Biology subjects

Altman, Y.

Publications and source records attributed to Altman, Y..

6 recordsLinked to original sources

bioRxiv2026

HSV-1 hijacks the DNA repair protein RAD51 at gene promoters to drive viral transcription

Productive infection by Herpes Simplex Virus type 1 (HSV-1) requires initiation of efficient viral gene expression. Upon nuclear entry, HSV-1 genomes are associated with several cellular factors, including DNA repair proteins. It is unclear how these cellular factors impact viral processes at early stages of infection. In this study, we investigate the role of RAD51, a core homologous recombination (HR) factor. We measured nascent viral transcription and show that RAD51 plays a pro-viral role in infection by promoting immediate-early viral gene expression. We demonstrate that RAD51 binds GC-rich gene promoter of ICP4 and directly promotes gene expression. We also reveal a previously unknown interaction between RAD51 and ADNP, a subunit of the ChAHP complex, known for its role in transcription regulation. We propose a model where RAD51 binds incoming genomes at promoter regions regulating the genome landscape and allowing for efficient transcription initiation.

cell biology↗

bioRxiv2025

Automation of high-throughput arrayed lentivirus production and titration

Generation of arrayed genome-wide CRISPR libraries in a ready-to-transduce lentiviral format remains laborious, time-consuming, and costly. To address these limitations, the present study developed a fully automated lentivirus production and titration workflow using a Biomek i7 Hybrid automated workstation, integrated with multiple instruments and managed by SAMI EX software. The workflow produced and titrated viruses in 96 and 384-well plate formats, respectively. It employed reverse transfection and triplicate wells per lentivector to reduce variability and yielded an average of three viral particles in transduction unit (TU) per producing HEK293T cell. Titration was performed using U937-mCherry suspension cells, with the percentage of transduced cells converted from U937 (X%) to HEK293T (Y%) values via a linear regression equation (Y% = 4.3X% + 9.3%). The titer calculation was based on the initial seeding cell number, the converted percentage of HEK293T transduced cells, and virus input volume. The titration demonstrated strong reproducibility across LSRFortessa (BD) and Aurora (Cytek) flow cytometers (R2 = 0.9). Among 1,760 unconcentrated virus preparations, median and mean titers reached approximately 1.2 x 106 TU/mL, with over 97% of samples exceeding the high-titer threshold of 2x105 TU/mL, thus demonstrating a robust, scalable, and cost-effective automation platform for high throughput arrayed lentiviral library production and titration.

microbiology↗

bioRxiv2025

Partial Inhibition of Viral Replication Machinery Enhances Recombination in Herpes Simplex Viruses

Herpes simplex viruses (HSV-1 and HSV-2) are widespread human pathogens, most commonly causing oral and genital lesions. These DNA viruses use recombination as a major driver of evolution. Intragenomic and intergenomic recombination events can be detected both in vivo and in vitro. As viral recombination is tightly linked to replication, deciphering mechanisms that specifically effect recombination remains a challenge. Here, we employed a triple-fluorescent color recombination assay to identify homology mediated and non-canonical recombination events between co-infecting HSV-1 strains. We developed a deep learning model that detects and classifies progeny plaques according to their colors. This setup enabled us to perturb the infection process using small molecule inhibitors targeting either viral or host proteins. We identified that inhibitors that reduce infectious viral progeny, increased viral homology mediated recombination. The antiviral drugs, including acyclovir, also increased recombination between HSV-1 and HSV-2 and aberrations in the progeny viral genomes. Taken together our results indicate that commonly used anti-herpes drugs increase intraspecies and interspecies recombination rates and genetic rearrangements. SignificanceHerpes simplex viruses cause significant morbidity in all human populations. Current therapies rely primarily on antivirals that target viral replication. Viral recombination plays a key role in replication and evolution of these dsDNA viruses. To better characterize the viral recombination process, we introduce a fluorescence-based HSV-1 recombination assay coupled with deep learning-based plaque classification, enabling high-throughput quantification of recombination rates. We found that clinically relevant moderate concentrations of commonly used antiviral replication inhibitors, enhance homology-mediated intraspecies recombination, HSV-1/HSV-2 interspecies recombination, as well as the accumulation of defective genomes. We conclude that partial inhibition of the herpes replication complex can promote viral diversification, with potential implications for HSV evolution and drug resistance.

microbiology↗

bioRxiv2025

PI5P4Kα Regulates Iron Balance to Promote Metabolic Fitness in Pancreatic Cancer

Phosphoinositide kinases generate distinct phosphoinositides that regulate processes that maintain cellular fitness. Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) have garnered interest for their role in cancer metabolism and cellular trafficking; however, their function in pancreatic ductal adenocarcinoma (PDAC) remains unexplored. Given the unique metabolic demands of PDAC cells, which heavily rely on altered trafficking pathways to support their growth, investigating PI5P4Ks in this context may reveal critical insights. We identify PI5P4K as a regulator of PDAC cell fitness through its key role in maintaining iron homeostasis. PI5P4K depletion causes metabolic disruptions and reduced intracellular iron import, leading to the induction of apoptosis in PDAC cells that is reversed by iron supplementation. Notably, we find that PI5P4K knockdown suppresses tumor growth in a xenograft mouse model of PDAC. These results not only illuminate the mechanistic underpinnings of PI5P4K function in PDAC but also position it as a promising therapeutic target for this disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/647654v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@17f52e5org.highwire.dtl.DTLVardef@1b78c1org.highwire.dtl.DTLVardef@194e09aorg.highwire.dtl.DTLVardef@125b3c9_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic representation of the novel function and implication of PI5P4K in PDAC. PI5P4K is upregulated in PDAC to support the ferro-addiction and heightened metabolic requirements of the tumor. When PI5P4K is inhibited, the PDAC cells undergo apoptotic cell death due to iron depletion. PI5P4K-depleted PDAC cells upregulate autophagy as an adaptive response but is not sufficient to defend against apoptotic cell death.

cancer biology↗

bioRxiv2023

A mitochondria-regulated p53-CCF circuit integrates genome integrity with inflammation

Genomic instability and inflammation are distinct hallmarks of aging, but the connection between them is poorly understood. Understanding their interrelationship will help unravel new mechanisms and therapeutic targets of aging and age-associated diseases. Here we report a novel mechanism directly linking genomic instability and inflammation in senescent cells through a mitochondria-regulated molecular circuit driven by p53 and cytoplasmic chromatin fragments (CCF). We show, through activation or inactivation of p53 by genetic and pharmacologic approaches, that p53 suppresses CCF accumulation and the downstream inflammatory senescence-associated secretory phenotype (SASP), without affecting cell cycle arrest. p53 activation suppressed CCF formation by promoting DNA repair, and this is reflected in maintenance of genomic integrity, particularly in subtelomeric regions, as shown by single cell genome resequencing. Activation of p53 in aged mice by pharmacological inhibition of MDM2 reversed signatures of aging, including age- and senescence-associated transcriptomic signatures of inflammation and age-associated accumulation of monocytes and macrophages in liver. Remarkably, mitochondria in senescent cells suppressed p53 activity by promoting CCF formation and thereby restricting ATM-dependent nuclear DNA damage signaling. These data provide evidence for a mitochondria-regulated p53 signaling circuit in senescent cells that controls DNA repair, genome integrity, and senescence- and age-associated inflammation. This pathway is immunomodulatory in mice and a potential target for healthy aging interventions by small molecules already shown to activate p53.

cell biology↗

bioRxiv2021

Single-cell sequencing of the Drosophila embryonic heart and muscle cells during differentiation and maturation

Heart morphogenesis is a complex process that is orchestrated during development via the interaction of different cell types and the activity of distinct gene programs within these cells. Here, we analyzed the development and differentiation of the Drosophila embryonic heart at the single-cell level to characterize in detail the genetic expression profiles and phenotypic differences of cardiac cell types during heart morphogenesis. We present an embryonic fly heart cell atlas at unprecedented resolution that integrates the entire catalogue of known heart cells. We identified new gene programs and cell type marker genes that allows characterization of the molecular genetics of fly cardiogenesis in granular detail. In cardioblasts we described the temporal process of cardioblast-to-cardiomyocyte differentiation. Two sets of pericardial cells, likely contributing to cardiomyocyte differentiation, are eliminated by programmed cell death at the end of embryogenesis, whereas as third set continues to shape/influence cardiac function into adulthood. To dissect the gene programs downstream of the cardiac homeodomain transcription factor tinman we analyzed cardiac cells with reduced levels of Tinman. Here we find that Tinman acts both as suppressor and as activator of identified direct Tin-target genes in a cell type-dependent manner. We also found a developmental switch that alters the fate of pericardial cells towards wing heart cell fate and identified an entire wing heart gene program suppressed by Tinman in pericardial cells. Lastly, we find that in pericardial cells Tinman controls a Wingless/WNT receptor switch through selective activation and repression of frizzled and frizzled2, respectively. This study paves the way for investigating other core cardiogenic genes in delineating cardiac regulatory networks.

developmental biology↗