Journal: Cancer biology & therapy

Article Title: Molecular profiles of different PD-L1 expression in patients with esophageal squamous cell carcinoma.

doi: 10.1080/15384047.2023.2256927

Figure Lengend Snippet: Figure 5. Association between tumor-infiltrating lymphocytes (TILs) and PD-L1 expression. (a) Representative mIHC staining figures of the group with high PD-L1 expression. (b) Representative mIHC staining figures of the group with low PD-L1 expression. (c) the ratio of PD-L1+ or PD-1+ CD8+ T cells to CD8+ T cells. (d) the ratio of PD-L1+ or PD-1+ CD68+ macrophage to CD68+ macrophage. (e) correlation between CPS and TILs in the tumoral and stromal region. (f) correlation matrix between TILs in tumor and stroma region. (***, p < .001; **, p < .01; *, p < .05).

Article Snippet: The immune biomarker panel included CD68 (1:500, Beijing Zhongshan Golden Bridge Biotechnology, ZM0060), CD8 (1:100, Beijing Zhongshan Golden Bridge Biotechnology, ZA0508), PD-1 (1:50, Beijing Zhongshan Golden Bridge Biotechnology, ZM0381) and PD-L1 (1:25, Roche Diagnostics, 740–4859).

Techniques: Expressing, Staining

Journal: Nature Medicine

Article Title: Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial

doi: 10.1038/s41591-022-01789-0

Figure Lengend Snippet: a , Classification into synovial pathotypes according to semiquantitative scores for CD3 + T cells, CD20 + B cells, CD68 + macrophages and CD138 + plasma cells, with representative examples from patients classified as lymphomyeloid (CD20 ≥ 2 and/or CD138≥2), diffuse-myeloid (CD68SL≥2, and CD20/CD138<2) or fibroid/pauci-immune (CD68SL/CD20/CD138<2). Right, 16-week CDAI 50% response in patients stratified by pathotype ( n = 152). Bar plots showing the proportion of CDAI 50% responders for rituximab (in blue) and tocilizumab (in yellow) within each pathotype, with corresponding exact numbers. Fisher's test, exact P values for P < 0.05. b , Approach to in silico deconvolution of synovial tissue using MCP-counter. c , MCP-counter scores for each cell type compared among CDAI 50% responders (R) and nonresponders (NR). Bar plots indicate nominal log 10 P values for tocilizumab and –log 10 P values for rituximab (two-sided Mann–Whitney test); dashed lines correspond to P = 0.05. Boxplots (right) show median and first and third quartiles, whiskers extending to the highest and lowest values. d – f , 16-week CDAI 50% response in patients stratified into B and T cell poor/rich ( d ) and macrophage/mDC poor/rich ( e ) according to median MCP-counter scores for individual cells (rich if above median, poor if below), or by combining B cell and macrophage/mDC scores from d , e ( f ). Exact P values shown when <0.05, two-sided Fisher's test comparing the proportions of responders to rituximab (in blue) and tocilizumab (in yellow). g – i , Longitudinal disease activity scores (CDAI), shown as mean ± s.d., for each month from baseline to 16 weeks for patients randomized to rituximab (in blue) or tocilizumab (in yellow) and classified as B and T cell poor/rich ( g ), macrophage/mDC poor/rich ( h ) and combined B cell/macrophage poor/rich ( i ). Comparison of CDAI between the two medications at individual time points by two-sided Mann–Whitney test, exact P values for <0.05 (adjustment for multiple comparisons by FDR). P values for the drug × time interaction term (two-way repeated-measures analysis of covariance) are shown when <0.05. c – i , n = 133 patients with baseline RNA-seq. NK, natural killer cells. mDC, myeloid dendritic cells.

Article Snippet: Briefly, tissue morphology was visualized using fluorescent antibodies CD68-AF532 (clone KP1, Novus), CD20-DL594 (clone IGEL/773, Novus) and CD3-AF647 (clone UMAB54, Origene) and Syto13 (ThermoFisher).

Techniques: In Silico, MANN-WHITNEY, Activity Assay, RNA Sequencing Assay

Journal: Nature Medicine

Article Title: Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial

doi: 10.1038/s41591-022-01789-0

Figure Lengend Snippet: a , Scheme showing the approach to DSP, including selection of ROIs: CD68 + lining and superficial sublining, CD20 – CD3 – deep sublining and CD3 + CD20 + lymphoid aggregates. b , MA plot showing mean expression (log 2 ) on the x axis and fold change on the y axis comparing responders and refractory patients across all ROIs. Genes significantly upregulated (FDR<0.05) in responders are shown in blue (top), and those upregulated in refractory in red (bottom); in grey, genes with FDR > 0.05; P values were calculated using a negative binomial linear model applied to count data using DESeq2 (Wald test) and were FDR adjusted n = 12 patients, six ROIs per patient. c , Example of individual genes differentially expressed in refractory (red) or responders (green). Scatterplots showing individual ROIs, boxplots showing median and first and third quartiles. FDR-adjusted P values calculated as in b are shown for differentially expressed genes between refractory and responder individuals; n = 12 patients (4 responders to rituximab, 4 responders to tocilizimab and 4 refractory). d , Examples of individual genes differentially expressed in refractory (red) or responders (green) in different ROIs. Scatterplots showing individual ROIs ( n = 12 patients, six ROIs per patient), boxplots showing median and first and third quartiles. FDR-adjusted P values calculated as in b are shown for differentially expressed genes between refractory and responder individuals. L, lining/superficial sublining; SL, deep sublining; A, lymphoid aggregates (as shown in a ).

Article Snippet: Briefly, tissue morphology was visualized using fluorescent antibodies CD68-AF532 (clone KP1, Novus), CD20-DL594 (clone IGEL/773, Novus) and CD3-AF647 (clone UMAB54, Origene) and Syto13 (ThermoFisher).

Techniques: Selection, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Cirrhotic Cardiomyopathy Following Bile Duct Ligation in Rats—A Matter of Time?

doi: 10.3390/ijms24098147

Figure Lengend Snippet: Immunohistochemical staining of CD68 positive cells in rat myocardium after bile duct ligation (BDL) versus controls. Exemplary histologic images are shown for both groups at day 31 after BDL. Scale bars correspond to 250 µm length. Positive cells were counted in 10 high power fields (HPF, 40×; 2560 × 1440 pixels) and displayed as mean ± standard error of the mean (SEM). (*** P d31 < 0.001; ** P d35 = 0.002; * P d42 = 0.017, P d56 = 0.019, P group < 0.001, P time = 0.29, P group*time = 0.48). Data were analyzed using a generalized mixed model analysis corrected for multiple comparisons using the Shaffer-simulated approach. The interaction effect of group and time is expressed as group*time. p ≤ 0.05 was considered significant.

Article Snippet: Macrophages in cardiac sections were detected using a cluster of differentiation 68 (CD68) antibody (Cat. No. BM4000S, OriGene Technologies GmbH, Herford, Germany) as the primary antibody.

Techniques: Immunohistochemical staining, Staining, Ligation