Biology subjects

Park, J. O.

Publications and source records attributed to Park, J. O..

10 recordsLinked to original sources

bioRxiv2026

Deformability screening identifies NUDT5 as a mediator of cellular mechanobiology

How cells deform, sense, and respond to mechanical cues drives physiological and disease processes ranging from development to cancer metastasis; however, unbiased approaches to identify mechanical mediators are lacking. We screened 1280 compounds to identify modulators of cancer cell deformability using a cellular filtration assay and identified 92 compounds that significantly reduced deformability of ovarian cancer cells; top hits also reduced migration and invasion. Connectivity mapping of the top 21 compounds identified NUDT5 (Nudix hydrolase 5) as a predicted mechanical mediator; transcriptomic analyses implicated NUDT5 in mechanobiology and metabolic processes. We confirmed that NUDT5 mediates intracellular ATP and cellular mechanical behaviors, including morphology and deformability. In ovarian cancer, increased NUDT5 levels were associated with higher tumor stage and worse patient survival; NUDT5 inhibition reduced migration and colony formation in vitro and peritoneal tumor burden in mice. These findings establish deformability-based screening as a platform for discovering mechanical mediators and identify NUDT5 as a therapeutic target in ovarian cancer. TeaserScreening cells based on deformability provides an unbiased approach to identify NUDT5 as a mediator of cell mechanics

cell biology↗

bioRxiv2025

Ensemble quantitation of absolute metabolite concentrations in T cells reveals conserved features of immunometabolism

T cell diversity and differentiation define individual adaptive immunity. Metabolism fuels adaptive immunity by driving proliferation, differentiation, and activation; however, how individual and lineage differences shape T cell metabolism remains unknown. Here we develop an ensemble method for absolute metabolome quantitation and quantify 84 metabolites in human primary T cells. Liquid chromatography-mass spectrometry of metabolites co-extracted from T cells and 13C-labeled reference cells reveals absolute concentrations en masse. Across subtypes and individuals, T cell metabolomes resemble one another. T cells possess thermodynamically forward-driven glycolysis, high adenylate energy charge, large amino acid pools, and favorable redox ratios for anabolism and antioxidant defense. Across metabolism, metabolite concentrations exceed their associated Michaelis constants and inhibitor constants two thirds and half of the time, respectively. The conserved features of T cell metabolomes underlie a design principle: metabolite levels prime T cells for increased energy demand, oxidative stress, and rapid regulation that accompany immune response.

biochemistry↗

bioRxiv2024

Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis

A long-standing observation is that in fast-growing cells, respiration rate declines with increasing growth rate and is compensated by an increase in fermentation, despite respiration being more efficient than fermentation. This apparent preference for fermentation even in the presence of oxygen is known as aerobic glycolysis, and occurs in bacteria, yeast, and cancer cells. Considerable work has focused on understanding the potential benefits that might justify this seemingly wasteful metabolic strategy, but its mechanistic basis remains unclear. Here we show that aerobic glycolysis results from the saturation of mitochondrial respiration and the decoupling of mitochondrial biogenesis from the production of other cellular components. Respiration rate is insensitive to acute perturbations of cellular energetic demands or nutrient supplies, and is explained simply by the amount of mitochondria per cell. Mitochondria accumulate at a nearly constant rate across different growth conditions, resulting in mitochondrial amount being largely determined by cell division time. In contrast, glucose uptake rate is not saturated, and is accurately predicted by the abundances and affinities of glucose transporters. Combining these models of glucose uptake and respiration provides a quantitative, mechanistic explanation for aerobic glycolysis. The robustness of specific respiration rate and mitochondrial biogenesis, paired with the flexibility of other bioenergetic and biosynthetic fluxes, may play a broad role in shaping eukaryotic cell metabolism.

systems biology↗

bioRxiv2023

Determination of Metabolic Fluxes by Deep Learning of Isotope Labeling Patterns

All life forms operate metabolism in constant flux. Metabolic fluxes offer a direct readout of cellular state, detailing the rates and driving forces of metabolic pathways. However, indirect, iterative solvers for mapping isotope patterns from tracing experiments onto metabolic fluxes leave much of cellular state uncharted. Here, we streamline metabolic flux quantitation by innovating a machine learning framework, ML-Flux, that deciphers complex isotope labeling patterns. We train neural networks using isotope pattern-flux pairs across central carbon metabolism from 26 key 13C-glucose, 2H-glucose, and 13C-glutamine tracers. ML-Flux takes variable-size isotope labeling patterns as input, imputes missing isotope patterns, and outputs mass-balanced metabolic fluxes. Computation of fluxes using ML-Flux is more accurate and faster than that of leading metabolic flux analysis software employing a least-squares method. Our biochemical networks and machine learning models constitute a curated and growing online knowledgebase of metabolic flux and free energy to democratize quantitative metabolic profiling.

systems biology↗

bioRxiv2023

Extracellular Domains of CAR Reprogram T-Cell Metabolism Without Antigen Stimulation

Metabolism is an indispensable part of T-cell proliferation, activation, and exhaustion, yet the metabolism of chimeric antigen receptor (CAR)-T cells remains incompletely understood. CARs are comprised of extracellular domains that determine cancer specificity, often using single-chain variable fragments (scFvs), and intracellular domains that trigger signaling upon antigen binding. Here we show that CARs differing only in the scFv reprogram T-cell metabolism differently. Even in the absence of antigens, some CARs increase proliferation and nutrient uptake in T cells. Using stable isotope tracers and mass spectrometry, we observe basal metabolic fluxes through glycolysis doubling and amino acid uptake overtaking anaplerosis in CAR-T cells harboring rituximab scFv, unlike other similar anti-CD20 scFvs. Disparate rituximab and 14g2a-based anti-GD2 CAR-T cells are similarly hypermetabolic and channel excess nutrients to nitrogen overflow metabolism. Since CAR-dependent metabolic reprogramming alters cellular energetics, nutrient utilization, and proliferation, metabolic profiling should be an integral part of CAR-T cell development.

systems biology↗

bioRxiv2023

Atlas of fetal metabolism during mid-to-late gestation and diabetic pregnancy

Mounting evidence supports an instructive role for metabolism in stem cell fate decisions. However, much is yet unknown about how fetal metabolism changes during mammalian development and how altered maternal metabolism shapes fetal metabolism. Here, we present a descriptive atlas of in vivo fetal murine metabolism during mid-to-late gestation in normal and diabetic pregnancy. Using 13C-glucose and LC-MS, we profiled the metabolism of fetal brains, hearts, livers, and placentas harvested from pregnant dams between embryonic days (E)10.5 and 18.5. Comparative analysis of our large metabolomics dataset revealed metabolic features specific to fetal tissues developed under a hyperglycemic environment as well as metabolic signatures that may denote developmental transitions during euglycemic development. We observed sorbitol accumulation in fetal tissues and altered neurotransmitter levels in fetal brains isolated from dams with maternal hyperglycemia. Tracing 13C-glucose revealed disparate nutrient sourcing in fetuses depending on maternal glycemic states. Regardless of glycemic state, histidine-derived metabolites accumulated during late development in fetal tissues and maternal plasma. Our rich dataset presents a comprehensive overview of in vivo fetal tissue metabolism and alterations occurring as a result of maternal hyperglycemia.

cell biology↗

bioRxiv2022

A parallel glycolysis supports rapid adaptation in dynamic environments

Glycolysis is a universal metabolic process that breaks down glucose to produce cellular energy currency ATP and biomass precursors1. The Entner-Doudoroff pathway is a glycolytic pathway that parallels the textbook glycolysis but yields half as many ATP2. In organisms that possess both glycolytic pathways, such as Escherichia coli, inactivating the less energy-efficient Entner-Doudoroff pathway does not alter growth rates3. The benefit of the Entner-Doudoroff pathway has instead been hypothesized to be metabolic flexibility as an auxiliary enzyme-efficient catabolic route4. However, its raison detre remains incompletely understood. Here we identify the advantage of employing parallel glycolytic pathways under dynamic nutrient environments. Upon carbon and nitrogen upshifts, wild-type cells accelerate growth faster than those with the Entner-Doudoroff pathway knocked out. Using stable isotope tracers and mass spectrometry, we find that the Entner-Doudoroff pathway flux increases disproportionately faster than that of the textbook glycolysis during nutrient upshifts. We attribute the fast response time of the Entner-Doudoroff pathway to its strong thermodynamic driving force and concerted regulation facilitating glucose uptake. Intermittent supply of nutrients manifests this evolutionary advantage of the parallel glycolysis. Thus, the dynamic nature of an ostensibly redundant pathways role in promoting rapid adaptation constitutes a metabolic design principle.

systems biology↗

bioRxiv2020

Rational Tuning of CAR Tonic Signaling Yields Superior T-Cell Therapy for Cancer

Chimeric antigen receptors (CARs) are modular proteins capable of redirecting immune cells toward a wide variety of disease-associated antigens. Here, we explore the effects of CAR protein sequence and structure on CAR-T cell function. Based on the empirical observation that CD20 CARs with similar sequences exhibit divergent tonic-signaling and anti-tumor activities, we devised engineering strategies that aimed to improve CAR-T cell function by tuning the intensity of tonic signaling. We found that CARs designed to exhibit low but non-zero levels of tonic signaling show robust effector function upon antigen stimulation while avoiding premature functional exhaustion by CAR-T cells. Through alterations of the CARs ligand-binding domain and overall protein conformation, we generated CD20 CAR variants that outperform the CD19 CAR in mouse models of human lymphoma. We further demonstrate that rational modification of protein confirmation can be generalized to improve GD2 CAR-T cell efficacy against neuroblastoma. These findings point to tonic signaling and basal T-cell activation as informative parameters to guide the rational design of next-generation CARs for cancer therapy.

bioengineering↗

bioRxiv2018

E. coli translation strategies differ across nutrient conditions

For cells to grow faster they must increase their protein production rate. Microorganisms have traditionally been thought to accomplish this increase by producing more ribosomes to enhance protein synthesis capacity, leading to the linear relationship between ribosome level and growth rate observed under most growth conditions previously examined. Past studies have suggested that this linear relationship represents an optimal resource allocation strategy for each growth rate, independent of any specific nutrient state. Here we investigate protein production strategies in continuous cultures limited for carbon, nitrogen, and phosphate, which differentially impact substrate supply for protein versus nucleic acid metabolism. Unexpectedly, we find that at slow growth rates, E. coli achieves the same protein production rate using three different strategies under the three different nutrient limitations. Upon phosphate (P) limitation, translation is slow due to a particularly low abundance of ribosomes, which are RNA-rich and thus particularly costly for phosphorous-limited cells. In nitrogen (N) limitation, translation is slowed by limited glutamine and stalling at glutamine codons, resulting is slow elongation. In carbon (C) limitation, translation is slowed by accumulation of inactive ribosomes not bound to mRNA. These extra ribosomes enable rapid growth acceleration upon nutrient upshift. Thus, bacteria tune ribosome usage across different limiting nutrients to enable balanced nutrient-limited growth while also preparing for future nutrient upshifts.

microbiology↗

bioRxiv2017

An evolutionary module in central metabolism

Metabolic enzyme function and evolution is influenced by the larger context of a biochemical pathway - deleterious mutations or perturbations in one enzyme can often be compensated by mutations to others. To explore strategies for mapping adaptive dependencies between enzymes, we used a combination of comparative genomics and experiments to examine interactions with the model metabolic enzyme Dihydrofolate Reductase (DHFR). Biochemically, DHFR shares a metabolic intermediate with numerous folate metabolic enzymes. In contrast, comparative genomics analyses of synteny and gene co-occurrence indicate a sparse pattern of evolutionary couplings in which DHFR is coupled to the enzyme thymidylate synthase (TYMS), but is relatively independent from the rest of folate metabolism. To test this apparent modularity, we used quantitative growth rate measurements and forward evolution in E. coli to demonstrate that the two enzymes are coupled to one another, and can adapt independently from the remainder of the genome. Mechanistically, the coupling between DHFR and TYMS is driven by a constraint wherein TYMS activity must not greatly exceed that of DHFR - both to avoid depletion of reduced folates and prevent accumulation of the metabolic intermediate dihydrofolate. Extending our comparative genomics analyses genome-wide reveals over 200 gene pairs with statistical signatures similar to DHFR/TYMS, suggesting the possibility that cellular pathways might be decomposed into small adaptive units.

systems biology↗