Search bioRxiv⌕ Search

Biology subjects

Ganesh, N.

Publications and source records attributed to Ganesh, N..

3 recordsLinked to original sources

Dynamic regulation of cystathionine gamma-lyase expression during normoxia, ischemia, and reperfusion in liver: interplay of transcription factors, microRNAs, and histone modifications

Cystathionine gamma-lyase (CTH), a key enzyme in hydrogen sulfide (H2S) biosynthesis, has been studied extensively in models of oxidative stress. Dysregulated CTH has been reported in cardiovascular disease, ischemia-reperfusion (I/R) injury, aging, and xenobiotic stress, where reactive oxygen species are central to pathology. Despite this, how CTH is regulated at the molecular level under basal, ischemic, and reperfusion conditions is largely unknown. We observed that CTH expression is dysregulated during ischemia and reperfusion in Huh7 hepatic cells, mouse liver, and human liver, and therefore systematically dissected its transcriptional, post-transcriptional, and epigenetic control. Promoter-deletion reporter assays identified the -275/+91 bp region as the core human CTH promoter. This region was predicted to harbour binding sites for Sp1, CREB, and NFY, which were confirmed through overexpression, knockdown or inhibition, and ChIP assays in Huh7 cells. Computational and experimental screening identified miR-150-5p and miR-510-5p as novel post-transcriptional regulators that bind directly to the CTH 3'-UTR. We also examined histone marks (H3K9ac, H3K9me3, H3K4me3, and H3K27me3) at the CTH promoter and found that H3K9ac, H3K4me3, and H3K27me3 correlate with CTH expression across basal, ischemic, and reperfusion conditions. Mechanistically, ischemia reduces Sp1 occupancy at the CTH promoter, raises miR-150-5p and miR-510-5p levels, lowers H3K9ac, collectively suppressing CTH. Reperfusion reverses this with greater Sp1 and CREB binding, lower miR-150-5p and miR-510-5p levels, and reduced H3K27me3, restoring CTH expression. Together, these findings reveal novel roles for Sp1, CREB, NFY, miR-150-5p, miR-510-5p, and histone modifications in the regulation of CTH during basal, ischemia and reperfusion conditions.

molecular biology↗

A High-Dimensional Interfacial Wave Assay for Early Biophysical Profiling of Therapeutic Antibodies

Therapeutic antibody performance depends not only on sequence and structure, but also on how the molecule responds to physico-chemical perturbations encountered in its environment. Whereas sequence and static structure can be inferred under controlled conditions, behaviour is a conditional, multidimensional response to environment, most directly characterised by applying defined perturbations and quantifying the resulting dynamics. Conventional early-stage developability methods capture isolated dimensions of this response under near-equilibrium conditions, deferring integrated behavioural assessment to late-stage characterisation, when the cost of correction is highest. We introduce Variations in Interfacial Behaviour under Excitation (VIBE), an interfacial wave method implemented via Liquid State Intelligence (LSI), a sensing architecture that transduces molecular perturbations at the air-liquid interface into high-dimensional wave patterns. A colloidal liquid substrate operated near a thermodynamic transition couples small molecular perturbations to large dynamical responses, integrating structural flexibility, charge distribution, and surface hydrophobicity into a single behavioural readout from microgram-scale samples. Applied to antibodies previously characterised by industrial benchmarks, the primary behavioural descriptor, VIBE1, functioned as a high-precision triage tool, flagging candidates carrying multiple biophysical liabilities. In a clinical-stage cohort, the proportion of high-VIBE1 antibodies declined progressively from early trials through approval, and high-VIBE1 candidates showed an elevated clinical failure rate. Concordance analysis against estab-lished methods confirmed that VIBE1 captures a composite signal spanning hydrophobicity, polyreactivity, self-interaction, and thermal stability rather than recapitulating any single conventional readout. These findings establish interfacial wave sensing as a low-material modality for early-stage developability assessment, repositioning molecular behaviour from late-stage validation to discovery-phase characterisation.

biophysics↗

Identification of Cyclin L1 as a host factor regulating Hepatitis B Virus replication

Background & AimsUnderstanding the regulatory interactions between Hepatitis B virus (HBV) and human host factors is key to the development of next-generation host-directed antiviral therapies and achieving a functional HBV cure. In this study, we aimed to investigate HBV-induced alterations in host gene expression in primary human hepatocytes (PHH) to identify host-specific factors that are regulated and exploited by the virus for replication and survival. MethodsWe performed whole transcriptome sequencing (WTS) of HBV-infected PHH to identify host pathways that could potentially influence the HBV life cycle. RNA-interference-based validation of putative targets to evaluate the function of dysregulated candidate genes resulted in the identification of Cyclin L1 (CCNL1) as a key host factor. ResultsRNAi-knockdown of CCNL1 revealed that it is essential for HBV gene expression, including HBV-surface antigen (HBsAg). Mechanistically, we found that CCNL1 can phosphorylate the C-terminal domain (CTD) of RNA Polymerase II (RNAPII) at serine 2 (S2), likely to regulate HBV transcription. Furthermore, the knockdown of CCNL1 inhibited the binding of total and phospho- (Ser2-Ser5) RNAPII, pan-acetylated H3ac, and H3K27ac to HBV cccDNA, implicating its function in the regulation of cccDNA-dependent viral transcription. Finally, enhanced CCNL1 expression in chronic hepatitis B patients, as compared to those with resolved infection, underscores a functional link between this host factor and CHB. ConclusionOur data demonstrates that CCNL1 regulates HBV RNA transcription and replication by modulating RNAPII phosphorylation and activity, making it a potential host susceptibility factor for HBV. LAY SUMMARYHepatitis B requires human host cell factors and biological processes to establish an efficient infection. Identifying host factors that support and/or restrict HBV infection is essential for understanding the molecular basis of chronic HBV infection and for developing host-targeting anti-HBV drugs. Here, we report that CCNL1 can serve as a potential host susceptibility factor for HBV, as reduced CCNL1 function results in reduced viral replication and gene expression. Graphical SummaryGraphical summary, highlighting the approach and validation experiments. From whole transcriptomics analysis, we identified known HBV-host factors such as SRPK1, CDK1, NXF1 among others as well as new factors such as CCNL1. Employing various RNAi approaches and different cell models including primary human hepatocytes, we validated the role of CCNL1 during HBV infection cycle. Pull-down experiments followed by ChIP-PCR further showed a reduction in cccDNA-based transcription upon knockdown of CCNL1. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/619969v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1ee9cd9org.highwire.dtl.DTLVardef@7bac2dorg.highwire.dtl.DTLVardef@164c3bborg.highwire.dtl.DTLVardef@6e497a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗