mirna arrays  (Thermo Fisher)

Journal: MedComm

Article Title: Dormant Metastases Exhibit a Unique Phenotype Primarily Promoted by the Ch25h Gene and Are Maintained in Dormancy by T Lymphocytes

doi: 10.1002/mco2.70437

Figure Lengend Snippet: Genes differentially expressed in the dormant metastasis group. Heat maps are presented to illustrate the differential expression data between the three metastatic groups obtained from RNA‐Seq (A), or RT‐qPCR in genes involved in the cholesterol synthesis pathway (B), in chemokine genes (C), and in surface marker genes (D). Only genes that displayed a greater than twofold difference in expression (log2>1) with a p ‐value less than 0.001 were identified and plotted in the heatmap. The expression values are presented as log2 values and are scaled by gene. In RT‐qPCR assays, the expression levels of the genes of interest were determined with respect to the levels of the β‐actin and GAPDH housekeeping genes. The data for the overt‐met group were set to 1. The values represent the means of three independent experiments performed in duplicate. The statistical analysis was performed using ANOVA, followed by Tukey's post hoc test.

Article Snippet: The miProfileMouse miRNome miRNA qPCR Array (catalog QM002; GeneCopoeia) was used to analyze 834 mouse miRNAs.

Techniques: Quantitative Proteomics, RNA Sequencing, Quantitative RT-PCR, Marker, Expressing

Journal: MedComm

Article Title: Dormant Metastases Exhibit a Unique Phenotype Primarily Promoted by the Ch25h Gene and Are Maintained in Dormancy by T Lymphocytes

doi: 10.1002/mco2.70437

Figure Lengend Snippet: MicroRNAs that are differentially expressed in the dormant metastasis group. (A) Heat map is presented to illustrate the differential expression data between the three metastatic groups. (B) miRNA enrichment analysis of miRNAs differentially expressed in dormant‐met group (miEAA). The expression of 834 miRNAs was measured using the ‘mouse miRNome qPCR arrays 18.0’ (Genecopoeia). Only miRNAs that displayed a greater than twofold difference ( p < 0.01) when comparing the dormant‐met group with the nude‐met and overt‐met groups were plotted. The expression levels of the miRNAs of interest were determined with respect to the levels of six housekeeping snRNAs (MK1‐MK6). The data for the overt‐met group were set to 1. The values are presented as the means of three independent experiments, each performed in duplicate. The statistical analysis was conducted using an ANOVA test, followed by a Tukey's post hoc test.

Article Snippet: The miProfileMouse miRNome miRNA qPCR Array (catalog QM002; GeneCopoeia) was used to analyze 834 mouse miRNAs.

Techniques: Quantitative Proteomics, Expressing

Journal: bioRxiv

Article Title: Perfusion Bioreactor Culture Incorporating Mechanical Confinement Enhances Mesenchymal Stem Cell Extracellular Vesicle Production and Wound Healing Potential

doi: 10.1101/2025.08.12.669872

Figure Lengend Snippet: A) Timeline of experiment setup and injection schedule. Mice received injections of 1.1×10 10 EVs or an equivalent volume of PBS on days 0, 3, 6, and 9. B) Representative photos of splinted wounds receiving each treatment over 14 days (n=4-6). C) Percent wound closure based on wound area over 14 days (n=4-6). D) Fold change of M1 markers CD86, iNOS, and TNF11 and E) M2 markers IL-10, CD206, and Arg1 in harvested tissue from mice receiving flask and bioreactor EV injections relative to tissue from mice receiving PBS, as quantified by qPCR. Data represents 4 biological replicates analyzed with 3 technical replicates each per treatment group (n=4). F) Length of regenerating epithelium from H&E staining as a percentage of the length of the wound bed (n=4-6). G) Collagen deposition from Masson’s Trichrome staining quantified as a percentage of the total tissue volume (n=4-6). G) Granulation tissue area from H&E staining (n=4-6). I) CD31 fluorescence intensity normalized to DAPI over multiple fields of view and representative confocal microscopy images taken at 10X magnification (n=4-5). All values expressed as mean +/- standard error of the mean (ns – no significance; * p<0.05; ** p<0.01).

Article Snippet: Resulting cDNA was analyzed in a human MSC exosome miRNA qPCR array (GeneCopoeia; QM0460B6) per the manufacturer’s protocol.

Techniques: Injection, Staining, Fluorescence, Confocal Microscopy

Journal: bioRxiv

Article Title: Perfusion Bioreactor Culture Incorporating Mechanical Confinement Enhances Mesenchymal Stem Cell Extracellular Vesicle Production and Wound Healing Potential

doi: 10.1101/2025.08.12.669872

Figure Lengend Snippet: A) Heat map of the miRNA content of 5 µm static and 5 µm bioreactor EVs represented as the log2(fold change) relative to flask EVs (n≥2). B) Volcano plot comparing the miRNA within static and flask EVs, with the horizontal line at 1.3 (p = 0.05) representing statistical significance (n≥2). C) Volcano plot comparing the miRNA within bioreactor and flask EVs, with the horizontal line at 1.3 (p = 0.05) representing statistical significance. The labeled points indicate those in common between both static and bioreactor EVs (n≥2). All data represents the average of at least 2 independent experiments.

Article Snippet: Resulting cDNA was analyzed in a human MSC exosome miRNA qPCR array (GeneCopoeia; QM0460B6) per the manufacturer’s protocol.

Techniques: Labeling

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: MicroRNAs as regulators of NLRP3 inflammasome activation in herpes simplex virus type 2 infection

doi: 10.3389/fcimb.2025.1602965

Figure Lengend Snippet: TaqMan Assay of the target miRNAs: Graphical representation of (A) miR-141, (B) miR-211 miRNA and (C) HSV-2 UL30 mRNA expression during HSV-2 infection at 8-, 16- and 24 hpi relative to mock-infected cells. LPS-treatment (10 µg/mL, 24 hours) were included as an additional control to assess the specificity of miRNA downregulation during HSV-2 infection. miR-141 and miR-211 levels were quantified using specific TaqMan assays and normalized to RNA-U6. HSV-2 UL30 expression was measured by SYBR Green qPCR and normalized to GAPDH. Data represent the mean ± SD of at least three independent experiments. Statistical analysis was performed using one-way ANOVA followed by Tukey’s multiple comparisons test. The number of asterisks indicates the level of significance (*p<0.05, **p<0.01, ***p<0.001).

Article Snippet: The miRNAs hsa-miR-141-3p and hsa-miR-211-5p were selected for this study based on preliminary screening using the Human Inflammatory and Immune Response miRNA PCR Array (Qiagen, Cat. No. MIHS-105ZA), which revealed their downregulation in HSV-2-infected THP-1 cells ( ).

Techniques: TaqMan Assay, Expressing, Infection, Control, SYBR Green Assay

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: MicroRNAs as regulators of NLRP3 inflammasome activation in herpes simplex virus type 2 infection

doi: 10.3389/fcimb.2025.1602965

Figure Lengend Snippet: miR-141 and miR-211 regulate inflammation by targeting NLRP3 and CASP1, respectively, during HSV-2 infection: (A) Target validation of NLRP3 by miR-141 and (B) Target validation of CASP1 by miR-211. The complementary sequences between the seed regions of the wild-type and mutant (Δ) 3′ UTRs of NLRP3 and CASP1 with the respective miR-141 and miR-211 binding sites are shown. Relative luciferase activity (%) was measured in HEK293T cells transfected with miRNA target/co-transfected with miRNA target and scrambled miRNAs or miRNA mimic of interest, to demonstrate target regulation. Also, cells were transfected with wild-type (wt) or mutated (mt) 3′ UTRs of NLRP3 and CASP1 along with respective miRNA mimics to validate sequence-specific targeting by miRNAs. (C) Immunoblot analysis of NLRP3 and CASP1 protein levels following transfection with miR-141 and miR-211 mimics or scrambled controls. GAPDH served as the loading control. Data represent the mean ± SD of three independent experiments.The number of asterisks, as shown in each of the graphs, indicates the level of significance of the data (**p<0.01, ***p<0.001).

Article Snippet: The miRNAs hsa-miR-141-3p and hsa-miR-211-5p were selected for this study based on preliminary screening using the Human Inflammatory and Immune Response miRNA PCR Array (Qiagen, Cat. No. MIHS-105ZA), which revealed their downregulation in HSV-2-infected THP-1 cells ( ).

Techniques: Infection, Biomarker Discovery, Mutagenesis, Binding Assay, Luciferase, Activity Assay, Transfection, Sequencing, Western Blot, Control

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: MicroRNAs as regulators of NLRP3 inflammasome activation in herpes simplex virus type 2 infection

doi: 10.3389/fcimb.2025.1602965

Figure Lengend Snippet: miR-141 and miR-211 modulates HSV-2 viral gene expression across different replication phases: THP-1-derived macrophages were transfected with either miR-141, miR-211, or scrambled control miRNA, followed by HSV-2 infection. At 8 hpi, viral gene expression was analyzed across different replication phases by measuring key viral transcripts: RL2 (immediate early phase), UL30 (early phase), and UL44 (late phase). (A-C) The effects of miR-141 on HSV-2 viral gene transcripts. miR-141 significantly reduced the expression of all viral genes in the HSV-2 infected cells. (D-F) The effects of miR-211 under identical experimental conditions. Similar to miR-141, miR-211 demonstrated potent antiviral activity. “-” and “+” indicate absence or presence of HSV-2, sc-miR, miR-211, or miR-141 as specified. Data represent the mean ± SD of at least three independent experiments. Statistical analysis between two groups was performed using an unpaired two-tailed Student’s t-test (***p < 0.001).

Article Snippet: The miRNAs hsa-miR-141-3p and hsa-miR-211-5p were selected for this study based on preliminary screening using the Human Inflammatory and Immune Response miRNA PCR Array (Qiagen, Cat. No. MIHS-105ZA), which revealed their downregulation in HSV-2-infected THP-1 cells ( ).

Techniques: Gene Expression, Derivative Assay, Transfection, Control, Infection, Expressing, Activity Assay, Two Tailed Test

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: MicroRNAs as regulators of NLRP3 inflammasome activation in herpes simplex virus type 2 infection

doi: 10.3389/fcimb.2025.1602965

Figure Lengend Snippet: miR-141 and miR-211 suppress HSV-2-induced inflammatory responses: THP-1-derived macrophages were transfected with either miRNA or scrambled controls before HSV-2 infection. The expression of key inflammatory markers (NLRP3, GSDM-D, IL-18, and IL-1β) was quantified using qRT-PCR. (A-D) Effects of miR-141 on inflammatory markers. miR-141 transfection significantly reduced NLRP3, GSDM-D, IL-18, and IL-1β expression compared to HSV-2-infected controls. (E-H) Effects of miR-211 under identical experimental conditions. miR-211 demonstrated similar anti-inflammatory effects, reducing NLRP3, GSDM-D, IL-18, and IL-1β expression. The “-” and “+” symbols indicate absence or presence of HSV-2, sc-miR, miR-211, or miR-141 as specified. Data represent the mean ± SD of at least three independent experiments. Statistical analysis between two groups was performed using an unpaired two-tailed Student’s t-test (*p<0.05, **p<0.01, ***p<0.001).

Article Snippet: The miRNAs hsa-miR-141-3p and hsa-miR-211-5p were selected for this study based on preliminary screening using the Human Inflammatory and Immune Response miRNA PCR Array (Qiagen, Cat. No. MIHS-105ZA), which revealed their downregulation in HSV-2-infected THP-1 cells ( ).

Techniques: Derivative Assay, Transfection, Infection, Expressing, Quantitative RT-PCR, Two Tailed Test

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: MicroRNAs as regulators of NLRP3 inflammasome activation in herpes simplex virus type 2 infection

doi: 10.3389/fcimb.2025.1602965

Figure Lengend Snippet: miR-141 and miR-211 exhibit anti-inflammatory effects upon HSV-2 infection: The anti-inflammatory roles of miR-141 and miR-211 were confirmed through Immunoblotting and ELISA. (A, B) The relative protein expression levels of the active inflammatory markers- Caspase-1, IL-1β, IL-18 and GSDM-D were observed to be significantly decreased in miR-141 and miR-211 transfected and HSV-2 infected cells as compared to untransfected but infected cells. These reduced expression levels were not observed in Sc-miR transfected cells emphasizing on the sequence-complementarity-based specific gene regulation by the respective miRNAs. HSV-2 ICP8 protein levels confirmed the progression of infection, whereas, GAPDH was used as the loading control. Furthermore, (C, D) The declined release of the pro-inflammatory cytokines, IL-1β and IL-18 obtained through the ELISA further evidenced the negative impact of these miRNAs on the regulation of inflammation induced by HSV-2 infection. Data represent the mean ± SD of three independent experiments. Statistical analysis was performed using one-way ANOVA followed by Tukey’s multiple comparisons test. The number of asterisks, as shown in each of the graphs, indicates the level of significance of the data (**p<0.01).

Article Snippet: The miRNAs hsa-miR-141-3p and hsa-miR-211-5p were selected for this study based on preliminary screening using the Human Inflammatory and Immune Response miRNA PCR Array (Qiagen, Cat. No. MIHS-105ZA), which revealed their downregulation in HSV-2-infected THP-1 cells ( ).

Techniques: Infection, Western Blot, Enzyme-linked Immunosorbent Assay, Expressing, Transfection, Sequencing, Control

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: MicroRNAs as regulators of NLRP3 inflammasome activation in herpes simplex virus type 2 infection

doi: 10.3389/fcimb.2025.1602965

Figure Lengend Snippet: Schematic representation of the key signaling pathways involved in HSV-2-induced inflammation and pyroptosis: 1. HSV-2 Entry: Herpes Simplex Virus Type 2 (HSV-2) enters the host cell, initiating inflammatory responses. 2. Inflammasome Assembly: Upon HSV-2 infection, the miRNAs, miR-141 and miR-211 that target NLRP3 and CASP, are downregulated- a mechanism that may be crucial in facilitating the assembly of the inflammasome complex containing NLRP3, ASC, and Pro-Caspase-1. 3. Activation of Caspase-1: The assembled inflammasome activates Caspase-1 by cleaving its precursor, pro-Caspase-1. Activated Caspase-1 facilitates downstream inflammatory responses. 4. Cytokine Maturation: Caspase-1 in its active form cleaves the pro-inflammatory cytokine precursor Pro-IL-1β into its active form, IL-1β, which is then secreted excessively to amplify the inflammatory response. 5. Pyroptosis and Pore Formation: Caspase-1 also converts Gasdermin-D (GSDM-D) by cleaving into its N-terminal active fragment (N-GSDM-D), forming membrane pores. This results in pyroptosis, a form of programmed cell death, and the release of excessive inflammatory cytokines. 6. Ectopic Expression of miRNAs: MicroRNAs hsa-miR-141 and hsa-miR-211 are potential therapeutic agents. Their ectopic expressions suppress the inflammasome assembly and activation by targeting the key components NLRP3 and Caspase-1, respectively, thus mitigating inflammatory responses and viral replication. 7. By restricting inflammasome activation , these miRNAs limit the severity of HSV-2 infection, demonstrating their potential as therapeutic agents to inhibit inflammation and control viral pathogenesis.

Article Snippet: The miRNAs hsa-miR-141-3p and hsa-miR-211-5p were selected for this study based on preliminary screening using the Human Inflammatory and Immune Response miRNA PCR Array (Qiagen, Cat. No. MIHS-105ZA), which revealed their downregulation in HSV-2-infected THP-1 cells ( ).

Techniques: Protein-Protein interactions, Virus, Infection, Activation Assay, Membrane, Expressing, Control