Breast cancer relapse free survival and lung metastasis free survival
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE5327 | GEO | 2007/05/14
SECONDARY ACCESSION(S): PRJNA96341
REPOSITORIES: GEO
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Project description:Validation of lung metastasis signature (LMS) and its association with risk of developing lung metastasis and with primary tumor size. Experiment Overall Design: 58 tumor samples
2008-06-13 | E-GEOD-5327 | biostudies-arrayexpress
Project description:This series represents 180 lymph-node negative relapse free patients and 106 lymph-node negate patients that developed a distant metastasis. Please see attached patient clinical parameters sheet for more information. Keywords: other
2005-02-23 | GSE2034 | GEO
Project description:This series represents 180 lymph-node negative relapse free patients and 106 lymph-node negate patients that developed a distant metastasis. Please see attached patient clinical parameters sheet for more information (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GSE2034&id=40089&db=GeoDb_blob26). Keywords: other
2005-02-22 | E-GEOD-2034 | biostudies-arrayexpress
Project description:Purpose: Herein we demonstrate that UV-induced melanomas of low metastatic potential in mice that overexpress HGF and harbor deletion of the Ink4a/p16 locus (HP strain) are converted to highly metastatic forms by virtue of hemizygous deletion of the metastasis suppressor genes Nme1 and Nme2 (HPN strain). The striking difference in metastatic activity between HP and HPN melanomas strains provided a powerful system for identifying molecular profiles associated with metastatic activity. Methods: Primary and metastatic melanoma RNAseq profiling. Results: RNA-seq analysis of primary melanomas identified a 32-gene expression signature that was strongly associated with the HPN genotype and lung metastatic activity (HPN lung metastasis signature, or HPN-LMS). Expression of the HPN-LMS was highly predictive of overall survival in human cohorts of cutaneous melanoma (SKCM) and uveal melanoma (UVM) patients of The Cancer Genome Atlas (TCGA). Conclusions: Three HPN-LMS genes (ARRDC3, NYNRIN, RND3) associated with longer survival in SKCM and/or UVM patients exhibited strong anti-invasion activity in human melanoma cells, consistent with roles as effectors of the metastasis suppressor functions of Nme1 and Nme2. The HP/HPN mouse paradigm has thus yielded a network of potential therapeutic targets and prognostic markers for clinical management of metastatic melanoma.
2021-08-02 | GSE181207 | GEO
Project description:Identification of genomic characteristics in a cohorte of human cutaneous primary melanoma associated with a distant metastasis free survival.
2007-04-01 | E-TABM-1 | biostudies-arrayexpress
Project description:Background: Many strategies to define subtypes and treat cancer relies on a presumption of either localized or widespread (poly)metastatic disease. We proposed an intermediate state of metastasis termed oligometastasis(es) characterized by limited metastatic progression and amenable to treatment by localized methods e.g. surgery or radiotherapy. Methods: To understand the biological basis of oligometastatic and polymetastatic progression, we analyzed microRNA expression patterns from lung tumor samples of patients with less than five metastases at first metastasis presentation and treated with metastasis-directed surgery. Results: Patients were stratified into four subgroups of oligo- and poly-metastatic progression based on the rate of metastatic progression over follow-up period. We prioritized microRNAs between the extremes of oligo- vs. poly-metastatic progression and validated their capacity to distinguish these phenotypes and predict survival in an independent validation dataset. Conclusions: Our results provide further evidence for the biological underpinnings of oligometastasis(es) and potential microRNA candidates to predict progression trajectories of patients and optimize corresponding metastasis-directed treatment. We collected tumor samples from 63 patients that (i) had between one and five metastasis(es) at first metastatic presentation and no clinical or radiologic evidence of metastases in the pleural, peritoneal, pericardial or retroperitoneal cavities,(ii) at the time of lung surgery, had every site of known metastases treated with definitive intent, and (iii) had a minimum of 16 months of follow-up after surgery was required. Total RNA were derived from FFPE metastatic tissue samples. Patient samples were subsequently classified into 3 groups: those from patients with high, intermediate and low rates of progression.
2012-06-13 | E-GEOD-38698 | biostudies-arrayexpress
Project description:PurposeChondrosarcomas are the second most common primary malignant bone tumors. Although histologic grade is the most important factor predicting the clinical outcome of chondrosarcoma, it is subject to interobserver variability. Isocitrate dehydrogenase 1 (IDH1) and IDH2 hotspot mutations were recently found to be frequently mutated in central chondrosarcomas. However, a few published articles have been controversial regarding the association between IDH1/IDH2 mutation status and clinical outcomes in chondrosarcomas.Experimental designWe performed hotspot sequencing of IDH1 and IDH2 genes in 89 central chondrosarcomas and targeted next-generation sequencing in 54 of them, and then correlated the IDH1/IDH2 mutation status with the patient's clinical outcome.ResultsAlthough no association was discovered between IDH mutation status and the patient's overall survival, IDH1/IDH2 mutation was found to be associated with longer relapse-free and metastasis-free survival in high-grade chondrosarcomas. Genomic profiling reveals TERT gene amplification and ATRX mutation, for the first time, in addition to TERT promoter mutation in a subset (6/30, 20%) of high-grade and dedifferentiated chondrosarcomas. These abnormalities in telomere genes are concurrent with IDH1/IDH2 mutation and with CDKN2A/2B deletion or TP53 mutation, suggesting a possible association and synergy among these genes in chondrosarcoma progression. We found 21% of patients with chondrosarcoma also had histories of second malignancies unrelated to cartilaginous tumors, suggesting possible unknown genetic susceptibility to chondrosarcoma.ConclusionsIDH1/IDH2 mutations are associated with longer relapse-free and metastasis-free survival in high-grade chondrosarcomas, and they tend to co-occur with TERT mutations and with CDKN2A/2B and TP53 alterations in a subset of high-grade chondrosarcomas.
| S-EPMC6980683 | biostudies-literature
Project description:microRNA exprssion profiling of HCC comparing primary tumor with lung metastasis. To explore differentially expressed microRNAs involved in process of HCC metastasis, and identify their biological functions. Two-condition experiment, primary tumor specimens vs. lung metastasis specimens. Biological replicates: 3 primary tumor replicates, 3 lung metastatic replicates. One replicate per array.
2012-01-24 | E-GEOD-26323 | biostudies-arrayexpress
Project description:Homeobox genes comprise a family of regulatory genes that contain a common homeobox domain and act as transcription factors. Changes in the expression of homeobox genes are observed in many cancers, including leukaemia, colon, skin, prostate, breast, and ovarian cancers. Recent studies indicate that homeobox A5 (HOXA5) may serve as a tumour suppressor gene in breast cells. However, the precise role of HOXA5 in lung cancer remains unclear. Using microarrays and an invasion/metastasis lung adenocarcinoma cell line model, we showed that the expression of HOXA5 is negatively correlated with cancer cell invasion ability. The ectopic expression of HOXA5 in highly invasive cancer cells suppressed cell migration, invasion, and filopodia formation in vitro and inhibited metastatic potential in vivo. The knockdown of HOXA5 expression via a HOXA5-specific siRNA was able to promote the invasiveness of lung cancer cells. Furthermore, HOXA5 expression was associated with improved overall survival and disease-free survival in non-small cell lung cancer patients with wild-type EGFR (P = 0.0199 and 0.0345, respectively). Genome-wide transcriptome and pathway analyses indicated that these effects of HOXA5 may be associated with the regulation of cytoskeletal remodelling. In summary, our studies provide new insights into how HOXA5 may contribute to the suppression of metastasis in lung cancer. We used microarrays to profile the global gene expression of HOXA5-overexpressing cells compared with mock control cells and identified the pathways involved in HOXA5-induced biofunctional alterations.
2016-08-25 | GSE50659 | GEO