EGAS00001000837-sc-20150303 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001001271 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Around 50 samples of pre-invasive lung cancer lesions showing subsequent clinical and pathological progression or regression
| EGAS00001000837 | EGA
Project description:Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Molecular profiling techniques have identified marked differences between progressive and regressive lesions. Here we present laser-captured stromal tissue, adjacent to previously profiled CIS lesions, to examine the role of the tumour microenvironment in spontaneous lesion regression. All samples in this dataset are paired with matched CIS lesions in dataset GSE108082.
2020-09-01 | GSE133690 | GEO
Project description:Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.
2019-01-01 | GSE94611 | GEO
Project description:Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.
2019-01-01 | GSE108123 | GEO
Project description:Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. We analysed 83 progressive lesions, 41 regressive and 33 normal epithelial control samples. DNA methylation and gene expression profiles were further validated using publicly available lung cancer data. Results: Somatic mutation burden was higher in progressive lesions than regressive CIS lesions, across base substitutions, rearrangements, insertions and deletions. Driver mutations were present in both progressive and regressive CIS lesions, but were more numerous in progressive cases. Progressive and regressive CIS lesions had distinct epigenomic and transcriptional profiles, with a strong chromosomal instability signature. Gene expression, methylation and copy number profiles can all predict accurately which CIS lesions will progress to lung cancer. Conclusion: Pre-invasive CIS lesions that will subsequently progress to invasive lung cancer can be distinguished from those that will regress using molecular profiling. Progression is associated with a strong chromosomal instability signature. These findings inform the development of novel therapeutic targets.
2019-01-01 | GSE108082 | GEO
Project description:Lung squamous cell carcinoma (SCC) is thought to arise from premalignant lesions in the airway epithelium, therefore studying these lesions is critical for understanding lung carcinogenesis. We performed RNA sequencing on laser-microdissected representative cell populations along the SCC pathological continuum of patient-matched normal basal cells, premalignant lesions, and tumor cells. We discovered transcriptomic changes and identified genomic pathways altered with initiation and progression of SCC within individual patients. We used immunofluorescent staining to confirm gene expression changes in premalignant lesions and tumor cells, including increased expression of SLC2A1, CEACAM5, and PTBP3 at the protein level and increased activation of MYC via nuclear translocation. Cytoband enrichment analysis revealed coordinated loss and gain of expression in chromosome 3p and 3q regions, respectively, during carcinogenesis. This is the first gene expression profiling of airway premalignant lesions with patient-matched samples that provides insight into the mechanisms of stepwise lung carcinogenesis. Profiling of mRNA expression in laser-microdissected normal airway basal cells, premalignant airway lesions, and lung SCC tumor cells by massively parallel RNA sequencing.
2014-07-03 | E-GEOD-49155 | biostudies-arrayexpress
Project description:Intercepting progression from pre-invasive to invasive lung adenocarcinoma
| PRJNA808146 | ENA
Project description:Intercepting progression from pre-invasive to invasive lung adenocarcinoma
| PRJNA808147 | ENA
Project description:Spontaneous regression is a well defined phenomenon commonly observed in human melanoma in its partial histopathological form but sporadically in its complete expression. Molecular mechanisms which might be involved in spontaneous regression are poorly understood so far. The Melanoblastoma bearing Libechov Minipig (MeLiM) model exhibits cutaneous melanomas which appear in utero or shortly after birth. These lesions are clinically and histologically highly comparable to their human counterparts. Nevertheless, in swine most of the highly invasive melanomas undergo complete spontaneous regression. Induction of regression is expressed by clinical features including changes in color, drying aspect and decrease in size; histologically we observed infiltration of histiocyte-like cells, fibrosis and lymphocytic infiltrate later. To characterize the regression phase on a transciptomic level, we performed time dependent gene expression profiling using the MeLiM model and porcine Affymetrix microarrays. We collected 5 different tumors of 5 siblings at 5 timepoints, from day 8 to day 91 after birth. After statistical analysis and reannotation of the 25 porcine microarrays we were able to identify 1411 genes regulated during regression. K-means clustering and subsequent functional clustering of these genes via Ingenuity Pathway analysis revealed significant pathways playing a role in melanoma regression. Genes involved in cell cycle, apoptosis, cellular movement, melanocyte-differentiation and pigmentation as well as genes of the immune reponse seem to be potential mediators of melanoma regression.
2008-09-10 | E-MEXP-1152 | biostudies-arrayexpress
Project description:In multiple sclerosis (MS), activated microglia and infiltrating macrophages phagocytose myelin focally in (chronic) active lesions. These demyelinating sites expand in time, but at some point turn inactive into a sclerotic scar. To identify molecular mechanisms underlying lesion activity and halt, we analyzed genome-wide gene expression in rim and peri-lesional regions of chronic active and inactive MS lesions, as well as in control tissue. Gene clustering revealed patterns of gene expression specifically associated with MS and with the presumed, subsequent stages of lesion development. Next to genes involved in immune functions, we found regulation of novel genes in and around the rim of chronic active lesions, such as NPY, KANK4, NCAN, TKTL1, and ANO4. Of note, the presence of many foamy macrophages in active rims was accompanied by a congruent upregulation of genes related to lipid binding, such as MSR1, CD68, CXCL16, and OLR1, and lipid uptake, such as CHIT1, GPNMB, and CCL18. Except CCL18, these genes were already upregulated in regions around active MS lesions, showing that such lesions are indeed expanding. In vitro downregulation of the scavenger receptors MSR1 and CXCL16 reduced myelin uptake. In conclusion, this study provides the gene expression profile of different aspects of MS pathology and indicates that early demyelination, mediated by scavenger receptors, is already present in regions around active MS lesions. Genes involved in early demyelination events in regions surrounding chronic active MS lesions might be promising therapeutic targets to stop lesion expansion.
2018-01-01 | GSE108000 | GEO