ArticleCell systems2024
Stimulus-response signaling dynamics characterize macrophage polarization states.
Article in Cell systems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Macrophage response specificity to ligand mixtures is improved by signaling pathway antagonism.Molecular systems biology · 2026Article
- Anthraquinone-Loaded Liposomes for TAM Reprogramming in Triple-Negative Breast Cancer: Mechanistic Rationale, Delivery Logic, and Translational Challenges.Pharmaceutics · 2026Review
- Macrophage polarization in inflammatory regulation: molecular mechanisms, therapeutic targets, and translational challenges.Cellular and molecular life sciences : CMLS · 2026Review
- RACK1 in host immune response to infections: molecular mechanisms and therapeutic potentials.Frontiers in immunology · 2026Review
- A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling.PLoS computational biology · 2025Article
- An era of immunological discoveries heralded by molecular biology.Trends in immunology · 2025Article
- Innate Immune Memory is Stimulus Specific.bioRxiv : the preprint server for biology · 2025Article
- Harnessing miRNA dynamics in HIV-1-infected macrophages: Unveiling new targeted therapeutics using systems biology.Computational and structural biotechnology journal · 2025Article
- Emerging Insights into the Role of Macrophages in Multiple Sclerosis: Pathogenesis and Potential Therapeutic Strategies.Journal of inflammation research · 2025Review
- Linking signaling dynamics and cell fate decisions through single-cell imaging: evidence and challenges.Frontiers in cell and developmental biology · 2025Review
- A data-driven model of macrophage polarization states reveals an IFN macrophage signature in active Crohn's disease.Frontiers in immunology · 2025Article
- NF-κB: master regulator of cellular responses in health and disease.Immunity & inflammation · 2025Review
- Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages.Molecular cell · 2024Article
- Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag.bioRxiv : the preprint server for biology · 2024Article
- Quantifying stimulus-response specificity to probe the functional state of macrophages.Cell systems · 2023Article
- NF-κB in monocytes and macrophages - an inflammatory master regulator in multitalented immune cells.Frontiers in immunology · 2023Review
- Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.Cell reports · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The functional state of cells is dependent on their microenvironmental context. Prior studies described how polarizing cytokines alter macrophage transcriptomes and epigenomes. Here, we characterized the functional responses of 6 differentially polarized macrophage populations by measuring the dynamics of transcription factor nuclear factor κB (NF-κB) in response to 8 stimuli. The resulting dataset of single-cell NF-κB trajectories was analyzed by three approaches: (1) machine learning on time-series data revealed losses of stimulus distinguishability with polarization, reflecting canalized effector functions. (2) Informative trajectory features driving stimulus distinguishability ("signaling codons") were identified and used for mapping a cell state landscape that could then locate macrophages conditioned by an unrelated condition. (3) Kinetic parameters, inferred using a mechanistic NF-κB network model, provided an alternative mapping of cell states and correctly predicted biochemical findings. Together, this work demonstrates that a single analyte's dynamic trajectories may distinguish the functional states of single cells and molecular network states underlying them. A record of this paper's transparent peer review process is included in the supplemental information.
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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.