Ontology Analysis if Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films

Published

July 31, 2014

Author(s)

Bryan A. Baker, Patrick S. Pine, Kaushik Chatterjee, Girish Kumar, Jennifer H. McDaniel, Marc L. Salit, Carl G. Simon Jr.

Abstract

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 with different chemistries, suggesting that substrate structure had stronger effects on cell function than substrate chemistry. 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.

Citation

Biomaterials

Pub Type

Journals

Keywords

3D scaffolds, cell differentiation, cell-material interactions, human bone marrow stromal cells, mRNA microarrays, pathway analysis, stem cells

Citation

Baker, B. , Pine, P. , Chatterjee, K. , Kumar, G. , McDaniel, J. , Salit, M. and Simon, C. (2014), Ontology Analysis if Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films, Biomaterials (Accessed October 8, 2025)