Journal: Molecular Cancer

Article Title: BRRIAR lncRNA alters breast cancer risk by modulating interferon signaling in cis and in trans

doi: 10.1186/s12943-025-02510-8

Figure Lengend Snippet: BRRIAR expression and immune activation in patient-derived samples. a High-resolution spatial transcriptomics map of one ER + breast tumor generated using the Curio Seeker platform. b Corresponding BRRIAR -positive cell states. c Spatial neighborhood analysis of BRRIAR -positive cells. Bars represent the proportion of neighbouring cell types within a defined radius. Error bars, SD ( n = 13 cells). p value was determined by Student’s t- test (* p < 0.05). d Scatter plot showing correlation between BRRIAR and RIG-I (left panel) or IRF7 (right panel) expression. Each black dot represents an individual cell at the co-expression peak. A linear regression line with its 95% confidence interval (blue shaded area) is overlaid. The correlation coefficient was calculated using Pearson correlation ( R ), and p values were determined using a two-sided t -test. e Spatially resolved BRRIAR expression across different tumor types using both 10x Visium and Curio Seeker platforms. BRRIAR -positive cells are depicted as colored dots. f-g Cytokine profiling for granzyme B, granzyme A, IFNγ and CCL5 secreted from HCMV-activated PBMCs (donors; D1-4) after f 48 h exposure to media harvested from T47D cells transfected with dsi-CON or dsi- BRRIAR then treated with 5’ppp-dsRNA for 3 h. The dsi-CON is a non-targeting control. Error bars, SEM ( n = 4). Or g 48 h exposure to media harvested from T47D cells transfected with IVT LacZ or IVT BRRIAR for 24 h. Error bars, SEM ( n = 4). p values were determined by two-way ANOVA with Sidak’s test (* p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001). h Proposed model for BRRIAR as a positive regulator of RIG-I activation in ER + breast tumor cells to promote IFN production and support an anti-tumor immune response

Article Snippet: T47D cells were transfected with 3p-hpRNA (0.5 μg/ml; Invivogen) using Lipofectamine 3000, or 5’ppp-dsRNA (1 μg/ml) and its non-phosphorylated control dsRNA (Invivogen) using 6.25 μg of LyoVec transfection reagent (Invivogen) as per the manufacturer’s protocol.

Techniques: Expressing, Activation Assay, Derivative Assay, Generated, Transfection, Control

Journal: bioRxiv

Article Title: Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states

doi: 10.64898/2025.12.19.695525

Figure Lengend Snippet: Nucleosome-nucleosome contacts as measured by Micro-C in epigenetic regions defined by published WT K562 ChIP datasets in a) scr-CTRL b) and H1-low conditions . Two biological replicates shown each. c) Ratio of N/N+odd contacts and N/N+even nucleosome contacts in epigenetic state regions. Error bar: standard deviation between biological replicates, n=2. d) Capillary electrophoresis (TapeStation) traces of the fragment size distribution produced by MNase titration with different amounts of enzyme. The estimated fragment length of the mononucleosome peak is indicated. e) Micro-C contact probability curves for the libraries obtained from the MNase titration in (d) . f-g) RICC-seq FLDs from irradiated cells and matched gDNA controls in h-i) j-k) scr-CTRL cells and H1-low cells, subset by histone mark gapped peaks. 1 biological replicate shown.

Article Snippet: Genomic DNA control plugs were equilibrated in 0.5 M Tris-HCl pH 8 on ice (three 15-min exchanges, then +400 μL Tris) and irradiated identically, followed by the same washes. ssDNA was eluted by incubating plugs in 0.1 N NaOH (200 μL, 15 min), neutralized with 1 M Tris-HCl pH 7.5 (100 μL) + 2 mM EDTA (RT, ∼4 h), and purified with the Zymo RNA Clean & Concentrator-5 kit (R1016) using modified speeds (binds at 3,800 RCF; washes at 10,000 RCF); columns were loaded with 600 μL RNA Binding Buffer then 900 μL absolute ethanol and eluted twice in 10 μL 10 mM Tris pH 8 (total ∼18 μL).

Techniques: Standard Deviation, Electrophoresis, Produced, Titration, Irradiation

Journal: bioRxiv

Article Title: Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states

doi: 10.64898/2025.12.19.695525

Figure Lengend Snippet: a) ATAC-seq accessibility signal over Cut&Tag H3K27me3 peaks +/- 5 kb around peak centers shown with a bin size of 100 bp. b) RICC-seq FLD plot over downregulated vs unchanging H3K27me3 peaks in H1-low vs scr-CTRL. n= 1 biological replicate shown as ratio over subset genomic DNA control. Signal normalized to mononucleosome peak. c) RICC-seq FLD plot over unchanging ATAC-seq peaks and genome-wide smoothed (30 nt rolling average). n=1 biological replicate shown corrected by biological replicate-specific correction factor and ratio over similarly subset and corrected sample-matched genomic DNA control. Signal normalized to mononucleosome peak. d) RICC-seq FLD plot over upregulated ATAC-seq peaks and genome-wide, as in (c). e) RICC-seq FLD plot over upregulated ATAC-seq peaks, H3K27me3, and H3K27ac, as in (c).

Article Snippet: Genomic DNA control plugs were equilibrated in 0.5 M Tris-HCl pH 8 on ice (three 15-min exchanges, then +400 μL Tris) and irradiated identically, followed by the same washes. ssDNA was eluted by incubating plugs in 0.1 N NaOH (200 μL, 15 min), neutralized with 1 M Tris-HCl pH 7.5 (100 μL) + 2 mM EDTA (RT, ∼4 h), and purified with the Zymo RNA Clean & Concentrator-5 kit (R1016) using modified speeds (binds at 3,800 RCF; washes at 10,000 RCF); columns were loaded with 600 μL RNA Binding Buffer then 900 μL absolute ethanol and eluted twice in 10 μL 10 mM Tris pH 8 (total ∼18 μL).

Techniques: Control, Genome Wide

Journal: Journal of Leukocyte Biology

Article Title: The macrocyclic peptide rhesus theta defensin 1 activates interferon and antiviral pathways in human monocytes

doi: 10.1093/jleuko/qiaf150

Figure Lengend Snippet: Effect of RTD-1 on gene expression in human monocytes. (A) Validation of RNA-seq analysis. qRT-PCR analysis was performed for select genes from monocytes treated with or without RTD-1. (Left) Gene expression was normalized to ACTB expression, and fold change was calculated with respect to control cells (data from 2 control and 2 RTD-1–treated monocyte samples). Blue: control (0.01% HOAC), red: 10 µg/mL RTD-1 treatment. The numbers indicate change in gene expression observed by RNA-seq analysis. (Right) Comparison of fold change observed by RNA-seq and qRT-PCR for genes in the left panel. (B) IPA generated graphical representation of the RTD-1–induced gene expression in human monocytes. The position of the nodes was tweaked for readability. Blue indicates inhibition and orange indicates activation, and the legend for IPA shapes is available at https://qiagen.my.salesforce-sites.com/KnowledgeBase/articles/Knowledge/Legend . (C) GSEA of changes in gene expression induced by RTD-1. ND, not differentially expressed in RNA-seq.

Article Snippet: Cells were treated with 10 μg/mL RTD-1 or with 0.01% HOAc (vehicle control) for 4 h at 37 °C and 5% CO 2 and harvested by centrifugation at 200 g for 8 min. For THP-1, cells were resuspended at 3.3 × 10 5 cells/mL in RPMI + 1% FBS and 1% P/S for 4 h at 37 °C in 5% CO 2 and then treated with 1, 3, or 10 μg/mL RTD-1 or 0.01% HOAc (vehicle) control for 20 h. Cells were then harvested at 200 g for 8 min. RNA was isolated using Quick RNA Miniprep kit (Zymo Research) from 3 experiments.

Techniques: Gene Expression, Biomarker Discovery, RNA Sequencing, Quantitative RT-PCR, Expressing, Control, Comparison, Generated, Inhibition, Activation Assay

Journal: Journal of Leukocyte Biology

Article Title: The macrocyclic peptide rhesus theta defensin 1 activates interferon and antiviral pathways in human monocytes

doi: 10.1093/jleuko/qiaf150

Figure Lengend Snippet: Regulation of gene expression by RTD-1 in THP-1 cells. (A) THP-1 cells were treated with RTD-1 or with 0.01% HOAc vehicle control as indicated and the RNA-seq data from 3 experiments was analyzed by hierarchical clustering. Validation of RNA-seq results using qRT-PCR. Gene expression observed in RNA-seq analysis was evaluated for a few genes using qRT-PCR. The gene expression was normalized to ACTB gene expression and fold change was calculated with respect to the vehicle control. Correlation between qRT-PCR and RNA-seq data (B) with 3 µg/mL RTD-1 and (C)with 10 µg/mL RTD-1.

Article Snippet: Cells were treated with 10 μg/mL RTD-1 or with 0.01% HOAc (vehicle control) for 4 h at 37 °C and 5% CO 2 and harvested by centrifugation at 200 g for 8 min. For THP-1, cells were resuspended at 3.3 × 10 5 cells/mL in RPMI + 1% FBS and 1% P/S for 4 h at 37 °C in 5% CO 2 and then treated with 1, 3, or 10 μg/mL RTD-1 or 0.01% HOAc (vehicle) control for 20 h. Cells were then harvested at 200 g for 8 min. RNA was isolated using Quick RNA Miniprep kit (Zymo Research) from 3 experiments.

Techniques: Gene Expression, Control, RNA Sequencing, Biomarker Discovery, Quantitative RT-PCR

Journal: Journal of Leukocyte Biology

Article Title: The macrocyclic peptide rhesus theta defensin 1 activates interferon and antiviral pathways in human monocytes

doi: 10.1093/jleuko/qiaf150

Figure Lengend Snippet: RTD-1 induced phosphorylation of STAT1. THP-1 cells were pretreated with DMSO or Ruxo for 1 h and then with 0.01% HOAc or RTD-1 as shown. The cells were harvested after 30 min and extracts were analyzed by Western blotting experiments using anti-phospho-STAT1 Y701 antibody or anti-ACTB antibody. (Left) One representative gel from 2 experiments. (Right) Ratio of quantification of the phospho-STAT1 Y701 and ACTB bands from Western blots was plotted with respect to RTD-1 concentration. Results are average of 2 experiments. Error bars indicate standard deviation.

Article Snippet: Cells were treated with 10 μg/mL RTD-1 or with 0.01% HOAc (vehicle control) for 4 h at 37 °C and 5% CO 2 and harvested by centrifugation at 200 g for 8 min. For THP-1, cells were resuspended at 3.3 × 10 5 cells/mL in RPMI + 1% FBS and 1% P/S for 4 h at 37 °C in 5% CO 2 and then treated with 1, 3, or 10 μg/mL RTD-1 or 0.01% HOAc (vehicle) control for 20 h. Cells were then harvested at 200 g for 8 min. RNA was isolated using Quick RNA Miniprep kit (Zymo Research) from 3 experiments.

Techniques: Phospho-proteomics, Western Blot, Concentration Assay, Standard Deviation

Journal: Journal of Leukocyte Biology

Article Title: The macrocyclic peptide rhesus theta defensin 1 activates interferon and antiviral pathways in human monocytes

doi: 10.1093/jleuko/qiaf150

Figure Lengend Snippet: Stimulation of ISRE reporter by RTD-1. The activity of Lucia luciferase secreted in the medium was assayed and the luminescence units are plotted. (A) THP-1 Dual cells were stimulated with HOAc (vehicle) or increasing concentrations of RTD-1. Results are from 3 experiments. * P < 0.05, 2-tailed t test, comparison with HOAc-treated sample. Error bars indicate standard deviation. (B) THP-1 Dual cells were pretreated with DMSO or Ruxo as indicated. Assay done in triplicate. * P < 0.05 when compared with HOAc-treated control, 2-tailed t test. # P < 0.05 when compared with RTD-1 treatment. Error bars indicate standard deviation. (C) THP-1 Dual cells were transferred to RPMI + 1% HI FBS + P/S + normocin medium and either 2.5 μg human IgG1 or anti-IFNAR1 antibodies were added to the culture. Cells were incubated for 2 h, and RTD-1 or IFN-β was added as indicated and the incubation continued for 18 h. Assay was done in triplicate. * P < 0.05 when compared with HOAc-treated control, 2-tailed t test. Error bars indicate standard deviation. (D) THP-1 Dual cells were treated with RTD-1, IFN-β, or both as shown. Assay was done in triplicate. * P < 0.05, 2-tailed t test. Error bars indicate standard deviation.

Article Snippet: Cells were treated with 10 μg/mL RTD-1 or with 0.01% HOAc (vehicle control) for 4 h at 37 °C and 5% CO 2 and harvested by centrifugation at 200 g for 8 min. For THP-1, cells were resuspended at 3.3 × 10 5 cells/mL in RPMI + 1% FBS and 1% P/S for 4 h at 37 °C in 5% CO 2 and then treated with 1, 3, or 10 μg/mL RTD-1 or 0.01% HOAc (vehicle) control for 20 h. Cells were then harvested at 200 g for 8 min. RNA was isolated using Quick RNA Miniprep kit (Zymo Research) from 3 experiments.

Techniques: Activity Assay, Luciferase, Comparison, Standard Deviation, Control, Incubation