Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: CBX family genes expression in colon cancer. ( A ) CBX expression level by qRT-PCR in three colon cancer cell lines (CACO-2, SW480, and HCT 116) compared to a normal colon cell line (NMC 460D). ( B ) CBX gene expression level in a colon cancer cDNA RT-qPCR array consisting of tumor ( N = 40) and normal samples ( N = 8). ( C ) Expression analysis of CBX family genes of colon tumor in UALCAN dataset (Normal = 41, Primary Tumor = 286). The star symbol indicates statistical significance (**: p ≤ 0.01, ***: p ≤ 0.001, ****: p ≤ 0.0001).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Expressing, Quantitative RT-PCR, Gene Expression

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: Association between CBX4 expression levels and clinical stage and grade of CRC patients. ( A ) CBX4 expression analyses performed using the UALCAN dataset with relative statistical comparison among groups. ( B ) CBX4 expression analyses in a colon cancer cDNA RT-qPCR array consisting of tumor ( n = 40) and normal samples ( n = 8) stratifying patients according to stage and grade. The star symbol indicates statistical significance (**: p ≤ 0.01).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Expressing, Comparison, Quantitative RT-PCR

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: Characterization of CBX4 in CRC organoids. ( A ) Representative images of ex vivo PDO culture obtained from colorectal cancer biopsies are reported. Scale bar: 10 µm. ( B ) Real-time qPCR analysis of CBX4 in two groups of PDOs: the first one derived from healthy tissues (CNT) and the second one derived from tumor tissues (Tumor). Results were normalized to RPS18 mRNA and analyzed by 2 −ΔΔCt method. ( C ) Analysis of the knockdown efficiency of siCBX4 assessed by RT-PCR in PDOs after 72 h. ( D ) Effect of CBX4 silencing on PDO viability assessed by ATP Lite assay after 72 h. The star symbol indicates statistical significance (**: p ≤ 0.01).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Ex Vivo, Derivative Assay, Knockdown, Reverse Transcription Polymerase Chain Reaction

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: Role of CBX4 silencing in CRC organoids ( A , B ). Representative images of our target molecules through immunofluorescence analysis. Localization of NFkB in tumor ex vivo PDOs before (CNT) and after siCBX4. Maximal projection images of PDO incubated NFkB (green signal) and cell nuclei were stained with Hoechst 33342 (blue signal). Scale bar: 10 µm. ( C ) Real time qPCR analysis of NF-κB, c-myc, TNF-α, and IL-1 in tumor ex vivo PDOs before (CTR) and after CBX4 silencing. Results were normalized to RPS18 mRNA and analyzed by 2 −ΔΔCt method. The star symbol indicates statistical significance (*: p ≤ 0.05, **: p ≤ 0.01).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Immunofluorescence, Ex Vivo, Incubation, Staining

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