Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia.

BACKGROUND: Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. METHODS: This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7-13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. RESULTS: The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). CONCLUSION: The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.

Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform.

Genetic polymorphisms of enzymes and transporters associated with the absorption, distribution, metabolism, and elimination (ADME) of drugs are one of the major factors that contribute to interindividual variations in drug response. In the present study, we aimed to elucidate the pharmacogenetic profiles of the Korean population using the Affymetrix Drug Metabolizing Enzyme and Transporters (DMET™) platform. A total of 1,012 whole blood samples collected from Korean subjects were genotyped using the DMET™ plus microarray. In total, 1,785 single nucleotide polymorphism (SNP) markers for 231 ADME genes were identified. The genotype and phenotype of 13 clinically important ADME genes implemented in the Clinical Pharmacogenetics Implementation Consortium guidelines were compared among different ethnic groups. Overall, the genotype frequencies of the Korean population were similar to those of the East Asian population. Several genes, notably CYP2C19 and VKORC1, showed marked differences in Koreans compared to Europeans (EURs) or Africans (AFRs). The percentage of CYP2C19 poor metabolizers was 15% in Koreans and less than 3% in EURs or AFRs. The frequencies of causative SNPs of the VKORC1 gene for the low warfarin dose phenotype were 90%, 60%, and 10% in Koreans, EURs and AFRs, respectively. Our findings can be utilized for optimal pharmacotherapy in Korean patients.

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.

Identification of genomic imbalances in oral clefts.

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.

Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer.

The silencing of tumor suppressor genes by promoter CpG island (CGI) methylation is an important cause of oncogenesis. Silencing of MLH1 and BRCA1, two examples of oncogenic events, results from promoter CGI methylation. Interestingly, both MLH1 and BRCA1 have a divergent promoter, from which another gene on the opposite strand is also transcribed. Although studies have shown that divergent transcription is an important factor in transcriptional regulation, little is known about its implication in aberrant promoter methylation in cancer. In this study, we analyzed the methylation status of CGI in divergent promoters using a recently enriched transcriptome database. We measured the extent of CGI methylation in 119 colorectal cancer (CRC) clinical samples (65 microsatellite instability high [MSI-H] CRC with CGI methylator phenotype, 28 MSI-H CRC without CGI methylator phenotype and 26 microsatellite stable CRC) and 21 normal colorectal tissues using Infinium MethylationEPIC BeadChip. We found that CGI within divergent promoters are less frequently methylated than CGI within unidirectional promoters in normal cells. In the genome of CRC cells, CGI within unidirectional promoters are more vulnerable to aberrant methylation than CGI within divergent promoters. In addition, we identified three DNA sequence motifs that correlate with methylated CGI. We also showed that methylated CGI are associated with genes whose expression is low in normal cells. Thus, we here provide fundamental observations regarding the methylation of divergent promoters that are essential for the understanding of carcinogenesis and development of cancer prevention strategies.

[Correlation analysis between the progression of HIV infection and HLA polymorphism].

Objective: To analyze the polymorphisms of human leukocyte differentiation antigens Ⅰ and Ⅱ (HLA-A, B, DRB1) alleles and explore the association between HIV infection and HLA loci, for discovering the distribution of HLA loci in HIV-infected with different disease progression in different parts of Henan Province. Methods: A total of 48 cases of slow progressers and 80 typical progressers in Weishi County, Shangcai County, Xihua County and Xuchang City of Henan Province were studied, and compared with 380 healthy blood donors.For analyzing HLA-A, B, DRB1 alleles and comparing difference among the study subjects, the method of polymerase chain reaction-sequence special oligonucleotide (PCR-SSO) was used. Results: The association of HLA alleles and HIV infection showed that HLA-B*40∶02, HLA-DRB1*04∶05 was significantly more common in healthy people, while HLA-B*15∶18, B*44∶02, B*67∶01 and HLA-DRB1*14∶01 were present in HIV/AIDS.HLA-A*02∶06, HLA-B*13∶02, B*40∶06 in slow progressers were higher than typical progressers from the grouped study, and HLA-B*46∶01 only appeared in the typical progressers. Conclusion: HLA-B*15∶18, B*44∶02, B*67∶01, and HLA-DRB1*14∶01 may be associated with HIV susceptibility.HLA-A*02∶06, HLA-B*13∶02, and B*40∶06 may be associated with delayed disease progression in HIV-infected people, while HLA-B*46∶01 may be associated with accelerated disease progression.

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.

Effect of acupuncture at Renying (ST 9) on gene expression profile of hypothalamus in spontaneously hypertensive rats.

OBJECTIVE: To investigate changes in gene expression profiles in the hypothalamus related to the effects of acupuncture at the Renying (ST 9) acupoint in spontaneously hypertensive (SH) rats. METHODS: We randomly divided 18 SH rats into Renying (ST 9) group and model control group, 9 body weight-matched Wistar-Kyoto rats were used as blank controls. Acupuncture was performed manually for 20-min daily over 28 d in the Renying (ST 9) group. Rat Gene 2.0 array technology was used for the determination of gene expression profiles and the screened key genes were verified by real-time quantitative polymerase chain reaction (RT-PCR) analyses. RESULTS: The different groups exhibited differential gene expression: compared with the blank control group, 48 genes were up-regulated and 91 genes were down-regulated in the model group; compared with the model group, 79 genes were up-regulated and 80 genes were down-regulated in Renying (ST 9) group. The RT-PCR results of the key genes including Chi3l1, Ephx2, Klk1, 5-HT1A and Cbs were consistent with that of gene chip analysis. CONCLUTION: Acupuncture at Renying (ST 9) could significantly lower the blood pressure of SH rats and affect their hypothalamic gene expression profile. Genes associated with the contraction of vascular smooth muscle and the regulation of inflammation, neurotransmitters may be involved in acupuncture's antihypertensive mechanism.

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.

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.

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.

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 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.

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.

The Genetic Basis of Peyronie Disease: A Review.

INTRODUCTION: Peyronie disease (PD) is a progressive fibrotic disorder of the penile tunica albuginea that results in fibrotic penile plaques and can lead to penile deformity. Characterized by aberrant fibrosis resulting in part from the persistence of myofibroblasts and altered gene expression, the molecular factors underpinning PD and other related fibrotic diatheses are just being elucidated. A genetic link to PD was first identified three decades ago using pedigree analyses. However, the specific genetic factors that predispose patients to aberrant fibrosis remain unknown, and the relations between these fibrotic conditions and other heritable diseases, including malignancy, are uncharacterized. AIM: To review the current landscape linking molecular and genetic factors to aberrant fibrosis in PD and related fibrotic diatheses, including Dupuytren disease. METHODS: Review and evaluation of the literature from 1970 to the present for genetic factors associated with PD were performed. MAIN OUTCOME MEASURES: Data describing the genetic factors associated with PD were obtained. RESULTS: We describe the known structural chromosomal abnormalities and single-nucleotide polymorphisms associated with fibrotic diatheses and discuss the spectrum of differential gene expression data comparing normal tissues with those derived from men with PD or Dupuytren disease. We discuss epigenetic mechanisms that might regulate gene expression and alter predisposition to fibrosis. CONCLUSION: Although the current understanding of the genetic factors associated with PD is limited, significant advances have been made during the past three decades. Further research is necessary to provide a more comprehensive understanding of the landscape of genetic factors responsible for the development of PD.

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.

A combined omics approach to evaluate the effects of dietary curcumin on colon inflammation in the Mdr1a(-/-) mouse model of inflammatory bowel disease.

The aim of this study was to provide insight into how curcumin reduces colon inflammation in the Mdr1a(-/-) mouse model of human inflammatory bowel disease using a combined transcriptomics and proteomics approach. Mdr1a(-/-) and FVB control mice were randomly assigned to an AIN-76A (control) diet or AIN-76A+0.2% curcumin. At 21 or 24weeks of age, colonic histological injury score (HIS) was determined, colon mRNA transcript levels were assessed using microarrays and colon protein expression was measured using 2D gel electrophoresis and LCMS protein identification. Colonic HIS of Mdr1a(-/-) mice fed the AIN-76A diet was higher (P<.001) than FVB mice fed the same diet; the curcumin-supplemented diet reduced colonic HIS (P<.05) in Mdr1a(-/-) mice. Microarray and proteomics analyses combined with new data analysis tools, such as the Ingenuity Pathways Analysis regulator effects analysis, showed that curcumin's antiinflammatory activity in Mdr1a(-/-) mouse colon may be mediated by activation of α-catenin, which has not previously been reported. We also show evidence to support curcumin's action via multiple molecular pathways including reduced immune response, increased xenobiotic metabolism, resolution of inflammation through decreased neutrophil migration and increased barrier remodeling. Key transcription factors and other regulatory molecules (ERK, FN1, TNFSF12 and PI3K complex) activated in inflammation were down-regulated by dietary intervention with curcumin.