Biology subjects

Bark, S. J.

Publications and source records attributed to Bark, S. J..

5 recordsLinked to original sources

bioRxiv2026

Human placental trophoblasts support sustained Treponema pallidum replication and reveal new candidate host pathways implicated in congenital syphilis

Congenital syphilis is a leading cause of preventable stillbirth, yet the mechanisms that enable Treponema pallidum subsp. pallidum, the etiological agent of syphilis, to traverse and persist within the human placenta are virtually unknown. This knowledge gap reflects, in part, the fastidious nature of T. pallidum, which has historically only been propagated in rabbit epithelial cells. Here, we demonstrate that T. pallidum replicates and can be propagated long-term in human placental trophoblast models. We identified three human trophoblast cell lines, JEG-3, BeWo, and HTR-8, that sustained robust T. pallidum replication for over 55 days. Confocal imaging with GFP-expressing T. pallidum demonstrated bacterial adherence to trophoblast cultures. To identify human placental pathways that may support T. pallidum replication and persistence, we performed bulk transcriptomic profiling of the three trophoblast lines co-cultured with T. pallidum for 3 or 7 days. Our findings revealed conserved host responses involving increased cholesterol synthesis, suppressed type I interferon signaling, and disrupted extracellular matrix organization. These data implicate host metabolic rewiring, innate immune attenuation, and extracellular matrix remodeling as candidate pathways that may promote T. pallidum invasion, replication and persistence within the placenta. Together, these models represent the first human placental systems capable of supporting efficient, long-term T. pallidum growth and provide a foundation for mechanistic studies of congenital syphilis pathogenesis.

microbiology↗

bioRxiv2026

Stress-Responsive Protein IFRD1 Protects Assembled Ribosomes via a Ribosome-Salvaging Mechanism

The ability of epithelial cells to cope with injury and undergo regeneration depends on tightly coordinated cellular responses. IFRD1 is a stress-responsive protein that is evolutionarily conserved and required for the cellular regeneration program paligenosis; however, how IFRD1 works in paligenosis is not known. Here we demonstrate that IFRD1 is primarily a cytosolic ribosome-binding protein, specifically binding 80S monosomes that are not actively engaged in translation. Using multiple in vivo and in vitro injury models, including cerulein-induced pancreatitis in mice and tunicamycin-induced ER stress in cell culture, we demonstrate that IFRD1 acts as a ribosome-salvaging factor, preventing ribosomes from degradation. In the absence of IFRD1 during ER stress, non-translating 80S ribosomes were unstable and prone to disassembly and selective degradation. The resulting accumulation of degraded ribosomal subunits overwhelmed cellular autophagic machinery, as evidenced by accumulation of the autophagy-tagging protein p62, even though overall autophagic flux remained unaffected. Ultimately, cells lacking IFRD1 showed reduced mTORC1 activity followed by increased cell death, consistent with patterns observed in cells lacking IFRD1 during paligenosis. Thus, we detail a previously unrecognized cellular function for IFRD1 in stabilizing and preserving the mature ribosome pool during metabolic and translational transitions such as paligenosis.

cell biology↗

bioRxiv2025

A scalable organoid model of urothelial aging for metabolic interrogation, infection modeling, and reversal of age-associated changes

Aging leads to a progressive decline in overall bladder function resulting in lower urinary tract symptoms and increased susceptibility to infections. However, tissue-specific mechanisms of aging, specifically the contributions of the aged urothelium remain elusive. Here, we introduce mouse bladder epithelium-derived organoids (mBEDOs) as a scalable platform to model urothelial aging. mBEDOs from aged mice recapitulate key features of age-associated cellular reprogramming, including oxidative stress, senescence, and DNA damage. We demonstrate the utility of mBEDOs for modeling Uropathogenic Escherichia coli (UPEC) infection, generating assembloids between mBEDOs and macrophages to model epithelial-immune interactions, and genetic perturbation. Using the mBEDO platform, we also identify urothelium-specific changes in purine, amino acid, and glycerophospholipid metabolism which may contribute to age-associated cellular perturbations. Lastly, supplementation with depleted metabolites, nicotinamide (NAM) and D-mannose, reduce DNA damage and oxidative stress and restore mitochondrial integrity in aged mBEDOs. These findings establish mBEDOs as an effective platform for investigating molecular and cellular underpinnings of urothelial aging and exploring metabolism-based interventions for age-associated bladder dysfunction.

bioengineering↗

bioRxiv2025

Autophagy-Dependent Regulation of YAP1 by STK38 Governs Recruitment of Differentiated Cells as Progenitor Cells During Regeneration

Paligenosis is a conserved cellular plasticity program that allows mature cells to reenter the cell cycle in response to tissue injury. Paligenosis progresses via three stages: autodegradation (with dramatic increase in autophagy and lysosomes), induction of metaplastic or fetal-like genes, and cell cycle entry. Hippo signaling, particularly the downstream effector YAP1, regulates cellular plasticity, but its role in paligenosis has not been studied. Here we first examine paligenosis in digestive-enzyme-secreting chief cells in mouse stomach. We identify Serine/Threonine Kinase 38 (STK38) as a non-canonical YAP1 kinase that phosphorylated and deactivated YAP1 in uninjured chief cells. During paligenosis, STK38 was degraded by autophagy in stage 1, dephosphorylating and activating YAP1. YAP1 activation was necessary and sufficient for the paligenosis that converts chief cells into metaplastic, proliferating progenitors. Additionally, we show STK38, like canonical Hippo kinases, interact with NF2. We also observed the same pattern of YAP1 induction via autophagic destruction of STK38 in other tissues and cell types, suggesting a universal logic model for how the massive autophagy activated in differentiated cells during tissue damage can consequently activate Hippo effectors to induce plasticity for tissue regeneration.

developmental biology↗

bioRxiv2024

A new role for IFRD1 in regulation of ER stress in bladder epithelial homeostasis

A healthy bladder requires the homeostatic maintenance of and rapid regeneration of urothelium upon stress/injury/infection. Several factors have been identified to play important roles in urothelial development, injury and disease response, however, little is known about urothelial regulation at homeostasis. Here, we identify a new role for IFRD1, a stress-induced gene that has recently been demonstrated to play a critical role in adult tissue proliferation and regeneration, in maintenance of urothelial function/ homeostasis in a mouse model. We show that the mouse bladder expresses IFRD1 at homeostasis and its loss alters the global transcriptome of the bladder with significant accumulation of cellular organelles including multivesicular bodies with undigested cargo, lysosomes and mitochondria. We demonstrate that IFRD1 interacts with several mRNA-translation-regulating factors in human urothelial cells and that the urothelium of Ifrd1-/- mice reveal decreased global translation and enhanced endoplasmic reticulum (ER) stress response. Ifrd1-/- bladders have activation of the unfolded protein response (UPR) pathway, specifically the PERK arm, with a concomitant increase in oxidative stress and spontaneous exfoliation of urothelial cells. Further, we show that such increase in cell shedding is associated with a compensatory proliferation of the basal cells but impaired regeneration of superficial cells. Finally, we show that upon loss of IFRD1, mice display aberrant voiding behavior. Thus, we propose that IFRD1 is at the center of many crucial cellular pathways that work together to maintain urothelial homeostasis, highlighting its importance as a target for diagnosis and/or therapy in bladder conditions.

cell biology↗