Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA149361 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:PURPOSE: To develop an index capable of detecting and quantifying the extent of liver RNA contamination in liver biopsies of metastatic breast cancer METHODS: We developed a microarray-based gene expression liver index by comparing the expression levels of genes in liver tissue biopsies and in primary breast cancer biopsies. The predictive performance of the index was then evaluated in defined mixtures of liver and breast cancer RNA. A calibration curve was established to allow estimation of the liver RNA content in unknown metastatic breast cancer samples. A set of liver biopsies and primary breast cancer biopsies were used to identify genes that were expressed significantly higher in liver tissue. These genes were used in a liver index, which was validated in a new set of liver and primary breast cancer biopsies. A set of liver/breast cancer RNA mixtures was used to establish a calibration curve to allow quantification of liver contamination in metastatic breast cancer samples. The prediction error of the calibration curve was assessed in a new set of liver/breast cancer RNA mixtures and applied to estimate the liver content in a set of unknown metastatic breast cancer biopsies.
2013-01-05 | E-GEOD-33116 | biostudies-arrayexpress
Project description:PURPOSE: To develop an index capable of detecting and quantifying the extent of liver RNA contamination in liver biopsies of metastatic breast cancer METHODS: We developed a microarray-based gene expression liver index by comparing the expression levels of genes in liver tissue biopsies and in primary breast cancer biopsies. The predictive performance of the index was then evaluated in defined mixtures of liver and breast cancer RNA. A calibration curve was established to allow estimation of the liver RNA content in unknown metastatic breast cancer samples.
2013-01-05 | GSE33116 | GEO
Project description:There is clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SET ER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to pre-analytical and analytical influences. We tested SET ER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SETER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients. Higher SET ER/PR index in metastatic samples predicted longer progression-free (PFS) and overall survival (OS) when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.534, 95% CI 0.299 to 0.955, p = 0.035; OS: HR 0.315, 95% CI 0.157 to 0.631, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1% to 98% of ESR1 transcripts (all had high SETER/PR index). A signature based on probe sets with good pre-analytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SET ER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript. We tested SET ER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SET ER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients. Higher SET ER/PR index in metastatic samples predicted longer progression-free (PFS) and overall survival (OS) when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.485, 95% CI 0.265 to 0.889, p = 0.019; OS: HR 0.314, 95% CI 0.155 to 0.637, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1% to 98% of ESR1 transcripts (all had high SET ER/PR index). A signature based on probe sets with good pre-analytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SET ER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript.
2019-05-30 | GSE124647 | GEO
Project description:To develop a classifier based on microRNAs for primary tumor site identification of liver core biopsies and to explore the influence of surrounding normal liver tissue on classification. Tissue samples from 333 patients, corresponding to one of the following ten assay classes, were obtained from archives of the pathology department, Copenhagen University Hospital, Rigshospitalet, Denmark: Lung cancer, breast cancer, gastric/cardia cancer, colorectal cancer, bladder cancer, pancreatic cancer, hepatocellular carcinoma, cholangiocarcinoma, squamous cell cancers of different origin, and normal liver tissue
2013-10-19 | E-GEOD-51429 | biostudies-arrayexpress
Project description:There is clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SETER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to pre-analytical and analytical influences. We tested SETER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SETER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients. Higher SETER/PR index in metastatic samples predicted longer progression-free (PFS) and overall survival (OS) when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.534, 95% CI 0.299 to 0.955, p = 0.035; OS: HR 0.315, 95% CI 0.157 to 0.631, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1% to 98% of ESR1 transcripts (all had high SETER/PR index). A signature based on probe sets with good pre-analytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SETER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript.
2019-05-30 | GSE124648 | GEO
Project description:Breast cancer molecular subtypes preferentially metastasize to specific organs and the anatomical location of the metastasis is associated with the length of survival post-recurrence. We used microarrays to provide a detailed characterization of breast cancer site-specific metastases with particular focus on identifying genes predictive of breast cancer liver metastatic proprnsity We performed global gene expression profiling on fine-needle aspirates of metastatic lesions from different anatomical sites obtained from breast cancer patients treated within the Swedish randomized trial (TEX) of first-line chemotherapy for locally advanced or metastatic breast cancer. Samples were collected before commencement of treatment.
2013-12-02 | E-GEOD-46141 | biostudies-arrayexpress
Project description:Patients diagnosed with estrogen receptor (ER) positive breast cancer have a prolonged risk of distal metastatic recurrence to vital organs. Metastatic disease is incurable at present due to the development of treatment resistant cell populations. Here we used single-cell RNA sequencing to evaluate the transcriptome heterogeneity of ER+ breast cancer patient-derived xenografts (PDX) tropic for three common breast cancer metastatic sites – bone, brain, and liver – compared to primary tumors grown in the mammary fat pad. Metastatic cell populations at each location were phenotypically distinct from primary tumor cells with unique transcriptional programs indicative of signaling programs driven by specific transcription factors. Cells that metastasized to brain and liver tissue adopted gene expression programs indicative of the target organ microenvironments. Discerning the organ-specific phenotypic adaptations of metastatic ER+ breast cancer cells may help tailor appropriate therapies for individual patients and to each metastatic site.
2020-05-09 | GSE131007 | GEO
Project description:Breast cancer is a hugely heterogeneous disease, and markers for disease subtypes and therapy response remain poorly defined. For that reason, we employed a retrospective study in node-positive breast cancer to identify molecular signatures of gene expression correlating with metastatic free survival. Patients were primarily included in FEC100 (fluorouracil, epirubicin and cyclophosphamide) arms of two multicentric phase III clinical trials (PACS01 and PEGASE01 - FNCLCC). Data from nylon microarrays containing 8.032 cDNA unique sequences, representing 5.776 distinct genes, have been used to develop a predictive model for treatment outcome. We obtained the gene expression profiles of 150 population-based patients, and used stringent univariate selection technique based on Cox regression combined with principal component analysis to identify signature associated with prognosis and impact of FEC100 chemotherapy. Our work identified a gene-signature of metastatic relapse. Most of the 14 selected genes have a clear role in breast cancer, neoplasia or chemotherapy resistance. Furthermore, we showed the interest of combining transcriptomic data with clinical data into a clinicogenomic model for patients subtyping. The described model adds predictive accuracy to that provided by the well established Nottingham prognostic index or by the genomic predictor alone. Keywords: Gene-expression profiling
2007-10-18 | GSE7017 | GEO
Project description:Breast cancer molecular subtypes preferentially metastasize to specific organs and the anatomical location of the metastasis is associated with the length of survival post-recurrence. We used microarrays to provide a detailed characterization of breast cancer site-specific metastases with particular focus on identifying genes predictive of breast cancer liver metastatic proprnsity
2013-12-02 | GSE46141 | GEO
Project description:The PI3Kalpha-specific inhibitor Alpelisib (BYL719) has been approved for the treatment of metastatic ER+/HER2- breast cancer patients in combination with Fulvestrant. After initial response, patients develop drug resistance and disease relapses. In order to identify signalling pathways contributing to the acquired resistance to BYL719 in breast cancer, we generated BYL719-resistant T47D cells and used them together with the parental cells to perform label-free quantitative phosphoproteomics.
2023-12-05 | PXD033956 | Pride