Biology subjects

Bosco, G.

Publications and source records attributed to Bosco, G..

14 recordsLinked to original sources

bioRxiv2026

Host DNA repair factors empower a mechanism of antiviral nucleoside analog resistance

How host functions affect resistance to antiviral drugs is poorly understood. Ganciclovir, a chain-terminating nucleoside analog, is a first-line therapy against human cytomegalovirus, a widespread herpesvirus that causes life-threatening disease in immunocompromised individuals and newborns. Ganciclovir resistance, which is caused by mutations that affect the viral kinase, UL97 and/or the viral polymerase, UL54, can cause treatment failures. Among these mutations, those reducing the exonuclease activity of the viral DNA polymerase permit ganciclovir incorporation without chain termination. However, the fate of DNA strands containing the incorporated nucleotide analog is unknown. We show here that template DNA containing ganciclovir fails to support DNA synthesis of the complementary strand by exonuclease-mutant polymerase. Moreover, while DNA synthesis and ganciclovir incorporation are limited in drug-treated fibroblasts infected by virus with wild-type polymerase, an exonuclease-resistant mutant virus can better synthesize full-length genomes and incorporate substantially more ganciclovir into DNA. Notably, ganciclovir is lost from DNA when drug is removed, suggesting that ganciclovir-containing templates are repaired. We identify the host nucleotide excision repair component, XPA, and the repair enzyme, polymerase kappa, as each being necessary for mutant virus ganciclovir resistance and polymerase kappa as being required for the mutants cidofovir resistance, demonstrating a role for host DNA repair machinery in a mechanism of antiviral resistance. We propose a model for this mechanism, which has relevance for at least one other antiviral drug and likely other nucleoside analog therapeutics, and highlights the participation of host DNA repair machinery during human cytomegalovirus DNA replication. IMPORTANCENucleoside analogues such as ganciclovir, which is a leading drug for preventing and treating human cytomegalovirus, are a critical defense against viral diseases, but antiviral resistance often results in treatment failures. This study reveals a critical role for host DNA repair in a mechanism of resistance to ganciclovir, and identifies at least one specific repair pathway that permits viral DNA synthesis in the presence of ganciclovir, defining a mechanism by which cellular DNA repair pathways conspire to enable antiviral drug resistance. This mechanism is relevant to at least one other antiviral drug and may apply to other antiviral and anticancer agents. The study also showcases the participation of host DNA repair machinery during human cytomegalovirus DNA synthesis.

microbiology↗

bioRxiv2026

A targetable dependency on nonsense-mediated decay for proteostasis and immune control in small cell lung cancer

Small cell lung cancer (SCLC) is among the deadliest cancers with excessive somatic alterations, expectedly resulting in immunogenic epitopes. However, patient benefit from immunotherapy is limited. We found abundant frameshift mutations in SCLC, regarded as highly immunogenic, counterbalanced by a hyperactive nonsense-mediated decay (NMD) pathway, responsible for frameshift-mRNA degradation. NMD activity correlated with tumor mutational burden (TMB) across cancers, suggesting that SCLC depends on NMD for cellular homeostasis and immune evasion. NMD inhibition impaired SCLC proliferation and induced ER stress-dependent apoptosis in a TMB-dependent manner, thereby enabling pharmacological inhibition in vivo which effectively controlled tumor growth. By integrating genome and transcriptome sequencing with MHC-I immunopeptidomics and functional in vitro and in vivo assays, we identified that NMD inhibition boosted neoantigen expression and presentation by tumor cells and increased T cell recognition, thus enhancing overall tumor immunogenicity and further improving immunotherapy efficacy in vivo. Our work shows that SCLC - as a TMBhigh cancer - relies on NMD for survival and immune escape, uncovering a novel TMB-dependent tractable vulnerability for this devastating disease.

cancer biology↗

bioRxiv2025

Human cytomegalovirus regulates host DNA repair machinery for viral genome integrity

The DNA damage response (DDR) encompasses a multitude of interconnected pathways that serve as a cellular defense to protect genome integrity. Dysregulation or failure of these pathways results in cancers and genetic disease. DNA viruses, including the herpesvirus cytomegalovirus (CMV), activate DDR signaling during their replicative program. The mechanisms by which they commandeer these responses for replication of their genome is less well understood. Here, we define a viral protein, UL138, that modulates the activity of host DDR pathways. The loss of UL138 results in structural variants, including inversion, deletions, duplication, with signature of homology-directed repair and other DDR pathways. The actions of UL138 are due, in part, to its modulation of pathways regulated by the cellular deubiquitinating complex that targets proliferating cell nuclear antigen (PCNA) and Fanconi Anemia effectors, FANCD2 and FANCI. However, we also show that UL138 accesses pathways independent of USP1-PCNA/FANCD2/FANCI. Disruption of UL138 or these pathways impacts viral genome replication and had consequences for viral genome integrity. This work provides mechanistic insight into the long-standing questions of how DNA viruses recruit, modulate and use cellular DDR pathways. It also puts forth CMV as a model system for further defining these pathways in human cells. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/683233v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@121e55borg.highwire.dtl.DTLVardef@58d8b7org.highwire.dtl.DTLVardef@fc1628org.highwire.dtl.DTLVardef@12b32a_HPS_FORMAT_FIGEXP M_FIG C_FIG Major findingsO_LIUL138 protects HCMV genome integrity through its interaction with USP1-PCNA/FANCD2/FANCI and repeat sequence-mediated pathways C_LIO_LIUL138 protects HCMV genome integrity in the UL region by mechanisms independent of repeat sequences and USP1-PCNA/FANCD2/FANCI C_LIO_LICollectively, US and UL regions of the HCMV genome have fundamentally different pathways acting on them and UL138 modulates DNA damage and repair pathway choice. C_LI

microbiology↗

bioRxiv2025

Task demands and visual context naturalness modulate gravitational expectation during ocular tracking of temporarily occluded ballistic trajectories

During ocular tracking of a target, contextual information provides useful cues to account for motion features the visual system is poorly sensitive to, like its acceleration. For example, the brain can rely on an internal model of gravity to intercept and track accelerated targets under gravity, and cues about the visual environment naturalness can facilitate its recruitment. Notably, in real life, these two tasks are often associated. Experimental evidence suggests that predictive information may be shared between the two tasks, albeit their concurrent execution can, in turn, affect the oculomotor performance. To gain further insight on how task demands and the naturalness of the visual context affect the weighting of sensory feedback and predictive feedforward information in ocular tracking, subjects tracked targets either congruent with gravity or perturbed during the trajectory with altered gravity. Targets were projected on either pictorial or neutral background, and, to enforce prediction, were occluded for variable intervals 550 ms after the perturbation. Sixty-nine participants were divided into two groups: one group performed only ocular tracking, the other also intercepted the targets. In general, subjects ocular tracking performance depended on the target acceleration level and the visual context, with effects of gravitational expectations being more evident with the pictorial naturalistic environment. This result reinforced the idea that gravity a priori information can be weighted based on the naturalness of the visual context. Another striking finding was that participants who only tracked the target showed systematic changes of the oculomotor performance with the acceleration level right after the perturbation, compatible with a strong reliance on gravitational expectation; instead, participants that also intercepted the target showed such systematic changes primarily after the targets occlusion, perhaps weighting more sensory information until then. Thus, concurrence of ocular tracking and manual interception seemingly influenced the temporal recruitment of internalized gravity information.

neuroscience↗

bioRxiv2025

Complex roles for proliferating cell nuclear antigen in human cytomegalovirus replication

DNA viruses at once elicit and commandeer host pathways, including DNA repair pathways for virus replication. Despite encoding its own DNA polymerase and processivity factor, human cytomegalovirus (HCMV) recruits the cellular processivity factor, proliferating cell nuclear antigen (PCNA) and specialized host DNA polymerases involved in translesion synthesis (TLS) to replication compartments (RCs) where viral DNA (vDNA) is synthesized. While the recruitment of TLS polymerases is important for viral genome stability, the role of PCNA is poorly understood. PCNA function in DNA repair is regulated by monoubiquitination (mUb) or SUMOylation of PCNA at lysine 164 (K164). We find that mUb-PCNA increases over the course of infection, and modification of K164 is required for PCNA-mediated restriction of virus replication. mUb-PCNA plays important known roles in recruiting TLS polymerases to DNA, which we have shown are important for viral genome integrity and diversity, represented by novel junctions and single nucleotide variants (SNVs), respectively. We find that PCNA drives SNVs on vDNA similar to Y-family TLS polymerases, but that this did not require modification at K164. Unlike TLS polymerases, PCNA was dispensable for preventing large scale rearrangements on vDNA. These striking results suggest separable PCNA-dependent and - independent functions of TLS polymerases on vDNA. By extension, these results imply roles for TLS polymerase beyond their canonical function in TLS in host biology. These findings highlight PCNA as a complex restriction factor for HCMV infection, likely with multiple distinct roles, and provides new insights into the PCNA-mediated regulation of DNA synthesis and repair in viral infection. IMPORTANCEGenome synthesis is a critical step of virus life cycles and a major target of antiviral drugs. Human cytomegalovirus, like other herpesviruses, encodes machinery sufficient for viral DNA synthesis and relies on host factors for efficient replication. We have shown that host DNA repair factors play important roles in HCMV replication, but our understanding of this is incomplete. Building on previous findings that specialized host DNA polymerases contribute to HCMV genome integrity and diversity, we sought to determine the importance of PCNA, the central polymerase regulator. PCNA associates with nascent viral DNA and restricts HCMV replication. While PCNA is dispensable for genome integrity, it contributes to genome diversity. Our findings suggest that host polymerases function on viral genomes by separable PCNA-dependent and - independent mechanisms. Through revealing complex roles for PCNA in HCMV replication, this study expands the repertoire of host DNA synthesis and repair proteins hijacked by this ubiquitous herpesvirus.

microbiology↗

bioRxiv2023

Rhythmic tapping to a moving beat: motion kinematics overrules motion naturalness.

Beat induction is the cognitive ability that allow humans to listen to a regular pulse in music and move in synchrony with it. Although auditory rhythmic cues are known to induce more consistent synchronization than flashing visual metronomes, this asymmetry can be canceled out by visual moving metronomes. Here, we investigated whether the naturalness of the visual motion or its kinematics could provide a synchronization advantage over flashing metronomes. Subjects tap in sync with visual isochronous metronomes defined by vertically or horizontally accelerating and decelerating motion, either congruent or not with natural gravity, and then continue tapping with no metronome. We found that motion kinematics was the predominant factor determining rhythm synchronization, as accelerating moving metronomes in either cardinal direction produced more precise and predictive tapping than decelerating or flashing conditions. Notably, a Bayesian observer model revealed that error correction during tapping synchronization and regression towards the mean in accuracy during tapping continuation in the absence of external cues are optimal control strategies independently of the moving properties of the visual metronomes. Our results support the notion that accelerating visual metronomes convey a strong sense of beat as seen in the cueing movements of an orchestra director.

neuroscience↗

bioRxiv2022

Single-cell RNA sequencing of conditional Pten knockout neurons in mice

PTEN is a well-known tumor suppressor whose mutations are also strongly associated with Autism Spectrum Disorder (ASD). The activity and function of PTEN in neurons have been studied extensively in various settings, whereas animal models offer the best opportunity to experimentally modify and test the role of PTEN in neuronal development in vivo. On the molecular level, PTENs importance in the mTOR pathways suppression is well-known but many other interactions have been suggested and yet others likely remain undiscovered. Therefore, to systematically explore the regulatory landscape downstream of PTEN on the genetic level, we have set out to establish a singlecell RNA sequencing (scRNA-seq) workflow to measure gene expression changes as a result of knocking out the Pten gene in vivo. We were able to collect brain tissue from four conditionally knocked out mouse samples and dissociate them into single live cells, which were subsequently flow-sorted and a scRNA-seq library was prepared. All of these steps were completed in a single day, yielding sequencing data from hundreds of cells suitable for cell clustering, cell type identification, and differential expression measurements. Having demonstrated its feasibility, this approach promises to aid hypothesis generation and discovery in mapping the function of Pten as well other genes whose regulatory networks remain to be fully defined.

neuroscience↗

bioRxiv2021

Internal oligo(dT) priming in bulk and single cell RNA sequencing

Significant advances in RNA sequencing have been recently made possible by the use of oligo(dT) primers for simultaneous mRNA enrichment and reverse transcription priming. The associated increase in efficiency has enabled more economical bulk RNA sequencing methods as well as the advent of high throughput single cell RNA sequencing, now already one of the most widely adopted new methods in the study of transcriptomics. However, the effects of off-target oligo(dT) priming on gene expression quantification have not been fully appreciated. In the present study, we describe the extent, the possible causes, and the consequences of internal oligo(dT) priming across multiple publicly available datasets obtained from a variety of bulk and single cell RNA sequencing platforms. In order to explore and address this issue, we developed a computational algorithm for identification of sequencing read alignments that likely resulted from internal oligo(dT) priming and their subsequent removal from the data. Directly comparing filtered datasets to those obtained by an alternative method reveals significant improvements in gene expression measurement. Finally, we infer a list of genes whose expression quantification is most likely to be affected by internal oligo(dT) priming.

genomics↗

bioRxiv2020

The Photoconvertible Fluorescent Probe, CaMPARI, Labels Active Neurons in Freely-Moving Intact Adult Fruit Flies

Linking neural circuitry to behavior by mapping active neurons in vivo is a challenge. Both genetically encoded calcium indicators (GECIs) and intermediate early genes (IEGs) have been used to pinpoint active neurons during a stimulus or a behavior but have drawbacks such as limiting the movement of the organism, requiring a priori knowledge of the active region or having poor temporal resolution. CaMPARI (calcium-modulated photoactivatable ratiometric integrator) was engineered to overcome these spatial-temporal challenges. CaMPARI is a photoconvertible protein that only converts from green to red fluorescence in the presence of high calcium concentration and violet (405 nm) light. This allows the experimenter to precisely mark active neurons within defined temporal windows. The photoconversion can then be quantified by taking the ratio of the red fluorescence to the green. CaMPARI promises the ability to trace active neurons during specific stimulus; however, CaMPARIs uses in adult Drosophila have been limited to photoconversion during fly immobilization. Here, we demonstrate a method that allows photoconversion of multiple freely-moving intact adult flies during a stimulus. Flies were placed in a dish with filter paper wet with acetic acid (pH=2) or neutralized acetic acid (pH=7) and exposed to photoconvertible light (60 mW) for 30 min (500 ms on, 200 ms off). Immediately following photoconversion, whole flies were fixed and imaged by confocal microscopy. The red:green ratio was quantified for the DC4 glomerulus, a bundle of neurons expressing Ir64a, an ionotropic receptor that senses acids in the Drosophila antennal lobe. Flies exposed to acetic acid showed 1.3-fold greater photoconversion than flies exposed to neutralized acetic acid. This finding was recapitulated using a more physiological stimulus of apple cider vinegar. These results indicate that CaMPARI can be used to label neurons in intact, freely-moving adult flies and will be useful for identifying the circuitry underlying complex behaviors.

neuroscience↗

bioRxiv2019

Transgeneratonal inheritance of ethanol preference is caused by maternal NPF repression

Rapid or even anticipatory adaptation to environmental conditions can provide a decisive fitness advantage to an organism. The memory of recurring conditions could also benefit future generations, however neuronally-encoded behavior isnt thought to be inherited across generations. We tested the possibility that environmentally triggered modifications could allow "memory" of parental experiences to be inherited. In Drosophila melanogaster, exposure to predatory wasps leads to inheritance of a predisposition for ethanol-rich food for five generations. Inhibition of Neuropeptide-F (NPF) activates germline caspases required for transgenerational ethanol preference. Further, inheritance of low NPF expression in specific regions of F1 brains is required for the transmission of this food preference: A maternally derived NPF locus is necessary for this phenomenon, implicating a maternal epigenetic mechanism of NPF-repression. Given the conserved signaling functions of NPF and its mammalian NPY homolog in drug and alcohol disorders, these observations raise the intriguing possibility of NPY-related transgenerational effects in humans.

molecular biology↗

bioRxiv2019

Neural circuitry of dialects through social learning in Drosophila.

Drosophila species communicate the presence of parasitoid wasps to naive individuals. This observation suggests a rudimentary Drosophila social structure. Communication between closely related species is efficient, while more distantly related species exhibit a dampened, partial communication. Partial communication between some species is enhanced following a period of cohabitation, suggesting that species-specific variations in communication "dialects" can be learned through social interactions. However, it remains unclear as to how the behavioral acquisition and how learning dialects is facilitated by distinct brain regions. In this study, we have identified six regions of the Drosophila brain essential for dialect learning, including the odorant receptor Or69a. Furthermore, we pinpoint subgroups of neurons such as motion detecting neurons in the optic lobe, layer 5 of the fan-shaped body, and the D glomerulus in the antennal lobe, where activation of each are necessary for dialect learning. These results demonstrate that Drosophila can display complex social behaviors with inputs to multiple regions of the Drosophila brain and unique subsets of neurons that must integrate olfactory, visual and motion cues.

neuroscience↗

bioRxiv2018

New Drosophila long-term memory genes revealed by assessing computational function prediction methods.

A major bottleneck to our understanding of the genetic and molecular foundation of life lies in the ability to assign function to a gene and, subsequently, a protein. Traditional molecular and genetic experiments can provide the most reliable forms of identification, but are generally low-throughput, making such discovery and assignment a daunting task. The bottleneck has led to an increasing role for computational approaches. The Critical Assessment of Functional Annotation (CAFA) effort seeks to measure the performance of computational methods. In CAFA3 we performed selected screens, including an effort focused on long-term memory. We used homology and previous CAFA predictions to identify 29 key Drosophila genes, which we tested via a long-term memory screen. We identify 11 novel genes that are involved in long-term memory formation and show a high level of connectivity with previously identified learning and memory genes. Our study provides first higher-order behavioral assay and organism screen used for CAFA assessments and revealed previously uncharacterized roles of multiple genes as possible regulators of neuronal plasticity at the boundary of information acquisition and memory formation.

neuroscience↗

bioRxiv2017

Drosophila species learn dialects through communal living

Many species are able to share information about their environment by communicating through auditory, visual, and olfactory cues. In Drosophila melanogaster, exposure to parasitoid wasps leads to a decline in egg laying, and exposed females communicate this threat to naive flies, which also depress egg laying. We find that species across the genus Drosophila respond to wasps by egg laying reduction, activate cleaved caspase in oocytes, and communicate the presence of wasps to naive individuals. communication within a species and between closely related species is efficient, while more distantly related species exhibit partial communication. Remarkably, partial communication between some species is enhanced after a cohabitation period that requires exchange of visual and olfactory signals. This interspecies \"dialect learning\" requires neuronal cAMP signaling in the mushroom body, suggesting neuronal plasticity facilitates dialect learning and memory. These observations establish Drosophila as genetic models for inter-species social communication and evolution of dialects.

genomics↗

bioRxiv2017

Machine learning analysis identifies Drosophila Grunge/Atrophin as an important learning and memory gene required for memory retention and social learning.

High throughput experiments are becoming increasingly common, and scientists must balance hypothesis driven experiments with genome wide data acquisition. We sought to predict novel genes involved in Drosophila learning and long-term memory from existing public high-throughput data. We performed an analysis using PILGRM, which analyzes public gene expression compendia using machine learning. We evaluated the top prediction alongside genes involved in learning and memory in IMP, an interface for functional relationship networks. We identified Grunge/Atrophin (Gug/Atro), a transcriptional repressor, histone deacetylase, as our top candidate. We find, through multiple, distinct assays, that Gug has an active role as a modulator of memory retention in the fly and its function is required in the adult mushroom body. Depletion of Gug specifically in neurons of the adult mushroom body, after cell division and neuronal development is complete, suggests that Gug function is important for memory retention through regulation of neuronal activity, and not by altering neurodevelopment. Our study provides a previously uncharacterized role for Gug as a possible regulator of neuronal plasticity at the interface of memory retention and memory extinction.

genetics↗