Sphingolipids control dermal fibroblast heterogeneity

Abstract

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual cells of the same type. However, we are only starting to characterize the function of these cell-to-cell differences in lipid composition. Here, we measured the lipidomes and transcriptomes of individual human dermal fibroblasts by coupling high-resolution mass spectrometry imaging with single-cell transcriptomics. We found that the cell-to-cell variations of specific lipid metabolic pathways contribute to the establishment of cell states involved in the organization of skin architecture. Sphingolipid composition is shown to define fibroblast subpopulations, with sphingolipid metabolic rewiring driving cell-state transitions. Therefore, cell-to-cell lipid heterogeneity affects the determination of cell states, adding a new regulatory component to the self-organization of multicellular systems.

Greasing the skin

In multicellular organisms, cells are parts of communities in which an individual contributes to the collective phenotype of the community. Appreciating the “social” organization of these cell communities is instrumental to dissecting their physiology and the pathological consequences of their abnormalities. Capolupo et al . investigated the lipid metabolism and gene expression of individual human skin cells and found that specific lipid compositions drive cell specialization. Specifically, the authors found that sphingolipids determine the transcriptional programs of fibroblasts populating in different layers of the human skin. These results reveal an unexpected role for membrane lipids in the establishment of cell identity and tissue architecture. —LZ

Abstract

Single-cell lipidomics and transcriptomics define sphingolipid compositions important for human skin fibroblast subsets.

Abstract

INTRODUCTION

External signals (e.g., hormones, cytokines, and growth factors) and cell-autonomous properties (e.g., the transcriptional and metabolic states of individual cells) concur to determine cell-fate decisions. Although the mode of action of external signals has been detailed extensively in decades of intense research, the molecular bases of cell-autonomous contribution to cell-fate decisions have been traditionally more elusive. Lipids are fundamental constituents of all living beings. They participate in energy metabolism, account for the assembly of biological membranes, act as signaling molecules, and interact with proteins to influence their function and intracellular distribution. Eukaryotic cells produce thousands of different lipids, each endowed with peculiar structural features and contributing to specific biological functions. With the development of lipidomics, we can now understand the lipid compositional complexity of cells and start making sense of lipidome dynamics. Lipidomes indeed vary among cell types and are reprogrammed in differentiation events. However, whether and how lipidome remodeling assists changes in cell identity is not understood.

RATIONALE

Human dermal fibroblasts are cell constituents of our skin that display cell-to-cell phenotypic heterogeneity as a result of their dynamic cell identity. Thus, individual dermal fibroblasts can adopt different cell specializations that are responsible for wound repair, fibrosis, or remodeling of the extracellular matrix. Whether lipid metabolism is differently shaped in fibroblasts with different phenotypes and if lipid composition participates in the establishment of fibroblast subtypes were unknown. Here, we addressed both the overall lipid composition and phenotypic states of hundreds of individual dermal fibroblasts looking for a possible role of lipids in the determination of dermal fibroblast identity.

RESULTS

We coupled high-resolution mass spectrometry imaging and single-cell mRNA sequencing to resolve both lipidomes and transcriptomes of individual dermal fibroblasts. We found that dermal fibroblasts exist in multiple lipid compositional states that correspond to transcriptional subpopulations in vitro and to fibroblasts populating different layers of the skin in vivo. We isolated the metabolic pathways that account for this correlation and found that sphingolipids are major markers of the different lipid compositional states that we named lipotypes. We also found that lipotype heterogeneity influences cell identity by diversifying the response of otherwise identical cells to extracellular stimuli and that manipulating sphingolipid composition is sufficient to reprogram cells toward different phenotypic states. We also found that lipid composition and signaling pathways are wired in self-sustained circuits that account for the metabolic and transcriptional fibroblast heterogeneity. Specifically, we observed that sphingolipids modulate fibroblast growth factor 2 (FGF2) signaling, with globo-series sphingolipids acting as positive regulators and ganglio-series glycosphingolipids as negative regulators. In turn, FGF2 signaling counteracts ganglioside production by sustaining the alternative metabolic pathway leading to the production of globo-series sphingolipids.

CONCLUSION

By studying the lipid composition of individual cells, we found that lipids play a driving role in the determination of cell states. We indeed uncovered an unexpected relationship between lipidomes and transcriptomes in individual cells. In fact, our results indicate that the acquisition of specific lipotypes influenced the activity of signaling receptors and fostered alternative transcriptional states. Cell states are intermediates in the process of cell differentiation in which state switches precede terminal commitment. As a consequence, lipidome remodeling could work as an early driver in the establishment of cell identity, and following lipid metabolic trajectories of individual cells could have the potential to inform us about key mechanisms of cell fate decision. Thus, this study stimulates new questions about the role of lipids in cell-fate decisions and adds a new regulatory component to the self-organization of multicellular systems.