Single‐Cell and Spatial Transcriptomics Decodes Wharton's Jelly‐Derived Mesenchymal Stem Cells Heterogeneity and a Subpopulation with Wound Repair Signatures

Abstract

The highly heterogeneous characteristics of Wharton's jelly mesenchymal stem cells (WJ-MSCs) may be responsible for the poor clinical outcomes and poor reproducibility of treatments based on WJ-MSCs. Exploration of WJ-MSC heterogeneity with multimodal single-cell technologies will aid in establishing accurate MSC subtyping and developing screening protocols for dominant functional subpopulations. Here, the characteristics of WJ-MSCs are systematically analyzed by single cell and spatial transcriptome sequencing. Single-cell transcriptomics analysis identifies four WJ-MSC subpopulations, namely proliferative_MSCs, niche-supporting_MSCs, metabolism-related_MSCs and biofunctional-type_MSCs. Furthermore, the transcriptome, cellular heterogeneity, and cell-state trajectories of these subpopulations are characterized. Intriguingly, the biofunctional-type MSCs (marked by S100A9, CD29, and CD142) selected in this study exhibit promising wound repair properties in vitro and in vivo. Finally, by integrating omics data, it has been found that the S100A9 + CD29 + CD142 + subpopulation is more enriched in the fetal segment of the umbilical cord, suggesting that this subpopulation deriving from the fetal segment may have potential for developing into an ideal therapeutic agent for wound healing. Overall, the presented study comprehensively maps the heterogeneity of WJ-MSCs and provides an essential resource for future development of WJ-MSC-based drugs.

Unveiling heterogeneity in MSCs: exploring marker-based strategies for defining MSC subpopulations

“…This integrated approach harnesses the biological knowledge of the candidate biomarker strategy while utilizing the technical capabilities of the high-throughput strategy to discover biomarkers associated with distinct functional subgroups in a more comprehensive and precise manner [16,[21][22][23][24]. In the realm of MSCs, with the use of prior knowledge and high-throughput technologies such as single-cell RNA sequencing (scRNA-seq), specific markers related to different functional subsets of mesenchymal stem cells can be more comprehensively and accurately mined [17][18][19][20][21][22][23][24]. Therefore, in the current review, we would discuss the MSC markers that have been identified so far.…”

“…Among these high-throughput technologies, single-cell RNA sequencing technology (scRNA-seq) is a significant innovation in the field of MSCs that has sparked widespread interest in recent years [17][18][19][20][21][22][23][24]. By deciphering the gene expression of each individual cell within a cell population, this technique reveals the astonishing complexity of cellular diversity and heterogeneity, bringing about a revolutionary breakthrough in cellular biology research [292,293].…”

“…The exploration of the majority of these markers (S100A9, F3, LRRC75A, SERPINF1, CMKLR1, GL1) in the context of scRNA-seq applications has primarily relied on the 10 × Genomics Chromium system [17][18][19][22][23][24], while the CD168 identification was conducted with the C1 platform [20] and the interaction between Lgr5 + and Lgr6 + MSCs were carried out by using the SMART-seq2 technology [21]. The reliability of these three platforms for developing novel MSC markers has been successfully validated.…”

“…Through these techniques, it becomes feasible to detect thousands of molecules, facilitating the comparison of differences between heterogenous cell populations. Notably, this approach allows for the identification of biomarkers associated with specific functions without being reliant on prior knowledge [16][17][18][19][20]…”

Proposal of a new genomic framework for categorization of pediatric acute myeloid leukemia associated with prognosis

“…These heterogeneities were occasionally associated with molecular categories or somatic mutations but were not exclusive (Fig. S7G-H), with possible factors, including cell-extrinsic factors 65,80 to be further investigated.…”