Biology subjects

Kim, E. J.

Publications and source records attributed to Kim, E. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Hepatic cholinergic T cell signaling mediates an adaptive response to alcohol-induced liver stress

Alcohol-associated liver disease (ALD) is a major cause of liver-related morbidity and mortality, yet no targeted, disease-modifying therapy exists and the immune mechanisms driving disease progression remain poorly defined. Acetylcholine-producing cholinergic immune cells have emerged as regulators of homeostasis across tissues and in disease, but their role in alcohol-induced hepatic stress is unknown. Here, we characterized the hepatic cholinergic immune landscape during alcohol-induced stress using flow cytometry and single-cell RNA-sequencing of ChAT-eGFP reporter mice. Alcohol feeding expanded hepatic cholinergic immune cells, with T cells constituting a substantial and dynamic fraction of this population that showed a broad increase in acetylcholine signaling and shifted towards a repressed, anergy-like transcriptional state. CD4 T cells underwent coordinated suppression of cholesterol biosynthesis, while CD8 T cells instead adopted a cytotoxic activation program. Together, these findings identify cholinergic T cell signaling, and cholesterol metabolism within CD4 T cells specifically, as a previously unrecognized adaptive response to alcohol-induced liver stress, nominating candidate therapeutic targets for a disease that is marred by critically limited treatment options.

immunology↗

bioRxiv2026

Predation risk reweights reward preference through coordinated amygdala-prelimbic dynamics

A fundamental challenge for animals and humans is resolving competing survival demands under naturalistic threat, yet circuit-level mechanisms remain poorly understood. We developed a paradigm recapitulating a predator-prey encounter: Long-Evans rats emerged from a nest to forage in an open arena, choosing between preferred and standard reward locations while facing a robotic predator. We simultaneously recorded single-unit activity from the basolateral amygdala (BLA) and the prelimbic cortex (PL). Rats shifted to the safer option under threat. BLA neurons responded predominantly to the predator, whereas PL neurons encoded reward value, threat context, and behavioral state. Population decoding revealed threat encoding in BLA and multiplexed representations in PL. Threat-responsive BLA neurons were preferentially recruited into BLA-PL synchrony before safe choices, and information flow became biased from BLA to PL following predator attack. These findings identify coordinated corticolimbic dynamics as a candidate mechanism through which threat reweights reward-guided action selection under ecological risk.

neuroscience↗

bioRxiv2026

Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastoma

Single-cell and spatial transcriptomic studies have provided insights into the developmental origins and intratumoural heterogeneity of SHH medulloblastoma (SHH-MB) and suggested how targeted drugs such as CDK4/6 inhibitors remodel tumour ecosystems, yet the interplay between local drug exposure, metabolism, cell state, and drug resistance remains poorly understood. Here we developed a same-section spatial pharmaco-multiomics framework that integrates MALDI-MSI-based spatial metabolomics with Visium whole-transcriptome profiling and high-resolution Xenium imaging to map palbociclib distribution, metabolite landscapes, and transcriptional programs within the same histological contexts of an SHH-MB PDOX model and primary human tumours. Palbociclib-rich tumour bulk exhibited broad suppression of E2F-driven proliferation and a shift toward neuronal differentiation, corroborating and extending prior findings. In contrast, drug-poor tumour-brain interfaces and perivascular regions retained E2F-high proliferative states and were enriched for mesenchymal-like stromal cells and ECM-remodelling genes, indicating anatomically constrained reservoirs of tolerance. Spatial metabolomics linked these interface niches to ganglioside (GM2) and sphingomyelin enrichment, while differentiated, drug-exposed regions displayed phosphatidylcholine, phosphatidic-acid signatures consistent with neuronal maturation. Integrated pathway analysis further revealed a "mitochondrial tuning" program, with upregulation of histidine, folate/one-carbon, CoA, and lipoate metabolism with redox and oxidative-phosphorylation support. These signatures were specific to therapy-exposed border cells. Rare palbociclib-positive, E2F-high resistant spots additionally exhibited mitotic checkpoint and DNA-repair signatures, implying a drug-induced resistance axis independent of scarcity. Together, our study provides a generalisable same-section spatial pharmaco-multiomics pipeline and a spatially resolved model of CDK4/6 response, nominating interface-focused metabolic and cell-intrinsic vulnerabilities for combination therapy.

cancer biology↗

bioRxiv2026

The bromodomain protein Bdf3 is sufficient to activate expression of a procyclin gene in bloodstream stage African trypanosomes

The early branching eukaryotic parasite, Trypanosoma brucei, lives extracellularly in the mammalian host, where it expresses variant surface glycoprotein (VSG). Antigenic variation of VSGs allows the parasite to evade the host immune response while in the bloodstream. Upon transition to the tsetse fly vector, the parasite remodels its surface to express procyclin protein from a limited set of EP and GPEET genes. While the environmental signals that trigger the switch from expressing VSG genes to expressing EP and GPEET genes are known, the molecular mechanism that initiates transcription of the EP and GPEET genes during parasite differentiation to the procyclic stage within the tsetse is not well understood. Previous work has shown that the chromatin interacting bromodomain protein Bdf3 is absent from the pol I promoter of the EP locus in bloodstream parasites, but appears there shortly after initiation of differentiation from the bloodstream to the procyclic stage. Here, we show that tethering of Bdf3 to the EP promoter using a dCas9-Bdf3 fusion protein and a guide RNA is sufficient to increase transcript levels of EP1 in bloodstream parasites, where the gene is normally silenced. This result supports the model that Bdf3 appears at the EP locus during differentiation to facilitate initiation of transcription, which is consistent with the role for Bdf3 as a transcriptional activator in other systems. Understanding gene regulatory mechanisms in this early branching eukaryote may help build a more complete picture for the conserved and unique features of gene regulatory proteins across diverse biological systems. ImportanceThe Trypanosoma brucei parasite is transmitted to a mammalian host via the tsetse fly vector, where it causes African trypanosomiasis, a fatal disease that causes a severe human and economic burden for people living in in areas of sub-Saharan African. While drug treatments have improved for some strains, some infections still require treatment with drugs that have serious side effects. One avenue for drug development is to try and manipulate the lifecycle of the parasite to make it poorly adapted to the mammalian host. However, this requires detailed knowledge of the mechanisms by which parasites regulate their genes as they progress through the lifecycle. Here, we show that the DNA interacting bromodomain protein Bdf3 may be a key driver for turning on insect-specific genes that code for insect-stage surface proteins. This finding could aid in the development of lifecycle manipulating drugs, and shed light on how gene regulatory mechanisms evolved.

molecular biology↗

bioRxiv2025

Structured and Target-Specific Development of Cortico-Cortical Connectivity in the Mouse Visual Cortex

The mammalian cortex exhibits highly stereotyped long-range connectivity, yet the developmental principles that specify precise cortico-cortical projection patterns remain poorly defined. Two dominant models propose that target specificity arises either from early inter-regional exuberant outgrowth followed by pruning, or through initially directed axonal targeting. To resolve this, we systematically mapped the postnatal development of V1 cortico-cortical projection neurons (CCPNs) to eleven higher visual areas (HVAs) in mice using rapid and complementary retrograde, anterograde, and single-cell tracing methods. We found that V1[->]HVA connectivity develops via spatiotemporally staggered axon extension and pruning programs, aligned with target position along the medial-lateral axis. Reciprocal HVA[->]V1 feedback emerges concurrently and is refined over time, yielding gradually aligned bidirectional connectivity. Notably, both multiplexed retrograde tracing and MAPseq-based single-cell profiling revealed that individual V1 neurons initialize and retain specific projection motifs with limited variation over development, arguing against global exuberance followed by selective, inter-areal pruning. Instead, our findings support a directed guidance model, in which distinct V1 CCPN subtypes establish selective projection patterns early, followed by local, target-dependent refinement. This structured yet heterogeneous developmental strategy provides an anatomical framework for how precise long-range cortical networks emerge. HIGHLIGHTSO_LIV1[->]HVA connections form via directed axonal targeting, establishing motifs early with little variation C_LIO_LIMedial targets are innervated earlier and refine gradually, lateral targets later and rapidly C_LIO_LIFeedforward and feedback V1-HVA circuits emerge concurrently C_LIO_LIBidirectional like-to-like V1-HVA connectivity refines across development C_LI

neuroscience↗

bioRxiv2025

Distinct Neurogenic Dynamics of Cortico-cortical Neuronal Subtypes in Layer 2/3 of the Mouse Visual Cortex

In the mammalian cerebral cortex, the birthdates of excitatory projection neurons are closely linked to their laminar positions, which are often associated with distinct long-range projection targets. Although broad relationships between neurogenic timing, laminar position, and projection patterns are well established, the degree to which birthdate specifies projection identity within the same cortical layer remains unclear. In the mouse primary visual cortex (V1), neurons projecting to lateral higher visual areas are relatively evenly distributed throughout layer 2/3, whereas those projecting to medial areas are biased toward more superficial sublayers. To determine whether these projection identities are linked to neurogenic timing, we combined EdU birthdating with retrograde viral tracing. Notably, we found that V1 layer 2/3 neurons projecting to lateral higher visual areas are preferentially born at embryonic day 15.5 (E15.5) compared to E16.5, whereas V1 neurons projecting to medial higher visual areas show no significant birthdate bias between E15.5 and E16.5. These findings suggest that distinct cortico-cortical projection subtypes in layer 2/3 are generated on different temporal schedules, linking neurogenic timing to fine-scale projection identity.

neuroscience↗

bioRxiv2025

Deficiency in POLE exonuclease causes synthetic lethality in highly aneuploid cancer cells

Aneuploidy is a hallmark of cancer and is associated with drug resistance and poor clinical outcomes across diverse cancer types. However, no therapies have been clinically established to target highly aneuploid tumors. By analyzing a real-world dataset comprising nearly half a million tumor samples subjected to comprehensive genomic profiling, we identified a striking mutual exclusivity between POLE exonuclease domain mutations and high aneuploidy burden. This observation was independently validated using data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). Probabilistic modeling revealed that the elevated quantity and unique spectrum of mutations induced by POLE exonuclease deficiency increase the likelihood of inactivating essential genes on chromosome arms harboring losses, leading to a synthetic lethal phenotype in highly aneuploid cells. Functional experiments demonstrated that POLE exonuclease activity is essential for the viability of highly aneuploid cancer cell lines but is dispensable in diploid cells. These findings suggest that selective inhibition of POLE exonuclease may represent a promising therapeutic strategy for targeting highly aneuploid tumors.

cancer biology↗

bioRxiv2025

Brain-wide connectivity patterns of feedforward and feedback cortico-cortical neurons in the mouse secondary visual cortex

Feedforward and feedback cortico-cortical neurons are distinct yet spatially intermingled subtypes distributed across cortical layers, playing specialized roles in sensory and cognitive processing. However, whether their presynaptic inputs differ to support these functions remains unknown. Using projection-and layer-specific monosynaptic rabies tracing, we mapped brain-wide long-distance inputs to multiple feedforward and feedback neuron types in VISl (also known as LM), the mouse secondary visual cortex. Overall, long-distance input patterns for these feedforward and feedback neurons were largely similar, as all received the majority of their inputs from VISp, the primary visual cortex, along with substantial inputs from various other cortical and visual thalamic regions. Despite their similarities, these feedforward and feedback types differed in the proportion of long-distance cortical inputs originating from specific visual, retrosplenial, and auditory cortices. These findings reveal the input connectivity patterns of cortico-cortical neurons based on feedforward and feedback projections, providing an anatomical framework for future studies on their functions and circuit integration. KEY POINTS1) Feedforward and feedback cortico-cortical projection neurons in VISl form largely distinct populations that are distributed across multiple cortical layers. 2) Four different feedforward and feedback cortico-cortical projection neuron types receive broadly similar patterns of long-distance input across the brain. 3) Despite overall similarities, feedforward and feedback neurons differ in the relative proportions of inputs from specific areas, including visual, retrosplenial, and auditory cortices.

neuroscience↗

bioRxiv2025

Strain-specific differences in toxT expression and virulence gene activation in Vibrio cholerae

The transcriptional activator ToxT is a key regulator of Vibrio cholerae virulence, controlling the expression of cholera toxin (CT) and the toxin co-regulated pilus (TCP). Insights into the regulation and function of toxT have largely come from studies on the classical biotype strain O395, which exhibits robust toxT expression. However, toxT expression is not fully consistent across V. cholerae strains. Here, we show that toxT transcription and protein production differ significantly among strains, particularly in El Tor biotype, which exhibit allele-dependent regulatory constraints. Using qRT-PCR and Western blotting, we demonstrate that alternative toxT alleles confer distinct transcriptional activator functions across El Tor biotype strains. Notably, IB5230, a pandemic El Tor strain, exhibits enhanced toxT and virulence gene expression even at 37{degrees}C, suggesting a potential adaptation for increased pathogenicity. Our results suggest that toxT autoregulatory feedback plays a more critical role in virulence gene activation than previously recognized. This study underscores previously unrecognized complexity in toxT regulation, emphasizing the need to reassess virulence control mechanisms in epidemic and emerging V. cholerae strains. Understanding these strain-specific differences is essential for refining models of cholera pathogenesis. Author SummaryCholera is a severe diarrheal disease caused by the bacterium Vibrio cholerae, which continues to pose a major threat to global health. The ability of V. cholerae to cause disease depends on the expression of two key virulence factors--cholera toxin (CT) and the toxin-coregulated pilus(TCP)-- controlled by the transcriptional activator ToxT. While much of our understanding of ToxT regulation is based on classical biotype strains, most recent cholera outbreaks have been driven by El Tor biotype strains. In this study, we demonstrate that toxT expression and its ability to activate virulence genes vary markedly across V. cholerae strains, depending on both the specific toxT allele and the genetic background. Using isogenic strains engineered to express different toxT alleles, we show that some alleles are transcriptionally silent in certain El Tor strains while others are active, despite having similar functional capabilities when expressed. Notably, a hypervirulent strain linked to the Haitian cholera outbreak maintained high toxT expression even at human body temperature, hinting at possible adaptive mechanisms for enhanced pathogenicity. Our findings suggest that virulence regulation in V. cholerae may be more variable than previously recognized, highlighting strain- and allele-specific differences in toxT expression. Understanding these strain- and allele-specific differences in virulence gene regulation is crucial for improving models of cholera pathogenesis and could inform the development of more effective interventions and vaccines against this evolving pathogen.

microbiology↗

bioRxiv2024

Warm temperature modifies cell fates to reduce stomata production in Arabidopsis

O_LIStomatal abundance decrease in Arabidopsis triggered by warm-temperature is attributed to PIF4-mediated repression of SPEECHLESS (SPCH) expression. We identified the unknown developmental and transcriptional basis of this adaptive response. C_LIO_LIWe traced stomatal lineages in vivo using cell-identity marker lines and mutants, quantified epidermal traits and conducted RNA sequencing under oscillating temperatures. C_LIO_LIProlonged warm-temperature or PIF4-overexpression altered cell-fates, inducing diverted stomatal precursors (DPs) that lacked stomatal fate, accounting for stomata reduction. DPs originated from meristemoids that lost SPCH expression, lacked MUTE expression and exited the cell cycle. Short warm-temperature pulses allowed later recovery of SPCH expression, and did not induce DPs or stomata reduction. Comparison of transcriptomes obtained during warm-temperature pulses with stomatal lineage cell-specific profiles identified gene expression changes and contrasted their reversibility. Though warm-temperature silenced key stomatal drivers, most lineages formed stomata through partly modified transcriptional landscapes that promoted uncommitted cell identities and included alternative pathways. C_LIO_LIExpression changes in stomatal regulators and cell-fate changes explain lineage progression under fluctuating temperatures. Since short-term temperature oscillations prevail in natural conditions, the requirement of long warm-temperature exposure to trigger DPs would prevent stomata reduction by occasional temperature rises. Promoting uncommitted lineage stages provides flexibility to stomatal development under environmental changes. C_LI

plant biology↗

bioRxiv2024

Distinct Disruptions in CA1 and CA3 Place Cell Function in Alzheimer's Disease Mice

The hippocampus, a critical brain structure for spatial learning and memory, is susceptible to neurodegenerative disorders such as Alzheimers disease (AD). The APPswe/PSEN1dE9 (APP/PS1) transgenic mouse model is widely used to study the pathology of AD. Although previous research has established AD-associated impairments in hippocampal-dependent learning and memory, the neurophysiological mechanisms underlying these cognitive dysfunctions remain less understood. To address this gap, we investigated the activities of place cells in both CA1 and CA3 hippocampal subregions, which have distinct yet complementary computational roles. Behaviorally, APP/PS1 mice demonstrated impaired spatial recognition memory compared to wild-type (WT) mice in the object location test. Physiologically, place cells in APP/PS1 mice showed deterioration in spatial representation compared to WT. Specifically, CA1 place cells exhibited significant reductions in coherence and spatial information, while CA3 place cells displayed a significant reduction in place field size. Both CA1 and CA3 place cells in APP/PS1 mice also showed significant disruptions in their ability to stably encode the same environment. Furthermore, the burst firing properties of these cells were altered to forms correlated with reduced cognition. Additionally, the theta rhythm was significantly attenuated in CA1 place cells of APP/PS1 mice compared to WT. Our results suggest that distinct alteration in the physiological properties of CA1 and CA3 place cells, coupled with disrupted hippocampal theta rhythm in CA1, may collectively contribute to impaired hippocampal-dependent spatial learning and memory in AD.

neuroscience↗

bioRxiv2024

Alzheimer's pathology disrupts flexible place cell coding and hippocampal-prefrontal neural dynamics during risky foraging decisions in mice

This study investigates how amyloid pathology influences hippocampal-prefrontal neural dynamics and decision-making in Alzheimers disease (AD) using 5XFAD mice, a well-established model system characterized by pronounced early amyloid pathology. Utilizing ecologically-relevant "approach food-avoid predator" foraging tasks, we observed that 5XFAD mice exhibited persistent risk-taking behaviors and reduced adaptability to changing threat conditions, indicative of impaired decision-making. Multi-regional neural recordings revealed rigid hippocampal CA1 place-cell fields, decreased sharp-wave ripple (SWR) frequencies, and disrupted medial prefrontal-hippocampal connectivity, all of which corresponded with deficits in behavioral flexibility during spatial risk scenarios. These findings highlight the critical role of SWR dynamics and corticolimbic circuit integrity in adaptive decision-making, with implications for understanding cognitive decline in AD in naturalistic contexts. By identifying specific neural disruptions underlying risky decision-making deficits, this work provides insights into the neural basis of cognitive dysfunction in AD and suggests potential targets for therapeutic intervention.

neuroscience↗

bioRxiv2024

Mosaic display of stable hemagglutinin monomers induces broad immune responses

The nature of the interplay between immunity and viral variation is infinitely adaptive. Infection frequently induces immune responses against variation-prone epitopes, rather than against spatially hidden conserved epitopes. It thus remains a substantial challenge to elicit the immune responses to the conserved epitopes providing broad-spectrum immunity. We developed an approach of scaffold-mediated mosaic display to present monomeric influenza virus hemagglutinins (HAs), which exposes highly conserved stem and interface epitopes. Stable monomers were rationally engineered from H1 and H3 subtypes and B type HA trimers, with amino acid mutations at the monomer-monomer interface and for disulfide bond formation, and fused to a self-assembling scaffold, to generate a mosaic HA monomer-displaying nanoparticle, 3HA-np. Immunization with 3HA-np induced broadly neutralizing antibodies (bnAbs) in mice and ferrets and protected against challenges with H1N1 and H3N2 viruses. Competitive immunoassays revealed that 3HA-np induced high interface- and stem-binding Ab titers as compared to head Ab titers, indicating that the monomeric and mosaic nature of 3HA-np elicit cross-reactive Abs. Our results suggest that exposure of the hidden conserved epitope by monomer-displaying nanoparticles is a promising approach to generate a universal influenza vaccine.

bioengineering↗

bioRxiv2023

Periaqueductal gray activates antipredatory neural responses in the amygdala of foraging rats

Pavlovian fear conditioning research suggests that the interaction between the dorsal periaqueductal gray (dPAG) and basolateral amygdala (BLA) acts as a prediction error mechanism in the formation of associative fear memories. However, their roles in responding to naturalistic predatory threats, characterized by less explicit cues and the absence of reiterative trial-and-error learning events, remain unexplored. In this study, we conducted single-unit recordings in rats during an approach food-avoid predator task, focusing on the responsiveness of dPAG and BLA neurons to a rapidly approaching robot predator. Optogenetic stimulation of the dPAG triggered fleeing behaviors and increased BLA activity in naive rats. Notably, BLA neurons activated by dPAG stimulation displayed immediate responses to the robot, demonstrating heightened synchronous activity compared to BLA neurons that did not respond to dPAG stimulation. Additionally, the use of anterograde and retrograde tracer injections into the dPAG and BLA, respectively, coupled with c-Fos activation in response to predatory threats, indicates that the midline thalamus may play an intermediary role in innate antipredatory defensive functioning.

neuroscience↗

bioRxiv2023

Distinct prefrontal projections conversely orchestrate social competition and hierarchy

Social animals compete for limited resources, resulting in a social hierarchy. Although different neuronal subpopulations in the medial prefrontal cortex (mPFC), a hub brain region of social hierarchy, encode distinct social competition behaviors, their identities and associated molecular underpinnings have not yet been identified. In this study, we found that mPFC neurons projecting to the nucleus accumbens (mPFC-NAc) encode social winning behavior, whereas mPFC neurons projecting to the ventral tegmental area (mPFC-VTA) encode social losing behavior by monitoring and manipulating neural circuit activity. High-throughput single-cell transcriptomic analysis and projection-specific genetic manipulation revealed that the expression level of POU domain, class 3, transcription factor 1 (Pou3f1) in mPFC-VTA neurons controls social hierarchy. Optogenetic activation of mPFC-VTA neurons increases Pou3f1 expression and lowers social rank. Together, these data demonstrate that discrete activity and gene expression in separate mPFC projections oppositely orchestrate social competition and hierarchy.

neuroscience↗

bioRxiv2022

Bell Jar: A Semi-Automated Registration and Cell Counting Tool for Mouse Neurohistology Analysis

To investigate the anatomical organization of neural circuits across the whole brain, it is essential to register the experimental brain tissues to a reference atlas accurately. This procedure is also a prerequisite to quantify the locations and numbers of cells of interest in specific regions. However, it remains challenging to do registration on experimental tissue due to the intrinsic variation among the specimens, tissue deformation introduced by histological processing, and the potential inconsistency in the judgment of the experimenter during manual annotation. Here, we introduce Bell Jar, a multi-platform analysis tool with semi-automated affine warping of atlas maps onto microscopic images of brain slices and machine learning-based cell detection. Bell Jars intuitive GUI and internal dependency management enable users of all skill levels to obtain accurate results without programming expertise. To compare the performance of Bell Jar with previously published methods1-4, we labeled neurons in the mouse visual cortex with either an engineered rabies virus or an adeno-associated virus (AAV) for neural circuit tracing5, and quantified Bell Jars performance at each step of the pipeline for image alignment, segmentation, and cell counting. We demonstrated that Bell Jars output is as reliable as manual counting by an expert; it is more accurate than currently available techniques even with noisy data and takes less time with fewer user interventions. Bell Jar is an easy-to-navigate application that provides a reproducible, automated analysis workflow to facilitate the precise mapping of histological images of the mouse brain to the reference atlas and the quantification of cellular signals it is trained to recognize.

neuroscience↗

bioRxiv2022

T cell-instructed inflammation drives immune checkpoint inhibitor therapy resistance

Resistance to immune checkpoint inhibitors (ICIs) is common, even in tumors with T cell infiltration. We thus investigated consequences of ICI-induced T cell infiltration in the microenvironment of resistant tumors. T cells increased in ICI-resistant tumors following treatment as did neutrophils, in contrast to ICI-responsive tumors. Resistant tumors were distinguished by high expression of IL-1 Receptor 1 (IL1R1), enabling a synergistic response to IL-1 and TNF to induce G-CSF, CXCL1, and CXCL2 via NF-{kappa}B signaling, supporting neutrophils. Perturbation of this inflammatory resistance circuit sensitized tumors to ICIs. Paradoxically, T cells drove this resistance circuit via TNF both in vitro and in vivo. Evidence of this inflammatory resistance circuit and its impact also translated to human cancers. These data support a novel mechanism of ICI resistance, wherein treatment-induced T cell activity can drive resistance in tumors responsive to IL-1 and TNF, with important therapeutic implications. Statement of SignificanceAlthough T cell-infiltrated cancers are frequently resistant to immune checkpoint inhibitor therapies, mechanisms of resistance beyond T cell exhaustion remain unclear. Here, we reveal the functional significance of tumor- infiltrating T cells in resistant tumors, which surprisingly instruct immunosuppressive inflammation in mouse and human cancers responsive to IL-1 and TNF.

immunology↗

bioRxiv2022

Non-catastrophic collapse of VEEV by lethal mutagenesis

RNA viruses replicate at a high mutation rate, providing a highly adaptive capacity to the population as well as vulnerability to an extinction due to additional mutations, which is the conceptual basis for lethal mutagenesis. However, the mechanistic understanding of lethal mutagenesis has remained unclear due to the lack of RNA mutagens with potent antiviral activity and the inherent inability to distinguish between infectious and non-infectious sub-populations within a viral population. In our study, we investigated how the replication competency and mutation frequency of Venezuelan Equine Encephalitis Virus (VEEV) change following treatment with the RNA mutagen {beta}-d-N4-hydroxycytidine, a potent antiviral RNA mutagen. By pairing limiting dilution with a long-read sequencing approach, we specifically determined genomic sequences of replication-competent viral clones from the total population. We found that replication-competent VEEV population maintained itself within a narrow mutation spectrum with a significantly lower mutation frequency than the total population. We also found that treatment with an RNA mutagen did not induce catastrophic destruction of the infectious population even at a high exposure, allowing replication-competent subpopulations with increased variability in mutational fitness and enhanced adaptability to new selection pressures, such as antiviral treatment, to continue to propagate. Together our study provides new understanding of viral population landscape and suggests a careful consideration of lethal mutagenesis as an antiviral strategy for high-capacity replicating viruses such as alphaviruses.

microbiology↗