Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions [RNA-seq]
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PROVIDER: PRJNA1177462 | ENA |
REPOSITORIES: ENA
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Project description:Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions
| PRJNA1178722 | ENA
Project description:Large-Scale CRISPR Screening in Primary Human 3D Gastric Organoids Enables Comprehensive Dissection of Gene-Drug Interactions [ATAC-seq]
| PRJNA1177460 | ENA
Project description:Investigating gene-drug interactions is critical for advancing personalized medicine by revealing how genetic variations shape individual responses to medications. To achieve this goal, it is essential to develop a robust human functional genomics system that can accurately recapitulate normal physiology and disease while effectively accounting for the complexity and heterogeneity among individuals. We explored this potential in primary 3D human gastric organoids by implementing a wide range of large-scale CRISPR-based genetic screens, including CRISPR knockout, CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and single-cell CRISPR screens. Our cisplatin sensitization screens targeting 1,952 DNA-binding proteins identified numerous known genes associated with DNA repair pathways, along with previously unrecognized cisplatin sensitization loci. Individual validation of top hits further confirmed the robustness of the screening results. Furthermore, using multiplexed single-cell CRISPR screens to simultaneously extract individual sgRNAs and single-cell transcriptomes, we uncovered a convergence within DNA repair pathways in cisplatin-treated organoids compared to cisplatin-naïve organoids. These methods distinguished high-dimensional synergistic effects between sgRNAs and drug perturbations by leveraging each cell's gene expression profiles, improving the resolution to link genotypes with drug response phenotypes in organoids. Finally, we identified TAF6L as a novel cisplatin sensitization gene. Mechanistically, TAF6L is crucial for the proliferation of cell recovery following cisplatin-induced DNA damage response. In summary, diverse CRISPR-based functional genomics platforms can be successfully applied to human organoids, revealing new gene-drug interactions with implications for human disease.
2025-06-26 | GSE280506 | GEO
Project description:Investigating gene-drug interactions is critical for advancing personalized medicine by revealing how genetic variations shape individual responses to medications. To achieve this goal, it is essential to develop a robust human functional genomics system that can accurately recapitulate normal physiology and disease while effectively accounting for the complexity and heterogeneity among individuals. We explored this potential in primary 3D human gastric organoids by implementing a wide range of large-scale CRISPR-based genetic screens, including CRISPR knockout, CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and single-cell CRISPR screens. Our cisplatin sensitization screens targeting 1,952 DNA-binding proteins identified numerous known genes associated with DNA repair pathways, along with previously unrecognized cisplatin sensitization loci. Individual validation of top hits further confirmed the robustness of the screening results. Furthermore, using multiplexed single-cell CRISPR screens to simultaneously extract individual sgRNAs and single-cell transcriptomes, we uncovered a convergence within DNA repair pathways in cisplatin-treated organoids compared to cisplatin-naïve organoids. These methods distinguished high-dimensional synergistic effects between sgRNAs and drug perturbations by leveraging each cell's gene expression profiles, improving the resolution to link genotypes with drug response phenotypes in organoids. Finally, we identified TAF6L as a novel cisplatin sensitization gene. Mechanistically, TAF6L is crucial for the proliferation of cell recovery following cisplatin-induced DNA damage response. In summary, diverse CRISPR-based functional genomics platforms can be successfully applied to human organoids, revealing new gene-drug interactions with implications for human disease.
2025-06-23 | GSE280257 | GEO
Project description:Investigating gene-drug interactions is critical for advancing personalized medicine by revealing how genetic variations shape individual responses to medications. To achieve this goal, it is essential to develop a robust human functional genomics system that can accurately recapitulate normal physiology and disease while effectively accounting for the complexity and heterogeneity among individuals. We explored this potential in primary 3D human gastric organoids by implementing a wide range of large-scale CRISPR-based genetic screens, including CRISPR knockout, CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and single-cell CRISPR screens. Our cisplatin sensitization screens targeting 1,952 DNA-binding proteins identified numerous known genes associated with DNA repair pathways, along with previously unrecognized cisplatin sensitization loci. Individual validation of top hits further confirmed the robustness of the screening results. Furthermore, using multiplexed single-cell CRISPR screens to simultaneously extract individual sgRNAs and single-cell transcriptomes, we uncovered a convergence within DNA repair pathways in cisplatin-treated organoids compared to cisplatin-naïve organoids. These methods distinguished high-dimensional synergistic effects between sgRNAs and drug perturbations by leveraging each cell's gene expression profiles, improving the resolution to link genotypes with drug response phenotypes in organoids. Finally, we identified TAF6L as a novel cisplatin sensitization gene. Mechanistically, TAF6L is crucial for the proliferation of cell recovery following cisplatin-induced DNA damage response. In summary, diverse CRISPR-based functional genomics platforms can be successfully applied to human organoids, revealing new gene-drug interactions with implications for human disease.
2025-06-23 | GSE280256 | GEO
Project description:Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies
| PRJNA348447 | ENA
Project description:BackgroundRapidly characterizing the operational interrelationships among all genes in a given organism is a critical bottleneck to significantly advancing our understanding of thousands of newly sequenced microbial and eukaryotic species. While evolving technologies for global profiling of transcripts, proteins, and metabolites are making it possible to comprehensively survey cellular physiology in newly sequenced organisms, these experimental techniques have not kept pace with sequencing efforts. Compounding these technological challenges is the fact that individual experiments typically only stimulate relatively small-scale cellular responses, thus requiring numerous expensive experiments to survey the operational relationships among nearly all genetic elements. Therefore, a relatively quick and inexpensive strategy for observing changes in large fractions of the genetic elements is highly desirable.ResultsWe have discovered in the model organism Halobacterium salinarum NRC-1 that batch culturing in complex medium stimulates meaningful changes in the expression of approximately two thirds of all genes. While the majority of these changes occur during transition from rapid exponential growth to the stationary phase, several transient physiological states were detected beyond what has been previously observed. In sum, integrated analysis of transcript and metabolite changes has helped uncover growth phase-associated physiologies, operational interrelationships among two thirds of all genes, specialized functions for gene family members, waves of transcription factor activities, and growth phase associated cell morphology control.ConclusionsSimple laboratory culturing in complex medium can be enormously informative regarding the activities of and interrelationships among a large fraction of all genes in an organism. This also yields important baseline physiological context for designing specific perturbation experiments at different phases of growth. The integration of such growth and perturbation studies with measurements of associated environmental factor changes is a practical and economical route for the elucidation of comprehensive systems-level models of biological systems.
| S-EPMC2880973 | biostudies-literature
Project description:Comprehensive Dissection of CircRNA-Associated-ceRNA Networks in Cardiac Transplant Rejection Immunity
| PRJNA685431 | ENA
Project description:We have utilized a version 2.0 of our Fusion gene microarray (version 1.0 described by PMID: 19152679 and GEO, GPL8078) to screen cancer cell lines for known fusion genes We assembled a comprehensive database of published fusion genes, including those which have been reported only in individual studies and samples, and fusion genes resulting from deep sequencing of cancer genomes and transcriptomes. From the total set of 548 fusion genes, we designed 197,846 unique oligonucleotides, targeting both chimeric transcript junctions as well as sequences internal to each of the fusion gene partners. We investigated the presence of fusion genes in a series of 67 cell lines originating from 15 different cancer types. Data from ten leukaemia cell lines with known fusion gene status were used to evaluate and calibrate an automated scoring algorithm. In five out of ten cell lines the correct fusion gene was the top most scoring hit, and one came second, all six passing a cut-off of 50 percent of theoretical maximum-score. Two additional fusion genes, BCAS4-BCAS3 from the MCF-7 breast cancer cell line and CCDC6-RET from the TPC-1 thyroid cancer cell line were validated as true positive fusion transcripts from the remaining 57 cell lines. A total of 67 cell lines from various cancer types were analysed for presence of known fusion genes
2011-02-10 | E-GEOD-24737 | biostudies-arrayexpress
Project description:Develop a novel de-glyco-assisted methylation site identification (DOMAIN) strategy which enables straightforward, fast, and reproducible analysis of protein methylation in a proteome-wide manner. Combining multidimensional fractionation and multiprotease digestion, our method enabled the identification of 573 methylated forms in 270 proteins, including 311 new methylation forms, in A549 cells. Combining this technique with stable isotope labeling quantitative proteomics and RNA interference, we determined the differential regulation of several putative methylated sites that are related to the protein arginine N-methyltransferase 3 (PRMT3). Collectively, our integrated proteomics workflow for comprehensive mapping of methylation sites enables a better understanding of protein methylation, while providing a rapid and effective approach for global protein methylation analysis in biomedical research.
2019-07-18 | PXD014574 | Pride