Biology subjects

Yoo, W.

Publications and source records attributed to Yoo, W..

7 recordsLinked to original sources

bioRxiv2026

DIPTAR: A synthetic biology platform for functional interrogation of protein degradation

Protein degradation regulates cellular homeostasis, yet many degradation events are difficult to study because they lack a readily selectable phenotype. Here, we develop Degradation-Induced Pyroptosis TArgeting Receptors (DIPTAR), a modular synthetic biology platform that couples protein degradation to CARD8-mediated pyroptosis. Using HIF-1 as a model substrate, we show that DIPTAR faithfully reports oxygen-dependent VHL-mediated degradation and enables pooled CRISPR screening to identify established and previously unrecognized regulators of HIF-1 stability. DIPTAR is functional across multiple cell types and can be programmed with diverse proteins, including BRD4, I{kappa}B, and p53, to convert distinct degradation stimuli into a common pyroptotic output. DIPTAR also detects pathogen-mediated perturbations of host degradation pathways, including both inhibition and induction of degradation-dependent signaling. By converting protein degradation into a robust selectable phenotype, DIPTAR provides a scalable platform for functional genetic discovery, interrogation of degradation pathways, degrader characterization, and investigation of host-pathogen interactions.

synthetic biology↗

bioRxiv2025

Human non-canonical inflammasomes activate CASP3 to limit intracellular Salmonella replication in macrophages.

Inflammasomes are multiprotein signaling platforms that activate inflammatory caspases to initiate innate immune signaling. In humans, canonical inflammasomes activate CASP1, which cleaves the pore-forming protein gasdermin D (GSDMD) and the cytokines IL-1{beta} and IL-18. In contrast, the non-canonical inflammasome detects bacterial lipopolysaccharide (LPS) through CASP4/5, which cleave GSDMD to drive pyroptosis. While CASP1 substrates are well characterized, CASP4/5 substrates remain less defined. Here, we show that in response to intracellular LPS and gram-negative bacterial infection, CASP4/5 directly cleave and activate the executioner caspases CASP3/7. CASP3 in turn cleaves and activates gasdermin E (GSDME). Surprisingly, CASP3, but not GSDME, was required for restricting intracellular Salmonella replication, suggesting that CASP4/5-induced apoptosis contributes to host defense. We further show that most GSDMD cleavage during non-canonical inflammasome activation is mediated by CASP1, and that GSDMD is the primary driver of pyroptosis. Finally, we confirm that CASP4/5 activate CASP3/7 and GSDME in human primary macrophages. These findings establish CASP4/5 as dual apoptotic initiator and inflammatory caspases and reveal a central role for the apoptotic signaling cascade in non-canonical inflammasome-mediated immunity.

cell biology↗

bioRxiv2023

IST1 regulates select endosomal recycling pathways

ESCRTs (Endosomal Sorting Complex Required for Transport) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intralumenal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/551359v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@14c2658org.highwire.dtl.DTLVardef@699063org.highwire.dtl.DTLVardef@867084org.highwire.dtl.DTLVardef@44f7b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Quisinostat is a brain-penetrant radiosensitizer in glioblastoma

In recent years, histone deacetylase inhibitors (HDACi) have garnered considerable interest for the treatment of adult and pediatric malignant brain tumors. However, owing to their broad-spectrum nature and inability to effectively penetrate the blood-brain barrier, HDACi have failed to provide significant clinical benefit to glioblastoma (GBM) patients to date. Moreover, global inhibition of HDACs results in widespread toxicity, highlighting the need for selective isoform targeting. While no isoform-specific HDACi are currently available, the second-generation hydroxamic acid-based HDACi quisinostat possesses sub-nanomolar specificity for class I HDAC isoforms, particularly HDAC1 and 2. Recently, we demonstrated that HDAC1 is the essential HDAC in GBM. Here, we provide the first report on the neuro-pharmacokinetic, pharmacodynamic and radiation-sensitizing properties of quisinostat in preclinical models of GBM. We demonstrate that quisinostat is a well-tolerated and brain-penetrant molecule that significantly extends survival when administered in combination with radiation in vivo. The pharmacokinetic-pharmacodynamic-efficacy relationship was established by correlating free drug concentrations and evidence of target modulation in the brain with survival benefit. Together, these data provide a strong rationale for clinical development of quisinostat as a radiosensitizer for the treatment of GBM.

cancer biology↗

bioRxiv2022

Microbiota-derived aspartate drives pathogenic Enterobacteriaceae expansion in the inflamed gut

Inflammation boosts the availability of electron acceptors in the intestinal lumen creating a favorable niche for pathogenic Enterobacteriaceae. However, the mechanisms linking intestinal inflammation-mediated changes in luminal metabolites and pathogen expansion remain unclear. Here, we show that mucosal inflammation induced by Salmonella enterica serovar Typhimurium (S. Tm) infection and chemical colitis results in increased intestinal levels of the amino acid aspartate. The S. Tm and E. coli genomes encode an aspartate ammonia-lyase (aspA) which converts aspartate into fumarate, an alternative electron acceptor. S. Tm and pathogenic E. coli used aspA-dependent fumarate respiration for growth in the murine gut only during inflammation. Such growth advantage was abolished in the gut of germ-free mice. However, mono-association of gnotobiotic mice with members of the classes Bacteroidia and Clostridia restored the benefit of aspartate utilization to the pathogens. Our findings demonstrate the role of microbiota-derived amino acids in driving respiration-dependent Enterobacteriaceae expansion during colitis.

microbiology↗

bioRxiv2021

Salmonella Typhimurium uses anaerobic respiration to overcome propionate-mediated colonization resistance

The gut microbiota benefits the host by limiting enteric pathogen expansion (colonization resistance) partially via the production of inhibitory metabolites. Propionate, a short-chain fatty acid produced by microbiota members, is proposed to mediate colonization resistance against Salmonella enterica serovar Typhimurium (S. Tm). Here, we show that S. Tm overcomes the inhibitory effects of propionate by using it as a carbon source for anaerobic respiration. We determined that propionate metabolism provides an inflammation-dependent colonization advantage to S. Tm during infection. Such benefit was abolished in the intestinal lumen of Salmonella-infected germ-free mice. Interestingly, S. Tm propionate-mediated intestinal expansion was restored when germ-free mice were monocolonized with Bacteroides thetaiotaomicron (B. theta), a prominent propionate producer in the gut, but not when mice were monocolonized with a propionate production-deficient B. theta strain. Taken together, our results reveal a novel strategy used by S. Tm to mitigate colonization resistance by metabolizing microbiota-derived propionate.

microbiology↗

bioRxiv2017

The SMuSh pathway is essential for survival during growth-induced compressive mechanical stress

Cells that proliferate within a confined environment build up mechanical compressive stress. For example, mechanical pressure emerges in the naturally space-limited tumor environment. However, little is known about how cells sense and respond to mechanical compression. We developed microfluidic bioreactors to enable the investigation of the effects of compressive stress on the growth of the genetically tractable model organism Saccharomyces cerevisiae. We used this system to determine that compressive stress is partly partly sensed through a module consisting of the mucin Msb2, and the cell wall protein Sho1, which act together as a sensor module in one of the two major osmosensing pathways in budding yeast. This signal is transmitted via the MAPKKK kinase Ste11. Thus, we term this mechanosensitive pathway the SMuSh pathway, for Ste11 through Mucin / Sho1 pathway. The SMuSh pathway delays cells in the G1 phase of the cell cycle and improves cell survival in response to growth-induced pressure. We also found that the Cell Wall Integrity (CWI) pathway contributes to the response to mechanical compressive stress. These latter results are confirmed in complimentary experiments in the accompanying manuscript from Mishra et al. When both the SMuSh and the CWI pathways are deleted, cells fail to adapt to compressive stress and all cells lyse at relatively low pressure when grown in confinement. Thus, we define a network that is essential for cell survival during growth under pressure. We term this new mechanosensory system the SCWISh (Survival through the CWI and SMuSh) network.\n\nSignificance StatementGrowth in confined environments leads to the build up of compressive mechanical stresses, which are relevant to diverse fields, from cancer to microbiology. In contrast to tensile stress, little is known about the molecular integration of compressive stresses. In this study, we elucidate the SMuSh pathway, which, together with the Cell Wall Integrity pathway, is essential for viability of the budding yeast S. cerevisiae when growing under mechanical pressure. Pressure-sensing requires the transmembrane mucin, Msb2, which is linked to the actin cortex. Our result raises the intriguing question of whether mucins, widely conserved in eukaryotes and frequently misregulated in cancers, might sense compressive stresses in other organisms, including humans.

cell biology↗