Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391450 | ENA |
REPOSITORIES: ENA
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Project description:A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors
| PRJNA391444 | ENA
Project description:A biobank of 30 molecularly characterized patient-derived xeongraft models of pediatric brain tumors [Affymetrix]
| PRJNA391448 | ENA
Project description:Genome-wide DNA methylation analysis on PCOS using Illumina HumanMethylation 450K BeadChips in 30 PCOS patients and 30 healthy controls
2016-08-22 | GSE80468 | GEO
Project description:We used the Illumina Infinium HumanMethylation EPIC beadchip array to profile 31 pediatric tumors with the histological diagnosis of anaplastic pilocytic astrocyoma (PA). PA with anaplasia has been defined in the 2016 WHO classification as a tumor with PA morphology and >4 mitoses per 10 HPF, with or without necrosis with a potential worse outcome. DNA Methylation based studies performed mainly in adults have put forward this subtype as a distinct entity. After performing the same techniques on pediatric samples, our findings argue that the diagnostic histomolecular criteria established for anaplasia in adult PA are not of diagnostic or prognostic value in a pediatric setting.
2019-11-08 | E-MTAB-8390 | biostudies-arrayexpress
Project description:Osteosarcoma (OS) and Ewing’s sarcoma (EW) are the two most common pediatric solid tumors, after brain tumors. Multimodal treatments have significantly improved prognosis in localized disease but outcome is still poor in metastatic patients, for whom therapeutic options are often inadequate. Preclinical drug testing to identify promising treatment options that match the molecular make-up of these tumors is hampered by the lack of appropriate and molecularly well-characterized patient-derived models. To address this need, a panel of patient-derived xenografts (PDX) was established by subcutaneous implantation of fresh, surgically resected OS and EW tumors in NSG mice. Tumors were re-transplanted to next mice generations and fragments were collected for histopathological and molecular characterization. A model was considered established after observing stable histological and molecular features for at least three passages. To evaluate the similarity of the model with primary tumor, we performed a global gene expression profiling and tissue microarrays (TMA), to assess tumor specific biomarkers on tissues from OS/EW tumors and their PDXs (1st and 3rd passage). Moreover, we verified the feasibility of these models for preclinical drug testing. We implanted 61 OS and 29 EW samples: 14/38 (37%) primary OS and 9/23 (39%) OS lung metastases successfully engrafted; while among EW, 5/26 (19%) primary samples and 1/3 (33%) metastases were established. Comparison between patient samples and PDXs, highlighted that histology and genetic characteristics of PDXs were stable and maintained over passages. In particular, correlative analysis between OS and EW samples and their PDXs was extremely high (Pearson’s r range r=0.94-0.96), while patient-derived primary cultures displayed reduced correlation with human samples (r=0.90-0.93), indicating that in vitro adaptation superimpose molecular alterations that create genetic diversion from original tumors. No significant differentially expressed gene profile was observed from the comparison between EW samples and PDXs (fold change > 2, adjusted p <0.05 at paired t-test). In OS, the comparison between OS patient-derived tumors and PDX indicated differences in 397 genes, mostly belonging to immune system functional category. This is in line with the idea that human immune cells are gradually replaced by murine counterparts upon engraftment in the mouse. As proof-of concept, two EW PDX and one OS PDX have been treated with conventional and innovated drugs to test their value in terms of drug-sensitivity prediction. Overall, our study indicated that PDX models maintained the histological and genetic markers of the tumor samples and represent reliable models to test sensitivity to novel drug associations.
2019-08-27 | E-MTAB-7568 | biostudies-arrayexpress
Project description:Sixteen pre-treatment samples of pathologically confirmed solitary fibrous tumors (SFT) were available for RNA profiling. They were collected from 16 patients who underwent initial surgery and/or diagnostic biopsy. Samples were macrodissected by pathologists, and frozen within 30 min of removal in liquid nitrogen in our biobank (Biobank authorization number 2008/70, APHM). All profiled specimens contained more than 70% tumor cells. Each patient gave written informed consent for molecular analysis, and the study was approved by our institutional ethics committee. Total RNA was extracted from frozen samples by using the All-In-One Norgen Biotek kit (Thorold, Canada) and integrity was controlled by Agilent analysis (Bioanalyzer, Palo Alto, CA). Gene expression profiling was done with Affymetrix U133 Plus 2.0 human oligonucleotide microarrays with labeling kit and protocol from manufacturer.
2013-11-12 | E-MTAB-1361 | biostudies-arrayexpress
Project description:Genome-wide DNA methylation analysis on PCOS using Illumina HumanMethylation 450K BeadChips in 30 PCOS patients and 30 healthy controls Case-control design
2016-08-22 | E-GEOD-80468 | biostudies-arrayexpress
Project description:14 PDX models of pmCRC were established, including 9 matched PD3D/PDX models, and treatment response to 17 SoC and targeted therapies was monitored, which resulted in drug-dependent inter- and intra-patient specific growth inhibition. Analysis of the molecular data of the models and patient tissue resulted in the identification of predictive biomarkers for treatment with 5-FU, irinotecan, trametinib, erlotinib, cetuximab and avastin, oxaliplatin, selumetinib, docetaxel and everolimus. Conclusions: The establishment of a preclinical drug testing platform based on in vitro and in vivo matched pmCRC models, molecularly characterized by multi-omics technology, facilitated the identification of predictive biomarkers for treatment response, as well as cancer relevant signatures for effective therapies, ready for validation in clinical cohorts.
2022-02-17 | PXD027419 | Pride
Project description:We identified XPO1 as an aberrantly activated, non-oncogene encoded targetable vulnerability in pediatric renal tumors (Wilms and malignant rhabdoid tumor [MRT]) using OncoTarget, a Master Regular-based precision cancer medicine tool. We demonstrate significant anti-tumor activity of selinexor and eltanexor, two selective XPO1 inhibitors, in patient derived xenograft mice models of Wilms and MRT, and report on a case of successful treatment of a pediatric cancer patient.
2022-03-09 | GSE198000 | GEO
Project description:Kidney tumors are among the most common solid tumors in children, comprising several distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first pediatric cancer organoid biobank. It contains tumor and matching normal organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumors, malignant rhabdoid tumors, renal cell carcinomas, and congenital mesoblastic nephromas. The malignant rhabdoid tumor organoids represent the first organoid model for tumors of non-epithelial origin. The tumor organoids retain key properties of native tumors, useful for revealing patient specific drug vulnerabilities. We further demonstrate that organoid cultures derived from Wilms tumors consist of multiple different cell types, including epithelial, stromal and blastemal-like. Our organoid biobank captures the cellular heterogeneity of pediatric kidney tumors, providing a representative collection of well-characterized models for basic cancer research, drug-screening, and personalized medicine.
| EGAS00001003853 | EGA