Biology subjects

Pennington, T. R.

Publications and source records attributed to Pennington, T. R..

3 recordsLinked to original sources

bioRxiv2026

The Microglia Forebrain Assembloid Model Recapitulates Human Brain Development and Neuroimmune Biology.

Microglia are innate immune cells of the CNS whose dysfunction contributes to inflammation and metabolic changes across neurodegenerative and CNS disorders. Across all stages of life, microglia are essential for immune surveillance, neural homeostasis, and synaptic pruning; however, their role in neurodevelopment is less understood. Microglia invade the brain during early neurogenesis, prior to neuronal/glial differentiation, but their potential role at this stage remains undescribed. To model neuroimmune interactions during human cortical development, we created an "assembloid" of human ESC-derived forebrain organoids combined with developmentally matched microglia during cortex formation. Functional contributions of microglia were compared to control organoids using histology and metabolomics.

neuroscience↗

bioRxiv2025

Glucose and Oxygen Metabolism Coordinate Human Cortical Developmental Decisions

Defining metabolic regulation of neurodevelopmental programs is essential to approach developmental disorders and injuries driven by alterations in metabolism. In vitro cultures are the only available method to temporally perturb and study living human brain cells throughout neurogenesis, however most culture systems use supraphysiologic conditions of essential nutrients, glucose and oxygen. We probed how environmental exposure to endogenous-like concentrations impact metabolic state and developmental progression of cortical cell types using organoids. Nutrient accessibility globally impacted metabolic state, yet developmental responses to metabolic changes were cell type-specific. Metabolomic and transcriptomic datasets reveal increased TCA metabolites and amino acids and oxidative phosphorylation (OXPHOS) genes, under physiologic glucose conditions. Oxygen level had a modest, yet specific, molecular impact on deep layer excitatory neurons. We assessed consequences of metabolic changes on fate and observed that physiologic glucose expanded the human-enriched population of cortical stem cells, outer radial glia, and their progeny, upper layer excitatory neurons. Alterations in oxygen, instead, affected production of neurogenic progenitors and neuronal differentiation, with higher oxygen availability supporting shifts toward mitochondrial metabolism necessary for maturing cell types. We functionally tested this transition by inhibiting glycolysis; total inhibition promoted neuronal differentiation, whereas inhibition of anaerobic glycolysis/lactate production led to oRG expansion. Lactate signaling was sufficient to suppress oRG development and promote self-renewal of neurogenic progenitors. These data suggest that refined metabolic switches and decreased reliance on glucose are required for transition from stem cell self-renewal to more mature, diversified progenitor subtypes, where switch from anaerobic to aerobic metabolism discretely impacts progenitor diversification.

neuroscience↗

bioRxiv2023

An engineered culture vessel and flow system to improve the in vitro analysis of volatile organic compounds

Volatile organic compounds (VOCs) are a biologically important subset of an organisms metabolome, yet in vitro techniques for the analysis of these small molecules vary substantially in practice, restricting the interpretation and reproducibility of study findings. Here, we present an engineered culture tool, termed the "Biodome", designed to enhance analyte sensitivity by integrating dynamic headspace sampling methodology for the recovery of VOCs from viable biological cultures. We validate the functionality of the device for in vitro volatile metabolomics utilizing computational modeling and fluorescent imaging of mammalian cell culture. We then leverage comprehensive two-dimensional gas chromatography coupled with a time-of-flight mass spectrometer and the enhanced sampling capabilities afforded by our tool to identify seven VOCs not found in the media or exogenously derived from the sampling method (typical pitfalls with in vitro volatilome analysis). We further work to validate the endogenous production of these VOCs using two independent approaches: (i) glycolysis-mediated stable isotopic labeling techniques using 13C6-D-glucose and (ii) RNA interference (RNAi) to selectively knockdown {beta}-oxidation via silencing of CPT2. Isotope labeling reveals 2-Decen-1-ol as endogenously derived with glucose as a carbon source and, through RNAi, we find evidence supporting endogenous production of 2-ethyl-1-hexene, dodecyl acrylate, tridecanoic acid methyl ester and a low abundance alkene (C17) with molecular backbones likely derived from fatty acid degradation. To demonstrate applicability beyond mammalian cell culture, we assess the production of VOCs throughout the log and stationary phases of growth in ampicillin-resistant DH5 Escherichia coli. We identified nine compounds with results supporting endogenous production, six of which were not previously associated with E. coli. Our findings emphasize the improved capabilities of the Biodome for in vitro volatile metabolomics and provide a platform for the standardization of methodology.

bioengineering↗