Biology subjects

Sarnow, P.

Publications and source records attributed to Sarnow, P..

6 recordsLinked to original sources

bioRxiv2026

Distinct virus-derived circular RNA molecule influences host response during SARS-CoV-2 infection

Virus-derived circular RNA molecules (VcircRNAs) are expressed by many RNA viruses during infection. Putative functions include modulating viral replication and interacting with the host immune response. Some function as non-coding RNA fragments that regulate gene expression through binding to complementary RNA sequences, whereas others contain internal ribosomal entry site (IRES) sequences or non-canonical modifications that allow them to be translated. Here, we confirm the expression of a distinct SARS-CoV-2 VcircRNA molecule, circ7b8N, that has not been previously identified. We found that circ7b8N is expressed and detectable in cell culture infections and in acute infections across SARS-CoV-2 variants and shows promise for detection in post-acute clinical samples. Conservation of circ7b8N junctions is limited to the nearest phylogenetic relatives within the betacoronavirus genus but are present in other human and bat-infecting coronaviruses. Host cell gene expression is modulated by the treatment with circ7b8N agnostic of viral infection. The discovery and subsequent confirmation of circ7b8N expressed by SARS-CoV-2 provides a new biomarker for infection, and its conservation across variants suggests functional importance. Author SummaryCircular RNAs are a well-documented class of molecules expressed by mammalian cells. However, circular RNA molecules expressed by RNA viruses remain largely uncharacterized regarding their generation, specific functions, and roles in host-pathogen interactions. Our computational predictions discovered thousands of distinct circular RNA molecules expressed by SARS-CoV-2. Among these, we confirmed the presence of circ7b8N, the most abundant SARS-CoV-2-derived circular RNA identified in our sequencing data. We found that circ7b8N localizes outside the nucleus and is detectable in clinical samples collected both during and after acute SARS-CoV-2 infection. Although overexpression of circ7b8N was not found to alter viral titers, it modulated the expression of host genes related to immune response activation and membrane remodeling. This suggests that circ7b8N may simultaneously provide pro- and anti-viral functions independent of influencing viral replication. Phylogenetic analyses of coronaviruses suggest that the expression of circ7b8N is a relatively recent evolutionary event, and it is conserved across SARS-CoV-2 variants from the first five years of the pandemic. The abundant presence of circ7b8N across variants in both sequencing data and clinical samples implies it plays a multifaceted role in SARS-CoV-2 pathogenesis.

microbiology↗

bioRxiv2023

Virus-derived circular RNAs populate hepatitis C virus-infected cells

It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a back- splicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into novel proteins that displayed pro-viral functions. Furthermore, a highly abundant, non-translated vcircRNA was shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus. Significance StatementProcessing of an RNA viral genome into hundreds of circular RNAs provides novel pro-viral functions and can promote translation of novel viral peptides.

microbiology↗

bioRxiv2021

Loquacious Modulates Flaviviral RNA Replication in Mosquito Cells

Arthropod-borne viruses infect both mosquito and mammalian hosts. While much is known about virus-host interactions that modulate viral gene expression in their mammalian host, much less is known about the interactions that involve inhibition, subversion or avoidance strategies in the mosquito host. A novel RNA-Protein interaction detection assay was used to detect proteins that directly or indirectly bind to dengue viral genomes in infected mosquito cells. Membrane-associated mosquito proteins SEC61A1 and Loquacious (Loqs) were found to be in complex with the viral RNA. Depletion analysis demonstrated that both SEC61A1 and Loqs have pro-viral functions in the dengue viral infectious cycle. Co-localization and pull-down assays showed that Loqs interacts with viral protein NS3 and both full-length and subgenomic viral RNAs. While Loqs coats the entire positive-stranded viral RNA, it binds selectively to the 3 end of the negative-strand of the viral genome. In-depth analyses showed that the absence of Loqs did not affect translation or turnover of the viral RNA but modulated viral replication. Loqs also displayed pro-viral functions for several flaviviruses in infected mosquito cells, suggesting a conserved role for Loqs in flavivirus-infected mosquito cells. Author SummaryThere is a wealth of information that dictates virus-host interactions in flavivirus-infected mammalian cells, yet there is only sparse information on the mechanisms that modulate viral gene expression in the mosquito host. Using a novel RNA-protein detection assay, the interactions of SEC61A1 and Loqs with the dengue viral genome were found to have proviral functions in infected mosquito cells. In particular, Loqs forms complexes with the positive-strand of the viral RNA and the very 3 end of the negative-strand viral RNA. Further analyses showed that Loqs modulates viral RNA replication of dengue virus and gene amplification of several other flaviviral genomes. These findings argue that Loqs is an essential proviral host factor in mosquitos.

microbiology↗

bioRxiv2020

An evolutionarily acquired microRNA shapes development of mammalian cortical projections

The corticospinal tract is unique to mammals and the corpus callosum is unique to placental mammals (eutherians). The emergence of these structures is thought to underpin the evolutionary acquisition of complex motor and cognitive skills. Corticospinal motor neurons (CSMN) and callosal projection neurons (CPN) are the archetypal projection neurons of the corticospinal tract and corpus callosum, respectively. Although a number of conserved transcriptional regulators of CSMN and CPN development have been identified in vertebrates, none are unique to mammals and most are co-expressed across multiple projection neuron subtypes. Here, we discover seventeen CSMN-enriched microRNAs (miRNAs), fifteen of which map to a single genomic cluster that is exclusive to eutherians. One of these, miR-409-3p, promotes CSMN subtype identity in part via repression of LMO4, a key transcriptional regulator of CPN development. In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is the first demonstration of an evolutionarily acquired miRNA in eutherians that refines cortical projection neuron subtype development. Our findings implicate miRNAs in the eutherians increase in neuronal subtype and projection diversity, the anatomic underpinnings of their complex behavior. Significance StatementThe mammalian central nervous system contains unique projections from the cerebral cortex thought to underpin complex motor and cognitive skills, including the corticospinal tract and corpus callosum. The neurons giving rise to these projections - corticospinal and callosal projection neurons - develop from the same progenitors, but acquire strikingly different fates. The broad evolutionary conservation of known genes controlling cortical projection neuron fates raises the question of how the more narrowly conserved corticospinal and callosal projections evolved. We identify a microRNA cluster selectively expressed by corticospinal projection neurons and exclusive to placental mammals. One of these microRNAs promotes corticospinal fate via regulation of the callosal gene LMO4, suggesting a mechanism whereby microRNA regulation during development promotes evolution of neuronal diversity.

neuroscience↗

bioRxiv2020

Host-derived Circular RNAs Display Proviral Activities in Hepatitis C Virus - Infected Cells

Viruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Surprisingly, circPSD3 also inhibited the cellular nonsense-mediated decay (NMD) pathway in liver cells. Thus, enhanced abundance of circPSD3 in virus-infected cells aids in viral replication and likely contributes to the known inhibition of NMD in HCV-infected cells. Findings from the global analyses of the circular RNA landscape argue pro-, and likely, anti-viral functions are executed by circRNAs that modulate both viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis. Author SummaryUsually, cells are infected by one or a few virus particles that carry genomes with limited expression capacity. Thus, the expression of viral genomes has to compete with a sea of cellular components that aid in viral translation, replication and virion production. Depending on their lifestyle, viruses have evolved to avoid or to subvert cellular pathways, especially those that display anti-viral functions. Host-derived circular RNA molecules have recently been discovered in the cytoplasm of cells, although, as-of yet, few functions have been assigned to them. Here, we describe alterations in the circular RNA landscape in hepatitis C virus-infected liver cells. Up-regulated and down-regulated circular RNAs were identified, and three of the upregulated RNAs were shown to promote HCV infection. One of them, circPSD3, inhibited the cellular nonsense-mediated RNA decay that is a powerful antiviral response in infected cells. Because circular RNAs are more stable than linear RNAs, they may have important functions during viral infection, dictating the outcomes of innate immune responses and viral pathogenesis.

microbiology↗

bioRxiv2018

Impact of a Patient-Derived Hepatitis C Viral RNA Genome with a Mutated MicroRNA Binding Site

Hepatitis C virus (HCV) depends on liver-specific microRNA miR-122 for efficient viral RNA amplification in liver cells. This microRNA interacts with two different conserved sites at the very 5 end of the viral RNA, enhancing miR-122 stability and promoting replication of the viral RNA. Treatment of HCV patients with oligonucleotides that sequester mir-122 resulted in profound loss of viral RNA in phase II clinical trials. However, some patients accumulated in their sera a viral RNA genome that contained a single cytidine to uridine mutation at the third nucleotide from the 5 genomic end. It is shown here that this C3U variant indeed displayed higher rates of replication than that of wild-type HCV when miR-122 abundance is low in liver cells. However, when miR-122 abundance is high, binding of miR-122 to site 1, most proximal to the 5 end in the C3U variant RNA, is impaired without disrupting the binding of miR-122 to site 2. As a result, C3U RNA displays a much lower rate of replication than wild-type mRNA when miR-122 abundance is high in the liver. These findings suggest that sequestration of miR-122 leads to a resistance-associated mutation that has only been observed in treated patients so far, and raises the question about the function of the C3U variant in the peripheral blood.\n\nAuthor SummaryWith the advent of potent direct-acting antivirals (DAA), hepatitis C virus (HCV) can now be eliminated from the majority of patients, using multidrug therapy with DAAs. However, such DAAs are not available for the treatment of most RNA virus infections. The main problem is the high error rate by which RNA-dependent RNA polymerases copy viral RNA genomes, allowing the selection of mutations that are resistant to DAAs. Thus, targeting host-encoded functions that are essential for growth of the virus but not for the host cell offer promising, novel approaches. HCV needs host-encoded microRNA miR-122 for its viral RNA replication in the liver, and depletion of miR-122 in HCV patients results in loss of viral RNA. This study shows that a single-nucleotide mutation in HCV allows viral RNA amplification when miR-122 abundances are low, concomitant with changes in its tropism.

microbiology↗