Biology subjects

Chen, K.-Y.

Publications and source records attributed to Chen, K.-Y..

8 recordsLinked to original sources

bioRxiv2026

Influenza A virus initiates genome selection through promoter-dependent nuclear export

Influenza A virus replicates its segmented RNA genome in the nucleus in the context of viral ribonucleoprotein (vRNP) complexes. Newly synthesised vRNPs are exported to the cytoplasm for virion assembly, whereas structurally similar complementary RNPs (cRNPs), which function as replication intermediates, are not incorporated into virions. The molecular basis for this selectivity remains unclear. Here, combining promoter mutagenesis, single-molecule fluorescence in situ hybridisation (smFISH), virus-like particle (VLP) assays and cryo-electron microscopy (cryo-EM), we find that cRNPs are retained in the nucleus and that export competence is encoded by promoter architecture, with the length of the single-stranded 3' promoter region as the principal contributing feature and promoter sequence and duplex architecture further modulating export efficiency. cRNPs carrying export-competent promoters are incorporated into virus-like particles, demonstrating a functional link between nuclear export and packaging competence. Cryo-EM analyses reveal that both 3' vRNA and cRNA promoters bind a common polymerase surface site but are associated with distinct polymerase conformational landscapes, with only the vRNA promoter being compatible with an encapsidase conformation of the polymerase. Together, our findings identify a promoter-dependent checkpoint that links RNA promoter architecture and polymerase conformation to RNP export and packaging. These results demonstrate that influenza virus initiates genome selection in the nucleus and reveal nuclear export as an early step in genome selection.

microbiology↗

bioRxiv2025

Airway microbiome-host transcriptome networks link microbial dysbiosis to survival outcomes and therapeutic opportunities in severe COVID-19

The lower respiratory tract microbiome may critically influence outcomes in severe COVID-19, yet remains understudied. We analyzed bronchoalveolar lavage fluid from 86 severe patients requiring mechanical ventilation, stratified into two groups. We identified 213 bacteria with differential abundance, 11 bacteria associated with differentially expressed genes, and 39 of them were associated with patient survival. The more serious group exhibited reduced microbial network complexity, suggesting ecosystem disruption. To explore therapeutic potential, we employed our previously published model and predicted that compounds like palbociclib, XMD-1499, RS-17053, and RS-504393 may shift host gene expression favoring beneficial microbial signatures. These results highlight an important link between microbial dysbiosis and COVID-19 severity, offering promising directions for microbiome-informed therapeutic strategies. Our findings underscore the importance of the lung microbiome in modulating host responses and clinical outcomes, and suggest that modulating microbial-host interactions may serve as a novel adjunctive approach in the treatment of severe COVID-19. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/661228v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@2fc879org.highwire.dtl.DTLVardef@1128d5dorg.highwire.dtl.DTLVardef@fef0eaorg.highwire.dtl.DTLVardef@17aa499_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors

Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified four molecules, including the broad-spectrum antiviral merimepodib/VX-497, which show anti-nsp5 activity and inhibit SARS-CoV-2 replication in A549-ACE2 cells with IC50 values in the 4-21 {micro}M range. The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.

microbiology↗

bioRxiv2021

Rapid, Reference-Free Human Genotype Imputation with Denoising Autoencoders

Genotype imputation is a foundational tool for population genetics. Standard statistical imputation approaches rely on the co-location of large whole-genome sequencing-based reference panels, powerful computing environments, and potentially sensitive genetic study data. This results in computational resource and privacy-risk barriers to access to cutting-edge imputation techniques. Moreover, the accuracy of current statistical approaches is known to degrade in regions of low and complex linkage disequilibrium. Artificial neural network-based imputation approaches may overcome these limitations by encoding complex genotype relationships in easily portable inference models. Here we demonstrate an autoencoder-based approach for genotype imputation, using a large, commonly-used reference panel, and spanning the entirety of human chromosome 22. Our autoencoder-based genotype imputation strategy achieved superior imputation accuracy across the allele-frequency spectrum and across genomes of diverse ancestry, while delivering at least 4-fold faster inference run time relative to standard imputation tools.

bioinformatics↗

bioRxiv2020

Mixed-stock analysis in the age of genomics: Rapture genotyping enables evaluation of stock-specific exploitation in a freshwater fish population with weak genetic structure

Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Eries commercial and recreational walleye (Sander vitreus) fisheries and estimate the relative harvest of weakly differentiated stocks (pairwise FST < 0.01). We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks with 95% reassignment accuracy, which was not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks constituted the majority of individuals harvested during peak walleye fishing season (July - September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May - June). Clear spatial structure in harvest composition existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.

genomics↗

bioRxiv2020

Identification of potential biomarkers or therapeutic targets of mesenchymal stem cells in multiple myeloma by bioinformatics analysis.

ObjectivesMesenchymal stem cells (MSCs) play important roles in multiple myeloma (MM) pathogenesis. Previous studies have discovered a group of MM-associated potential biomarkers in MSCs derived from bone marrow (BM-MSCs). However, no study of the bioinformatics analysis was conducted to explore the key genes and pathways of MSCs derived from adipose (AD-MSCs) in MM. The aim of this study was to screen potential biomarkers or therapeutic targets of AD-MSCs and BM-MSCs in MM. MethodsThe gene expression profiles of AD-MSCs (GSE133346) and BM-MSCs (GSE36474) were downloaded from Gene Expression Omnibus (GEO) database. Gene Oncology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) network of differentially expressed genes (DEGs) were performed. ResultsA total of 456 common downregulated DEGs in two datasets were identified and the remaining DEGs in GSE133346 were further identified as specific DEGs of AD-MSCs. Furthermore, a PPI network of common downregulated DEGs was constructed and seven hub genes were identified. Importantly, cell cycle was the most significantly enrichment pathway both in AD-MSCs and BM-MSCs from MM patients. ConclusionWe identified key genes and pathways closely related with MM progression, which may act as potential biomarkers or therapeutic targets of MM.

bioinformatics↗

bioRxiv2018

Mammalian stringent-like response mediated by the cytosolic NADPH phosphatase MESH1

Nutrient deprivation triggers stringent response in bacteria, allowing rapid reallocation of resources from proliferation toward stress survival. Critical to this process is the accumulation/degradation of (p)ppGpp regulated by the RelA/SpoT homologues. While mammalian genomes encode MESH1, a homologue of the bacterial (p)ppGpp hydrolase SpoT, neither (p)ppGpp nor its synthetase has been identified in mammalian cells. Therefore, the function of MESH1 remains a mystery. Here, we report that human MESH1 is an efficient cytosolic NADPH phosphatase, an unexpected enzymatic activity that is captured by the crystal structure of the MESH1-NADPH complex. MESH1 depletion promotes cell survival under ferroptosis-inducing conditions by sustaining the level of NADPH, an effect that is reversed by the simultaneous depletion of the cytosolic NAD(H) kinase, NADK, but not its mitochondrial counterpart NADK2. Importantly, MESH1 depletion also triggers extensive transcriptional changes that are distinct from the canonical integrated stress response but resemble the bacterial stringent response, implicating MESH1 in a previously uncharacterized stress response in mammalian cells.

biochemistry↗

bioRxiv2018

Arabidopsis inositol phosphate kinases, IPK1 and ITPK1, constitute a metabolic pathway in maintaining phosphate homeostasis

Emerging studies have implicated a close link between inositol phosphate (InsP) metabolism and cellular phosphate (Pi) homeostasis in eukaryotes; however, whether a common InsP species is deployed as an evolutionarily conserved metabolic messenger to mediate Pi signaling remains unknown. Here, using genetics and InsP profiling combined with Pi starvation response (PSR) analysis in Arabidopsis thaliana, we showed that the kinase activity of inositol pentakisphosphate 2-kinase (IPK1), an enzyme required for phytate (inositol hexakisphosphates; InsP6) synthesis, is indispensable for maintaining Pi homeostasis under Pi-replete conditions, and inositol 1,3,4-trisphosphate 5/6-kinase 1 (ITPK1) plays an equivalent role. Although both ipk1-1 and itpk1 mutants exhibited decreased levels of InsP6 and diphosphoinositol pentakisphosphate (PP-InsP5; InsP7), disruption of another ITPK family enzyme, ITPK4, which correspondingly caused depletion of InsP6 and InsP7, did not display similar Pi-related phenotypes, which precludes these InsP species as effectors. Notably, the level of D/L-Ins(3,4,5,6)P4 was concurrently elevated in both ipk1-1 and itpk1 mutants, which implies a potential role for InsP4 in regulating Pi homeostasis. However, the level of D/L-Ins(3,4,5,6)P4 is not responsive to Pi starvation that instead manifests a shoot-specific increase in InsP7 level. This study demonstrates a more nuanced picture of intersection of InsP metabolism and Pi homeostasis and PSR than has previously been elaborated, and additionally establishes intermediate steps to phytate biosynthesis in plant vegetative tissues.\n\nSignificance StatementRegulation of phosphate homeostasis and adaptive responses to phosphate limitation is critical for plant growth and crop yield. Accumulating studies implicate inositol phosphates as regulators of phosphate homeostasis in eukaryotes; however, the relationship between inositol phosphate metabolism and phosphate signaling in plants remain elusive. This study dissected the step where inositol phosphate metabolism intersects with phosphate homeostasis regulation and phosphate starvation responses.

plant biology↗