Journal: Frontiers in Immunology

Article Title: Hsa-miR-31 Governs T-Cell Homeostasis in HIV Protection via IFN-γ-Stat1-T-Bet Axis

doi: 10.3389/fimmu.2021.771279

Figure Lengend Snippet: miR-31 is correlated with disease progression during both acute and chronic HIV-1 infection. (A) Unsupervised clustering of the 251 miRNAs. After normalization and filtering of the microarray data, 251 miRNAs were retained for further analysis. Average linkage hierarchical clustering was performed using a centered correlation metric. Twenty-three samples from the FBD study were clustered into 2 groups: the left cluster was a mixture of elite controllers, viremic controllers and progressors; the right was mainly progressors with one exception. (B) Venn diagram showing the numbers of candidate miRNAs filtered with different criteria. The miRNAs in the lower left and right circles were generated by significance analysis of microarrays (SAM) of participants stratified by the CD4+ T cell count (<250 cells/μL vs. >450 cells/μL) and viral load (<2000 copies/mL vs. >10000 copies/mL), respectively. The identified 15 miRNA candidates were marked in red in (A) . (C) Correlation between expression levels of miR-31 and CD4+ T cell counts in HIV-1 infected individuals (FBD, former blood donor cohort). miR-31 expression was quantified by quantitative RT-PCR, and the relationship between relative level of miR-31 and CD4+ T cell count was examined by Spearman correlation (n = 50). Red dots represent patients that eventually reached the defined endpoints. (D) Kaplan-Meier survival curves of FDB patients stratified by median whole blood miR-31 level during the late phase of chronic infection. (E–G) Kaplan-Meier survival curves of another HIV patient cohort (an acute-phase prospective men who have sex with men (MSM) cohort) stratified by plasma miR-31 levels before and after infection. Absolute CD4+ T cell count below 350 cells/μL, initiation of long-term ART, progression to AIDS and death were defined as endpoints of the study. Patients were separated into two groups stratified by the median miR-31 level in plasma collected before infection (E) , during acute infection phase (F) , during early phase of chronic infection (G) .

Article Snippet: PAXgene Blood miRNA Kit (QIAGEN, Hilden, Germany) was used for extraction and purification of total RNA, including miRNA, from whole blood stabilized in PAXgene Blood RNA Tubes (PreAnalytix, BD, UK).

Techniques: Biomarker Discovery, Infection, Microarray, Generated, Cell Counting, Expressing, Quantitative RT-PCR, Clinical Proteomics

Journal: Frontiers in Immunology

Article Title: Hsa-miR-31 Governs T-Cell Homeostasis in HIV Protection via IFN-γ-Stat1-T-Bet Axis

doi: 10.3389/fimmu.2021.771279

Figure Lengend Snippet: Loss of miR-31 triggers CD4+ T cell activation. (A) miR-31 levels in different immune cell subtypes. Data were obtained from a miRNA RTqPCR data from Rossi et al ’s work (see the text for reference). (B) Comparison of absolute naïve CD4+ T cell counts in blood of HIV-1 infected individuals (FBD, n = 50) stratified by miR-31 expression. (C, D) Correlation between miR-31 levels and frequencies of CD38+ T cells (C) or HLA-DR+ T cells in blood of HIV infected individuals (FBD, n=44) (E) Gene set enrichment analysis (GSEA) of “naïve” signature in antagomiR-31- versus antagoNC- treated naïve CD4+ T cells. NES, normalized enrichment score. (F) Heatmap of representative genes associated with activation versus naïve state of T cells. Shown is log2 fold changes of gene expression in antagomiR-31-treated naïve CD4+ T cells relative to that in antagoNC-treated cells (n=3). (G) Effects of antagomiR-31 treatment on CD25 expression of naïve CD4+ T cells, assessed by frequency of CD25+ cells and median fluorescent intensity (MFI) of CD25. Average fold changes were 4.45 and 2.25, respectively (n = 8). Blue, antagomir-31 treated group; red, antagoNC-treated group. Representative FACS data for CD25 were shown in the left panel. (H) Schema of the in vitro assay used for examining the role of miR-31 in HIV-1 infection. CD4+ T cells were sorted, followed by transfection with antagomiR-31 or antagoNC. After 48 hours, cells were stimulated with a mix of anti-CD3 and anti-CD28 antibodies and infected with HIV-1 IIIB 5 days later. (I, J) Cells and supernatants were collected on days 5 and 11 post infection and respectively subjected to flow cytometry for determination of P24-expressing CD4+ T cells (I) and ELISA for quantification of released P24 proteins (J) (n = 3).

Article Snippet: PAXgene Blood miRNA Kit (QIAGEN, Hilden, Germany) was used for extraction and purification of total RNA, including miRNA, from whole blood stabilized in PAXgene Blood RNA Tubes (PreAnalytix, BD, UK).

Techniques: Activation Assay, Comparison, Infection, Expressing, Gene Expression, In Vitro, Transfection, Flow Cytometry, Enzyme-linked Immunosorbent Assay

Journal: Toxicology Reports

Article Title: Placental microRNAs: Responders to environmental chemicals and mediators of pathophysiology of the human placenta

doi: 10.1016/j.toxrep.2020.08.002

Figure Lengend Snippet: miRNAs in the placenta that are responsive to exposure to environmental toxicants.

Article Snippet: Toxic Metals , Placenta, JEG-3 cells , N = 32 , 861 , miR-26a, miR-155 , AllPrep DNA/RNA/miRNA Univerisal Kit (Qiagen) , Human miRNA Oligo microarray (Agilent); qRT-PCR , miRNA U6 , (Brooks, Martin et al. 2016).

Techniques: Extraction, Microarray, Isolation

Journal: Microorganisms

Article Title: Coinfection of Dermal Fibroblasts by Human Cytomegalovirus and Human Herpesvirus 6 Can Boost the Expression of Fibrosis-Associated MicroRNAs

doi: 10.3390/microorganisms11020412

Figure Lengend Snippet: Expression of fibrosis-associated miRNAs in response to HCMV/HHV-6A coinfection of human dermal fibroblasts. Cell samples were collected at the indicated days post-infection (d.p.i.) and analyzed by qPCR microarray. ( a ) Scatterplot representation (threshold put at 2-fold change in coinfected vs. uninfected control cells). Red and blue dots represent up-regulated and down-regulated factors, respectively. Results are expressed as mean values of duplicate samples in two independent experiments. ( b ) Detailed values of down- and up-regulated factors: dark blue, down-regulation >10-fold; light blue, down-regulation between 9.9- and 2-fold; light red, up-regulation between 2- and 9.9-fold; medium red, up-regulation between 10- and 99.9-fold; dark red, up-regulation >100-fold.

Article Snippet: In short, 10 ng aliquots of RNA were retrotranscribed by the miRCURY LNA miRNA RT Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

Techniques: Expressing, Infection, Microarray, Control

Journal: Microorganisms

Article Title: Coinfection of Dermal Fibroblasts by Human Cytomegalovirus and Human Herpesvirus 6 Can Boost the Expression of Fibrosis-Associated MicroRNAs

doi: 10.3390/microorganisms11020412

Figure Lengend Snippet: Expression of fibrosis-associated miRNAs most up- or down-regulated by HCMV/HHV-6A coinfection in human dermal fibroblasts. Cell samples were collected at the indicated days post-infection (d.p.i.) and analyzed by individual miRNA assays. Results are expressed as mean values of fold-change ± S.D. of duplicate samples in two independent experiments.

Article Snippet: In short, 10 ng aliquots of RNA were retrotranscribed by the miRCURY LNA miRNA RT Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

Techniques: Expressing, Infection

Journal: Biomedical reports

Article Title: Lipolysis by downregulating miR-92a activates the Wnt/β-catenin signaling pathway in hypoxic rats.

doi: 10.3892/br.2020.1340

Figure Lengend Snippet: Figure 1. Analysis of miR‑92a expression in the epididymal fat of hypoxic rats. (A) B3L, B6L and B9L were from normoxic rats. (B) D2L, D6L, and D9L were from hypoxic rats. (C) Relative expression of miRNAs in the normoxic and hypoxic rats. miR‑92a expression levels in the hypoxic rats were reduced compared with the normoxic rats based on the miRNA micro array analysis. miR, microRNA; Rno, Rattus norvegicus.

Article Snippet: The following reagents and instruments were used: miRcute miRNA Isolation kit (Tiangen Biotech Co., Ltd.), miRcute miRNA cDNA First Strand Synthesis kit (Tiangen Biotech Co., Ltd.), miRcute MiRNA Quantitative Fluorescence Detection kit (cat. no. FP401; Tiangen Biotech Co., Ltd.), SuperReal PreMix SYBR‐Green (cat. no. FP204; Tiangen Biotech Co., Ltd.), TIANScript II cDNA First Strand Synthesis kit (cat. no. KR107; Tiangen Biotech Co., Ltd.) and RT‐qPCR amplifier (BIOER FQD‐96A; Hangzhou Bioer Co., Ltd.).

Techniques: Expressing, Microarray

Journal: Biomedical reports

Article Title: Lipolysis by downregulating miR-92a activates the Wnt/β-catenin signaling pathway in hypoxic rats.

doi: 10.3892/br.2020.1340

Figure Lengend Snippet: Figure 3. Analysis of miR‑92a binding with Fzd10. (A) Wild‑type and mutant‑type binding sequences of miR‑92a with Fzd10. (B) Dual luciferase reporter assay. Wild‑type miR‑92a bound and degraded wild‑type Fzd10 mRNA in the Fzd10+miR92a group. Single Fzd10 or mutated Fzd10 mRNA did not result in altered fluorescence values of the empty carrier pRL‑TK, and miR‑92a was not significantly altered the fluorescence values of the mutated Fzd10 mRNA in the mFzd10+miR92a group. miR/miRNA, microRNA; Fzd10, frizzled 10; mFzd10, mutated Fzd10.

Article Snippet: The following reagents and instruments were used: miRcute miRNA Isolation kit (Tiangen Biotech Co., Ltd.), miRcute miRNA cDNA First Strand Synthesis kit (Tiangen Biotech Co., Ltd.), miRcute MiRNA Quantitative Fluorescence Detection kit (cat. no. FP401; Tiangen Biotech Co., Ltd.), SuperReal PreMix SYBR‐Green (cat. no. FP204; Tiangen Biotech Co., Ltd.), TIANScript II cDNA First Strand Synthesis kit (cat. no. KR107; Tiangen Biotech Co., Ltd.) and RT‐qPCR amplifier (BIOER FQD‐96A; Hangzhou Bioer Co., Ltd.).

Techniques: Binding Assay, Luciferase, Reporter Assay, Fluorescence

Journal: Placenta

Article Title: MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth.

doi: 10.1016/j.placenta.2024.08.004

Figure Lengend Snippet: Fig. 2. Upregulated and downregulated human placenta miRNAs associ- ated spontaneous preterm labor. MiRNAs isolated from human placentas after SPTB (n = 6) were compared with miRNAs of placentas obtained from STB (n = 6).

Article Snippet: MiRNAs were isolated with the NucleoSpin miRNA kit (Macherey-Nagel).

Techniques: Isolation

Journal: Placenta

Article Title: MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth.

doi: 10.1016/j.placenta.2024.08.004

Figure Lengend Snippet: Fig. 3. Functional annotation clustering of miRNA targets associated with spontaneous preterm birth. Clustering was performed via DAVID Functional Annotation Bioinformatics Microarray Analysis. The three most affected pathway clusters and ten most affected pathways from each of the clusters are shown. The size of the ball represents the number and colour represents the percentage of affected genes in the pathway.

Article Snippet: MiRNAs were isolated with the NucleoSpin miRNA kit (Macherey-Nagel).

Techniques: Functional Assay, Microarray

Journal: Placenta

Article Title: MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth.

doi: 10.1016/j.placenta.2024.08.004

Figure Lengend Snippet: Fig. 4. Expression of miR-489-3p, miR-766-3p, and miR-889-3p in SPTB and STB placentas. Relative miRNA levels from the basal plates (maternal side of the placenta) were normalized to the miRNA levels of the “housekeeping miRNA” hsa-miR-103a-3p. Differences were analyzed with a nonparametric Mann–Whitney U test. Asterisk indicates statistically significant changes. Box and whiskers display quartiles. The band inside the box denotes the median, and the ends of the whiskers denote the minimum and maximum values; the square inside the box represents the mean value.

Article Snippet: MiRNAs were isolated with the NucleoSpin miRNA kit (Macherey-Nagel).

Techniques: Expressing, MANN-WHITNEY

Journal: Placenta

Article Title: MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth.

doi: 10.1016/j.placenta.2024.08.004

Figure Lengend Snippet: Fig. 5. Effect of hsa-miR-489-3p and hsa-miR-766-3p miRNA mimic transfections on SLIT2 mRNA expression. Ten nM and 50 miRNA mimic transfections were applied to the HEK-293T cells. The effect of the transfection on SLIT2 mRNA exprssion was measured via qPCR, and the result was compared to the result of the miRNA mimic negative control transfection. Negative control values were set to 1.00 (miR-neg), to which the rest of the samples were compared. Lines show the median value of the nine replicates. Statistical significance was determined via a Mann–Whitney U test.

Article Snippet: MiRNAs were isolated with the NucleoSpin miRNA kit (Macherey-Nagel).

Techniques: Transfection, Expressing, Negative Control, MANN-WHITNEY

Journal: Placenta

Article Title: MicroRNA expression profile in the basal plate of human placenta associates with spontaneous preterm birth.

doi: 10.1016/j.placenta.2024.08.004

Figure Lengend Snippet: Fig. 6. Binding of miRNAs in 3′ UTR of SLIT2. The figure shows luciferase reporter-based assays used to detect the binding of miR-489-3p (a) and miR-766-3p (b) mimics to the 3′ UTR of SLIT2 mRNA. 10 nM and 50 nM mimic concentrations were used. Constructs were cotransfected with miR-489-3p mimic (a), miR-677-3p mimic (b), or miRNA mimic negative control into the HEK-293T cells. Luciferase activities were measured via dual luciferase reporter assay, in which Firefly luciferase was the experimental reporter and Renilla luciferase the control reporter. Negative control values were set to 1.00 (WT/miR-neg), to which the rest of the samples were compared. Lines show the median value of the nine replicates. Statistically significant changes were determined using the Mann–Whitney U test.

Article Snippet: MiRNAs were isolated with the NucleoSpin miRNA kit (Macherey-Nagel).

Techniques: Binding Assay, Luciferase, Construct, Negative Control, Reporter Assay, Control, MANN-WHITNEY