Biology subjects

Kim, Z.

Publications and source records attributed to Kim, Z..

3 recordsLinked to original sources

bioRxiv2026

Spiperone targets HBV cccDNA via ER stress induced innate immune activation and epigenetic silencing

Chronic hepatitis B persists due to the stability of nuclear covalently closed circular DNA (cccDNA), which maintains viral transcription despite prolonged antiviral therapy, highlighting the need for strategies that suppress cccDNA via host-targeted mechanisms. Here, we identify Spiperone, a clinically approved compound, as a repurposed anti-HBV candidate with strong translational potential. Spiperone robustly reduced HBsAg, HBeAg, viral DNA, and pgRNA across HepG2.2.15, HBV-infected HepG2-NTCP-C4 and HepaRG cells, and multiple in vivo models, including HBV transgenic, hydrodynamic injection, and AAV- HBV1.04x models. Notably, intrahepatic cccDNA was significantly diminished. In combination, Spiperone potentiated tenofovir activity, exhibiting synergistic effects, while both intraperitoneal and oral administration reduced antigenemia and viremia. Mechanistically, Spiperone activated the PERK-eIF2-ATF4 arm of the ER stress response, coupled with mitochondrial perturbation and cytosolic release of oxidized mitochondrial DNA, leading to activation of IFI16-STING-IRF3 signaling. This cascade induced type I interferon (IFN-I) and interferon-stimulated genes. ChIP-qPCR further demonstrated reduced enrichment of activating histone marks on cccDNA, consistent with transcriptional repression. Collectively, these findings position Spiperone as a host-directed antiviral that converges ER stress-linked innate immunity and epigenetic repression to suppress cccDNA, supporting its advancement in combination strategies toward a functional cure for chronic HBV infection.

microbiology↗

bioRxiv2025

Proteomic Signatures of Hepatitis B Virus Mutations Reveal Genotype-Specific Host Responses and Biomarker Candidates

Hepatitis B virus (HBV) remains a global health challenge, with viral genetic heterogeneity and mutation-driven resistance complicating treatment outcomes. While previous genomic and transcriptomic studies have characterized HBV mutations, the proteomic consequences of these variants remain underexplored. In this study, we applied liquid chromatography- mass spectrometry (LC-MS)-based proteomics and systems biology approaches to serum samples from 60 HBV-infected patients, stratified by mutation-defined genotype signatures. Four genotype groups were generated, including those harboring mutation related to liver disease progression (rt269/s184) and basal core promoter/precore mutations (A1762T/G1896A). Comparative analyses of 406 high-abundance plasma proteins revealed distinct proteomic signatures, particularly in the ##AG group lacking mutation related to liver disease progression motifs. This group exhibited elevated CRISPLD2 and HSPD1 expression, implicating a dual axis of anti-inflammatory buffering and chaperone-mediated viral processes. Network and co-expression analyses identified modules enriched in focal adhesion, extracellular matrix remodeling, angiogenesis, and PI3K/Akt signaling--pathways tightly linked to hepatocarcinogenesis. Protein-protein interaction enrichment further highlighted disruption of chaperone networks, cytoskeletal regulation, and unfolded protein response. These findings provide molecular evidence for genotype-specific host-virus interactions, nominate CRISPLD2 and HSPD1 as biomarker candidates, and suggest therapeutic strategies targeting PI3K/Akt and microenvironmental pathways. Our results underscore the value of proteomics in refining genotype-informed risk stratification and personalized management in chronic HBV.

systems biology↗

bioRxiv2025

T7 RNA polymerase-based gene expression from a transcriptionally silent rDNA spacer in the endosymbiont-harboring trypanosomatid Angomonas deanei

Eukaryotic life has been shaped fundamentally by the integration of bacterial endosymbionts. The trypanosomatid Angomonas deanei that contains a {beta}-proteobacterial endosymbiont, represents an emerging model to elucidate initial steps in symbiont integration. Although the repertoire of genetic tools for A. deanei is growing, no conditional gene expression system is available yet, which would be key for the functional characterization of essential or expression of toxic proteins. Development of a conditional expression system based on endogenous RNA polymerase II (POLII) is hampered by the absence of information on transcription signals in A. deanei as well as the unusual genetic system used in the Trypanosomatidae that relies on read-through transcription. This mode of transcription can result in polar effects when manipulating expression of genes in their endogenous loci. Finally, only few resistance markers are available for A. deanei yet, restricting the number of genetic modifications that can be introduced into one strain. To increase the range of possible genetic manipulations in A. deanei, and in particular, build the base for a conditional expression system that does not interfere with the endogenous gene expression machinery, here we (i) implemented two new drug resistance markers, (ii) identified the spacer upstream of the rDNA array on chromosome 13 as transcriptionally silent genomic locus, and (iii) used this locus for engineering an ectopic expression system that depends on the T7 RNA polymerase expressed from the {delta}-amastin locus. We show that transgene expression in this system is independent of the activity of endogenous RNA polymerases, reaches expression levels similar to the previously described POLII-dependent expression from the {gamma}-amastin locus, and can be applied for studying endosymbiosis. In sum, the new tools expand the possibilities for genetic manipulations of A. deanei and provide a solid base for the development of an ectopic conditional expression system.

genetics↗