Identification of genomic imbalances in oral clefts

Abstract Objective This article presents a clinical and cytogenomic approach that focuses on the diagnosis of syndromic oral clefts (OCs). Methods The inclusion criteria were individuals with OC presenting four or more minor signs and no major defects (non-syndromic oral clefts [NSOCs]) as well as individuals with OC presenting at least another major defect, regardless of the number of minor signs (syndromic oral clefts [SOCs]). The exclusion criteria included NSOC with less than four minor signs, SOC with known etiology, as well as atypical oral clefts. Results Of 1647 individuals with OC recorded in the Brazilian Database of Craniofacial Anomalies, 100 individuals were selected for chromosome microarray analysis (CMA). Among these, 44 individuals were clinically classified as NSOC and 56 as SOC. CMA was performed for both groups, and abnormal CMA was identified in 9%, all previously classified as SCO. The clinical and CMA data analyses showed a significant predominance of abnormal CMA in individuals classified as SOC (p = 0.0044); prematurity, weight, length, and head circumference at birth were significantly lower in the group with abnormal CMA. Besides, minor signs were significantly higher in this group (p = 0.0090). Conclusion The rigorous selection of cases indicates that the significant variables could help in early recognition of SOC. This study reinforces the importance of applying the CMA technique to establish the diagnosis of SOC. This is an important and universal issue in clinical practice for intervention, care, and genetic counseling.

Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri

Background: Gene expression analysis via microarray is widely used in phytobacteria to validate differential gene expression associated with virulence or to compare biological profiles of wild type and mutant strains. Here, we employed DNA microarrays to study the early stages of the infection process (24, 72 and 120 h post-inoculation) of Xanthomonas citri subsp. citri (Xac) infecting Citrus sinensis to interrogate the expression profiles of hypothetical genes. Results: Under infective conditions, 446 genes were up- and 306 downregulated. Outstanding among genes upregulated during infection were those involved in synthesizing the Type 3 Secretion System and effectors, xanthan gum and quorum-sensing induction, and flagellum synthesis and regulation. Additionally, 161 hypothetical genes were up- and 100 were downregulated, 49 of which are known to have a significant biological role. To understand hypothetical gene co-regulation or -expression, nine expression profiles including 158 genes were identified during the three infection phases. Of these, 47 hypothetical genes were identified as having expression profiles associated with at least one connected to a gene associated with adaptation and virulence. Conclusions: Expression patterns of six differentially expressed genes were validated by quantitative reverse transcription polymerase chain reaction, thus demonstrating the effectiveness of this tool in global gene expression analysis in Xac.

Identify the molecular target of nasopharyngeal carcinoma by bioinformatics analysis / 天津医药

Objective To study the pathogenesis of nasopharyngeal carcinoma and identify potential biomarkers or therapeutic targets. Methods Microarray data (GSE12452 and GSE13597) were downloaded from Gene Expression Omnibus. Processing of original microarray data and screening of differentially expressed genes were performed through bioinformatics analysis. Then, GO and KEGG pathway enrichment analysis was performed for these genes using DAVID database. Real time-PCR and Western blot assay were used to detect the expression levels of the identified genes. Results A total of 260 overlap DEGs were obtained including 16 GO entries and 4 signal pathways. Eighteen potential therapeutic targets that relative to cell cycle were identified by gene enrichment analysis. Expression levels of 12 selected genes were confirmed by real-time PCR. Finally, 4 selected genes were confirmed by Western blot assay. Conclusion By bioinformatics analysis of two sets of microarray data and molecular biology research, four genes were found including CDC6, CDK1,MCM2 and CCNB1, which might be potential key genes that can be developed for therapy targets of NPC in the future.

Sequencing analysis of HPV-other type on an HPV DNA chip

OBJECTIVES: To identify the specific human papillomavirus (HPV) genotypes from HPV-other type on an HPV DNA chip test by sequencing. METHODS: Among 13,600 women undergoing a routine gynecology examination including Pap smear and/or HPV test by DNA chip test in the healthcare system at Gangnam Center from July 2012 to February 2013, we prospectively collected and performed sequencing for a total of 351 consecutive cervicovaginal samples consisting of 180 samples that tested positive for HPV-other type and 171 samples that tested positive for either high-risk HPV or low-risk HPV. RESULTS: Of a total of 351 samples, individual HPV genotypes were successfully sequenced in 215 cases: 119 HPV-other type, 82 HPV-high-risk, and 14 HPV-low-risk. Based on the sequencing for 119 HPV-other type samples, 91.6% were detected as HPV types that were not included on the DNA chip; however, 7.6% (9/119) were proven to be high-risk HPV types: HPV 18 (n=4), HPV 33 (n=3), HPV 35 (n=1), and HPV 59 (n=1). For correlation analysis of all high-risk and HPV 16/18, the correlation rate was 76.2% and 86.6% with kappa-value of 0.38 and 0.69, respectively. CONCLUSION: HPV-other type on DNA chip test may still have possibility of high-risk HPV, i.e., HPV 18 and thus the significance of HPV-other type in detecting cervical disease remains to be investigated.

Effects of propranolol on in vitro cultured hemangioma endothelial cells and their mechanisms / 中华皮肤科杂志

Objective To evaluate effects of propranolol on the proliferation and apoptosis of in vitro cultured hemangioma endothelial cells (HemEC),and to explore their molecular mechanisms.Methods Hemangioma tissues were resected from 7 children with proliferative hemangioma,and used for in vitro culture of HemEC.Meanwhile,cultured human umbilical vein endothelial cells (HUVEC) served as controls.The 2 kinds of cells were treated with propranolol at different concentrations of 0,25,50,75,100,125 and 150 μmol/L for 24,48 and 72 hours separately.Methyl thiazolyl tetrazolium (MTT) assay was performed to evaluate cellular proliferative activity,and flow cytometry to determine the apoptosis rate.Some cultured HemEC were divided into 2 groups to be treated with 100 μmol/L propranolol-containing culture medium (propranolol group) and culture medium alone (blank control group),respectively,for 18 hours.Total RNA in the 2 groups was extracted separately.Differentially expressed genes in HemEC between the above 2 groups were identified by DNA microarray technology,and verified by real-time quantitative PCR.Results The treatment with 25 μmol/L propranolol for 24 and 48 hours caused a slight proliferation of HemEC (P ＜ 0.05).The survival rate of HemEC was decreased after the treatment with propranolol at the concentration of ≥ 100 μmol/L for more than 24 hours,while the proliferation of HUVEC was inhibited by the treatment with propranolol at the concentration of ≥ 100 μ mol/L for more than 48 hours.During 24-72 hours of treatment with 100-150 μmol/L propranolol,the survival rates of HemEC were significantly lower than those of HUVEC (P ＜ 0.05).After the treatment with 100-150 μmol/L propranolol,the apoptosis rate of HemEC gradually increased with the increase in treatment duration and concentrations of propranolol (all P ＜ 0.05).Compared with the blank control group,186 differentially expressed genes (＞ 1.5-fold changes) were screened out by DNA microarray technology,including 128 upregulated genes and 58 down-regulated genes.Real-time quantitative PCR showed that the mRNA expression of proprotein convertase subtilisin/kexin type 9 (PCSK9) and fatty acid binding protein 3 (FABP3) in the propranolol group were (9.88 ± 2.19) and (21.90 ± 8.18) times that in the blank control group respectively (t =7.028,4.427 respectively,P ＜ 0.05).Conclusions Propranolol at high concentrations can inhibit the proliferation of HemEC and HUVEC,and its inhibitory effect on HemEC is stronger than that on HUVEC.The inhibitory effect of propranolol on HemEC may be related to the inhibition of HemEC proliferation and promotion of HemEC apoptosis.

Comparative study of the different methods of small RNA high-throughput sequencing library preparation in human brain tissues / 中华老年医学杂志

Objective The aim of this study is to investigate the effects of the initial amount of total RNA input,adapter dilution and PCR amplification cycles on the results of small RNA library preparation and high-throughput sequencing.Methods Based on the sequencing reads number,the number of detected miRNAs and the accuracy of quantitative detection,we explored the effects of initial Total RNA,dilution ratio and PCR cycles on the quality of microRNA library preparation and high-throughput sequencing,respectively.Results For libraries preparation of the normal RNA input(1 μg),the adapter dilution combined with 22 PCR cycles could gain the best quality of sequencing.In the low-input libraries(10 ng),adapter dilution and increased PCR cycles would also improve the quality of sequencing,but as compared with the 1 μg library,there was lower correlation with microarray quantitative results in general.Conclusions The initial amount of RNAs input has the biggest effects on the quality of sequencing,and the quantity accuracy rate of low-input libraries is lower than the normal libraries generally.Increasing the PCR amplification cycles properly is indispensable to low-input libraries.

Pathogenesis of t(8;21) acute myeloid leukemia and the progress of next generation sequencing technique in leukemia / 解放军医学杂志

Acute myeloid leukemia (AML),the most common disease in acute leukemia,is a highly heterogeneous invasive hematological disease.The t(8;21)(q22;q22) translocation is the most common chromosomal translocation in AML,generating AML1-ETO fusion gene and encoding AML1-ETO fusion protein.This article summarizes the two-hit hypothesis in AML occurrence,the pathogenesis of t(8;21)AML,all features involved in t(8;21)AML,and the function of the components in AML1-ETO fusion protein,providing important basic information for the treatment and prognosis of t(8;21)AML.Meanwhile,this article also summarizes the progress of next generation sequencing technique in leukemia,providing a new technique for the accurate therapy of (8;21)AML.

Expression and clinical study of Lin28A/B in head and neck squamous cell carcinoma / 中国耳鼻咽喉头颈外科

OBJECTIVE Through the research of analyzing the expression level of Lin28A/B proteins in tissues of head and neck squamous cell carcinoma and the expression of the downstream miRNA genes in order to provide a new clue for the diagnoses and treatment of the head and neck squamous cell carcinoma.METHODS A retrospective study was performed in 20 patients with head and neck squamous cell carcinoma and the clinical data were recorded.The expression level of Lin28A/B proteins were detected by immunohistochemistry in HNSCCs tissues and their matched normal tissues.tThe expression level of miRNA were analyzed in 6 HNSCC patients and other 6 patients with benign pathological changes,with the application of gene chips to detect the expression.Methods of Western Blot and RT-PCR were both utilized to detect expression levels of proteins and transcriptive levels of miRNAs correspondingly,in Scc23,Tca8113 and FADU cell lines.RESULTS Over-expression of Lin28A/B were found in head and neck squamous cell carcinoma tissues and the expression had a significant relation to advanced stage or lymph node metastasis.In addition,Lin28A was expressed in cytoplasm,while Lin28B was expressed in the nucleus.Correspondingly,in miRNA array,downregulated let-7a,let-7b,let-7g and let-7f-1 were detected in HNSCCs compared with the control group.In vitro study,the over-expression of Lin28A/B was found in Scc23 and Tca8113.The results of the CE and NE confirm that Lin28A was expressed in cytoplasm,while Lin28B was expressed in the nucleus and the results were consistent with that of Immunohistochemistry.On the contrary,RT-PCR showed that Let-7a transcription was relatively low in Scc23 and Tca8113 0.46±0.02 and 0.60±0.13.CONCLUSION As a RNA-binding protein,Lin28A/B selectively inhibit the biosynthesis of let-7 family.This study showed that the overexpression of Lin28A/B in head and neck squamous cell carcinoma tissues were related to the level of malignancy and the abnormal expression of let-7 family were also found.In contrast to the Lin28A,the Lin28B was expressed in the nucleus and this result provides some new idea for the further study of functional researches and expanding experiments in next step.

Differential expression of autophagy-related genes in melanocytes under oxidative stress / 中华皮肤科杂志

Objective To evaluate the effect of hydrogen peroxide (H2O2) on autophagy in melanocytes,and to explore its possible regulatory mechanisms.Methods Normal human melanocytes at exponential growth phase were divided into several groups:blank control group receiving no treatment,positive control group treated with 100 nmol/L sirolimus solution,and experiment groups treated with H2O2 solution at different volume fractions of 10-7-10-3 respectively.After 4-hour treatment,cell counting kit-8 (CCK-8) assay and flow cytometry were performed to evaluate the cellular proliferative activity and detect apoptosis of melanocytes respectively.Acridine orange staining was performed to detect autophagosome formation,transmission electron microscopy to observe ultrastructural changes of autophagosomes,and Western blot analysis to measure the expression of autophagy-specific protein Beclin 1 and microtubuleassociated protein 1 light chain 3B (LC3B).A total of 84 autophagy-related genes were analyzed by RT2 Profiler PCR Array,so as to screen differentially expressed autophagy-related genes.Results After the treatment with H2O2 at different volume fractions of 10-3,5 × 10-4,10-4,5 × 10-5,10-5,5 × 10-6 and 10-6,experiment groups showed significantly decreased cellular proliferative activity,but significantly increased apoptosis rate compared with the blank control group (F =286.95,301.23,respectively,both P ＜ 0.05).With the increase in volume fractions of H2O2,the cellular proliferative activity was significantly gradually decreased (P ＜ 0.05),while the apoptosis rate showed an opposite trend (P ＜ 0.05),except that the 5 ×10-6 H2O2 group showed no significant differences in the apoptosis rate compared with the 10-5 H2O2 group and 10-6 H2O2 group.Acridine orange staining and electron microscopy showed autophagosome formation in the 10-5 H2O2 group,10-6 H2O2 group and positive control group.Western blot analysis revealed that Beclin1 expression and LC3B-Ⅱ/LC3B-Ⅰ ratio were significantly higher in the 10-5 H2O2 group,10-6 H2O2 group and positive control group than in the blank control group (all P ＜ 0.05).RT2 Profiler PCR Array showed significant up-regulation of ATG12,ATG3,ULK1,PIK3CG,PTEN and PIK3C3 genes and significant downregulation of EIF2AK3 gene in the 10-5 H2O2 group,10-6 H2O2 group and positive control group compared with the blank control group.In the 10-5 H2O2 group and positive control group,the mTOR gene was significantly up-regulated,and the ULK2 gene was significantly down-regulated.The 10-6 H2O2 group showed no obvious changes in the expression of mTOR gene,but significant up-regulation of AMPK and JNK1 genes.Conclusion H2O2 at volume fractions of 10-5 and 10-6 can induce autophagy in melanocytes,likely by influencing the expression of some related signaling molecules.

Gene expression profiling and functional analysis of cerebral artery after experimental subarachnoid hemorrhage / 天津医药

Objective To explore the difference of gene expression profiling between normal basilar arteries and basilar arteries of cerebral vasospasm (CVS) after subarachnoid hemorrhage (SAH) in rabbits. Methods cDNA chip of normal basilar arteries and basilar arteries of CVS after SAH in rabbits were downloaded from GEO database. The chip was analyzed and screened by Bioconductor software, and function enrichment and pathway analysis of the differentially expressed genes were analyzed by Cytoscape software. Then 6 adult male Japanese rabbits were used, and randomly divided into normal control group (n=3) and SAH model group (n=3). Rabbit SAH models were established by cisterna secondary-blood-injection method. RNA data of normal basilar artery specimens on the 0 day and basilar artery specimens after SAH on the 5-day were used to validate the parts of differentially expressed genes by qRT-PCR. Results A total of 4356 differentially expressed genes were found in normal basilar arteries and basilar arteries of CVS after SAH in rabbits. Among them, 920 genes were considered to be significant with P-value<0.05, such as GRIK1, MYH13, ZNF45, SAA3, RLN1, MSR1 and others. Function enrichment analysis indicated that the differentially expressed genes were involved in regulation of Ca2+transmembrane transporter activity, negative regulation of ion transmembrane transport, regulation of potassium ion transport, positive regulation of JAK-STAT signaling cascades and other biological processes. Pathway analysis showed that calcium signaling pathway, cGMP-PKG signaling pathway, HIF-1 signaling pathway, PI3K-Akt signaling pathway and other signaling pathways maybe related with the differentially expressed genes. qRT-PCR verification showed that the expression of MSR1 in SAH model group was consistent with that of the chip result. Conclusion The gene expressions of basilar arteries of CVS after SAH in rabbits are significantly different, and MSR1 gene can be used as a potential target for studying the pathological mechanism of CVS.

Expression profiles of Th17 pathway-related genes in patients with syphilis serofast reaction analyzed by PCR-Array technique / 中华微生物学和免疫学杂志

Objective To detect the expression of Th17 pathway-related genes in patients with syphilis serofast reaction and to investigate the mechanism of Th17 cells in syphilis serofast reaction. Meth-ods Peripheral blood samples were collected from patients with syphilis serofast reaction ( n=8 ) , patients who were syphilis-seronegative after treatment (n=8) and healthy subjects (n=8). Total RNA was extrac-ted from each blood sample and then reversely transcribed into cDNA. PCR-Array analysis was performed to quantify the expression levels of Th17 pathway-related genes. Results The expression levels of genes with a fold change >2 (up or down regulated) were defined as differentially expressed. (1) Compared with the control group, the patients with syphilis serofast reaction showed increased expression of genes encoding fork-head box protein 3 (Foxp3) and IL-10, but decreased expression of genes encoding C-C motif chemokine 22 (CCL22), colony stimulating factor 2 (CSF2), CSF3, chemokine (C-X-C motif) ligand 6 (CXCL6), IL-17A, IL-17D, IL-21, IL-23R, IL-9, interferon regulatory factor 4 (IRF4), RAR-related orphan receptorα( RORα) , RAR-related orphan receptor γ ( RORγ) and signal transducer and activator of transcription 3 (STAT3). (2) Compared with the seronegative syphilis group, the expression levels of genes encoding Foxp3 and IL-10 in patients with syphilis serofast reaction were up-regulated, while the expression of genes encoding CCL22, CSF2, CSF3, IL-17A, IL-21, IL-23R, IRF4, RORγ and STAT3 were down-regulated. (3) The expression levels of genes encoding CXCL6 and IL-9 in seronegative syphilis group were lower than those in control group. Conclusion The abnormal expression of Th17 pathway-related genes might relate to the pathogenesis of serofast state of syphilis.

Screening of Alzheimer's disease-associated gene expression changes through peripheral blood monocytes extracted gene microarray analysis in patients with Alzheimer's disease / 中华老年医学杂志

Objective To screen the amyloid protein-β(Aβ)degradation-associated genes through peripheral blood monocytes(PBMC)-extracted gene microarray analysis in patients with Alzheimer's disease(AD).Methods PBMC were isolated from blood of elderly AD patients versus age-matched healthy individuals(control).The cDNA(mRNAs)were analyzed using gene microarray.And real-time quantitative polymerase chain reaction detection and enzyme activity analysis were used to verify the primary outcome of gene chip.Results The expression of cathepsin D mRNA in peripheral blood monocytes was 104.70±15.96 in AD patients as compared with the control group 49.86±5.19,and the activity of cathepsin D was (22 620 ± 1 389) RFU in AD versus (32 210 ± 2 284) RFU in control (both P＜0.05).Conclusions The results suggest that the decreased levels of cathepsin D could be the stage markers related to the pathophysiology of AD process.Based on the microarray data,we select cathepsin D genes for further study.

Analysis of the relationship between MTHFR C677T polymorphism and unknown reason Embryo arrest by gene chip / 中国医师杂志

Objective To investigate the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism and unexplained embryo arrest relationship.Methods By the method of gene chip analysis of MTHFR gene C677T polymorphism;select August 2014 and September 2015 in Zhoukou City Center Hospital infertility clinic unexplained Embryo arrest was more than or equal to 2 349 times pregnant women as the case group,and 421 without abortion history of health by women as the control group.The genotype and allele frequency distribution of embryo arrest and C677T MTHFR were compared between the experimental and control groups.Results MTHFR C677T genotype C/C in experimental and control groups were distributed with significant difference [P ＜ 0.001,x2 =70.484,OR =0.267,95％ CI (0.195 ～ 0.366)].Genotype C/T in experimental and control groups was distributed without significant difference [P =0.714,x2 =0.156,OR =1.06,95％ CI (0.795 ～ 1.412)].T/T genotype in experimental and control groups was distributed with significant difference [P ＜ 0.001,x2 =98.812,OR =7.961,95％ CI (5.055 ～ 12.537)].C allele in experimental and control groups was distributed with significant difference [P ＜0.001,x2 =13.287,OR =0.291,95％ CI (0.236 ～0.361)].Allele t in experimental and control group was distributed with significant difference [P ＜0.001,x2 =13.287,OR =3.431,95％ CI (2.772 ～4.246)].Conclusions Embryo arrest was not associated with C677T gene mutations in MTHFR gene,and the high expression of T/T gene might be a risk factor for women of childbearing age.

Comparison of Analytical and Clinical Performance of HPV 9G DNA Chip, PANArray HPV Genotyping Chip, and Hybrid-Capture II Assay in Cervicovaginal Swabs

BACKGROUND: Human papillomavirus (HPV) infection can be detected by using several molecular methods, including Hybrid-Capture II (HC2) assay and variable HPV DNA chip tests, although each method has different sensitivities and specificities. METHODS: We performed HPV 9G DNA Chip (9G) and PANArray HPV Genotyping Chip (PANArray) tests on 118 cervicovaginal swabs and compared the results with HC2, cytology, histology, and direct sequencing results. RESULTS: The overall and high-risk HPV (HR-HPV) positivity rates were 62.7% and 44.9% using 9G, and 61.0% and 30.5% using PANArray, respectively. The positivity rates for HR-HPV with these two chips were significantly lower than 55.1% when HC2 was used. The sensitivity of overall HPV positivity in detecting histologically confirmed low-grade cervical squamous intraepithelial lesions or higher was 88.7% for all three tests. The specificity was 58.5% for 9G and 61.5% for PANArray, which was significantly lower than the 72.3% for HC2. With the HR-HPV+ genotype threshold, the sensitivity decreased to 75.5% for 9G and 52.8% for PANArray, which was significantly lower than the 88.7% for HC2. Comparison of the two chips showed concordant results in 55.1% of the samples, compatible results in 16.9%, and discordant results in 28.0%, exhibiting poor agreement in detecting  certain HPV genotypes. Compared with direct sequencing, 9G yielded no discordant results, whereas PANArray yielded 31 discordant results (26.7%). CONCLUSIONS: Compared with HC2, the HPV genotyping tests showed lower sensitivity in histologic correlation. When the two chips were compared, the 9G was more sensitive and accurate for detecting HR-HPV than the PANArray.

Detection of disease-causing gene in a Hui congential cataract pedigree by exon combined target region capture sequencing chip / 中华实验眼科杂志

Background Congenital cataract is an important cause of blindness and amblyopia in children,and about 50％ of congenital cataract is hereditary.Objective The aim of this study was to determine the diseasecausing gene of one Hui congenital cataract pedigree by using exon combined target region capture sequencing chip of eye diseases.Methods This study was approved by Ethic Committee of Ningxia People's Hospital and followed Declaration of Helsinki.One Hui congenital cataract pedigree was recruited in Ningxia Eye Hospital in 2011.All the disease history of the members in this family were collected and recorded,and the eye examinations were performed.The peripheral blood specimens were collected from family members and 300 healthy individuals for the extraction of DNA.Exon combined target region capture sequencing chip of eye diseases was used to screen the candidate diseasecausing mutations,then PCR and direct sequencing were used to confirm the disease-causing mutations.Results This H ui family included 61 members of 6 generations,and 18 patients were diagnosed in serial 5 passages,conforming to autosomal dominant inheritance pattern.Among 18 cataract patients,7 individuals were associated with nystagmus and strabismus,and 4 patients had high myopia.Eight candidate pathogenetic mutations were detected by exon combined target region capture sequencing chip of eye diseases and bioinformatics method,with 5 mutations in noncoding regions and 3 in coding regions.The mutation P24T of CYRGD gene was confirmed as pathogenic mutation of this pedigree by using PCR and direct sequencing methods.These mutations co-segregated with affected members of the family,and the mutations were not found in the unaffected family members and 300 unrelated controls.Conclusions P24T of CYRGD gene mutation is confirmed as pathogenic mutation of this pedigree.Exon combined target region capture sequencing chip provides a new approach to detect disease-causing mutations of congenital cataract with diversity clinical phenotypes.

Bioinformatics analysis of prostate cancer metastasis with highly expressed gene VCAN based on microarray / 中国医师杂志

Objective To investigate the function and regulatory mechanisms of VCAN gene and protein in metastatic prostate cancer.Methods The data of whole genomic expression profiles got from the prostate cancer metastasis were obtained from gene expression omnibus (GEO) database,a set of bioinformatics tools,such as BRB-Array Tools,protparam,SMART,SignalP 4.0,TMHMM,NetPhos2.0,PredictProtein,SWISS-MODEL,GO,KEGG and STRING softwares were used to accomplish data-mining and bioinformatics analysis.Results There were 73 co-expressed differentially genes in prostate cancer metastasis,21 up-regulated and 52 down-regulated.Bioinformatics analysis indicated that VCAN gene encoded 3396 amino acids,VCAN was also contained one Immunoglobulin domain,two hyaluronan-binding domain,one epidermal growth factor-like domain,one calcium-binding EGF-like domain,one C-type lectin domain and one domain abundant in complement control proteins,and a furthermore analysis suggested that VCAN played essential roles in such important biological function including cell adhesion,hyaluronic acid binding,calcium-binding,glycosaminoglycan binding,extracellular matrix and cell adhesion molecules.Conclusions Bioinformatics analysis had a high efficiency in analyzing microarray data and revealing internal biology information.VCAN may play an important role in the prostate cancer metastasis,Thus,VCAN might be a novel biomarker for the diagnosis of prostate cancer metastasis or a new target for its treatment.

Application of gene chip in nephritic syndrome research / 天津医药

Nephrotic syndrome is a common kidney disease in childhood. Its pathogenesis has not been fully elucidat?ed. In recent years, gene chip is maturing and widely used in many fields. Its application in nephrotic syndrome could pro?vide important information of its pathogenesis and treatment target at gene level. This article reveiwed the current application of the gene chip technology and its prospects in the nephrotic syndrome.

Establishment of a rapid and accurate gene microarray for identifying Mycobacterium species / 重庆医学

Objective To establish a rapid and accurate method for the identification of Mycobacterium species by the gene microarray and to verify its clinical application value .Methods According to the gene sequence of 23 species of Mycobacteria ,the specific probes were designed and the gene chips were prepared .23 Mycobacterial standard strains ,9 non‐mycobacterial strains ,103 clinically isolated mycobacterial strains were detected by PCR‐based reverse blot hybridization assay in the gene chip .Results 23 mycobacterial standard strains ,9 non‐mycobacterial strains were detected by gene chip ,the results showed that the specificity was 100% .Of 103 mycobacterial clinically isolated strains ,87 strains were identified as Mycobacterium tuberculosis compounds (MTC) and 16 strains as non‐tuberculosis mycobacteria (NTM ) including 5 strains of M .abscessus ,3 strains of M .intracellulare ,3 strains of M .avium ,2 strains of M .fortuitum ,1 strain of M .kansas ,1 strain of M .marinum and 1 strain of M .gordonae .The identification results of 103 clinically isolated strains were completely consistent with the sequencing results .The lowest detection limit by this method was 103 copies/mL .Conclusion The gene microarray technique for rapidly identifying Mycobacteria and differentiate MTC and NTM has the advantages of simpleness ,rapidness ,high accuracy ,high specificity and high sensitivity .

Rapid laboratory identification of Mycobacterium abscessus / 中华检验医学杂志

Objective To identify Mycobacterium abscessus rapidly with HAIN molecular assay genotype kit、gene chip and hsp65 gene sequencing,and to assess the clinical value of these three methods.Methods 13 clinical non-tuberculous Mycobacterium (NTM) of in-patient samples were collected from January2014 to January 2015,in the Department of Clinical Laboratory,Yinzhou People's Hospital,and meanwhile,these strains were identified with HAIN molecular assay genotype Mycobacterium kit and gene chip respectively.The hsp65 gene sequencing was used as the standard method to be compared with HAIN and gene chip.Results The results of HAIN kit and hsp65 gene sequencing showed that all the 13 strains were subspecies Mycobacterium abscessus,while that of gene chip showed that these strains were Mycobacteriumchelonae complex strains,and the subtypescould not be identified.Conclusion These results obtained from the HAIN molecular assay genotype mycobacterium system are in agreement with those obtained from the hsp65 gene sequencing,whereas the HAIN kit method is easier to use.

Overexpression of Plasminogen Activator Inhibitor-1 in Advanced Gastric Cancer with Aggressive Lymph Node Metastasis / Journal of the Korean Cancer Association, 대한암학회지

PURPOSE: The purpose of this study is to investigate differentially expressed genes using DNA microarray between advanced gastric cancer (AGC) with aggressive lymph node (LN) metastasis and that with a more advanced tumor stage but without LN metastasis. MATERIALS AND METHODS: Five sample pairs of gastric cancer tissue and normal gastric mucosa were taken from three patients with T3N3 stage (highN) and two with T4N0 stage (lowN). Data from triplicate DNA microarray experiments were analyzed, and candidate genes were identified using a volcano plot that showed > or = 2-fold differential expression and were significant by Welch's t test (p < 0.05) between highN and lowN. Those selected genes were validated independently by reverse-transcriptase-polymerase chain reaction (RT-PCR) using five AGC patients, and tissue-microarray (TMA) comprising 47 AGC patients. RESULTS: CFTR, LAMC2, SERPINE2, F2R, MMP7, FN1, TIMP1, plasminogen activator inhibitor-1 (PAI-1), ITGB8, SDS, and TMPRSS4 were commonly up-regulated over 2-fold in highN. REG3A, CD24, ITLN1, and WBP5 were commonly down-regulated over 2-fold in lowN. Among these genes, overexpression of PAI-1 was validated by RT-PCR, and TMA showed 16.7% (7/42) PAI-1 expression in T3N3, but none (0/5) in T4N0 (p=0.393). CONCLUSION: DNA microarray analysis and validation by RT-PCR and TMA showed that overexpression of PAI-1 is related to aggressive LN metastasis in AGC.