Journal: PLOS Biology

Article Title: Expression of intron-containing HIV-1 RNA induces NLRP1 inflammasome activation in myeloid cells

doi: 10.1371/journal.pbio.3003320

Figure Lengend Snippet: (A) Flow cytometry analysis (left panel) of MDMs infected with WT or mutant (M10 or M10-4xCTE) Lai∆envGFP/G viruses (MOI 1) in the presence of SIV3 + /Vpx VLPs, compared to mock (no virus infection). % infection (GFP + ) in MDMs was quantified at 3 dpi (right panel). (B) Immunoblotting analysis of whole cell lysates from MDMs infected with HIV-1 (WT, M10, or M10-4xCTE constructs) in the absence (untreated, DMSO) or presence of RT inhibitor (EFV, 1 μM) at 3 dpi. HIV-1 proteins (p55 Gag and p24 Gag ) were visualized using anti-HIV-1 IgG, β-actin was used as a loading control. (C) RT-qPCR quantification of unspliced (usRNA), and multiply-spliced (Tat/Rev) transcripts (msRNA) ( D ) in whole cell lysates from MDMs infected with WT, M10, or M10-4xCTE virus ± EFV, at 3 dpi compared to uninfected (mock) lysates. HIV-1 unspliced and spliced transcripts were quantified by RT-qPCR. Production of bioactive type-I IFN (E) , and secretion of IL-1β ( F ) in culture supernatants from MDMs infected with WT, M10, or M10-4xCTE virus ± EFV were harvested at 3 dpi and quantified using type I IFN bioassay or ELISA, respectively. (G, H) Transient knockdown of MAVS, STING and UNC93B1 by siRNA transfection in primary MDMs. Knockdown efficiency was quantified by RT-qPCR (G) at day 2 post-transfection and reported as relative expression normalized to that observed with scramble siRNA (siControl), and protein level analyzed by immunoblotting (H) . siRNA-transfected MDMs were infected with Lai∆envGFP/G (MOI 1) for 3 days (I–L) . Culture supernatants were harvested and analyzed at 3 dpi for p24 Gag (I) , IL-1β (J) , and IP-10 (K) secretion by ELISA. (L) Bioactive type I IFN in the culture supernatants from infected MDMs at 3 dpi quantified using interferon bioassay. The values were normalized to that of mock-infected control in each donor. The means ± SEM are shown, with each symbol representing an independent donor. The means ± SEM are shown, and each symbol represents an independent donor. Statistical significance was determined by two-way ANOVA followed by Tukey’s multiple comparisons (C, D) , or Dunnett’s post-test, comparing HIV-infected MDMs to uninfected (mock) control (E, F) , or with specific siRNAs to that from siControl (K, L) . P -values: **** < 0.0001; *** < 0.001; ** < 0.01; * < 0.05; ns: not significant ( p ≥ 0.05). The data underlying this figure can be found in .

Article Snippet: At day 2 post-transfection, cells were either infected with HIV-1 (as described above), or stimulated as follows to determine functional knockdown: AIM2 (cells were treated with ultra-pure LPS (100 ng/m, Invivogen) for 2 h, followed by transfection with linearized DNA (1 μg/mL) for 4 h); NLRP1 and CARD8 (cells were primed with Pam3CSK4 (0.5 μg/mL, InvivoGen) for 4 h, followed by stimulation with Val-boroPro (10 μM, InvivoGen) for 24 h; NLRP3 and caspase-1 (cells were primed with ATP (5 mM, Thermo Scientific) for 6 h, followed by activation with nigericin (10 μM) for 60 min; Caspase-4 (cells were transfected with ultra-pure LPS (5 μg/ml, InvivoGen) for 6 hrs; UNC93B1 (cells were treated with Resiquimod (5 μg/ml, Invivogen) for 24 h. At the indicated timepoints, culture supernatants were harvested for IL-1β and IP-10 ELISA, and cells were lysed for RNA or protein analysis.

Techniques: Flow Cytometry, Infection, Mutagenesis, Virus, Western Blot, Construct, Control, Quantitative RT-PCR, Bioassay, Enzyme-linked Immunosorbent Assay, Knockdown, Transfection, Expressing

Journal: Nature Immunology

Article Title: Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells

doi: 10.1038/s41590-025-02279-4

Figure Lengend Snippet: a , b , pDC heterogeneity in IFNAR-deficient mice. Shown are the gating scheme and a representative staining for Sca1 and CD69 in splenic pDCs from a naive Ifnar1 −/− mouse ( a ) and the fractions of pDC subsets in B6 WT versus Ifnar1 −/− mice ( b ). Bars represent means of biological replicates ± s.d. (B6 WT, n = 6 mice; Ifnar1 −/− , n = 5 mice) from 2 experiments. Significance of differences between pDC-A subsets is indicated. c , Cell-intrinsic role of IFNAR signaling in pDC heterogeneity. BM from WT or Ifnar1 −/− mice (CD45.2 + ) was mixed 1:1 with the BM from WT competitor (CD45.1 + ) mice and transferred into irradiated CD45.1 + recipients. Shown are the fractions of pDC subsets within donor (D)- or competitor (C)-derived splenic pDCs from recipients of WT:WT or Ifnar1 −/− :WT BM. Bars represent means of biological replicates ± s.d. (WT:WT, n = 7 mice; Ifnar1 −/− :WT, n = 4 mice) from 2 experiments. Significance of differences between pDC-A subsets is indicated. d , Transcriptome analysis of prospectively isolated pDC subsets. pDC-A/B/C subsets defined by Sca1 and CD69 expression were sorted from splenocytes of three individual naive WT mice and analyzed by bulk RNA-seq. Total pDCs from Ifnar1 −/− mice (phenotypic pDC-A) and from WT mice 12 h after CpG-A administration (phenotypic pDC-C) were sorted and analyzed in parallel (three separate mice per condition). Shown is the heatmap of top differentially expressed transcripts across individual samples. e – g , The history of Ifnb1 gene expression in pDC subsets as determined by lineage tracing in Ifnb1 tdTom-iCre Rosa26 LoxStopLox-EYFP reporter mice. e , Representative plots showing expression of EYFP and Tom in gated subsets of splenic pDCs from naive reporter mice. f , Percentage of EYFP + cells within pDC subsets in the spleen (left) and BM (right). Bars represent means, symbols represent biological replicates (mice) from two experiments and lines connect paired samples from the same mouse. g , Percentage of Tom + cells within pDC subsets in the spleen with groups ‘cDC2’ and ‘pDC+CpG-A’ shown as controls. Bars represent means ± s.d.; symbols represent biological replicates (mice) from one experiment, representative of three experiments. h , Representative gating scheme and staining for Sca1 and CD69 in splenic pDCs from a naive S ting1 −/− mouse. i , The fractions of pDC subsets in B6 WT, Sting1 −/− or Cgas −/− mice. Bars represent means of biological replicates ± s.d. (B6 WT, n = 11 mice; Sting1 −/− , n = 9 mice; Cgas −/− , n = 8 mice) from 4 experiments. Significance of differences between pDC-A subsets is indicated. j , Total BM from WT or S ting1 −/− knockout (KO) donor mice was transferred into irradiated WT or S ting1 −/− host mice. Shown is the fraction of pDC subsets within splenic pDCs in the resulting chimeric mice with the indicated donor (D) and host (H) genotypes. Bars represent means of biological replicates ± s.d. (WT (D):WT (H), n = 7 mice; WT (D):KO (H), n = 5 mice; all else, n = 4 mice) from 1 experiment. Significance of differences between pDC-A subsets is indicated. k , Fractions of pDC subsets within total splenic pDCs in mice with null alleles of the indicated TLR pathway genes. Bars represent means of biological replicates ± s.d. (B6 WT, n = 20 mice; Tlr9 −/− , n = 13 mice; Tlr7 −/− , n = 19 mice; Tlr7 −/− Tlr9 −/− , n = 14 mice; Unc93b1 −/− , n = 11 mice) from 12 experiments. Significance of differences between pDC-A subsets is indicated. l , Fractions of pDC subsets within total splenic (left) or BM (right) pDCs in mice deficient for Sting1 alone or with Tlr9 . Bars represent means of biological replicates ± s.d. ( Sting1 −/− Tlr9 −/− , n = 6 mice; all else, n = 8 mice) from 2 experiments. Significance of differences between pDC-A subsets is indicated. m , Fractions of pDC subsets within total splenic (left) or BM (right) pDCs in SPF or GF B6 WT mice. Bars represent means of biological replicates ± s.d. (SPF spleen, n = 15 mice; GF spleen, n = 23 mice; SPF BM, n = 11 mice; GF BM, n = 20 mice) from 6 experiments. Significance of differences between pDC-A subsets is indicated. Statistical significance was analyzed using unpaired two-sided Student’s t -test ( b , m ), paired two-sided Student’s t -test ( f (right)), one-way ANOVA followed by Tukey’s test ( c , f (left), i – l ) or paired one-way ANOVA followed by Tukey’s test ( g ); * P < 0.05; ** P < 0.005; *** P < 0.0005; **** P < 0.00005. Comparisons with control omitted from statistical analysis: gray bar ( g ). NS, not significant.

Article Snippet: Unc93b1 −/− (C57BL/6J- Unc93b1 3d /Mmucd) mice were obtained from the Mutant Mouse Resource & Research Centers (MMRRC) repository.

Techniques: Staining, Irradiation, Derivative Assay, Isolation, Expressing, RNA Sequencing, Gene Expression, Knock-Out, Control

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Distributions of mRNA in BRCA and identification of DEm-RNA association with immunity and prognostic of BRCA patients. A Volcano plot of Differently expressed mRNA B Venn diagram of immune-related genes and DEmRNAs associated with prognosis in BRCA patients C A heat map of UNC93B1 and its co-expressed mRNA. Significance identifier: ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques:

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Differential expression of UNC93B1 in pancancer and BRCA. A Differential expression of UNC93B1 in 33 tumours from the TCGA database B Differential expression of UNC93B1 in a variety of tumours from the paired TCGA database C Differential expression of UNC93B1 in unpaired BRCA samples D Differential expression of UNC93B1 in paired BRCA samples E Differential expression of UNC93B1 in the GSE45827 dataset. Significance identifier: *, p< 0.05; **, p<0.01; ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Quantitative Proteomics

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Clinical correlation analysis of UNC93B1 expression. A - G Expression of UNC93B1 in different patient groups with different clinicopathological factors H Overall survival curve of UNC93B1 from TCGA database I The ROC curve of UNC93B1. Significance identifier: *, p< 0.05; ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Expressing

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Subgroup prognostic analysis of survival and UNC93B1 expression. A - I Kaplan-Meier survival curves of UNC93B1 expression in relation to overall survival (OS) in different patient subgroups with different clinicopathological factors

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Expressing

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Functional enrichment analysis of UNC93B1 in BRCA. A Results of GO analysis B Results of KEGG analysis C - D Results of GSEA analysis. A positive abscissa indicates that UNC93B1 expression is positively correlated with this pathway; a negative abscissa indicates the opposite

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Functional Assay, Expressing

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: UNC93B1 expression and tumor immunity. A In the bar graph, UNC93B1 expression was correlated with 24 immune infiltration cells B - I UNC93B1 expression was positively correlated with 8 immune infiltration cells. Significance identifier: ns (no significance, p≥0.05); *, p< 0.05; **, p<0.01; ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Expressing

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Immunoinfiltration analysis of UNC93B1 in BRCA. A Subgroup comparison of the infiltration levels of a total of 17 immune cells in the UNC93B1 low- and high-expression groups B UNC93B1 was significantly associated with LAG-3 C UNC93B1 was significantly associated with HAVCR-2 D UNC93B1 was significantly associated with TNFRSF4 E UNC93B1 was significantly associated with PDCD1 F UNC93B1 was significantly associated with CTLA4 G UNC93B1 was significantly associated with CD274. Significance identifier: *, p< 0.05; **, p<0.01; ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Comparison, Expressing

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Evaluation of the expression of UNC93B1 in clinical breast cancer samples. A - B Detection of UNC93B1 and β-ACTIN expression in BRCA and adjacent tissues by Western blotting and quantitative analysis by Western blotting. The four proteins on the left are the WB results of adjacent tissues, and the four on the right are the WB results of BRCA tissues C - D Immunohistochemical images of UNC93B1 protein expression in normal tissue C versus BRCA D in Human Protein Atlas (HPA) data E Quantitative analysis of immunohistochemical images. Significance identifier: *, p< 0.05; ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Expressing, Western Blot, Immunohistochemical staining

Journal: Discover Oncology

Article Title: UNC93B1: a novel immune−related prognostic biomarker in breast cancer

doi: 10.1007/s12672-025-03124-8

Figure Lengend Snippet: Effect of UNC93B1 knockdown on the proliferation and invasion of BRCA cells. A - B After transfection of siRNA, qPCR was performed to assess the level of UNC93B1 gene expression in MDA-MB-231 and SK-BR-3 cells C - D The proliferation of MDA-MB-231 and SK-BR-3 was examined by CCK-8 E - F The proliferation of MDA-MB-231 and SK-BR-3 was examined by colony-formation assays G - H The migration of MDA-MB-231 and SK-BR-3 was examined by transwell assays. Significance identifier: ***, p<0.001

Article Snippet: The siRNAs targeting UNC93B1 were designed, synthesized, and purchased from Sangon Biotech (Shanghai).

Techniques: Knockdown, Transfection, Gene Expression, CCK-8 Assay, Migration