI).Heterogeneity was assessed using Cochran's Q test and horizontal pleiotropy was evaluated using MR-Egger intercept tests. RESULTS AND CONCLUSION:The inverse variance-weighted analysis demonstrated a positive association between genetically predicted rheumatoid arthritis and osteoporosis(OR=1.123,95%CI:1.077-1.171;P=4.02×10-8).Heterogeneity test(P=0.388)indicated no significant heterogeneity among the single nucleotide polymorphisms.MR-Egger intercept(P=0.571)tests did not detect horizontal pleiotropy,and sensitivity analysis showed no evidence of bias in the study results.There was no causal relationship between rheumatoid arthritis and BMD at the five different sites.The total body BMD(OR=1.000,95%CI:0.988-1.012;P=0.925),lumbar spine BMD(OR=0.999,95%CI:0.982-1.016;P=0.937),femoral neck BMD(OR=1.001,95%CI:0.986-1.016;P=0.866),heel BMD(OR=0.996,95%CI:0.989-1.004;P=0.419),and forearm BMD(OR=1.063,95%CI:0.970-1.031;P=0.996)indicated no significant association.MR-Egger intercept analysis did not detect potential horizontal pleiotropy(total body BMD:P=0.253;lumbar spine BMD:P=0.638;femoral neck BMD:P=0.553;heel BMD:P=0.444;forearm BMD:P=0.079).Rheumatoid arthritis may contribute to the development of osteoporosis through the interaction between chronic inflammation and bone formation,resorption,and absorption.Additionally,the use of glucocorticoids and the presence of autoantibodies(such as anti-citrullinated protein antibody)in patients with rheumatoid arthritis showed associations with osteoporosis.Future research should focus on monitoring systemic inflammatory markers,standardized use of glucocorticoids,and regular screening for osteoporosis risk in patients with rheumatoid arthritis.

Two-sample Mendelian randomization analysis of the relationship between statins and the risk of osteoarthritis / 中国组织工程研究

BACKGROUND:Observational studies have suggested that statins may have a protective effect against osteoarthritis,including knee osteoarthritis and hip osteoarthritis.However,the association between statins and the risk of osteoarthritis remains unclear. OBJECTIVE:To investigate the association between statins and the risk of osteoarthritis through Mendelian randomization analysis using summary data from large-scale population-based genome-wide association studies(GWAS). METHODS:Firstly,single nucleotide polymorphism data related to statins were obtained from the latest 9th edition of the FinnGen database,while data of osteoarthritis,knee osteoarthritis and hip osteoarthritis were obtained from the IEU Open GWAS,UK Biobank,and ArcOGEN(Genetics of Osteoarthritis)databases,respectively.The inverse variance weighted method was used as the primary analysis approach to evaluate the causal effects.The weighted median method,simple median method,weighted mode-based method,and MR-Egger regression were used as supplementary analyses.The causal relationship between statins and the risk of osteoarthritis,knee osteoarthritis and hip osteoarthritis was assessed using odds ratios(OR)with 95%confidence intervals(CI).Sensitivity analyses were conducted to validate the reliability of the results,including the Cochran's Q test for heterogeneity and the MR-Egger-intercept test for horizontal pleiotropy,as well as leave-one-out analysis to identify potentially influential single nucleotide polymorphisms. RESULTS AND CONCLUSION:The inverse variance weighted analysis demonstrated a negative causal relationship between genetically predicted statins and the risk of osteoarthritis(OR=0.998,95%CI:0.996-0.999,P=0.01),knee osteoarthritis(OR=0.964,95%CI:0.940-0.989,P=0.005),and hip osteoarthritis(OR=0.928,95%CI:0.901-0.955,P=4.28×10-7).MR-Egger intercept analysis did not detect potential horizontal pleiotropy(osteoarthritis:P=0.658;knee osteoarthritis:P=0.600;hip osteoarthritis:P=0.141).The results of this study provide evidence that statins reduce the risks of osteoarthritis,knee osteoarthritis and hip osteoarthritis as described in observational studies.Further research is needed to explore the specific mechanisms of statin treatment for osteoarthritis.

Gut microbiota and drug-associated osteonecrosis:a two-sample Mendelian randomization study / 中国组织工程研究

BACKGROUND:Osteonecrosis due to drugs is a serious adverse reaction occurring after the application of such drugs.Increasing evidence suggests that the gut microbiota composition is associated with osteonecrosis due to drugs.However,the causal relationship of the gut microbiota to osteonecrosis due to drugs is still unclear. OBJECTIVE:To evaluate the potential causal relationship between the gut microbiota and the risk of osteonecrosis due to drugs using the Mendelian randomization method. METHODS:A two-sample Mendelian randomization study was performed using the summary statistics of gut microbiota from the largest available genome-wide association study meta-analysis(n=13 266)conducted by the MiBioGen consortium as well as the summary statistics of osteonecrosis due to drugs obtained from the FinnGen consortium R9 release data(264 cases and 377 013 controls).Inverse variance weighted,MR-Egger,weighted median,weighted model and simple model were used to examine the causal association between gut microbiota and osteonecrosis due to drugs.Sensitivity analysis was used to test whether the results of the Mendelian randomization analysis were reliable.Reverse Mendelian randomization analysis was performed on all the bacteria as an outcome for effect analysis and sensitivity analysis. RESULTS AND CONCLUSION:Inverse variance weighted estimates suggested that Lentisphaerae(phylum),Lentisphaeria(class),Melainabacteria(class),Gastranaerophilales(order),Rhodospirillales(order),Victivallales(order)and Bifidobacterium(genus)had protective causal effects on osteonecrosis due to drugs.Methanobacteria(class),Bacillales(order),Methanobacteriaceae(family),Lachnospiraceae(family),Methanobacteriales(order),Holdemania(genus),Holdemania(UCG010 group)(genus),Odoribacter(genus)and Tyzzerella3(genus)had negative causal effects on osteonecrosis due to drugs.According to the results of reverse Mendelian randomization analysis,Clostridiaceae1(family),Peptostreptococcaceae(family),Streptococcaceae(family),Clostridiumsensustricto1(genus)and Streptococcus(genus)showed negative causal effects on osteonecrosis due to drugs.However,Eisenbergiella(genus)showed protective causal effects on osteonecrosis due to drugs.None of the bidirectional sensitivity analysis revealed heterogeneity or horizontal pleiotropy.When gut microbiota were used as exposure and osteonecrosis due to drugs as the outcome,Mendelian randomization analysis found that seven bacterial traits were positively correlated to osteonecrosis due to drugs,nine bacterial traits were negatively related to osteonecrosis due to drugs.When osteonecrosis due to drugs were used as exposure and gut microbiota as the outcome,reverse Mendelian randomization analysis found a negative correlated relationship with five bacterial traits and a positive causal relationship with one bacterial trait.By changing the diversity and composition of gut microbiota,it is expected to improve the incidence and prognosis of osteonecrosis due to drugs,providing new ideas for the study of orthopedic diseases.

Causal effects of serum trace elements and nutrients on osteonecrosis:a Mendelian randomization analysis / 中国组织工程研究

BACKGROUND:Multiple clinical observational studies have suggested a close relationship of serum trace elements and nutrients with osteonecrosis,but it remains unclear whether there is a genetic causal effect between serum trace elements and nutrients on osteonecrosis. OBJECTIVE:To investigate the causal effects of serum trace elements and nutrients on osteonecrosis using the Mendelian randomization approach. METHODS:The exposure factors of serum trace elements and vitamins with mononucleotide polymorphisms were obtained from the published UK Biobank database and publicly available databases of genome-wide association studies.The outcome event of osteonecrosis was derived from the FinnGen Biobank database.Mendelian randomization methods were employed to explore the causal relationship between seven trace elements and three nutrients with osteonecrosis.Causal inference was conducted using inverse variance weighting,MR-Egger,and weighted median methods.F-statistic was calculated to ensure the robustness of instrumental variables.Cochran's Q test and leave-one-out method were used for heterogeneity testing.MR-Egger regression and MR-PRESSO were employed for horizontal pleiotropy testing.PhenoScanner database was utilized to remove mononucleotide polymorphisms with horizontal pleiotropy to ensure the reliability of the results. RESULTS AND CONCLUSION:Causal relationships were found between serum selenium,phosphate,vitamin C,vitamin E,and osteonecrosis through Mendelian randomization analysis.Serum selenium,vitamin C,and vitamin E were found to have a protective effect on osteonecrosis,while excessive intake of phosphate increased the risk of osteonecrosis.No heterogeneity or horizontal pleiotropy was observed during the study,and Mendelian randomization statistical power(Power value>80%)indicated the reliability of the aforementioned four results.These findings have important clinical implications for the development of targeted preventive and therapeutic measures for osteonecrosis.

Effect of type 2 diabetes mellitus on bone mineral density in different age groups:a two-sample Mendelian randomization study / 中国组织工程研究

BACKGROUND:Epidemiologic studies have shown a correlation between type 2 diabetes mellitus and bone mineral density,but the causal association between the two and whether it is age-related remains unknown. OBJECTIVE:To study the correlation between type 2 diabetes mellitus and whole body bone mineral density at unspecified age and at all ages based on the Mendelian randomization technique. METHODS:The genome-wide association study(GWAS)data of type 2 diabetes mellitus and bone mineral density at all ages were selected from the IEU GWAS database of the University of Bristol.The exposure data were single nucleotide polymorphisms with significant correlation with type 2 diabetes mellitus as instrumental variables,and bone mineral density at all ages was selected as the outcome variable.Two-sample Mendelian randomization analysis of type 2 diabetes mellitus and bone mineral density was performed using inverse variance weighted method,weighted median estimator,and MR-Egger regression.The βvalue was used to evaluate the causal relationship between type 2 diabetes mellitus and bone mineral density at all ages. RESULTS AND CONCLUSION:A total of 118 single nucleotide polymorphisms were extracted from the GWAS summary data as instrumental variables.The MR-Egger regression results showed that there was no horizontal pleiotropy,but there was heterogeneity.Therefore,this study was based on the inverse variance weighted results.Inverse variance weighted results showed that type 2 diabetes mellitus may be a potential protective factor for bone mineral density and is associated with age:age-unspecified bone mineral density[β=0.038,95%confidence interval(CI):1.01-1.07,P=0.002],bone mineral density over 60 years old(β=0.052,95%CI:1.01-1.09,P=0.027),bone mineral density between 45-60 years old(β=0.049,95%CI:1.01-1.09,P=0.009),bone mineral density between 30-45 years old(β=0.033,95%CI:0.99-1.07,P=0.127).bone mineral density of 15-30 years old(β=0.025,95%CI:0.95-1.10,P=0.506),bone mineral density of 0-15 years old(β=0.006,95%CI:0.96-1.04,P=0.716).Similar results were obtained from the MR-Egger regression and weighted median estimator analyses.These findings indicate that type 2 diabetes mellitus may be one of the protective factors of bone mineral density,and there is a correlation with age.

Causal relationship between trunk and lower limb fat mass and intervertebral disc degeneration based on a Mendelian randomization analysis / 中国组织工程研究

BACKGROUND:It has been found in recent observational studies that assessing localized fat mass is crucial in the evaluation of disc degeneration.Although obesity has been recognized as a risk factor for disc degeneration,the causal relationship between fat mass,which is a key factor in obesity,and intervertebral disc degeneration has been unclear in previous studies. OBJECTIVE:To investigate the causal risk factors of intervertebral disc degeneration associated with different distributions of fat mass,thereby enhancing the understanding of the pathogenesis of intervertebral disc degeneration and contributing to the development of preventive,therapeutic,and prognostic strategies. METHODS:Genetic markers associated with trunk and lower limb fat mass were extracted as instrumental variables from the publicly available IEU Open GWAS under the conditions of strong correlation and fulfillment of linkage disequilibrium.These markers were combined with the Mendelian randomization analysis to investigate the relationship between body fat and intervertebral disc degeneration.We used the latest version 9 database of FinnGen and assessed the results using several regression models,including inverse variance weighting,MR-Egger regression,simple mode,weighted mode,and weighted median estimator.We also assessed the heterogeneity of the genetic markers using Cochran's Q test,and multiplicity was assessed using the MR-Egger intercept test.Additionally,we used the leave-one-out method to determine the sensitivity of individual genetic markers to the causal effect of the exposure and outcome.The results were presented as odds ratios(OR)and 95%confidence intervals(CI). RESULTS AND CONCLUSION:The results from the inverse variance weighting method revealed that there was a positive causal relationship between trunk fat mass and the risk of developing intervertebral disc degeneration(OR=1.25,95%CI:1.15-1.35,P＜0.001).Additionally,there was an inverse causal relationship between bilateral lower limb fat mass and the risk of developing intervertebral disc degeneration(OR=0.7,95%CI:0.63-0.78,P＜0.001;OR=0.69,95%CI:0.62-0.76,P＜0.001).Furthermore,the MR-Egger intercept analysis did not detect any potential horizontal pleiotropy.No bias single nucleotide polymorphisms were detected,while heterogeneity tests were present,and the leave-one-out sensitivity analysis suggested reliable results.The results above demonstrate a positive causal relationship between trunk fat mass and intervertebral disc degeneration.As trunk fat mass increases,the risk of intervertebral disc degeneration rises.With an increase in both lower limb fat mass,the risk of intervertebral disc degeneration decreases.Fat content and distribution affects the risk of developing intervertebral disc degeneration and should be given more attention.

Causal relationship between periodontitis and asthma: a two-sample Mendelian randomization study / 口腔疾病防治

Objective@#To explore the bidirectional causal relationships between periodontitis and asthma using the two-sample Mendelian randomization (MR) method to provide a basis for exploring the etiology and formulating preventive and therapeutic measures of periodontitis and asthma.@*Methods@#We performed two-sample bidirectional Mendelian randomization analysis using publicly released European genome-wide association studies (GWAS) statistics for periodontitis (n = 34 615) and asthma (n = 408 422). The inverse variance weighted (IVW) method was employed as the main approach to estimate the bidirectional causal relationships between periodontitis and asthma. In addition, weighted median (WM), MR-Egger regression, maximum likelihood, and Mendelian randomization robust adjusted profile score (MR-RAPS) were used as supplementary analyses. Sensitivity analyses were conducted using Cochran's Q test, Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO), and leave-one-out analysis.@*Results@#A total of 12 and 43 single-nucleotide polymorphisms (SNPs) were included as instrumental variables for periodontitis and asthma, respectively. The results of IVW, WM, MR-Egger regression, maximum likelihood, and MR-RAPS showed that periodontitis was not causally related to the risk of asthma (IVW: OR: 1.003, 95% CI: 0.973-1.035, P = 0.828, WM: OR: 0.990, 95% CI: 0.951-1.031, P = 0.641; MR-Egger regression: OR: 0.988, 95% CI: 0.960-1.028, P = 0.573; maximum likelihood: OR: 1.003, 95% CI: 0.972-1.035, P = 0.834; MR-RAPS: OR: 1.002, 95% CI: 0.970-1.036, P = 0.890) among the European population, and no causal effect of asthma on periodontitis was found (IVW: OR: 1.021, 95% CI: 0.938-1.111, P = 0.633, WM: OR: 1.011, 95% CI: 0.894-1.142, P = 0.866; MR-Egger regression: OR: 1.042, 95% CI: 0.824-1.319, P = 0.731; maximum likelihood: OR: 1.021, 95% CI: 0.938-1.112, P = 0.631; MR-RAPS: OR: 1.017, 95% CI: 0.931-1.110, P = 0.713) among the European population. Cochran's Q test showed no heterogeneity among the included instrumental variables, MR-PRESSO test found no horizontal pleiotropy, and the leave-one-out method did not identify outlier SNPs.@*Conclusion@#The results of this study, based on European genetic data, do not support a bidirectional causal association between periodontitis and asthma in the European population.

Association study between mammalian sterile 20-like kinase 1 SNPs and colorectal cancer / 安徽医科大学学报

Objective @#To explore the association between mammalian sterile 20-like kinase 1(MST1)gene poly- morphism and haplotype and the risk of colorectal cancer,rectal cancer,and colon cancer in the Han population in Baotou area by case-control association study@*Methods @#A total of 390 patients with colorectal cancer diagnosed by pathology and 413 normal physical examination population were collected,and 2 ml of peripheral blood was taken for subsequent gene genotyping.Single nucleotide polymorphisms(SNPs)of MSTI gene were screened according to the genetic polymorphism data of Chinese Han population provided by the National Center for Biotechnology Information-Haplotype Mapping database.Gene genotyping was performed by Taqman method.Logistic regression was used to calculate the association between each SNP and the risk of colorectal cancer,colon cancer,and rectal cancer under codominant,dominant,overdominant,and recessive genetic models.@*Results @#Four SNPs of MSTI gene were screened,namely rs8000,rs2234197,rs2267853,and rs6073629.Among them,SNP rs2234197 was associated with the risk of rectal cancer.Compared with the GG+AA genotype,the AG genotype could reduce the risk of rectal cancer, OR[95%confidence interval(CI)]=0.657(0.442-0.976).SNP rs8000 was associated with the risk of colon cancer.Compared with the TT+GT genotype,theGG genotype could reduce the risk of colon cancer [OR(95%CI)=0.425(0.182, -0.992)].@*Conclusion @#MSTI gene SNP rs2234197 AG genotype and SNP rs8000 GG genotype may be protective factors for rectal cancer and colon cancer,respectively.

Research progress in risk factors of post-transplantation diabetes mellitus / 器官移植

Solid organ transplantation has significantly prolonged the survival of patients with end-stage diseases. However, long-term use of immunosuppressants will increase the risk of post-transplantation diabetes mellitus (PTDM) in the recipients, thereby elevating the risk of infection, cardiovascular disease and death. In recent years, with persistent improvement of diagnostic criteria of PTDM, clinicians have deepened the understanding of this disease. Compared with type 2 diabetes mellitus, PTDM significantly differs in pathophysiological characteristics and clinical progression. Hence, different treatment strategies should be adopted. Early identification of risk factors of organ transplant recipients, early diagnosis and intervention are of significance for improving the quality of life of recipients, prolonging the survival of grafts and reducing the fatality of recipients. Therefore, the diagnosis, incidence and risk factors of PTDM were reviewed in this article, aiming to provide reference for clinicians to deliver prompt diagnosis and intervention for PTDM.

Identification of Scolopendra Dispensing Granules by Allele-specific PCR / 中国实验方剂学杂志

ObjectiveTo establish an allele-specific polymerase chain reaction （PCR） method for identifying Scolopendra dispensing granules， so as to ensure the quality and therapeutic effects of Scolopendra and its preparations. MethodThe primer interval suitable for the PCR was selected based on the cytochrome c oxidase subunit 3（COX-3） gene sequence of Scolopendra， and the single nucleotide polymorphism （SNP） loci of Scolopendra and its adulterants were mined from the interval for the design of specific primers. The samples of Scolopendra and its adulterants were collected. The PCR system was established and optimized regarding the annealing temperature， cycles， Taq enzymes， DNA template amount， PCR instruments， and primer concentrations， and the specificity and applicability of this method were evaluated. ResultThe PCR system was composed of 12.5 μL 2×M5 PCR Mix， 0.4 μL forward primer （10 μmol·L-1）， 0.4 μL reverse primer （10 μmol·L-1）， 2.5 μL DNA template， and 9.2 μL sterile double distilled water. PCR parameters： Pre-denaturation at 94 ℃ for 3 min， 30 cycles （94 ℃ for 20 s， 62 ℃ for 20 s， 72 ℃ for 45 s）， and extension at 72 ℃ for 5 min. After PCR amplification with the system and parameters above， the electrophoresis revealed a bright band at about 135 bp for Scolopendra and no band for the adulterants. ConclusionThe established allele-specific PCR method can accurately identify the medicinal materials， decoction pieces， and standard decoction freeze-dried powder of Scolopendra， as well as the intermediates and final products of Scolopendra dispensing granules， which is of great significance for ensuring the quality and clinical efficacy of Scolopendra and its preparations.

Evaluation of the participation of ABCA1 transporter in epicardial and mediastinal adipose tissue from patients with coronary artery disease

ABSTRACT Objective: Recent studies have shown a relationship between adipose tissue and coronary artery disease (CAD). The ABCA1 transporter regulates cellular cholesterol content and reverses cholesterol transport. The aim of this study was to determine the relationship between single nucleotide polymorphisms (SNPs) R230C, C-17G, and C-69T and their expression in epicardial and mediastinal adipose tissue in Mexican patients with CAD. Subjects and methods: The study included 71 patients with CAD and a control group consisting of 64 patients who underwent heart valve replacement. SNPs were determined using TaqMan probes. mRNA was extracted using TriPure Isolation from epicardial and mediastinal adipose tissue. Quantification and expression analyses were done using RT-qPCR. Results: R230C showed a higher frequency of the GG genotype in the CAD group (70.4%) than the control group (57.8%) [OR 0.34, 95% CI (0.14-0.82) p = 0.014]. Similarly, C-17G (rs2740483) showed a statistically significant difference in the CC genotype in the CAD group (63.3%) in comparison to the controls (28.1%) [OR 4.42, 95% CI (2.13-9.16), p = 0.001]. mRNA expression in SNP R230C showed statistically significant overexpression in the AA genotype compared to the GG genotype in CAD patients [11.01 (4.31-15.24) vs. 3.86 (2.47-12.50), p = 0.015]. Conclusion: The results suggest that the GG genotype of R230C and CC genotype of C-17G are strongly associated with the development of CAD in Mexican patients. In addition, under-expression of mRNA in the GG genotype in R230C is associated with patients undergoing revascularization.

The importance of deep genotyping in crop breeding / La importancia de la genotipificación profunda en el mejoramiento genético

ABSTRACT One of the greatest challenges facing humanity is the development of sustainable strategies to ensure food availability in response to population growth and climate change. One approach that can contribute to increase food security is to close yield gaps and enhancing genetic gain; to such end, what is known as "molecular breeding" plays a fundamental role. Since a crop breeding program is mainly based on the quality of the germplasm, its detailed genetic characterization is mandatory to ensure the efficient use of genetic resources and accelerating development of superior varieties. Deep genotyping is an essential tool for a comprehensive characterization of the germplasm of interest and, fortunately, the technology is now accessible at a reasonable cost. What must be ensured is the correct interpretation of the genotypic information and on that basis develop efficient practical molecular crop breeding strategies that respond to the real needs of the breeding program.

RESUMEN Uno de los mayores desafíos que enfrenta la humanidad es el desarrollo de estrategias sostenibles para asegurar la disponibilidad de alimentos en respuesta al crecimiento de la población y el cambio climático. Un enfoque que puede contribuir a aumentar la seguridad alimentaria es cerrar las brechas de rendimiento y mejorar la ganancia genética; para tal fin, lo que se conoce como "mejoramiento molecular" juega un papel fundamental. Dado que un programa de mejoramiento de cultivos se basa principalmente en la calidad del germoplasma, su caracterización genética detallada es fundamental para garantizar el uso eficiente de los recursos genéticos y acelerar el desarrollo de variedades superiores. La genotipificación profunda es una herramienta esencial para una caracterización integral del germoplasma de interés y, afortunadamente, en la actualidad se puede acceder a la tecnología a un costo razonable. Lo que debe asegurarse es la interpretación correcta de la información genotípica y sobre esa base desarrollar estrategias eficientes y prácticas de mejoramiento molecular de cultivos que respondan a las necesidades reales del programa de mejoramiento.

Identificación de polimorfismos obesogénicos en mexicanos / Identification of obesogenic polymorphisms in Mexicans

Introducción. La obesidad es una enfermedad metabólica caracterizada por el aumento del índice de la masa corporal. El riesgo de obesidad depende de factores ambientales, del estilo de vida y de la presencia de variantes genéticas originadas por mutaciones únicas y polimorfismos de un solo nucleótido (SNPs). Estudios han mostrado la importancia de la etnia en la heredabilidad de las variantes genéticas asociadas al desarrollo de la obesidad. En México, la prevalencia de sobrepeso y la obesidad es del 38.8 % y 32.4 %, respectivamente. Objetivo. El objetivo de este estudio es determinar SNPs que influyen de manera distintiva en el desarrollo de la obesidad de mexicanos. Materiales y métodos. Se realizó un estudio bibliográfico en la base de datos Pubmed con 70 artículos que estudian la asociación de diferentes SNPs con el desarrollo de la obesidad en mexicanos. Resultados. Se identifican los SNPs rs17782313 (MC4R), rs6548238 (TMEM18), rs6265 (BDNF) y rs7488665 (SH2B1) con un comportamiento diferencial respecto a los resultados obtenidos en población caucásica y el SNPs rs6232 del gen PCSK1 asociado con la aparición de la obesidad en edades juveniles en la población mexicana. Conclusiones. Concluyendo que la caracterización detallada de los genes de mayor incidencia en las distintas etnias contribuye a establecer estrategias personalizadas en particular de la población mexicana y que permitan desarrollar un sistema de alta sensibilidad para determinar la susceptibilidad a la obesidad(AU)

Introduction. Obesity is a metabolic disease characterized by an increase in the body mass index. The risk of obesity depends on environmental factors, lifestyle and the presence of genetic variants caused by single mutations and single nucleotide polymorphisms (SNPs). Studies have shown the importance of ethnicity in the heritability of genetic variants associated with the development of obesity. In Mexico, the prevalence of overweight and obesity is 38.8% and 32.4%, respectively. Objective. The objective of this study is to determine SNPs that have a distinctive influence on the development of obesity in Mexicans. Materials and Methods. A bibliographical study was carried out in the Pubmed database and 70 papers were found that study the association of different SNPs with the development of obesity in Mexicans. Results. The SNPs rs17782313 (MC4R), rs6548238 (TMEM18), rs6265 (BDNF) and rs7488665 (SH2B1) with a differential behavior with respect to the results obtained in the Caucasian population, and the SNPs rs6232 of the PCSK1 gene associated with the appearance of obesity in youth in the Mexican population. Conclusions. Concluding that the detailed characterization of the genes with the highest incidence in the different ethnic groups contributes to establish personalized strategies in particular of the Mexican population and that allow the development of a highly sensitive system to determine susceptibility to obesity(AU)

Performance of the tetra-primer PCR technique compared to PCR-RFLP in the search for rs12979860 (C/T) and rs8099917 (T/G) single nucleotide polymorphisms (SNPs) in the IFNL4 gene / Desempenho da técnica tetra-primer PCR em relação a PCR-RFLP na pesquisa de polimorfismos de nucleotídeos únicos (SNPs) rs12979860 (C/T) e rs8099917 (T/G) no gene IFNL4

Single nucleotide polymorphisms (SNPs, rs12979860 e rs8099917) in the Interferon Lambda 4 gene (IFNL4, formerly IFNL3and/or IL28B) has been associated with failure in the innate immune response, sustained virological response in hepatitis C, and HTLV-1-associated myelopathy (HAM) development. To search for these polymorphisms several methodologies can be employed, such as sequencing, real-time or quantitative polymerase chain reaction (qPCR), restriction fragment length polymorphism analysis in PCR products (PCR-RFLP), and tetra-primer PCR. The present study compared the performance of the tetra-primer PCR in relation to the PCR-RFLP, both optimized in the Research HTLV Laboratory of the Center of Immunology of Instituto Adolfo Lutz in São Paulo. One hundred DNA samples obtained from patients of STD/Aids Reference Centre in São Paulo, previously analyzed for IL28B SNPs by PCR-RFLP were selected for analysis, after confirming that they represent all IL28B SNPs patterns described in the literature. The results obtained showed concordance between the PCR-RFLP and the tetra-primer PCR SNPs results, and because of the low cost, easy to perform, and minor employment of biological specimen and reagents, the tetra-primer PCR is of choice to be used in routine. (AU)

Polimorfismos de nucleotídeos únicos (single nucleotide polymorphisms, SNPs rs12979860 e rs8099917) no gene que codifica o Interferon Lambda 4 (IFNL4, antigamente IFNL3 e/ou IL28B) têm sido associados às falhas na resposta imune inata e resposta virológica sustentada na hepatite C, e a mielopatia associada ao HTLV-1 (HTLV-1-associated myelopathy, HAM). A pesquisa destes polimorfismos pode empregar diversas metodologias: sequenciamento, reação em cadeia da polimerase em tempo real ou quantitativa (quantitative polymerase chain reaction, qPCR), análise de fragmentos de restrição enzimática em produtos de PCR (restriction fragment length polymorphism in PCR products, PCR-RFLP) e a tetra-primer PCR. Este estudo comparou o desempenho da tetra-primer PCR em relação a PCR-RFLP, ambas otimizadas no Laboratório de Pesquisa em HTLV do Centro de Imunologia do Instituto Adolfo Lutz de São Paulo. Foram selecionadas 100 amostras de DNA obtidas de pacientes do Centro de Referência e Treinamento em DST/Aids de São Paulo cujos SNPs na IL28B foram anteriormente determinados por PCR-RFLP e representaram todos os perfis descritos em literatura. Os resultados obtidos mostraram concordância entre elas, e pelo fato da tetra-primer PCR ter menor custo, ser de fácil execução, empregar menos tempo, insumos e material biológico, é a técnica de escolha para uso em rotina. (AU)