Journal: International Journal of Molecular Sciences

Article Title: Expression of Alternative Splice Variants of 6-Phosphofructo-2-kinase/Fructose-2,6-bisphosphatase-4 in Normoxic and Hypoxic Melanoma Cells

doi: 10.3390/ijms22168848

Figure Lengend Snippet: The response of malignant melanoma cells to low oxygen concentration. ( A ) Upper panel: Malignant melanoma lines, WM115 and WM266-4, were cultured with 100 µM pimonidazole (hypoxyprobe) in normoxic (N) and hypoxic conditions (H) for 16 h. The formation of pimonidazole–protein adducts were detected using Western Blot. Lower panel: Ponceau S stained membrane is shown as an internal control for equal protein loading. ( B ) Upper panels: Melanoma cells were cultured for 16 h in normoxia and hypoxia. Then HIF-1 alpha subunit accumulation was verified using the Western Blot. β-actin is shown as an internal control for equal loading. Lower panels: Densitometry analysis of Western Blot bands intensity normalized to β-actin. Relative densitometry value is the average of four independent experiments. The mean ± SEM is shown. Student’s t -test was used to evaluate the influence of hypoxia on HIF-1 alpha subunit stabilization. * p < 0.05 by Student’s t -test, ** p < 0.01 by Student’s t -test, p -value between 0.05 and 0.1 by Student’s t -test was given as an indication of the trend. ( C ) CAIX and PFKFB4 expression was analyzed by RT-qPCR in both melanoma cell lines under hypoxic and normoxic conditions. Expression data for each transcript was normalized to that for the reference gene TBP. Means ± SEM of at least five independent experiments are presented relative to expression in normoxic controls. The Student t -test was used to evaluate the differences between normoxic and hypoxic expression of CAIX and PFKFB4 . ** p < 0.01 by Student’s t -test. ( D ) Upper panels: Melanoma cells were cultured for 16 h in normoxia and hypoxia. Then CAIX and PFKFB4 expression was verified using the Western Blot. β-actin is shown as an internal control for equal loading. Lower panels: Densitometry analysis of Western Blot bands intensity normalized to β-actin. Each relative densitometry value is the average of at least four independent experiments. The mean ± SEM is shown. Studen’st t -test was used to evaluate the influence of hypoxia on CAIX and PFKFB4 expression. * p < 0.05 by Student’s t -test, ** p < 0.01 by Student’s t -test, p -value between 0.05 and 0.1 by Student’s t -test was given as an indication of the trend.

Article Snippet: Two human melanoma cell lines WM115 and WM266-4 were obtained from Rockland Immunochemicals (Limerick, PA, USA).

Techniques: Concentration Assay, Cell Culture, Western Blot, Staining, Membrane, Control, Expressing, Quantitative RT-PCR

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