Journal: Nutrients

Article Title: Biotin Deficiency Alters the Expression Profile of Colonic microRNAs: Possible Contribution to the Alterations in Expression of Proteins Involved in the Maintenance of Colonic Physiology and Inflammation

doi: 10.3390/nu18040612

Figure Lengend Snippet: Validation of the identified miRNAs in: ( I ) colon [(A) mmu-miR-199a-3p; (B) mmu-miR-199a-5p; (C) mmu-miR-21a-3p; (D) mmu-miR-21a-5p, (E) mmu-miR-34a-5p; (F) mmu-miR-126a-3p; (G) mmu-miR-126a-5p; (H) mmu-miR-7b-5p] and ( II ) small intestinal tissue [(A) mmu-miR-146a-5p; and (B) mmu-miR-142a-3p] of biotin-deficient and their pair-fed control mice. The levels of miRNA expression were analyzed using RNA samples extracted from mouse intestinal tissue by RT-qPCR analysis. Data are means ± SE of 4 pairs of animals (n = 4). All miRNA expression results were normalized relative to internal control miRNAs RNU1A1 and UniSp6, and comparison was made relative to simultaneously performed controls as described in Methods. Statistical significance was evaluated by the Student’s t -test using GraphPad Prism software. * p < 0.05; ** p < 0.01.

Article Snippet: Transient transfection of NCM460 cells was done using 200 nM miRNA mimic miR-190a-5p (MCE MedChemExpress, Cat# HY- R00361 ) and miR-199a-5p (MCE MedChemExpress, Cat# HY- R00399 ) with appropriate negative control miRNA mimic (MCE MedChemExpress, Cat# HY- R04602 ) for 48 h, using RNAiMax (Cat# 13778150) transfection reagent to achieve maximum transfection efficiency (Invitrogen, Carlsbad, CA, USA).

Techniques: Biomarker Discovery, Control, Expressing, Quantitative RT-PCR, Comparison, Software

Journal: Scientific Reports

Article Title: Changes in circulating small non-coding RNAs after castration in a cohort of prostate cancer patients

doi: 10.1038/s41598-026-38334-9

Figure Lengend Snippet: Identification of differentially expressed sncRNAs in the two treatment arms. Generalised linear models identified sncRNAs present in significantly altered levels at W12 and W24 in contrast to W0. The analyses are based on the following distribution of samples across the three timepoints: O-arm W0 (n = 27), W12 (n = 28), and W24 (n = 24) and G-arm W0 (n = 29), W12 (n = 29), and W24 (n = 26). In ( a ), volcano plots illustrate the sncRNAs that are significant at FDR q-value < 0.05 and regulated more than onefold (red dots). Blue and green dots mark sncRNAs that are < onefold regulated and have q-values > 0.05, respectively. The dotted lines indicate an FDR q-value of 0.05 and a fold change of 1. The name is displayed for the 10 most significant sncRNAs in each contrast. Top row from the left: differentially expressed sncRNA in the group of patients that had subcapsular orchiectomies (O-arm) for contrasts W12, W24, and W12 + W24 in reference to W0. The bottom row shows the same for the group of patients receiving GnRH-agonist (G-arm). In ( b ), the number of sncRNAs identified at FDR q-value < 0.05 in each contrast, is plotted according to the subtype (miRNAs, piRNAs, pre-miRNAs, snoRNAs, snRNAs, and tRNAs). The plots on top shows the number of sncRNAs identified in higher levels post-intervention (i.e. at W12 and W24) and the plots below shows sncRNAs identified in lower levels after intervention.

Article Snippet: Quantification was performed using the TaqManTM Fast Advanced Master Mix, no UNG (Thermo Fisher Scientific, MA, USA, Cat No. A44360) with the TaqManTM Pri-miRNA Assay (hsa-miR-153-1) (Thermo Fisher Scientific, MA, USA, Assay ID: Hs03303182_pri, Cat No. A44360) and ACTB as housekeeping gene (Thermo Fisher Scientific, MA, USA, Assay ID: Hs01060665_g1, Cat No. 4331182) according to the manufacturer’s instructions.

Techniques:

Journal: Scientific Reports

Article Title: Changes in circulating small non-coding RNAs after castration in a cohort of prostate cancer patients

doi: 10.1038/s41598-026-38334-9

Figure Lengend Snippet: Longitudinal expression patterns and experimental validation of testicular expression of selected sncRNAs. Subpanels ( a-f ) show longitudinal traces of six sncRNAs for both the O and G-arm. Boxplots are shown for each timepoint (W0, W12 and W24) and treatment arm, and on top of the boxplot, points representing each participant are shown and connected with a line. Within each treatment arm, the colours represent a single participant. In g and f , results from RT-qPCR quantification of expression in the testis, skin, prostate, and epididymis are shown for miR-153-P1_pri and SNORD38A. The relative expression levels in six different commercially available RNA samples are shown. Expression was normalized to the housekeeping gene ACTB. Error bars are based on biological replicates for testis tissue (n = 3). Error bars for skin, prostate, and epididymis are based on technical variability (1 sample, 3 technical replicates for each). In ( i ), small RNA in situ hybridisation of SNORD38A in a testis tissue sample from the tumour-free periphery of an orchiectomy specimen shows a prominent expression in spermatogonia (arrows) and some expression in Leydig (arrow heads) and peritubular cells. The dashed box indicates the magnified area shown below. The bar indicates 50 and 20 μm, respectively.

Article Snippet: Quantification was performed using the TaqManTM Fast Advanced Master Mix, no UNG (Thermo Fisher Scientific, MA, USA, Cat No. A44360) with the TaqManTM Pri-miRNA Assay (hsa-miR-153-1) (Thermo Fisher Scientific, MA, USA, Assay ID: Hs03303182_pri, Cat No. A44360) and ACTB as housekeeping gene (Thermo Fisher Scientific, MA, USA, Assay ID: Hs01060665_g1, Cat No. 4331182) according to the manufacturer’s instructions.

Techniques: Expressing, Biomarker Discovery, Quantitative RT-PCR, In Situ, Hybridization

Journal: Scientific Reports

Article Title: Changes in circulating small non-coding RNAs after castration in a cohort of prostate cancer patients

doi: 10.1038/s41598-026-38334-9

Figure Lengend Snippet: Identification of differentially expressed sncRNAs in the two treatment arms. Generalised linear models identified sncRNAs present in significantly altered levels at W12 and W24 in contrast to W0. The analyses are based on the following distribution of samples across the three timepoints: O-arm W0 (n = 27), W12 (n = 28), and W24 (n = 24) and G-arm W0 (n = 29), W12 (n = 29), and W24 (n = 26). In ( a ), volcano plots illustrate the sncRNAs that are significant at FDR q-value < 0.05 and regulated more than onefold (red dots). Blue and green dots mark sncRNAs that are < onefold regulated and have q-values > 0.05, respectively. The dotted lines indicate an FDR q-value of 0.05 and a fold change of 1. The name is displayed for the 10 most significant sncRNAs in each contrast. Top row from the left: differentially expressed sncRNA in the group of patients that had subcapsular orchiectomies (O-arm) for contrasts W12, W24, and W12 + W24 in reference to W0. The bottom row shows the same for the group of patients receiving GnRH-agonist (G-arm). In ( b ), the number of sncRNAs identified at FDR q-value < 0.05 in each contrast, is plotted according to the subtype (miRNAs, piRNAs, pre-miRNAs, snoRNAs, snRNAs, and tRNAs). The plots on top shows the number of sncRNAs identified in higher levels post-intervention (i.e. at W12 and W24) and the plots below shows sncRNAs identified in lower levels after intervention.

Article Snippet: Hsa-Mir-202_pri decreased significantly in the O-arm but did not change in the G-arm.

Techniques: