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Similarity of PDXs between passages and lineages using Affymetrix mRNA expression data

ABSTRACT: PDX tumors at various passages post first implantation in nude mice

ORGANISM(S): Homo sapiens

PROVIDER: GSE78806 | GEO | 2016/03/02

SECONDARY ACCESSION(S): PRJNA313969

REPOSITORIES: GEO

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Project description:PDX tumors at various passages post first implantation in nude mice PDX tumors were profiled at different passages when they reached ~400mm3

2016-03-02 | E-GEOD-78806 | biostudies-arrayexpress

Study of the molecular stability of patient-derived tumor xenograft (PDX) for human renal cell carcinoma (RCC) in nude mice during subsequent passages in mice

Project description:We established a large panel of preclinical models of human RCC directly from patients, faithfully reproducing the biological features of the original tumor. RCC tissues were collected for 8 years from 336 patients undergoing surgery, xenografted subcutaneously in nude mice, and serially passaged into new mice up to 13 passages. Tissue samples from the primary tumor and tumors grown in mice through passages were analyzed at the histology, genetic and for of them at the molecular levels for biological tissue stability. We established a large panel of 30 RCC models and 5 them of the clear cell type (clear cell renal cell carcinoma, CCC) were characterized at the mRNA expression level. We used Affymetrix whole genome microarrays to analyze the stability of the PDX models comparing the primary tumor (P0) with the subsequent passages in mice (P1 â¦).

2016-06-29 | E-GEOD-83820 | biostudies-arrayexpress

Affymetrix SNP array data for different passages of mesenchymal stem cells.

Project description:Cells in culture undergo replicative senescence and unequivocally stop proliferation after a limited number of cell divisions. In this study, we have expanded mesenchymal stem cells (MSC) from human adipose tissue and analyzed genetic and epigenetic sequels. The subpopulation of highly proliferative cells and the in vitro differentiation potential decayed already within early passages. Relevant chromosomal aberrations were not detected by karyotyping and SNP-microarrays.

2013-02-15 | GSE27135 | GEO

Study of the molecular stability of patient-derived tumor xenograft (PDX) for human renal cell carcinoma (RCC) in nude mice during subsequent passages in mice

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Affymetrix SNP array data for different passages of mesenchymal stem cells.

2013-02-15 | E-GEOD-27135 | biostudies-arrayexpress

mCRPC LuCaP PDXs ChIP-seq

Project description:Informed consent was obtained to collect human mCRPC tissues and generate the patient-derived xenograft tumors as described previously (Labrecque et al., 2019; Nguyen et al., 2017). The study was approved by the University of Washington Human Subjects Division institutional review board (no. 39053). All animal studies were approved by University of Washington IACUC and performed according to NIH guidelines. Molecular characterization of AR+ mCRPC LuCaP PDXs 70CR, 78CR, 81CR, 96CR, 105CR, 136CR and 147CR was previously described (Labrecque et al., 2019; Nguyen et al., 2017). LuCaP PDX 167CR was established from a liver metastasis of 77-year-old Caucasian male who died of abiraterone-, carboplatin- and docetaxel-resistant CRPC. LuCaP 167CR expresses AR, responds to castration and is negative for synaptophysin. PDX cellular morphology recapitulates the original liver metastasis (Supplementary Figure S8A).

2022-04-06 | GSE163220 | GEO

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks.

Project description: Not available

| S-EPMC3630002 | biostudies-literature

Bulk RNA-seq of archived Acute Myeloid Leukemia (AML) samples propagated in a mouse Xenograft model over several passages

Project description:Cryopreserved AML PDX samples were collected with minimal harm to the sample by taking a biopsy punch from the vial of cell and transfering it into lysis buffer. 96 AML PDX samples collected in such manner were processed using prime-seq to generate high quality expression profiles.

2021-08-01 | E-MTAB-10175 | biostudies-arrayexpress

FiTAc-seq analysis of PDX 14-07 and MMTV-rtTA/tetO/Her2 tumors treated with abemaciclib

Project description:We measured changes in H3K27ac after treatment of PDX 14-07 or MMTV-rtTA/tetO-Her2 tumors implanted in nude mice with abemaciclib

2020-09-03 | GSE157384 | GEO

Identification of tumor antigens in the HLA peptidome of patient-derived xenograft tumors in mouse

Project description:Personalized cancer immunotherapy targeting patient-specific cancer/testis (CTA) antigens and neoantigens may benefit from large-scale tumor HLA peptidome (immunopeptidome) analysis, which aims to accurately identify antigens presented by tumor cells. While significant efforts have been invested in analyzing the HLA peptidomes of fresh tumors, it is often impossible to obtain sufficient volumes of tumor tissues for comprehensive HLA peptidome characterization. This work attempted to overcome some of these obstacles by using patient-derived xenograft tumors (PDX) in mice as the tissue sources for HLA peptidome analysis. PDX tumor provide a proxy for expansion of the patient tumor by re-grafting them through several passages to immune compromised mice. The HLA peptidomes of human biopsies were compared to those derived from PDX tumors. Larger HLA peptidomes were obtained from the significantly larger PDX tumors as compared to the patient biopsies. The HLA peptidomes of different PDX tumors derived from the same source tumor biopsy were very reproducible, even following subsequent passages to new naïve mice. A large number of CTA-derived HLA peptides were discovered, as well as several neoantigens. Taken together, use of PDX tumors for HLA peptidome analysis serves as a highly expandable and stable source of reproducible and authentic peptidomes, opening up new opportunities for defining large HLA peptidomes when only small tumor biopsies are available. This approach provides a large source for tumor antigens identification potentially useful for personalized immunotherapy.

2020-05-27 | PXD016060 | Pride

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