Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer

ABSTRACT: Poor therapeutic response in subsets of breast cancer (BC) patients poses an ongoing challenge. Here, we present a series of 14 patient-derived triple-negative BC organoids, established with the aim of modeling resistant disease with greater fidelity using biomarkers and developing an in-vitro system grounded in clinical data for testing alternative treatment strategies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE303509 | GEO | 2026/07/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer

Project description:Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer

| PRJNA1295546 | ENA

Emerging Biomarker-Guided Therapies in Prostate Cancer.

Project description: Not available

| S-EPMC9319825 | biostudies-literature

Promising use of metformin in treating neurological disorders: biomarker-guided therapies.

Project description: Not available

| S-EPMC10749596 | biostudies-literature

CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends

Project description:Spatial transcriptomics provides insights into tissue architecture by linking gene expression with spatial localization. Current deconvolution methods rely heavily on single-cell RNA sequencing (scRNA-seq) references, which are costly and often unavailable, especially if the tissue under evaluation is limited as in a core biopsy specimen. We present a novel tool, CITEgeist, that deconvolutes spatial transcriptomics data using antibody capture from the same slide as the reference, directly leveraging cell surface protein measurements from the same tissue section. This approach circumvents the limitations of scRNA-seq as a reference, offering a cost-effective and biologically grounded alternative. Our method employs mathematical optimization to estimate cell type proportions and gene expression profiles, incorporating sparsity constraints for robustness and interpretability. Benchmarks against state-of-the-art deconvolution methods show improved accuracy in cell type resolution, particularly in dense tumor microenvironments, while maintaining computational efficiency. This antibody-based tool advances spatial transcriptomics by providing a scalable, accurate, and reference-independent solution for deconvolution in complex tissues. We validate this tool by using a combined approach of simulated data and clinical samples by applying CITEgeist to translational pre-treatment and post-treatment ER+ breast tumors from an ongoing clinical trial, emphasizing the applicability and robustness of CITEgeist.

2026-03-19 | GSE289326 | GEO

Clinical outcome of biomarker-guided therapies in adult patients with tumors of the nervous system.

Project description: Not available

| S-EPMC10007909 | biostudies-literature

High-throughput dynamic BH3 profiling may quickly and accurately predict effective therapies in solid tumors.

Project description: Not available

| S-EPMC8023011 | biostudies-literature

A Non-Contrast Multi-Parametric MRI Biomarker for Assessment of MR-Guided Focused Ultrasound Thermal Therapies.

Project description: Not available

| S-EPMC10768718 | biostudies-literature

RNA-seq Analysis of Differential Gene Expression in Obese Compared with Non-Obese Breast Cancer Patients

Project description:Breast cancer (BC), the most common malignant tumor type, ranked top in incidence with high prevalence and mortality among females worldwide. Obesity poses a serious public health issue worldwide, it consider as one of BC risk factors. Obesity has profound effects on cancer cell transcriptome that can affect the outcome of cancer therapy. The information regarding the potential effects of obesity on BC transcriptome to identify novel transcripts biomarker and pathways related to disease progression are still elusive. Therefore, the RNA-seq analysis was performed to investigate the whole blood differential epressed genes profile in the blood liquid biopsy of obese compared with non-obese BC patients to provide a better understanding of the biological status and shed new insights into potential molecular mechanisms interaction and biomarkers in the relationship between obesity and BC.

2020-09-04 | GSE148892 | GEO

Hsa_circ_0001583 a novel biomarker for breast cancer related to immune response

Project description:The differently expressed circRNAs were analysis by microarray. There were 256 differentially upregulated circRNAs and 277 differentially downregulated circRNAs based on fold change ≥2.0 and p<0.05. We found hsa_circ_0001583 expression was up-regulated in BC groups (p<0.05) by RT-qPCR. Therefore, we though hsa_circ_0001583 may serve as a novel kind of biomarker for BC.

2021-02-02 | GSE165884 | GEO

Forkhead Box F1 acts as a novel prognostic biomarker and induces caspase-dependent apoptosis in bladder cancer

Project description:Down-regulated expression of Forkhead Box F1 (FOXF1) in malignant tumors were reported in several kinds of cancer before, but its role in bladder cancer (BC) was not clear. This study aims to demonstrate the prognostic value and of FOXF1 in BC patients. Here, a retrospectively recruited BC cohort and public datasets were utilized to identify the predictive ability of FOXF1 and its relationship between clinical information in BC patients. The expression level of FOXF1 is notably higher in BC tissues than para-cancerous mucosae. Low FOXF1 expression is correlated to unfavorable clinicopathological features and poor prognosis. Further, in bladder tumor cells, the expression levels of FOXF1 mRNA and protein were tested by quantitative real-time PCR and western blot. The viability of cells was examined by CCK-8, EdU, and clonogenic capacity assays. Cell apoptosis was detected by flow cytometry. We note that FOXF1 activating could impair cell viability and induce apoptosis in BC. Then, caspase 3 as a downstream gene of FOXF1 was spotted by RNA-Seq and PPI. The anti-tumor effect of FOXF1 were also validated in animal models. In conclusion, down-regulated FOXF1 expression is a potential independent indicator for unfavorable clinical outcomes of BC patients, FOXF1 inhibits BC cells proliferation and induces cell apoptosis via caspase signaling pathway. This study exhibits FOXF1 express pattern, demonstrates the prognostic predictive ability of FOXF1 and prove the anti-tumor mechanisms of FOXF1 in BC, it has reference value to clinical decision, activation FOXF1 expression could be used as a new strategy in tumor therapeutics.

2023-07-18 | GSE229810 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data