Top PDF MicroRNA expression variability in human cervical tissues.

MicroRNA expression variability in human cervical tissues.

MicroRNA expression variability in human cervical tissues.

The role of miRNAs in cervical cancer is still poorly understood, however various studies have already been carried out. Lui et al. have characterized the profiles of miRNAs and other small RNA segments in six human cervical cell lines and five normal cervical samples using a direct sequencing method [15]. They found reduced expression of miR-143 and increased expression of miR-21 in 29 matched pairs of human cervical cancer and normal cervical specimens [15]. Another study showed that miRNA profiles in cervical squamous cell carcinoma depend on Drosha, which is an RNase III enzyme involved in the miRNA biogenesis pathway [16]. Martinez and co-workers have demonstrated that HPV alter the expression of miRNAs in cervical carcinoma cell lines [17]. In a fourth study, 10 early stage invasive squamous cell carcinomas (ISSC) and 10 normal cervical squamous epithelial biopsies were profiled for miRNA misexpres- sion using TaqMan real-time quantitative PCR [18]. This study identified 68 up-regulated and 2 down-regulated miRNAs between the ISCCs and normal epithelial tissues, with miR- 199s, miR-9, miR-199a*, miR-199a, miR-199b, miR-145, miR- 133a, miR-133b, miR-214 and miR-127 being among the miRNAs most overexpressed. By contrast, only two of the miRNAs, miR-149 and miR-203 showed significant down- regulation [18]. A study analyzing eight cervical cancer cell lines, two HPV16+ W12 subclones [19] and five age-matched normal cervix and cervical cancer tissues was also reported [20]. The authors showed that miR-126, miR-143 and miR-145 were down-regulated and miR-15b, miR-16, mi-146 and miR-155 were up-regulated. Their data also indicated that decreased miR- 143 and miR-145 expression and increased miR-146a expression are relevant for cervical carcinogenesis. Finally, Hu and co- workers have recently identified miR-200a and miR-9 as predictors of patient survival in cervical carcinoma [21]. These studies were unable to clarify the role of miRNAs in cervical cancer due to
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MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2.

MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2.

contribute to the metastasis of cancer cells and consequently facilitate the advanced development of human cancers like NSCLC. We further characterized ZEB2 as a functional target of miR-132 by luciferase reporter gene assays, RT-PCR and Western blot analysis, respectively. ZEB2/SIP1, as a member of the deltaEF-1 family of two-handed zinc-finger factors, is frequently expressed in a variety of human cancers, including pancreatic [31], breast [32], gastric [33,34], renal [35], head and neck [36], glioma [37], hepatocellular [38], ovarian [39], squamous and non-small cell lung carcinomas [14,15]. The important role of transcription factor ZEB2 has been strongly underlined in numerous papers, due to its function in inducing epithelial- mesenchymal transition (EMT) and facilitating the metastasis of cancer cells [37,40,41]. For instance, Nam EH, et al. reported that ZEB2 could induce EMT and invasion of human cancer cells via specifically repressing the expression of E-cateherin and up-regulating vimentin expression [42]. In addition, Cong N and his colleague found that down-regulated microRNA-200 family was able to promote EMT through wnt/b-catenin pathway by targeting E-cadherin repressors ZEB1/ZEB2 in gastric adenocarcinoma [33]. In the present study, we found that ZEB2 had a frequently high expression in metastatic NSCLC cells and clinical lymph node tissues. And ZEB2 was responsible for miR- 132-modulated migration and invasion of NSCLC cells. Notably, we observed that E-cadherin or vimentin, the downstream effector of ZEB2, was also down-regulated or up-regulated by miR-132, indicating that miR-132 may exert functions in migration and invasion of NSCLC cells through modulating EMT. These in vitro data implied the necessary contribution of attenuated miR-132 in promoting cell metastasis in cancers. Recent studies revealed an mesenchymal- epithelial transition (MET) in metastases that allowed establishment of cancer cells in a remote site [43]. However, the potential role of miR-132 in this process still need to be further illustrated.
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MicroRNAs in veterinary cardiology

MicroRNAs in veterinary cardiology

DCM is the primary cardiopathy of large dogs and has high rates of morbidity and mortality (TIDHOLM et al., 2001). Studies in man have shown that several microRNAs are involved in the pathogenesis of DCM and are used as biomarkers for the disease in human patients, such as miR-423-5p microRNA for diagnosis of heart failure secondary to DCM (IKEDA & PU, 2010; FAN et al., 2013). A study with Doberman Pinscher dogs evaluated the expression of 401 microRNAs in serum and reported no differences in expression in any animal with DCM (STEUDEMANN et al., 2013). This may be explained in part by the small number of animals in the study or by the type of sample analyzed. In contrast, several studies in people have used cardiac tissue samples instead of blood samples, since microRNAs are expressed differently in various tissues and cells (SATOH et al., 2010; POWERS et al., 2015).
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Real Time PCR and Importance of Housekeepings Genes for Normalization and Quantification of mRNA Expression in Different Tissues

Real Time PCR and Importance of Housekeepings Genes for Normalization and Quantification of mRNA Expression in Different Tissues

β-actin showed maximum variations in its expression in the blood cells, being inappropriate for standardization. For the samples of human skeletal muscles exposed to creatine supplementation on short-term and high intensity exercise, the β-actin gene was considered a valid option for real-time PCR analysis (Murphy et al. 2003). In the studies with lymphoid cells in cattle (BL-3), β-actin was stable when analyzed by the program NormFinder (Anstaett et al. 2010). In the patients undergoing renal transplantation, acute rejection and antirejection therapy, the gene β-actin is influenced in its expression, which makes it unsuitable for standardization (Gibbs et al. 2003). During the analysis of the expression of interstitial cells in the heart valves in sheep, the gene β-actin was considered invalid (Yperman et al. 2004). According to Fu et al. (2010) in normal ovarian tissue, or in ovaries with endometriomas or various types of tumors, β-actin showed low stability among the groups. Several data have shown that the genes of references, such as β- actin, depending of the tissue, may be inappropriate as internal standard because of its variability (Bustin 2002). Several authors confirmed that the β-actin used as housekeeping presented differential expression in various tissues (Selvey et al. 2001; Barber et al. 2005).
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Cigarette smoking decreases global microRNA expression in human alveolar macrophages.

Cigarette smoking decreases global microRNA expression in human alveolar macrophages.

specific polarized phenotypes. However, the extent to which these phenotypes accurately depict macrophage phenotypes in vivo has been difficult to determine, partly because purification of human macrophages from the tissues in which they are embedded is usually not possible. Human alveolar macrophages are unique in this aspect since relatively pure populations can be obtained from bronchoalveolar lavage fluid. A consistent alteration in gene expression profiles of human alveolar macrophages from cigarette smokers compared to nonsmokers has been reported by two Figure 4. Expression profiling of a second data set indicates a global repression of total miRNA abundance in alveolar macrophages of cigarette smokers. Nonsmoker, light smoker, and heavy smoker miRNA expression ratios were determined by TLDA assays using RNA from alveolar macrophages (cohort 3). The endogenous control, RNU48, was used to normalize the data. A) Smoker-to-nonsmoker expression ratios are represented by black circles (light smokers) and red circles (heavy smokers) in order from lowest to highest for 277 and 281 detected miRNAs, respectively. B) The number of miRNAs with a greater than 2-fold change between the two smoker groups and the nonsmokers are displayed.
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The differential expression of OCT4 isoforms in cervical carcinoma.

The differential expression of OCT4 isoforms in cervical carcinoma.

It is well known that human OCT4 gene functions as a master regulator for the pluripotency and self-renewal of ESCs. Recent investigations indicate that Oct4 is detected in some somatic tumors such as hepatoma [28] and breast cancer [29]. In addition, the expression level of OCT4 in HPV16-positive cervical cancer cells (HeLa and Caski) was higher than that in HPV- negative cervical cancer cells (C-33A) [7]. In our study, IHC analysis of 50 CC tissues showed that positive OCT4 staining was not only localized in the nucleus, but also in the cytoplasm, which is different from the previous description about OCT4 as a nuclear protein. OCT4 en- codes two chief isoforms that are generated by alternative splicing, OCT4A and OCT4B, com- posed of 360 and 265 amino acids, respectively. Both OCT4A and OCT4B have an N-terminal transcriptional activation domain, a central POU domain, and a C-terminal cell type-specific transactivation domain, they have identical POU DNA-binding and C-terminal transactivation domains but different N-terminus [12,20]. It is suggested that OCT4A and OCT4B can be dis- tinguished by their distinct subcellular localization [30]. To characterize OCT4 isoform and confirm their specificity and cellular localization, the polyclonal antibody SC-8629 against the C-terminus of OCT4 and mouse monoclonal antibody (SC-5279) against the N-terminus of OCT4 were used to detect nuclear OCT4A in 10 cervical cancer samples. As show in S2 Fig., both OCT4 antibodies revealed nuclear localization of OCT4 in positive control cells Tera-1 [31]. In cervical cancer samples, nuclear staining of OCT4 was detected by SC-5279 but both
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Interferon-β induced microRNA-129-5p down-regulates HPV-18 E6 and E7 viral gene expression by targeting SP1 in cervical cancer cells.

Interferon-β induced microRNA-129-5p down-regulates HPV-18 E6 and E7 viral gene expression by targeting SP1 in cervical cancer cells.

Normal cervix and cervical cancer tissues were obtained from women ranging in age from 28 to 77 years old. Four normal cervical samples were obtained from patients who underwent hysterectomy to treat other types of diseases such as myoma or adenomyosis. None of the patients had undergone hormone therapy, radiotherapy or chemotherapy before surgery. The stages and histological grades of these tumors were established according to the criteria of the International Federation of Gynecology and Obstetrics (FIGO). Each tissue sample was immediately snap- frozen in liquid nitrogen and stored at 280uC until RNA extraction. Prior written and informed consent was obtained from each patient, and the study was approved by the ethics committee of the Medical Faculty of Shanghai Jiao Tong University. Clinical and pathological data relating to the clinical samples are presented in Table 1.
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Chronological changes in microRNA expression in the developing human brain.

Chronological changes in microRNA expression in the developing human brain.

In summary, we have established the first miRNA and non- coding RNA expression atlas of the developing human brain. Expression signatures varied significantly between fetal, early postnatal, and adult brain tissue samples, analogous to patterns of temporal regulation previously observed in animal model systems. Despite attempts to match samples with respect to demographic variables, factors pertaining to sample selection and handling can skew the results of post-mortem expression studies. Experimental and statistical methods were adopted to optimize sensitivity and accuracy of measured miRNA expression levels, yet some caveats still remain. The coronal sections of cerebrum from which RNA was extracted are heterogeneous in terms of cell type. Expression levels were averaged across multiple samples from a given developmental age to minimize regional effects, but the relative contribution of specific cellular populations to detected expression levels could conceivably vary across time points. Also, average post-mortem interval was higher for postnatal compared to prenatal samples (Table 1), however our previous work demon- strates that few microRNAs (8%) have expression which is influenced by post-mortem interval [38]. Additionally, the pre- and postnatal sample set used is biased towards African-American individuals while the adult timepoints were from Caucasian individuals, which could conceivably confound results if there are large ethnic differences in microRNA expression in the brain. However, data from other tissues indicate that ethnic differences are likely to be modest [39]. Despite these caveats, the valuable expression data presented here and the proposed classification scheme should guide future studies of miRNA expression and function in both normal and pathogenic development.
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Universidade de Brasília UnB Instituto de Ciências Biológicas Departamento de Biologia Celular Perfil de expressão de miRNAs endócrinos em ilhotas pancreáticas: Modulação da sua expressão por citocinas proinflamatórias associadas com a

Universidade de Brasília UnB Instituto de Ciências Biológicas Departamento de Biologia Celular Perfil de expressão de miRNAs endócrinos em ilhotas pancreáticas: Modulação da sua expressão por citocinas proinflamatórias associadas com a

MicroRNAs (miRNA) are small non-coding RNAs that inhibit gene expression through binding to complementary messenger RNA sequences. MiRNAs have been predicted to target genes important for pancreas development, proper endocrine cell function and metabolism. We previously described that miRNA-7 (miR-7) was the most abundant and differentially expressed islet miRNA, with 200- fold higher expression in mature human islets than in acinar tissue. Here we have analyzed the temporal and spatial expression of miR-7 in human fetal pancreas from 8 to 22 weeks of gestational age (wga). Human fetal (8-22 wga) and adult pancreases were processed for immunohistochemistry, in situ hybridization, and quantitative RT-PCR of miRNA and mRNA. MiR-7 was expressed in the human developing pancreas from around 9 wga and reached its maximum expression levels between 14 and 18 wga, coinciding with the exponential increase of the pancreatic endocrine hormones. Throughout development miR-7 expression was preferentially localized to endocrine cells and its expression persisted in the adult pancreas. The present study provides a detailed analysis of the spatiotemporal expression of miR-7 in developing human pancreas. The specific localization of miR-7 expression to fetal and adult endocrine cells indicates a potential role for miR-7 in endocrine cell differentiation and/or function. Future functional studies of a potential role for miR-7 function in islet cell differentiation and physiology are likely to identify novel targets for the treatment of diabetes including the
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TNF-α mediated increase of HIF-1α inhibits VASP expression, which reduces alveolar-capillary barrier function during acute lung injury (ALI).

TNF-α mediated increase of HIF-1α inhibits VASP expression, which reduces alveolar-capillary barrier function during acute lung injury (ALI).

The release of cytokines or proinflammatory factors during the systemic inflammation in ALI injures pulmonary vascular endo- thelial cells and alveolar epithelial cells, which increases the permeability of the pulmonary capillary membrane. Consequent- ly, liquid protein permeates from the vessel lumen into the interstitial space and alveolus, followed by external respiratory dysfunction, which subsequently leads to a lethal abnormal Figure 4. VASP was downregulated via the TNF-a-induced activation of HIF-1a during acute lung injury in vivo. Balb/c mice were peritoneally injected with 0.01 mg/g LPS to model ALI or the same dose of saline in the vehicle group. The animals were treated for 0–8 hours. (A) After 0–8 hours of stimulation, the sera of the animal models were prepared via orbital blood collection, and ELISA was performed to detect the concentration of TNF-a in the serum. In the vehicle groups, the TNF-a concentration in the serum remained at a very low level (,30 pg/mL) and displayed no obvious changes over time (p.0.05 vs. vehicle). In contrast, the sera from mice treated with LPS for 0–8 hours all displayed much higher TNF-a concentrations (.450 pg/mL), which peaked at 4 hours (.700 pg/mL), compared with the vehicle groups (**p,0.01 and ***p,0.001 vs. vehicle). (B) After LPS treatment, the supernatant liquid of lung tissues was prepared from the excised left lungs, and ELISA was performed to detect the concentration of TNF-a in the lung tissues. The TNF-a concentration in the lung tissues also remained at a very low level (,0.3 pg/mg) in the vehicle groups and displayed no obvious changes over time (p.0.05 vs. vehicle). Conversely, the TNF-a concentration in the lung tissues from LPS- induced ALI mice was dramatically higher than that of the vehicle groups (.2.0 pg/mg; **p,0.01 and ***p,0.001 vs. vehicle) and peaked at 4 hours (.3.4 pg/mg). (C) The HIF-1a and VASP expression levels in mouse lung tissues were detected by western blotting. GAPDH served as a loading control. Representative blots from three independent experiments with similar results are shown. The relative protein expression levels obtained for HIF-1a or VASP/GAPDH are shown in the bar graphs. Compared with the vehicle group, the HIF-1a levels in the lung tissues were evidently elevated by 142.3% in the 4-hour group (***p,0.001) and 119.3% in the 8-hour group (**p,0.01 vs. vehicle). Correspondingly, VASP expression decreased by 43.1% in the 4-hour group (**p,0.01 vs. vehicle) and 43.5% in the 8-hour group (**p,0.01 vs. vehicle). The test was repeated three times with identical results. The data are presented as the mean 6 SEM. *p,0.05, **p,0.01, ***p,0.001.
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Signaling pathways in a Citrus EST database

Signaling pathways in a Citrus EST database

In Arabidopsis thaliana, several different genes have been associated with the ABA response including PGGT-I (Johnson et al., 2005), the gene encoding the b-subunit of protein geranylgeranyltransferase type I (PGGT I). Cross-talk between ABA and Inositol 1,4,5-triphosphate dephosphorylation is also important in this signal trans- duction since mutation in fry1, the inositol polyphosphate 1-phosphatase encoding gene, leads to super-induction of ABA- and stress-responsive genes (Xiong et al., 2002). Other genes involved in the ABA response participate in the RNA metabolism like hyl1 (Lu et al., 2002), a gene en- coding a double-stranded RNA binding protein that is re- lated to activity of MAP kinases (Lu et al., 2002); abh1 (Hugouvieux et al., 2001), a gene encoding an mRNA cap binding protein that modulates the ABA signaling by af- fecting transcription of early ABA signaling elements; and sad1, that encodes a polypeptide similar to multifunctional Sm-like snRNP proteins required for mRNA splicing, ex- port and degradation (Xiong et al., 2001). Other non-trans- cription factor-encoding genes are also involved in the ABA response such as genes encoding NADPH oxidase, rboHD and F (Kwak et al., 2003), showing that reactive ox- ygen species are second messengers in ABA signaling. Sugar signaling pathways
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Recapitulation of tumor heterogeneity and molecular signatures in a 3D brain cancer model with decreased sensitivity to histone deacetylase inhibition.

Recapitulation of tumor heterogeneity and molecular signatures in a 3D brain cancer model with decreased sensitivity to histone deacetylase inhibition.

culture; for example neurosphere medium is usually serum free and supplemented with epidermal growth factor and basic fibroblast growth factor. The RCCS aggregates are formed in the same medium as used for 2D cell culture, thus removing the influence of media composition on comparisons between RCCS and 2D culture using the same cell line. The recent demonstration of a 3D culture system with automated and quantitative analysis, similarly generates tumor spheroids with a size range of 300– 500 mm in diameter [24]. Although matrix invasion and angiogenic differentiation was induced when tumor cells were co-cultured with embryoid bodies, we believe that the ,10-fold larger RCCS aggregates display more acute cellular heterogeneity with clearly delineated proliferating rim, necrotic core and peri- necrotic rim with direct observation of hypoxic stress and senescent cells in this region. Indeed we have also shown that a proportion of RCCS brain tumor aggregates exhibit a vasculo- genic phenotype and angiogenic gene expression profile in the absence of any form of co-culture, a phenomenon termed ‘vasculogenic mimicry’ (Smith et al, manuscript in preparation). Moreover as the immediate tumor microenvironment is generated by the secretion of endogenous ECM rather than exogenous and artificial substrates, the resulting paracrine signaling and resulting global gene expression changes in the RCCS may be more informative than other 3D methods. In support of the importance of cancer cell-ECM interactions with regards to mimicking physiological aspects of tumor biology, Loessner and colleagues describe a 3D culture consisting of a sophisticated synthetic hydrogel matrix with incorporated biomimetic features. This method permitted exposure to similar biochemical and bio- mechanical stimuli in all directions due a homogenous dispersion Table 2. Differentially expressed genes amongst U87 2D/3D culture and primary HGG.
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Assessment Of NPK In Human Male And Female Urine For Its Fertilising Potential In Agriculture

Assessment Of NPK In Human Male And Female Urine For Its Fertilising Potential In Agriculture

discharge into water is reduced by about 60% irrespective of the type of treatment [10]. Pure urine is sterile but there is the likelihood of cross-contamination with the use of urine separating (Ecosan) toilets [28]. According to Jönsson et al. (2000) separated urine contains a greater part of the total nutrients in normal sewage; 80% of N, 55% of P, and 60% of K in just 1.5% of the volume of the sewage. According to Rheiberger (1936), there are comparable levels of creatine, urea and ammonia nitrogens in urine among primates such as man, mangabeys, baboons and chimpanzees. However, he identified sex differences in creatinine nitrogen coefficients of the male mangabeys, baboons and chimpanzees to be higher than those in the female counterparts. In small cases there was reversal of the magnitude seen in the macaques species precluding an assumption as to the validity of the observation. In analysing sex differences in urine with respect to lysine and α - amino nitrogen, the mean excretion of α - amino nitrogen whether ―total,‖ ―free,‖ or ―bound,‖ was higher for females than for males [22]. Thus, it is possible that the higher rate of amino acid excretion observed in females might be correlated with the sexual cycle, although no evidence of this was observed in the case of the four amino acids studied by Thompson and Kirby (1949) when samples from the same subjects were taken at various stages of the menstrual cycle. The influence of sex (gender) on the level of NPK in human urine has received no attention. Therefore, there is a need to study the effect from the Ecological Sanitation (ECOSAN) perspective, especially under local conditions. This is because gender ECOSAN urinals are going to spring up with the advent of industries and ECOSAN concepts, especially in the developing countries. The use of urine in agriculture has been studied in countries such as Sweden, Germany, Switzerland, South Africa, Burkina Faso and Nigeria. In all these studies, the fertilizing ability of human urine was established as being comparable to that of chemical fertilizers, such as 21% N ammonia. However, in Ghana little U
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Global MicroRNA Expression Profiling of Mouse Livers following Ischemia-Reperfusion Injury at Different Stages.

Global MicroRNA Expression Profiling of Mouse Livers following Ischemia-Reperfusion Injury at Different Stages.

Previous studies identified a bunch of differentially expressed genes that mediated the physi- ological and biochemical events triggered by hepatic ischemia-reperfusion injury [6–8]. For example, Toll-like receptor 4 (TLR4) was overexpressed in liver transplantation. Down-regula- tion of TRL4 attenuated liver ischemia-reperfusion injury [9]. MicroRNAs are a class of short noncoding RNA molecules (21–30 nucleotide long) widely endogenously expressed in plants, animals, and viruses [10–12], and mainly function posttranscriptionally through mRNA decay and translational repression by base-pairing to the 3’ untranslated regions of target mRNAs [10, 13–15]. Recent studies have uncovered a regulatory role of microRNAs in ischemia-reper- fusion injury in organ transplantation surgery. For example, 40 differentially expressed micro- RNAs associated with proinflammatory et al. processes were identified in ischemia-reperfusion injury post-liver transplantation [16]. Nine microRNAs were differentially expressed in renal ischemia-reperfusion injury [17]. miR-223 was up-regulated in the hepatic ischemia-reperfu- sion injury [18]. In contrast, miR-146a was down-regulated in the early stage of hepatic ische- mia-reperfusion injury [19]. Seventy-eight microRNAs with more than two fold expression difference were identified in the mice livers upon ischemia-reperfusion injury [20].
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Atrial Fibrillation associated chromosome 4q25 variants are not associated with PITX2c expression in human adult left atrial appendages.

Atrial Fibrillation associated chromosome 4q25 variants are not associated with PITX2c expression in human adult left atrial appendages.

esis is that these SNPs affect complex traits by regulating the expression of nearby genes, thus these SNPs may be classified as cis-acting expression quantitative trait loci (eQTLs). It is also challenging to determine which are the causal SNPs, as the index SNPs may not be causal but in linkage disequilibrium (LD) with causal SNPs. Recent findings from the ENCODE project show that most of the GWAS SNPs, or SNPs in strong LD with the GWAS SNPs, are within regulatory regions. These regions were identified due to their location within a DNAseI hypersensitive region or within a site in which histone modification or transcription factor binding indicates regulatory activity, as determined by chromatin-immunoprecipitation and next genera- tion sequencing [13]. We hypothesized that the four SNPs independently associated with AF in the chromosome 4q25 region would be associated with PITX2c expression. To study this, we used SNP arrays to obtain genotypes and quantitative RT-PCR (qRT-PCR) to measure PITX2c expression in left atrial append- ages obtained from 239 subjects of European ancestry, including 40 samples from subjects with no history of AF. We found that these AF-associated SNPs were not associated with PITX2c mRNA expression in adult left atrial appendages in all subjects combined, or in the subgroup of subjects with no history of AF. However, we identified several SNPs in introns of the ENPEP gene, on the opposite side of the PITX2 gene relative to the location of the AF- associated SNPs, which were modestly associated with PITX2c mRNA expression levels. Thus, the mechanism of the AF- associated SNPS on 4q25 remains unknown.
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A novel method for identification and quantification of consistently differentially methylated regions.

A novel method for identification and quantification of consistently differentially methylated regions.

differential in samples and more likely to be DMRs [17]. Unfortunately, this method lacks the statistic test for determining the significance. A quantitative approach for DMR identification and characterization (QDMR) has been proposed recently using Shannon entropy which measures variation or change in a series of events and has been applied to the study of differential expression genes [18]. In the QDMR, a pointwise method is used in which a weighted entropy score is calculated for each probe to represent the extent of methylation differences across multiple samples. Unlike ranking-based feature selection method, the QDMR provides a statistic for each probe to test the divergence of methylation levels with respect to average methylation level across samples. The methylation statuses of neighboring CpG sites are not independent of each another [7], and it is possible to have positive correlations of methylation intensities in nearby probes across the genome, especially in tiling arrays or from data using sequencing technologies that generate dense data in a specific region of the genome [19,20]. Aggregating information from neighboring probes, however, cannot be taken into account using the pointwise approach, although appropriately incorporating this information into the analysis of DMRs may reduce false positives, because the methylated fragments are always longer than the probe length used in the array. Here, Identification of Consistently Differentially Methylated Regions (ICDMR), an unsupervised approach, is proposed to directly analyze methylation intensity data generated from tiling arrays to locate DMRs across a large set of samples simultaneously. This method considers all correlations of signals between nearby probes, i.e., those that are biologically significant and those that are not. The former correlation arises from changes in DNA methylation status, whereas the latter arises from the intrinsic correlation of probes, such as the linear correlation arising from overlapping probes or from the hybridized DNA fragments spanning multiple probes on the array [21,22]. The proposed method provides a way to calculate the concor- dance between adjacent probes, where concordance measures the consistency of methylation status between two probes among individuals. A population-based distribution is also used to assess the significance of the concordance. Thus, contiguous probes with significant concordance can then be integrated to form a consistently DMR. In other words, the proposed method searches for the region(s) showing different methylation statuses among individuals in a population, where these differences are consistent across the probes in the region.
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The causal link between HPV and cervical cancer and its implications for prevention of cervical cancer

The causal link between HPV and cervical cancer and its implications for prevention of cervical cancer

Dif- ference in prevalence of human papillo- mavirus genotypes in cytomorphologically normal cervical smears is associated with a history of cervical intraepithelial neop[r]

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Association between DNMT3A mutations and prognosis of adults with de novo acute myeloid leukemia: a systematic review and meta-analysis.

Association between DNMT3A mutations and prognosis of adults with de novo acute myeloid leukemia: a systematic review and meta-analysis.

Acute myeloid leukemia (AML) are a group of heterogeneous diseases with respect to biological and clinical outcomes, which have been considered to be related to cytogenetic and gene lesions in hematopoietic stem or progenitor cells [1,2,3]. It is extremely important for patients with de novo AML to assess risk status based on cytogenetic and molecular abnormalities. Cytogenetic abnormalities have been utilized widely to evaluate the risk status of patients [3,4,5,6]. However, only several molecular lesions were applied to risk stratification in clinical practice, such as FMS-like tyrosine kinase 3 (FLT3) [7,8], Nucleophosmin1 (NPM1) [9,10], CCAAT/enhancer-binding protein alpha (CEBPA) [11,12]. Whereas DNMT3A [13,14,15], Isocitrate dehydrogenase1 (IDH1), IDH2 [16,17] and TET2 [18,19] have not been fully assessed. DNMT3A plays a role in de novo methylation of specific
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Syngeneic cardiac and bone marrow stromal cells display tissue-specific microRNA signatures and microRNA subsets restricted to diverse differentiation processes.

Syngeneic cardiac and bone marrow stromal cells display tissue-specific microRNA signatures and microRNA subsets restricted to diverse differentiation processes.

specific manner (Figure 5). Four subsets were distinctively modulated in CStC. The first subset comprises 5 miRs (142-5p, 216a-5p, 27b-3p, 30d-5p, and 511-5p) that were all up-regulated by AM in CStC to a significantly higher level than in BMStC (mean fold difference of 15.2, 17.5, 3.5, 2.3, and 3.1, respectively). A second subset consists of 7 miRs (1, 133b, 184, 204-5p, 24-1-5p, 362-5p, and 503-5p) up-regulated by OM in CStC and significantly higher than in BMStC (fold difference of 4.5, 42.4, 71.8, 432.7, 3.4, 6.3, and 6.6, respectively). The third subset includes 3 miRs (1, 135a-5p, and 27b-3p) up-regulated by CM in CStC to a significantly higher extent than in BMStC (fold difference of 5.0, 60.0, and 1.7, respectively). Finally, miR-204-5p was up-regulated in CStC also by EM, with a significant fold difference of 22.3 compared to in BMStC. Conversely, two miRs (130a-3p and 511-5p) were up-regulated by OM and CM, respectively, in BMStC but not in CStC (with significant fold differences of 2.9 and 5.7). In addition, miR-222-3p was down- regulated by all differentiation media but EM in both cell types, showing a significant higher expression in BMStC vs. CStC cultured in GM (3.2), AM (3.4), and EM (1.7); miR-29a-3p was Figure 5. miRs for which the effect of the media differed between CStC and BMStC. Mean expression levels 6 SEM are plotted for 16 miRs showing a significant interaction effect between tissue origin and media, at 2-way ANOVA, for both Cardiac (CStC) and Bone Marrow (BMStC) Stromal Cells (open circle and filled squares, respectively). Post-hoc comparison between CStC and BMStC indentified miRs differentially modulated by differentiation media. *P,0.05, **P,0.01, ***P,0.001. GM, growth medium; AM, Adipogenic Medium; OM, Osteogenic Medium; CM, Cardiomyogenic Medium; EM, Endothelial Medium.
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Sonoporation delivery of monoclonal antibodies against human papillomavirus 16 E6 restores p53 expression in transformed cervical keratinocytes.

Sonoporation delivery of monoclonal antibodies against human papillomavirus 16 E6 restores p53 expression in transformed cervical keratinocytes.

Non-invasive, pathogen-targeted treatments belong to the new era in cancer research and may be the ‘‘magic bullet’’, as originally envisioned 100 years ago by Paul Ehrlich, needed for future progress [51]. Our interdisciplinary approach allows for precise targeting of HPV16 infected cervical carcinoma cells–we can select a viral protein antibody target and guide the placement of the HIFU beam with millimetre accuracy. This type of ultrasound mechanical stimulation induces a rapid hyperpolarization of the cell membrane potential when the microbubble is in direct contact Figure 3. Detection of 4 mg/mL tubulin antibody within CaSki and SiHa cells. (A) Immunofluorescence detection of the tubulin antibody 48 hours following exposure of the cells to sonoporation or sham no HIFU treatment. Nuclei were counterstained blue with DAPI (left photo). Green signal indicates internalized tubulin antibody detected by the application of a secondary fluorophore (centre photo). Images merged (right photo). Cells were visualized using 4006 magnification. (B) Tubulin antibody positive cells (%) 48 hours following both chemical transfection and sonoporation with 4 mg/mL antibody. Sonoporation resulted in a higher antibody transfection efficiency than that obtained with the traditional chemical reagent, HiPerFect (P,0.001, n = 3). Statistical analysis was performed using a two-way ANOVA with Student’s two-sample t-tests post hoc. Error bars represent mean +/2 SEM. ‘‘*’’ denotes significance.
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