ArticleCancer discovery2023
OncoLoop: A Network-Based Precision Cancer Medicine Framework.
Article in Cancer discovery, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06615830 (HIPANC-002 - Observational Performance Study of Transcriptome-Based OncoTreat/OncoTarget Testing With Patient-Derived Organoids in Metastatic Pancreatic Cancer), which is not on this map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
HIPANC-002 - Observational Performance Study of Transcriptome-Based OncoTreat/OncoTarget Testing With Patient-Derived Organoids in Metastatic Pancreatic Cancer
Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review on the culture methods and applications of 3D tumoroids for cancer research and personalized medicine.Cellular oncology (Dordrecht, Netherlands) · 2025Pooled it
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- Development and validation of a model for predicting central lymph node metastasis in colorectal cancer based on CT textural features and clinical indicators.Translational cancer research · 2026Article
- A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer.The Journal of experimental medicine · 2026Article
- Mammalian aging involves genome-wide splicing degeneration leading to functional decline.bioRxiv : the preprint server for biology · 2026Article
- pyVIPER: a fast and scalable Python package for protein activity estimation and master regulator analysis of single-cell RNA sequencing data.BMC bioinformatics · 2026Article
- Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states.Nature genetics · 2026Article
- Multi-omics evaluation of cell lines as models for metastatic prostate cancer.Communications biology · 2026Article
- Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies inScience advances · 2026Article
- Pan-cancer inference and validation of hypermorphic, hypomorphic and neomorphic mutations.Nature genetics · 2026Article
- System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells.Cell reports. Medicine · 2025Article
- Omics-Mediated Treatment for Advanced Prostate Cancer: Moving Towards Precision Oncology.International journal of molecular sciences · 2025Review
- Identification and targeting of regulators of SARS-CoV-2-host interactions in the airway epithelium.Science advances · 2025Article
- ATAD2 Drives Prostate Cancer Progression to Metastasis.Molecular cancer research : MCR · 2025Article
- Systems Biology of the Cancer Cell.Annual review of biomedical engineering · 2025Review
- Molecular characterization of the sea lamprey retina illuminates the evolutionary origin of retinal cell types.Nature communications · 2024Article
- Network analysis to identify driver genes and combination drugs in brain cancer.Scientific reports · 2024Article
- Computer-aided drug discovery strategies for novel therapeutics for prostate cancer leveraging next-generating sequencing data.Expert opinion on drug discovery · 2024Review
- Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers.Cell chemical biology · 2024Article
Corrections and comments
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Authors and funding
24 authors.
Funding
Abstract
Prioritizing treatments for individual patients with cancer remains challenging, and performing coclinical studies using patient-derived models in real time is often unfeasible. To circumvent these challenges, we introduce OncoLoop, a precision medicine framework that predicts drug sensitivity in human tumors and their preexisting high-fidelity (cognate) model(s) by leveraging drug perturbation profiles. As a proof of concept, we applied OncoLoop to prostate cancer using genetically engineered mouse models (GEMM) that recapitulate a broad spectrum of disease states, including castration-resistant, metastatic, and neuroendocrine prostate cancer. Interrogation of human prostate cancer cohorts by Master Regulator (MR) conservation analysis revealed that most patients with advanced prostate cancer were represented by at least one cognate GEMM-derived tumor (GEMM-DT). Drugs predicted to invert MR activity in patients and their cognate GEMM-DTs were successfully validated in allograft, syngeneic, and patient-derived xenograft (PDX) models of tumors and metastasis. Furthermore, OncoLoop-predicted drugs enhanced the efficacy of clinically relevant drugs, namely, the PD-1 inhibitor nivolumab and the AR inhibitor enzalutamide. SIGNIFICANCE: OncoLoop is a transcriptomic-based experimental and computational framework that can support rapid-turnaround coclinical studies to identify and validate drugs for individual patients, which can then be readily adapted to clinical practice. This framework should be applicable in many cancer contexts for which appropriate models and drug perturbation data are available. This article is highlighted in the In This Issue feature, p. 247.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.