Journal: BioMed Research International

Article Title: MicroRNAs as Salivary Markers for Periodontal Diseases: A New Diagnostic Approach?

doi: 10.1155/2016/1027525

Figure Lengend Snippet: Comparison of methods from current investigations regarding miRNAs in periodontal disease.

Article Snippet: Naqvi et al. 2014 [ ] , Human THP-1-differentiated macrophages , miRNeasy kit (Qiagen) , NanoString nCounter miRNA assay (NanoString Technologies) , Quantitative real-time PCR EvaGreen Master Mix (Biotium) , — , RNU6B , Student's t -test (two-tailed) , miR-29b miR-32 miR-146a miR-891.

Techniques: Comparison, RNA Extraction, Biomarker Discovery, Control, In Vitro, Microarray, Isolation, TaqMan microRNA Assay, SYBR Green Assay, Labeling, Real-time Polymerase Chain Reaction, Virus, Quantitative RT-PCR, In Vivo, Expressing, Mann-Whitney U-Test

Journal: Gene

Article Title: Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

doi: 10.1016/j.gene.2012.09.093

Figure Lengend Snippet: Distinct miRNA profiles of mK-ras-LE cells in 2-D and rBM 3-D cultures. A) mK-ras-LE cells were grown in 2-D and rBM 3-D culture. Morphology of the cells was visualized using fluorescent staining for F-actin. The images of rBM 3-D culture were captured at the central planes of cell clusters using a confocal fluorescent microscope on day 12 post-seeding. The images were captured at 600x magnification. Representative images of each culture condition were displayed. B) Total cell RNA was extracted from mK-ras-LE cells in 2-D and rBM 3-D cultures. miRNA expression profiles were compared between the two culture conditions using miRNA microarrays. A heatmap of the significantly differentially expressed miRNAs was generated using geWorkbench suite (n = 3, P < 0.01, FDR < 0.05). C) The expression of miR-17, miR-92b, and miR-21 was measured using qRT-PCR in total cell RNA collected from 2-D and rBM 3-D cultures of mK-ras-LE cells. A fold change of each miRNA of interest was obtained by setting the values of each miRNA in 2-D culture to one and normalization to the values of U6. D) Similar to part C except that the expression of miR-200a was compared between 2-D and rBM 3-D cultures. E) The culture conditions were similar to part A. The cell lysates were collected from the cell colonies extracted from the culture. The protein levels of ZEB2, PTEN, and -actin were determined using immunoblots. The data were presented in averages and standard deviations obtained from three independent experiments. and indicated a P value < 0.05 and 0.01, respectively.

Article Snippet: 2.4. miRNA microarray analysis The miRNA expression profiling service was provided by LC Sciences (Houston, TX) using μParaflo® technology and proprietary probe hybridization (Cy3 and Cy5 dendrimer dyes) that enables highly sensitive and specific direct detection of mouse miRNAs.

Techniques: Staining, Microscopy, Expressing, Generated, Quantitative RT-PCR, Western Blot

Journal: Gene

Article Title: Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

doi: 10.1016/j.gene.2012.09.093

Figure Lengend Snippet: Disparate expression of miRNAs between rBM 3-D and 2-D cultures of mK-ras-LE cells. Total cell RNA was extracted from rBM 3-D and 2-D cultures. miRNA arrays were carried out and analyzed as described in Methods. A fold change of each miRNA was obtained by setting the values from 2-D culture to one. The results were average of three miRNA microarrays. The miRNAs bearing documented tumor-modulating properties were highlighted in bold.

Article Snippet: 2.4. miRNA microarray analysis The miRNA expression profiling service was provided by LC Sciences (Houston, TX) using μParaflo® technology and proprietary probe hybridization (Cy3 and Cy5 dendrimer dyes) that enables highly sensitive and specific direct detection of mouse miRNAs.

Techniques: Expressing

Journal: Gene

Article Title: Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

doi: 10.1016/j.gene.2012.09.093

Figure Lengend Snippet: miRNA expression associated with aincar morphogenesis. A) A549 and A549LC cells were cultured in 2-D (A1 & A2) and rBM 3-D (A3 & A4) cultures. Morphology was recorded using an inverse phase contrast microscope. Polarized monolayer of the cells and the central lumen were pointed at by white arrows. B) The expression of miR-17, miR-92, and miR-21 was measured using qRT-PCR in total cell RNA collected from 2-D and rBM 3-D of A549 and A549LC cells. A fold change of each miRNA was obtained by setting the values of each miRNA from A549 cells in 2-D culture to one and normalization to the values of U6. C) Similar to part A except that the expression of miR-200a was compared across the groups. D) The culture conditions were similar to part A. The RNA levels of pri-miR-21 and VMP1 were measured in A549 cells using qRT-PCR. A fold change of each RNA was obtained by setting the values of RNA from A549 cells in 2-D culture to one and normalization to the values of 36B4. The data were presented in averages and standard deviations obtained from three independent experiments. , , and indicated a P value < 0.05, 0.01, and 0.001, respectively.

Article Snippet: 2.4. miRNA microarray analysis The miRNA expression profiling service was provided by LC Sciences (Houston, TX) using μParaflo® technology and proprietary probe hybridization (Cy3 and Cy5 dendrimer dyes) that enables highly sensitive and specific direct detection of mouse miRNAs.

Techniques: Expressing, Cell Culture, Microscopy, Quantitative RT-PCR

Journal: Respiratory Research

Article Title: Exosomal microRNAs of tuberculous pleural effusion orchestrating TGF-β signaling mediate pleural fibrosis

doi: 10.1186/s12931-026-03541-5

Figure Lengend Snippet: Differentially expressed miRNA in exosomes from tuberculous pleural effusion and transudative pleural effusion (as control) by miRNAs sequencing. A Heatmap of differential exosomes miRNAs expression in pleural effusion between control individuals and tuberculous pleurisy patients; n = 9. RPKM values are represented by gradient colors and shown for each sample. Red represents a higher RPKM; blue represents a lower RPKM. Results are based on nine RNA sequencing samples. B Venn diagram showing the overlap between differentially expressed miRNAs in TPE exosomes and transudate exosomes. C Volcanic map of differential exosomes miRNAs expression in pleural effusion between control individuals and tuberculous pleurisy patients. Adjusted P value < 0.05 and fold change > 1 was set as restrictive conditions to identify the differentially expressed genes. D Pathway enrichment analysis showed the significant target genes of differentially expressed miRNAs associated with various KEGG pathways. E The expression of three differentially expressed miRNAs in TPE exosomes and transudate exosomes was verified by RT-qPCR and normalized by the U6. Data are expressed as mean ± SEM. n = 6, **** P < 0.0001 (Paired student’s t-test)

Article Snippet: Exosomes from pleural effusion were obtained by ultracentrifugation of samples isolated from nine control individuals and nine patients with tuberculous pleurisy patients and processed by Novogene Co., Ltd (Beijing, China) for miRNA microarray analysis (lllumina SE50).

Techniques: Control, Sequencing, Expressing, RNA Sequencing, Quantitative RT-PCR

Journal: Respiratory Research

Article Title: Exosomal microRNAs of tuberculous pleural effusion orchestrating TGF-β signaling mediate pleural fibrosis

doi: 10.1186/s12931-026-03541-5

Figure Lengend Snippet: miR-503-5p regulated Smurf1/Smad7 signaling pathway. A , B Venn diagram showing overlap between differentially up-regulated miRNAs in TPE exosomes and miRNAs targeting Smurf1 or Smad7 predicted by the miRTarBase. The online analysis database “miRTarBase” ( https://miRTarBase.cuhk.edu.cn/ ) was used. C Human PMCs were transfected with miR-503-5p mimics (50 nmol/ml) or negative control (NC) for 24 h, after which miR-503-5p expression levels in cells were determined by qRT-PCR and normalized by the U6. D - E Human PMCs were transfected with miR-25-3p mimics or miR-503-5p mimics or miR-92a-3p mimics (50 nmol/ml) or negative control (NC) for 24 h, after which intracellular mRNA levels of Smurf1 were measured by RT-qPCR and normalized to GAPDH ( D ). The protein expression of Smurf1 and TGF-β receptor (TGFBR) were detected by western blotting. Bar graphs revealed changes in relative ratio of Smurf1 and TGFBR to GAPDH. F Human PMCs were transfected with miR-503-5p mimics (50 nmol/ml) or negative control (NC) for 24 h, after which mRNA expression of Smurf1, TGFBR and COL1A1 were detected by qRT-PCR. G Human PMCs were incubated with miR-503-5p mimics. After 24 h, Smurf1 protein was detected by immunofluorescence staining and nuclei with DAPI staining. Bar scale: 50 μm. H - K Human PMCs were transfected with miR-503-5p mimics (50 nmol/ml) or negative control (NC) for 24 h. miR-503-5p expression levels in cells were determined by qRT-PCR and normalized by the U6 ( H ). The protein expression of S Smurf1, TGFBR and COL1A1 were detected by western blotting ( I ). Bar graphs revealed changes in the relative ratio to GAPDH ( J ). mRNA levels of S Smurf1, TGFBR and COL1A1 were measured by RT-qPCR and normalized to GAPDH ( K ). Data are mean ± SEM. n = 3. * P < 0.05 (student’s t-test)

Article Snippet: Exosomes from pleural effusion were obtained by ultracentrifugation of samples isolated from nine control individuals and nine patients with tuberculous pleurisy patients and processed by Novogene Co., Ltd (Beijing, China) for miRNA microarray analysis (lllumina SE50).

Techniques: Transfection, Negative Control, Expressing, Quantitative RT-PCR, Western Blot, Incubation, Immunofluorescence, Staining

Journal: Respiratory Research

Article Title: Exosomal microRNAs of tuberculous pleural effusion orchestrating TGF-β signaling mediate pleural fibrosis

doi: 10.1186/s12931-026-03541-5

Figure Lengend Snippet: Triple miRNAs inhibitor attenuated TPE-Exo induced pleural fibrosis. C57BL/6 mice were intra-pleural injected by using PBS (100 µl/mouse), TPE-Exo (100 µl/mouse), TPE-Exo plus control inhibitor, or TPE-Exo plus triple miRNAs inhibitor with carbon particles (0.1 mg/mouse) as descriptions in the Methods. TPE-Exo from 50 ml TPE was administered at days 1, 5, 9. In TPE-Exo plus triple miRNAs inhibitor group, TPE-Exo was co-incubated with triple miRNAs inhibitor which restrained expressions of miR-150-3p, miR-424-3p and miR-503-5p. All mice were euthanized at day 21, and tissues were taken for analysis. A Representative Masson’s trichrome staining images of visceral pleura from lung sections, parietal pleura from chest wall and diaphragm sections. Original magnification, ×400. B Changes in pleural thickness. C Changes in collagen percentages of visceral and parietal pleura. Data are expressed as mean ± SEM. n = 6 mice. *** P < 0.001 (One-way ANOVA followed by the Bonferroni’s test)

Article Snippet: Exosomes from pleural effusion were obtained by ultracentrifugation of samples isolated from nine control individuals and nine patients with tuberculous pleurisy patients and processed by Novogene Co., Ltd (Beijing, China) for miRNA microarray analysis (lllumina SE50).

Techniques: Injection, Control, Incubation, Staining

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Comparison of the expression profiles of miRNAs(A-C) and mRNAs (D-F) between HbH-CS patients and healthy controls. (A) Scatter plot showing the distribution of miRNA expression. (B) Volcano plot showing the differential expression of miRNAs. (C) The clustering heatmap showed differentially expressed miRNAs between patients with HbH-CS patients and healthy controls. (D) Scatter plot showing the distribution of mRNA expression. (E) Volcano plot showing the differential expression of mRNAs. (F) The clustering heatmap showed differentially expressed mRNAs between patients with HbH-CS patients and healthy controls.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Comparison, Expressing, Quantitative Proteomics

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Bioinformatics analysis. (A) Venn diagram showed stratified operations of miRNAs from the original data and online database. (B) Intersection plot of mRNAs from our previous ArrayStar human mRNA array and miR-223-3p target gene predicted by online database. (C) Prediction plot of miR-223-3p target gene. Yellow circled node, miR-223-3p; blue rectangle type node, mRNA. (D, E) The qRT-PCR was performed to detect the relative expression levels of miR-223-3p (D) and TGFBR3 (E) in the samples from healthy normal subjects and HbH-CS patients. Normal group, n = 17; HbH-CS group, n = 17, mean ± SEM, ** p < 0.01, *** p < 0.001.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Quantitative RT-PCR, Expressing