Biology subjects

Seo, D.

Publications and source records attributed to Seo, D..

11 recordsLinked to original sources

bioRxiv2026

Targeting of ELMO2 by the Shigella E3 Ligase IpaH4.5 Reveals Key Differences Between ELMO Paralogs

The IpaH class of effector proteins secreted by Shigella flexneri ubiquitinate specific immune factors, targeting them for proteasomal degradation. ELMO1-3 are key signaling molecules involved in cell motility and phagocytosis, but the distinct roles of these three proteins remain unclear. Here, we identify ELMO2 as a substrate of S. flexneri IpaH4.5 using an unbiased screening approach in human cell lysate. Using in vitro and cellular assays, we show that IpaH4.5 specifically targets ELMO2 for ubiquitination but has no activity against its paralogs ELMO1 and ELMO3. Using chimeric proteins, we show that IpaH4.5 specificity is dictated by divergence within the ELMO2 Armadillo Repeat Region, identifying this domain as a key determinant of ELMO paralog specialization. Consistent with this divergence, we find that commonly used ELMO antibodies lack paralog specificity and that ELMO2 is the predominant paralog expressed across multiple human cell lines. Further, functional assays demonstrate that IpaH4.5-mediated degradation of ELMO2 disrupts RAC activation downstream of the ELMO/DOCK complex, suggesting that this signaling pathway is perturbed during infection. We conclude that ELMO2 plays an as-yet unidentified role in counteracting bacterial infection and is therefore targeted by IpaH4.5.

microbiology↗

bioRxiv2026

Microfluidic Mechanical Reactivation of Aged Stem Cells

Stem cell aging significantly impairs therapeutic efficacy, requiring innovative strategies to restore potency. We present a microfluidic cell-compressing platform for reactivation (-CPR) designed to apply controlled hydrodynamic deformation to late-passage stem cells. This mechanical stimulation facilitates functional reactivation without external chemical cues. Within a defined window, -CPR effectively reduces oxidative stress, SA-{beta}-Gal activity, and {gamma}H2AX foci, while simultaneously restoring proliferation and canonical stemness markers (OCT4, SOX2, and KLF4). Mechanical stimulation via -CPR induces coordinated structural remodeling: nuclei become more compact, actin cortex organization is restored, -actinin redistributes to focal adhesions, and microtubule networks are restructured, suggesting a rebalanced intracellular tension. Transcriptomic and proteomic analyses reveal that this process reprograms extracellular matrix remodeling and DNA repair pathways while attenuating pro-fibrotic and senescence-associated secretory phenotype (SASP)-associated pathways. Crucially, this reactivation occurs without compromising fundamental MSC hallmarks, preserving intrinsic immunophenotypes and multilineage differentiation potential. Functionally, -CPR-processed stem cells demonstrate restored in vitro wound closure and enhanced tissue repair in vivo, with efficacy appearing dependent on mechanical dosage. This platform establishes a non-genetic, mechanobiological approach to restoring stem cell function, offering a scalable strategy for functional reactivation and potentially paving the way toward comprehensive cellular rejuvenation.

bioengineering↗

bioRxiv2026

The Vector Competence and Vectorial Capacity of Aedes albopictus for Ross River Virus in the United States as a Function of Temperature

Ross River virus (RRV) is a medically significant arbovirus endemic to Australia where it causes an average of 5000 reported human cases per year. Due to concern for possible transmission outside of its endemic range, we examined the vector competence and vectorial capacity of RRV by Aedes albopictus (Skuse 1894) to contribute to risk assessments for outbreaks in the United States. We tested Ae. albopictus mosquitoes exposed to RRV at three temperatures and five time points post-infection for infection and dissemination. We also collected saliva from exposed individuals incubated at the same three temperatures to determine the presence of viral RNA. Additionally, we assessed the impact of viral infection on life expectancy as a function of temperature. Rates of infection were unaffected by time and temperature and 89.3% of individuals were infected. 85-100% of infected individuals displayed dissemination by day 7 at all temperatures. The extrinsic incubation period as determined by the saliva collection was approximately 6 days and 78.6-100% of individuals tested expressed salivary viral RNA at some point in the experiment which is comparable to the rates of overall infection. The vectorial capacity of RRV with Ae. albopictus as a vector ranged from 10.23-23.37 indicating that these mosquitoes are competent potential vectors for RRV. Due to prior outbreaks RRV has caused outside of its endemic range, these findings warrant further investigation in the transmission potential of RRV in the United States. Author SummaryThe last 30 years has seen a steady increase in mosquito-borne illness globally, much of which has been driven by viruses such as dengue establishing in new areas as a consequence of the spread of its primary vectors and environmental changes. In order to mitigate the continued increase in the prevalence of mosquito-borne illness, it is necessary to determine which viruses are likely to spread beyond their native range. Ross River virus (RRV) is a mosquito-borne virus which, while nonlethal, commonly causes a litany of debilitating side-effects for extended periods of time. RRV is endemic to Australia, however the recent introduction of a known RRV vector to California as well as the widespread prevalence of a suspected RRV vector, Ae. albopictus, across the country, could prime RRV for an outbreak in the continental United States. As part of a risk assessment for the outbreak potential of RRV in the continental United States, we investigated the vector competence and vectorial capacity of Ae. albopictus. We find that this species is a competent vector for this virus across a range of relevant temperatures.

ecology↗

bioRxiv2024

RBP4 functions as an antagonistic ligand of orphan DR6

Death receptor (DR) is a unique transmembrane receptor mediating extrinsic factor-induced programmed cell death pathways. For most DRs, the regulatory mechanism has been revealed to involve agonistic death ligand (e.g., TRAIL, TNF-)-driven receptor clustering and activation, offering an in-depth understanding of the mechanistic basis for cell death regulation and therapeutic strategies. However, only death receptor 6 (DR6) remains orphan, and its molecular mechanism is poorly understood. Here, we identified retinol binding protein 4 (RBP4), a major vitamin-A carrier protein, as an antagonistic ligand of DR6. Single-molecule photobleaching and single-receptor tracking analyses revealed that RBP4 drives DR6 dimerization on the plasma membrane to prevent DR6 prodegenerative heterointeractions and consequent neurodegenerative processes. DR6 homodimerization predominantly depends on an extracellular intrinsically disordered region, allowing the agonistic propensity of increasing Ca2+ levels. Collectively, our study establishes the distinct molecular mechanism of DR6 and highlights the non-canonical role of RBP4 as a cell death regulator.

molecular biology↗

bioRxiv2024

Activation and Evasion of the FEAR Pathway by RNA Viruses

We recently identified the FACT-ETS-1 Antiviral Response (FEAR) pathway as an interferon-independent innate immune response that restricts DNA virus replication and is countered by poxvirus-encoded A51R proteins (Rex et al., 2024, Nature Microbiology). The human FEAR pathway is mediated by the FACT complex, consisting of hSpt16 and SSRP1 subunits, that remodels chromatin to activate expression of the antiviral transcription factor, ETS-1. To counter this pathway, poxvirus A51R proteins tether SUMOylated hSpt16 subunits to microtubules to prevent ETS-1 expression. While these observations indicate a role for the FEAR pathway in DNA virus restriction, it was unclear if RNA viruses interact with this pathway. Here, we show that RNA viruses are also restricted by the FEAR pathway, yet encode mechanisms distinct from poxviruses to counter this response. We show vesicular stomatitis virus (VSV), a rhabdovirus, utilizes its matrix (M) protein to promote proteasome-dependent degradation of SUMOylated hSpt16 and to block ETS-1 nuclear import. Strains encoding mutant M proteins that cannot antagonize the FEAR pathway exhibit replication defects in human cells that can be rescued by hSpt16 or ETS-1 depletion. Moreover, FACT inhibitor treatment enhanced the replication of oncolytic VSV strains encoding defective M proteins in restrictive cancer cells, suggesting FEAR pathway inhibition may improve oncolytic virotherapy. Strikingly, we provide evidence that the inability of VSV M to degrade SUMOylated Spt16 in lepidopteran insect cells results in abortive infection, suggesting VSV-Spt16 interactions influence virus host range. Lastly, we show that human and murine paramyxovirus target SUMOylated Spt16 proteins for degradation in human and murine cells utilizing a conserved N-terminal motif in their accessory "C" proteins. Collectively, our study illustrates that DNA and RNA viruses have independently evolved diverse mechanisms to antagonize SUMOylated host Spt16 proteins, underscoring the physiological importance of the FEAR pathway to antiviral immunity.

microbiology↗

bioRxiv2024

GLARE: DISCOVERING HIDDEN PATTERNS IN SPACEFLIGHT TRANSCRIPTOME USING REPRESENTATION LEARNING

AO_SCPLOWBSTRACTC_SCPLOWSpaceflight studies present novel insights into biological processes through exposure to stressors outside the evolutionary path of terrestrial organisms. Despite limited access to space environments, numerous transcriptomic datasets from spaceflight experiments are now available through NASAs GeneLab data repository, which allows public access to these datasets, encouraging further analysis. While various computational pipelines and methods have been used to process these transcriptomic datasets, learning-model-driven analyses have yet to be applied to a broad array of such spaceflight-related datasets. In this study, we propose an open-source pipeline, GLARE: GeneLAb Representation learning pipelinE, which consists of training different representation learning approaches from manifold learning to self-supervised learning that enhance the performance of downstream analytical tasks. We illustrate the utility of GLARE by applying it to gene-level transcriptional values from the results of the CARA spaceflight experiment, an Arabidopsis root tip transcriptome dataset that spanned light, dark, and microgravity treatments. We show that GLARE not only substantiated the findings of the original study concerning cell wall remodeling but also revealed additional patterns of gene expression affected by the treatments, including evidence of hypoxia. This work suggests there is great potential to supplement the insights drawn from initial studies on spaceflight omics-level data through further machine-learning-enabled analyses.

plant biology↗

bioRxiv2023

A FACT-ETS-1 Antiviral Response Pathway Restricts Viral Replication and is Countered by Poxvirus A51R Proteins

The FACT complex is an ancient chromatin remodeling factor comprised of Spt16 and SSRP1 subunits that regulates specific eukaryotic gene expression programs. However, whether FACT regulates host immune responses to infection was unclear. Here, we identify an antiviral pathway mediated by FACT, distinct from the interferon response, that restricts poxvirus replication. We show that early viral gene expression triggers nuclear accumulation of specialized, SUMOylated Spt16 subunits of FACT required for expression of ETS-1, a downstream transcription factor that activates a virus restriction program. However, poxvirus-encoded A51R proteins block ETS-1 expression by outcompeting SSRP1 for binding to SUMOylated Spt16 in the cytosol and by tethering SUMOylated Spt16 to microtubules. Moreover, we show that A51R antagonism of FACT enhances both poxvirus replication in human cells and viral virulence in mice. Finally, we demonstrate that FACT also restricts unrelated RNA viruses, suggesting a broad role for FACT in antiviral immunity. Our study reveals the FACT-ETS-1 Antiviral Response (FEAR) pathway to be critical for eukaryotic antiviral immunity and describes a unique mechanism of viral immune evasion.

microbiology↗

bioRxiv2022

A dual gene-specific mutator system installs all transition mutations at similar rates in vivo

Targeted in vivo hypermutation accelerates directed evolution of proteins through concurrent DNA diversification and selection. Among recently developed methods, the systems employing a fusion protein of a nucleobase deaminase and T7 RNA polymerase present gene-specific targeting. However, their mutational spectra have been largely limited to exclusive or dominant C:G[->]T:A mutations. Here we describe eMutaT7transition, a new gene-specific mutator system, that installs all the transition mutations (C:G[->]T:A and A:T[->]G:C) at comparable rates. By using two mutator proteins in which two efficient deaminases, PmCDA1 and TadA-8e, are separately fused to T7 RNA polymerase, we obtained similar numbers of C:G[->]T:A and A:T[->]G:C mutations at a sufficiently high rate ([~]3.4 x 10-5 mutations per base per generation or [~]1.3 mutations per 1 kb per day). Through eMutaT7transition-mediated TEM-1 evolution for antibiotic resistance, we generated many mutations also found in clinical isolates. Overall, with a fast mutation rate and wider mutational spectrum, eMutaT7transition is a potential first-line method for gene-specific in vivo hypermutation.

synthetic biology↗

bioRxiv2022

Existence of blood circulating immune-cell clusters (CICs) comprising antigen-presenting cells and B cells

Cell-to-cell physical interactions are involved in almost every physiological processes in multicellular organisms. Although the dynamics of these interactions could be highly diverse and complex in many circumstances, certain cell-to-cell interactions among immune cells have been well studied due importance in understanding disease pathogenesis and immune therapy development1. Dendritic cells (DCs) and B cells are directly involved in adaptive immune response against pathogens. Interaction mechanism between these two celltypes is well-known to occur in germinal centers either indirectly via helper T (Th) cells or directly via cell contact. However, there are animal in vitro and in vivo evidence that such direct DC-to-B cell contact can occur outside germinal centers like in peripheral blood or collagen matrix and display antiviral immune-related activity2,3. Here, we provide evidence that certain types of antigen presenting cells (APCs) can form robust cell clusters with B cells and circulate in blood. From healthy human blood immune single cell RNA-seq datasets, we detected APC subpopulations (0.34{+/-}0.19% of total PBMCs) that were also enriched with well-known naive B cell markers. We visually observed DC:B doublets and multiplets ([~]0.69% of total live PBMCs) in wildtype mouse blood using flow cytometry and microscopic imaging, thus proving the existence of circulating immune-cell clusters (CICs) composed of APCs and B cells. BCR repertoire of these healthy mouse CICs were similar to circulating B cells. Noticeably, frequency of these APC:B CICs were higher COVID-19 patients than healthy donors and their B cell subtype composition (e.g. naive, plasmablast, IgM+, IgG+) varied with disease severity.

immunology↗

bioRxiv2021

The Mixed Blessing of AMPK Signaling in Cancer Treatments

Nutrient acquisition and metabolism pathways are altered in cancer cells to meet bioenergetic and biosynthetic demands. A major regulator of cellular metabolism and energy homeostasis, in normal and cancer cells, is AMP-activated protein kinase (AMPK). AMPK influences cell growth via its modulation of the mechanistic target of Rapamycin (mTOR) pathway, specifically, by inhibiting mTOR complex mTORC1, which facilitates cell proliferation, and by activating mTORC2 and cell survival. Given its conflicting roles, the effects of AMPK activation in cancer can be counter-intuitive. Prior to the establishment of cancer, AMPK acts as a tumor suppressor. However, following the onset of cancer, AMPK has been shown to either suppress or promote cancer, depending on cell type or state. To unravel the controversial roles of AMPK in cancer, we developed a computational model to simulate the effects of pharmacological maneuvers that target key metabolic signalling nodes, with specific focus on AMPK, mTORC, and their modulators. Model simulations clarify the competing effects and the roles of key metabolic signalling pathways in tumorigenesis, which may yield insights on innovative therapeutic strategies.

systems biology↗

bioRxiv2020

Size-dependent protein segregation creates a spatial switch for Notch and APP signaling

Aberrant cleavage of Notch by {gamma}-secretase is implicated in numerous diseases, but how cleavage is regulated in space and time is unclear. Here, we report that cadherin-based adherens junctions (cadAJs) are sites of high cell-surface {gamma}-secretase activity, as well as sites of constrained physical space that excludes {gamma}-secretase substrates having large extracellular domains (ECDs) like Notch. ECD shedding initiates drastic spatial relocalization of Notch to cadAJs, allowing enzyme-substrate interactions and downstream signaling. Spatial mutations by adjusting the ECD size or the physical constraint alter signaling. Dysregulation of this spatial switch promotes precocious differentiation of ventricular zone neural progenitor cells in vivo. We show the generality of this spatial switch for amyloid precursor protein proteolysis. Thus, cadAJs create spatially distinct biochemical compartments regulating cleavage events involving {gamma}-secretase and preventing aberrant activation of receptors. One Sentence SummaryNotch cleavage by {gamma}-secretase is regulated through dynamic spatial control of receptors, adhesion molecules, and activating proteases

cell biology↗