scholarly journals Peritoneal Effluent MicroRNA Profile in Encapsulating Peritoneal Sclerosis

Author(s):  
Kun-Lin Wu ◽  
Che-Yi Chou ◽  
An-Lun Li ◽  
Chien-Lung Chen ◽  
Jen-chieh Tsai ◽  
...  

Abstract Encapsulating peritoneal sclerosis (EPS) is a catastrophic complication of chronic peritoneal dialysis (PD). Late diagnosis is associated with high mortality. With the advancement of new diagnostic technologies, such as microRNA (miRNA), we attempted to develop a noninvasive test to assist in the diagnosis of EPS. The eight-hour PD effluents were collected from 71 non-EPS and 56 EPS patients. The screening set included 28 samples (20 of non-EPS vs. 8 of EPS). After analyzing the ratio values of two miRNA expression levels from the high-throughput real-time PCR-array of 377 miRNAs, eight candidate miRNAs were selected. The prediction model was conducted using 127 samples (71 of non-EPS vs 56 of EPS) to produce an area under the curve (AUC) value of the miRNA classifier. Candidate miRNAs were also verified by single real-time PCR. The ratios of the five miRNAs with the top five ROC values were selected to calculate the combined AUC by multiple logistic regression. The AUC value to detect EPS with the five miRNA ratios was 0.8929 with an accuracy of 78.7%. The accuracy of the EPS diagnosis was further optimized to 94.1% after considering clinical characteristics (AUC value 0.9931). A signature-based model of clinical characteristics and miRNA expression in PD effluents can efficiently assist in the diagnosis of EPS, thus preventing the catastrophic prognosis.

2021 ◽  
Author(s):  
Kun-Lin Wu ◽  
Che-Yi Chou ◽  
An-Lun Li ◽  
Chien-Lung Chen ◽  
Jen-chieh Tsai ◽  
...  

Abstract Background: Encapsulating peritoneal sclerosis (EPS) is a catastrophic complication of chronic peritoneal dialysis (PD). Late diagnosis is associated with high mortality. With the advancement of new diagnostic technologies, such as microRNA (miRNA), we attempted to develop a noninvasive test to assist in the diagnosis of EPS. Methods: MiRNA expression profiles of PD effluents from patients with or without EPS were examined by a high-throughput real-time PCR array to first screen candidate miRNAs. Candidate miRNAs were verified by single real-time PCR. The model for EPS prediction was evaluated by multiple logistic regression. Results: We collected eight-hour PD effluents from 71 non-EPS and 56 EPS patients. The screening set included 28 samples (20 of non-EPS vs. 8 of EPS). After analyzing the ratio values of two miRNA expression levels from the PCR-array of 377 miRNAs, eight candidate miRNAs were selected. The prediction model was conducted using 127 samples (71 of non-EPS vs 56 of EPS) to produce an area under the curve (AUC) value of the miRNA classifier. The ratios of the five miRNAs with the top five ROC values were selected to calculate the combined AUC by logistic regression. The AUC value to detect EPS with the five miRNA ratios was 0.8929 with an accuracy of 78.7%. The accuracy of the EPS diagnosis was further improved to 94.1% after considering clinical characteristics (AUC value 0.9931). Conclusions: A signature-based model of clinical characteristics and miRNA expression in PD effluents can efficiently assist in the diagnosis of EPS, thus preventing the catastrophic prognosis.


2020 ◽  
Vol 14 (2) ◽  
pp. 109-118 ◽  
Author(s):  
Qiuling Ma ◽  
Yong Shao ◽  
Wei Chen ◽  
Cheng Quan ◽  
Yanhui Zhu ◽  
...  

Aim: To investigate whether cervical cancer (CC) and cervical intraepithelial neoplasia (CIN) can be screened by analyzing gene expression profiling of peripheral blood. Methods: RNA-sequencing analysis of blood was performed on 11 CC patients, 21 CIN patients and 19 healthy controls (H). Fifty-nine genes were validated by quantitative real-time PCR using blood samples from 46 H, 83 CC and 32 CIN patients. Results: There were significant differences in the expression levels of six genes between CC and H, five genes between CIN and H and four genes between CC and CIN (p < 0.05). Four genes discriminated cervical lesions from H with a sensitivity of 82.61%, a specificity of 87.83% and an area under the curve of 0.8981. Three genes discriminated CC from CIN with a sensitivity of 53.13%, a specificity of 96.39% and an area under the curve of 0.7786. Conclusion: Our findings provided a promising noninvasive quantitative real-time PCR diagnostic assay of CC and CIN.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2650-2650
Author(s):  
Aisha L Walker ◽  
Shirley Steward ◽  
Michael Wang ◽  
Matthew P Smeltzer ◽  
Russell E. Ware

Abstract Abstract 2650 Background: Hydroxyurea has both laboratory and clinical efficacy for children, adolescents, and adults with Sickle Cell Anemia (SCA), and its benefits are primarily due to its ability to increase fetal hemoglobin (HbF). However, HbF induction by hydroxyurea is highly variable among patients, and its mechanism of HbF reactivation remains unclear. MicroRNAs (miRNA) are small non-coding RNAs that can regulate gene expression by inhibiting transcription or translation of targeted proteins. Recently, miRNAs have been implicated in cellular regulation and differentiation including hematopoiesis and hemoglobin switching. In an effort to elucidate the mechanisms behind hydroxyurea-mediated HbF induction, we tested the hypothesis that hydroxyurea modulates miRNA expression in sickle reticulocytes in vivo and this modulation is associated with changes in HbF levels. Methods: As part of the prospective Hydroxyurea Study of Long-term Effects (HUSTLE, NCT00305175), total RNA was purified from CD71+ reticulocytes isolated from the peripheral blood of SCA patients, either prior to hydroxyurea treatment or after reaching stable maximum tolerated dose (MTD); non-SCA adults were included as controls. Initially, differential miRNA expression associated with disease and/or hydroxyurea exposure was determined by microarray and then confirmed by real-time PCR in a cross-sectional analysis of hydroxyurea-treated (n=13) and untreated (n=22) SCA patients, plus controls (n=8). Subsequently to identify hydroxyurea-mediated changes in miRNA expression and its association with HbF induction, miRNA levels were measured by real-time PCR in paired samples collected from patient reticulocytes at baseline and at hydroxyurea MTD (n=41). Statistical correlation to HbF levels used Spearman correlation coefficient and mixed model analysis. Results: Microarray analysis identified 108 miRNAs expressed in CD71+ reticulocytes, 10 of which were significantly different in SCA patients with or without hydroxyurea exposure and normal controls. Real-time PCR confirmed that miRNA expression of human miRNA (hsa-mir) 29a, 130b, 215, and 494 were upregulated, while hsa-mir-223 was downregulated, in untreated SCA patients compared to non SCA controls. Additional analysis of 41 paired samples showed that 3 miRNAs, hsa-mir 148a, 151-3p, and 494, were significantly upregulated with hydroxyurea treatment (Table 1). At MTD, HbF levels increased an average of 17% from a mean of 8.9 ± 6.1% at baseline (range 0.0–22.9%) to a mean of 25.9 ± 9.0% at MTD (range 9.4–55.9%).Significant associations between hsa-mir 26b miRNA expression and HbF levels were identified, both at baseline (rs= -.34; p=0.03) and at MTD (rs= -.32; p=0.04). Using mixed model analysis, change in hsa-mir 151-3p expression was significantly associated with the change in HbF (p=0.047) from baseline to MTD. Conclusion: We identified specific miRNAs that are significantly associated with sickle cell anemia, hydroxyurea treatment, and hydroxyurea-mediated HbF induction. These studies suggest that miRNA regulation, specifically hsa-mir 26b and 151-3p, may be involved in hydroxyurea-mediated HbF induction in patients with sickle cell anemia. Future studies to identify the relevant protein targets may lead to a better understanding of hydroxyurea's mechanisms of action and patient response to the drug including the observed inter-patient variability in HbF response. Results from real-time PCR shows differential miRNA expression in non-SCA controls compared to untreated SCA patients from cross-sectional analysis, and upregulation of 3 miRNAs in SCA patients at baseline compared to MTD from paired-sample analysis. Negative fold change indicates a downregulation. Disclosure: Off Label Use: Hydroxyurea used to treat sickle cell anemia in children. Disclosures: Off Label Use: Hydroxyurea used to treat sickle cell anemia in children.


2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
R Ragusa ◽  
A Di Molfetta ◽  
S Del Turco ◽  
G Basta ◽  
M Rizzo ◽  
...  

Abstract Background VAD use in heart failure (HF) children have undergone rapid progress in the last three decades through pump technological innovation and improvement of perioperative care. Studies in HF adults showed that VAD put native heart at rest and lead to molecular changes in cardiac muscle, including at microRNA (miRNA) level. However, little is known on changes induced by VAD implant in cardiac miRNA expression and their putative targets in HF children. Purpose The aims of this study were to evaluate: 1) modification of miRNA expression in cardiac muscle from HF children after VAD support; 2) the putative targets of selected miRNAs by in silico analysis; 2) the role of the identify miRNAs on putative targets by in vitro study. Methods Cardiac biopsies were collected from HF children at the moment of VAD implant [n=8; 20 (7.5–64.5) months, 2 males; 19 (15.75–32.25) LVEF%] and at the time of heart transplant after VAD support [n=5; 32 (5–204) months; 4 males; 13.5 (10–18) LVEF%]. Cardiac miRNA expression was evaluated by NGS. The potential miRNA targets were identified by bioinformatics analyses and their cardiac expression by real-time PCR was evaluated. HL-1 cell line was used for testing the regulatory role of selected miRNA on predicted targets by miRNA mimic transfection study. Results At NGS, 465 miRNA were found on average in each sample and the cardiac expression levels of miR19a-3p, miR-1246 and miR-199b-5p decreased in HF children after VAD support compared to pre-implant (Fig. 1A-B). In silico analysis showed that more than 5000 potential gene targets regulated by miR-19a-3p, miR-1246 and miR-199b-5p. Among them, adiponectin receptors (AdipoR1, AdipoR2, T-CAD) were identified as common targets for 3 miRNAs. Real-time PCR data showed that levels of all adiponectin receptors increased significantly whilst the expression of 3 miRNAs decreased after VAD support (Fig. 1C). Moreover, AdipoR2 and T-CAD were inversely related to miRNA levels (Fig. 1D). In vitro studies confirmed the regulatory role of miR-1246 and miR-199b-5p on AdipoR2 (Fig. 1E-F), whilst only miR-199b-5p reduced the expression of T-CAD (Fig. 1G). Finally, AdipoR1 expression levels are not modified compared to control by miRNAs mimic transfection (data not shown). Conclusion In HF children the use of VAD could modify the expression of several miRNAs potentially involved in the regulation of several pathophysiological mechanisms underlying HF. Specifically, the reductions of miR-1246, mir-19a-3p, miR-199b-5p were associated with an increase of the adiponectin receptors AdipoR2 and T-CAD mRNA, suggesting the existence of a miRNAs related fine tuning of the adiponectin system at cardiac tissue level by VAD implant, able to favour the protective effect of adiponectin in HF cardiac muscle. FUNDunding Acknowledgement Type of funding sources: Public grant(s) – EU funding. Main funding source(s): FP7-ICT-2009 Project, Grant Agreement 24863 Figure 1


Biologia ◽  
2016 ◽  
Vol 71 (6) ◽  
Author(s):  
Adikeshavan Thilagavathy ◽  
Varadahally R. Devaraj

AbstractMicroRNAs (miRNAs) play key roles in plant responses to biotic and abiotic stresses by modulating their own expression and a wide array of target mRNAs. Reverse transcription quantitative real-time PCR is a sensitive and widely used method to study miRNA expression profile. Accurate analysis and interpretation of results require the selection of an appropriate reference gene. Reference genes selected should have a constant expression level under different stress conditions. Six reference candidates, including two miRNAs (miRNA 156 and miRNA 172), an rRNA (5S rRNA), a snRNA (U6) and two protein coding genes (actin and protein phosphatase 2A), were selected for normalization of miRNA expression in


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 105-105
Author(s):  
Amanda Dixon-McIver ◽  
Phil East ◽  
Charles A. Mein ◽  
Jean-Baptiste Cazier ◽  
Gael Molloy ◽  
...  

Abstract MicroRNAs (miRNAs) are single stranded non-coding RNAs of ∼ 22 nucleotides involved in gene regulation. Several examples of an association between disrupted expression of miRNAs and cancer have been shown. Using a real-time quantitative PCR, designed to amplify only from the mature miRNA (TaqMan® -MicroRNA Looped-PCR assay, Applied Biosystems), we measured the expression levels of 157 miRNAs in 100 acute myeloid leukaemia (AML) patients representing the spectrum of known karyotypes common in AML, 2 leukaemic cell lines (KG1 and NB4), and the bone marrow from 2 healthy donors. ANOVA analysis using a 5% false discovery rate threshold was performed to identify differentially expressed miRNAs between leukaemia samples and normal bone marrow. MiRNAs specific to karyotype groupings were also identified in the same way. A method was developed to demonstrate the spatial localisation, in situ, of specific miRNA identified in the quantification and confirm the expression of miRNA with relation to karyotype. Commercial locked nucleic acid (LNA) oligonucleotides (Exiqon) were obtained for two miRNAs (miRNA-127 and miRNA-154), as well as for positive and negative control probes. LNAs were labelled with digoxigenin and probes applied to both cytospins and/or trephines of a sample set representative of the different AML subtypes. Detection of hybridisation signals was either by colorimetric or fluorescent reaction and visualised by confocal microscopy. Unsupervised cluster analysis revealed an association of miRNA expression with the karyotype of the samples. Promyelocytic leukaemias (APML) bearing the t(15;17) translocation, show a distinct pattern characterised by the high expression of a subset of 10 miRNAs located in the human 14q32 imprinted domain, including miR-127 and miR-154. ANOVA data analysis revealed the de-regulation of 33 miRNAs across the leukaemic set in respect to bone marrow from healthy donors. Seventeen miRNAs were up-regulated and 16 down-regulated. MiRNAs miR-155, miR-181a, miR-181b, miR-181c, miR-142-5p, miR-221, and miR-222, were among those commonly highly expressed. Down-regulated were miR-26a, miR-34c, and miR-199a. MiRNAs miR-10a and miR-125b showed the highest variability throughout the samples, being associated with specific subgroups. In situ hybridisation analysis of miR-127 and miR-154 confirmed the results obtained by real-time PCR of their expression associated with APML. This study, conducted on about a third of the miRNAs reported in the Sanger database (microrna.sanger.ac.uk), demonstrates the potential for using miRNA expression to sub-classify cancer. The expression analysis of larger number of miRNAs coupled with the in situ hybridisation of leukaemic cells will allow the investigation of miRNA expression on stored samples during the disease course and provide valuable insights into the leukaemogenic process.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4815-4815
Author(s):  
Flavia Z Piazera ◽  
Doralina Amaral Rabello ◽  
Felipe Araújo Saldanha ◽  
Fábio Pitella Silva ◽  
Fábio Morato Oliveira ◽  
...  

Abstract INTRODUCTION: Epigenetic changes have proved increasingly important in the genesis of various tumors including acute and chronic lymphoid malignancies.Its basic features do not cause changes in the DNA sequence, but removing selective expression of genes dependent DNA packaging level. The histone methylation is one of the leading and most studied epigenetic events. SETD family of methyltransferases comprises 10 genes encoding proteins with SET domain. SETMAR encodes a protein that contains an N-terminal SET domain and a C-terminal mariner transposase domain. SETMAR-catalyzed methylation of H3K4 and H3K36 may lead to an open chromatin structure, which may facilitate its transposase-dependent processes. SETMAR was associated with carcinogenesis of acute myeloid leukemia by losing disjuntion checkpoint in cells treated with inhibitors of protein topo II. However, the role of SETMAR in CLL leukemogenesis remains unknown. METHODS: In the present study, we evaluated the relative expression of SETMAR between a group of 59 CLL patients and 10 healthy controls by real-time PCR. As normal controls, we used peripheral blood mononuclear cells (PBMC) from 10 age-matched hematological healthy donors (age 50 to 84 years).We analyzed the correlation between SETMAR expression patterns with CLL clinical characteristics such as chromosomal aberrations, ZAP-70 expression and white blood cell (WBC) count. Total RNA was isolated and cDNAs were synthesized. Quantification of SETMAR was performed by Real Time PCR (qPCR) and normalized to endogenous (beta-actin) expression. Results were analyzed by the comparative2-ΔΔCt method. The amount of target gene, normalized to the endogenous control gene and relative to a reference sample, was converted into relative quantification. Based on the continuous distribution of SETMAR expression on CLL samples, we adopted the median value as the cutoff to dichotomize CLL patients in "low" and "high" SETMAR expression. Clinical and laboratory information were then compared between groups. Statistical analysis was performed by GraphPad Prism version 5. The Mann-Whitney U-test was used to examine differences between SETMAR expression (low or high) groups versus platelets, WBC count and ZAP-70 status and also to compare the groups of CLL patients with normal versus abnormal karyotypes. Association of SETMAR expression profile with karyotype was done using Fisher's exact test. RESULTS: The clinical characteristics of CLL patient cohort used in this study is summarized in table 1. Initially, we compared SETMAR gene expression profiles between CLL patients and control samples, using the Mann-Whitney test. SETMAR gene expression was higher in CLL samples (p= 0.00117),with statistical difference (p<0.05) (Fig. 1). Table 1. Clinical and laboratorial characteristics of CLL patients. Characteristics PATIENTS (%) GENDER Male 24(40,7%) Female 35(59,3%) AGE 63 (32-98 years) TUMOR STAGE Binet A 39(66%) Binet B 13(22%) Binet C 7(12%) CYTOGENETIC ANALYSIS 13q deletion 5(8,3%) 17p deletion 4(6,7%) 12tryssomy 16(26,7%) Normal 15(25%) Others 20(33,3%) ZAP-70 expression >20% 39(67,2%) <20% 19(32,8%) CLL patients with lower expression of SETMAR had a higher WBC count and a higher incidence of cytogenetic abnormalities (CTG) (p=0.001) when compared to those with higher expression (p=0.0262) (Fig. 2). However, differential SETMAR expression had no impact on platelets count (p = 0.092), ZAP-70 protein expression (p = 0.25) and tumor stage of Binet (p= 0.38). Figure 2- A) SETMAR relative expression gene and cytogenetic abnormalities, with p=0,001 and B) SETMAR relative expression and WBC counts with p= 0,0262. The cohort of 59 clinical specimens of CLL patients used in the present study revealed quite heterogeneous patterns of SETMAR expression and its association with clinical variables. Future efforts will be necessary to increase the assessment of SETMAR expression in a larger number of CLL patients in order to evaluate its impact on survival, as well as to unveil its correlation with response to established cancer therapy and in the course of the disease. CONCLUSION: We observed that although the expression of SETMAR is elevated in the majority of CLL patients when compared to healthy controls, a lower expression of SETMAR in patients is associated with chromosomal instability and progression of the tumor mass (increased leukocytosis). Figure 2. Figure 2. Figure 3. Figure 3. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Maxime Pichon ◽  
Benoit Pichard ◽  
Thierry Barrioz ◽  
Chloé Plouzeau ◽  
Vincent Croquet ◽  
...  

ABSTRACT The noninvasive detection of Helicobacter pylori and its resistance to clarithromycin could revolutionize the management of H. pylori-infected patients by tailoring eradication treatment without any need for endoscopy when histology is not necessary. Several real-time PCR tests performed on stools have been proposed, but their performances were either poor or they were tested on too few patients to be properly evaluated. We conducted a prospective, multicenter study including 1,200 adult patients who were addressed for gastroduodenal endoscopy with gastric biopsies and who were naive for eradication treatment in order to evaluate the performance of the Amplidiag H. pylori+ClariR assay recently developed by Mobidiag (Espoo, Finland). The results of the Amplidiag H. pylori+ClariR assay performed on DNA from stools (automatic extraction with the EasyMag system [bioMérieux]) were compared with those of culture/Etest and quadruplex real-time PCRs performed on two gastric biopsy samples (from the antrum and corpus) to detect the H. pylori glmM gene and mutations in the 23S rRNA genes conferring clarithromycin resistance. The sensitivity and specificity of the detection of H. pylori were 96.3% (95% confidence interval [CI], 92 to 98%) and 98.7% (95% CI, 97 to 99%), respectively. The positive and negative predictive values were evaluated to be 92.2% (95% CI, 92 to 98%) and 99.3% (95% CI, 98 to 99%), respectively. In this cohort, 160 patients (14.7%) were found to be infected (positive by culture and/or PCR). The sensitivity and specificity for detecting resistance to clarithromycin were 100% (95% CI, 88 to 100%) and 98.4% (95% CI, 94 to 99%), respectively.


Sign in / Sign up

Export Citation Format

Share Document