Identification of differentially expressed genes associated with lung adenocarcinoma via bioinformatics analysis.

Lung adenocarcinoma (LUAD) with extremely high morbidity as well as mortality is still in the exploration stage of pathogenesis and treatment. This study aimed to screen and identify differentially expressed genes (DEGs) associated with LUAD via bioinformatics analysis. Three LUAD microarray datasets, GSE116959, GSE68571 and GSE40791, were selected from the Gene Expression Omnibus (GEO) database to analyze the DEGs. 128 DEGs were identified in all, incorporating 36 upregulated and 92 downregulated. Function and pathway enrichment analyses showed that metabolic pathways were their main signaling pathways. After that, seven hub genes including VWF, SPP1, PECAM1, TOP2A, CDK1, UBE2C and KIF23 were mined by the protein-protein interaction (PPI) network. Gene expression analysis, TNM and survival analysis of these hub genes were performed via Gene Expression Profiling Interactive Analysis (GEPIA) online database. Further analysis indicated that TOP2A, CDK1, UBE2C and KIF23 were related to the stage of LUAD patients and overall survival. Then, we verified the relative expression levels of TOP2A, CDK1, UBE2C and KIF23 in LUAD cell lines by qRT-PCR. In conclusion, this study indicated that the four hub genes screened out by bioinformatics analysis were differentially expressed in LUAD compared to normal sample and might be prognostic markers of LUAD.

PPARGC1A is upregulated and facilitates lung cancer metastasis.

Lung cancer remains a leading cause of cancer-related mortality, with metastatic progression remaining the single largest cause of lung cancer mortality. Hence it is imperative to determine reliable biomarkers for lung cancer prognosis. We performed quantitative real-time PCR (qRT-PCR) analysis to explore epithelial-mesenchymal transition (EMT) inducers that regulate EMT process in three patients with advanced lung cancer disease. Peroxisome proliferator-activated receptor gamma (PPARGC1A) was uniformly the topmost overexpressed gene in all three human non-small cell lung cancer (NSCLC) patient samples. Further evaluation in human normal lung and metastatic lung cancer cell lines revealed that the expression of PPARGC1A was upregulated in metastatic lung cancer cell lines. Metagenomic analysis revealed direct correlation among PPARGC1A, zinc-finger transcription factor snail homolog 1 (SNAI1), and metastatic lung disease. Upregulation of PPARGC1A transcript expression was independent of a differential upregulation of the upstream AMP-dependent protein kinase (AMPK) activation or steady state expression of the silent mating type information regulation 2 homolog 1 (SIRT1). Xenograft tail vein colonization assays proved that the high expression of PPARGC1A was a prerequisite for metastatic progression of lung cancer to brain. Our results indicate that PPARGC1A might be a potential biomarker for lung cancer prognosis.

Allele-specific methylation contributed by CpG-SNP is associated with regulation of ALOX5AP gene expression in ischemic stroke.

Previous studies have shown that CpG-SNPs might have influence on gene function via allele-specific DNA methylation (ASM). However, association study between DNA methylation and the promoter CpG-SNPs in ALOX5AP gene with IS has not been reported. The present study aims to explore the relationship among CpG-SNPs, methylation levels, and messenger RNA (mRNA) expression levels of ALOX5AP gene. Firstly, we made a two-stage association study to identify a potential associated CpG-SNP (rs4073259) by SNaPshot genotyping approach (P = 0.015, OR = 0.672, 95% CI 0.487-0.927; P = 0.035, OR = 0.809, 95% CI 0.664-0.985, respectively). In addition, the methylation levels of 17 CpG sites located in the promoter of ALOX5AP were tested by MethylTarget sequencing. The methylation level of GG genotype carriers is significantly higher than those with the AG and AA genotypes (P < 0.05). And the GG genotype carriers with higher DNA methylation levels have a decreased mRNA expression levels of ALOX5AP (P < 0.05). Finally, we found that the G allele with higher methylation level has got a lower transcription activity than the A allele by luciferase assay (P = 0.000).The study provided evidence that IS-associated CpG-SNP rs4073259 may affect the expression level of ALOX5AP through allele-specific methylation and consequently the phenotype of the disease.

MicroRNA-490 regulates lung cancer metastasis by targeting poly r(C)-binding protein 1.

Lung cancer remains a leading cause of cancer-related mortality, with metastatic progression remaining the single largest cause of lung cancer mortality. Hence, it is imperative to determine reliable biomarkers of lung cancer prognosis. MicroRNA-490-3p has been previously reported to be a positive prognostic biomarker for hepatocellular cancer. However, its role in human lung cancer has not yet been elucidated. Here, we report that hsa-miR-490-3p expression is significantly higher in human lung cancer tissue specimens and cell line. Gain- and loss-of-function studies of hsa-miR-490-3p showed that it regulates cell proliferation and is required for induction of in vitro migration and invasion-the latter being a hallmark of epithelial to mesenchymal transition. In situ analysis revealed that hsa-miR-490-3p targets poly r(C)-binding protein 1 (PCBP1), which has been previously shown to be a negative regulator of lung cancer metastasis. Reporter assays confirmed PCBP1 as a bona fide target of miR-490-3p, and metagenomic analysis revealed an inverse relation between expression of miR-490-3p and PCBP1 in metastatic lung cancer patients. In fact, PCBP1 expression, as detected by immunohistochemistry, was undetectable in advanced stages of lung cancer patients' brain and lymph node tissues. Xenograft tail vein colonization assays proved that high expression of miR-490-3p is a prerequisite for metastatic progression of lung cancer. Our results suggest that hsa-miR-490-3p might be a potential biomarker for lung cancer prognosis. In addition, we can also conclude that the lung cancer cells have evolved refractory mechanisms to downregulate the expression of the metastatic inhibitor, PCBP1.

Mitochondrial DNA haplogroup D4b is a protective factor for ischemic stroke in Chinese Han population.

Mitochondrial DNA (mtDNA) haplogroups affect the assembly and stability of the mitochondrial respiratory chain, which is potentially related to susceptibility to ischemic stroke (IS). However, the role of mtDNA in IS has not been comprehensively studied. The purpose of this study was to explore whether mtDNA polymorphisms and haplogroups are involved in the etiology of IS in the Chinese Han population. We recruited 200 patients with IS and 200 matched controls and genotyped them for 18 mtDNA single nucleotide polymorphisms defining the major Eastern Asian haplogroups by SNaPshot minisequencing. We also sequenced the hypervariable segment I (HVS-I), position 16051-16400. The prevalence of haplogroup D4b was significantly lower in IS patients than in healthy controls (0 and 8 %, respectively, corrected P = 2 × 10(-5), odds ratio = 0.028, 95 % confidence interval = 0.002-0.468).The positive association between haplogroup D4b and IS may be related to the protective effect of haplogroup D4b against oxidative damage, which decreases the risk of IS. Our study provides the first evidence that haplogroup D4b is a potential genetic protective factor for IS in the Chinese Han population.

Long noncoding RNA MEG3 regulates cell proliferation and apoptosis by disrupting microRNA-9-5p-mediated inhibition of NDRG1 in prostate cancer.

BACKGROUND: Long noncoding RNA MEG3 has been described to be involved in the regulation of gene expression and cancer progression. However, the role of lncMEG3 in prostate cancer (PCa) remains largely uncharted. METHODS: Differential expression of lncMEG3 was identified in PCa tissues using RNA-sequencing analysis. qRT-PCR was performed to examine the level of lncMEG3. Additionally, cellular fractionation and fluorescent in situ hybridization techniques were employed to determine the localization. Subsequently, functional assays were conducted to evaluate the impact of lncMEG3 and miR-9-5p on PCa proliferation and apoptosis in vitro and in vivo. The interaction between lncMEG3 and miR-9-5p was confirmed using RNA immunoprecipitation. Moreover, luciferase reporter assays were also utilized to investigate the relationship between miR-9-5p and NDRG1. RESULTS: We observed downregulation of lncMEG3 in PCa cells and tissues. Patients with lower levels of lncMEG3 had a higher likelihood of experiencing biochemical recurrence. Overexpression of lncMEG3 resulted in the inhibition of PCa cell proliferation and the promotion of apoptosis. Moreover, lncMEG3 is competitively bound to miR-9-5p, preventing its inhibitory effect on the target gene NDRG1. This ultimately led to the inhibition of PCa cell proliferation and the promotion of apoptosis. Furthermore, increasing lncMEG3 levels also demonstrated inhibitory effects on PCa proliferation and promotion of apoptosis in vivo. CONCLUSIONS: Our findings uncover a crucial role for lncMEG3 in inhibiting PCa proliferation and promoting apoptosis through disruption of miR-9-5p-mediated inhibition of NDRG1.

[A study on paternity testing with 96 autosomal SNPs].

OBJECTIVE: To explore the feasibility of applying autosomal single nucleotide polymorphisms (SNPs) on parentage testing. METHODS: All SNP genotyping results of HapMap (r27) were downloaded from the website. With self-made computer programs, SNPs were extracted when their minor allele frequency (MAF) were ≥ 0.30 among all of the 11 HapMap populations. Ninety-six SNPs were chosen and integrated into the Illumina Goldengate bead arrays on the condition that no linkage disequilibrium was found between them. Three father-child-mother trios (9 samples in total) were tested with the arrays. Cumulative paternity index (CPI) was then calculated and compared with genotyping results using 15 short tandem repeats (STRs)(Identifiler(TM)). RESULTS: Family 1 was found to have nine SNPs or seven STRs that did not conform to the Mendelian laws, Family 2 had 13 such SNPs or seven STRs, and Family 3 only had one such SNP but no STR. For Family 3, when all of the 96 SNPs were used in combine, the CPI was 1207, which had contrasted with the CPI by the 15 STRs, i.e., 355 869. CONCLUSION: When applied to paternity testing, the paternity exclusion (PE) value for a SNP is usually less than 1/3 of that of a STR. The proportion of SNPs not comforming to the Mendelian laws for the tested SNPs may not be as high as that of inconsistent STRs over all tested STRs. Because of the low mutation rate of a SNP, the CPI will be greatly reduced even if one SNP did not conform to the Mendelian laws. Therefore, highly accurate testing methods are required to reduce artificial errors when applying SNPs for paternity testing.

Epidemiological evidences from China assume that psychiatric-related diseases may be associated with Toxoplasma gondii infection.

In recent years, the effect of Toxoplasma gondii infection on psychiatric-related aspects has been increasingly recognized. T. gondii has a high affinity for brain tissue where tachyzoites may form tissue cysts and persist life long. In recent years, 15 serological surveys about T. gondii infection and psychiatric diseases have been carried out in different areas in China. Studies showed that the prevalence of antibodies against T. gondii in psychotic patients was much higher than in normal persons; statistically differences were significant. Studies also reported that raising cats or enjoying the habit of eating raw or under cooked meet were potential risk factors for the infection of T. gondii. The epidemiological and serological evidence support the hypothesis that some psychiatric diseases such as schizophrenia or mental retardation might be linked to T. gondii infection.

A promoter polymorphism (rs17222919, -1316T/G) of ALOX5AP gene is associated with decreased risk of ischemic stroke in two independent Chinese populations.

No coding sequence variants of the gene encoding 5-lipoxygenase-activating protein (ALOX5AP) leading to amino acid substitutions have been identified. Therefore, variants in the ALOX5AP promoter region have received attention recently. The purpose of this study was to explore whether the promoter polymorphism rs17222919 is involved in the etiology of ischemic stroke (IS) in the Chinese Han population. We investigated the rs17222919 polymorphism by TaqMan genotyping in two independent Chinese Han samples: the first comprised 910 IS patients and 925 healthy inhabitants from the northern Henan Province, while the second included 1003 IS patients and 889 healthy controls from the southern Henan Province. Functional characterization of rs17222919 was performed by an in vitro luciferase assay. After adjusting for conventional risk factors, the G allele frequencies in the IS groups were significantly lower than that in the control groups of the two independent Chinese cohorts (19.0% vs. 22.9%, P = 0.004, odds ratio (OR) = 0.792, 95% confidence interval (CI) = 0.675-0.929; 18.8% vs. 22.9%, P = 0.002, OR = 0.782, 95% CI = 0.668-0.915, respectively). This was also observed in the large-artery atherosclerosis (LAA) and stroke of other undetermined etiology (SUE) subtypes (P = 0.019, OR = 0.815, 95% CI = 0.687-0.967; P = 0.021, OR = 0.815, 95% CI = 0.685-0.970, respectively). Additionally, the TG genotype and G allele frequencies were significantly lower in the IS compared with the control group in two female cohorts (P<0.05). Finally, the in vitro luciferase assay demonstrated that the G allele has a significantly lower transcription activity than the T allele (P = 0.031). Our study provides evidence that the promoter single nucleotide polymorphism (SNP) rs17222919 is a potential genetic protective factor for IS in the Chinese Han population.

New fluorescent sensor for Cu(2+) and S(2-) in 100% aqueous solution based on displacement approach.

An On-Off-On type fluorescent sensor (HL) has been developed, which exhibited high selectivity and sensitivity for Cu(2+) over other common ions in 100% aqueous solution. Once HL combined with Cu(2+), blue fluorescence was almost completely quenched and the L-Cu ensemble was formed. Moreover, the ensemble showed high specificity for S(2-) based on the displacement approach, and no interferences were observed in the presence of other anions. Such fluorescence modulation behavior simulates the performance of an IMPLICATION logic gate. In addition, the fluorescent sensor was successfully applied to fluorescent cellular imaging implying potential applications in physiological and environmental systems.

Association between VKORC1 gene polymorphisms and ischemic cerebrovascular disease in Chinese Han population.

The vitamin K epoxide reductase subunit 1 gene (VKORC1) plays a key role in vitamin K recycling, and there is a close association between VKORC1 gene single-nucleotide polymorphisms (SNPs) and the required dose of warfarin, an anticoagulant. However, the association between VKORC1 SNPs and ischemic cerebrovascular disease (ICVD) has not been defined. This case-control study involved 370 patients with ICVD and 408 healthy individuals (controls) from Chinese Han population. Two VKORC1 gene SNPs (1639A/G and 1173T/C) were genotyped by PCR-RFLP method. The G allele frequencies of the 1639A/G locus and C allele frequencies of the 1173T/C locus were higher in the ICVD group than in the control group (p = 0.014 and p = 0.008, respectively). Haplotype analysis showed that 1639G-1173C was associated with an increased risk of ICVD (odds ratio (OR) = 1.163, 95 % confidence interval (CI) = 1.137~2.288), while 1639A-1173T was associated with decreased risk of ICVD (OR = 0.620, 95 % CI = 0.437~0.880). Our findings suggested that individuals carrying the 1639G or 1173C allele might be at increased risk for ICVD. Furthermore, the 1639G-1173C haplotype was a risk factor for ICVD, and 1639A-1173T was a protective factor in Chinese Han population.

A novel risk haplotype of ALOX5AP gene is associated with ischemic stroke in Chinese Han population.

Previous studies have implicated that two at-risk haplotypes (HapA and HapB) of gene-encoding 5-lipoxygenase-activating protein (ALOX5AP) were significantly associated with stroke. The aim of this study was to explore the association between haplotypes of ALOX5AP gene and risk for ischemic stroke (IS) in Chinese Han population. A total of 492 patients with IS and 490 matched control subjects were recruited. Six ALOX5AP SNPs (SG13S377, SG13S114, SG13S41, SG13S89, SG13S32 and SG13S35) were genotyped by SNaPshot minisequence technique. A common genetic variant SG13S114/AA in the ALOX5AP gene was associated with IS in this Chinese cohort (OR = 2.514, 95 % CI = 1.667 ~ 3.790). HapA (TGA) and HapB (AAAG) had no significant difference in the patients (36.3 and 18.5 %, respectively) and controls (37.6 and 16.3 %, respectively) (P = 0.631 and P = 0.375, respectively). But, the frequency of Hap (GAAG) was significantly higher in the patients than that in the controls after Bonferroni's adjustment (P = 0.006). To conclude, SG13S114/AA of the ALOX5AP gene was associated with an increased risk for IS. A novel risk haplotype, Hap (GAAG) was a genetic risk factor for IS in this Chinese population.

Evaluation of 96 SNPs in 14 populations for worldwide individual identification.

Great advances have been made recently in searching for individual identification single-nucleotide polymorphisms (IISNPs or IDSNPs). Such SNPs as suggested by SNPforID scientists and by Pakstis et al., are promising, although they were selected from older or smaller databases rather than the most recent database. Here, we describe a new computational strategy for developing IDSNPs based on HapMap. We searched through HapMap r27 for SNPs having minor allele frequencies ≥0.30 in all its 11 populations and found more than 1881 qualified SNPs. We examined 96 of them with 183 DNA samples from three Chinese populations using Illumina arrays. The average allele frequency for these 96 SNPs among the three populations was 0.495/0.505, the average number of identical SNP genotypes shared by two individuals among the 14 populations (three Chinese and 11 HapMap) was 37.9, and the random matching probability for two unrelated Hans to match in all 96 genotypes was 9.793 × 10(-39). Thus, most of these 96 SNPs are universally applicable.

Sex-dependent association of phosphodiesterase 4D gene polymorphisms with ischemic stroke in Henan Han population.

BACKGROUND: Recent evidence has implicated the gene for phosphodiesterase 4D (PDE4D) as susceptibility gene for ischemic stroke (IS) in Icelandic population. However, there are few reports on the associations between PDE4D gene polymorphisms and IS in Chinese individuals. The present study aimed to investigate the possible association of genetic polymorphisms in PDE4D gene with IS in Henan Han population. METHODS: A total of 400 patients with IS and 400 matched controls were examined using a case-control design. Two single nucleotide polymorphism (SNPs) (rs918592 and rs2910829) in PDE4D gene were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Odds ratios (OR) and 95% confidence intervals (95%CI) were calculated to test the association between the genetic factors and IS. Genetic parameter and association studies were carried out with SPSS 16.0. RESULTS: Among the two SNPs tested, the rs918592 was significantly associated with IS (OR: 1.351, 95%CI: 1.110 - 1.645), especially in male patients (OR: 1.427, 95%CI: 1.105 - 1.844). Haplotype analysis showed that A-T was associated with an increased risk of the IS (OR: 2.114, 95%CI: 2.005 - 2.230) while G-T was associated with decreased risk of IS (OR: 0.419, 95%CI: 0.302 - 0.583). Protecting effect of haplotype G-T was also significant in males (OR: 0.264, 95%CI: 0.162 - 0.431). CONCLUSIONS: The present study demonstrated a strong association of rs918592 with IS. Haplotype A-T increased the risk of IS while haplotype G-T had a protective effect in Henan Han population. The association was sex-dependent with male patients showing stronger effect.

HCV subtype characterization among injection drug users: implication for a crucial role of Zhenjiang in HCV transmission in China.

BACKGROUND: HCV transmission is closely associated with drug-trafficking routes in China. However, the transmission route of HCV in Eastern China remains unclear. Here, we investigate the role of Zhenjiang city of Jiangsu province, an important transportation hub linking Shanghai with other regions of China, in HCV transmission. METHODOLOGY/PRINCIPAL FINDINGS: A total of 141 whole blood samples were collected from injection drug users (IDUs) in Zhenjiang and then tested for HCV infection. Of them, 115 HCV positive plasmas were subjected to RNA extraction, RT-PCR amplification, and sequencing. The subtype characterization and the evolutionary origin of HCV strains circulating in Zhenjiang were determined using polygenetic or phylogeographic analyses. Seven HCV subtypes 1b, 2a, 3a, 3b, 6a, 6e and 6n were detected among Zhenjiang IDUs, showing a complex HCV epidemic. The most predominant subtypes were 3a (38%) and 1b (26.8%). Among these subtypes, subtypes 3b, 6n and 6e originated from Southwestern China (i.e., Yunnan and/or Guangxi), subtypes 2a and 6a from Southern China (i.e., Guangdong), subtype 1b from Central (i.e., Henan) and Northwestern (i.e., Xinjiang) China, and subtype 3a from Southwestern (i.e., Yunnan) and Northwestern (i.e., Xinjiang) China. From Zhenjiang, subtypes 1b and 2a were further spread to Eastern (i.e., Shanghai) and Northern (i.e., Beijing) China, respectively. CONCLUSIONS/SIGNIFICANCE: The mixing of seven HCV subtypes in Zhenjiang from all quarters of China indicates that as an important middle station, Zhenjiang plays a crucial role in HCV transmission, just as it is important in population migration between other regions of China and Eastern China.

High Prevalence of Hepatitis C virus Among Injection Drug Users in Zhenjiang, Jiangsu, China.

The constant increase in the number of drug users and rapidly spread of Hepatitis C virus (HCV) and Human immunodeficiency virus (HIV) among drug users result in a serious public health problem in China. To investigate HCV prevalence among drug users in Zhenjiang city, Jiangsu, China, 207 drug users from Zhenjiang were enrolled in this study during 2009 and the prevalence of HCV, HIV and syphilis infection were detected. HCV prevalence among injection drug users (IDUs) was 81.6%, significantly higher than that (22.9%) among oral drug users (P < 0.001), suggesting a strong association of HCV infection with injection drug use (IDU). Most drug users were more than 25 years old (89.2%), single (60.5%, including single and divorced/widowed), and had a history of drug abuse over 6 years (92.9%). HCV prevalence among drug users with middle (72.6%) or high (83.8%) school diplomas was significantly higher than that among those with lower (46.9%) education level (P = 0.007). HCV prevalence among IDUs did not obviously change along with the increase in duration of drug use and in frequency of injection per day, suggesting less association of HCV infection with both variables. These results suggest that most Chinese addicts might start drug use after their middle/high school education. To reduce drug use and to prevent HIV and HCV transmission via IDU, large-scale drug prevention educations should be urgently conducted in all China's middle and high schools.