Genomics Analysis of Metabolic Pathways of Human Stem Cell-Derived Microglia-Like Cells and the Integrated Cortical Spheroids

Abstract

Brain spheroids or organoids derived from human pluripotent stem cells (hiPSCs) are still not capable of completely recapitulating in vivo human brain tissue, and one of the limitations is lack of microglia. To add built-in immune function, coculture of the dorsal forebrain spheroids with isogenic microglia-like cells (D-MG) was performed in our study. The three-dimensional D-MG spheroids were analyzed for their transcriptome and compared with isogenic microglia-like cells (MG). Cortical spheroids containing microglia-like cells displayed different metabolic programming, which may affect the associated phenotype. The expression of genes related to glycolysis and hypoxia signaling was increased in cocultured D-MG spheroids, indicating the metabolic shift to aerobic glycolysis, which is in favor of M1 polarization of microglia-like cells. In addition, the metabolic pathways and the signaling pathways involved in cell proliferation, cell death, PIK3/AKT/mTOR signaling, eukaryotic initiation factor 2 pathway, and Wnt and Notch pathways were analyzed. The results demonstrate the activation of mTOR and p53 signaling, increased expression of Notch ligands, and the repression of NF-κB and canonical Wnt pathways, as well as the lower expression of cell cycle genes in the cocultured D-MG spheroids. This analysis indicates that physiological 3-D microenvironment may reshape the immunity of in vitro cortical spheroids and better recapitulate in vivo brain tissue function for disease modeling and drug screening.

Aggregation‐induced integrated stress response rejuvenates culture‐expanded human mesenchymal stem cells

“…The downstream target genes ATF4, DDIT3, and PPP1R15A were elevated following 3D aggregation for the three cell types. Similar to our previous study (Bejoy et al, 2019), the ATF-4 and GADD34 upregulation occurs at the messenger RNA level. The rest genes did not show significant differences between 2D and 3D conditions.…”

Magnetic nanoparticle loaded human adipose derived mesenchymal cells spheroids in levitated culture

“…Metabolic reprograming in 3D aggregates has been commonly attributed to limitation of oxygen diffusion. Another mechanism involving actin‐mediated cellular re‐shaping was found to activate PI3K/Akt pathway and to induce metabolic shift toward glycolysis 32,33 . In our study, cells originating from monolayer were pelleted inducing a “forced” 3D like situation.…”

Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective

“…Although genomics [141][142][143][144][145][146][147][148] and proteomics [149,150] approaches have been widely applied to studying spheroids and organoids, there have been comparatively few studies of metabolism in these models [35,108,124,[151][152][153][154][155][156][157][158][159][160][161][162][163][164] and very few stable isotope tracers-based studies [35,121,124,162]. From the perspective of SIRM, not all 3D matrices are equal.…”