Journal: Nature

Article Title: Loss of colonic fidelity enables multilineage plasticity and metastasis

doi: 10.1038/s41586-025-09125-5

Figure Lengend Snippet: (a) International Cancer Genome Consortium data of top 20 mutated cancer genes with high functional impact mutations in colorectal cancer (CRC). (b) Representative ATRX staining of human normal and CRC tissue microarray. Examples of positive and negative staining are shown. Scale bars, 500 µm. (c) Quantification of ATRX expression using immunohistochemistry H-score method analysed using QuPath. Samples are separated into normal, non-metastatic (stage I and II) and metastatic (stage III and IV) groups, n = 8 vs 47 vs 25 tumours. (d) Summary data indicating presence (H-score > 10) or absence (H-score <10) of ATRX staining in non-metastatic and metastatic samples. Number of tumours in each group indicated on graph, n = 47 vs 25 tumours. (e) Summary data indicating presence or absence of ATRX mutation in CRIS-B vs all other CRIS transcriptional subtypes. Data extracted from TCGA dataset where CRIS tumour annotation is known. Number of tumours in each group indicated on graph, n = 43 vs 278 tumours. (f) Overall survival data of patients with CRIS-B tumours separated on presence or absence of ATRX mutation. Data extracted from TCGA dataset, n = 37 vs 6 patients. For (c) data are mean ± SD. P values were calculated using ordinary one-way ANOVA with multiple comparisons. For (d) and (e) p values were calculated using two-sided Fisher’s exact test. For (f) P value was calculated using Log-rank (Mantel-Cox) test. (g) Lollipop plot of TCGA PanCancer mutational data for ATRX. ATRX mutations were analysed using cBioPortal (07/12/23) with TCGA PanCancer Atlas Studies selected. (h) Western-blot analysis of AKP ATRX KO organoids for ATRX and β-actin. n = 2 technical replicates. (i) Representative images of haematoxylin and eosin (H&E) stained lung metastases in mice injected with AKP Control or AKP Atrx KO2 organoid cells via tail vein. Scale bars, 500 µm. (j) Quantification of number of lung metastases per mouse, n = 7 vs 8 mice. (k) Quantification of total lung tumour burden per mouse, n = 7 vs 8 mice. (l) Summary data indicating presence or absence of lung metastases. Number of mice with lung metastases or no metastases indicated on graph, n = 7 vs 8 mice. For (j) and (k) data are mean ± SD. P values were calculated using two-tailed Mann-Whitney test. For (l) p value was calculated using two-sided Fisher’s exact test.

Article Snippet: The commercial colon cancer human tissue array used was CO804b (Biomax) (Extended Data Fig. ).

Techniques: Functional Assay, Staining, Microarray, Negative Staining, Expressing, Immunohistochemistry, Mutagenesis, Western Blot, Injection, Control, Two Tailed Test, MANN-WHITNEY

Journal: bioRxiv

Article Title: Antagonizing the serotonin receptor HTR2B drives antigen-specific cytotoxic T-cell responses and controls colorectal cancer growth

doi: 10.1101/2025.02.26.640476

Figure Lengend Snippet: TCGA-COAD data were analyzed. (A) Kaplan-Meier survival analysis of HTR 2B expression (derived from TCGA data) in 220 colon adenocarcinomas patient’s cohort. “HTR 2B -high” versus “HTR 2B -low” data were segregated based on the cohort’s top or bottom 25% with intratumoral HTR 2B expression. Mantel-cox log rank test. (B) Representative images of HTR 2B and Ki67 in the control (lamina propria) and lamina propria of colon adenocarcinoma (COAD) tissue. The original magnification is 200X, and the inset images are 600X. (C) Representative images of serotonin (5-HT), neurofilament-A (NF-A) in the control (lamina propria) and lamina propria of colon adenocarcinoma (COAD) tissue IHC. Original magnification 200X. (D) RNA-seq datasets (n=30 samples) were segregated into “HTR 2B -high” and “HTR 2B -low” (highest fifteen and lowest fifteen intra-tumoral HTR 2B expression), and the differential expression of selected genes was analyzed. (E) Principal component analysis (PCA) of “HTR 2B -high” versus “HTR 2B -low” datasets (n=15 patients/group). (F) Venn diagram showing numbers of mutually exclusive or shared genes in each group. (G) A volcano plot shows differentially expressed genes (DEGs) of “HTR 2B -high” versus “HTR 2B -low” datasets (n=15 patients/groups) are shown. (H) Heatmap statistics differentially expressed selected gene sets. (I) Gene ontology of altered biological processes. (J) Gene set enrichment analysis (GSEA) of the curated gene sets that affect the regulatory and effector functions of the T cells. (K) Intra-tumoral immune cell signatures were analyzed by deconvolution using TIMER2.0 of HTR 2B -high and -low datasets. (L) A TIDE computational analysis of the association between the tumor-infiltrating CD8 T cells (CTL) level (expression of CD8A, CD8B, GZMA, GZMB, and PRF1. Overall, patient survival with the intratumoral HTR 2B gene expression level. For each patient cohort, tumor samples were divided into HTR 2B -high (samples with HTR 2B expression one standard deviation above the average, shown in the left survival plot) and HTR 2B -low (remaining samples shown in the right survival plot) groups.

Article Snippet: The human colon adenocarcinoma tissue microarray (Novus Biological, Catalog # NBP2-78088) was stained with the antibodies and detected using chromogenic reagent DAB.

Techniques: Expressing, Derivative Assay, Control, RNA Sequencing, Gene Expression, Standard Deviation