Biology subjects

Chen, A. W.

Publications and source records attributed to Chen, A. W..

5 recordsLinked to original sources

bioRxiv2026

Ferroptosis of selective progenitor cell types during embryogenesis ensures proper organ morphogenesis

Ferroptosis, a form of non-apoptotic cell death, is induced by lipid peroxidation resulting from an intracellular accumulation of labile iron (1). While apoptosis is involved in embryonic development (2), the role of ferroptosis in embryogenesis is unknown. Here, we report that the ferroptosis process occurs in the embryonic lung and kidney at mid- and late-gestation. In these tissues, pro-ferroptotic cells include subpopulations of the Sox9+ distal lung epithelial cells and the Flk1+ vascular progenitors in the kidney glomeruli. Lipidomic analysis reveals mixed lipid peroxidation as the driver for ferroptosis. The role of ferroptosis in the morphogenesis of these organs was confirmed by triple positivity of TfR1, 4-HNE and TUNEL, mitochondrial defects, cell membrane breakage, dead cell remnants, single-cell RNA-sequencing of a ferroptosis gene signature. Genetic manipulation of Gpx4, an endogenous inhibitor of ferroptosis. Further, genetic knockout or transgenic overexpression of Gpx4 affects lung and kidney development and results in cystic lungs and kidneys. Notably, conditional deletion Gpx4 results in hypoplasia of the lung epithelia and of the renal glomeruli, while transgenic overexpression of Gpx4 resulted in atelectasis with collapsed lung alveoli and hypertrophic glomeruli. Together, these findings show that ferroptosis regulates lung and kidney morphogenesis by acting in key progenitor cell populations during gestation. Supplementation of iron or polyunsaturated fatty acid during pregnancy has implications for organogenesis.

developmental biology↗

bioRxiv2025

Isoflurane and Surgical Stress Disrupt Fatty Acid and Carbon Metabolism Leading to Cardiomyopathy

Aging alters cardiac resilience to anesthetic and surgical stress, yet the molecular basis of these effects remains poorly understood. To define age-dependent cardiac transcriptional responses to isoflurane exposure and operative (ISO/OP) stress, we analyzed gene expression profiles across young adult (3m), late middle-aged (17m), and geriatric mice (27m) following short-term 2 h ISO/OP exposure. At 24 h after cessation, all age groups exhibited distinct cardiac transcriptional signatures separating ISO/OP from sham controls. In young adult hearts, transcriptional alterations 24 hours after cessation of ISO/OP were characterized by dysregulation of small molecule catabolic processes, fatty acid metabolism, disruptions to protein processing in endoplasmic reticulum and cytoskeletal organization. Late middle-aged mice displayed amplified perturbations in lipid metabolism alongside suppression of muscle system and calcium signaling pathways, while old mice showed robust activation of PPAR and AMPK signaling and downregulation of genes governing contractility and morphogenesis. In contrast, geriatric mice showed upregulation of fatty acid metabolic pathways, robust activation of PPAR and AMPK signaling, coupled with suppression of muscle differentiation and actin organization following ISO exposure, indicating a maladaptive metabolic reprogramming. Overlapping DEGs across all age groups converged on pathways regulating oxidative stress, Ca2+ handling, hypertrophy, and energy metabolism, suggesting a conserved but age-intensified cardiac stress response. Longitudinal profiling in aged mice revealed persistent transcriptomic remodeling five weeks after stress. Crucially, this remodeling was observed even after ISO exposure alone, indicating that general anesthesia is a primary driver of this long-term effect. This persistent signature was marked by mitochondrial dysfunction and dysregulation of genes associated with diabetic cardiomyopathy, extracellular matrix integrity, and neurodegenerative signaling. Together, these findings identify isoflurane exposure as a potent inducer of persistent, age-dependent metabolic and structural reprogramming in the heart, implicating impaired lipid utilization and mitochondrial homeostasis as central mechanisms linking the perioperative period, and specifically anesthetic exposure, to long-term cardiovascular vulnerability.

pharmacology and toxicology↗

bioRxiv2023

Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation

The capacity for bacterial extracellular electron transfer via secreted metabolites is widespread in natural, clinical, and industrial environments. Recently, we discovered biological oxidation of phenazine-1-carboxylic acid (PCA), the first example of biological regeneration of a naturally produced extracellular electron shuttle. However, it remained unclear how PCA oxidation was catalyzed. Here, we report the mechanism, which we uncovered by genetically perturbing the branched electron transport chain (ETC) of the soil isolate Citrobacter portucalensis MBL. Biological PCA oxidation is coupled to anaerobic respiration with nitrate, fumarate, dimethyl sulfoxide, or trimethylamine-N-oxide as terminal electron acceptors. Genetically inactivating the catalytic subunits for all redundant complexes for a given terminal electron acceptor abolishes PCA oxidation. In the absence of quinones, PCA can still donate electrons to certain terminal reductases, albeit much less efficiently. In C. portucalensis MBL, PCA oxidation is largely driven by flux through the ETC, which suggests a generalizable mechanism that may be employed by any anaerobically respiring bacterium with an accessible cytoplasmic membrane. This model is supported by analogous genetic experiments during nitrate respiration by Pseudomonas aeruginosa. Author summaryMany bacteria have extremely flexible metabolisms, and we are only beginning to understand how they manifest in the environment. Our study focuses on the role of phenazine-1-carboxylic acid (PCA), a molecule that some bacteria synthesize and secrete into their surroundings. PCA is an "extracellular electron shuttle," a molecule that readily transfers electrons between cells and oxidizing/reducing compounds or other cells. Until our investigation, the role of PCA electron-shuttling had only been studied in one direction: how it takes electrons away from cells, and the effect this has on their viability. Here we present a detailed account of the opposite process and its mechanism: what happens when PCA delivers electrons to cells? Our findings indicate that this previously underappreciated process is generalizable to any anaerobically respiring bacterium. Consequently, we expect that electron donation by PCA is widespread in environments where PCA is plentiful and oxygen is sparse, such as in some agricultural soils. The universality of the extracellular electron shuttle oxidation mechanism we describe for PCA suggests that it should also occur with similar small molecules, of which there are thousands, deepening the implication that this is a significant process in the environment and motivating further research into its consequences.

microbiology↗

bioRxiv2023

α-carboxysome size is controlled by the disordered scaffold protein CsoS2

Carboxysomes are protein microcompartments that function in the bacterial CO2 concentrating mechanism (CCM) to facilitate CO2 assimilation. To do so, carboxysomes assemble from thousands of constituent proteins into an icosahedral shell which encapsulates the enzymes rubisco and carbonic anhydrase to form structures typically >100 nm and >300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here we show that the size of -carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats which bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of -carboxysomes.

biochemistry↗

bioRxiv2019

α-carboxysome formation is mediated by the multivalent and disordered protein CsoS2

Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO2-concentrating mechanism, feeding high concentrations of CO2 to the enzyme Rubisco for fixation. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the -carboxysome, there is little molecular insight into protein-protein interactions which drive the assembly process. Here we show that the N-terminus of CsoS2, an intrinsically disordered protein found in the -carboxysome, possesses a repeated peptide sequence that binds Rubisco. X-ray structural analysis of the peptide bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate CsoS2 acts as an interaction hub to condense Rubisco and enable efficient -carboxysome formation.

biochemistry↗