Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthetic lethality-mediated precision oncology via the tumor transcriptome

ABSTRACT: Precision oncology has made significant advances in the last few years, mainly by targeting actionable mutations in cancer driver genes. However, the proportion of patients whose tumors can be targeted therapeutically remains limited. Recent studies have begun to explore the benefit of analyzing tumor transcriptomics data to guide patient treatment, raising the need for new approaches for systematically accomplishing that. Here we show that computationally derived genetic interactions can successfully predict patient response.

ORGANISM(S): Homo sapiens

PROVIDER: GSE166449 | GEO | 2021/02/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Patient-derived micro-organospheres (MOS) enable clinical precision oncology

Project description:Patient-derived xenografts (PDX) and organoids (PDO) have been shown to model clinical response to cancer therapy. However, it remains challenging to use these models to guide timely clinical decisions for cancer patients. Here we used droplet emulsion microfluidics with temperature control and dead-volume minimization to rapidly generate thousands of Micro- Organospheres (MOS) from low-volume patient tissues, which serve as an ideal patient-derived model for clinical precision oncology. A clinical study of newly diagnosed metastatic colorectal cancer (CRC) patients using a MOS-based precision oncology pipeline reliably predicted patient treatment outcome within 14 days, a timeline suitable for guiding treatment decisions in clinic. Furthermore, MOS capture original stromal cells and allow T cell penetration, providing a clinical assay for testing immuno-oncology (IO) therapies such as PD-1 blockade, bispecific antibodies, and T cell therapies on patient tumors.

2022-09-01 | GSE184242 | GEO

Synthetic lethality-mediated precision oncology via the tumor transcriptome

Project description:Synthetic lethality-mediated precision oncology via the tumor transcriptome

| PRJNA700986 | ENA

A Single-Cell Tumor Immune Atlas for Precision Oncology

Project description:The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell resolved tumor immune cell atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we developed SPOTlight, a computational tool that identified striking spatial immune cell patterns in tumor sections. We expect the atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification strategies for prognosis and immuno-therapy response.

2020-10-27 | GSE158803 | GEO

Molecular and functional landscape of malignant serous effusions for precision oncology

Project description:Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells from patient biopsies. Here, we comprehensively characterize a pan-cancer cohort of 150 malignant serous effusion (MSE) samples at the cellular, molecular, and functional level. We find that MSE-derived cancer cells retain the genomic and transcriptomic profiles of their corresponding primary tumors, validating their use as a patient-relevant model system for solid tumor biology. Integrative analyses reveal that baseline gene expression patterns relate to global ex vivo drug sensitivity, while high-throughput drug-induced transcriptional changes in MSE samples are indicative of drug mode of action and acquired treatment resistance. A case study exemplifies the added value of multi-modal MSE profiling for patients who lack genetically stratified treatment options. In summary, our study provides a functional multi-omics view on a pan-cancer solid tumor cohort and underlines the feasibility and utility of MSE-based precision oncology.

2024-10-04 | PXD052582 | Pride

CPTAC: Microscaled Proteogenomic Methods for Precision Oncology

Project description:CPTAC: Microscaled Proteogenomic Methods for Precision Oncology

| PRJNA574689 | ENA

Towards Optimization of Precision Oncology in Metastatic Uterine Tumors

Project description:Precision oncology and its diagnostic tools are essential for developing personalized cancer treatments. The purpose of this study was to integrate data on the digital patterns of reticulin fiber scaffolding and the immune cell infiltrate, transcriptomic and epigenetic profiles in aggressive uterine adenocarcinoma (uADC), uterine leiomyosarcoma (uLMS) and their respective lung metastases (LM-uADC and LM-uLMS), with the aim of obtaining key tumor microenvironment (TME) biomarkers that can help improve metastatic prediction and shed light on potential therapeutic targets.

2022-12-16 | GSE216313 | GEO

Synthetic lethality-mediated precision oncology via the tumor transcriptome.

Project description:Precision oncology has made significant advances, mainly by targeting actionable mutations in cancer driver genes. Aiming to expand treatment opportunities, recent studies have begun to explore the utility of tumor transcriptome to guide patient treatment. Here, we introduce SELECT (synthetic lethality and rescue-mediated precision oncology via the transcriptome), a precision oncology framework harnessing genetic interactions to predict patient response to cancer therapy from the tumor transcriptome. SELECT is tested on a broad collection of 35 published targeted and immunotherapy clinical trials from 10 different cancer types. It is predictive of patients' response in 80% of these clinical trials and in the recent multi-arm WINTHER trial. The predictive signatures and the code are made publicly available for academic use, laying a basis for future prospective clinical studies.

| S-EPMC9310669 | biostudies-literature

A Single-Cell Tumor Immune Atlas for Precision Oncology

Project description:A Single-Cell Tumor Immune Atlas for Precision Oncology

| PRJNA666613 | ENA

Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_drug_treated]

Project description:Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells. These patients frequently develop malignant serous effusions (MSE). The value of MSE-based tumor cell characterization for guiding precision oncology is, however, currently unclear. Here, we present a comprehensive characterization of a pan-cancer cohort of 150 MSE samples at the cellular, molecular, and functional level. Our integrative analysis reveals dynamic cellular heterogeneity in MSE, and uncovers links between tumor driver mutations and ex vivo growth patterns. Strong concordance between genomic and transcriptional profiles of MSE and their corresponding solid tumors validates their use as a model system for solid tumor biology. We link baseline gene expression patterns to global ex vivo drug sensitivity, and demonstrate that drug-induced transcriptional changes in MSE are highly indicative of compound mode of action. Two case studies exemplify the utility of our approach in investigating acquired resistance to targeted therapy and identifying treatment options for relapsed solid tumors. In summary, our study provides a functional multi-omics view on a pan-cancer MSE cohort and underlines the utility of MSE-based precision oncology.

2024-08-26 | GSE240951 | GEO

Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_baseline]

2024-08-26 | GSE240952 | GEO