Abstract
Objectives
Osteoarthritis (OA) is a major concern in the United States and worldwide. Development and validation of robust decellularization techniques is critical in generating suitable bioscaffolds for future OA treatment options.
Data descriptions
In the present study, proteins from porcine auricular cartilage before and after decellularization were extracted, digested, and identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data represents protein profiles of both non-decellularized and decellularized porcine auricular cartilage. This data is intended to be useful to scientists who are interesting in generating biomaterials for potential relevant clinical applications using decellularized cartilage tissue.
Keywords: Osteoarthritis, Porcine, Cartilage, Decellularization, Proteomics, LC-MS/MS
Objective
Osteoarthritis (OA) is one of the leading causes of disability worldwide [1, 2]. Tissue engineering approaches using 3-dimensional scaffolds are promising for the early treatment of cartilage degeneration in OA joints [3]. Development and validation of robust decellularization techniques is critically important in generating suitable scaffolds to provide support for tissue growth. Our dataset comprises quantitative proteomic analysis of porcine auricular cartilage before and after decellularization. We believe that this data would be beneficial for researchers who are interested in generating biomaterials using decellularized cartilage as a future alternative treatment option for individuals suffering from OA.
Data description
This is a raw data set of our research article presenting our findings on creating and validating biological scaffold from porcine auricular cartilage using a decellularization protocol developed in our lab [4]. We performed decellularization using a combination of chemical and physical methods. Surfactants, acid and bases, and enzymes were included in the chemical and enzymatic treatment to remove cells [5–7]. Proteins from nondecellularized and decellularized scaffolds were digested with trypsin and the resulting peptide were chromatographically separated on a reverse-phase C18 column analyzed on a Linear Ion Trap mass spectrometer using a Data Dependent Acquisition workflow [4]. Peptide spectral matching was performed by a database search using Sequest HT algorithms in a Proteome Discoverer 2.2 (Thermo Fisher Scientific). Raw spectrum data were searched against the UniProtKB/Swiss-Prot protein database for Sus scrofa (May 25, 2019). Dataset includes raw data files and peak list files (Table 1) [8].
Table 1.
Overview of data files/data sets
| Label | Name of data file/data set | File types (file extension) |
Data repository and identifier (DOI or accession number) |
|---|---|---|---|
| Data file 1 | DecellularizedRawData | Raw data (.raw) | MassIVE (10.25345/C5HQ3S890) [8] |
| Data file 2 | NondecellularizedRawData | Raw data (.raw) | MassIVE (10.25345/C5HQ3S890) [8] |
| Data file 3 | DecellularizedPeaklist | Peak list (.mzML) | MassIVE (10.25345/C5HQ3S890) [8] |
| Data file 4 | NondecellularizedPeaklist | Peak list (.mzML) | MassIVE (10.25345/C5HQ3S890) [8] |
Limitations
Current data is of scaffolds generated from porcine auricular cartilage and may differ from biomaterials generated from decellularization of other tissues.
The data is generated using a linear ion trap mass spectrometer and thus the mass resolution is slightly less compared to other high-resolution platforms like Orbitrap data.
Acknowledgements
Authors acknowledge support from the Biomolecular Research Center RRID:SCR_019174, at Boise State University with funding from the National Science Foundation, Grants #0619793, #0923535, and #2320410; the M. J. Murdock Charitable Trust; Duane and Lori Stueckle, and the Idaho State Board of Education.
Abbreviations
- OA
Osteoarthritis
- LC-MS/MS
Liquid chromatography-tandem mass spectrometry
Author contributions
Conceptualization, R.N.S. and J.T.O.; methodology, R.N.S., X.P.; writing—original draft preparation, R.N.S. and X.P.; writing—review and editing, R.N.S., X.P., and J.T.O.
Funding
This research was supported by Institutional Development Awards (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under Grants #P20GM103408 and #P20GM109095.
Data availability
Proteomic dataset has been deposited in MassIVE repository and is available at: https://doi.org/10.25345/C5HQ3S890.
Declarations
The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare no competing interests.
Footnotes
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
References
- 1.Cross M, Smith E, Hoy D, Nolte S, Ackerman I, Fransen M, et al. The global burden of hip and knee osteoarthritis: estimates from the global burden of Disease 2010 study. Ann Rheum Dis. 2014;73:1323–30. doi: 10.1136/annrheumdis-2013-204763. [DOI] [PubMed] [Google Scholar]
- 2.Escobar Ivirico JL, Bhattacharjee M, Kuyinu E, Nair LS, Laurencin CT. Regenerative Engineering for knee osteoarthritis treatment: Biomaterials and Cell-Based technologies. Engineering. 2017;3:16–27. doi: 10.1016/J.ENG.2017.01.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Tamaddon M, Gilja H, Wang L, Oliveira JM, Sun X, Tan R, et al. Osteochondral Scaffold Early OA Treat. 2020;1:3–17. doi: 10.3877/cma.j.issn.2096-112X.2020.01.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Stone RN, Frahs SM, Hardy MJ, Fujimoto A, Pu X, Keller-Peck C, et al. Decellularized Porcine Cartilage Scaffold; validation of decellularization and evaluation of biomarkers of Chondrogenesis. Int J Mol Sci. 2021;22:6241. doi: 10.3390/ijms22126241. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Kim YS, Majid M, Melchiorri AJ, Mikos AG. Applications of decellularized extracellular matrix in bone and cartilage tissue engineering. Bioeng Transl Med. 2019;4:83–95. doi: 10.1002/btm2.10110. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Heath DE. A review of Decellularized Extracellular Matrix Biomaterials for Regenerative Engineering Applications. Regen Eng Transl Med. 2019;5:155–66. doi: 10.1007/s40883-018-0080-0. [DOI] [Google Scholar]
- 7.Gilpin A, Yang Y. Decellularization strategies for Regenerative Medicine: from Processing techniques to applications. Biomed Res Int. 2017;2017:1–13. doi: 10.1155/2017/9831534. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Oxford JT. Proteomic evaluation of decellularization of porcine auricular cartilage. MassIVE. 2023 doi: 10.25345/C5HQ3S890. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Proteomic dataset has been deposited in MassIVE repository and is available at: https://doi.org/10.25345/C5HQ3S890.