Proteomic Analysis of Low and High Risk Metastisising CSCC
Ontology highlight
ABSTRACT: This project assesses the risk of metastasis in formalin-fixed and paraffin embedded primary cutaneous squamous cell carcinoma using DIA-MS proteomics.
Project description:Cutaneous squamous cell carcinoma (cSCC) is the leading cause of death in recessive dystrophic epidermolysis bullosa (RDEB) patients but remains poorly studied on a proteomic level. We aim to characterize the RDEB-SCC proteome by comparing it to the proteomes of UV-light induced cSCC of non-aggressive and aggressive behavior with which RDEB cSCC share either the well-differentiated morphology or the aggressive behavior, respectively. We applied a direct trypsinization protocol using an acid labile surfactant and label-free quantitation to study formalin-fixed, paraffin-embedded tissues from patients with RDEB cSCC (n=6), low-risk cSCC (n=5) and metastasizing cSCC (n=13) by liquid chromatography tandem-mass spectrometry.
Project description:DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 83 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. 83 FFPE primary OTSCC tumour samples were analysed in one experimental run.
Project description:DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 83 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array.
Project description:We retrospectively identified cases of invasive vulvar squamous cell carcinoma. Formalin fixed, paraffin embedded tissues samples were retrieved. Sections were confirmed by H&E staining prior to analysis. Sections were processed by ribosomal RNA depletion and RNA-sequencing (KAPA RNA HyperPrep with RiboErase) (HMR). 23 patient samples had RNA of sufficient quality for analysis. HPV status was determined by a consensus of high-risk HPV RNA-ISH and HPV DNA PCR. Only samples that were positive in both assays were considered 'HPV-positive'.
Project description:Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma tissues obtained at the time of surgical resection. Gene-expression profiling was performed using formalin-fixed, paraffin-embedded hepatocellular carcinoma tissues obtained at the time of surgical resection.
Project description:The aim of this study was to evaluate whether micro-RNA signature in tumor tissues from low-risk Endometrial Cancer women can be correlated with the occurrence of recurrences MicroRNA expression was assessed by chip analysis in 7 formalin-fixed paraffin-embedded (FFPE) LREC primary tumors from women whose follow up showed recurrences (R+) and in 14 FFPE LREC primary tumors from women whose follow up did not show any recurrence (R-), matched for grade and age.