Journal: Cell

Article Title: DE NOVO EPIGENETIC PROGRAMS INHIBIT PD-1 BLOCKADE-MEDIATED T-CELL REJUVENATION

doi: 10.1016/j.cell.2017.06.007

Figure Lengend Snippet: Key Resources Table

Article Snippet: Anti-mouse/human Tcf1 (clone C63D9) , Cell Signaling , Cat#14456S.

Techniques: Virus, Recombinant, DNA Methylation Assay, Plasmid Preparation, Cloning, cDNA Synthesis, Microarray, Software, Methylation Sequencing, Flow Cytometry

Journal: Cell reports

Article Title: UTX promotes CD8 + T cell-mediated antiviral defenses but reduces T cell durability

doi: 10.1016/j.celrep.2021.108966

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit anti-TCF1 mAb, AF647, clone C63D9 , Cell Signaling , Cat#6709S; RRID: AB_2797631.

Techniques: Purification, Generated, Recombinant, Staining, Isolation, Cell Isolation, RNA Sequencing Assay, DNA Sequencing, Software

Journal: bioRxiv

Article Title: Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks

doi: 10.1101/430611

Figure Lengend Snippet: (A) PCA plot of HR+ luminal cells depicting expression of WNT4 and TNFSF11 (RANKL) in log normalized counts. (B) Non-negative matrix factorization identifies a specific gene signature of hormone signaling in HR+ luminal cells. Heatmap depicting the top 20 genes expressed in each HR+ cell metagene, highlighting marker genes in HR+ metagene 8. (C) Gene set enrichment analysis of HR+ cell metagene 8, showing enrichment of genes shown to be upregulated during the luteal phase of the menstrual cycle (NES = 2.16, p < 1e-9) . (D) Ridge plots depicting the distribution of HR+ metagene 8 (hormone signaling) expression in HR+ luminal cells across samples, and quantification of the average expression of metagene 8 in nulliparous (NP) versus parous (P) samples (n = 22 samples, p = 0.04, Mann-Whitney test). (E) Immunostaining for TCF7, p63, and KRT7, and quantification of the percentage of TCF7+ cells within the p63+ basal/myoepithelial cell compartment for nulliparous (NP) versus parous (P) samples (n=15 samples; p < 0.002, Mann-Whitney test).

Article Snippet: Antibodies, TSA reagents, and dilutions used are as follows: p63 (1:2000; CST 13109, clone D2K8X), KRT7 (1:4000; Abcam AB68459, clone EPR1619Y), KRT23 (1:2000; Abcam AB156569, clone EPR10943), ER (1:4000; Thermo Scientific RMM-9101-S, clone SP1), PR (1:3000; CST 8757, clone D8Q2J), TCF7 (1:2000; CST 2203, clone C63D9), FITC-TSA (2 min; Perkin Elmer NEL701A001KT), Cy3-TSA (3 min; Perkin Elmer NEL744001KT), Cy5-TSA (7 min; Perkin Elmer NEL745E001KT).

Techniques: Expressing, Marker, MANN-WHITNEY, Immunostaining

Journal: bioRxiv

Article Title: Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks

doi: 10.1101/430611

Figure Lengend Snippet: (A) Heatmap showing the similarity between each sample’s single-cell expression distribution across HR+ cell metagene 8, measured as (1 - Jensen-Shannon distance). Hierarchical clustering identifies two sets of samples representing high or low expression of the “hormone signaling” metagene (ward D2). (B) PCA plot of HR+ luminal cells in nulliparous or parous women depicting expression of HR+ cell metagene 8. (C) Binomial probability distribution for the number of samples with high hormone signaling. The binomial probability of high hormone signaling is modeled as the average length of the luteal phase of the menstrual cycle, in days, divided by the average total length of the menstrual cycle (P = 0.44) . (D) Volcano plot highlighting the differential expression of canonical hormone-responsive genes between parous and nulliparous samples in HR+ luminal cells. (E) Immunostaining for PR, KRT23, and KRT7, and quantification of the percentage of PR+ cells within the KRT23-/KRT7+ luminal cell compartment for nulliparous (NP) versus parous (P) samples (n=15 samples; p < 0.03, Mann-Whitney test). (F) Immunostaining for p63, TCF7, and KRT7 in ducts versus TDLUs, and quantification of the percentage of TCF7+ cells within the p63+ basal/myoepithelial cell compartment (n = 14 samples; p = 0.64, Wilcoxon signed-rank test).

Article Snippet: Antibodies, TSA reagents, and dilutions used are as follows: p63 (1:2000; CST 13109, clone D2K8X), KRT7 (1:4000; Abcam AB68459, clone EPR1619Y), KRT23 (1:2000; Abcam AB156569, clone EPR10943), ER (1:4000; Thermo Scientific RMM-9101-S, clone SP1), PR (1:3000; CST 8757, clone D8Q2J), TCF7 (1:2000; CST 2203, clone C63D9), FITC-TSA (2 min; Perkin Elmer NEL701A001KT), Cy3-TSA (3 min; Perkin Elmer NEL744001KT), Cy5-TSA (7 min; Perkin Elmer NEL745E001KT).

Techniques: Expressing, Immunostaining, MANN-WHITNEY

Journal: Immunity

Article Title: Circulating NK cells establish tissue residency upon acute infection of skin and mediate accelerated effector responses to secondary infection

doi: 10.1016/j.immuni.2023.11.018

Figure Lengend Snippet:

Article Snippet: TCF1/TCF7 (C63D9) Rabbit mAb (Alexa Fluor® 488 Conjugate) , Cell Signaling Technology , Cat. #6444S; RRID: AB_2797627.

Techniques: Purification, Virus, Modification, Recombinant, Staining, Lysis, RNA Sequencing, Generated, Software

Journal: Cell Reports Medicine

Article Title: Local delivery of IL-15 and anti-PD-L1 nanobody by in vitro- transcribed circILNb elicits superior antitumor immunity in cold tumors

doi: 10.1016/j.xcrm.2025.102413

Figure Lengend Snippet: circILNb reprograms tumor-specific tdLN and tumor CD8 + T cells (A) (Left) Timeline of the experiment designed to evaluate the p-STAT5 levels of CD8 + T cells in tdLN and (right) legends and abbreviations for different treatment groups. B16F10-OVA tumor-bearing mice were intratumorally injected with circIL, circNb, and circILNb (0.5 mg/kg circRNA per mouse). The circLuc was used as control circScram. p value was determined by two-tailed unpaired t test. Data are mean ± SEM. (B) (Left) Representative sample histogram of pSTAT5 after circRNAs treatment. Summary data for (middle) pSTAT5 MFI and (right) pSTAT5 + cells. Gated on live CD3 + CD8 + cells ( n = 3). (C) Timeline of the experiment designed to evaluate the population and activity of CD8 + T cells in tdLN or tumor. B16F10-OVA tumor-bearing mice were intratumorally injected with circIL, circNb, and circILNb (0.5 mg/kg circRNA per mouse). circLuc was used as control circScram. p value was determined by two-tailed unpaired t test. Data are mean ± SEM. (D) (Left) Representative sample histogram of ki67 expression and (right) quantification of the ki67 MFI of tdLN CD8 + T cells. Gated on live CD3 + CD8 + cells ( n = 5). (E) Counts of tetramer + cells in the tdLN, gated on live CD8 + CD44 + tetramer + cells ( n = 5). (F) The tdLN frequency of Ttsm cells, gated on live CD8 + CD44 + tetramer + TCF1 + TOX − cells ( n = 3). (G) (Left) Representative contour plots, (middle) frequency, and (right) counts of Tsle in tumor, gated on live CD8 + tetramer + PD1 + TCF1 + TIM3 - cells ( n = 4). (H) (Left) Frequency and (right) counts of tetramer + cells in the tumor, gated on live CD8 + cells ( n = 3). (I) Counts of IFN-γ + cells in the tumor, gated on live CD8 + tetramer + cells ( n = 5). (J) Counts of GrzmB + cells in the tumor, gated on live CD8 + tetramer + cells ( n = 5). " n " indicates biologically independent samples.

Article Snippet: PE/Cy7 anti-mouse TCF1 (clone: C63D9) , Cell Signaling Technology , Cat#90511S; RRID: AB_3086656.

Techniques: Injection, Control, Two Tailed Test, Activity Assay, Expressing

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: TCF1 and LEF1 act as T-cell intrinsic HTLV-1 antagonists by targeting Tax.

doi: 10.1073/pnas.1419198112

Figure Lengend Snippet: Fig. 1. TCF1 and LEF1 are expressed at low levels in HTLV-1–infected T cells. (A) TCF1 and LEF1 mRNA expression is invariably low in HTLV-1–infected cell lines. Total RNA was extracted for each cell line and subjected to quantitative real-time PCR (qPCR) analysis. Results are shown as relative mRNA expression of TCF1 or LEF1 normalized to that of 18S rRNA. (B) TCF1 and LEF1 protein expression of cell lines used in A. α-tubulin expression was used as a control. (C) TCF1 and LEF1 mRNA expression is lower in fresh ATL cases. Peripheral CD4 T cells from a healthy donor (HD) and four ATL patients were subjected to RNA extraction and following qPCR analysis. Results are shown as relative mRNA expression of TCF1 or LEF1 normalized to that of 18S rRNA. “Fold exp.” indi- cates fold expression of normalized mRNA level of TCF1 or LEF1.

Article Snippet: Rabbit monoclonal antibodies for TCF1 (C63D9) and LEF1 (C12A5) were purchased from Cell Signaling Technology.

Techniques: Infection, Expressing, Real-time Polymerase Chain Reaction, Control, RNA Extraction

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: TCF1 and LEF1 act as T-cell intrinsic HTLV-1 antagonists by targeting Tax.

doi: 10.1073/pnas.1419198112

Figure Lengend Snippet: Fig. 2. TCF1 and LEF1 each interact with Tax and impair its transactivating ability. (A) TCF1 and LEF1 each repress Tax-mediated activation of WT-Luc (Top), NFκB-Luc (Middle), and AP1-Luc (Bottom). Reporter assays were performed in Jurkat cells. (B) Physical interactions between TCF1 and Tax (Upper), and LEF1 and Tax (Lower). (C) A ΔPBM mutant of Tax has impaired binding to TCF1 (Upper) and LEF1 (Lower) compared with WT Tax. (D) Physical interactions between Tax and CREB are inhibited by TCF1 or LEF1 in a dose-dependent manner. Tax-specific bands are denoted with an asterisk. All immunoprecipi- tations were performed in 293FT cells. “Ls” indicates the whole cell lysate.

Article Snippet: Rabbit monoclonal antibodies for TCF1 (C63D9) and LEF1 (C12A5) were purchased from Cell Signaling Technology.

Techniques: Activation Assay, Mutagenesis, Binding Assay

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: TCF1 and LEF1 act as T-cell intrinsic HTLV-1 antagonists by targeting Tax.

doi: 10.1073/pnas.1419198112

Figure Lengend Snippet: Fig. 3. TCF1 and LEF1 each inhibit HTLV-1 replication by antagonizing Tax. (A) TCF1 and LEF1 each inhibits HTLV-1 production (Upper) and protein ex- pression (Lower). pX1MT-M (0.5 μg) was transfected with or without TCF1 or LEF1 into 293FT cells. 48 h later, supernatants were collected for p19 ELISA and cells were lysed for Western blot. (B) TCF1 and LEF1 each inhibit Tax transcription (Lower) but not HBZ transcription (Upper). pX1MT-M (0.5 μg) was transfected with or without TCF1 or LEF1 into 293FT cells. 44 h later, RNA was extracted for qPCR analysis. (C) TCF1 and LEF1 each slightly en- hance Tax-mediated 3′ LTR-Luc (Left) activation, whereas they significantly suppress 5′ LTR activation (Right). Reporter assays were performed in Jurkat cells. (D) Jurkat or normal human CD4 T cells were either cultured alone (Upper) or cocultivated with lethally irradiated (150 Gy) MT-2 cells (Lower) at a 2:1 ratio. 48 h later (when MT-2 cells were all dead), cells were stained for intracellular Tax and TCF1 or LEF1. Numerals indicate percentages of gated populations. Fold exp. indicates fold expression.

Article Snippet: Rabbit monoclonal antibodies for TCF1 (C63D9) and LEF1 (C12A5) were purchased from Cell Signaling Technology.

Techniques: Transfection, Enzyme-linked Immunosorbent Assay, Western Blot, Activation Assay, Cell Culture, Irradiation, Staining, Expressing

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: TCF1 and LEF1 act as T-cell intrinsic HTLV-1 antagonists by targeting Tax.

doi: 10.1073/pnas.1419198112

Figure Lengend Snippet: Fig. 4. Tax down-regulates the expression of TCF1 and LEF1 via STAT5a. (A) P/I stimulation (Upper) or Tax overexpression (Lower) inhibits TCF1/LEF1 transcription in Jurkat. For P/I stimulation, cells were treated with 50 ng/mL of PMA and 500 ng/mL of ionomycin (P/I) for 5 h and then subjected to RNA extraction and qPCR analysis. Overexpression of Tax was achieved by elec- troporation and 24 h later, RNA was extracted for qPCR. (B) Tax induction in JPX-9 down-regulates the expression of TCF1 and LEF1. JPX-9 was cultured in RPMI supplemented with 20 μM of cadmium (Cd) to induce Tax expression. At indicated time points, cells were lysed for Western blot analysis. (C) P/I stimulation or Tax overexpression induces STAT5a expression in Jurkat. P/I stimulation and Tax overexpression were performed as in A. (D) Over- expression of STAT5a down-regulates TCF1 and LEF1. Jurkat was transfected with wild type (WT) or constitutively active (CA) STAT5a by electroporation. 24 h later, RNA was extracted for qPCR. Fold exp. indicates fold expression.

Article Snippet: Rabbit monoclonal antibodies for TCF1 (C63D9) and LEF1 (C12A5) were purchased from Cell Signaling Technology.

Techniques: Expressing, Over Expression, RNA Extraction, Cell Culture, Western Blot, Transfection, Electroporation