Biology subjects

Lim, Y. S.

Publications and source records attributed to Lim, Y. S..

8 recordsLinked to original sources

bioRxiv2026

Host recovery after skin barrier disruption is individual-specific and associated with microbial functions

The human skin is repeatedly exposed to mechanical and environmental stress, particularly in common skin diseases such as eczema, and yet the determinants of recovery remain poorly understood. Using longitudinal, multimodal profiling of skin physiology, structure (Raman spectroscopy), and microbial communities (shotgun metagenomics), we investigated in a human cohort (n=36 subjects, x2 sites, x6 timepoints) how host-microbe interactions could jointly shape recovery. Despite baseline variability in physiological parameters, we established that our protocol enables a defined disruption of the stratum corneum. While recovery trajectories for host attributes were notably consistent across age groups and body sites, individual-specific differences in recovery timelines were observed. To assess the role of the skin microbiome, several key time-dependent changes in microbial species were identified including enrichment of select Cutibacterium and Staphylococcus species and depletion of Corynebacterium and Malassezia species. Clustering of microbiome stability profiles across subjects and sites identified 6 distinct groups which associate with varying host-recovery patterns and microbial functions. Finally, joint hazards modelling of recovery timing revealed significant contributions from microbial taxa, functions and stability groups, highlighting the under-appreciated role of host-microbial interactions in response to skin stress and in the recovery process.

genomics↗

bioRxiv2026

Two orthogonal MAP3K-driven pathways of NLRP1 inflammasome activation revealed by poisonous beetles.

Environmental toxins that cause irritant dermatitis remain poorly understood as activators of innate immune pathways. Here, we identify rove beetle (Paederus) and blister beetle (Meloidae) toxins as previously unrecognized triggers of the human NLRP1 inflammasome in keratinocytes. Rove beetles, likely through the ribosome inhibitor pederin, activate NLRP1 via translational stalling and the ZAK-dependent ribotoxic stress response. In contrast, the phosphatase inhibitor cantharidin from blister beetles induces NLRP1 through TAK1-driven hyperphosphorylation of its linker region, independent of ZAK. In their hyperactivated states, ZAK and TAK1 share overlapping phosphosites on the NLRP1 disordered linker, including a common essential TZ motif. In addition, we show that TAK1 and ZAK are jointly responsible for NLRP1 linker phosphorylation and activation caused by dsRNA and CHIKV infection. These findings reveal medically relevant insect toxins as activators of NLRP1, and uncover parallel MAP3 kinase pathways as converging upstream activating signals for the human NLRP1 inflammasome. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/701189v1_ufig1.gif" ALT="Figure 1000"> View larger version (50K): org.highwire.dtl.DTLVardef@ee34b9org.highwire.dtl.DTLVardef@c79ec9org.highwire.dtl.DTLVardef@189c373org.highwire.dtl.DTLVardef@17ec853_HPS_FORMAT_FIGEXP M_FIG C_FIG KEY POINTSTwo dermatitis-causing beetle species induce NLRP1-driven pyroptosis of human keratinocytes Rove beetles, likely via pederin, activate NLRP1 via ribosome inhibition and ZAK[a]-driven RSR Cantharidin from blister beetles activates human via TAK1-, instead of ZAK[a]-driven hyperphosphorylation of the NLRP1 linker region Shared phosphosites by TAK1 and ZAK[a] on NLRP1 contribute to dsRNA-driven NLRP1 activation

immunology↗

bioRxiv2025

Clarifying the priming requirement and activator specificity for the NLRP3 inflammasome in human keratinocytes in vitro

While NLRP3 has been extensively studied in myeloid cells, its existence and regulation in epithelial cells, including keratinocytes, are unclear. In fact, whether human keratinocytes express a functional NLRP3 inflammasome at all remains a matter of debate in the inflammasome field. Here, we provide additional evidence that NLRP3 is repressed in human keratinocytes cultured under non-inflammatory conditions but can be sharply induced by interferon-{gamma} (IFN{gamma})--but not lipopolysaccharide (LPS). In this IFN{gamma}-primed state, not all established NLRP3 activators are specific to NLRP3. We report that nigericin-driven keratinocyte pyroptosis occurs via both NLRP1 and NLRP3, whereas Staphylococcus aureus -hemolysin (Hla) exclusively and nonredundantly activates NLRP3, even though both require K+ efflux. Furthermore, in the presence of T cells, certain virulent S. aureus strains can cause NLRP3-dependent pyroptotic death in keratinocytes in vitro through the cooperative actions of superantigens (SAgs) and Hla. In summary, our findings establish the strict inducibility and functional relevance of the NLRP3 inflammasome in non-myeloid, epithelial cells in vitro. These results resolve conflicting reports and position keratinocytes as a context-specific, non-hematopoietic cellular model for studying NLRP3 activation in host-microbe interactions at barrier tissues. KEY FINDINGSO_LIAdditional evidence that NLRP3 is absent in resting, nonstimulated human keratinocytes in vitro C_LIO_LIIFN{gamma}, but not LPS, is a potent priming signal for NLRP3 in human keratinocytes in vitro C_LIO_LIIn IFN{gamma}-primed keratinocytes, S. aureus -hemolysin (Hla) selectively activates NLRP3, whereas nigericin activates both NLRP1 and NLRP3 in vitro C_LIO_LISAg and Hla kill keratinocytes via NLRP3-driven pyroptosis in the presence of T cells in vitro C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/669639v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@4996f4org.highwire.dtl.DTLVardef@155a2a9org.highwire.dtl.DTLVardef@12a21a0org.highwire.dtl.DTLVardef@105bc15_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Integrated detection and quantification of aberrant transcripts with novel splicing events

Splicing misregulation, such as the inclusion of previously unknown cryptic exons, is implicated in numerous diseases. Recent methods have increased accurate and efficient detection of such splicing alterations occurring in disease phenotypes. However, the quantification and differential analyses of non-canonical splicing alterations remains focused at a splice event level, thus preventing a complete view of the effects on the downstream transcriptomic landscape. Here, we present a novel and integrated pipeline, SpliCeAT, that (1) detects and quantifies differential non-canonical splicing events from short-read bulk RNA-seq data, (2) augments the canonical transcriptome with novel transcripts containing these non-canonical splicing events, and (3) performs transcript-level differential analysis to identify and quantify aberrant cryptic exon-containing transcripts based on this augmented transcriptome. Using TDP-43, an ALS/FTD-associated RNA-binding protein as an example, we identified and catalogued aberrant splicing events in embryonic mouse brains from deletion of TDP-43 in neural progenitor cells. The accuracy of our integrated pipeline was further confirmed and validated with long-read isoform sequencing. Furthermore, by comparing neuronal TDP-43 knockouts in mice with a publicly available human dataset with TDP-43 pathology, we identified and validated 4 common genes, namely, Kalrn/KALRN, Poldip3/POLDIP3, Rnf144a/RNF144A, and Unc13a/UNC13A, with cryptic exons. In summary, our integrated pipeline, novel splice events are identified, incorporated and quantified at the transcript level, thereby enabling more complete transcriptome profiling of well-annotated genomes in in the case of pathological splicing misregulation.

genomics↗

bioRxiv2024

A chemically defined and xeno-free hydrogel system for regenerative medicine.

Biofabricated scaffolds facilitate bona fide cellular interactions, cell type specification, and the formation of three-dimensional tissue architecture from human pluripotent stem cells (hPSCs). However, xenogenic biomaterials are poorly defined, and synthetic biomaterials remain underdeveloped and understudied, hindering regulatory approval for clinical use and preventing the translation of lab-grown therapies. Here, we describe a protein screen-based hydrogel system biofabricated from clinical-grade human components. We show that "Alphagel", a base hydrogel comprising human embryonic matrices, supports the trilineage differentiation of hPSCs into neural, cardiac, and liver tissue. Alphagel is also shown to be biocompatible and biodegradable in vivo. Further, upon adding select proteins from maturing human foetal liver to Alphagel, we show that the resulting hydrogel (termed "Hepatogel") enhances the differentiation of hPSC-derived hepatocytes (H-iHeps) compared with Matrigel. Importantly, when injected into mice livers, Hepatogel significantly improves the retention of H-iHeps compared to standard aqueous cell injections. Altogether, our results provide proof of concept that customisable and organ-specific hydrogel systems are a valuable tool for developing clinically translatable therapies for regenerative medicine and tissue engineering.

bioengineering↗

bioRxiv2020

A sustained type I IFN-neutrophil-IL-18 axis drives pathology during mucosal viral infection

Neutrophil responses against pathogens must be balanced between protection and immunopathology. Factors that determine these outcomes are not well-understood. In a mouse model of genital herpes simplex virus-2 (HSV-2) infection, which results in severe genital inflammation, antibody-mediated neutrophil depletion reduced disease. Comparative single cell RNA-sequencing analysis of vaginal cells against a model of genital HSV-1 infection, which results in mild inflammation, demonstrated sustained expression of interferon-stimulated genes (ISGs) only after HSV-2 infection primarily within the neutrophil population. Both therapeutic blockade of IFN/{beta} receptor 1 (IFNAR1) and genetic deletion of IFNAR1 in neutrophils concomitantly decreased HSV-2 genital disease severity and vaginal IL-18 levels. Therapeutic neutralization of IL-18 also diminished genital inflammation, indicating an important role for this cytokine in promoting neutrophil-dependent immunopathology. Our study reveals that sustained type I IFN signaling is a driver of pathogenic neutrophil responses, and identifies IL-18 as a novel component of disease during genital HSV-2 infection.

immunology↗

bioRxiv2020

Fungi.guru: comparative genomic and transcriptomic database for the Fungi kingdom

The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi precludes us from tailoring them to our needs and tapping into their metabolic diversity. To remedy this, we gathered genomic and gene expression data of 19 most widely-researched fungi to build a database, fungi.guru, which contains tools for cross-species identification of conserved pathways, functional gene modules, and gene families. We exemplify how our database can elucidate the molecular function, biological process and cellular component of genes involved in various biological processes, by identifying a secondary metabolite pathway producing gliotoxin in Aspergillus fumigatus, the catabolic pathway of cellulose in Coprinopsis cinerea and the conserved DNA replication pathway in Fusarium graminearum and Pyricularia oryzae. The database is available at www.fungi.guru.

bioinformatics↗

bioRxiv2018

Fungal symbionts produce prostaglandin E2 to promote their intestinal colonization

Candida albicans is a ubiquitous fungal symbiont that resides on diverse human barrier surfaces. Both mammalian and fungal cells can convert arachidonic acid into the lipid mediator, prostaglandin E2 (PGE2), but the physiological significance of fungal-derived PGE2 remains elusive. Here we report that a C. albicans mutant deficient in PGE2 production suffered a loss of competitive fitness in the murine gastrointestinal (GI) tract and that PGE2 supplementation mitigated this fitness defect. Impaired fungal PGE2 production affected neither the in vitro fitness of C. albicans nor hyphal morphogenesis and virulence in either systemic or mucosal infection models. Fungus-derived PGE2 improved intra-GI fitness of C. albicans by diminishing the killing of C. albicans by phagocytes. Consequently, ablation of colonic phagocytes abrogated the fitness boost conferred by fungal PGE2. These observations suggest that C. albicans has evolved the capacity to produce PGE2 from arachidonic acid, a host-derived precursor, to promote its own colonization of the host gut. Analogous mechanisms might undergird host-microbe interactions of other symbiont fungi.\n\nAuthor SummaryCandida albicans is a symbiont fungus that resides in the gut of a majority of people without provoking disease. However, resident C. albicans can bloom and turn pathogenic in a subset of individuals who are immunocompromised due to infections or chemotherapy or who suffer a disruption of their intestinal microbial community due to antibiotic use. However, the fungal and host factors that regulate the fitness of C. albicans as a symbiont or an invasive pathogen remain poorly understood. Here we focused on the physiological role of fungus-derived prostaglandin E2 (PGE2) in the fitness of C. albicans using a PGE2-deficient C. albicans strain and mouse models of infections and intestinal symbiosis. We found that fungal PGE2, contrary to previously described functions of promoting virulence, played no role in fungal pathogenicity in vivo. Instead, fungal PGE2 specifically augmented the ability of C. albicans to colonize the gut, in part by reducing fungal killing by intestinal phagocytes. Our results suggest that fungal PGE2 synthetic pathways may be prophylactically targeted in individuals susceptible to invasive infections.

microbiology↗