Human Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells Acquire Rejuvenation and Reduced Heterogeneity

Abstract

Despite the uniform selection criteria for the isolation of human mesenchymal stem cells (MSCs), considerable heterogeneity exists which reflects the distinct tissue origins and differences between individuals with respect to their genetic background and age. This heterogeneity is manifested by the variabilities seen in the transcriptomes, proteomes, secretomes, and epigenomes of tissue-specific MSCs. Here, we review literature on different aspects of MSC heterogeneity including the role of epigenetics and the impact of MSC heterogeneity on therapies. We then combine this with a meta-analysis of transcriptome data from distinct MSC subpopulations derived from bone marrow, adipose tissue, cruciate, tonsil, kidney, umbilical cord, fetus, and induced pluripotent stem cells derived MSCs (iMSCs). Beyond that, we investigate transcriptome differences between tissue-specific MSCs and pluripotent stem cells. Our meta-analysis of numerous MSC-related data sets revealed markers and associated biological processes characterizing the heterogeneity and the common features of MSCs from various tissues. We found that this heterogeneity is mainly related to the origin of the MSCs and infer that microenvironment and epigenetics are key drivers. The epigenomes of MSCs alter with age and this has a profound impact on their differentiation capabilities. Epigenetic modifications of MSCs are propagated during cell divisions and manifest in differentiated cells, thus contributing to diseased or healthy phenotypes of the respective tissue. An approach used to reduce heterogeneity caused by age- and tissue-related epigenetic and microenvironmental patterns is the iMSC concept: iMSCs are MSCs generated from induced pluripotent stem cells (iPSCs). During iMSC generation epigenetic and chromatin remodeling result in a gene expression pattern associated with rejuvenation thus allowing to overcome age-related shortcomings (e.g., limited differentiation and proliferation capacity). The importance of the iMSC concept is underlined by multiple clinical trials. In conclusion, we propose the use of rejuvenated iMSCs to bypass tissue- and age-related heterogeneity which are associated with native MSCs.

Keywords: MSC; epigenetics; heterogeneity; iMSC; iPSC; rejuvenation.

FIGURE 1

“Young” MSCs cluster separated from adult MSCs and PSCs. Pluripotent stem cells (PSCs, red color bar) of embryonic or reprogrammed (iPSCs) origin cluster separated from MSCs. Within the MSCs one cluster contains all samples related to “young” origin: fetal MSCs, umbilical cord (UC) MSCs and iMSCs (derived from iPSCs), marked with a yellow color bar. Adult MSCs (blue color bar) of various origins are spread over the remaining clusters.

FIGURE 2

MSCs of distinct origin share a large common gene signature but differ in smaller specific gene signatures. (A) The Venn diagram comparing gene expression in five MSC datasets on the Illumina Human HT-12 platform shows that most (9966) genes are expressed (detection-p-value < 0.05) in common. Specific to distinct types are subsets containing smaller numbers of genes: fetal MSCs-401, iMSCs-374, adipose-tissue-MSCs-29, bone-marrow-MSCs-130, and UC-MSCs-558. Over-representation analysis of Gene ontologies (GOs) in the specific subsets revealed GO terms of which the 20 most significant are listed here. (B) Significant GO terms in fetal MSCs relate to developmental and morphogenetic processes. (C) Significant GO terms in UC-MSCs relate to defense/inflammatory response, lung development, gastrulation. (D) Significant GO terms in iMSCs relate to hormone metabolism, neuronal development, interferon, and TNF signaling.

FIGURE 3

Heterogeneity in adipose-tissue and bone-marrow-derived MSCs reflects tissue of origin. Subsets of genes exclusively expressed in adipose tissue-derived MSCs (29 genes in Figure 2A) and bone-marrow-derived MSCs (130 genes in A) were analyzed for over-representation of GO terms. (A) Most significantly over-represented GO terms in adipose tissue-derived MSCs include vascular, muscle and neuronal development which may be considered characteristic for adipose tissue. (B) Most significantly over-represented GO terms in bone-marrow-derived MSCs include skeletal system and limb development pointing at osteogenic properties.

FIGURE 4

Tissue of origin determines heterogeneity of amniotic-fluid-derived MSCs (AF-MSCs), urine-derived renal progenitor cells (UdRPCs), and hepatic stellate cells (HSCs). (A) Genes expressed in common in MSCs on the Illumina platform (9966 genes) were compared with AF-MSCs, UdRPCs, and HSCs. Subsets of genes exclusively expressed in AF-MSCs (301 genes in A),UdRPCs (476), and HSCs (2280) were analyzed for over-representation of GO terms. (B) Most significantly over-represented GO terms in AF-MSCs include developmental and signaling processes which may be considered characteristic for embryonic development. (C) Most significantly over-represented GO terms in UdRPCs include lipid transport and detoxification pointing at renal properties. (D) Most significantly over-represented GO terms in HSCs include metabolic, cristae and mitochondrial processes pointing characterizing liver.

FIGURE 5

Characteristics of iMSCs overlap with those of MSCs from young origin. Overlapping over-represented GO terms between iMSCs, fetal MSCs, and UC-MSCs were identified. The overlap is connected to developmental processes (A–C).

FIGURE 6

Cluster analysis displays agglomeration of young (iMSCs, fetal, and UC-MSCs) MSCs in epigenetics-related gene signatures. (A) Heatmap using the aged-rejuvenation gene signature from our previous publication (Spitzhorn et al., 2017) yields coherent clusters of PSCs and iMSCs with fetal and UC-MSCs. (B) Also the heatmap using the epigenetics-related gene signature from the publication by Avgustinova and Benitah (2016) yields coherent clusters of PSCs and iMSCs with fetal and UC-MSCs, however, a bit more fragmented than in (A).

FIGURE 7

Generation of rejuvenated and more homogenous iMSCs via reprogramming of MSCs or terminally differentiated cells to iPSCs. Distinct MSC subpopulations such as bone marrow MSCs and adipose tissue MSCs have high levels of heterogeneity due to their microenvironments and epigenetic programs. This gets more similar as well as rejuvenated in iMSCs. MSCs as well as iMSCs home into sites of injury and exert beneficial effects which are predominantly due to paracrine signaling and are even superior for the iMSCs as several studies demonstrated.