Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films.
Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. Previous work has shown that hBMSC culture in nanofiber scaffolds can induce osteogenic differentiation in the absence of osteogenic supplements (OS). Analysis using ontology databases revealed that nanofibers and OS regulated similar pathways and that both were enriched for TGF-β and cell-adhesion/ECM-receptor pathways. The most notable difference between the two was that nanofibers had stronger enrichment for cell-adhesion/ECM-receptor pathways. Comparison of nanofibers scaffolds with flat films yielded stronger differences in gene expression than comparison of nanofibers made from different polymers, suggesting that substrate structure had stronger effects on cell function than substrate polymer composition. These results demonstrate that physical (nanofibers) and biochemical (OS) signals regulate similar ontological pathways, suggesting that these cues use similar molecular mechanisms to control hBMSC differentiation.
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA.
Bryan A
BA
Baker
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA.
P Scott
PS
Pine
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA; Department of Materials Engineering, Indian Institute of Science, Bangalore 560012, India.
Kaushik
K
Chatterjee
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA; Division of Biology, Office of Science & Engineering Laboratories, Center for Devices & Radiological Health, Food & Drug Administration, Silver Spring, MD 20993, USA.
Girish
G
Kumar
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA.
Nancy J
NJ
Lin
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA.
Jennifer H
JH
McDaniel
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA.
Marc L
ML
Salit
Biosystems & Biomaterials Division, National Institute of Standards & Technology, Gaithersburg, MD 20899, USA. Electronic address: carl.simon@nist.gov.
Carl G
CG
Simon
D001672:Biocompatible Materials / Q000737:chemistry; D002448:Cell Adhesion / Q000502:physiology; D002454:Cell Differentiation / Q000502:physiology; D002478:Cells, Cultured; D015870:Gene Expression; D006801:Humans; D059630:Mesenchymal Stem Cells / Q000378:metabolism*; D046228:Microarray Analysis; D057139:Nanofibers / Q000737:chemistry; D010012:Osteogenesis / Q000502:physiology; D011108:Polymers / Q000737:chemistry; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D023822:Tissue Engineering / Q000379:methods; D054457:Tissue Scaffolds / Q000737:chemistry*; D059467:Transcriptome; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism
D001672:Biocompatible Materials; D011108:Polymers; D012333:RNA, Messenger; D016212:Transforming Growth Factor beta
3D scaffolds; Cell differentiation; Cell–material interactions; Human bone marrow stromal cells; Pathway analysis; mRNA microarrays