ArticleIntegrative biology : quantitative biosciences from nano to macro2016
Dynamic transcription factor activity networks in response to independently altered mechanical and adhesive microenvironmental cues.
Article in Integrative biology : quantitative biosciences from nano to macro, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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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.
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Who cites it
19 citing papers in PubMed, 24 citations in OpenAlex.
- BART-spatial unravels biologically significant transcriptional regulators from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- Bridging systems biology and tissue engineering: Unleashing the full potential of complex 3DBiophysics reviews · 2024Review
- Bioengineered Hydrogels Recapitulate Fibroblast Heterogeneity in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Nanoparticle dose and antigen loading attenuate antigen-specific T-cell responses.Biotechnology and bioengineering · 2023Article
- Injectable, macroporous scaffolds for delivery of therapeutic genes to the injured spinal cord.APL bioengineering · 2021Article
- Extracellular Matrix Proteins Confer Cell Adhesion-Mediated Drug Resistance Through Integrin αFrontiers in cell and developmental biology · 2021Article
- Cyclin E overexpression confers resistance to trastuzumab through noncanonical phosphorylation of SMAD3 in HER2+ breast cancer.Cancer biology & therapy · 2020Article
- Towards systems tissue engineering: Elucidating the dynamics, spatial coordination, and individual cells driving emergent behaviors.Biomaterials · 2020Review
- Adrenergic Blockade Promotes Maintenance of Dormancy in Prostate Cancer Through Upregulation of GAS6.Translational oncology · 2020Article
- Injectable, Hyaluronic Acid-Based Scaffolds with Macroporous Architecture for Gene Delivery.Cellular and molecular bioengineering · 2019Article
- Cargo-less nanoparticles program innate immune cell responses to toll-like receptor activation.Biomaterials · 2019Article
- Predicting growth rate from gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Synergy of Paracrine Signaling During Early-Stage Mouse Ovarian Follicle DevelopmentCellular and molecular bioengineering · 2018Article
- Dynamic microRNA activity identifies therapeutic targets in trastuzumab-resistant HER2Biotechnology and bioengineering · 2018Article
- Design of Large-Scale Reporter Construct Arrays for Dynamic, Live Cell Systems Biology.ACS synthetic biology · 2018Article
- Embryonic stem cell secreted factors decrease invasiveness of triple-negative breast cancer cells through regulome modulation.Cancer biology & therapy · 2018Article
- Systems analysis of dynamic transcription factor activity identifies targets for treatment in Olaparib resistant cancer cells.Biotechnology and bioengineering · 2017Article
- Peptide-Conjugated Nanoparticles Reduce Positive Co-stimulatory Expression and T Cell Activity to Induce Tolerance.Molecular therapy : the journal of the American Society of Gene Therapy · 2017Article
- A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions.BMC systems biology · 2017Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
Abstract
Multiple aspects of the local extracellular environment profoundly affect cell phenotype and function. Physical and chemical cues in the environment trigger intracellular signaling cascades that ultimately activate transcription factors (TFs) - powerful regulators of the cell phenotype. TRACER (TRanscriptional Activity CEll aRrays) was employed for large-scale, dynamic quantification of TF activity in human fibroblasts cultured on hydrogels with a controlled elastic modulus and integrin ligand density. We identified three groups of TFs: responders to alterations in ligand density alone, substrate stiffness or both. Dynamic networks of regulatory TFs were constructed computationally and revealed distinct TF activity levels, directionality (i.e., activation or inhibition), and dynamics for adhesive and mechanical cues. Moreover, TRACER networks predicted conserved hubs of TF activity across multiple cell types, which are significantly altered in clinical fibrotic tissues. Our approach captures the distinct and overlapping effects of adhesive and mechanical stimuli, identifying conserved signaling mechanisms in normal and disease states.
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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.