RNA sequencing of invasive vulvar squamous cell carcinoma (VSCC)
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ABSTRACT:
PROVIDER: PRJNA760903 | ENA |
REPOSITORIES: ENA
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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'.
2022-01-01 | GSE183454 | GEO
Project description:BACKGROUND: Regional lymph node (LN) status is a well-known prognostic factor for vulvar carcinoma (VC) patients. Although the reliable LN assessment in VC is crucial, it presents significant diagnostic problems. PURPOSE: We aimed to identify specific mRNA markers of VC dissemination in the LN and to address the feasibility of predicting the risk of nodal recurrence by the patterns of gene expression. EXPERIMENTAL DESIGN: Sentinel and inguinal LN samples from 20 patients who had undergone surgery for stage T1-3, N0-2, M0 primary vulvar squamous cell carcinoma were analyzed. Gene expression profiles were assessed in four metastatic [LN(+)] and four histologically negative [LN(-)] lymph node samples obtained from four VC patients, by the Affymetrix U133 Plus 2.0 gene expression microarrays. Of the set of genes of the highest expression in the metastatic LNs compared to LN(-), seven candidate marker genes were selected PERP, S100A8, FABP5, SFN, CA12, JUP and CSTA, and the expression levels of these genes were further analyzed by the real-time reverse transcription polymerase chain reaction (qRT-PCR) in 71 LN samples. RESULTS: Five of the genes, PERP, S100A8, FABP5, SFN and CA12, were significantly increased in LN(+) compared to LN(-) samples. In the initial validation of the seven putative markers of metastatic LN, the Cox proportional hazard model pointed to SFN and CA12 expression to significantly relate to the time to groin recurrence in VC patients. CONCLUSIONS: PERP, S100A8, FABP5, SFN and CA12 have a potential of marker genes for the molecular testing of LN involvement in VC patients. Gene expression profiles of 8 tissue samples representing 4 metastatic [N(+)] and 4 histologically negative [N(-)] LN samples
2011-07-31 | E-GEOD-28442 | biostudies-arrayexpress
Project description:BACKGROUND: Regional lymph node (LN) status is a well-known prognostic factor for vulvar carcinoma (VC) patients. Although the reliable LN assessment in VC is crucial, it presents significant diagnostic problems. PURPOSE: We aimed to identify specific mRNA markers of VC dissemination in the LN and to address the feasibility of predicting the risk of nodal recurrence by the patterns of gene expression. EXPERIMENTAL DESIGN: Sentinel and inguinal LN samples from 20 patients who had undergone surgery for stage T1-3, N0-2, M0 primary vulvar squamous cell carcinoma were analyzed. Gene expression profiles were assessed in four metastatic [LN(+)] and four histologically negative [LN(-)] lymph node samples obtained from four VC patients, by the Affymetrix U133 Plus 2.0 gene expression microarrays. Of the set of genes of the highest expression in the metastatic LNs compared to LN(-), seven candidate marker genes were selected PERP, S100A8, FABP5, SFN, CA12, JUP and CSTA, and the expression levels of these genes were further analyzed by the real-time reverse transcription polymerase chain reaction (qRT-PCR) in 71 LN samples. RESULTS: Five of the genes, PERP, S100A8, FABP5, SFN and CA12, were significantly increased in LN(+) compared to LN(-) samples. In the initial validation of the seven putative markers of metastatic LN, the Cox proportional hazard model pointed to SFN and CA12 expression to significantly relate to the time to groin recurrence in VC patients. CONCLUSIONS: PERP, S100A8, FABP5, SFN and CA12 have a potential of marker genes for the molecular testing of LN involvement in VC patients.
2011-08-01 | GSE28442 | GEO
Project description:Identification of copy number alterations of HPV-positive and HPV-negative vulvar squamous cell carcinomas (VSCC) and vulvar intraepithelial neoplasias (VIN), with special focus on VIN with and without VSCC, the latter group being defined as VIN with no VSCC development during >10 year follow-up.
2018-07-01 | E-MTAB-6113 | biostudies-arrayexpress
Project description:UNCOVERING VULVAR CARCINOMA: AN INTEGRATIVE APPROACH
| PRJNA343113 | ENA
Project description:Genome-wide expression array measurements for 9 head and neck squamous cell carcinomas (HNSCC) stratified by worst pattern of invasion (WPOI) Jayakar et al. (2016). Apolipoprotein E promotes invasion in oral squamous cell carcinoma. Li et al. (2013). Validation of the risk model: high-risk classification and tumor pattern of invasion predict outcome for patients with low-stage oral cavity squamous cell carcinoma. Comparison of transcription profiles between OSCC tumors with a more invasive (WPOI 5) versus a less invasive (WPOI 3) pattern of invasion using two independent Illumina platforms.
2016-04-01 | E-GEOD-79795 | biostudies-arrayexpress
Project description:Background: Vulvar squamous cell carcinoma (vSCC) is a rare but debilitating disease. One vSCC subtype comprises tumor cells that grow and expand as a cohesive sheet of cells that “pushes” and compresses the associated lymphoplasmacytic (LPC) stroma. Another vSCC subtype features tumor cells that grow in loose association with other tumor cells and infiltrate the associated fibromyxoid (FMX) stroma consisting mainly of extracellular matrix. Clinically, infiltrative vSCC with FMX stroma (Inf/FMX) is significantly associated with lymph node metastases and recurrence. Methods: An unbiased proteomic approach was used to identify pathways that could produce these different vSCC subtypes. Formalin-fixed and paraffin-embedded tissues from 10 cases of pushing vSCC with LPC stroma (Push/LPC) and 8 cases of Inf/FMX were subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Results: Analysis identified 2,265 different proteins in the 18 samples of vSCC. Of these, 344 proteins were differentially expressed (p<0.05) by at least 4-fold between vSCC subtypes. Of these, 59 were higher and 285 lower in Inf/FMX compared to Push/LPC tumors. Consistent with the desmoplastic morphology and increased picrosirius red staining, expression of subunits of several collagens (Col 1, 3, 6, 14, 18) was higher in the more aggressive Inf/FMX tumors. In contrast, signal transducer and activator of transcription 1 (STAT1), an important regulator of several inflammatory pathways, was expressed at lower levels in the Inf/FMX tumors. This finding was confirmed by immunohistochemistry using an antibody to STAT1. An informatics analysis of the differing profiles identified differences in the integrin signaling pathway and inflammation mediated by chemokine and cytokine signaling pathway. This analysis also linked decreased expression of proteins involved antigen processing and presentation and increased expression of those with cell-matrix adhesion as processes with the more aggressive Inf/FMX vSCC subtype. Conclusions: Comparing the proteomic profiles of vSCC morphologic subtypes indicates that increased expression of collagen subunits and decreased expression of STAT1 are associated with a more aggressive tumor subtype. Informatic analyses further identify alterations in cell interaction with matrix and immune function differ with tumor aggressiveness. Identification of these pathways provides a molecular basis for understanding aggressiveness of vSCC.
2017-12-12 | PXD006901 | Pride
Project description:Quantitative proteomic profiling the lung squamous carcinoma cells
2016-07-14 | MSV000079911 | MassIVE
Project description:Preinvasive squamous cell cancer (PSCC) are local transformations of bronchial epithelia that are frequently observed in current or former smokers. Their different grades and sizes suggest a continuum of dysplastic change with increasing severity, which may culminate in invasive squamous cell carcinoma (ISCC). As a consequence of the difficulty in identifying and obtaining PSCC samples, the molecular pathology that underlies their histological variability remains largely unknown. To address this issue, we have measured gene expression in the distinct stages of this proposed model of squamous carcinogenesis, i.e. low- and high-grade PSCC, lymph node-negative and positive ISCC compared with matched normal bronchial epithelia, using Human Exon 1.0 ST arrays and RNA obtained from microdissected formalin-fixed and paraffin embedded (FFPE) biopsies.
2017-06-09 | E-MTAB-3950 | biostudies-arrayexpress
Project description:To analyze the changes of proteins in esophageal squamous cell carcinoma after treatment with Peptide 58
2024-01-26 | PXD035683 | Pride