ArticleNature biotechnology2025
Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Harnessing metabolomics and proteomics in a clinical trial for pulmonary arterial hypertension: insights from post-hoc analysis of the REHAB-PH trial.EBioMedicine · 2026Trial
- Preprocessing Large-Scale Proteomics Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Proteome-guided drug discovery maps and mitigates therapeutic degrader toxicity.Nature chemical biology · 2026Article
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- DT-TRAP enables accurate target recognition via simplified dosing and low-temperature incubation.Journal of pharmaceutical analysis · 2026Article
- Systematic optimization and benchmarking of synchro-PASEF for high-throughput phosphoproteome profiling.bioRxiv : the preprint server for biology · 2026Article
- Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2026Article
- Robotic perturbation proteomics and AI agents enable scalable drug mechanism discovery.bioRxiv : the preprint server for biology · 2026Article
- Dose-Dependent Inhibition of Protein Glycosylation Reveals Crosstalk between Glycosylation and Phosphorylation in EGF Signaling Pathways.Analytical chemistry · 2026Article
- Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition.Communications biology · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.Nucleic acids research · 2026Article
- Article
- Proteomics in Antitumor Drug Target Discovery, Toxicity, Resistance, and Precision Oncology.Drug design, development and therapy · 2026Review
- Phosphoproteomic and Acetylomic Characterization of Colorectal Cancer Cells Treated with Kinase Inhibitors.ACS pharmacology & translational science · 2025Article
- Acquired resistance in cancer: towards targeted therapeutic strategies.Nature reviews. Cancer · 2025Review
- Nontargeted Toxicological/Chemical Analysis in Complex Mixtures for Risk Assessment and Key Driver Discovery.Environment & health (Washington, D.C.) · 2025Article
- Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics.Analytical chemistry · 2025Review
- AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships.Computational and structural biotechnology journal · 2025Review
- BRAFbioRxiv : the preprint server for biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Proteomics is making important contributions to drug discovery, from target deconvolution to mechanism of action (MoA) elucidation and the identification of biomarkers of drug response. Here we introduce decryptE, a proteome-wide approach that measures the full dose-response characteristics of drug-induced protein expression changes that informs cellular drug MoA. Assaying 144 clinical drugs and research compounds against 8,000 proteins resulted in more than 1 million dose-response curves that can be interactively explored online in ProteomicsDB and a custom-built Shiny App. Analysis of the collective data provided molecular explanations for known phenotypic drug effects and uncovered new aspects of the MoA of human medicines. We found that histone deacetylase inhibitors potently and strongly down-regulated the T cell receptor complex resulting in impaired human T cell activation in vitro and ex vivo. This offers a rational explanation for the efficacy of histone deacetylase inhibitors in certain lymphomas and autoimmune diseases and explains their poor performance in treating solid tumors.
Indexed as
Identifiers
What OpenQuestion holds
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.