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

Journal: Nature communications

Article Title: The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis

doi: 10.1038/ncomms4000

Figure Lengend Snippet: (a) The schema shows naturally occurring d-flow (lesser curvature, LC) and stable flow ( s-flow) regions (greater curvature, GC) in the aortic arch. Also shown is the surgically induced d-flow in partial carotid ligation model in which three of the four caudal branches of the left common carotid artery (LCA) are ligated, while the contralateral right common carotid artery (RCA) remains untouched as an internal control. (b) Endothelial-enriched total RNAs obtained from intima of mouse (C57BL/6) left carotid (flow-disturbed LCA) and right carotid (contralateral control, RCA) at 48 h post-ligation, were analyzed by gene array (Illumina BeadChip). Hierarchical clustering analyses of mechanosensitive miRNAs found in LCA endothelium compared to that of RCA are shown as heat maps. The color represents the expression level of the gene. Red represents high expression, while green represents low expression. The expression levels are continuously mapped on the color scale provided at the top of the figure. Each column represents a single sample pooled from 3 different LCAs or RCAs, and each row represents a single miRNA probe (n=3). (c–f) Validation of miRNA microarray results by qPCR Quantitative PCR (qPCR), using additional independent RNA samples, was used to validate the above miRNA array data. Ten miRNAs (5 up-, 5 down-regulated miRNAs at 48 hours post-ligation) were selected based on fold-change by flow. The qPCR study validated the microarray results for (c) 5 up-regulated (miR-712, -330*, -699, -223, and 770–5p) and (d) 5 down-regulated (miR-195, -30c, -29b, -26b and let-7d) miRNAs at the 48 h time point (n=5 each, data shown as mean ± s.e.m; * p<0.05 as determined by paired t- test). To further validate whether the mechanosensitive genes that were identified in vivo responded specifically to shear stress, we tested expression of these miRNAs in vitro using immortalized mouse aortic endothelial cells (iMAECs) that were subjected to laminar (LS) or oscillatory stress (OS), mimicking s-flow and d-flow in vivo , respectively . Among the 9 different miRNAs examined, 7 miRNAs were differentially expressed under oscillatory shear (n=6 each, data shown as mean ± s.e.m; * p<0.05 as determined by paired t- test) (e) . These results showed that miR-712 was the most consistently and robustly upregulated miRNA both in vivo and under flow conditions in vitro.

Article Snippet: Intimal RNAs from three LCAs or RCAs were pooled to obtain ~30 ng total RNA . miRNA microarray was performed using Illumina Mouse v2 MicroRNA expression BeadChip array (Illumina) at the Emory Biomarker Service Center .

Techniques: Ligation, Control, Expressing, Biomarker Discovery, Microarray, Real-time Polymerase Chain Reaction, In Vivo, Shear, In Vitro

Journal: Nature communications

Article Title: The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis

doi: 10.1038/ncomms4000

Figure Lengend Snippet: (a) Expression of miR-712 was determined by qPCR using endothelial-enriched RNA obtained from LCA and RCA following partial carotid ligation in C57Bl6 mouse (0–48h) (n=4, data shown as mean ± s.e.m; * p<0.05 as determined by paired t- test). (b, c) Expression of pre-miR-712 and mature miR-712 by d-flow in LCA and RCA endothelium following partial ligation at 24 and 48 hours as above in (b) was quantitated by miScript miRNA qPCR assay ( n=8 each; *p<0.05 as determined by Student’s t- test). (d, e) Expression of pre-miR-712 and mature miR-712 was measured by miScript miRNA qPCR in immortalized mouse aortic endothelial cells (iMAECs) exposed to laminar (LS), oscillatory shear (OS) or static (ST) for 24 h (n=6, data shown as mean ± s.e.m; * p<0.05 as determined by Student’s t- test). (f) Aortic arch (LC and GC) and LCA and RCA obtained at 2-days post ligation obtained from control C57Bl6 mice were subjected to fluorescence in situ hybridization using digoxigenin-labeled miR-712 probe and anti-digoxigenin antibody, which was detected by tyramide signal amplification method using Cy-3 and confocal microscopy (shown in red), (n=6). Blue: DAPI nuclear stain; Green: auto-fluorescent elastic lamina; Arrows indicate cytosolic miR-712 expression. White scale bars = 20 μm. (g) shows the potential structure and processing of pre-ribosomal RNA gene, RN45s, which is composed of 18S, 5.8S and 28S rRNA sequences with 2 intervening spacers ITS1 and ITS2. The sequences matching murine miR-712 in ITS2 and its putative human counterpart miR-663 in ITS1 are indicated as well. (h–j) Expression of DICER , DGCR8 and XRN1 in mouse RCA and LCA (2-day post ligation) were determined by qPCR (n=4, data shown as mean ± s.e.m; * p<0.05 as determined by paired t- test). (k, l) XRN1 expression in iMAECs and HUVECs exposed to LS or OS for 24 h was determined by qPCR (n=3 each, data shown as mean ± s.e.m; * p<0.05 as determined by Student’s t- test). (m) miR-712 expression was induced by treating iMAECs with XRN1 siRNA but not by DGCR8 siRNA and DICER1 siRNA (n=3 each, data shown as mean ± s.e.m; * p<0.05 as determined by Student’s t- test).

Article Snippet: Intimal RNAs from three LCAs or RCAs were pooled to obtain ~30 ng total RNA . miRNA microarray was performed using Illumina Mouse v2 MicroRNA expression BeadChip array (Illumina) at the Emory Biomarker Service Center .

Techniques: Expressing, Ligation, Shear, Control, Fluorescence, In Situ Hybridization, Labeling, Amplification, Confocal Microscopy, Staining

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Study design flowchart. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure. DEcircRNAs, differentially expressed circRNAs; DEmiRNAs, differentially expressed miRNAs; DEmRNAs, differentially expressed mRNAs

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Boxplots, volcano plots and Venn diagram of mRNAs for GSE103465. (A) Boxplot of GSE103465. (B) Volcano plots of DEmRNAs based on GSE103465. (C) Venn diagram of mRNAs for GeneCards and GSE103465, where the intersection section is predicted DEmRNAs asscociated with angiogenesis in RIF. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Boxplots, volcano plots and Venn diagram of miRNAs for GSE121219. (A) Boxplot of GSE121219. (B) Volcano plots of DEmiRNAs based on GSE121219. (C) Venn diagram of miRNAs for miRDIP and GSE121219, where the intersection section is predicted DEmiRNAs asscociated with angiogenesis in RIF. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Boxplots, volcano plots and Venn diagram of circRNAs for GSE147442. (A) Boxplot of GSE147442 after standardization. (B) Volcano plots of DEcircRNAs based on GSE147442. (C) Venn diagram of miRNAs for starBase 2.0 and GSE147442, where the intersection section is predicted DEcircRNAs asscociated with angiogenesis in RIF. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Figure 5 CircRNA-miRNA-mRNA regulatory network, which consists of 8 DEcircRNAs, 10 DEmiRNAs and 45 DERNAs. DEcircRNA, differentially expressed circular RNA; DEmiRNA, differentially expressed micro RNA; DERNA, differentially expressed RNA. Arrow-shape nodes: circRNAs, triangle nodes: miRNAs, ellipse-shaped nodes: mRNAs

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: A PPI network and circRNA–miRNA–hub gene regulatory subnetwork. (A) A PPI network of the fifty-five target genes associated with angiogenesis in RIF. (B) Six hub genes extracted by cytoHubba plug-in. (C) CircRNA–miRNA–hub gene regulatory subnetwork, consisting of 3 circRNAs, 3 miRNAs, and 3 mRNAs. PPI, protein–protein interaction; circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: Oncotarget

Article Title: miR-125a-5p is a prognostic biomarker that targets HDAC4 to suppress breast tumorigenesis

doi:

Figure Lengend Snippet: (A) miR-125a-5p expression in human normal breast cells (H184B5F/M10 cells) and breast cancer cell lines (MDA-MB-435, MDA-MB-231, MCF-7, MCF-7/Her18, R2d, R2N1d) was detected using q-PCR. (B) The R2N1d breast cancer cell line was transfected with control miRNA (5 μg), miR-125a-5p (5 μg), anti-miR-125a-5p (150 nmol/L), or anti-miR-125a-5p (150 nmol/L) + miR-125a-5p (5 μg), and miR-125a-5p expression was detected using q-PCR 48 hr post-transfection. (C–F) R2N1d cells were transfected as in (B). At the indicated times after transfection, the cells growth rate was evaluated by determining XTT assay (C) . The cells migration rate was evaluated with a wound-healing assay (D) . The cells invasion rate was evaluated using a transwell invasion chamber (E) . The proliferation marker, Ki-67 and the cells motility marker, MMP2 were evaluated with western blotting (F). Data are the means ± SD of three experiments. * P < 0.05 vs . untreated control; two-tailed Student's t test. Scale bar = 200 um.

Article Snippet: To investigate whether miRNAs are associated with survival in patients with breast cancer, we profiled miRNA expression in serum samples from five breast cancer patients ( ) who survived for less than 1 year after diagnosis (short-survival group) and five breast cancer patients who survived for more than 5 years after diagnosis (long-survival group) using an miRNA microarray (human 384 SeraMir qPCR Profiler array, System Biosciences).

Techniques: Expressing, Transfection, Control, XTT Assay, Migration, Wound Healing Assay, Marker, Western Blot, Two Tailed Test