ANGIOPREDICT - an FP7-funded project enabling personalised medicine for patients with metastatic colorectal cancer.
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001005423 | EGA |
REPOSITORIES: EGA
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Project description:In ANGIOPREDICT, academic cancer biologists and industry-based biotechnology researchers worked with clinicians to identify biomarkers to predict whether individual metastatic colorectal cancer patients will respond positively to bevacizumab containing therapy. In this retrospective study, copy number profiles were determined using whole genome shallow sequencing, and progression free survival and treatment data was collected.
| EGAS00001002724 | EGA
Project description:Background: Human papillomavirus has been shown to have a causal role in the development of head and neck squamous cell carcinoma and represents a distinct and well-defined pathology. While HPV-positive HNSCC is associated with a better response to treatment and prognosis, a subset of patients do not respond favorably to current standard of care thus suffering unnecessary morbidity and delay to receive effective therapy. Methods: RNA from nineteen patients with HPV-positive HNSCC was subjected to gene expression analysis using Affymetrix microarrays. HPV-status was confirmed by detection of HPV16 E7 with RT-PCR. Results: In addition to specific genetic biomarkers (including LCE3D, KRTDAP, HMOX1, KRT19, MDK, TSPAN1), differentially expressed genes were highly represented in the cell processes of genomic stability, cell cycle, and DNA damage. Conclusions: This pilot study suggests possible biomarkers that predict response to chemoradiation therapy. These data can potentially lead to an assay that can be used clinically to predict HPV-positive HNSCC patients that will not benefit from chemoradiation, thus helping clinicians to lower morbidity and get selected patients to surgery faster.
2014-12-19 | GSE40020 | GEO
Project description:We analyzed gene expression profiles of human testicular biopsies in men with idiopathic nonobstructive azoospermia who underwent therapy with hCG/rFSH. Using new generation oligonucleotide microarray platform GeneChip® Human Gene 1.0 ST, we identified genes which could be potential prognostic biomarkers of azoospermia treatment. We analyzed 6 testicular biopsy samples with Affymetrix Human Gene 1.0 ST microarrays. 3 of them were obtained from patients with NOA, who positively responded to hormonal therapy and 3 non-respoders.
2015-12-31 | E-GEOD-51111 | biostudies-arrayexpress
Project description:Background: Cardiac arrest (CA) represents the third leading cause of death worldwide. Among survivors, severe neurological sequelae are frequent but difficult to predict. Novel prognostic biomarkers would offer clinicians the possibility to deliver personalized healthcare. The potential of small circulating noncoding RNAs (microRNAs) to predict neurological outcome and survival after CA has been reported. Objective: This study aims to identify circulating circular RNAs (circRNAs) associated with clinical outcome after CA. Methods and Results: Methods and Results: Whole blood samples obtained 48h after return of spontaneous circulation from 23 sex-matched survivors and 23 deceased cardiac arrest (CA) patients were enrolled in this study. Whole transcriptome RNA sequencing identified candidate RNAs associated with neurological outcome and survival. Conclusion: We have identified candidate RNAs associated with clinical outcome after CA whose predictive value remains to be confirmed in large populations.
2022-11-02 | GSE197764 | GEO
Project description:Background: Human papillomavirus has been shown to have a causal role in the development of head and neck squamous cell carcinoma and represents a distinct and well-defined pathology. While HPV-positive HNSCC is associated with a better response to treatment and prognosis, a subset of patients do not respond favorably to current standard of care thus suffering unnecessary morbidity and delay to receive effective therapy. Methods: RNA from nineteen patients with HPV-positive HNSCC was subjected to gene expression analysis using Affymetrix microarrays. HPV-status was confirmed by detection of HPV16 E7 with RT-PCR. Results: In addition to specific genetic biomarkers (including LCE3D, KRTDAP, HMOX1, KRT19, MDK, TSPAN1), differentially expressed genes were highly represented in the cell processes of genomic stability, cell cycle, and DNA damage. Conclusions: This pilot study suggests possible biomarkers that predict response to chemoradiation therapy. These data can potentially lead to an assay that can be used clinically to predict HPV-positive HNSCC patients that will not benefit from chemoradiation, thus helping clinicians to lower morbidity and get selected patients to surgery faster. HPV-positive head and neck squamous cell carcinoma (HNSCC) has a good prognosis with a large percentage of patients responding to therapy. However, a certain percentage of patients do not respond. Gene expression data from Affymetrix Human Exon 1.0ST microarrays was utilized to compare patients that responded to therapy with those that did not respond.
2014-12-19 | E-GEOD-40020 | biostudies-arrayexpress
Project description:Body fluids from cancer patients are informative regarding disease conditions in tumor tissues. Thus, biomarkers detected by liquid biopsy can guide clinicians in designing personalized therapies and may serve as a proxy for treatment success. However, biomarkers that predict the existence of druggable target structures cannot be reliably defined in blood samples due to genetic tumor heterogeneity and presence of molecules from non-tumorous cells. To test the applicability of RNA signatures as liquid biopsy biomarkers, expression data from hepatocellular carcinoma (HCC) cells after inhibition of Hippo pathway effectors is investigated. We show that the oncogene yes-associated protein (YAP) transcriptionally controls a panel of long non-coding RNAs (lncRNAs), which support HCC progression via tumor cell-intrinsic mechanisms. These lncRNAs are detectable and overexpressed in YAPS127A transgenic mouse livers as well as in a subgroup of human HCC tissue and serum samples. Using a machine learning algorithm, a 4 gene lncRNA signature is defined that correlates with the nuclear abundance of YAP in HCC tissues (CYTOR, SNHG1, SNHG17, MIR4435-2HG). Importantly, YAP accumulation in human HCCs is significantly associated with lncRNA signature serum abundance in two independent patient cohorts. Evaluation of expression data and confirmatory experiments illustrate that the lncRNA signature is a robust predictor for YAP activity in other tumor types such as lung adenocarcinoma. Liquid biopsy-based detection of lncRNAs in cancer patients is informative for the activity of transcriptional regulators and can serve as diagnostic tool that guides clinicians in the design of targeted therapies.
2023-03-15 | GSE207723 | GEO
Project description:Body fluids from cancer patients are informative regarding disease conditions in tumor tissues. Thus, biomarkers detected by liquid biopsy can guide clinicians in designing personalized therapies and may serve as a proxy for treatment success. However, biomarkers that predict the existence of druggable target structures cannot be reliably defined in blood samples due to genetic tumor heterogeneity and presence of molecules from non-tumorous cells. To test the applicability of RNA signatures as liquid biopsy biomarkers, expression data from hepatocellular carcinoma (HCC) cells after inhibition of Hippo pathway effectors is investigated. We show that the oncogene yes-associated protein (YAP) transcriptionally controls a panel of long non-coding RNAs (lncRNAs), which support HCC progression via tumor cell-intrinsic mechanisms. These lncRNAs are detectable and overexpressed in YAPS127A transgenic mouse livers as well as in a subgroup of human HCC tissue and serum samples. Using a machine learning algorithm, a 4 gene lncRNA signature is defined that correlates with the nuclear abundance of YAP in HCC tissues (CYTOR, SNHG1, SNHG17, MIR4435-2HG). Importantly, YAP accumulation in human HCCs is significantly associated with lncRNA signature serum abundance in two independent patient cohorts. Evaluation of expression data and confirmatory experiments illustrate that the lncRNA signature is a robust predictor for YAP activity in other tumor types such as lung adenocarcinoma. Liquid biopsy-based detection of lncRNAs in cancer patients is informative for the activity of transcriptional regulators and can serve as diagnostic tool that guides clinicians in the design of targeted therapies.
2023-03-15 | GSE207722 | GEO
Project description:Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.
2014-04-01 | GSE53629 | GEO
Project description:Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei (Δxyr1) grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.
2017-02-09 | GSE66982 | GEO
Project description:NK cells were first isolated from PBMCs using EasySep⢠Human NK cell enrichment kit (STEMCELL biotechnology). The magnetically isolated NK cells were stained with anti-CD3 FITC, anti-CD56 Pe-Cy7 and LIVE/DEAD® red stain for a further enrichment, whereby the CD3 negative and CD56 positive live cells were sorted with MoFlo⢠cell sorter (Beckman Coulter). The sorted NK cell populations were sent to AROS Applied Biotechnology A/S (Aarhus N, Denmark) to be analysed using GeneChip® Human Transcriptome Array 2.0 (Affymetrix, USA). The transcription profile of NK cells from day 14 post stem cell transplantation was compared with those from healthy donors.
2018-10-31 | E-MTAB-5474 | biostudies-arrayexpress