Biology subjects

Chau, S.

Publications and source records attributed to Chau, S..

8 recordsLinked to original sources

bioRxiv2026

Endonuclease G governs an antiviral RNA surveillance system in budding yeast

Endonuclease G family DNA/RNA nucleases localize to the mitochondrial intermembrane space and prevent escape of mitochondrial DNA to the cytosol or nucleus. While extramitochondrial Endonuclease G also targets nuclear DNA during cell death, RNA regulatory roles of this family remain enigmatic. Here we discover an RNA surveillance system in Saccharomyces cerevisiae governed by Nuc1, the yeast Endonuclease G homolog. This system limits replication of L-A, an RNA mycovirus that endemically infects this organism. Whereas L-A resides in the cytosol, we find that Nuc1's antiviral function requires its mitochondrial intermembrane space localization. To understand Nuc1's indirect antiviral mechanism we investigated its genetic interactions with REX1 and REX2, RNA exonucleases that control 3' end processing of tRNA and rRNA intermediates in the nucleus. We demonstrate that the nuc1{triangleup} antiviral defect is massively amplified by rex1{triangleup} rex2{triangleup} leading to L-A RNA levels that surpass mature rRNAs and overwhelm the cells. NUC1 concurrently controls a pool of mis-processed tRNA and rRNA species that accumulate in rex1{triangleup} rex2{triangleup} mutants. Linking these mis-processed RNAs with L-A control, we show they are significantly reduced in L-A infected cells, suggesting that L-A depletes them to enhance its replication. Our findings identify a previously unrecognized RNA surveillance function of Nuc1 that prevents aberrant rRNA and tRNA species from promoting replication of the L-A mycovirus.

molecular biology↗

bioRxiv2026

The yeast mitochondrial Porin represses Snf1/AMP Kinase signaling to attenuate viral replication

Although fungi are broadly infected with mycoviruses, the antiviral mechanisms fungal cells use to oppose viral replication are not well understood. Here we discover a new mitochondrially controlled signaling mechanism in the budding yeast Saccharomyces cerevisiae that limits replication of L-A, an RNA mycovirus that endemically infects this organism. We show that Por1, the mitochondrial voltage dependent anion channel, prevents hyper-replication of L-A in stationary phase cells that have exhausted media nutrients. By investigating known stationary phase regulators, we find that deletion of the AMP-activated Kinase homolog SNF1 reverses hyper-replication of L-A observed in por1{Delta} cells. This epistatic relationship suggests that Por1 negatively regulates Snf1 in stationary phase cells and derepressed Snf1 promotes L-A hyper-replication. We confirm this model, first demonstrating that POR1 prevents the accumulation of activated Snf1 throughout stationary phase. By investigating Snf1 signaling targets we show that this POR1-SNF1 regulatory mechanism acts in stationary phase cells to limit amino acid availability that sustain L-A replication. POR1-SNF1 signaling represents a novel physiological control mechanism to limit viral replication in a eukaryotic cell.

genetics↗

bioRxiv2025

A microRNA CRISPR screen reveals miR-483-3p as an apoptotic regulator in prostate cancer

The development of traditional protein-targeted cancer therapies is a slow and arduous process, often taking years or even decades. In contrast, RNA-based therapies targeting crucial microRNAs (miRNAs) offer a faster alternative due to the sequence specific nature of miRNA inhibitor binding. This, combined with the capacity of individual miRNAs to influence multiple cellular pathways, makes these small RNAs attractive targets for cancer therapy. While miRNA are known to be dysregulated in prostate cancer (PCa), identifying their individual contributions to disease progression and the identification of therapeutically actionable miRNA targets in PCa has been challenging due to limited screening tools. To overcome this, we developed miRKOv2, a miRNA-only CRISPR knockout library enabling systematic, genome-wide loss-of-function screens to identify miRNAs essential for PCa cell survival. Our screens uncovered 69 potential essential miRNA candidates, with miR-483 demonstrating the most significant impact on PCa cell viability. Functional characterization demonstrated that miR-483 disruption significantly potentiated apoptosis in PCa cell lines. Mechanistically, we uncovered a novel regulatory axis wherein miR-483-3p directly modulates a BCLAF1/PUMA/BAK1 apoptotic signaling network, highlighting its critical role in maintaining PCa cell survival. Our findings provide novel insights into the complex regulatory role of miRNA in PCa progression and offer a potential therapeutic strategy for targeting miRNA-mediated pathways in metastatic disease.

cancer biology↗

bioRxiv2023

Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV

Older individuals and people with HIV (PWH) were prioritized for COVID-19 vaccination, yet comprehensive studies of the immunogenicity of these vaccines and their effects on HIV reservoirs are not available. We followed 68 PWH aged 55 and older and 23 age-matched HIV-negative individuals for 48 weeks from the first vaccine dose, after the total of three doses. All PWH were on antiretroviral therapy (cART) and had different immune status, including immune responders (IR), immune non-responders (INR), and PWH with low-level viremia (LLV). We measured total and neutralizing Ab responses to SARS-CoV-2 spike and RBD in sera, total anti-spike Abs in saliva, frequency of anti-RBD/NTD B cells, changes in frequency of anti-spike, HIV gag/nef-specific T cells, and HIV reservoirs in peripheral CD4+ T cells. The resulting datasets were used to create a mathematical model for within-host immunization. Various regimens of BNT162b2, mRNA-1273, and ChAdOx1 vaccines elicited equally strong anti-spike IgG responses in PWH and HIV- participants in serum and saliva at all timepoints. These responses had similar kinetics in both cohorts and peaked at 4 weeks post-booster (third dose), while half-lives of plasma IgG also dramatically increased post-booster in both groups. Salivary spike IgA responses were low, especially in INRs. PWH had diminished live virus neutralizing titers after two vaccine doses which were rescued after a booster. Anti-spike T cell immunity was enhanced in IRs even in comparison to HIV- participants, suggesting Th1 imprinting from HIV, while in INRs it was the lowest. Increased frequency of viral blips in PWH were seen post-vaccination, but vaccines did not affect the size of the intact HIV reservoir in CD4+ T cells in most PWH, except in LLVs. Thus, older PWH require three doses of COVID-19 vaccine to maximize neutralizing responses against SARS-CoV-2, although vaccines may increase HIV reservoirs in PWH with persistent viremia.

immunology↗

bioRxiv2022

On the synergies between ribosomal assembly and machine learning tools for microbial identification

Genome assembly tools are used to reconstruct genomic sequences from raw sequencing data, which are then used for identifying the organisms present in a metagenomic sample. More recently, machine learning approaches have been applied to a variety of bioinformatics problems, and in this paper, we explore their use for organism identification. We start out by evaluating several commonly used metagenomic assembly tools, including PhyloFlash, MEGAHIT, MetaSPAdes, Kraken2, Mothur, UniCycler, and PathRacer, and compare them against state-of-the art deep learning-based machine learning classification approaches represented by DNABERT and DeLUCS, in the context of two synthetic mock community datasets. Our analysis focuses on determining whether ensembling metagenome assembly tools with machine learning tools has the potential to improve identification performance relative to using the tools individually. We find that this is indeed the case, and analyze the level of effectiveness of potential tool ensembling for organisms with different characteristics (based on factors such as repetitiveness, genome size, and GC content). Author SummaryMetagenomic studies focus on the challenging problem of identifying the presence and abundance of different species in a sample. This process typically involves the creation of digital reads from the sample which correspond to small parts of the genome sequence, and then have to be assembled together by a genome assembly tool. More recently, machine learning approaches have been applied to a variety of bioinformatics problems, and in this paper, we explore their use for organism identification, and how they might complement traditional bioinformatics approaches. We conduct experiments with two representative state-of-the-art machine learning approaches and six metagenomic assembly tools in the context of two synthetic datasets. We find that for organisms with certain characteristics (levels of repetitiveness, GC content, and genome size), ensembling metagenome assembly tools with machine learning tools has the potential to improve species identification performance relative to using the tools individually.

bioinformatics↗

bioRxiv2022

Diverse innate immune factors protect yeast from lethal viral pathogenesis

In recent years, newly characterized anti-viral systems have proven to be remarkably conserved from bacteria to mammals, demonstrating that unique insights into these systems can be gained by studying microbial organisms. Despite the enthusiasm generated by these findings, the key microbial model organism Saccharomyces cerevisiae (budding yeast) has been minimally exploited for studies of viral defense, primarily because it is not infected with exogenously transmitted viruses. However, most yeast strains are infected with an endogenous double stranded RNA (dsRNA) virus called L-A, and previous studies identified conserved antiviral systems that attenuate L-A replication. Although these systems do not completely eradicate L-A, we show here that they do prevent proteostatic stress and lethality caused by L-A over-proliferation. Exploiting this new finding, we demonstrate that the genetic screening methods available in yeast can be used to identify additional conserved antiviral systems. Using these approaches, we discovered antiviral functions for the yeast homologs of polyA-binding protein (PABPC1) and the La-domain containing protein Larp1, which are both involved in viral innate immunity in humans. We also identified new antiviral functions for the RNA exonucleases REX2 and MYG1, both of which have distinct but poorly characterized human and bacterial homologs. These findings highlight the potential of yeast as a powerful model system for the discovery and characterization of conserved antiviral systems. Significance StatementThe budding yeast Saccharomyces cerevisiae has been minimally exploited for investigation of host-virus interactions despite its chronic infection with a double-stranded RNA virus called L-A. Controverting its presumed harmless nature, we show here that L-A causes pathogenesis in cells lacking parallel-acting viral attenuation pathways. Taking advantage of the genetic tools available in budding yeast, we identify several highly conserved proteins to play a role in antiviral defense. Some of these have been recently identified in humans to be involved in viral innate immunity, thus highlighting the potential of budding yeast as a model organism to identify and investigate new antiviral systems.

microbiology↗

bioRxiv2021

Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B

Safe and effective vaccines are needed to end the COVID-19 pandemic caused by SARS-CoV-2. Here we report the preclinical development of a lipid nanoparticle (LNP) formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutralizing antibody response against SARS-CoV-2. Further tests in mice and hamsters indicated that PTX-COVID19-B induced robust humoral and cellular immune responses and completely protected the vaccinated animals from SARS-CoV-2 infection in the lung. Studies in hamsters also showed that PTX-COVID19-B protected the upper respiratory tract from SARS-CoV-2 infection. Mouse immune sera elicited by PTX-COVID19-B vaccination were able to neutralize SARS-CoV-2 variants of concern (VOCs), including the B.1.1.7, B.1.351 and P.1 lineages. No adverse effects were induced by PTX-COVID19-B in both mice and hamsters. These preclinical results indicate that PTX-COVID19-B is safe and effective. Based on these results, PTX-COVID19-B was authorized by Health Canada to enter clinical trials in December 2020 with a phase 1 clinical trial ongoing (ClinicalTrials.gov number: NCT04765436). One Sentence SummaryPTX-COVID19-B is a SARS-CoV-2 mRNA vaccine that is highly immunogenic, safe, and effective in preventing SARS-CoV-2 infection in mice and hamsters and is currently being evaluated in human clinical trials.

immunology↗

bioRxiv2019

Meiotic viral attenuation through an ancestral apoptotic pathway

The programmed release of apoptogenic proteins from mitochondria is a core event of apoptosis, though ancestral roles of this phenomenon are not known. In mammals, one such apoptogenic protein is Endonuclease G (EndoG), a conserved nuclease that fragments the DNA of dying cells. In this work, we show that budding yeast executes meiotically programmed mitochondrial release of an EndoG homologue, Nuc1, during sporulation. In contrast to EndoGs ostensible pro-death function during apoptosis, Nuc1 mitochondrial release attenuates the cytosolic dsRNA mycovirus, Killer, protecting spores from a lethal accumulation of its encoded toxin. Our identification of cell-protective viral attenuation as a target of this rudimentary apoptotic pathway illuminates a primordial role for mitochondrial release of EndoG.\n\nOne Sentence SummaryYeast sporulation induces release of mitochondrial endonuclease G to accomplish viral attenuation.

genetics↗