Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integration of Proteomics, Phosphoproteomics and Kinomics Enables the Discovery of Anticancer Drugs for Pancreatic Cancer

ABSTRACT: Here we performed proteomic examination of surgical specimens. This lead to the prediction of a number of drugs that induced apoptosis in the patient-derived cell lines.

INSTRUMENT(S): Synapt G2 HDMS

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Algirdas Kaupinis

PROVIDER: MSV000089751 | MassIVE | Tue Jun 28 21:29:00 BST 2022

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Integration of Proteomics, Phosphoproteomics and Kinomics Enables the Discovery of Anticancer Drugs for Pancreatic Cancer

Project description:Here we performed phosphoproteomic, kinome examination of surgical specimens and patient-derived cancer cell lines.Kinomics and phosphoproteomics identified changes in the activity of a number of identical protein kinases in PDAC tumors and tissue culture cells. This allowed us to use these kinases as small molecular inhibitor targets for successful in vitro PDAC cell eradication.

2022-06-27 | MSV000089736 | MassIVE

Targeted transcriptomic analysis of pancreatic adenocarcinoma in EUS-FNA samples by NanoString technology

Project description:Background: Integration of transcriptomic testing into EUS-FNA samples is a growing need for precision oncology in pancreatic ductal adenocarcinoma (PDAC). The NanoString platform is suitable for transcriptome profiling in low yield RNA samples. Methods: Inclusion of patients that underwent EUS-FNA cytological diagnosis of pancreatic ductal adenocarcinoma using 19G and/or 22G needles and subsequent surgical resection. Formalin fixed paraffin embedded (FFPE) cytological and surgical samples underwent RNA extraction and transcriptomic analysis using a custom 52-gene NanoString panel of stromal PDAC features. Cell type abundance was quantified in FFPE specimens and correlated. Results: 18 PDAC patients were included. Mean EUS-FNA passes was 2 + 0.7. All FFPE passed the RNA quality control for genomic analysis. Hierarchical clustering on the global gene expression data showed that genes were differentially expressed between EUS and surgical samples. A more enriched cancerassociated fibroblasts and epithelial-mesenchymal transition transcriptomic profile was observed across surgical specimens whereas immunological biomarkers were more represented in EUS-FNA samples. Cytological examination confirmed a scanty representation of CAF and more immunological cell abundance in cytological samples in comparison to surgical specimens. Conclusion: Targeted transcriptomic NanoString profiling of PDAC samples obtained by EUS-FNA is a feasible approach for pre-surgical molecular analysis although stromal CAF/EMT mRNA biomarkers are underrepresented.

2023-05-04 | GSE225953 | GEO

Perturbation-informed signatures from crosswise integration of transcriptome and chromatin accessibility analyses predict susceptibility to candidate anticancer drugs (cisplatin validation dataset) [RNA-seq]

Project description:Transcriptome and chromatin state of cell lines with high (Jurkat) and low (BxPC-3) sensitivity to cisplatin was acquired after 6 h 3 uM treatment with the anticancer drug, in order to validate a drug prediction pipeline based on the construction of a perturbation-informed signature.

2022-08-17 | GSE207611 | GEO

2022-08-17 | GSE207607 | GEO

Genome-wide analysis of gene expression in surgical specimens of primary glioblastoma multiform

Project description:We used a genome-wide coding gene expression profiling to identify a gene signature for the molecular classification or prognostic prediction of primary GBMs. Total RNA obtained from 21 surgical specimens of primary glioblastoma multiform.

2012-07-12 | E-GEOD-25630 | biostudies-arrayexpress

Affymetrix SNP array data for Non-Smoking Female Lung Cancer in Taiwan

Project description:Genome-Wide Screening of Genomic Alterations and Transcriptional Modulation in Non-Smoking Female Lung Cancer in Taiwan Sixty-one pairs of cancer and normal lung tissue specimens from non-smoking females were collected at National Taiwan University Hospital and Taichung Veterans General Hospital. The selection criteria of clinical specimens depend on pathology report, physical examination and cigarette-smoking history. Surgical lung tissue specimens were immediately snap-frozen in liquid N2 and stored at -80 °C. Surgical specimens would be further processed for RNA and DNA extraction. Only those samples passed quality controls were processed for gene expression profiling analysis and single nucleotide polymorphism (SNP) analysis respectively.

2012-12-31 | E-GEOD-33355 | biostudies-arrayexpress

Treatment with anticancer drugs for advanced pancreatic cancer: a systematic review.

Project description:BackgroundPatients with advanced pancreatic cancer have a poor prognosis and high burden of cancer-related symptoms. It is necessary to assess the trade-off of clinical benefits and possible harms of treatments with anticancer drugs (TAD). This systematic review aims to compare the effectiveness of TAD versus supportive care or no treatment, considering all patient-important outcomes.MethodsWe searched PubMed, Embase, Cochrane Library, and Epistemonikos. Two reviewers performed selection, data extraction and risk of bias assessment. We assessed certainty of the evidence using the GRADE approach.ResultsWe included 14 randomised controlled trials. Chemotherapy may result in a slight increase in overall survival (MD: 2.97 months (95%CI 1.23, 4.70)) and fewer hospital days (MD: -6.7 (-8.3, -5.1)), however, the evidence is very uncertain about its effect on symptoms, quality of life, functional status, and adverse events. Targeted/biological therapy may result in little to no difference in overall survival and a slight increment in progression-free survival (HR: 0.83 (95%CI 0.63, 1.10)), but probably results in more adverse events (RR: 5.54 (95%CI 1.24, 23.97)). The evidence is very uncertain about the effect of immunotherapy in overall survival and functional status.ConclusionsThe evidence is very uncertain about whether the benefits of using treatment with anticancer drugs outweigh their risks for patients with advanced pancreatic cancer. This uncertainty is further highlighted when considering immunotherapy or a second line of chemotherapy and thus, best supportive care would be an appropriate alternative. Future studies should assess their impact on all patient-important outcomes to inform patients in setting their goals of care.

| S-EPMC10422698 | biostudies-literature

miR-27b synergizes with anticancer drugs

Project description:Drug resistance, caused by complex and redundant mechanisms, is a major obstacle in cancer treatment, especially in liver and kidney cancers. Combinational therapy of miRNAs, which concurrently target multiple pathways, with anticancer drugs represent a new strategy to improve the drug response. By a systems approach, we identified that miR-27b, a miRNA deleted in liver and kidney cancers, sensitizes cancer cells to a broad spectrum of anticancer drugs in vitro and in vivo. Two samples transfected with nontarget miRNA control or miR-27b mimics followed by 48 hours doxorubicin treatment

2014-01-07 | E-GEOD-53872 | biostudies-arrayexpress

Genome-wide analysis of microRNA expression in surgical specimens of primary glioblastoma multiform

Project description:MicroRNA has a great potential in predicting survival of cancer patient. We used a genome-wide microRNA expression profiling to identify a miRNA signature for the prediction of clinical outcome of primary GBM patients. Total RNA obtained from 82 surgical specimens of primary glioblastoma multiform and 5 normal brain tissues from areas surrounding arteriovenous malformations (AVM) as control.

2012-07-12 | E-GEOD-25631 | biostudies-arrayexpress

Expression data from glioblastoma surgical specimens

Project description:Expression data from glioblastoma surgical specimens

| PRJNA741898 | ENA