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Ex-vivo screening platform to identify tumor-specific therapies

ABSTRACT: Ex-vivo screening platform to identify tumor-specific therapies

PROVIDER: PRJNA417676 | ENA |

REPOSITORIES: ENA

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Ex-vivo screening platform to identify tumor-specific therapies

Project description:We report the generation of a preclinical IBC patient-derived xenograft (PDX)-derived ex vivo tumor tissue model and show that it closely replicates the tissue architecture of the original PDX tumor harvested from mice and show that its genetic signature highly correlates with that of the original tumor. We used microarrays to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.

2018-04-07 | GSE106685 | GEO

High-throughput transcriptomics platform for screening hepatotoxicants

Project description:High-throughput transcriptomics platform for screening hepatotoxicants

| PRJNA638385 | ENA

A safety screening platform for individualized cardiotoxicity assessment

Project description:A safety screening platform for individualized cardiotoxicity assessment

| PRJNA971626 | ENA

High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

Project description:High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

| PRJNA683595 | ENA

Ex Vivo Lung Perfusion as a Human Platform for Preclinical Small Molecule Testing

Project description:Ex Vivo Lung Perfusion as a Human Platform for Preclinical Small Molecule Testing

| PRJNA486099 | ENA

An ex vivo physiologic and hyperplastic vessel culture model to study intra-arterial stent therapies

Project description:An ex vivo physiologic and hyperplastic vessel culture model to study intra-arterial stent therapies

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A cyanobacterial screening platform for mutant variants of a Form II Rubisco

Project description:Cyanobacterial Form II Rubisco screening platform

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Development of a split-toxin CRISPR screening platform to systematically identify upstream regulators of human myoblast fusion

Project description:Muscle defects are a common feature in human developmental disorders and often lead to severe functional impairment. These defects arise from intricate tissue crosstalk and rare genetic mutations, underscoring the need to systematically identify cell-autonomous mechanisms regulating human myogenesis. Despite the clinical significance, our understanding of human development remains limited, due in part to the absence of a scalable genetic approach to study this process. Here, we introduce a rationally designed high-throughput CRISPR screening platform that integrates human myoblast models, muscle-specific CRISPR knockout libraries, and a split-toxin strategy that acts as a functional readout for myoblast fusion—a fundamental step of human myogenesis. This screening strategy enables selection of CRISPR-induced fusion-defective myocytes in a quantifiable manner. Leveraging this platform, our initial genetic screen uncovered a large group of new hits essential for human myoblast fusion. The majority of these hits converge into 23 protein complexes, most of which have not previously been functionally linked to myogenesis in any species. Notably, mutations in 41 of our fusion screen hits cause human diseases presenting abnormal skeletal muscle morphology. Applying a new single-cell CRISPR & RNA-seq approach, we show that majority of these hits control human myoblast fusion as well as influence early-stage myogenic differentiation. Together, this work presents a new systematic approach to study human myogenesis and uncovers promising candidates governing human muscle differentiation and fusion. A broader application of this split-toxin based CRISPR screening platform would accelerate the study of cell-autonomous mechanisms of human muscle development and diseases at scale.

2025-10-24 | GSE293514 | GEO

Human Ex Vivo Lung Perfusion: A Model System to study Lung diseases and direct targeted therapies

Project description:Human Ex Vivo Lung Perfusion: A Model System to study Lung diseases and direct targeted therapies

| PRJNA610580 | ENA

High-throughput transcriptomics platform for screening hepatotoxicants

Project description:We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.

2021-09-01 | GSE152128 | GEO

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