Ontology highlight
ABSTRACT:
PROVIDER: PRJNA884683 | ENA |
REPOSITORIES: ENA
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Project description:To further development of our gene expression signature for survival prediction, we conducted expression profiles of lung squamous carcinoma samples with overall survival information as the training cohort.
2015-09-25 | GSE73403 | GEO
Project description:Tumour-infiltrating lymphocytes are a major predictor for overall survival and response to immunotherapy for several malignancies. However, while tumour-infiltrating CD8 T cells have been extensively studied, little is known about the role of the humoral immune system within the tumour microenvironment (TME). Here we show that plasma cells are present in the TME and actively secrete human papillomavirus (HPV)-specific IgG antibodies in HPV-positive head and neck squamous cell carcinoma patients. Compared to circulating memory B cells, plasma cells in the TME were enriched for HPV-reactivity with little bystander recruitment of influenza-specific cells. HPV-specific plasma cells in the TME correlated with the antibody titres in peripheral blood and produced antibodies with a high degree of somatic hypermutation directed against HPV E2, E6 and E7 antigens. A striking proportion of HPV-specific antibodies produced in situ were directed against E2, which might thus be a promising target for immunotherapies in HPV-associated cancers. Overall, we show that antigen-specific activated and germinal centre B cells as well as plasma cells can be found in the TME, with plasma cells producing antibodies specific for tumour-associated antigens in situ. These findings provide a better understanding of humoral immune responses in human cancer and suggest that tumour-infiltrating B cells could be harnessed for the development of novel therapeutic agents.
2020-07-20 | GSE149327 | GEO
Project description:The immune system plays a key role in the protective response against oral cancer, however the tumour microenvironment (TME) is able to impair this anti-cancer response by modulating T helper (Th) responses and promoting an anti-inflammatory environment. Regulatory T cells (Tregs) and Th2 effector cells (Teff) have been associated with bad prognosis in oral squamous cell carcinoma (OSCC), however it is unknown the main chemoattractant or immunomodulatory mechanisms associated with the enrichment of these subsets in OSCC. We characterised T helper-like lineages in Teff and Tregs and evaluated the main immunomodulatory changes induced by the TME in OSCC. Our phenotypic data revealed a higher distribution of tumour-infiltrating CCR8+ and Th2-like Treg in OSCC in comparison with non-malignant samples, whereas the percentages of Th1 cells were reduced in cancer. We then analysed the presence of CCR8 ligands and the chemoattractant effect of tumour secretomes, however despite observing higher presence of CCR8 ligand CCL18, we only observed reduced migration of Teff to tumour secretomes. The direct effect of the TME was then analysed by exposing T cell subsets to cancer secretomes and we observed that the TME induced higher expression of CCR8 and immunomodulatory molecules on both subsets. Finally, the proteomic analysis of the TME suggests that these changes were associated with the rapid membrane-associated vitamin D signalling pathway. In summary, the TME from OSCC promotes immunomodulatory changes by regulating CCR8 expression and disbalancing the Th1/Th2 repertoire.
2021-04-29 | PXD023049 | Pride
Project description:To identify gene expression biomarkers associate with asbestos-related lung squamous cell carcinoma, we analyzed gene expression profiles for a total of 56 lung squamous cell carcinomas using 44K Illumina Gene Expression microarrays. Twenty-six cases had lung asbestos body counts above levels associated with urban dwelling (ARLC-SCC: asbestos-related lung cancer-squamous cell carcinoma) and 30 cases had no lung asbestos bodies (NARLC-SCC: non-asbestos related lung cancer- squamous cell carcinoma). Genes differentially expressed between ARLC-SCC and NARLC-SCC were identified on fold change and P-value, and then prioritised using gene ontology. Total RNA was obtained from fresh frozen lung tumour tissue and stratified by asbestos phenotype. Gene expression profiling was performed to identify differences in the gene profiles of asbestos-related and non-asbestos related lung squamous cell carcinomas.
2012-01-30 | E-GEOD-23822 | biostudies-arrayexpress
Project description:The composition and remodelling of the extracellular matrix (ECM) are important factors in the development and progression of cancers, and the ECM is implicated in promoting tumour growth and restricting anti-tumour therapies through multiple mechanisms. The characterisation of differences in ECM composition between normal and diseased tissues may aid in identifying novel diagnostic markers, prognostic indicators and therapeutic targets for drug development. Using tissue from non-small cell lung cancer (NSCLC) patients undergoing curative intent surgery, we characterised quantitative tumour-specific ECM proteome signatures by mass spectrometry, identifying 161 matrisome proteins differentially regulated between tumour tissue and nearby non-malignant lung tissue. We defined a collagen hydroxylation functional protein network that is enriched in the lung tumour microenvironment. We validated two novel putative extracellular markers of NSCLC, the collagen cross-linking enzyme peroxidasin and a disintegrin and metalloproteinase with thrombospondin motifs 16 (ADAMTS16), for discrimination of malignant and non-malignant lung tissue. These proteins were up-regulated in lung tumour samples, and high PXDN and ADAMTS16 gene expression was associated with shorter survival of lung adenocarcinoma and squamous cell carcinoma patients, respectively. These data reveal tumour matrisome signatures in human NSCLC.
2023-06-16 | PXD041066 | Pride
Project description:Primary tumor recurrence occurs commonly after surgical resection of lung squamous cell carcinoma (SCC). The aim of this study was to identify genes involved in recurrence in lung squamous cell carcinoma patients. Array comparative genomic hybridization (aCGH) was performed on DNA extracted from tumour tissue from 62 patients with primary lung squamous cell carcinomas. aCGH data was analysed to identify genes affected by copy number alterations that may be involved in SCC recurrence. Candidate genes were then selected for technical validation based on differential copy number between recurrence and non-recurrence SCC tumour samples. Genes technically validated advanced to tests of biological replication by qPCR using an independent test set of 72 primary lung SCC tumour samples. 18q22.3 loss was identified by aCGH as significantly associated with recurrence (p=0.038). Although aCGH copy number loss associated with recurrence was found for seven genes within 18q22.3, only SOCS6 copy number loss was both technically replicated by qPCR and biologically validated in the test set. DNA copy number profiling using 44K element array comparative genomic hybridization microarrays of 62 primary lung squamous cell carcinomas.
2011-12-25 | E-GEOD-32058 | biostudies-arrayexpress
Project description:Lung cancer remains the leading cause of cancer death worldwide. Overall 5-year survival is about 10-15% and despite curative intent surgery, treatment failure is primarily due to recurrent disease. Conventional prognostic markers are unable to determine which patients with completely resected disease within each stage group are likely to relapse. To identify a gene signature associated with recurrent squamous cell carcinoma (SCC) of lung, we analyzed primary tumour gene expression for a total of fifty-one SCCs (stage I-III) on 22,323 element microarrays, comparing expression profiles for individuals who remained disease-free for a minimum of 36 months with those from individuals whose disease recurred within 18 months of complete resection. Cox proportional hazards modeling with leave-one-out cross-validation identified a 70-gene capable of predicting the likelihood of tumor recurrence and a 79-gene signature predictive for overall survival. These two signatures were pooled to generate a 111-gene classifier which achieved an overall predictive accuracy for disease recurrence of 72% (77% sensitivity, 67% specificity) in an independent set of fifty-eight stage I-III SCCs. This classifier also predicted differences in survival (log-rank P=0.0008, hazard ratio (HR), 3.8 [95% confidence interval, 1.6-8.7]), and was superior to conventional prognostic markers such as TNM stage or N stage in predicting patient outcome. Genome-wide profiling has revealed a distinct gene expression profile for recurrent lung SCC which may be clinically useful as a prognostic tool. Keywords: non-small cell lung carcinoma, squamous cell, tumor recurrence, expression profiling
2006-11-21 | GSE5123 | GEO
Project description:Lung cancer remains the leading cause of cancer death worldwide. Overall 5-year survival is about 10-15% and despite curative intent surgery, treatment failure is primarily due to recurrent disease. Conventional prognostic markers are unable to determine which patients with completely resected disease within each stage group are likely to relapse. To identify a gene signature associated with recurrent squamous cell carcinoma (SCC) of lung, we analyzed primary tumour gene expression for a total of fifty-one SCCs (stage I-III) on 22,323 element microarrays, comparing expression profiles for individuals who remained disease-free for a minimum of 36 months with those from individuals whose disease recurred within 18 months of complete resection. Cox proportional hazards modeling with leave-one-out cross-validation identified a 70-gene capable of predicting the likelihood of tumor recurrence and a 79-gene signature predictive for overall survival. These two signatures were pooled to generate a 111-gene classifier which achieved an overall predictive accuracy for disease recurrence of 72% (77% sensitivity, 67% specificity) in an independent set of fifty-eight stage I-III SCCs. This classifier also predicted differences in survival (log-rank P=0.0008, hazard ratio (HR), 3.8 [95% confidence interval, 1.6-8.7]), and was superior to conventional prognostic markers such as TNM stage or N stage in predicting patient outcome. Genome-wide profiling has revealed a distinct gene expression profile for recurrent lung SCC which may be clinically useful as a prognostic tool. Expression profiling using 22K element microarrays of 51 primary lung squamous cell carcinomas.
2010-07-01 | E-GEOD-5123 | biostudies-arrayexpress
Project description:We studied overall difference in gene expression between head and neck squamous cell carcinoma tumours and normal mucosa. Samples were collected from patients during surgery and almost in all cases, paired samples were collected: tumour tissue and normal mucosa from the opposite side. Tumour samples were TNM staged by pathologist and tested for human papillomavirus infection (HPV) high-risk types 16 and 18 by PCR of E6 and E7 mRNA. If possible, patients were followed up and their disease-free and overall survival is available (up to 11 years after surgery).
2020-12-31 | E-MTAB-8588 | biostudies-arrayexpress
Project description:Tongue squamous cell carcinoma is a tumour type with rather low five year survival, around 60%. The poor survival rate has been ascribed to late detection, a high frequency of locoregional recurrence, the occurrence of secondary primary tumours and death due to comorbidity. One reason for development of recurrence is thought to be the existence of transformed cells in areas adjacent to the primary tumour, cancerization field effect. The aim of this study was to map the changes in the tumour free tongue tissue adjacent to tongue tumours compared with healthy control tongue tissue to better understand the cancerization field effect. Tissue biopsies were collected from tumour (T) and tumour free tissue adjacent to the tumour (TF) from patients with tongue squamous cell carcinoma. Control tissue was collected from latter border of the tongue of tumour free healthy volunteers (C). All samples were homogenized and RNA was extracted. The RNA was biotin labelled and run on Illumina HT-12 bead chip array.
2016-12-21 | E-MTAB-4678 | biostudies-arrayexpress