Journal: The Journal of Cell Biology

Article Title: Galectin-9 regulates dendritic cell polarity and uropod contraction by modulating RhoA activity

doi: 10.1083/jcb.202404079

Figure Lengend Snippet: cDC2 cell purity and supplementary phenotype analysis. (A) Gating strategy to determine cDC2 purity after isolation from PBMCs. cDC2s were stained for CD1c, CD11c, CD14, and CD20. A first gate is set based on the physical FCS-A/SSC-A parameters followed by selecting on negative cells for CD14 and CD19. cDC2s are then identified as positive cells for CD11c and CD1c. (B) Surface galectin-9 and CCR7 expression in galectin-9 and CCR7-positive cDC2s. Graph shows average ± SEM gMFI of five individual donors. One-way ANOVA followed by Dunnett’s test for multiple comparisons was performed. *P < 0.05; **P < 0.01; ***P < 0.001. gMFI, geometric mean fluorescence intensity.

Article Snippet: Human cDC2s were isolated from peripheral blood mononuclear cells derived from healthy individuals (Sanquin, Nijmegen, The Netherlands) using the MACS CD1c + isolation kit (130-119-475; Miltenyi Biotec) according to the manufacturer’s instructions.

Techniques: Isolation, Staining, Expressing, Fluorescence

Journal: Frontiers in immunology

Article Title: Genomic Multiple Sclerosis Risk Variants Modulate the Expression of the ANKRD55 - IL6ST Gene Region in Immature Dendritic Cells.

doi: 10.3389/fimmu.2021.816930

Figure Lengend Snippet: FIGURE 5 | Digital droplet PCR (ddPCR) quantification of gene transcript copy numbers in pDC, mDC, CD14+ monocytes, PBMC fraction minus monocytes (F-), and moDC. Analysis was performed in 350 pg cDNA (A, E, F) or 30 ng of cDNA (B–D). (C) ddPCR quantification of ANKRD55 transcript copy numbers in moDC treated with AM-580. (D) ANKRD55 copy numbers in moDC matured or not with IFN-g/LPS measured at 6 h after addition of stimulus. (F) Transcript levels of markers specific for mDC (CD1c) and pDC (IL3RA, CLEC4C).

Article Snippet: To verify the purity of each subpopulation, cells were analyzed by flow cytometry (MACSQuant® flow cytometer, Miltenyi Biotec) using antihuman CD1c (BCDA-1)-APC antibody (Miltenyi Biotec, Ref. 130-110-595) for mDC and CD303 (BDCA-2)-APC antibody (Miltenyi Biotec, Ref. 130-114-177) for pDC, as shown in Supplementary Figure S1.

Techniques:

Journal: Cell

Article Title: Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma.

doi: 10.1016/j.cell.2020.11.041

Figure Lengend Snippet: Figure 2. Myeloid-derived cell components in primary and relapsed HCC (A) t-SNE plot showing the subtypes of myeloid-derived cells derived from PT and RT patients. Each cluster is color-coded according to cell type. Cluster an- notations are indicated in the figure. (B) t-SNE plot showing PT and RT myeloid cells, clustered and color-coded, according to patient. (C) Heatmap showing the expression of marker genes in each subtype of myeloid-derived cells. (D) Boxplot showing the fraction of myeloid subgroups in PT (green) and RT (blue). (E) Representative images of IHC staining in Formalin-fixed paraffin-embedded (FFPE) tissues, indicating CD45+IDO+ (DC1or DC3) or CD45+CD1C+ (DC2) cells, in paired RT and PT samples. Scale bar, 20 mm. (F) Violin plot, presenting the fractions of DCs in paired PT and RT samples from validation cohort 2, based on IHC staining results. All statistical analyses are paired (F) or unpaired Wilcoxon tests (D). N represents the number of patients. See also Figure S2 and Table S3.

Article Snippet: Paired primary and relapsed samples were used for double staining of CD1C (Cat# TA505384, Origene) and IDO (Cat# 86630, CST) antibodies, staining of CD45 (Cat# 13917, CST) antibody, and double staining of CD8 (Cat# ab17147, Abcam) and CD161 (Cat# ab197979, Abcam) antibodies.

Techniques: Derivative Assay, Expressing, Marker, Immunohistochemistry, Biomarker Discovery

Journal: Cell

Article Title: Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma.

doi: 10.1016/j.cell.2020.11.041

Figure Lengend Snippet: Figure 7. Characteristics of malignant cells and their effects on the tumor ecosystem (A) Bar chart showing the enrichment of specific pathways, based on the HALLMARK gene set of upregulated genes, in primary or recurrent malignant cells. (B) Violin plots showing the proliferation, hepatic scores, immune escape, and immune surveillance scores of malignantcells from PT (green) and RT (blue) samples. (C) Violin plot showing the expression of selected immune escape genes in tumor cells from PT (green) and RT (blue) samples. (D) Violin plot showing the expression of CTLA4 and CD274 in primary and relapsed malignant cells. (E) Boxplot showing the fraction of CD274+ tumor cells in RT and PT samples. (F) Bubble chart showing the interaction between malignant cells and DC subtypes, based on selected ligand and receptor pairs. These scores are normalized expression levels, and the sizes of the bubbles indicate the significance of the interactions, calculated by CellPhoneDB. (G) Immunofluorescence images showing the interaction between DCs and malignant cells, based on the CD80-PDL1, using antibodies CD45, IDO, CD1c, cd80, and PD-L1. Scale bars, 100 mm. (H) Schematic diagram of the unique tumor ecosystem in relapsed HCC. The p values in (B–D) were calculated by Student’s t test, and in (E) by the Wilcoxon test. See also Figure S7 and Tables S3 and S6.

Article Snippet: Paired primary and relapsed samples were used for double staining of CD1C (Cat# TA505384, Origene) and IDO (Cat# 86630, CST) antibodies, staining of CD45 (Cat# 13917, CST) antibody, and double staining of CD8 (Cat# ab17147, Abcam) and CD161 (Cat# ab197979, Abcam) antibodies.

Techniques: Expressing

Journal: Cell Death & Disease

Article Title: Hypoxic human proximal tubular epithelial cells undergo ferroptosis and elicit an NLRP3 inflammasome response in CD1c + dendritic cells

doi: 10.1038/s41419-022-05191-z

Figure Lengend Snippet: Representative serial section immunohistochemical (IHC) staining of control/non-fibrotic (left panel) and fibrotic (middle panel) kidney tissue probed for ( A ) aquaporin-1, ( B ) GPX4, ( C ) 4-HNE and ( D ) CD1c. Regions of CD1c + DC co-localisation with aqupaporin-1 + PTEC displaying evidence of ferroptotic cell death (↓ GPX4 and ↑ 4-HNE) are highlighted with black arrows. Scale bars represent 60 µm. Quantitative analysis (positive pixel intensity/µm 2 total area) of IHC staining in control and fibrotic tissue is presented (right panels). Symbols represent values for individual donor tissue. Results represent mean ± SEM of values from four randomly selected areas for each tissue sample. * P < 0.05, *** P < 0.001, Welch’s t test.

Article Snippet: Serial sections were probed with antibodies against AQP-1 (Cat. No. sc-20810; Santa Cruz Biotechnology, Dallas, TX, USA), GPX4 (Cat. No. ab41787; Abcam, Cambridge, MA, USA), 4-HNE (Cat. No. ab46544; Abcam) or CD1c (Cat. No. AF5910; R&D Systems, Minneapolis, MN, USA).

Techniques: Immunohistochemical staining, Immunohistochemistry, Control

Journal: Cell Death & Disease

Article Title: Hypoxic human proximal tubular epithelial cells undergo ferroptosis and elicit an NLRP3 inflammasome response in CD1c + dendritic cells

doi: 10.1038/s41419-022-05191-z

Figure Lengend Snippet: A Heatmap representing secreted cytokine levels following 24-h co-culture (DC & PTEC) of flow cytometry sorted CD1c + DC with pre-conditioned normoxic (N; 21% O 2 ) or hypoxic (H; 1% O 2 ) PTEC in the absence (Nil) or presence of poly I:C. PTEC alone and DC alone cultures are included as controls; n = 4. The colour bar represents the z-score. Yellow indicates low expression; purple indicates high expression. IL-12p70, IL-17, interferon (IFN)-α and IFN-γ were not detectable in any culture conditions (data not shown). B , C Secreted IL-1β ( B ) and IL-18 ( C ) protein levels (measured by LEGENDplex™ assay; pg/ml) following 24-h co-culture (DC & PTEC) of flow cytometry sorted CD1c + DC with pre-conditioned normoxic (white bars) or hypoxic (grey bars) PTEC in the absence (Nil) or presence of poly I:C. PTEC alone and DC alone cultures are included as controls; N.D. not detectable. Bar graphs represent mean ± SEM. Symbols represent individual donor PTEC experiments; n = 4. **** P < 0.0001, one-way ANOVA with Tukey’s multiple-comparison test. D Flow cytometric detection of intracellular IL-1β protein following 4-h co-culture of magnetic bead-enriched CD1c + DC with pre-conditioned hypoxic PTEC in the presence of poly I:C. Co-cultures were treated prior to the 4-h culture period with either brefeldin A or VX-765 to enable intracellular IL-1β accumulation/detection. Representative flow cytometric histograms of IL-1β staining (black unfilled) compared with unstained control (grey filled) for PTEC (gated on live, single, CD45 − cells) and CD1c + DC (gated on live, single, CD45 + lineage − HLA-DR + CD1c + cells) are presented. One representative of three individual donor PTEC experiments is shown. E Fold changes (relative to –Fer-1) in secreted IL-1β levels (measured by ELISA; pg/ml) following 24-h co-culture (DC & PTEC) of magnetic bead-enriched CD1c + DC with pre-conditioned hypoxic PTEC and poly I:C in the absence (-Fer-1) or presence of ferrostatin-1 (+Fer-1). Bar graphs represent mean ± SEM. Symbols represent individual donor PTEC experiments; n = 7. ns not significant, paired t test.

Article Snippet: Serial sections were probed with antibodies against AQP-1 (Cat. No. sc-20810; Santa Cruz Biotechnology, Dallas, TX, USA), GPX4 (Cat. No. ab41787; Abcam, Cambridge, MA, USA), 4-HNE (Cat. No. ab46544; Abcam) or CD1c (Cat. No. AF5910; R&D Systems, Minneapolis, MN, USA).

Techniques: Co-Culture Assay, Flow Cytometry, Expressing, Comparison, Staining, Control, Enzyme-linked Immunosorbent Assay

Journal: Cell Death & Disease

Article Title: Hypoxic human proximal tubular epithelial cells undergo ferroptosis and elicit an NLRP3 inflammasome response in CD1c + dendritic cells

doi: 10.1038/s41419-022-05191-z

Figure Lengend Snippet: A NLRP3 mRNA expression relative to housekeeping gene β-2-microglobulin ( B2M) in flow cytometry sorted CD1c + DC freshly isolated (0 h) or following 24-h co-culture (DC & PTEC) with pre-conditioned normoxic (white bar) or hypoxic (grey bar) PTEC in the presence of poly I:C. DC alone cultures are included as controls. Bar graphs represent mean ± SEM. Symbols represent individual donor PTEC experiments; n = 7. * P < 0.05, one-way ANOVA with Tukey’s multiple-comparison test. B Heatmap representing secreted cytokine levels following 24-h co-culture (DC & PTEC) of magnetic bead-enriched CD1c + DC with pre-conditioned hypoxic PTEC and poly I:C in the absence (NIL) or presence of inflammasome inhibitors (VX-765, MCC950) or DAMP inhibitors (apyrase, isotype control or HMGB1 antibody); n = 6. The colour bar represents the z-score. Yellow indicates low expression; purple indicates high expression. C , D Fold changes (relative to NIL inhibitor) in secreted IL-1β ( C ) and IL-18 ( D ) protein levels (measured by LEGENDplex™ assay) following 24-h co-culture (DC & PTEC) of magnetic bead-enriched CD1c + DC with pre-conditioned hypoxic PTEC and poly I:C in the absence (NIL) or presence of inflammasome inhibitors (VX-765, MCC950) or DAMP inhibitors (apyrase, isotype control or HMGB1 antibody). Bar graphs represent mean ± SEM. Symbols represent individual donor PTEC experiments; n = 6. * P < 0.05; ** P < 0.01; **** P < 0.0001, one-way ANOVA with Tukey’s multiple-comparison test.

Article Snippet: Serial sections were probed with antibodies against AQP-1 (Cat. No. sc-20810; Santa Cruz Biotechnology, Dallas, TX, USA), GPX4 (Cat. No. ab41787; Abcam, Cambridge, MA, USA), 4-HNE (Cat. No. ab46544; Abcam) or CD1c (Cat. No. AF5910; R&D Systems, Minneapolis, MN, USA).

Techniques: Expressing, Flow Cytometry, Isolation, Co-Culture Assay, Comparison, Control

Journal: Cell Death & Disease

Article Title: Hypoxic human proximal tubular epithelial cells undergo ferroptosis and elicit an NLRP3 inflammasome response in CD1c + dendritic cells

doi: 10.1038/s41419-022-05191-z

Figure Lengend Snippet: A , B Immunofluorescent labelling of frozen sections from control/non-fibrotic ( A ) and fibrotic kidney tissue ( B ) stained for ASC (green), CD1c (red), aquaporin-1 (AQP-1) (white) and DAPI (blue). Scale bars represent 50 µm for small frames (left panels) and 20 µm for large frames (right panels). ASC-speck-positive CD1c + DC are highlighted with white arrows. C Quantification (mean cells/mm 2 ) of ASC-speck-negative CD1c + DC (white bars) and ASC-speck-positive CD1c + DC (grey bars) in control/non-fibrotic kidney tissue ( n = 4) and fibrotic kidney tissue ( n = 4). Symbols represent values for individual donor tissue. Results represent mean ± SEM of values from five randomly selected areas for each tissue sample. * P < 0.05, ** P < 0.01, Welch’s t test.

Article Snippet: Serial sections were probed with antibodies against AQP-1 (Cat. No. sc-20810; Santa Cruz Biotechnology, Dallas, TX, USA), GPX4 (Cat. No. ab41787; Abcam, Cambridge, MA, USA), 4-HNE (Cat. No. ab46544; Abcam) or CD1c (Cat. No. AF5910; R&D Systems, Minneapolis, MN, USA).

Techniques: Control, Staining

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Group 1 CD1 genes in rabbit.

doi: 10.4049/jimmunol.166.1.403

Figure Lengend Snippet: FIGURE 1. Comparison of deduced amino acid sequences of rabbit and human CD1 genes. Dots depict amino acid identity, and spaces have been introduced to maximize homology. Arrows mark the boundaries of the structural domains. A, CD1a. The boxed area represents a serine-containing motif that is similar to one (SD/EXSL, where X is any amino acid) found in the cytoplasmic tails of MHC class I molecules. B, CD1b. The boxed areas represent a tyrosine-containing motif (YXXZ, where X is any amino acid and Z is a hydrophobic amino acid) found in human CD1b, CD1c, and CD1d molecules that is required for trafficking to the endosome. C, CD1e. The GenBank accession numbers for the rabbit CD1 genes are CD1A1 (AF276977), CD1A2 (AF276978), CD1B (AF276979), and CD1E (AF276980).

Article Snippet: Cells that survived selection were then screened with the panel of anti-CD1 mAbs to detect surface expression of rabbit CD1 proteins. mAbs and flow cytometric analysis The mAbs used in this study were anti-human CD1b (clone SN13/K5-1B8; Ancell, Bayport, MN), anti-human CD1c (clone M241, Ancell; clone L161, Serotec, Raleigh, NC; clones F10/2A3.1 and F10/21A3, provided by Dr. Steven Porcelli, Albert Einstein School of Medicine, New York, NY), anti-human CD1a (clone NA1/34-HLK, Serotec; clone OKT6, provided by Dr. Steven Porcelli), anti-rabbit thymocyte (clones LAT-1, LAT-2, and LAT-3, provided by Dr. Stewart Sell, Albany Medical College, Albany, NY), anti-rabbit IgM (clone 367), and anti-rabbit MHC class II (clone 2C4).

Techniques: Comparison

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Group 1 CD1 genes in rabbit.

doi: 10.4049/jimmunol.166.1.403

Figure Lengend Snippet: FIGURE 6. Phylogenetic analysis of the deduced amino acid sequences of known CD1 proteins using the multiple alignment software, CLUSTALX. The rabbit CD1 proteins are in bold type, and the group 1 and group 2 classi- fications are noted. The cottontail rabbit CD1d (marked as rabbit CD1d) and the nonrabbit CD1 protein sequences were obtained from GenBank, and their respective accession numbers are as follows: cottontail rabbit CD1d, M26249; human CD1a, P06126; human CD1b, P29061; human CD1c, P29017; human CD1d, P15813; human CD1e, P15812; mouse CD1d1.1, I49582; sheep CD1b25, CAA85359; sheep CD1b42, S47246; sheep CD1d, AJ006722; guinea pig CD1b2, AF145484; guinea pig CD1b3, AF145485; guinea pig CD1e, AF145490; and pig CD1a, AF059492.

Article Snippet: Cells that survived selection were then screened with the panel of anti-CD1 mAbs to detect surface expression of rabbit CD1 proteins. mAbs and flow cytometric analysis The mAbs used in this study were anti-human CD1b (clone SN13/K5-1B8; Ancell, Bayport, MN), anti-human CD1c (clone M241, Ancell; clone L161, Serotec, Raleigh, NC; clones F10/2A3.1 and F10/21A3, provided by Dr. Steven Porcelli, Albert Einstein School of Medicine, New York, NY), anti-human CD1a (clone NA1/34-HLK, Serotec; clone OKT6, provided by Dr. Steven Porcelli), anti-rabbit thymocyte (clones LAT-1, LAT-2, and LAT-3, provided by Dr. Stewart Sell, Albany Medical College, Albany, NY), anti-rabbit IgM (clone 367), and anti-rabbit MHC class II (clone 2C4).

Techniques: Software