title: Dynamic transcription factor activity networks in response to independently altered mechanical and adhesive microenvironmental cues.
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.
authors.affiliation: Chemical and Biological Engineering Department, Northwestern University, Evanston, IL, USA. broadbelt@northwestern.edu.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Peñalver Bernabé
authors.forename: Seungjin
authors.initials: S
authors.lastname: Shin
authors.forename: Peter D
authors.initials: PD
authors.lastname: Rios
authors.forename: Linda J
authors.initials: LJ
authors.lastname: Broadbelt
authors.forename: Lonnie D
authors.initials: LD
authors.lastname: Shea
authors.forename: Stephanie K
authors.initials: SK
authors.lastname: Seidlits
mesh_terms: D000269:Adhesives; D020816:Amino Acid Motifs; D002448:Cell Adhesion; D002478:Cells, Cultured; D060833:Cellular Microenvironment; D055119:Elastic Modulus; D005347:Fibroblasts / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D017930:Genes, Reporter; D006801:Humans; D020100:Hydrogels / Q000737:chemistry; D007150:Immunohistochemistry; D016023:Integrins / Q000378:metabolism; D008024:Ligands; D010641:Phenotype; D011092:Polyethylene Glycols / Q000737:chemistry; D011336:Probability; D012212:Rheology; D015398:Signal Transduction; D012984:Software; D013314:Stress, Mechanical; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D000269:Adhesives; D020100:Hydrogels; D016023:Integrins; D008024:Ligands; D014157:Transcription Factors; D011092:Polyethylene Glycols