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Quantitative proteomics analysis of different sources of hMSCs

ABSTRACT: Mesenchymal stem cells (MSCs) are an attractive therapeutic tool for tissue engineering and re-generative medicine due to their regenerative and trophic properties. The best-known and most widely used are bone marrow MSCs, but they are now being harvested and developed from a wide range of adult and perinatal tissues. MSCs from different sources are believed to have dif-ferent secretion potentials and production, which may influence their therapeutic effects. To prove it, we performed a quantitative proteomic analysis based on the TMT technique of MSCs from 3 different sources: wharton’s jelly (WJ), dental pulp (DP) and bone marrow (BM). Our analysis has focused on MSC biological properties of interest for tissue engineering. We identified a total of 611 human proteins differentially expressed. WJ-MSCs shown the greatest variation compared to the other sources. WJ produced more extra-cellular matrix (ECM) proteins and ECM-affiliated proteins and appeared to more able to modulate the inflammatory and immune response. BM-MSCs display enhanced differentiation and paracrine communication capabilities. DP-MSC appeared to promote exosome production. The results obtained confirm the existence of differences between WJ, DP and BM-MSC and the need to select the MSC origin according to the therapeutic objective sought.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Paulo MARCELO

LAB HEAD: Paulo MARCELO

PROVIDER: PXD043912 | Pride | 2023-09-20

REPOSITORIES: Pride

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Project description:Purpose: Most studies conducted towards understanding the differences among the adult sources of MSCs (BM-MSC and AD-MSC) and UC-MSCs have focused on their phenotypic properties which cannot provide an idea of the functional characteristics changing at the molecular level. Even NGS studies done before, each each study focuses on a different profiling methodology, which makes it difficult to establish a molecular equivalency among the various datasets. We undertake an integrative omics comparison between UC-MSC and two other popular sources of adult MSC (BM-MSC and AD-MSC), with the reasoning that a joint modeling of the changes occurring at the various functional levels will provide greater in-depth insight into the molecular heterogeneity related to different sources of MSCs. Methods: human Mesenchymal Stem Cell (MSC) mRNA cultured under basal conditions in Xeno-free media were subjected to deep sequencing. Three different MSC sourcers : adipose (AD-MSC), bone-marrow (BM-MSC) and Wharton-jelly umbilical cord (UC-MSC) were used and three donors from each tissues source along with three biological replicates for each donor were sequenced using the Illumina PE 150 platform. The sequence reads that passed quality filters Q30≥ 80% were analyzed using DESeq2. Results: Using an optimized data analysis workflow, we identified 24,804 transcripts among the three different sources of MSCs. Among these 2127 transcripts (~10%) were found to be differentially expressed among the three sources of MSC, with a\Log2FC| ≥2 and FDR <0.05. Hierarchical clustering of differentially expressed genes uncovered significant differences among the neonatal source (UC-MSC) and adult-MSCs (AD-MSC and BM-MSC). Altered gene expression profiles among the sources was also confirmed using a proteomics study of the same three sources of MSC with the same donors. Further, secretory immune-regulatory molecules which were confirmed to be differentially expressed among the MSC sources using the integrated transcriptomics-proteomics approach was validated using a Luminex cytokine profiling study. Conclusions: Our study represents the first detailed integrated analysis of differential gene expression profiling among source-specific human Mesenchymal Stem Cells using a multi-omics approach to validate the observed transcriptomic changes at both the translational as well as secretory levels. Our results offer a comhrehensive evaluation of the differences in immune signaling that exists among the different sourcrs of MSC based on their tissue of origina nd which subsequently plays a decisive role in determining the "regenrative siganture" of these MSCs based on the match between "immune-signature" and "disease type".

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Quantitative proteomics analysis of different sources of hMSCs

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