title: Proteomic analysis of naturally-sourced biological scaffolds.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Qiyao
authors.initials: Q
authors.lastname: Li
authors.affiliation: Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA 02114, USA.
authors.forename: Basak E
authors.initials: BE
authors.lastname: Uygun
authors.affiliation: Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA 02114, USA.
authors.forename: Sharon
authors.initials: S
authors.lastname: Geerts
authors.affiliation: Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA 02114, USA.
authors.forename: Sinan
authors.initials: S
authors.lastname: Ozer
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Scalf
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Gilpin
authors.affiliation: Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Harald C
authors.initials: HC
authors.lastname: Ott
authors.affiliation: Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Hospitals for Children, Boston, MA 02114, USA.
authors.forename: Martin L
authors.initials: ML
authors.lastname: Yarmush
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
authors.affiliation: Division of Otolaryngology, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA. Electronic address: welham@surgery.wisc.edu.
authors.forename: Nathan V
authors.initials: NV
authors.lastname: Welham
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: bfrey@chem.wisc.edu.
authors.forename: Brian L
authors.initials: BL
authors.lastname: Frey
mesh_terms: D000818:Animals; D015153:Blotting, Western; D003094:Collagen / Q000494:pharmacology; D024042:Collagen Type I / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D004338:Drug Combinations; D005260:Female; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000378:metabolism; D007797:Laminin / Q000494:pharmacology; D008099:Liver / Q000187:drug effects / Q000378:metabolism; D008168:Lung / Q000378:metabolism; D011509:Proteoglycans / Q000494:pharmacology; D040901:Proteomics / Q000379:methods*; D011917:Rats, Inbred Lew; D054457:Tissue Scaffolds / Q000737:chemistry*
chemical_list: D024042:Collagen Type I; D004338:Drug Combinations; D036341:Intercellular Signaling Peptides and Proteins; D007797:Laminin; D011509:Proteoglycans; C059485:matrigel; D003094:Collagen; D004247:DNA
keywords: Decellularized human lung; Decellularized rat liver; Mass spectrometry; Matrigel; Matrisome; Proteomics