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To profile the landscape of sebaceous tumours RNA

ABSTRACT: ebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract RNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted RNA will be used for RNA sequencing.

PROVIDER: EGAS00001007803 | EGA |

REPOSITORIES: EGA

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To profile the landscape of sebaceous tumours WES

Project description:Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract DNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted DNA will be used for exome sequencing.

| EGAS00001003553 | EGA

EGAS00001007803-sc-2024-05-20T08:25:33Z - samples

Project description:Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract RNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted RNA will be used for RNA sequencing.

| EGAD00001015368 | EGA

EGAS00001003553-sc-2024-05-20T08:23:02Z - samples

| EGAD00001015367 | EGA

Molecular profile of hidradenitis suppurativa

Project description:Hidradenitis Suppurativa molecular taxonomy and key signaling pathways were studied by whole transcriptome profiling. Dysregulated genes were detected by comparing lesional and non lesional skin obtained from female HS patients and matched healthy controls using the Agilent array platform

2019-09-10 | GSE137141 | GEO

Microdialysis analysis of common inflammatory skin diseases highlights abnormalities in nonlesional skin of patients with atopic dermatitis

Project description:Insight into the pathophysiology of inflammatory skin diseases, especially at the proteomic level, is severely hampered by the lack of adequate in situ data. Skin microdialysis samples from patients with atopic dermatitis (AD, n=6), psoriasis vulgaris (PSO, n=7) or prurigo nodularis (PN, n=6), as well as healthy controls (n=7) were subjected to proteomics and multiplex cytokine analysis. Single-cell RNA sequencing of skin biopsy specimens was used to identify the cellular origin of cytokines. Among the top 20 enriched GO annotations, NAD metabolic process, regulation of secretion by cell, and pyruvate metabolic process were elevated in microdialysates from lesional AD skin compared with both nonlesional skin and controls. The top 20 enriched KEGG pathways in these three groups overlapped almost completely. In contrast, nonlesional skin from patients with PSO or PN and control skin showed no overlap with lesional skin in this KEGG pathway analysis. Lesional skin from patients with PSO, but not AD or PN, showed significantly elevated protein levels of IL-22 and MCP-1 compared to nonlesional skin. IL-8 was elevated in lesional vs nonlesional AD and PSO skin, whereas IL-12p40 was higher only in lesional PSO skin. Integrated single-cell RNA-seq data revealed identical cellular sources of these cytokines in AD, PSO and PN. Based on microdialysate, proteomic data of lesional PSO and PN skin, but not lesional AD skin, differed significantly from those of nonlesional skin. IL-8, IL-22, MCP-1 and IL-12p40 might be suitable markers for minimally invasive molecular profiling.

2024-08-22 | PXD050245 | Pride

Project description:Vitiligo RNA Seq from lesional and non-lesional tissue

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Molecular profile of apocrine glands in hidradenitis suppurativa

Project description:Molecular taxonomy and key signaling pathways of apocrine glands of patients with hidradenitis suppurativa were studied by whole transcriptome profiling. Dysregulated genes were detected by comparing lesional and non lesional skin obtained from male and female HS patients using the Agilent array platform.

2020-02-06 | GSE144801 | GEO

Transcriptomics of FFPE-derived primary brain tumours

Project description:Primary brain cancers are highly heterogeneous and include the most prevalent and aggressive glioblastomas. To understand the key factors underlying brain tumourigenesis, we have built our own database based on RNA sequencing from FFPE-derived biomaterial.

2025-01-15 | GSE272042 | GEO

Characterization of tumour microenvironment landscape of mouse oral cancer tumours

Project description:Access of CD8+ T cells inside tumour nests is shaped by the tumour microenvironment (TME). Cancer-associated fibroblasts (CAFs) are among the most abundant TME components and have been associated with poor survival and T cells exclusion. However, the mechanisms that link CAFs presence with T cell blockade are unclear and there is a huge unmet medical need to increase T cell accessibility inside tumour cores. Here, we established single cell RNAseq of syngeneic murine models of head and neck squamous cell carcinoma that recapitulate different tumour-stroma organizations and evolutions (MOC1 and MOC2). MOC1 tumours are immune indolent and transition from a T cell infiltrated to an immune excluded/desert TME over time. MOC2 are more aggressive and are rich in myeloid cells while being T cell desert.

2026-09-01 | GSE277135 | GEO

Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.

Project description:Purpose: Human papilloma virus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than HPV(-) negative cancer. This may be due, in part, to the higher number of tumour infiltrating lymphocytes (TIL) in HPV(+) tumours. We used RNAseq to evaluate whether these differences in clinical behaviour could be explained simply by a numerical difference in TILs or whether there was a fundamental difference between TILs in these two settings. Patients and methods: Twenty-three consecutive HNSCC cases with high and moderate TIL density were subjected to RNAseq analysis. Differentially expressed genes (DEG) between 10 HPV(+) and 13 HPV(-) tumours were identified with EdgeR. Immune subset analysis was performed using, FAIME (Functional Analysis of Individual Microarray Expression) and Immune gene transcript count analysis. Results: 1634 genes were differentially expressed. There was a dominant immune signature in HPV(+) tumours. After normalizing expression profiles for numerical differences in T cells and B cells, 437 significantly DEGs still remained. A B-cell associated signature emerged, which segregated HPV(+) from HPV(-) cancers and included CD200, STAG3, GGA2, SPIB and ADAM28. Differential expression of these genes was confirmed by real-time quantitative PCR and immunohistochemistry. Conclusion: In our dataset, the difference associated with T-cells between patients with HPV(+) and (-) HNSCC was predominantly numerical. However, when TIL numbers are corrected, a distinct differential B-cell signature was revealed. mRNA profiles of 10 HPV driven (HPV+) and 13 HPV independant (HPV-) head and neck squamous cell carcinoma (HNSCC) tumours were generated by RNA-Seq, using Illumina HiSeq 2000.

2016-09-01 | E-GEOD-72536 | biostudies-arrayexpress

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