Proteome Analyses and Single-Cell RNA Sequencing Reveal Age-Dependent Re-Wiring of Central Carbon Metabolism in Myeloid-Biased Subsets of Human Hematopoietic Stem Cells

Background: Diminishing potential to replace damaged tissues is a hallmark for aging of somatic stem cells, but the mechanisms leading to aging remain elusive. Applying comprehensive proteomics studies on human hematopoietic stem and progenitor cells (HPCs) as well as 5 other cell populations that constitute the bone marrow niche, we have acquired a systems understanding of the mechanisms involved in aging of HPCs.

Methods and materials: We present a proteome-wide atlas of age-associated alterations in HPCs along with 5 other cell populations including mesenchymal stromal cells (MSC) that comprise the bone marrow niche. For each, the abundance of a large fraction of the ~12,000 proteins identified was assessed in a cohort of 59 human subjects from different age groups. In selected samples, transcriptomics, metabolomics, and single cell RNA-Sequencing studies were simultaneously performed.

Results:As the HPCs become older, one of the most prominent changes is the increase in abundance of proteins involved in the pathways for central carbon metabolism. This change is found only in HPCs and is reminiscent of the Warburg effect where glycolytic intermediates are rerouted towards pentose phosphate shunt and anabolism. Transcriptomic data confirm the increase in abundance of mRNA for the respective glycolytic enzymes in older HPCs. Metabolomics analyses provide further proofs demonstrating the trend towards anabolism upon aging. Altered abundance of early regulators of HPC differentiation reveals a reduced functionality and a bias towards myeloid differentiation at the expense of lymphoid development. Simultaneously, significant and complementary alterations in the bone marrow niche are observed. Whereas key factors responsible for homing, egress and adhesion of HPCs, e.g. SDF1/CXCL12, VCAM1, FN1, integrins α4, αL, β1 andβ2 decrease in abundance in MSCs, soluble factors responsible for myeloid differentiation, e.g.TGF-beta1, increase in abundance in the cellular niche with age. Transcriptomic analyses of single-sorted HPCs have demonstrated unequivocally that the mRNA levels of age-dependent increase in glycolytic enzymes are expressed at significantly higher levels in myeloid-biased versus than those in lymphoid-biased HPCs, whereas age-unaffected enzymes have similar mRNA levels in both subsets. The increase in abundance of glycolytic enzymes is hence linked with skewing of myeloid-biased HPCs in older human subjects.

Conclusion: We have generated a comprehensive atlas of alterations in proteome landscapes of human HPCs and niche cells in bone marrow upon aging. In addition to findings that recapitulate the results derived from murine studies, the major novelties are (a) the alterations in central carbon metabolism in aging human HPCs, (b) the complementary decrease in levels of adhesive molecules and respective ligands in MSCs and HPCs. Single-cell studies have demonstrated that the age-related increase in abundance of the glycolytic enzymes is linked to the myeloid-biased HPCs. These data represent a valuable resource and serve as a basis for development of strategies targeting metabolic changes to enhance HPC regeneration.