Journal: Nature Communications

Article Title: The integrated molecular and histological analysis defines subtypes of esophageal squamous cell carcinoma

doi: 10.1038/s41467-024-53164-x

Figure Lengend Snippet: a The immune cell infiltration profiling across our cohort is shown, clustered by the level of estimated immune cell infiltration. Each row represents an immune cell type as estimated by the method used by Danaher et al. Immune cells are natural killer (NK) cells, neutrophils, B cells, macrophages, CD4 + mature cells, regulatory T cells (Treg), CD56dim NK cells, total T cells (T cells), CD8 + T cells, cytotoxic cells, exhausted CD8 + T cells (exhausted CD8), dendritic cells (DC) and mast cells. Consensus clustering was performed. Each column represents a patient sample. Three immune infiltration clusters were identified: C1, C2 and C3. b Levels of gene expression of XCL1 and XCL2 for n = 120 samples are shown among the three immune subtypes as a box and whisker plot. Significance in each pairwise comparison is shown using the two-sided Wilcoxon rank-sum test. c IHC analysis revealed that the C2 immune subtype had significantly increased levels of CD8 (67 samples) and CD56 (75 samples) expression. Significance was determined using a two-sided Wilcoxon test; * p < 0.05, *** p < 0.001. d The survival analysis of all profiled immune cell types against overall survival for 102 samples is shown. The hazard ratio (HR) derived from the multivariate Cox regression model is shown as a whisker plot. The blue square indicates the HR value, and the error bars represent 95% confidence intervals. Significance is determined using a two-sided log-rank test (■ p < 0.1; * p < 0.05). e A Kaplan–Meier curve is shown for NK cell estimates against overall survival for our cohort (China, 102 samples) and TCGA (90 samples). Multivariant survival analysis was performed for the China cohort. HR and p -value derived from the log-rank test are shown. f The number of cases of the four transcriptomic subtypes is shown among the three immune subtypes C1, C2 and C3. Fisher´s exact test was used to test if there is any difference in the proportion of transcriptomic subtypes between different immune subtypes (**** p < 0.0001). g The scatter plot of expression levels between LGR6 and three NK cell markers, XCL1 , XCL2 and CD160 , is shown. Two-sided Pearson’s correlation coefficient and associated p -value are displayed. h IHC (Immunohistochemistry) staining of XCL1 and LGR6 from one patient, Sample 427, and IHC of CD160 and LGR6 from a different patient, Sample 341, are shown. The IHC results show that XCL1 and LGR6 , CD160 and LGR6 are co-expressed in tumour cells. Furthermore, to provide a more comprehensive understanding of our findings, we included a larger visualisation of IHC results depicting CD160, LGR6, XCL1, and CD56 in both normal control and tumour samples for Sample 333 in Supplementary Fig. . In b , c , the box bounds the interquartile range divided by the median, with the whiskers extending to a maximum of 1.5 times the interquartile range beyond the box. Source data are provided as a Source Data file.

Article Snippet: Antibodies used in this study were listed as follows, anti-SFRP1 (1:200, Atlas antibodies, HPA064870), anti-XCL1 (1:400, Atlas antibodies, HPA057725), anti-LGR6 (1:100, Abcam,126747), anti-CD160 (1:300, Origene, TA349762), anti-CD8 (Genetech, GT211207), anti-CD4 (Maixin Biotechnology).

Techniques: Expressing, Whisker Assay, Comparison, Derivative Assay, Immunohistochemistry, Staining, Control

Journal: Nature Communications

Article Title: The integrated molecular and histological analysis defines subtypes of esophageal squamous cell carcinoma

doi: 10.1038/s41467-024-53164-x

Figure Lengend Snippet: a GSEA normalised enrichment score (NES) of EP300 Mut (mutated) versus Wt (wildtype) samples (green bars) and EP300 high versus low expression samples (red bars), against representative (upregulated) gene sets of four transcriptomic subtypes and upregulated genes in XCL -high ESCC cell lines (XCL_up). The values of FDR were shown within the bars. b GSEA plots of ‘stemness_up’ and ‘differentiated_up’ gene sets for the EP300 Mut (mutated) versus Wt (wildtype) comparison, and the ‘stemness_up’ and ‘XCL1_up’ gene sets for the EP300 high versus low-expression comparison. FDR q -values were shown. c Gene expression of CD160 between EP300 mutated and wildtype samples. Wilcoxon rank-sum test was used to compare the level between groups. d Pathway functional mutation enrichment adjusted for tumour mutation burden and the correlation between functional mutation enrichment ratio and tumour cellularity are plotted together for each hallmark gene set. P -values derived from the Kruskal–Wallis test comparing the enrichment ratio among the four subtypes were used for y -axis values. For significant hallmark gene sets, they were coloured to represent the subtype which had the highest enrichment for this gene set. e Significance P -values (−log10 transformed) comparing the enrichment scores among the four subtypes against P -values comparing GSVA values among the four subgroups are plotted for each hallmark gene set. For significant hallmark gene sets that passed both significance thresholds ( P < 0.05), they were coloured to represent the subtype which had the highest enrichment for that gene set in both functional mutation and pathway expression levels. f The intra-tumour heterogeneity for 102 samples, measured as the Shannon density, is shown across the four transcriptomic and immune subtypes, using the Wilcoxon rank-sum test. g The survival analysis of the Shannon density index against overall survival is shown using a multivariate analysis. The P -value derived from the log-rank test was shown, along with the hazard ratio and 95% confidence interval. All significance is shown in the figure, * P < 0.05, ** P < 0.01, and **** P < 0.0001. In c , f , the box bounds the interquartile range divided by the median, with the whiskers extending to a maximum of 1.5 times the interquartile range beyond the box. Source data are provided as a Source Data file.

Article Snippet: Antibodies used in this study were listed as follows, anti-SFRP1 (1:200, Atlas antibodies, HPA064870), anti-XCL1 (1:400, Atlas antibodies, HPA057725), anti-LGR6 (1:100, Abcam,126747), anti-CD160 (1:300, Origene, TA349762), anti-CD8 (Genetech, GT211207), anti-CD4 (Maixin Biotechnology).

Techniques: Expressing, Comparison, Functional Assay, Mutagenesis, Derivative Assay, Transformation Assay

Journal: Cell reports

Article Title: Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity

doi: 10.1016/j.celrep.2023.112769

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CD160-AF700 , Novus Biologicals , CatNBP2-90074AF700; RRID:AB_2941072 Clone-275.

Techniques: Luminex, Recombinant, Red Blood Cell Lysis, Staining, Translocation Assay, Flow Cytometry, Sequencing, Software