Genome-Wide Methylation Changes Associated with Replicative Senescence and Differentiation in Endothelial and Bone Marrow Mesenchymal Stromal Cells

Angelica Giuliani; Maria Giulia Bacalini; Deborah Ramini; Emanuela Mensà; Chiara Giordani; Luciano Xumerle; Paolo Garagnani; Fabiola Olivieri; Antonio Domenico Procopio; Maria Rita Rippo; Jacopo Sabbatinelli

doi:10.3390/cells12020285

Genome-Wide Methylation Changes Associated with Replicative Senescence and Differentiation in Endothelial and Bone Marrow Mesenchymal Stromal Cells

Cells. 2023 Jan 11;12(2):285. doi: 10.3390/cells12020285.

Authors

Angelica Giuliani¹, Maria Giulia Bacalini², Deborah Ramini³, Emanuela Mensà¹, Chiara Giordani¹, Luciano Xumerle⁴, Paolo Garagnani^{5

6

7

8}, Fabiola Olivieri^{1

3}, Antonio Domenico Procopio^{1

3}, Maria Rita Rippo¹, Jacopo Sabbatinelli^{1

9}

Affiliations

¹ Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, 60126 Ancona, Italy.
² IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy.
³ Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy.
⁴ Personal Genomic S.R.L, 37134 Verona, Italy.
⁵ Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy.
⁶ Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40126 Bologna, Italy.
⁷ CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza"-Unit of Bologna, 40126 Bologna, Italy.
⁸ Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 141 86 Huddinge, Sweden.
⁹ Laboratory Medicine Unit, Azienda Ospedaliero Universitaria delle Marche, 60126 Ancona, Italy.

Abstract

Bone marrow mesenchymal stromal cells (BMSCs) are multipotent cells able to self-renew and differentiate, depending on the microenvironment, into adipocytes and osteoblasts. These cells have a limited number of replications and enter replicative senescence during in vitro expansion. The role of DNA methylation (DNAm) assumes importance in cell function and commitment; however, its exact contribution to BMSC differentiation and replicative senescence is still unclear. We performed a genome-wide DNAm analysis on BMSCs cultured in vitro at early passages and induced to differentiate into adipocytes and osteoblasts, and on replicative senescent BMSCs and HUVECs, to identify DNAm patterns of senescence and differentiation. We also compared BMSCs and HUVECs in replicative senescence and found that, in both cellular systems, genome-wide hypomethylation was accompanied by a higher-than-expected overlap of differentially methylated positions (DMPs) and concordance in terms of direction of the change. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on lineage-independent senescence-associated DMPs revealed 16 common pathways, including Insulin resistance, Molecule adhesion, and Wnt/β-catenin signaling. In both adipogenesis and osteogenesis, we observed a general demethylation of CpG sites compared with undifferentiated BMSCs with a higher number of DMPs in osteogenesis. KEGG analysis resulted in 30 pathways enriched in osteoblasts and only 2 in adipocytes when compared to undifferentiated cells. When comparing differentiated BMSCs with senescent ones, osteogenesis exhibited a greater overlap with senescence in terms of number of DMPs and direction of methylation change compared to adipogenesis. In conclusion, this study may be useful for future research on general mechanisms that occur in replicative senescence and furthermore to identify trajectories of BMSC differentiation and common aspects of differentiated and senescent cells.

Keywords: DNA methylation; adipocytes; bone-marrow mesenchymal stromal cells; cellular senescence; endothelial cells; osteoblasts.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bone Marrow*
Cell Differentiation / genetics
Cellular Senescence / genetics
DNA Methylation / genetics
Mesenchymal Stem Cells* / metabolism

Grants and funding

This research was funded by Università Politecnica delle Marche, Italy, RSA Grant to MRR and Ministero della Salute, Italy, Ricerca Corrente to IRCCS INRCA to FO.