scholarly journals Identification of Circulating miR-22-3p and miR-93-5p as Stable Endogenous Control in Tuberculosis Study

Diagnostics ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 868
Author(s):  
Workneh Korma ◽  
Adane Mihret ◽  
Azeb Tarekegn ◽  
Yunhee Chang ◽  
Dasom Hwang ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Addis Ababa ◽  
Transcript Level ◽  
Healthy Controls ◽  
Small Nuclear Rna ◽  
Diagnosis And Prognosis ◽  
Latently Infected ◽  
Biological Interpretation ◽  
Mirna 93 ◽  
The Stability

The diagnosis and prognosis of tuberculosis remains challenging and necessitates the development of a new test that can accurately diagnose and monitor treatment responses. In this regard, miRNA is becoming a potential diagnostic and prognostic biomarker which differentiates treatment respondents from non-respondents for various non-infectious and infectious diseases, including tuberculosis. The concentration of miRNAs varies based on cell type, disease, and site of infection, implicating that selection of an optimal reference gene is crucial, and determines the quantification of transcript level and biological interpretation of the data. Thus, the study evaluated the stability and expression level of five candidate miRNAs (let-7i-5p, let-7a-5p, miRNA-16-5p, miRNA-22-3p and miRNA-93-5p), including U6 Small Nuclear RNA (RNU6B) to normalize circulating miRNAs in the plasma of 68 participants (26 healthy controls, 23 latent, and 19 pulmonary tuberculosis infected) recruited from four health centers and three hospitals in Addis Ababa, Ethiopia. The expression levels of miRNAs isolated from plasma of culture confirmed newly diagnosed pulmonary tuberculosis patients were compared with latently infected and non-infected healthy controls. The qPCR data were analyzed using four independent statistical tools: Best Keeper, Genorm, Normfinder and comparative delta-Ct methods, and the data showed that miRNA-22-3p and miRNA-93-5p were suitable plasma reference miRNAs in a tuberculosis study.

scholarly journals The Herpesvirus saimiri Small Nuclear RNAs Recruit AU-Rich Element-Binding Proteins but Do Not Alter Host AU-Rich Element-Containing mRNA Levels in Virally Transformed T Cells

2004 ◽  
Vol 24 (10) ◽  
pp. 4522-4533 ◽  
Author(s):  
Heidi L. Cook ◽  
Hannah E. Mischo ◽  
Joan A. Steitz
Keyword(s):  
T Cells ◽  
Posttranscriptional Regulation ◽  
Binding Proteins ◽  
Herpesvirus Saimiri ◽  
Mrna Levels ◽  
Small Nuclear Rna ◽  
Small Nuclear Rnas ◽  
Latently Infected ◽  
The Stability

ABSTRACT Herpesvirus saimiri (HVS) encodes seven Sm-class small nuclear RNAs, called HSURs (for Herpesvirus saimiri U RNAs), that are abundantly expressed in HVS-transformed, latently infected marmoset T cells but are of unknown function. HSURs 1, 2, and 5 have highly conserved 5′-end sequences containing the AUUUA pentamer characteristic of AU-rich elements (AREs) that regulate the stability of many host mRNAs, including those encoding most proto-oncogenes and cytokines. To test whether the ARE-containing HSURs act to sequester host proteins that regulate the decay of these mRNAs, we demonstrate their in vivo interaction with the ARE-binding proteins hnRNP D and HuR in HVS-transformed T cells using a new cross-linking assay. Comprehensive Northern and microarray analyses revealed, however, that the levels of endogenous ARE-containing mRNAs are not altered in T cells latently infected with HVS mutants lacking HSURs 1 and 2. HSUR 1 binds the destabilizing ARE-binding protein tristetraprolin induced following activation of HVS-transformed T cells, but even in such stimulated cells, the levels of host ARE-containing mRNAs are not altered by deletion of HSURs 1 and 2. Instead, HSUR 1 itself is degraded by an ARE-dependent pathway in HVS-transformed T cells, suggesting that HVS may take advantage of the host ARE-mediated mRNA decay pathway to regulate HSUR expression. This is the first example of posttranscriptional regulation of the expression of an Sm small nuclear RNA.

scholarly journals Clinical value evaluation of microRNA-324-3p and other available biomarkers in patients with HBV-infection-related hepatocellular carcinoma

2021 ◽  
Author(s):  
Li Zhao ◽  
Qian Yang ◽  
Jianbo Liu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Hepatitis B ◽  
Diagnostic Performance ◽  
Cox Regression ◽  
Hbv Infection ◽  
Healthy Controls ◽  
Survival Prognosis ◽  
Diagnosis And Prognosis ◽  
Hcc Cells

Abstract Background Patients with hepatitis B virus (HBV) infection are at high risk of hepatocellular carcinoma (HCC). This study aimed to evaluate the expression of microRNA-324-3p (miR-324-3p) in HBV-related HCC, and explore the clinical significance of serum miR-324-3p and other available biomarkers in the diagnosis and prognosis of HBV-related HCC. Methods Expression of miR-324-3p in HBV-infection-related cells and patients was estimated using quantitative real-time PCR. The receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic performance of serum miR-324-3p, AFP and PIVKA-II in the differentiation of HBV-related HCC from healthy controls and chronic hepatitis B (CHB). The relationship between serum miR-324-3p and patients’ clinical features was assessed using Chi-square test, and the value of miR-324-3p to predict overall survival prognosis was evaluated using Kaplan-Meier methods and Cox regression assay in patients with HBV-related HCC. Results HBV-related HCC cells had significantly increased miR-324-3p compared with normal and HBV-unrelated HCC cells, and serum miR-324-3p in HCC patients with HBV infection was also higher than that in healthy controls and CHB. Serum miR-324-3p had relatively high diagnostic accuracy for the screening of HCC case with HBV infection, and the combination of miR-324-3p, AFP and PIVKA-II showed the improved diagnostic performance. Additionally, high serum miR-324-2p in HBV-related HCC patients was associated with cirrhosis, tumor size, clinical stage and poor overall survival prognosis. Conclusion Serum increased miR-324-3p may be involved in the progression of HBV-related hepatitis to HCC, and may serve as a candidate biomarker for the diagnosis and prognosis of HBV-related HCC.

scholarly journals DNA Methylation Profiling for the Diagnosis and Prognosis of Patients with Nontuberculous Mycobacterium Lung Disease

2021 ◽  
Vol 43 (2) ◽  
pp. 501-512
Author(s):  
Jee Youn Oh ◽  
Young Kyung Ko ◽  
Jeong-An Gim
Keyword(s):  
Dna Methylation ◽  
Lung Disease ◽  
Poor Prognosis ◽  
Wnt Signaling Pathway ◽  
Fold Change ◽  
Nontuberculous Mycobacterium ◽  
Healthy Controls ◽  
Log2 Fold Change ◽  
Diagnosis And Prognosis ◽  
Ntm Lung Disease

The incidence of nontuberculous Mycobacterium (NTM) lung disease is rapidly increasing; however, its diagnosis and prognosis remain unclear while selecting patients who will respond to appropriate treatment. Differences in DNA methylation patterns between NTM patients with good or poor prognosis could provide important therapeutic targets. We used the Illumina MethylationEPIC (850k) DNA methylation microarray to determine the pattern between differentially methylated regions (DMRs) in NTM patients with good or poor prognosis (n = 4/group). Moreover, we merged and compared 20 healthy controls from previous Illumina Methylation450k DNA methylation microarray data. We selected and visualized the DMRs in the form of heatmaps, and enriched terms associated with these DMRs were identified by functional annotation with the “pathfinder” package. In total, 461 and 293 DMRs (|Log2 fold change| > 0.1 and p < 0.03) were more methylated in patients with four poor and four good prognoses, respectively. Furthermore, 337 and 771 DMRs (|Log2 fold change| > 0.08 and p < 0.001) were more methylated in eight NTM patients and 20 healthy controls, respectively. TGFBr1 was significantly less methylated, whereas HLA-DR1 and HLA-DR5 were more methylated in patients with poor prognosis (compared to those with good prognosis). LRP5, E2F1, and ADCY3 were the top three less-methylated genes in NTM patients (compared with the controls). The mTOR and Wnt signaling pathway-related genes were less methylated in patients with NTM. Collectively, genes related to Th1-cell differentiation, such as TGFBr1 and HLA-DR, may be used as biomarkers for predicting the treatment response in patients with NTM lung disease.

scholarly journals Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA

Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3827
Author(s):  
Jae Young Hur ◽  
Kye Young Lee
Keyword(s):  
Therapeutic Potential ◽  
Extracellular Vesicle ◽  
Clinical Settings ◽  
Biomarker Detection ◽  
Diagnosis And Prognosis ◽  
Double Stranded Dna ◽  
Fundamental Research ◽  
The Stability ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.

scholarly journals Stability of a one-dimensional morphoelastic model for post-burn contraction

2021 ◽  
Vol 83 (3) ◽  
Author(s):  
Ginger Egberts ◽  
Fred Vermolen ◽  
Paul van Zuijlen
Keyword(s):  
Wound Healing ◽  
Residual Stresses ◽  
Truncation Error ◽  
Signaling Molecules ◽  
Discrete Problem ◽  
One Dimensional ◽  
Stability Constraint ◽  
Biological Interpretation ◽  
The Stability ◽  
The One

AbstractTo deal with permanent deformations and residual stresses, we consider a morphoelastic model for the scar formation as the result of wound healing after a skin trauma. Next to the mechanical components such as strain and displacements, the model accounts for biological constituents such as the concentration of signaling molecules, the cellular densities of fibroblasts and myofibroblasts, and the density of collagen. Here we present stability constraints for the one-dimensional counterpart of this morphoelastic model, for both the continuous and (semi-) discrete problem. We show that the truncation error between these eigenvalues associated with the continuous and semi-discrete problem is of order $${{\mathcal {O}}}(h^2)$$ O ( h 2 ) . Next we perform numerical validation to these constraints and provide a biological interpretation of the (in)stability. For the mechanical part of the model, the results show the components reach equilibria in a (non) monotonic way, depending on the value of the viscosity. The results show that the parameters of the chemical part of the model need to meet the stability constraint, depending on the decay rate of the signaling molecules, to avoid unrealistic results.

scholarly journals Modeling the patient and health system impacts of alternative xpert® MTB/RIF algorithms for the diagnosis of pulmonary tuberculosis in Addis Ababa, Ethiopia

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Abraham Tesfaye ◽  
Daniel Fiseha ◽  
Dawit Assefa ◽  
Eveline Klinkenberg ◽  
Silvia Balanco ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Health System ◽  
Addis Ababa

scholarly journals The expression of miR-211-5p in atherosclerosis and its influence on diagnosis and prognosis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanxia Zhang ◽  
Huiyun Wang ◽  
Yu Xia
Keyword(s):  
Roc Curve ◽  
Cox Regression ◽  
Survival Curve ◽  
Prognostic Significance ◽  
Significant Negative Correlation ◽  
Diagnostic Value ◽  
Expression Level ◽  
Healthy Controls ◽  
Cox Regression Analysis ◽  
Diagnosis And Prognosis

Abstract Background The purpose of this study was to evaluate the diagnostic and prognostic significance of miR-211-5p in atherosclerosis (AS) by detecting the expression level in serum of patients with AS. Methods A total of 85 healthy controls and 90 asymptomatic AS patients participated in this study. The expression level of miR-211-5p in all subjects were measured by qRT-PCR. Spearman correlation coefficient was used to evaluate the correlation of miR-211-5p with CRP and CIMT. The ROC curve was established to assess the diagnostic value of miR-211-5p in AS. The Kaplan–Meier survival curve and multivariate COX regression analysis were used to evaluate the prognostic significance of miR-211-5p in AS. Results The expression levels of miR-211-5p in AS patients were significantly lower than in healthy controls (P < 0.001), and miR-211-5p showed a significant negative correlation with CRP (r =  − 0.639, P < 0.001) and CIMT (r =  − 0.730, P < 0.001). The AUC of the ROC curve was 0.900, the specificity and the sensitivity were 84.7% and 78.9%, respectively, which indicating that miR-211-5p had diagnostic value for AS. Survival analysis showed that patients with low miR-211-5p expression were more likely to have cardiovascular end-point events (Log rank P = 0.013). Conclusion Serum miR-211-5p could be used as a new biomarker for the diagnosis of AS, and the low expression of miR-211-5p is associated with the poor prognosis of AS.

scholarly journals Sputum Smear Positive Pulmonary Tuberculosis Diagnostic Dropout Rate in Public Health Facilities, Addis Ababa, Ethiopia

2019 ◽  
Vol 2019 ◽  
pp. 1-6
Author(s):  
Daniel Melese Desalegn ◽  
Kumera Terfa Kitila ◽  
Boja Dufera Taddese ◽  
Tinsae Kidanemariam Hailu ◽  
Tariku Takle Dinku ◽  
...  
Keyword(s):  
Public Health ◽  
Pulmonary Tuberculosis ◽  
Addis Ababa ◽  
Dropout Rate ◽  
Sputum Smear ◽  
P Value ◽  
Smear Microscopy ◽  
Sputum Smear Microscopy ◽  
Public Health Facilities ◽  
Smear Positive Pulmonary Tuberculosis

Background. Prolonged laboratory diagnostic process of tuberculosis can lead to failure to complete the diagnosis and increase dropout rate of smear positive pulmonary tuberculosis (PTB) cases. This implies such dropout patients without completing diagnosis are critical as infected individuals remain untreated in the community, providing more opportunities for transmission of the disease and adversely affecting the epidemic. The aim of this research is to determine the level of smear positive PTB diagnosis dropout rate of spot-morning-spot sputum microscopy diagnosis method in public health facilities, in Addis Ababa, Ethiopia. Methods. Retrospective review of patient documents in 13 public health facilities’ TB laboratory in Addis Ababa was conducted from October 2011 to March 2016. Data was computerized using Epi-info software and analysed using SPSS version 20.0 software. Descriptive numerical summaries were used to present the findings. Association between the dropout rate and demographic variables was assessed by Chi-square (X2). Bivariate model using Odds Ratio (OR) with a 95% Confidence Interval (CI) was calculated. P-Value less than 0.05 was taken as statistically significant. Results. Of 41,884 presumptive TB patients registered during the 53 months for laboratory investigation, 5.9% were positive for the first spot sputum smear microscopy. Among these positive cases, 142 (5.8%) and 298 (12.1%) did not come back to the laboratory to submitted early morning and second spot sputum specimens, respectively. The diagnostic dropout for morning sputum specimen in hospitals was 5.6% (58/1039) and in health centres was 5.9% (84/1424). However, higher proportion of dropout for second spot sputum specimen in hospitals was 16.4% (170/1039), compared to the health centres, 8.9% (128/1424). Diagnostic dropout of sputum smear microscopy had no significant association with sociodemographic variable (P value >0.05), while it had significant association with facility type (P value <0.05). Conclusion. In this study smear positive pulmonary tuberculosis diagnostic dropout rate was high compared to WHO reported for the new strategy shift implying the importance of shifting to same-day approach. Hence, shifting from conventional to same day is crucial to minimize the TB diagnostic dropout rate in the study area and other similar settings. Further research is needed/recommended in the local setting to compare the yield and dropout rates between same-day and conventional sputum smear microscopy approach.

The stability of mRNA encoding IL-4 is increased in pulmonary tuberculosis, while stability of mRNA encoding the antagonistic splice variant, IL-4δ2, is not

Tuberculosis ◽  
2007 ◽  
Vol 87 (3) ◽  
pp. 237-241 ◽  
Author(s):  
Keertan Dheda ◽  
Jung-Su Chang ◽  
Jim F. Huggett ◽  
Louise U. Kim ◽  
Margaret A. Johnson ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Splice Variant ◽  
The Stability

scholarly journals Serum miR-1228-3p and miR-181a-5p as Noninvasive Biomarkers for Non-Small Cell Lung Cancer Diagnosis and Prognosis

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Wei-Xiao Xue ◽  
Meng-Yu Zhang ◽  
Rui Li ◽  
Xiao Liu ◽  
Yun-Hong Yin ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Roc Analysis ◽  
Cox Regression ◽  
Small Cell ◽  
Healthy Controls ◽  
Small Cell Lung ◽  
Cox Regression Analysis ◽  
Diagnosis And Prognosis ◽  
Noninvasive Biomarkers ◽  
Nsclc Patients

Background. Lung cancer is the leading cause of cancer-related mortality worldwide, and non-small cell lung cancer (NSCLC) accounts for over 80% of all lung cancers. Serum microRNAs (miRNAs), due to their high stability, have the potential to become valuable noninvasive biomarkers. This present study was aimed to identify the serum miRNAs expression signatures for the diagnosis and prognosis of NSCLC using bioinformatics analysis. Methods. A total of 12 miRNAs profiling studies have been identified in Pubmed, Gene Expression Omnibus (GEO), and ArreyExpress databases. Differentially expressed miRNAs (DEmiRNAs) were analyzed according to GEO2R online tool and RRA method from R. Then, prediction of DEmiRNAs’ target genes from TargetScan, PicTar, miRDB, Tarbase, and miRanda database. Furthermore, we using reverse transcription– quantitative polymerase chain reaction (RT-qPCR) to evaluate the expression levels of DEmiRNAs in serum samples obtained from NSCLC patients and healthy controls. Subsequently, the clinical significance of the tested miRNAs was determined using receiver operating characteristic (ROC) analysis and Cox regression analysis. Results. A total of 27 DEmiRNAs were identified and 5 of them (miR-1228-3p, miR-1228-5p, miR-133a-3p, miR-1273f, miR-545-3p) were significantly up-regulated and 4 of them (miR-181a-5p, miR-266-5p, miR-361-5p, miR-130a-3p) were significantly down-regulated in NSCLC patients compared with healthy controls. RT-qPCR validated that miR-1228-3p (P =0.006) and miR-181a-5p (P =0.030) were significantly differentially expressed in the serum of NSCLC patients and healthy controls. ROC analysis on miR-1228-3p and miR-181a-5p revealed the area under the curve (AUC) of 0.685 (95% confidence interval [CI], 0.563–0.806; P =0.006) and 0.647 (95% CI, 0.506–0.758; P =0.049). ROC analysis on miR-1228-3p combined miR-181a-5p revealed the AUC of 0.711 (95% CI, 0.593–0.828; P =0.002). Multivariate Cox regression analysis demonstrated that the high serum miR-1228-3p level was an independent factor for the poor prognosis of NSCLC patients. Conclusions. Serum miR-1228-3p and miR-181a-5p are potential noninvasive biomarkers for the diagnosis and prognosis of NSCLC patients.

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