Proteomic analysis of naturally-sourced biological scaffolds

Qiyao Li, Basak E. Uygun, Sharon Geerts, Sinan Ozer, Mark Scalf, Sarah E. Gilpin, Harald C. Ott, Martin L. Yarmush, Lloyd M. Smith, Nathan V. Welham, Brian L. Frey

Research output: Contribution to journalArticlepeer-review

67 Scopus citations


A key challenge to the clinical implementation of decellularized scaffold-based tissue engineering lies in understanding the process of removing cells and immunogenic material from a donor tissue/organ while maintaining the biochemical and biophysical properties of the scaffold that will promote growth of newly seeded cells. Current criteria for evaluating whole organ decellularization are primarily based on nucleic acids, as they are easy to quantify and have been directly correlated to adverse host responses. However, numerous proteins cause immunogenic responses and thus should be measured directly to further understand and quantify the efficacy of decellularization. In addition, there has been increasing appreciation for the role of the various protein components of the extracellular matrix (ECM) in directing cell growth and regulating organ function. We performed in-depth proteomic analysis on four types of biological scaffolds and identified a large number of both remnant cellular and ECM proteins. Measurements of individual protein abundances during the decellularization process revealed significant removal of numerous cellular proteins, but preservation of most structural matrix proteins. The observation that decellularized scaffolds still contain many cellular proteins, although at decreased abundance, indicates that elimination of DNA does not assure adequate removal of all cellular material. Thus, proteomic analysis provides crucial characterization of the decellularization process to create biological scaffolds for future tissue/organ replacement therapies.

Original languageEnglish (US)
Pages (from-to)37-46
Number of pages10
StatePublished - Jan 2016
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Bioengineering
  • Ceramics and Composites
  • Biophysics
  • Biomaterials
  • Mechanics of Materials


  • Decellularized human lung
  • Decellularized rat liver
  • Mass spectrometry
  • Matrigel
  • Matrisome
  • Proteomics


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