Association of Polymorphisms in the 3'UTR of Genes in the ERK1/2 Signaling Pathway with Non-small Cell Lung Cancer / 昆明医科大学学报

Objective To investigate the association between four single nucleotide polymorphisms(SNP)(rs9340 in MAPK1,rs14804 in NRAS,rs712 and rs7973450 in KRAS)in the 3'UTR of ERK1/2 signaling pathway-related genes and non-small cell lung cancer(NSCLC).Methods A total of 478 NSCLC patients and 480 healthy controls were enrolled in this study.Four SNPs were genotyped by using TaqMan assays.The association between the four SNPs and NSCLC was analyzed.Results The distribution frequency difference of the allele of rs9340 was statistically significant between the control group and the non-small cell squamous cell carcinoma(SCC)group(P = 0.009),suggesting that the G allele of rs9340 may be a protective factor for non-small cell lung squamous cell carcinoma(OR = 0.67,95%CI:0.50～0.91).In addition,in the<50 years age group,the distribution frequency difference of the allele of rs9340 was statistically significant between the control group and the NSCLC group(P = 5.07×10-4),indicating that the G allele of rs9340 may be a protective factor for NSCLC(OR = 0.46,95%CI:0.29～0.72).Conclusion The SNP rs9340 in MAPK1 may be associated with the risk of NSCLC.

Application research of PGT in blocking the inheritance of novel mutations in the PKHD1 gene in autoso-mal recessive polycystic kidney disease pedigrees / 实用医学杂志

Objective To investigate the application value of single nucleotide polymorphism(SNP)linkage analysis based on next-generation sequencing(NGS)technology in preimplantation genetic testing(PGT)of families with autosomal recessive polycystic kidney disease(ARPKD).Methods A family with ARPKD was selected,where the female member had a pregnancy ultrasound revealing polycystic kidney in the fetus.Genetic testing showed compound heterozygous mutations of the polycystic kidney/polycystic liver disease 1 gene(PKHD1),c.10444C>T(paternal)and c.4303del(maternal),with the c.4303del mutation being reported for the first time.Targeting the coding region of the PKHD1 gene,335 high-density tightly linked SNP sites were selected in the upstream and downstream 2M regions using multiplex polymerase chain reaction(PCR)and NGS.The couple′s SNP risk haplotypes carrying gene mutations were constructed.After in vitro fertilization,blastocyst culture was performed.Trophoblastic cells obtained from the biopsy were subjected to whole-genome amplification,and NGS was used for linkage analysis and low-depth chromosomal aneuploidy screening of the embryos.Sanger sequencing was used to verify the results of embryo linkage analysis.Results Among the 6 biopsied embryos,4 were mutation-free and euploid,1 exhibited heterozygous for the mutation and mosaic while another unstable sequencing data,making it impossible to judge.One of the mutation-free and developmentally healthy euploid embryos was implanted into the maternal uterus,resulting in the full-term delivery of a healthy baby.Conclusion Application of NGS-based SNP linkage analysis in PGT can effectively blocking the vertical transmission of ARPKD within families,while avoiding abortion issues caused by aneuploid embryos.This study is also the first PGT report target-ing the PKHD1 gene c.4303del mutation.

Analysis of Association Between Immune Cells and Breast Cancer Based on Two-sample Mendelian Randomization Method / 肿瘤防治研究

Objective To explore the causal relationship among 731 types of immune cells and breast cancer. Methods Genome-wide association data for immune cells and breast cancer were used. Mendelian randomization analysis was performed using the inverse variance weighting (IVW) and weighted median (WM) methods, and sensitivity analysis was conducted to assess heterogeneity and pleiotropy. Results A total of 19 immune cell phenotypes were identified to potentially have a causal association with breast cancer, using IVW as the main analysis method (P>0.05) and correcting P values using the false discovery rate method at a significance level of 0.05, excluding reverse causality. Of these, eight and 11 immune phenotypes may increase and decrease the risk of breast cancer, respectively. Conclusion This study explored the causal relationship between immune cells and breast cancer. Results show that certain immune cell phenotypes could serve as predictive markers for the early diagnosis of breast cancer and the development of new immunotherapeutic strategies.

Research on the association between the DYS570 microvariant and Y-SNP haplogroup in Kunming / 中国法医学杂志

Objective To investigate the association between microvariants at locus DYS570 and Y-SNPs haplogroup.Methods 89 Y-SNPs and 34 Y-STRs in AIYSNP42,AIYSNP47 and YfilerTM Platinum kits were used to detect the genotype of 116 microvariants at locus DYS570 in Kunming,and the Set-B kit was used to detect the core repeat sequences of the DYS570 locus.The data were statistically analyzed by direct counting method.Then,a network map was drawn by Network 10.2,in order to visualize the genetic information of the sample.Results The results demonstrated that 111 DYS570/18.3-21.3 samples had a core repeat sequence of TTT[TITC]18-21,belonging to subgroup O2a2b1a1a1a4-F14494.A DYS570/20.3 sample had a core repeat sequence of[TTTC]15TTC[TTTC]5,belonging to O2a1b1a1a1a1e-F1365 subgroup.A DYS570/17.1 sample had a core repeat sequence of[TTTC]17 T,belonging to the O2a1b1a1a1a-F11 subgroup.Three DYS570(19.2)samples had[TTTC]3 TT[TTTC]16,belonging to the D1a1a-M15 haplogroup.Conclusion The results indicated that the microvariant with the same core repeat structure at locus DYS570 was associated with haplogroups,and the ancestry origin of samples can be inferenced from microvariant characteristics during the practice of forensic medicine.

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.

The association of CYP11A1 gene polymorphisms with the polycystic ovary syndrome patients

SUMMARY OBJECTIVE: The objective of this study was to investigate the allele frequencies of polymorphisms in genes CYP11A1 rs4886595 and CYP11A1 rs4887139 that are responsible for the steroidogenesis mechanism in polycystic ovary syndrome patients and control females. METHODS: Samples were obtained from the Department of Obstetrics and Gynecology in the Near East University Hospital from September 2019 to December 2019. Only the nonobese patients between the ages of 18-40 years were included in this study following informed consent. Obese patients and patients more than 40 years of age were excluded from the study. Nonobese women and normal ovulation were included in the control group. DNA was isolated from blood samples. Real-time polymerase chain reaction (PCR) was used to analyze single nucleotide polymorphisms (SNPs) in various genes linked to polycystic ovary syndrome. The studies were carried out using the samples obtained from 120 women, of whom 55 were nonobese and had normal ovulation, and 65 were polycystic ovary syndrome patients. The allelic frequencies of SNPs in genes linked to polycystic ovary syndrome were calculated using real-time PCR outcomes. RESULTS: The variation of the CYP11A1 rs4887139 G>A did not show any significance, while the variation of CYP11A1 rs4886595 C>A showed significant differences between the patient and the control groups (p=0.01), respectively. CONCLUSION: Future research ought to focus on elucidating the susceptible causes of polycystic ovary syndrome with a wide range of SNPs and more sample size. The genome-wide association studies in polycystic ovary syndrome patients of different origin will be important to identify candidate genes as well as proteins that are implied in polycystic ovary syndrome risk.

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.

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)

Research progress on emerging biomarkers in kidney transplantation / 器官移植

The hosts could show complex and diverse immune responses to the allografts. Whether biomarkers can be employed to explain the complexity of graft immune responses and the degree of disease damage are of significance. Conventional biomarkers, such as estimated glomerular filtration rate and blood concenrtation of immunosuppressant, lack of sensitivity and specificity in accurately identifying between immune and non-immune renal allograft injuries. Although renal biopsy is the "gold standard" for the diagnosis of postoperative complications, it still has disadvantages, such as invasiveness and high price, etc. Emerging biomarkers have potential advantages in the non-invasive diagnosis of subclinical injury of renal allograft, prediction of treatment response and individualized adjustment of immunosuppressive regimen. In this article, emerging biomarkers including blood, urine and tissue biomarkers that have been applied and are expected to be applied in clinical practice in the field of kidney transplantation were reviewed, and the range of application and effect of these biomarkers were evaluated, aiming to promote appropriate and rational application of these promising emerging biomarkers in clinical practice.

Role of melatonin receptor 1B gene polymorphism and its effect on the regulation of glucose transport in gestational diabetes mellitus / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Melatonin receptor 1B (MT2, encoded by the MTNR1B gene), a high-affinity receptor for melatonin, is associated with glucose homeostasis including glucose uptake and transport. The rs10830963 variant in the MTNR1B gene is linked to glucose metabolism disorders including gestational diabetes mellitus (GDM); however, the relationship between MT2-mediated melatonin signaling and a high birth weight of GDM infants from maternal glucose abnormality remains poorly understood. This article aims to investigate the relationship between rs10830963 variants and GDM development, as well as the effects of MT2 receptor on glucose uptake and transport in trophoblasts. TaqMan-MGB (minor groove binder) probe quantitative real-time polymerase chain reaction (qPCR) assays were used for rs10930963 genotyping. MT2 expression in the placenta of GDM and normal pregnant women was detected by immunofluorescence, western blot, and qPCR. The relationship between MT2 and glucose transporters (GLUTs) or peroxisome proliferator-activated receptor γ (PPARγ) was established by western blot, and glucose consumption of trophoblasts was measured by a glucose assay kit. The results showed that the genotype and allele frequencies of rs10830963 were significantly different between GDM and normal pregnant women (P<0.05). The fasting, 1-h and 2-h plasma glucose levels of G-allele carriers were significantly higher than those of C-allele carriers (P<0.05). Besides, the protein and messenger RNA (mRNA) expression of MT2 in the placenta of GDM was significantly higher than that of normal pregnant women (P<0.05). Melatonin could stimulate glucose uptake and GLUT4 and PPARγ protein expression in trophoblasts, which could be attenuated by MT2 receptor knockdown. In conclusion, the rs10830963 variant was associated with an increased risk of GDM. The MT2 receptor is essential for melatonin to raise glucose uptake and transport, which may be mediated by PPARγ.

Effects and mechanisms of SNP-9 on Parkinson''s disease cell model induced by rotenone / 中国药科大学学报

@#In this article, the effects and mechanisms of SNP-9 on Parkinson''s disease (PD) cell model were investigated.SH-SY5Y cells were treated with rotenone to establish PD cell model; the effects of rotenone and SNP-9 on cell viability were detected by MTT assay; Hoechst/PI double staining assay was used to detect the effects of rotenone and SNP-9 on cell apoptosis; DCFH-DA probe was used to detect the effects of rotenone and SNP-9 on cellular reactive oxygen species (ROS) levels; and Western blot was used to detect the effects of rotenone and SNP-9 on protein levels of tyrosine hydroxylase (TH), α-synuclein (α-syn), Bcl-2 and Bax.The results showed that SNP-9 could alleviate abnormalities in cell viability, levels of TH and α-syn, apoptosis, ROS and apoptotic relative protein Bax/Bcl-2 induced by rotenone.Our findings suggest that SNP-9 may alleviate rotenone-induced injury in neuronal cells by regulating cell apoptosis related pathway.

Single nucleotide polymorphism at rs7903146 of transcription factor 7-like 2 gene among subjects with type 2 diabetes mellitus in Myanmar / Journal of the ASEAN Federation of Endocrine Societies

Objectives@#To investigate the association between the single nucleotide polymorphism (SNP) rs7903146 in the transcription factor 7-like 2 (TCF7L2) gene and type 2 diabetes mellitus (T2DM) and to examine the impact of this variant on pancreatic beta-cell function in the Myanmar population.@*Methodology@#A case-control study was undertaken in 100 subjects with T2DM and 113 controls. The SNP rs7903146 was genotyped using the allele-specific polymerase chain reaction method. Plasma glucose and serum insulin levels were determined using the enzymatic colorimetric method and ELISA respectively. Beta-cell function was calculated by the HOMA-β formula.@*Results@#The frequencies of carrier genotypes (CT and TT) were higher in subjects with T2DM than in controls. The minor T alleles of rs7903146 were found to statistically increase type 2 diabetes risk than the C allele with an allelic odds ratio of 2.07 (95% CI 1.39-3.09, p=0.0004). The mean HOMA-β level of the group with non-carrier genotype (CC) was significantly higher than that of the groups with carrier genotypes (CT and TT) in subjects with T2DM and controls with a p-value of 0.0003 and less than 0.0001, respectively.@*Conclusion@#The rs7903146 variant of the TCF7L2 gene was found to be associated with T2DM and low β-cell function among Myanmar subjects.

The association between the DYS527a/b and DYF387S1a/b multi-allele pattern and Y-SNP haplogroups / 中国法医学杂志

Objective To investigate the association of the DYS527a/b and DYF387S1a/b multi-allele pattern with Y-SNP haplogroups.Methods Samples from 295 unrelated males who carrying the DYS527a/b multi-allele pattern were amplified by the YFilerPlus? kit.The genotypes of their frequency distributions,including three multi-copy loci(DYS527a/b,DYF387S1a/b,DYS385a/b)and other single-copy loci were obtained.The DYS527a/b multi-allele pattern and their haplotypes were examined for the associations with Y-chromosome haplogroups using the AIYSNP42 kit,which contains 42 Y-SNP loci.Based on the above results,the association between the DYS527a/b multi-allele patter and its constituent Y-STR haplotypes and related haplogroups was discussed.Results Among the 295 samples,the DYS527a/b tri-allele pattern and tetra-allele pattern accounted for 97.29%and 2.71%respectively,while the DYF387S1a/b tri-allele pattern and tetra-allele encompassed 54.24%and 4.75%.Null allele was detected in DYS448 in 13.22%of the samples.Here,7 Y-SNPs were deticted such as O-M175 and C-M131 which encompassed 45.76%and 45.08%.The haplogroups of R1-M173,N-M231,D1-M174,J-M304 and F-M89 were less than 13 cases,with frequencies ranging from 4.41%～0.34%.There were Y-STR genotypes differences among haplogroups,as haplogroup O-M175 was represented by 4 genotypes of Y-STR profiles characterized by DYS385a/b(12/12,as well as 12/17,12/18,12/19),DYS392(13),DYS593(16)and DYS393(12),and haplogroup C-M130 was characterized by DYS527a/b(19/20/21),DYS385a/b(11),DYS593(17),DYS390(23),Y_GATA_H4(11),and DYS444(13)and so on.Conclusion The DYS527a/b multi-allele pattern is frequently observed in the Kunming population with haplogroup C-M130.In the samples from haplogroups O,C,R1 and N,the DYS527a/b and DYF387S1a/b haplotypes frequently exhibit the multi-allele pattern.Given the frequencies of different haplogroups and the association between Y-SNP haplogroups and Y-STR loci,it could be helpful to look for more details in the paternal lineage search.

Application of single nucleotide polymorphism(SNP)analysis in bacterial molecular typing / 中国人兽共患病学报

Single nucleotide polymorphisms(SNPs),third generation molecular genetic markers,have attracted extensive attention because of their importance in research on genetic diseases,gene evolution,adaptation,species,medicine and other fields.SNPs are found in large numbers,with a wide distribution,stable genetics and high throughput.Moreover,SNPs are suitable for rapid and large-scale screening.These genetic markers have been widely used in molecular typing for a variety of bacteria.Herein,the current status of SNP technology is discussed and compared with other typing methods,and its applica-tions in bacterial molecular typing are reviewed.

A systematic survey of LU domain-containing proteins reveals a novel human gene, LY6A, which encodes the candidate ortholog of mouse Ly-6A/Sca-1 and is aberrantly expressed in pituitary tumors / 医学前沿

The Ly-6 and uPAR (LU) domain-containing proteins represent a large family of cell-surface markers. In particular, mouse Ly-6A/Sca-1 is a widely used marker for various stem cells; however, its human ortholog is missing. In this study, based on a systematic survey and comparative genomic study of mouse and human LU domain-containing proteins, we identified a previously unannotated human gene encoding the candidate ortholog of mouse Ly-6A/Sca-1. This gene, hereby named LY6A, reversely overlaps with a lncRNA gene in the majority of exonic sequences. We found that LY6A is aberrantly expressed in pituitary tumors, but not in normal pituitary tissues, and may contribute to tumorigenesis. Similar to mouse Ly-6A/Sca-1, human LY6A is also upregulated by interferon, suggesting a conserved transcriptional regulatory mechanism between humans and mice. We cloned the full-length LY6A cDNA, whose encoded protein sequence, domain architecture, and exon-intron structures are all well conserved with mouse Ly-6A/Sca-1. Ectopic expression of the LY6A protein in cells demonstrates that it acts the same as mouse Ly-6A/Sca-1 in their processing and glycosylphosphatidylinositol anchoring to the cell membrane. Collectively, these studies unveil a novel human gene encoding a candidate biomarker and provide an interesting model gene for studying gene regulatory and evolutionary mechanisms.

Association of PI3K/AKT/mTOR pathway autophagy-related gene polymorphisms with pulmonary tuberculosis susceptibility in a Chinese population

ABSTRACT Background: Autophagy can inhibit the survival of intracellular microorganisms including Mycobacterium tuberculosis (Mtb), and the PI3K/AKT/mTOR pathway plays a crucial role. This study investigated the association between PI3K/AKT/mTOR pathway autophagy-related gene polymorphisms and pulmonary tuberculosis (PTB) susceptibility. Methods: KEGG pathway and gene ontology (GO) databases were searched for genes belonging to the PI3K/AKT/mTOR and autophagy pathways. Thirty SNPs in nine genes were identified and tested for their associations with tuberculosis in 130 patients with PTB and 271 controls. We constructed genetic risk scores (GRSs) and divided the participants into 3 subgroups based on their GRSs:0-5, 6-10, and 11-16. Results: This analysis revealed that the AKT1 (rs12432802), RPTOR (rs11654508, rs12602885, rs2090204, rs2589144, and rs2672897), and TSC2 (rs2074969) polymorphisms were significantly associated with PTB risk. A decreasing trend was observed (P trend 0.020), in which a lower GRS was associated with a higher risk of PTB ([6-10] vs. [0-5]: OR (95%CI) 0.590 (0.374-0.931); [11-16] vs. [0-5]: OR (95%CI) 0.381 (0.160-0.906)). Conclusions: Polymorphisms in AKT1, RPTOR, and TSC2 may influence susceptibility to PTB.

Polyalanine polymorphism in the signal peptide of Glutathione peroxidase 1 (GPX1) gene & its association with osteoporosis

Background & objectives: Osteoporosis is a systemic skeletal disease, characterized by a low bone mass leading to increased bone fragility and hence, a greater susceptibility to the risk of fracture. Since age-related oxidative stress is one of the factors that has been implicated in developing low bone mineral density (BMD), leading to osteoporosis, this study wanted to explore the expression of antioxidant enzymes in individuals with osteoporosis. The present study focused on mapping polymorphism in an important antioxidant enzyme glutathione peroxidase 1 (GPx1) among osteoporosis and healthy Asian Indians. Methods: Dual-energy X-ray absorptiometry was used to assess BMD of individuals and was classified into normal (n=96) and osteoporotic (n=88) groups. Biochemical parameters such as vitamin D, total oxidant status (TOS), and GPx1 enzyme activity were estimated from plasma samples of recruited individuals. Quantitative real-time qRT-PCR was carried out using GAPDH as an endogenous control. Genomic DNA was isolated from whole blood, and polymorphisms were evaluated by sequencing. Results: The BMD was lower in osteoporotic individuals, and further analysis of biochemical parameters indicated significantly low 25-hydroxy vitamin D and GPx1 with higher TOS levels in osteoporotic as compared to healthy individuals. Furthermore, qRT-PCR revealed low expression of GPX1 in osteoporotic individuals. GPX1 sequence analysis of the promoter and two exons revealed the lower frequency of five alanine repeats in the osteoporotic individuals. Interpretation & conclusions: In this study, the in silico analysis revealed the lower frequency of five alanine repeats in exon 1 of GPX1 and high TOS to be associated with osteoporosis. However, no polymorphism was found in exon 2 of GPX1 among the two study groups.

Possible association between a polymorphism of EPAS1 gene and persistent pulmonary hypertension of the newborn: a case-control study

Abstract Objective: To explore possible genes related to the development of persistent pulmonary hypertension of the newborn (PPHN). Methods: The authors identified 285 single nucleotide polymorphisms (SNPs) of 11 candidate genes (BMPR2, EPAS1, PDE3A, VEGFA, ENG, NOTCH3, SOD3, CPS1, ABCA3, ACVRL1, and SMAD9), using an Illumina Asian Screening Array-24 v1.0 BeadChip Array. The FastLmmC and R package was used for statistical analyses. The chi-square test and Cochrane-Armitage trend test were used to compare the allele and genotype frequencies between the groups and to test the genetic models, respectively. Results: A total of 45 PPHN infants and 294 control subjects were analyzed. The most common cause of PPHN was meconium aspiration syndrome. Among the 285 SNPs, 17 SNPs from 6 candidate genes (BMPR2, EPAS1, PDE3A, VEGFA, ENG, and NOTCH3) were significantly associated with PPHN (P < 0.05). After using the Bonferroni correction (P < 0.00018), only the rs17034984 SNP located in intron 1 of the EPAS1 gene remained significantly different between the PPHN and control subjects (P = 0.00014). The frequency of the TC/TT genotype of rs17034984 in the gene with the dominant model was significant in the patients with PPHN (OR = 5.38, 95% CI: 2.15-13.49). The T allele frequency of rs17034984 in the gene showed a significant difference compared with the control subjects (OR = 4.89, 95% CI: 2.03-11.82). Conclusions: The present study suggests that the rs17034984 variant of EPAS1 gene is associated with PPHN.

Prevalence of risk alleles in the lysyl oxidase-like 1 gene in pseudoexfoliation glaucoma patients in India

Purpose: The purpose of this study was to genotype two previously identified SNPs (rs1048661:R141L, and rs3825942:G153D) in the lysyl oxidase?like 1 (LOXL1) gene and determine their association with pseudoexfoliation glaucoma (XFG) in patients from Pune, India. Methods: All subjects underwent detailed phenotyping, and DNA extraction was performed on blood samples by using standardized techniques. Exon 1 of the LOXL1 gene containing the SNPs (rs3825942:G153D; rs1048661:R141L) were Sanger sequenced, and the results were analyzed using sequence analysis software SeqScape 2.1.1. Results: Data were analyzed from 71 patients with XFG and 81 disease?negative, age?matched controls. There was a strong association between the G allele of rs3825942 and XFG with an odds ratio of 10.2 (CI: 3.92–26.6; P < 0.001). The G allele of rs1048661 also showed an increase in risk relative to the T allele (OR = 1.49; CI: 0.88–2.51; P = 0.13), but this was not significant. Haplotype combination frequencies were estimated for rs1048661 and rs3825942; the GG haplotype was associated with a significant increase in risk (OR = 3.91; CI: 2.27–6.73; P < 0.001). Both the GA and TG haplotypes were associated with decreased XFG risk, although the latter was not significant (GA: OR = 0.08; CI: 0.03–0.21; P < 0.001; TG: OR = 0.67; CI: 0.40–1.13; P = 0.13). Conclusion: The risk G allele in rs3852942 (G153D) is strongly associated with the development of XFG in the Western Indian population. Genetic screening strategies to identify LOXL1 risk alleles in the population can assist in case definition and early diagnosis, targeting precious resources to high?risk patients.

Effects and mechanisms of SNP-9 on Aβ25-35-induced damage in bEnd.3 cells / 中国药科大学学报

@#In order to investigate the effects of neuroprotective peptide SNP-9 which is derived from silk fibroin hydrolysate on the injury of the blood-brain barrier in Alzheimer′s disease (AD), Aβ25-35 was used to damage brain microvascular endothelial cells bEnd.3 to establish AD injury model and drug intervention was performed.MTT assay was used to detect the effects of SNP-9 and Aβ25-35 on cell viability.RT-qPCR was used to determine the effects of SNP-9 and Aβ25-35 on the mRNA levels of tight junctions (TJs)-related ZO-1, occludin and claudin-5.Western blot was used to detect the effects of SNP-9 and Aβ25-35 on the protein levels of TNF-α, phosphorylated NF-κB, NF-κB, IκBα and RAGE.The results showed that SNP-9 reduced bEnd.3 cell damage induced by Aβ25-35, and improved the abnormal mRNA levels of ZO-1, occludin and claudin-5 in model cells.It alleviated the abnormal protein levels of TNF-α, phosphorylated NF-κB, IκBα and RAGE induced by Aβ25-35. These results suggest that SNP-9 may regulate the levels of TNF-α in model cells by influencing RAGE/NF-κB pathway, and then ameliorate TJs-related abnormalities and alleviate bEnd.3 cell injury induced by Aβ25-35.