Less invasive diagnostics for identification and monitoring of cancer associated mutations in blood
Ontology highlight
ABSTRACT:
DISEASE(S): Patients Suffering From Tumors Such As Colorectal, Lung And Pancreatic Cancer And Precancerous Disease
PROVIDER: 2628163 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Primary outcome(s): Comparison of the gene expression profile in hair follicle between cancer patients and healthy volunteer
| 2628246 | ecrin-mdr-crc
Project description:Longitudinal monitoring of liver function in vivo is hindered by the lack of high-resolution non-invasive imaging techniques. Using the anterior chamber of the mouse eye as a transplantation site, we have established a platform for longitudinal in vivo imaging of liver spheroids at cellular resolution. Transplanted liver spheroids engraft on the iris, become vascularized and innervated, retain hepatocyte-specific and liver-like features and can be studied by in vivo confocal microscopy. Employing fluorescent probes administered intravenously or spheroids formed from reporter mice, we showcase potential use of this platform exemplified by monitoring hepatocyte cell cycle activity, bile secretion and lipoprotein uptake. Moreover, we show that hepatic lipid accumulation during diet-induced hepatosteatosis is mirrored in intraocular grafts in vivo. The here described technology will provide a crucial tool to study liver physiology and disease progression in both pre-clinical and basic research as well as a drug screening platform in the pharma industry.
2024-01-15 | GSE245944 | GEO
Project description:Background: The incidence of human papillomavirus (HPV) associated oropharyngeal carcinomas has increased rapidly over the last thirty years. These tumours behave as a distinct biological entity when compared to classical smoking- and alcohol-related disease. To gain more information regarding the pathway through pre-malignancy in HPV positive/HPV negative oropharyngeal carcinoma (OSCC), we investigated genomewide expression profiles in histopathologically confirmed tumour samples with site-matched normal epithelial controls. Methods: Twenty-four patients with primary oropharyngeal squamous cell carcinoma (4 with stage III and 20 with stage IV disease) were included in this prospective clinical trial (UKCRN11945). The tumour tissues were each assessed by a histopathologist with HPV status and typing by p16INK4A, consensus PGMY PCR, type-specific HPV16 DNA & RNA PCR and DNA sequencing. Fresh tissue samples were subjected to whole transcriptome analysis using the Illumina Bead Array (~47,000 transcripts) and the results validated with quantitative Real Time-PCR (qRT-PCR). In a separate cohort of twelve OSCC patients, laser capture micro-dissection of formalin fixed paraffin embedded (FFPE) tissue allowed RNA extraction from regions of in situ malignant change (with matched normal and invasive SCC samples). Results: The majority of OSCC patients (28/36) displayed evidence of high risk HPV positivity. Predictable fold changes of RNA expression in HPV-associated disease included multiple transcripts within the p53 oncogenic pathway (e.g. CDKN2A/CCND1). Other candidate transcripts found to have altered levels of expression in this study have not previously been established in HPV16 associated oropharyngeal cancer. These were involved in cell differentiation, proliferation and invasion and demonstrated considerable overlap with expression analysis data in other oncogenic pathways (SFRP1/CRCT1/DLG2/SYCP2/CRNN). SYCP2 showed the highest consistent fold change from baseline in both fresh frozen and FFPE tissue (qRT-PCR fresh frozen tissue [P<0.04]; FFPE tissue pre-invasive [P<0.01]; FFPE tissue invasive [P<0.01]), and aberrant expression of this meiosis-specific protein may contribute to genetic instability during HPV-associated cancer development. Conclusion: Investigation of differentially expressed genes in HPV-positive tumours may reveal unique pathways that can explain their different natural history and biological properties. The data from this study reveal SYCP2 (amongst others) as a potential biomarker in HPV positive oropharyngeal carcinoma, and if corroborated on a larger scale, may facilitate the development of a non-invasive screening tool. Twenty four samples (12 matched invasive oropharyngeal carcinoma and normal epithelial controls).
2015-11-01 | E-GEOD-56142 | biostudies-arrayexpress
Project description:Evaluation of cell free circulating DNA (cfDNA) has recently been proposed for tracking disease relapse in colorectal cancer (CRC). Such assays could overcome the issues of classical monitoring, but requires personalized assay design due to absence of common alteration. On the contrary, early methylation alterations are restricted to delimited genomic loci allowing comprehensive assay design for population study. Our objective was to identify new cancer specific methylation biomarkers fitted to assess cfDNA over treatment, thus monitoring response in the metastatic CRC (mCRC) setup. Genome wide methylation profiling of colorectal cancer cell lines (surrogate to pure tumor tissue) was carried out and compared to publically available normal healthy colon mucosa (cancer unrelated). Identified loci were validated in additional publically available cohorts. Digital PCR assays were designed for selected markers and assessed in cfDNA of self-declared healthy donors (>40 years old), and of mCRC patients. Longitudinal assessment was performed in a subset of colorectal cancer patients treated with different therapy regimen (chemotherapy or targeted agents). Samples from the current GEOset were extracted by Wizard SV Genomic DNA Purification System (Promega). DNA samples were checked for integrity by 1% agarose gel, and quantity via Picogreen quantification. All samples were bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) with a minimum input of 500ng and following manufacturer’s instructions. Infinium HumanMethylation450 BeadChip arrays were carried out according to the Illumina Infinium HD methylation protocol.
2017-10-10 | GSE86078 | GEO
Project description:Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. Given their functional and clinical relevance, small EVs have emerged as a promising target among the liquid biopsy approaches for cancer detection. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive. In this study, we established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC). By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitundial cohorts, we uncovered 28 EV-miRs for detecting mCRC, and 131 EV-miRs for long-term monitoring of tumor size progression. Among these candidates, we further pinpointed a 15-EV-miR signature with dual detection and monitoring functions for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker – aside from its diagnostic power, its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Furthermore, target spectrum of this 15-EV-miR signature of mCRC suggested an involvement of small EVs in programming the mesenchymal–epithelial transition (MET) transition for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche. Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in tumor therapeutic monitoring.
2022-09-14 | GSE188627 | GEO
Project description:Rational biomarker development for the early and minimally invasive monitoring of AML
| PRJNA667439 | ENA
Project description: Not available
| S-EPMC3986488 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Sustained clinical remission (CR) without drug treatment has not been achieved in patients with rheumatoid arthritis (RA). This implies a substantial difference between CR and the healthy state, but it has yet to be quantified. We report a longitudinal monitoring of the drug response at multi-omics levels in the peripheral blood of patients with RA. Our data reveal that drug treatments alter the molecular profile closer to that of HCs at the transcriptome, serum proteome and immunophenotype level. Patient follow-up suggests that the molecular profile after drug treatments is associated with long-term stable CR. In addition, we identify molecular signatures that are resistant to drug treatments. These signatures are associated with RA independently of known disease severity indexes and are largely explained by the imbalance of neutrophils, monocytes, and lymphocytes. This high-dimensional phenotyping provides a quantitative measure of molecular remission and illustrates a multi-omics approach to understanding drug response.
2018-07-16 | GSE93777 | GEO
Project description:RNA-seq for monitoring expression levels in mutants that do not anchor chromatin at the nuclear periphery.
2015-12-11 | GSE74067 | GEO
Project description:Monitoring and contamination incidence of gnotobiotic experiments performed in microisolator cages
| PRJEB41815 | ENA