Journal: Nucleic Acids Research

Article Title: Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8

doi: 10.1093/nar/gkag190

Figure Lengend Snippet: Basal IFN activation of DGCR8 KO cells relies on the dsRNA-sensing pathway. ( A ) RT-qPCR analysis of the ISGs IFIT3, OAS3 , and IFIT2 in WT and two DGCR8 KO PA-1 clones treated with BX795, ruxolitinib (RUXO), or vehicle control (DMSO). GAPDH serves as a normaliser. Data are presented relative to the average expression of each gene in the KO2 DMSO condition. ( B ) RT-qPCR analysis of the ISGs DDX58, IFIH1, IFIT2 , and IFIT3 in WT and two independent DGCR8 KO PA-1 clones transfected with poly(I:C). Expression is normalised as 2^-ΔCt, serving GAPDH as normaliser. ( C ) Expression levels of the IFNB1 mRNA in WT and two DGCR8 KO PA-1 clones after G3-YDNA transfection by RT-qPCR. BV-2 cells were used as a positive control for DNA stimulation. GAPDH was used as the normaliser. Expression is represented relative to the average expression of the WT + G3-YDNA condition. ( D, E ) MAVS ( D ) and IFIH1 ( E ) KO clones in DGCR8 KO HEK293T cells. Western blot analysis was used to confirm complete KO of MAVS protein ( D , left). RT-qPCR analysis of the ISGs IFIT2 and MX1 in DGCR8 KO and double KO (dKO) cell lines. Expression is represented relative to DGCR8 KO, and GAPDH is used as normaliser. Bars represent the average of three biological replicates. Error bars plot mean ± SD. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. P -values are determined by one-way ANOVA followed by Dunnett multiple comparison post-hoc test.

Article Snippet: Cells were transfected at 70% confluency, in six-well plates, and transfected with 5 μl of Invitrogen Lipofectamine 2000 Transfection Reagent and 1 μg of Y-shaped-DNA cGAS agonist (G3-YSD) (#tlrl-ydna, Invivogen) or dsRNA analogue polyinosinic:polycytidylic acid (poly(I:C)) (HMW #tlrl-pic, Invivogen).

Techniques: Activation Assay, Quantitative RT-PCR, Clone Assay, Control, Expressing, Transfection, Positive Control, Western Blot, Comparison

Journal: Nucleic Acids Research

Article Title: Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8

doi: 10.1093/nar/gkag190

Figure Lengend Snippet: 3′ UTR-localised transposable elements form dsRNA in DGCR8 KO cells. ( A ) Read distribution of the J2-based dsRNA immunoprecipitation (dsRNA-seq) in PA-1 WT and two independent DGCR8 KO clones. Reads mapping to > 1 category are counted in each. ( B, C ) Differential TE loci expression in dsRNA-seq IPs from DGCR8 KO1 ( B ) and DGCR8 KO2 ( C ) cells versus WT. Significantly downregulated (log2FC < -1 and p-adj < 0.05) and upregulated (log2FC > 1 and p-adj < 0.05) TE loci are shown for each clone. ( D ) Fraction of upregulated TE loci (log2FC > 1 and p-adj < 0.05) in DGCR8 KO1 and KO2 dsRNA-Seq on each TE family. ( E ) Representation of TE classification; ‘self-expressed’ TEs are those annotated in intergenic regions or introns of a non-expressed protein-coding gene. Gene-dependent TEs are those inserted within exons, 5′ UTRs, 3′ UTRs, extended 3′ UTRs, introns of an expressed gene, or expressed on antisense orientation. ( F ) Fraction of self-expressed versus gene-dependent dsRNA-forming TE loci in both DGCR8 KO clones. ( G ) Fraction of intragenic versus intergenic dsRNA-forming TE loci in both DGCR8 KO clones. ( H ) Genomic distribution of dsRNA-forming TE loci in WT, DGCR8 KO1 and KO2 cells, versus those enriched (up) in KO1 or KO2 versus WT (log2FC > 1 and p-adj < 0.05) and depleted (down) in KO1 or KO2 versus WT (log2FC > -1 and p-adj < 0.05). Proportions represent the average of three biological replicates.

Article Snippet: Cells were transfected at 70% confluency, in six-well plates, and transfected with 5 μl of Invitrogen Lipofectamine 2000 Transfection Reagent and 1 μg of Y-shaped-DNA cGAS agonist (G3-YSD) (#tlrl-ydna, Invivogen) or dsRNA analogue polyinosinic:polycytidylic acid (poly(I:C)) (HMW #tlrl-pic, Invivogen).

Techniques: Immunoprecipitation, Clone Assay, Expressing

Journal: Nucleic Acids Research

Article Title: Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8

doi: 10.1093/nar/gkag190

Figure Lengend Snippet: DGCR8 binds SINE-rich mRNAs. ( A ) Absolute number of TEs per gene in: mRNAs bound by DGCR8 with at least one accumulated dsRNA-TE (log2FC > 1 and p-adj < 0.05) in either of the DGCR8 KO clones, mRNAs bound by DGCR8 without any accumulated dsRNA-TEs (yellow) and unbound mRNAs, with binding defined by Macias et al. (see Materials and methods). ( B ) Density of TEs per gene in the three gene categories defined in ( A ). ( C ) Average number of SINE, LINE and LTR elements per 3′ UTR of the three gene categories defined in ( A ). ( D ) Minimum Free Energy (MFE) violin plots for the three gene categories defined in ( A ). ( E ) Aggregate plot of mean pA ± RNA 3′ end-seq from HeLa cells (Gockert et al. 2022). Signal was plotted over 300 nt TSS-upstream to 300 nt TES-downstream regions of annotated SINE elements in 3′ UTRs of mRNAs with logFC > 1 & padj < 0.05 in DGCR8 KO2/WT dsRNA-Seq ( n = 1044). The transcriptional unit (TU) body area (TSS to TES) was normalised to 300 nt for each SINE. Mean values and 90% confidence intervals (lighter shade around the curves) of log2-transformed coverage data are displayed in the aggregate plot with binning of 5 and a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} ${{10}^{ - 1}}$\end{document} multiplication factor. ( F ) Aggregate plot of mean pA ± RNA 3′ end-seq from HeLa cells, as in ( E ). Signal was plotted over 25 nt upstream to 25 nt downstream regions of expressed mature miRNA ( n = 63). Mean values and 90% confidence intervals (lighter shade around the curves) of log2-transformed coverage data are displayed in the aggregate plot with binning of 5 and a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} ${{10}^{ - 1}}$\end{document} multiplication factor. ( G ) Immunoprecipitation of overexpressed Flag-DGCR8 in HeLa cells and co-immunoprecipitated DROSHA, ZCCHC8, and DHX9 levels by western blot. Benzonase (benz) treatment serves to test RNA-dependent interactions. ( H ) Proximity labelling assay of WT and mTurboID-DGCR8 mESCs. Biotinylated proteins were enriched using streptavidin beads, followed by western blot against DGCR8, DROSHA, ZCCHC8, and DHX9. Vinculin was used as a negative control. ( I ) Enrichment of SINE and LINE elements in genes co-bound by pairs of proteins (DGCR8, DROSHA, DHX9) compared with genes bound by only one protein. Fold change was calculated by comparing the median TE count in co-bound genes to the higher median TE count of singly-bound genes. ( A–D ) P -values are determined by Wilcoxon rank sum test. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: Cells were transfected at 70% confluency, in six-well plates, and transfected with 5 μl of Invitrogen Lipofectamine 2000 Transfection Reagent and 1 μg of Y-shaped-DNA cGAS agonist (G3-YSD) (#tlrl-ydna, Invivogen) or dsRNA analogue polyinosinic:polycytidylic acid (poly(I:C)) (HMW #tlrl-pic, Invivogen).

Techniques: Clone Assay, Binding Assay, Transformation Assay, Immunoprecipitation, Western Blot, Negative Control

Journal: Nucleic Acids Research

Article Title: Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8

doi: 10.1093/nar/gkag190

Figure Lengend Snippet: Loss of DGCR8 leads to immune system activation in 22qDS cells. ( A ) Western blot analyses of DGCR8 protein levels in PA-1 WT, DGCR8 HET, and DGCR8 KO cells. GAPDH serves as loading control (left). Quantification of three independent biological replicates (right). The dashed line represents the WT mean. ( B ) Quantification of IFNB1 mRNA levels by RT-qPCR in PA-1 WT, DGCR8 HET, and DGCR8 KO cells, both untreated and after stimulation with poly(I:C). Expression is represented as 2^-ΔCt, using GAPDH as a normaliser. ( C ) Influenza A Virus RNA levels by RT-qPCR after infection of PA-1 WT, DGCR8 HET, and DGCR8 KO. Expression was normalised to 18S rRNA and plotted relative to WT cells. ( D ) DGCR8 mRNA levels by RT-qPCR in control (healthy cells) and 22qDS immortalised fibroblasts (GM07215F). Data are normalised to GAPDH and expressed relative to WT cells. ( E ) IFNB1 expression levels by RT-qPCR in control (healthy cells) versus 22qDS immortalised fibroblasts (GM07215F), after poly(I:C) stimulation. Data are normalised to RN7SK and represented relative to stimulated healthy (WT) fibroblasts. ( F ) IFNB1 expression levels by RT-qPCR in control (healthy cells) versus 22qDS-derived primary fibroblasts (GM02944), after poly(I:C) stimulation. Data are normalised to GAPDH and represented relative to healthy stimulated cells. ( G ) Percentage of ISGs with a log2FC (22qDS/control) > 0 (up) or log2FC (22qDS/control) < 0 (down) from the following datasets: blood (Lin et al. ), T-lymphocytes (Raje et al. 2022), iPSCs-derived neurons (Lin et al. ), and cerebral cortex organoids from 22qDS-iPSCs (Khan et al. ). ( H ) Correlation between the log2FC (22qDS/control) of 22q11.2 deleted genes and ISGs. The log2FC of the mean of ISGs is plotted on the y -axis. The log2FC of the mean of 22q11.2 genes or the DGCR8 gene is plotted on the x -axis. Each dot represents one dataset, these being: blood ( n = 79 patients, n = 68 controls) (Lin et al. 2021), T-lymphocytes ( n = 13 patients, n = 6 controls) (Raje et al. 2022), iPSCs-derived neurons ( n = 8 patients, n = 7 controls) (Lin et al. 2016), hPSCs, NPCs and neurons ( n = 20 patients, n = 29 controls) (Nehme et al. ) and cerebral cortex organoids differentiated from 22qDS-iPSCs after 25, 50, 50, and 100 days ( n = 15 patients, n = 14 controls) (Khan et al. 2020). On the right, a table representing the top15 22q11.2 genes with the highest correlation index (all genes in ). ( I ) In homeostasis, DGCR8 and dsRNA-BPs such as DHX9 bind and resolve dsRNA structures of TE-rich mRNAs. After unwinding, RNAs are exported to the cytoplasm, where they are unseen by dsRNA receptors (left). In the absence of DGCR8, dsRNA structures remain unresolved. In the cytoplasm, these TE-rich RNAs are recognised by the MDA5 sensor, triggering IFN activation (right). Figure was created in BioRender ( https://BioRender.com/jt7uab7 ). In RT-qPCR, bars represent the average of three biological replicates. Error bars plot mean ± SD. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. P -values are determined by one-way ANOVA followed by Dunnett multiple comparison post-hoc test.

Article Snippet: Cells were transfected at 70% confluency, in six-well plates, and transfected with 5 μl of Invitrogen Lipofectamine 2000 Transfection Reagent and 1 μg of Y-shaped-DNA cGAS agonist (G3-YSD) (#tlrl-ydna, Invivogen) or dsRNA analogue polyinosinic:polycytidylic acid (poly(I:C)) (HMW #tlrl-pic, Invivogen).

Techniques: Activation Assay, Western Blot, Control, Quantitative RT-PCR, Expressing, Virus, Infection, Derivative Assay, Comparison

Journal: Molecules

Article Title: Rapid Discovery of CD38 Inhibitor via DNA-Encoded Natural Product Library Screening

doi: 10.3390/molecules31050864

Figure Lengend Snippet: Structural diversity of Fenbendazole-based benzimidazole analogues. ( a ) Chemical formula illustrates the structural variations at the R1 and R2 positions of the Fenbendazole scaffold among the selected benzimidazole derivatives. ( b – j ) Details of individual structures are provided.

Article Snippet: Fenbendazole analogues were also obtained from commercial sources as follows: Albendazole (TargetMol, China, #T6372), Oxibendazole (MedChemExpress, USA, #HY-B0299), Parbendazole (MedChemExpress, USA, #HY-115364), Bendamustine (Cayman, Tianjin, China, #23693), Mebendazole (MedChemExpress, USA, #HY-17595), Flubendazole (J&K, Beijin, China, #129961), Oxfendazole (Aladdin, Shanghai, China, # O279005), Nocodazole (Beyotime, Shanghai, China, #S1765), and Thiabendazole (Yeasen, Shanghai, China, #60261ES76).

Techniques: Analogues

Journal: Molecules

Article Title: Rapid Discovery of CD38 Inhibitor via DNA-Encoded Natural Product Library Screening

doi: 10.3390/molecules31050864

Figure Lengend Snippet: SPR binding analysis of Fenbendazole (4) derivatives to the extracellular domain of human CD38. Top panels ( a – f ) show the binding sensorgrams for each compound at the indicated concentrations, with each concentration represented by a distinct colored curve. Bottom panels display the corresponding equilibrium binding isotherms fitted to determine binding affinity; the calculated K D value is annotated on each plot. The chemical structure of each analyzed compound is provided adjacent to its binding data to aid in structure–activity relationship analysis.

Article Snippet: Fenbendazole analogues were also obtained from commercial sources as follows: Albendazole (TargetMol, China, #T6372), Oxibendazole (MedChemExpress, USA, #HY-B0299), Parbendazole (MedChemExpress, USA, #HY-115364), Bendamustine (Cayman, Tianjin, China, #23693), Mebendazole (MedChemExpress, USA, #HY-17595), Flubendazole (J&K, Beijin, China, #129961), Oxfendazole (Aladdin, Shanghai, China, # O279005), Nocodazole (Beyotime, Shanghai, China, #S1765), and Thiabendazole (Yeasen, Shanghai, China, #60261ES76).

Techniques: Binding Assay, Concentration Assay, Activity Assay

Journal: Molecules

Article Title: Rapid Discovery of CD38 Inhibitor via DNA-Encoded Natural Product Library Screening

doi: 10.3390/molecules31050864

Figure Lengend Snippet: Inhibitory Activity of Fenbendazole Analogues on CD38 Enzymatic Functions. ( a ) Inhibition curves of the tested compounds (final concentration: 100 μM) against CD38 hydrolase activity using e-NAD as the substrate. ( b ) Quantification of hydrolytic product levels after 10 min of reaction across experimental groups. ( c ) Inhibition curves of the tested compounds (final concentration: 50 μM) against CD38 cyclase activity using NGD as the substrate. ( d ) Quantification of cyclized product levels after 10 min of reaction across groups. ( e – g ) Dose-dependent inhibition of CD38 hydrolase by Fenbendazole and Oxibendazole. Dose–response curve and corresponding IC 50 value for Fenbendazole ( f ) and Oxibendazole ( h ) against human CD38 hydrolase activity. Data points represent the mean ± SD of triplicate measurements. Calculated IC 50 values are indicated within each panel.

Article Snippet: Fenbendazole analogues were also obtained from commercial sources as follows: Albendazole (TargetMol, China, #T6372), Oxibendazole (MedChemExpress, USA, #HY-B0299), Parbendazole (MedChemExpress, USA, #HY-115364), Bendamustine (Cayman, Tianjin, China, #23693), Mebendazole (MedChemExpress, USA, #HY-17595), Flubendazole (J&K, Beijin, China, #129961), Oxfendazole (Aladdin, Shanghai, China, # O279005), Nocodazole (Beyotime, Shanghai, China, #S1765), and Thiabendazole (Yeasen, Shanghai, China, #60261ES76).

Techniques: Activity Assay, Analogues, Inhibition, Concentration Assay

Journal: Molecules

Article Title: Rapid Discovery of CD38 Inhibitor via DNA-Encoded Natural Product Library Screening

doi: 10.3390/molecules31050864

Figure Lengend Snippet: Schematic diagram of in silico predicted key CD38–ligand interactions at the binding pocket. Cartoon representations of CD38 in complex with Topiroxostat ( a ), Fenbendazole ( d ), and Oxibendazole ( g ). The protein is depicted as a rainbow-colored cartoon, while the small molecules are shown as stick-and-ball models. In silico predicted three-dimensional representations showcasing the binding modes of CD38 with Topiroxostat ( b ), Fenbendazole ( e ), and Oxibendazole ( h ). Carbon atoms are shown in deep cyan, sulfur in yellow, oxygen in red, nitrogen in slate, and hydrogen in white. In silico predicted a two-dimensional schematic representation of the binding mode of CD38 in complex with Topiroxostat ( c ), Fenbendazole ( f ), and Oxibendazole ( i ). The color coding for the different types of intermolecular interactions is provided at the bottom of the figures.

Article Snippet: Fenbendazole analogues were also obtained from commercial sources as follows: Albendazole (TargetMol, China, #T6372), Oxibendazole (MedChemExpress, USA, #HY-B0299), Parbendazole (MedChemExpress, USA, #HY-115364), Bendamustine (Cayman, Tianjin, China, #23693), Mebendazole (MedChemExpress, USA, #HY-17595), Flubendazole (J&K, Beijin, China, #129961), Oxfendazole (Aladdin, Shanghai, China, # O279005), Nocodazole (Beyotime, Shanghai, China, #S1765), and Thiabendazole (Yeasen, Shanghai, China, #60261ES76).

Techniques: In Silico, Binding Assay