Journal: Oncogene

Article Title: HAO1-mediated oxalate metabolism promotes lung pre-metastatic niche formation by inducing neutrophil extracellular traps

doi: 10.1038/s41388-022-02248-3

Figure Lengend Snippet: A Effect of 67NR and 4T1 exosomes treatment on HAO1 expression in alveolar epithelial cells by Western blot analysis. B Effect of transfection of RNA isolated from 67NR and 4T1 exosomes on HAO1 expression in alveolar epithelial cells by Western blot analysis. C Effect of poly (I:C) treatment on HAO1 expression in alveolar epithelial cells by Western blot analysis. D Effect of poly (I:C) inhalation on HAO1 expression in mice lung by Western blot analysis. E Detection of oxalate production in alveolar epithelial cells treated with poly(I:C) or poly(I:C) + CCPST. Means ± s.e.m are provided ( n = 3). F Detection of TLR3 expression in alveolar epithelial cells infected with sg-control or sg-Tlr3 lentivirus. G Detection of HAO1 expression in alveolar epithelial cells treated with 4T1 exosomes, 4T1 exosomes + CU CPT 4a or 4T1 exosomes + sg-Tlr3 lentivirus by Western blot analysis. H Detection of oxalate production in alveolar epithelial cells treated with 4T1 exosomes, 4T1 exosomes + CU CPT 4a or 4T1 exosomes + sg-Tlr3 lentivirus. I Effect of IRF3 over-expression on IRF3, P-IRF3 and HAO1 expression in alveolar epithelial cells by Western blot analysis. J Diagram of the HAO1 promoter showing the location of IRF3 binding sites. K Luciferase activity of HAO1-promoter construct after transfection of IRF3 plasmid in alveolar epithelial cells. L Detection of IRF3, P-IRF3 and HAO1 expression in alveolar epithelial cells treated with 4T1 exosomes or 4T1 exosomes + shIRF3 by Western blot analysis. M Detection of oxalate production in alveolar epithelial cells treated with 4T1 exosomes or 4T1 exosomes + shIRF3. Means ± s.e.m are provided ( n = 3). N Schematic diagram of the role of HAO1-mediated oxalate metabolism at pre-metastatic stage and metastatic stage. *** P < 0.001, **** P < 0.0001 according to two-tailed Student’s t test.

Article Snippet: The potassium oxalate (20 μM, Aladdin), DNase I (100 U/ml, Aladdin), CCPST (200 μM, Key organics), PMA (10 nM, MedChemExpress), apocynin (10 μM, MedChemExpress), SB 203580 (500 nM, MedChemExpress) and CU CPT 4a (27 μM, Tocris) were used for cell treatment.

Techniques: Expressing, Western Blot, Transfection, Isolation, Infection, Control, Over Expression, Binding Assay, Luciferase, Activity Assay, Construct, Plasmid Preparation, Two Tailed Test

Journal: Genome biology

Article Title: A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers.

doi: 10.1186/s13059-017-1385-x

Figure Lengend Snippet: Fig. 4 Immunomodulators can alter the fractional abundance of the c1 mDC phenotype. a Top: Schematic of bulk expression data (Bi) from publicly available perturbation data. Bottom: Each cell’s expression profile (C1j) is correlated with all Bi so as to compare similarities of the single-cell cluster 1 to all bulk expression profiles. b Volcano plot of negative log meta-analysis false discovery rate (FDR) vs mean difference in “TLR stimulation score” between c1 and c3–5. Scores are computed from weighted correlations between single-cell profiles and transcriptional patterns from human DCs (see “Methods”) after 48 h of stimulation with media control (black) or agonists for either TLR2 (PAM3CSK4, dark blue), TLR3 (Poly I:C, green), TLR4 (LPS, orange), TLR7/8 (Gard, purple), or TLR9 (CpG, light blue). Tests reproduced with FDR < 0.01 in both stratified analyses are highlighted in blue. c Proportion of CD64Hi,PDL1Hi cells among mDCs from PBMCs isolated from HIV-negative individuals cultured in the absence or the presence of VSV-G pseudotyped HIV-1, alone or in combination with TLR ligands (TLRL: TLR2L, PGNA, n = 11; TLR3L, Poly I:C, n = 11; TLR4L, LPS, n = 8; TLR8L, CL097, n = 11; Methods). Statistical significance was calculated using Kruskal–Wallis and Dunn’s tests (**, p < 0.01). d Proportions of CD64Hi, PD-L1Hi cells among mDCs from healthy individuals (indigo) and elite controllers (olive) cultured in the absence or the presence of Poly I:C and polymer nanoparticles loaded with single-stranded (ss) or double stranded (ds) 100 nucleotide HIV-1 DNA (see “Methods”; n = 8, HIV negative individuals; n = 7, ECs). Statistical significance was calculated using either two-tailed Wilcoxon signed-rank test (black) or two-tailed Mann–Whiney test (red) to compare differences within or among patient groups, respectively (**, p < 0.01; *, p < 0.05). e Proportion of proliferating CD4+ or CD8+ T cells after culture with Hi or Lo mDC from a HD stimulated with TLRL3 and nanoparticles containing gag single-stranded DNA (*, p < 0.05; two-tailed Wilcoxon signed-rank test. n = 6). f Volcano plot of negative log IDR vs mean difference in upstream regulatory score between c1 and c3–5 based on single-cell correlations with short hairpin RNA- perturbation profiles from mouse DCs stimulated with LPS for 6 h (adapted from Chevrier et al. [32]; see “Methods”). The net effect (activate, inhibit, both) of each perturbation is denoted by color (red, blue, gray, respectively), as is its breadth (size). g Proportions of CD64Hi,PD-L1Hi cells among EC mDCs cultured in the presence or absence of virus and DMSO (control, magenta) or BX795 TBK1 inhibitor (cyan; n = 10; see “Methods”). Statistical significance was calculated using a two-tailed Wilcoxon signed-rank test (*, p < 0.05)

Article Snippet: In the TLR antagonist studies, mDCs from PBMCs were treated with VSV-G pseudotyped HIV-1 (see “In vitro infection with HIV-1 virus”) alone or in combination with a TLR3 (CUCPT4A, 60 nM, Tocris), TLR4 (600 ng/mL, LPS-RS, InvivoGen), or TBK-1 inhibitor (BX795, 1 μM, InvivoGen) (Fig. 4b, g, Additional file 1: Figure S10).

Techniques: Expressing, Control, Isolation, Cell Culture, Polymer, Two Tailed Test, shRNA, Virus