Journal: Nature

Article Title: AIM2 in regulatory T cells restrains autoimmune diseases.

doi: 10.1038/s41586-021-03231-w

Figure Lengend Snippet: Fig. 4 | AIM2 promotes Treg cells in vitro and restrains AKT–mTOR via the RACK1–PP2A complex. a, b, RT–PCR (a) and flow cytometry (b) of FOXP3 in wild-type and Aim2−/− CD4+ T cells activated with the indicated amounts (a) or 2 ng ml−1 (b) of TGFβ for 4 days; n = 5 experiments in a and n = 4 experiments in b. c, Flow cytometry of IFNγ+ or IL-17A+ CD4+ T cells of indicated genotypes, 4 days after differentiation under indicated polarizing conditions; n = 4 experiments. cTH17, classic TH17; pTH17, pathogenic TH17. d–g, Wild-type and Aim2−/− CD4+ T cells were stimulated as in b. d, Enrichment scores of indicated gene sets, based on RNA-seq datasets. e, f, ECAR (e) and OCR (f) levels during glycolysis, and OCR levels during fatty acid oxidation (g), by Seahorse analysis; n = 10 experiments for e; n = 5 experiments for f; and n = 3 experiments for g. h, Immunoblotting of indicated proteins in wild-type and Aim2−/− CD4+ T cells stimulated as in b with indicated treatment for 24 h. Representative of three

Article Snippet: Ectopic expression of PP2A and RACK1 in Treg cells To generate the retrovirus expressing PP2A and RACK1, we first cloned PP2A (OriGene Technologies, MR204384L4) and RACK1 (OriGene Technologies, MR204575L3) into retroviral vectors MSCV-IRES-Thy1.1 (MIT, Addgene 17442) and MSCV-IRES-GFP (MIG, Addgene 20672) respectively, and generated MIT-PP2A and MIG-RACK1 retrovirus in 293T cells by transient transfection.

Techniques: In Vitro, Reverse Transcription Polymerase Chain Reaction, Flow Cytometry, RNA Sequencing, Western Blot

Journal: Blood Advances

Article Title: Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma

doi: 10.1182/bloodadvances.2021005682

Figure Lengend Snippet: FBXO11 tumor-derived mutants show impaired ability to induce BCL6 and SNAIL degradation. (A) Representative western blot for FBXO11 and BCL6 protein expression in HEK-293T cells transfected with BCL6 in combination with GFP, WT FBXO11, or FBXO11 mutants at the indicated time points after treatment with CHX. FBXO11 mutants were detected by anti-FBXO11 antibody, and BCL6 was detected by anti-BCL6 antibody. β-actin was used as a loading control. GFP was used for transfection efficiency. One representative experiment of 2 independently performed experiments is shown. (B) Impaired degradation of SNAIL by FBXO11 mutants. Representative western blot for FBXO11 and SNAIL protein expression in HEK-293T cells transfected with SNAIL and WT FBXO11 or the indicated FBXO11 mutants at the indicated time points after treatment with CHX. FBXO11 mutants were detected by anti-Flag antibody. β-actin was used as a loading control. One representative experiment of 2 independently performed experiments is shown. (C) Degradation kinetics of BCL6 by FBXO11 mutants. BCL6 abundance was measured from western blot gels as in (A) by ImageJ software and normalized for the GFP intensity of the corresponding lane. The ratio between the relative levels of BCL6/GFP at each time 0 was set as 100%. Data are from 1 of 2 independent experiments, each with comparable results. (D) SNAIL abundance was measured from western blot gels, as in (B), using ImageJ software and normalized for β-actin intensity of the corresponding lane. The ratio between the relative levels of SNAIL/β-actin at each time 0 was set as 100%. Data are from 1 of 2 independent experiments, each with comparable results.

Article Snippet: FLAG-tagged SNAIL (clone ID: 16218) and FLAG-tagged BCL6 (clone ID: 31391) plasmids were purchased from Addgene (Cambridge, MA).

Techniques: Derivative Assay, Western Blot, Expressing, Transfection, Software

Journal: Blood Advances

Article Title: Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma

doi: 10.1182/bloodadvances.2021005682

Figure Lengend Snippet: FBXO11 deletion accelerates lymphomagenesis in Eμ-myc–transgenic mice. (A) Kaplan-Meier survival analysis of Eμ-myc (n = 33), Eμ-myc/FBXO11fl/fl;CD19-Cretg/+ (KO) (n = 21) and Eμ-myc/FBXO11fl/+;CD19-Cretg/+ (HET) (n = 16) mice, with a median survival time of 121, 89, and 85 days, respectively. Eμ-myc (n = 33) are a combination of Eμ-myc/FBXO11fl/fl (n = 23) and Eμ-myc/FBXO11fl/+ (n = 10). P < .0001 log-rank (Mantel-Cox) test. (B) B220 and IgM expression in lymphomas from Eμ-myc (n = 17), Eμ-myc/FBXO11fl/fl;CD19-Cretg/+ (KO) (n = 16), and Eμ-myc/FBXO11fl/+;CD19-Cretg/+ (HET) (n = 9) mice. (C) B220 and IgD expression in lymphomas from Eμ-myc (n = 16), Eμ-myc/FBXO11fl/fl;CD19-Cretg/+ (KO) (n = 10), and Eμ-myc/FBXO11fl/+;CD19-Cretg/+ (HET) (n = 5) mice. (D) Representative flow cytometry of B220 and IgM expression in lymphoma from Eμ-myc, Eμ-myc/FBXO11-KO, and Eμ-myc/FBXO11 HET mice. (E) Representative H&E stains (top row) and immunohistochemistry for cleaved caspase 3 (middle row) and Ki-67 (bottom row) performed on Eμ-myc primary lymphoma with the indicated genotypes (original magnification ×200). Scale bars, 50 μm. Insets show high-magnification images. (F) Quantification of macrophages in Eμ-myc lymphoma with the indicated genotypes (n = 6 mice for each genotype). Data are mean (± standard deviation [SD]) macrophages per 40× field. Quantification of cleaved caspase 3+ (G) and Ki-67+ (H) cells in Eμ-myc lymphoma with the indicated genotypes (n = 4 mice for each genotype). Data are mean ± SD. (I) BCL6 stability in Eμ-myc/FBXO11-KO lymphoma cells. Western blot showing BCL6 protein expression after treatment with CHX for the indicated times in 3 immortalized Eμ-myc/FBXO11fl/fl lymphoma cell lines transduced with a tamoxifen-inducible CreERT2 vector. Cre recombinase was activated by treatment with 10 nM 4-hydroxytamoxifen (4-OHT) for 4 hours to induce deletion of the FBXO11 floxed gene. A20 is a mouse BCL6+ B lymphoma cell line used as control. **P < .01, ***P < .001, unpaired 2-tailed Student t test.

Article Snippet: FLAG-tagged SNAIL (clone ID: 16218) and FLAG-tagged BCL6 (clone ID: 31391) plasmids were purchased from Addgene (Cambridge, MA).

Techniques: Transgenic Assay, Expressing, Flow Cytometry, Immunohistochemistry, Standard Deviation, Western Blot, Transduction, Plasmid Preparation

Journal: Blood Advances

Article Title: Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma

doi: 10.1182/bloodadvances.2021005682

Figure Lengend Snippet: FBXO11 deletion in BL cell lines leads to BCL6 protein stabilization. (A) BLC6 stability in human BL lines in which FBXO11 is knocked out. Representative western blot showing BCL6 protein expression in 3 independent FBXO11 KO RAJI cell lines (clone #1 obtained with sgRNA#1, clones #2 and #3 obtained with sgRNA#2; supplemental Figure 5B-E) after treatment with CHX for the indicated times. FARAGE cell line, which is homozygous for deletion of the FBXO11 gene, was used as control for BCL6 stability. One representative experiment of 3 independently performed experiments is shown. (B) Representative western blot showing BCL6 protein expression in WT or FBXO11-KO DAUDI cell line after treatment with CHX for the indicated times. β-actin was used as a loading control. One representative experiment of 3 independently performed experiments is shown. (C) Degradation kinetics of BCL6 in BL WT or FBXO11-KO cells. BCL6 abundance was measured from western blot gels as in (A-B) using ImageJ software and normalized for the β-actin intensity of the corresponding lane. (D) Quantitative real-time PCR expression analysis of the BCL6 target genes DUSP5, CDKN1A, and CD69 mRNA in RAJI and 2 FBXO11-KO RAJI cell lines (#1 and #2). Data are mean ± standard deviation. (E) Hierarchical clustering (Euclidean distance, average linkage) of 172 genes detected as differentially expressed between the FBXO11-WT or -KO RAJI cell lines. (F) Analysis of genes detected as differentially expressed between WT cell lines and KO clones. Forty-seven of 172 differentially expressed genes can be connected to each other using Ingenuity Pathway Analysis (QIAGEN IPA) in a BCL6-centered network. **P < .01, ***P < .001, unpaired 2-tailed Student t test.

Article Snippet: FLAG-tagged SNAIL (clone ID: 16218) and FLAG-tagged BCL6 (clone ID: 31391) plasmids were purchased from Addgene (Cambridge, MA).

Techniques: Western Blot, Expressing, Clone Assay, Software, Real-time Polymerase Chain Reaction, Standard Deviation

Journal: Blood Advances

Article Title: Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma

doi: 10.1182/bloodadvances.2021005682

Figure Lengend Snippet: BCL6 degradation impairs BL growth and potentiates MYC inhibition. (A) Western blot analyses for BCL6 expression on the indicated BL cell lines. Cells were treated for 60 minutes with BI-3802 (1 or 5 μM), BI-3812 (1 μM), or vehicle (-) before collection. Data are representative of 2 experiments. β-actin was used as loading control. (B) Western blot analysis for BCL6 on immortalized lymphoma cell lines obtained from FBXO11-WT (Eμ-myc) or -KO (Eμ-myc/FBXO11fl/fl;CD19-Cretg/+) mice. Cells were treated for 1 hour with BI-3802 (1 or 5 μM), BI-3812 (1 μM), or vehicle (-) before collection. Data are representative of 2 experiments with similar results. β-actin was used as loading control. (C) Effects of BCL6 degradation on WT and FBXO11-KO RAJI (clones #1 and #2) cell growth. Cells were kept at constant concentrations of the degrader BI-3802 as indicated (1 μM or 5 μM) and split to 100 000 cells per milliliter every 3 days. Split rates were multiplied to derive growth curves. Data are mean ± standard error of the mean (SEM) and are representative of ≥3 independent experiments. *P < .05, **P < .01, unpaired 2-tailed Student t test. (D) Growth of tumor xenografts in NSG mice of WT and FBXO11-KO RAJI (clones #1 and #2) cells treated with BI-3802 (5 μM) for 24 hours before injection. Data (n = 5 mice per group) are shown as mean ± SEM. **P < .01, paired 2-tailed Student t test. (E) Growth curves of WT and FBXO11-KO RAJI (clones #1 and #2) cells treated with Omomyc mini-protein (2 or 5 μM), alone or in combination with BI-3802 (5 μM). Total cell number was quantified at the indicated time points. Data are mean ± SEM of triplicates from a single experiment representative of 2 repeats. **P < .01, ***P < .001, unpaired 2-tailed Student t test. (F) Growth curves of WT and FBXO11-KO RAJI (clones #1 and #2) cells infected with a doxycycline-inducible lentiviral vector expressing Omomyc. Cells were treated only with doxycycline to induce Omomyc expression (Omomyc), or BI-3802 (5 μM) or a combination of doxycycline and BI-3802 (Omomyc + BI-3802). Total cell number was quantified at the indicated time points. Data are mean ± SEM of triplicates from a single experiment representative of two repeats. **P < .01, ***P < .001, unpaired 2-tailed Student t test.

Article Snippet: FLAG-tagged SNAIL (clone ID: 16218) and FLAG-tagged BCL6 (clone ID: 31391) plasmids were purchased from Addgene (Cambridge, MA).

Techniques: Inhibition, Western Blot, Expressing, Clone Assay, Injection, Infection, Plasmid Preparation

Journal: Blood Advances

Article Title: Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma

doi: 10.1182/bloodadvances.2021005682

Figure Lengend Snippet: Combined targeting of MYC and BCL6 severely impairs BL growth in mice by reducing proliferation and increasing apoptosis. (A) Growth of tumor xenografts of RAJI cells transduced with doxycycline-inducible Omomyc vector in NSG mice. Lymphoma cells were treated with BI-3802 (5 μM) for 24 hours before injection. Mice were administered normal water (red line) or doxycycline water (blue line) from day 0. Data are mean ± standard error of the mean of 8 tumors per group. *P < .05, paired 2-tailed Student t test. (B) Representative H&E stains (top row) and immunohistochemistry for cleaved caspase 3 (middle row) and Ki-67 (bottom row) performed on RAJI lymphoma arising in NSG mice and treated with the BCL6 degrader BI-3802 together with Omomyc, as in (A) (original magnification ×200). Scale bars, 50 μm. Quantification of cleaved caspase 3+ (C) and Ki-67+ (D) cells in RAJI lymphoma with the indicated treatment. Data were obtained from 4 areas in 4 independent tumors for each treatment. Data are mean ± standard deviation. **P < .01, unpaired 2-tailed Student t test. (E) Representative immunofluorescence performed on RAJI lymphoma grafted in NSG mice and treated with the BCL6 degrader BI-3802 together with Omomyc, as in (A). Cells were stained for Ki-67 (green), Omomyc (red), and DAPI (blue) for the nucleus (original magnification, ×200). Scale bars, 100 μm. Higher-magnification images of the white boxes are shown in the far right panels. Pink arrow-heads in inset images indicate Ki-67−/Omomyc+ nuclei. (F) Quantification of the experiment described in (E). Three sections for each treatment were used to score the number of Ki-67+/Omomyc− and Ki-67+/Omomyc+ nuclei. ***P < .001.

Article Snippet: FLAG-tagged SNAIL (clone ID: 16218) and FLAG-tagged BCL6 (clone ID: 31391) plasmids were purchased from Addgene (Cambridge, MA).

Techniques: Transduction, Plasmid Preparation, Injection, Immunohistochemistry, Standard Deviation, Immunofluorescence, Staining

Journal: Nature Communications

Article Title: Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer

doi: 10.1038/s41467-024-55330-7

Figure Lengend Snippet: Fig. 3 | JUNB-HDAC1 complex represses inflammatory signals and cJUN. a Heatmap showing expression of cytokines present in the core enrichment of the gene sets shown in Supplementary Fig. 3a–d, for JUNB silencing (siJUNB; n = 3 biological replicates) versus control siRNA (siCtrl; n = 2 biological replicates) in CAPAN1 cells. Cell color indicates z score. b qRT-PCR analysis for indicated target genes in siJUNB conditions (red), normalized to siCtrl (gray), in CAPAN1. Relative mRNA expression with mean ± s.d. shown. n = 3 biological replicates. Two-tailed Student’s t-test with Welch’s correction. Coverage of JUNB ChIP-seq data in CAPAN121, as well as publicly available H3K27ac25 data, for loci of cJUN (c), IL1A/B (d), and CXCL9/10/11 (e). ChIP-qPCR validation regions are indicated. f Gene set enrichment analysis for curated signatures (C2) of the Molecular Signature Data- base (MSigDB) for siJUNB versus siCtrl in CAPAN1 cells. Normalized enrichment score (NES) and FDR q value are indicated. Immunoblot for JUNB, HDAC1, and β- actin after JUNB pulldown, IgG isotype control or input in CAPAN1 (g) and CAPAN2 (h). n = 3 biological replicates. i, j, ChIP-qPCR for regions indicated in (c–e), showing signal relative to input for JUNB (i) and HDAC1 (j) pulldown with

Article Snippet: Patient-derived primary cell line GCDX62 was maintained in a 3:1 mixture of Keratinocyte-SFM (KSF; Thermo Fisher Scientific; supplemented with 2% (v/v) FCS, 1% (v/v) Penicillin-streptomycin, bovine pituitary extract (BPE), and human epidermal growth factor) and RPMI 1640 containing 10% (v/v) FCS. cJUN overexpression (cJUN-OE; construct pMSCV-cJUN, no. 34898, addgene) and empty vector (EV; construct MSCV, no. 68469, addgene) control cell lines of CAPAN2 and GCDX62 were generated previously21, and were maintained in their normal growth medium supplemented with 1μg/mL puromycin. siRNA transfection For transient knockdownexperiments, 5 × 105 cellswere seeded in 6-well plates and immediately transfected with a mixture of 10μL Lipofectamine2000 (Thermo Fisher Scientific), 6μL of 20μM target-specific siRNA (or non-targeting siRNA as control), and 200μL Opti-MEM (Thermo Fisher Scientific) after 15min incubation of the transfection mixture at room temperature (RT).

Techniques: Expressing, Control, Quantitative RT-PCR, Two Tailed Test, ChIP-sequencing, ChIP-qPCR, Biomarker Discovery, Western Blot