The strategy is based on the analysis of three pairs of human melanoma cell lines with an aggressive variant derived under different physiological contexts: human, mouse, and rat. In each pair, the …
Among the 229 genes, 116 were associated to IPA canonical functions. Column 1 indicates the top functions. Column 2 shows the −log(p-value) as horizontal histogram relative to the Fisher exact test …
The Ensembl genome browser (http://www.ensembl.org, view on karyotype) was used to map the 229 hypermethylated genes to the human genome. Sex chromosomes were excluded from the analysis. Each …
Promoter methylation scores correspond to the average methylation values at CpG positions located in the promoter regions showing an increased methylation above 20% in WM266-4 compared to WM115 …
Nine methylation clusters containing 29 genes on six chromosomes.
(A) Shown is the localization of all the CpGs analysed (lollipops) on the four selected genes (MYH1, PCDHB15, PCDHB16, and BCL2L10). The CpGs present on the 450 k array are in bold type (black …
Hypermethylation (methylation difference ≥20%: dotted line) for all candidate genes analysed by bisulfite-pyrosequencing.
(A) The heatmap shows the median DNA methylation of analysed CpGs for each gene in metastatic (n = 10) and primary (n = 49) patient samples. Primary samples are divided by a black line indicating …
The median DNA methylation of the analysed CpG for each gene is indicated as percentage and overall survival in months. Primary samples are divided by a small black line indicating the cut-off at 1 …
(A) Kaplan–Meier curve of patients based on the methylation score in the 49 primary melanoma samples. (B) Hazard ratio plot calculated from our methylation score on the 49 primary melanoma samples. …
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Cell line (Homo sapiens) | WM115 | ATCC | CRL-1676 | |
Cell line (Homo sapiens) | WM-266–4 | ATCC | CRL-1675 | |
Cell line (Homo sapiens) | WM983A | Coriell Institute | WC00048 | |
Cell line (Homo sapiens) | WM983B | Coriell Institute | WC00066 | |
Cell line (Homo sapiens) | M4Be | Bailly and Doré, 1991 | Not applicable | |
Cell line (Homo sapiens) | TW12 | Bailly and Doré, 1991; Bertucci et al., 2007; Thomas et al., 1995 | Not applicable | |
Cell line (Homo sapiens) | M4BeS2 | Clark et al., 2000 | Not applicable | |
Biological sample (Homo sapiens) | Department of Pathology, IUCT-O Toulouse Hospital (France) | Primary melanomas (n=12), lymph node metastases (n = 7), and cutaneous metastases (n=3) | ||
Biological sample (Homo sapiens) | Department of Experimental Oncology, European Institute of Oncology, Milan (Italy) | Primary melanoma (n = 5) | ||
Biological sample (Homo sapiens) | Saint John’s Cancer Institute (formerly John Wayne Cancer institute [USA]) | Primary melanomas (n=12) | ||
Recombinant DNA reagent | Department of Pathology of the Portuguese Oncology Institute of Porto (IPO-Porto) | Primary melanomas (n=20) | ||
Commercial assay or kit | DNeasy Tissue kit | Qiagen | 69504 | |
Commercial assay or kit | QiaAmp kit | Qiagen | 965672 | |
Commercial assay or kit | FFPE RNA/DNA Purification Plus Kit | FFPE RNA/DNA Purification Plus Kit | 54300 | |
Commercial assay or kit | EpiTect 96 Bisulfite Kit | Qiagen | 59104 | |
Commercial assay or kit | Infinium Human Methylation 450 K BeadChips | Illumina | WG-310–1003 | |
Commercial assay or kit | PyroGold SQA reagent kit | Qiagen | 972824 | |
Recombinant DNA reagent | HotStarTaq DNA polymerase | Qiagen | 203207 | |
Software and algorithm | GenomeStudio | Illumina | Version 2011.1 | |
Software and algorithm | R studio | RStudio, Inc | RStudio 2021.09.2 382 ‘Ghost Orchid’ Release. R version 4.1.2 | |
Software and algorithm | PyroMark software | Qiagen | V1.0 | |
Software and algorithm | GraphPad Prims8 | Dotmatics | Version 8 | |
Software and algorithm | QIAGEN’s Ingenuity Pathway Analysis | Qiagen | 836508 |
Variables | n (%) |
---|---|
Mean age (SD) | 66.40 (15.88) |
Gender | |
Male | 26 (53) |
Female | 23 (47) |
American Joint Committee on Cancer eighth stages | |
IV | 12 (24) |
III | 12 (24) |
IIIA | 1 (2) |
IIIB | 2 (4) |
IIIC | 2 (4) |
II | 2 (4) |
IIA | 3 (6) |
IIB | 6 (12) |
IIC | 6 (12) |
IB | 2 (4) |
unknown | 1 (2) |
Mutations | |
NRAS | 1 (2) |
BRAF | 6 (12) |
Unknown | 42 (86) |
Ingenuity Pathway Analysis (IPA) software networks results.
Bisulphite pyrosequencing primer, sequences, and CpG location.
Survival data and signature score for each patient sample.
R scripts.