Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes

ABSTRACT: We generated PDX models of aggressive NSCLC, which represent the DNA methylation features modelling of primary NSCLC

ORGANISM(S): Homo sapiens

SUBMITTER: Ming-Sound Tsao

PROVIDER: E-MTAB-10156 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Label-free proteomics quantification of pancreatic ductal adenocarcinoma patient-derived xenografts with treatment combining Gemcitabine and nab-Paclitaxel

Project description:Tumor-stroma interactions are critical in pancreatic ductal adenocarcinoma (PDAC) progression and therapeutics. Patient-derived xenograft (PDX) models faithfully recapitulate tumor-stroma interactions in PDAC, but conventional antibody-based immunoassay is largely inadequate to resolve or quantify tumor and stromal proteins. A species-deconvolved proteomics approach embedded in the ultra-high-resolution (UHR)-IonStar workflow can unambiguously quantify the proteins from tumor (human-derived) and stroma (mouse-derived) in PDX samples, enabling unbiased investigation of their proteomes with excellent quantitative reproducibility. With this strategy, 3 PDAC PDXs were analyzed. They were showed differential responses to treatment with Gemcitabine combined with nab-Paclitaxel (GEM+PTX), which is a first-line treatment regimen for PDAC. For each PDAC PDX, samples were collected after 24 hour and 192 hour with/without treatment, and each condition contained four biological replicates.

2023-07-05 | PXD042267 | Pride

Pharmacological inhibition of TREM1 attenuates patient derived xenograft models

Project description:To characterize the transcriptional changes in PDX tumors during TREM1 inhibition by microarray

2023-09-27 | E-MTAB-13257 | biostudies-arrayexpress

MRX34 Biomarker study in animals bearing Hep3B orthotopic liver tumors

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-05 | E-GEOD-58893 | biostudies-arrayexpress

RNA-seq of human U87MG-GFP perivascular glioma stem cells

Project description:Glioblastoma stem cells (GSCs) have been reported to be found near the blood vessels. We wanted to identify the perivascular GSCs by combining the label retention approach with vascular perfusion. GSCs, like most of the stem cells, are in a quiescent state. Label retention approach involves staining the cells with a uniform membrane labeling dye (PKH26) and allowing them to grow in vivo in NOD SCID mice. Slow-dividing stem cells will retain the dye to a greater extent and perivascular cells are identified by injecting the mice with vascular perfusion dye (Hoechst 33342) 5 min prior to sacrifice. Perivascular GSCs (positive for Hoechst 33342 and pKH26 dye - dubbed as H+P+) were compared with the rest of the perivascular glioma cells (H+P-).

2022-01-01 | E-MTAB-9607 | biostudies-arrayexpress

Whole transcriptome profiling of 79 patient derived xenograft (PDX) models

Project description:RNA-Seq and a species-specific mapping strategy were used to profile the human and mouse transcriptomes of tumour samples taken from 79 PDX models representing multiple cancer types (19 x breast, 37 x lung, 8 x colorectal, 7 x ovarian, 3 x endometrial, 2 x pancreatic, 2 x ampullary, 1 x leukaemia).

2016-03-01 | E-MTAB-3980 | biostudies-arrayexpress

M12-8: MRX34 Biomarker study in animals bearing Hep3B orthotopic liver tumors [Illumina]

Project description:To identify direct tumor mRNA targets of miR-34a, tumor RNAs isolated from whole tumors from animals treated with negative control and MRX34 Hep3B cells were surgically implanted into the livers of Nod/Scid mice and allow to grow for multiple weeks. Once serum AFP levels reached levels consistent with tumor growth of ~80-100 mg, animals were subjected to a single IV injection of MRX34. Twenty-four hours later animals were sacrificed, tumors resected and RNA isolated for subsequent microarray analysis.

2014-11-05 | E-GEOD-58892 | biostudies-arrayexpress

M12-28: MRX34 Biomarker study in animals bearing HuH7 orthotopic liver tumors [Affymetrix]

Project description:To identify direct tumor mRNA targets of miR-34a, tumor RNAs isolated from whole tumors from animals treated with negative control and MRX34 HuH7 cells were surgically implanted into the livers of Nod/Scid mice and allow to grow for multiple weeks. Once serum AFP levels reached levels consistent with tumor growth of ~80-100 mg, animals were subjected to a single IV injection of MRX34. Twenty-four hours later animals were sacrificed, tumors resected and RNA isolated for subsequent microarray analysis.

2014-11-05 | E-GEOD-58800 | biostudies-arrayexpress

Genomic profiling of patient-derived xenografts identify high level âpassengerâ gene aberrations associated with better prognosis in non-small cell lung cancer

Project description:Patient-derived tumor xenografts (PDXs) increasingly are being used as preclinical models to study human cancers and to evaluate novel therapeutics, as they reflect clinical cancers more closely than established tumor cell lines. With >100 PDXs established from resected non-small cell lung carcinomas (NSCLC), we reported previously that xenograftability correlates significantly with poorer patient prognosis. In this study, genomic, transcriptomic, and proteomic profiling of 36 PDXs showed greater similarity in somatic alterations between PDX and primary tumors than with cell lines, using publicly available data on the latter. A higher number of somatic alterations among 865 frequently altered genes in the PDX tumors was associated with better overall patient survival (HR=0.15, p=0.00015) compared to patients with corresponding PDXs characterized by a lower number of alterations; this was validated with the TCGA lung cancer patient dataset (HR=0.28, p=0.000022). These passenger-like alterations, identified in PDXs, link cell-cell signaling and adhesion to patient prognosis. Total RNAs from xenograftswere amplified by DASL kit and hybridized to Illumina HT12v4 chip

2016-10-26 | E-GEOD-68929 | biostudies-arrayexpress

Characterizing the Chemoresistant Ovarian Cancer Population using the Heterogeneous PDX

Project description:The patient-derived xenograft (PDX) model retains the heterogeneity of patient tumors, allowing a means to not only examine efficacy of a therapy across a population, but also study crucial aspects of cancer biology in response to treatment. Herein we describe the development and characterization of an ovarian-PDX model in order to study the development of chemoresistance. We demonstrate that PDX tumors are not simply composed of tumor-initiating cells, but recapitulate the original tumor’s heterogeneity, oncogene expression profiles, and clinical response to chemotherapy. Combined carboplatin/paclitaxel treatment of PDX tumors enriches the cancer stem cell populations, but persistent tumors are not entirely composed of these populations. RNA-Seq analysis of treated PDX tumors compared to untreated tumors demonstrates a consistently contrasting genetic profile after therapy, suggesting similar, but few, pathways are mediating chemoresistance. The pathways most significantly altered included Protein Kinase A signaling, GNRH signaling, and sphingosine-1-phosphate signaling. Pathways and genes identified by this methodology represent novel approaches to targeting the chemoresistant population in ovarian cancer 6 pairs of Patient-Derived Xenografts (PDX) were ananlyzed using RNA-seq for a total of 12 samples. Each pair consists of a treated and untreated PDX of ovarian cancer. Treated Ovarian cancer PDXs were treated with 4 weeks of a combination of carboplatin and taxol. RNA was isolated and converted to cDNA. RNA-seq was conductred on the Illumina HiSeq 2000 with 50 bp paired end sequencing

2015-06-17 | E-GEOD-58586 | biostudies-arrayexpress

leChRO-seq for 2 pancreatic cancer patient-derived xenografts treated with Vehicle or Gemcitabine/Paclitaxel in mouse

Project description:Evaluation of nascent RNA in PDX

2023-03-21 | E-MTAB-11740 | biostudies-arrayexpress