6444s rrid ab 396457 rabbit anti human tox af488  (Cell Signaling Technology Inc)

Journal: Cell reports

Article Title: Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function

doi: 10.1016/j.celrep.2024.114506

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Anti-human/mouse TCF1/TCF7 AF647 (clone C63D9) , Cell Signaling , 6709; RRID:AB_2797631.

Techniques: Control, Blocking Assay, Virus, Recombinant, Protease Inhibitor, Lysis, Enzyme-linked Immunosorbent Assay, Staining, Cell Isolation, DNA Library Preparation, Purification, RNA HS Assay, Mutagenesis, Software

Journal: Cell Reports Medicine

Article Title: Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity

doi: 10.1016/j.xcrm.2024.101640

Figure Lengend Snippet: CXCR6 expression increases upon ICB and is repressed by TCF1 (A and B) Left: tumor area (y axis, mean ± SEM) over time (x axis) of Mc38Ova hi (A) or B16Ova (B) implanted in wild-type (WT) mice and treated with anti-PD1 (A), anti-PD-L1 + anti-TIM3 (B), or isotype control. Right: frequency of CXCR6 + cells (y axis, mean ± SEM) in the indicated subsets (x axis) of CD8 + TILs harvested from tumors treated as above (A: n = 4–6 per group, 1 experiment. B: n = 3–4 per group, 1 experiment). (C) Expression (row-normalized TPM, color bar) of top differentially expressed genes (rows) between WT OTI (E8i-Cre - , Tcf7 FL/FL ) and Tcf7 cKO OTI (E8i-Cre + , Tcf7 FL/FL ) cells at different time points after T cell activation (columns) ( n = 3, 1 experiment). (D) Mean expression (color bar) and fraction of expressing cells (dot size) of key genes (rows) in different CD8 + T cell clusters (columns) as determined by scRNA-seq of cells from B16Ova tumors implanted in WT or Tcf7 cKO mice ( n = 3 per group combined, 1 experiment). (E) Frequency of CXCR6 + cells (y axis, mean ± SEM) in the indicated subsets (x axis) of CD8 + TILs from B16Ova tumors from WT (black) or Tcf7 cKO (green) mice ( n = 3–7 per group, representative of 2 experiments). (F) Percent input (y axis, mean ± SEM) following chromatin immunoprecipitation (ChIP) PCR of the Cxcr6 locus with anti-TCF1 or rabbit IgG control antibodies (x axis) in WT or Tcf7 cKO CD8 + T cells ( n = 8, 5 experiments combined). (G–I) Luciferase activity (RLU, relative light unit, y axis, mean ± SEM) in HEK293T cells transfected with Cxcr6 locus-containing pGL4.10 luciferase reporters together with either empty vector (control) or vectors encoding the indicated transcription factors (x axis). Firefly luciferase activity is presented relative to constitutive Renilla luciferase activity ( n = 3, representative of 2 experiments). Statistical significance was determined by linear mixed model (A left, B left), Student’s unpaired t test (A right, B right, E, F comparing WT to Tcf7 cKO anti-TCF1 samples), Student’s paired t test (F comparing WT samples), or one-way ANOVA with Tukey’s multiple comparisons test (G, H, I). NS = not significant, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: Anti-Mouse/Human TCF1 Clone C63D9 , Cell Signaling Technology , Cat:# 2203S; RRID: AB_2199302.

Techniques: Expressing, Control, Activation Assay, Chromatin Immunoprecipitation, Luciferase, Activity Assay, Transfection, Plasmid Preparation

Journal: Cell Reports Medicine

Article Title: Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity

doi: 10.1016/j.xcrm.2024.101640

Figure Lengend Snippet:

Article Snippet: Anti-Mouse/Human TCF1 Clone C63D9 , Cell Signaling Technology , Cat:# 2203S; RRID: AB_2199302.

Techniques: Virus, Recombinant, Purification, SYBR Green Assay, Staining, Reporter Assay, In Vitro, Activation Assay, Generated, Luciferase, Plasmid Preparation, Sequencing, Software, CRISPR

Journal: Cell Reports Medicine

Article Title: Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity

doi: 10.1016/j.xcrm.2024.101640

Figure Lengend Snippet: CXCR6 expression increases upon ICB and is repressed by TCF1 (A and B) Left: tumor area (y axis, mean ± SEM) over time (x axis) of Mc38Ova hi (A) or B16Ova (B) implanted in wild-type (WT) mice and treated with anti-PD1 (A), anti-PD-L1 + anti-TIM3 (B), or isotype control. Right: frequency of CXCR6 + cells (y axis, mean ± SEM) in the indicated subsets (x axis) of CD8 + TILs harvested from tumors treated as above (A: n = 4–6 per group, 1 experiment. B: n = 3–4 per group, 1 experiment). (C) Expression (row-normalized TPM, color bar) of top differentially expressed genes (rows) between WT OTI (E8i-Cre - , Tcf7 FL/FL ) and Tcf7 cKO OTI (E8i-Cre + , Tcf7 FL/FL ) cells at different time points after T cell activation (columns) ( n = 3, 1 experiment). (D) Mean expression (color bar) and fraction of expressing cells (dot size) of key genes (rows) in different CD8 + T cell clusters (columns) as determined by scRNA-seq of cells from B16Ova tumors implanted in WT or Tcf7 cKO mice ( n = 3 per group combined, 1 experiment). (E) Frequency of CXCR6 + cells (y axis, mean ± SEM) in the indicated subsets (x axis) of CD8 + TILs from B16Ova tumors from WT (black) or Tcf7 cKO (green) mice ( n = 3–7 per group, representative of 2 experiments). (F) Percent input (y axis, mean ± SEM) following chromatin immunoprecipitation (ChIP) PCR of the Cxcr6 locus with anti-TCF1 or rabbit IgG control antibodies (x axis) in WT or Tcf7 cKO CD8 + T cells ( n = 8, 5 experiments combined). (G–I) Luciferase activity (RLU, relative light unit, y axis, mean ± SEM) in HEK293T cells transfected with Cxcr6 locus-containing pGL4.10 luciferase reporters together with either empty vector (control) or vectors encoding the indicated transcription factors (x axis). Firefly luciferase activity is presented relative to constitutive Renilla luciferase activity ( n = 3, representative of 2 experiments). Statistical significance was determined by linear mixed model (A left, B left), Student’s unpaired t test (A right, B right, E, F comparing WT to Tcf7 cKO anti-TCF1 samples), Student’s paired t test (F comparing WT samples), or one-way ANOVA with Tukey’s multiple comparisons test (G, H, I). NS = not significant, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001.

Article Snippet: Anti-Mouse/Human TCF1 PE Clone C63D9 , Cell Signaling Technology , Cat:# 14456S RRID: AB_2798483.

Techniques: Expressing, Control, Activation Assay, Chromatin Immunoprecipitation, Luciferase, Activity Assay, Transfection, Plasmid Preparation

Journal: Cell Reports Medicine

Article Title: Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity

doi: 10.1016/j.xcrm.2024.101640

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Article Snippet: Anti-Mouse/Human TCF1 PE Clone C63D9 , Cell Signaling Technology , Cat:# 14456S RRID: AB_2798483.

Techniques: Virus, Recombinant, Purification, SYBR Green Assay, Staining, Reporter Assay, In Vitro, Activation Assay, Generated, Luciferase, Plasmid Preparation, Sequencing, Software, CRISPR

Journal: Med (New York, N.Y.)

Article Title: Preclinical study and phase II trial of adapting low-dose radiotherapy to immunotherapy in small cell lung cancer.

doi: 10.1016/j.medj.2024.06.002

Figure Lengend Snippet: Figure 3. LDRT15 Gy/5 f + aPD-1 treatment recruits TCF1+ PD-1+ CD8+ stem-like T cells (A) UMAP plot of 5,113 CD8+ T cells from scRNA-seq of untreated tumors and tumors treated with aPD-1, LDRT15 Gy/5 f, or LDRT15 Gy/5 f + aPD-1, colored by cell type. (B) Heatmap showing the expression of marker genes across CD8+ T cell subtypes. (C) Distribution of CD8+ T cell subtypes across treatment groups. Top bar plot showing the relative proportion of cells from four different treatment groups for each CD8+ T cell subtype. Bottom right heatmap showing enrichment scores of each CD8+ T cell subtype across treatment groups. The left bar plot shows the total number of CD8+ T cells in each treatment group.

Article Snippet: The following primary antibodies were used: human CD3 (ZSGB-BIO, ZM-0417, 1:200), human CD8 (ZSGBBIO, ZA-0508, 1:400), human PD-1 (ZSGB-BIO, ZA-0381, 1:100), human TCF1 (CST, 2203, 1:400), human pan-CK (ZSGB-BIO, ZM-0069, 1:600) and DAPI.

Techniques: Expressing, Marker

Journal: Cell Reports Medicine

Article Title: IL-7-primed bystander CD8 tumor-infiltrating lymphocytes optimize the antitumor efficacy of T cell engager immunotherapy

doi: 10.1016/j.xcrm.2024.101567

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Article Snippet: Anti-mouse/human TCF1 AF488 (clone: C63D9) , Cell Signaling , Cat# 6444S; RRID: AB_2797627.

Techniques: Purification, Recombinant, Formulation, Flow Cytometry, Amplification, Software, Staining

Journal: Nature Medicine

Article Title: Regorafenib plus nivolumab in unresectable hepatocellular carcinoma: the phase 2 RENOBATE trial

doi: 10.1038/s41591-024-02824-y

Figure Lengend Snippet: a , Schematic summary of the design of exploratory analyses. b , Box plots showing the fold change in proportions of immune cell types among PBMCs in long-term responders (LR; n = 9), early progressors (EP; n = 9) and both ( n = 18). c , PCC of each cell type between C1D1 and C1D15. d , Bar plots showing the TCR diversity, as represented by the inverse Simpson index for CD8 + T cells in LR ( n = 15) and EP ( n = 14) between C1D1 and C1D15. e , Box plots showing the fold change in the proportions of CD8 + T cell subclusters among NK/T cells among LR ( n = 9), EP ( n = 9) and both ( n = 18). f , Violin plots showing the module score for gene sets related to inflammatory signature (left) and nivolumab responsiveness in each CD8 + T cell cluster (right). g , Heat map showing expression levels of CD8 and genes related to cytotoxicity and T cell exhaustion among MKI67 + CD8 + T cells. h , Proportion of Ki-67 + cells among CD8 + T cells and PD-1 + CD8 + T cells, before and after treatment, among LR ( n = 7) and EP ( n = 8). i , Proportion of Granzyme B + perforin + cells among CD8 + T cells and PD-1 + CD8 + T cells, before and after treatment, among LR ( n = 7) and EP ( n = 8). Gating strategy of CD8 + T cells is shown in Extended Data Fig. . * P < 0.05, ** P < 0.01, *** P < 0.005, **** P < 0.001, according to a Wilcoxon signed-rank test for paired groups and two-tailed Mann–Whitney U -test for unpaired groups. Data are presented as mean ± s.d. In each box plot, the box represents the interquartile range, and whiskers represent minima and maxima. RCC, renal cell carcinoma.

Article Snippet: The following directly conjugated, unconjugated or secondary antibodies were used to identify cell markers of CD8 + T cells in human PBMCs: rabbit anti-human TCF1/TCF7 at 1:100 dilution (C63D9, Cell Signaling Technology, 2203S), donkey anti-rabbit IgG at 1:100 dilution (Poly4064, BioLegend, 406410), mouse anti-human CD3-V500 at 1:100 dilution (UCHT1, BD Biosciences, 561416), mouse anti-human Ki-67-BV605 at 1:100 dilution (Ki-67, BioLegend, 350522), mouse anti-human Perforin-BV711 at 1:100 dilution (dG9, BioLegend, 308130), pembrolizumab (PD-1, Selleck Chemicals, A2005), mouse anti-human IgG4 Fc-FITC at 1:100 dilution (HP6025, Southern Biotech, 9200-02), mouse anti-human CD45-PerCP-Cy5.5 at 1:100 dilution (HI30, BD Biosciences, 564105), mouse anti-human CD14-PE-TR at 1:200 dilution (61D3, eBioscience, 61-0149-42), mouse anti-human CD19-PE-TR at 1:200 dilution (HIB19, eBioscience, 61-0199-42), mouse anti-human Granzyme B Alexa Fluor 700 at 1:100 dilution (GB11, BD Biosciences, 560213) and mouse anti-human CD8-APC-H7 at 1:100 dilution (SK1, BD Biosciences, 560179).

Techniques: Expressing, Two Tailed Test, MANN-WHITNEY

Journal: Nature Medicine

Article Title: Regorafenib plus nivolumab in unresectable hepatocellular carcinoma: the phase 2 RENOBATE trial

doi: 10.1038/s41591-024-02824-y

Figure Lengend Snippet: a , Volcano plot showing proportional changes in total CD8 + T-cell subclusters at C1D1 between long-term responders (LR; n = 15) and early progressors (EP; n = 13). The unpaired T test was performed for unpaired groups. b , Heatmap of CD8 + T surrogate marker genes among total CD8 + T cells and subclusters. Red and blue astrerisks indicate genes significantly upregulated at C1D1 and C1D15, respectively. c , Gating strategy of CD8 + T-cells PBMC in LR and EP. d , Representative flow cytometry plots for KI-67-expressing cells among CD8 + T-cells. e , Representative flow cytometry plots for granzyme B- and perforin-expressing CD8 + T-cells. f , Heatmap of proliferation marker gene among CXCR3 + CD8 + T-cell and CXCR3 − CD8 + T-cell subclusters from an independent HCC cohort treated with anti-PD-1 monotherapy (Chuah et al. 2022). g , Heatmap of CD8 + T surrogate marker genes among CXCR3 + CD8 + T-cell subcluster from the independent HCC cohort treated with anti-PD-1 monotherapy (Chuah et al. 2022). *P < 0.05, according to a two-sided Wilcoxon signed-rank test for paired groups.

Article Snippet: The following directly conjugated, unconjugated or secondary antibodies were used to identify cell markers of CD8 + T cells in human PBMCs: rabbit anti-human TCF1/TCF7 at 1:100 dilution (C63D9, Cell Signaling Technology, 2203S), donkey anti-rabbit IgG at 1:100 dilution (Poly4064, BioLegend, 406410), mouse anti-human CD3-V500 at 1:100 dilution (UCHT1, BD Biosciences, 561416), mouse anti-human Ki-67-BV605 at 1:100 dilution (Ki-67, BioLegend, 350522), mouse anti-human Perforin-BV711 at 1:100 dilution (dG9, BioLegend, 308130), pembrolizumab (PD-1, Selleck Chemicals, A2005), mouse anti-human IgG4 Fc-FITC at 1:100 dilution (HP6025, Southern Biotech, 9200-02), mouse anti-human CD45-PerCP-Cy5.5 at 1:100 dilution (HI30, BD Biosciences, 564105), mouse anti-human CD14-PE-TR at 1:200 dilution (61D3, eBioscience, 61-0149-42), mouse anti-human CD19-PE-TR at 1:200 dilution (HIB19, eBioscience, 61-0199-42), mouse anti-human Granzyme B Alexa Fluor 700 at 1:100 dilution (GB11, BD Biosciences, 560213) and mouse anti-human CD8-APC-H7 at 1:100 dilution (SK1, BD Biosciences, 560179).

Techniques: Marker, Flow Cytometry, Expressing