Journal: Oncogene

Article Title: Activating and sustaining c-Myc by depletion of miR-144/451 gene locus contributes to B-lymphomagenesis

doi: 10.1038/s41388-017-0055-5

Figure Lengend Snippet: miR-144/451 deletion accelerates tumorigenesis in aged mice. a Representative gloss tumor images from aged miR-144/451 −/ − mice. b Histopathological image with H&E staining showing typical lymphoma cells. c Flow cytometric analysis showing B-cell identity of the lymphoma cells based on B220/CD19 staining. d Gloss view of a large spleen with AML and e multiple liver adenoma in aged mice. f Genomic DNA PCR showing loss of heterogeneity of miR-144/451 − /+ genotype. M1 and M2 represent mouse 1 and mouse 2, and T1 and T2 represent tumors from M1 and M2, respectively

Article Snippet: Antibodies against mouse CD45R (B220, Cat# 553079) and CD19 (Cat# 553786) were purchased from BD Biosciences.

Techniques: Staining

Journal: Oncogene

Article Title: Activating and sustaining c-Myc by depletion of miR-144/451 gene locus contributes to B-lymphomagenesis

doi: 10.1038/s41388-017-0055-5

Figure Lengend Snippet: miR−144/451 expression is down regulated in murine B-lymphoma cells. a , b Quantitative real-time PCR (qRT-PCR) analysis to quantify the gene transcriptions. a miR-451 in murine B-cell lymphoma line 38B9 and Myc3. b Primary mouse B-cell lymphomas induced by constitutive Myc expression. c , d qRT-PCR analysis showing the miR-144 levels. c Murine B-lymphoma cell line 38B9 and Myc3. d Primary B-cell lymphomas. In all four graphs, the Y-axis shows relative expression and the miR-451 or miR-144 levels from normal bone marrow-derived CD19 + B220 + B-lymphocytes are assigned an arbitrary relative value of 1. (**) p value < 0.01 ( t -test). Experiments were repeated three times. Note, both miR-451 and miR-144 are dramatically down regulated in mouse B-lymphoma cells compared with normal B-lymphocytes

Article Snippet: Antibodies against mouse CD45R (B220, Cat# 553079) and CD19 (Cat# 553786) were purchased from BD Biosciences.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Derivative Assay

Journal: Molecular Cell

Article Title: Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mice and Humans

doi: 10.1016/j.molcel.2020.10.012

Figure Lengend Snippet: Aldehyde Catabolism Is Essential for Lymphoid Development (A) Spleen histology (hematoxylin and eosin [H&E stain]) and immunohistochemistry for B220 or CD3. (B) Quantification of splenic B, T, myeloid, and erythroid precursors assessed by flow cytometry (n = 23, 20, 19, 17, left to right). (C) Bone marrow immunohistochemistry for B220. (D) Thymus histology (H&E stain). (E) Representative flow cytometry plots showing bone marrow B cell development and quantification of total B220 + cells (mean ± SEM; n = 23, 20, 19, 15, left to right). (F and G) Representative flow cytometry plots and quantification of the thymic Lin − population (F) and Lin − CD4 − CD8 − (DN) populations defined by CD44 and CD25 expression (G). Mice analyzed for thymic Lin − populations were 2–30 weeks old (n = 23, 20, 19, 15, left to right). Mice analyzed for thymic DN populations were older than 30 weeks (n = 7, 7, 5, 5 mice, left to right). All bar graphs are shown with mean ± SEM. The p values were determined by two-tailed Mann-Whitney U test except for (G), where pairwise χ 2 tests of average distributions were performed. Scale bars indicate 100 μm. See also and .

Article Snippet: Bone marrow cells (1 × 10 6 ) as prepared above were stained with antibodies against CD45R/B220 (PE, clone RA3-6B2, BD PharMingen) and IgM (APC, clone II/41, BD PharMingen).

Techniques: Staining, Immunohistochemistry, Flow Cytometry, Expressing, Two Tailed Test, MANN-WHITNEY

Journal: Molecular Cell

Article Title: Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mice and Humans

doi: 10.1016/j.molcel.2020.10.012

Figure Lengend Snippet:

Article Snippet: Bone marrow cells (1 × 10 6 ) as prepared above were stained with antibodies against CD45R/B220 (PE, clone RA3-6B2, BD PharMingen) and IgM (APC, clone II/41, BD PharMingen).

Techniques: Recombinant, Sequencing, Clone Assay, Software

Journal: Nature Communications

Article Title: The immune landscape of human thymic epithelial tumors

doi: 10.1038/s41467-022-33170-7

Figure Lengend Snippet: ( a ) Schematic diagram of the overall study design and workflow. ( b ) t-SNE plots of total cells from human TETs ( n = 22) and the normal thymus ( n = 3) by CyTOF using a Phenograph clustering scheme. Samples were grouped according to WHO histological subtype, Masaoka stage or our alternative classification, and each color represents an independent group or stage (N, normal human thymus; T1, type 1; T2, type 2; T3, type 3; the abbreviations below are consistent with these definitions). ( c ) t-SNE plot of total cells from all samples ( n = 25) by CyTOF using a Phenograph clustering scheme, colored by cell cluster. ( d ) Bar plots showing the frequencies of cluster 1 and cluster 2 subsets among the four groups of samples ( n = 3, 9, 7 and 6 for N, T1, T2 and T3, respectively. Data are presented as the mean ± s.e.m. P values in the figure were determined by an unpaired two-tailed Student’s t test). ( e-f ) Sheet and pie charts summarizing samples in each alternative classification by WHO histological subtype ( e ) or Masaoka stage ( f ). Each color represents a WHO histological subtype or Masaoka stage. ( g ) Same t-SNE plot as ( c ), colored by cell type. ( h ) t-SNE plot of immune cells (EPCAM-CD45 + ) from all samples obtained by CyTOF using a Phenograph clustering scheme, colored by cell type. ( i ) t-SNE analysis of immune cells from all samples colored by the relative expression of CyTOF markers (CD45, CD3, CD4, CD8a, CD20, CD14, CD141, CD56, CD11c, CD66b, HLA-DR and CD39). ( j ) Same t-SNE plots of immune cells as ( h ) from samples of each group (N, T1, T2, T3), colored by cell type. ( k ) Bar plots showing the frequencies of the main immune cell subsets among the four groups of samples ( n = 3, 9, 7 and 6 for N, T1, T2 and T3, respectively. Data are presented as the mean ± s.e.m. P values in the figure were determined by an unpaired two-tailed Student’s t test). ( l ) Representative flow cytometric plot of CD3 + T cells and CD3 - CD4 + CD8 + lymphocytes from TETs of each type. Source data are provided as a Source Data file.

Article Snippet: Antibodies against CD45 (60287-1-IG, diluted 1:500), CCL25 (25285-1-AP, diluted 1:500), CHI3L1 (12036-1-AP, diluted 1:400), AIRE (22517-1-AP, diluted 1:500), KRT14 (60320-1-IG, diluted 1:800) and GNB3 (12036-1-AP, diluted 1:400) were procured from Proteintech Group.

Techniques: Two Tailed Test, Expressing

Journal: Nature Communications

Article Title: The immune landscape of human thymic epithelial tumors

doi: 10.1038/s41467-022-33170-7

Figure Lengend Snippet: ( a ) t-SNE plot of CD45 + CD3 + T cells from all samples (n = 25), colored by cell subset. (DN, CD3 + CD4 - CD8 - ; DP, CD3 + CD4 + CD8 + ). ( b ) Heatmap showing relative normalized protein expression for the T-cell subsets from CyTOF, normalized total matrix. ( c ) t-SNE plots of CD45 + CD3 + T cells from human TETs (n = 22) and the normal thymus (n = 3) by CyTOF using the Phenograph clustering scheme. Samples were grouped according to WHO classification, Masaoka stage or our alternative classification, and each color represents a T-cell subset. ( d – f ) Composition of the CD45 + CD3 + T-cell compartment showing the average frequencies of major T-cell subsets for each WHO histological subtype ( d ) (n = 3, 3, 7, 6 and 5 for N, A, AB, B and TC, respectively), Masaoka stage ( e ) (n = 3, 11, 4, 5 and 2 for N, I, II, III and IV, respectively) or our alternative classification ( f ) (n = 3, 9, 7 and 6 for N, T1, T2 and T3, respectively). Each color represents a T-cell subset, same as in ( c ). ( g ) Bar plots showing the frequencies of the main T-cell subsets among the four groups of samples (n = 3, 9, 7 and 6 for N, T1, T2 and T3, respectively. Data are presented as the mean ± s.e.m. P values in the figure were determined by an unpaired two-tailed Student’s t test). (DP, CD3 + CD4 + CD8 + ). ( h ) Representative flow cytometric plot of CD3 + CD4 - CD8 - T cells, CD3 + CD4 + T cells, CD3 + CD8 + T cells and CD3 + CD4 + CD8 + T cells from TETs of three types. ( i ) Representative immunofluorescence (IF) staining images showing CD3 (pale blue), CD8 (green), CD4 (red) and DAPI (nuclei, blue) in the normal human thymus and TET samples (scale bar: 100 μm). (M: Medulla; C: Cortex; M-like: Medulla-like structure; C-like: Cortex-like structure). Experiment was performed in three independent samples for each group with similar results. Source data are provided as a Source Data file.

Article Snippet: Antibodies against CD45 (60287-1-IG, diluted 1:500), CCL25 (25285-1-AP, diluted 1:500), CHI3L1 (12036-1-AP, diluted 1:400), AIRE (22517-1-AP, diluted 1:500), KRT14 (60320-1-IG, diluted 1:800) and GNB3 (12036-1-AP, diluted 1:400) were procured from Proteintech Group.

Techniques: Expressing, Two Tailed Test, Immunofluorescence, Staining