Biology subjects

Kelly, M.

Publications and source records attributed to Kelly, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Variation in hypoxia tolerance is driven by evolutionary changes in gene regulation in the eastern oyster

Understanding the genomic basis of stress tolerance is crucial for predicting biological responses to environmental change. Here, we investigated the genomic basis of divergence in hypoxia tolerance between two populations of eastern oyster (Crassostrea virginica) from Louisiana and Texas, USA. We combined low-coverage whole-genome sequencing data with previously generated transcriptomic evidence to understand the mechanisms underlying population-specific variation in hypoxia tolerance. Genome-wide analyses revealed substantial population differentiation (global FST = 0.21), indicative of a clear genetic break between our study populations. We combined estimates of genomic differentiation (FST) with diversity metrics to generate a set of exploratory candidate regions showing signatures consistent with recent selection. Several candidate genes identified through this approach were associated with the maintenance of homeostasis under environmental stress. We additionally tested whether genes previously identified as differentially expressed (DE) under hypoxia exhibit elevated genomic divergence between populations. While these hypoxia DEGs did show higher than expected between-population differentiation, this pattern also holds for other environmentally responsive genes. This suggests that transcriptomically responsive genes in general may generally show elevated divergence among populations, possibly due to a weaker effect of purifying selection. Furthermore, we found that hypoxia DEGs did not show an enrichment of nonsynonymous fixed differences (p = 0.9155, as compared to the genome-wide background), suggesting that the elevated divergence seen in these genes is not driven by rapid protein-coding evolution. Together, our results support a model in which population-scale differences in hypoxia tolerance occur primarily through evolution of gene regulation acting on environmentally responsive pathways.

genomics↗

bioRxiv2026

Dynamic Schlafen 11 (SLFN11) expression revealed by single-cell RNA sequencing of clonal human cancer cells

Schlafen 11 (SLFN11) is a key determinant of sensitivity to DNA-damaging therapies in multiple cancers including leukemia, Ewing sarcoma, head and neck cancers, mesothelioma and small cell lung cancer (SCLC). Here, utilizing immunofluorescence microscopy and single-cell RNA sequencing we characterized SLFN11 expression across eight different human cancer cell lines and found cell-to-cell heterogenous expression both at the protein and RNA levels. Gene set enrichment and pathway analyses show that SLFN11 is coexpressed with a distinct stress-response state and enhanced genome maintenance programs while being inversely correlated with protein translation pathways. Publicly available single-cell RNA-sequencing datasets of human SCLC tumors confirmed the heterogeneous distribution of SLFN11 expression and confirmed its association with replication-related transcriptional programs. These findings indicate that heterogeneous SLFN11 expression reflects dynamic regulation at the single-cell level. They also underscore the limitations of bulk proteomic and transcriptome profiling and point to a potential reservoir of intrinsic chemotherapy resistance.

cancer biology↗

bioRxiv2026

DVT-primed neutrophils reshape the brain microenvironment to promote brain metastasis

Brain metastasis (BrM) is a devastating complication of triple-negative breast cancer (TNBC), yet how host macroenvironmental conditions influence brain metastatic susceptibility remains poorly understood. Here, we investigated the impact of deep vein thrombosis (DVT), a common complication in patients with cancer, on TNBC brain metastasis. Analysis of a large clinical cohort identified DVT as an independent risk factor for BrM in patients with metastatic breast cancer. Using two syngeneic TNBC models, we demonstrated that DVT selectively enhanced brain metastasis without significantly affecting primary tumor growth or lung metastasis. Mechanistically, DVT increased neutrophil accumulation in the brain metastatic microenvironment, and neutrophil depletion completely abrogated the metastasis-promoting effect of DVT. Single-cell RNA sequencing of CD45+ cells in peripheral blood revealed that DVT reprogrammed circulating neutrophils toward migratory and inflammatory transcriptomic profiles characterized by neutrophil extracellular trap (NET) formation. DVT increased CXCR2 expression on circulating neutrophils and enhanced neutrophil recruitment in brain. Moreover, DVT significantly increased circulating NETs. Collectively, our findings identify DVT as a systemic driver of TNBC brain metastasis and reveal that DVT primes circulating neutrophils toward enhanced vascular recruitment and NET formation, providing a mechanistic link between cancer-associated thrombosis and brain metastatic susceptibility.

molecular biology↗

bioRxiv2026

Functional disruption of vgsc reveals haplosufficiency with implications for insecticide resistance and genetic control in Anopheles gambiae

Pyrethroid insecticides on bednets have been the mainstay of malaria control since the millennium by killing mosquitoes. The target of these pyrethroids is the voltage-gated sodium channel (VGSC). Resistance mutations at the pyrethroid binding site (L995F/S) have spread widely, but functional tools to dissect vgsc itself have lagged behind the population-genetic surveillance data. Manipulation of vgsc via knockout or functional mutation would be a vital step towards understanding its contribution to insecticide resistance, as well as exploring its utility as a genetic control target. Here we generate and characterise two CRISPR-edited An. gambiae lines: an exonic knockout (vgscKO) and an intronic CRISPR-mediated cassette exchange intermediate (vgscInt) sited near SNPs linked to L995F. Both insertions are viable and fertile in heterozygosity but homozygous lethal, demonstrating that vgsc is haplosufficient and therefore the locus represents a viable target for population suppression genetic control strategies. These insertions can also be used as balancers for studying vgsc mutations without the confounding effects of wild type alleles. We investigate the insecticide resistance phenotype of vgscKO and demonstrate that knocking out one copy of vgsc produces reduced susceptibility to deltamethrin and DDT at sub-discriminating doses, with implications for vgsc-mediated mechanisms of insecticide resistance.

genetics↗

bioRxiv2026

Discovery and Targeting of a Cryptic Human Proteome

First-in-class therapeutics require first-in-class biology. Yet despite decades of genomic and proteomic cataloging, vast regions of the human transcriptome remain dark and their encoded proteins invisible. Here we present RyboCypher, an integrated RNA-sequencing and AI-assisted proteogenomics platform that systematically maps the RyboCypher-derived "dark" transcriptome to unannotated peptides, predicting and empirically identifying cryptic proteins across the uncharted genome. Applied to cancer cell lines, patient tumors, and matched healthy tissues, RyboCypher resolved [~]8.3 million dark RNA isoforms and [~]16 million candidate ORFs. Interrogating these against [~]0.5 billion MS/MS spectra from cellular proteomics, membrane proteomics, and immunopeptidomics datasets (comprising a total of >8,000 raw MS data files ([~]7TB of MS data), derived from 2,229 patient samples), we empirically identified [~]80,000 cryptic peptides ([~]10,000 cancer-associated or cancer-upregulated) at <1% FDR. Altogether, these datasets establish the CypherAtlas, a comprehensive proteogenomic atlas of an unreported proteome comprising thousands of novel proteins, including membrane proteins with targetable extracellular domains, and intracellular proteins accessible through antigen presentation. By linking dark-RNA transcripts, predicted proteins, and patient-level metadata across RyboDyns proprietary experimental data, CypherAtlas further provides the training substrate for multi-modal models such as DarkCypher, which is being developed to prioritize cryptic targets and to forecast their expression in new patient samples. As proof of therapeutic potential, we disclose evidence for a cancer-associated, cryptic protein expressed from the YBX1 locus, (cryptic YBX1; cYBX1) and demonstrate selective in vitro tumor cell killing through a cryptic peptide-MHC (pMHC) complex derived from this protein with a TCR-mimic (TCRm) antibody when formatted as antibody drug conjugates (ADCs). Together, RyboCypher and CypherAtlas establish the dark proteome as a vast and previously inaccessible reservoir of novel targetable biology, laying the foundation for the next generation of first-in-class therapeutics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/743124v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@104c385org.highwire.dtl.DTLVardef@1c065ccorg.highwire.dtl.DTLVardef@5b717forg.highwire.dtl.DTLVardef@1788694_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

Distinct molecular mechanisms shape thermal tolerance and its plasticity in a splash pool copepod

Understanding how organisms respond to changes in temperature is becoming increasingly important in our rapidly changing world. While species differ substantially in their thermal tolerance, the exact molecular mechanisms underpinning this trait variation remain largely unknown. Species with broad geographical distribution provide a unique opportunity to examine variable responses to temperature, as populations experience a diverse range of thermal regimes that differ in the intensity, frequency, and duration of thermal stress. We used a splash pool copepod (Tigriopus californicus) with a large geographic range across the North American coast (Baja California to Alaska) to examine variation in thermotolerance and the plasticity of thermotolerance in five populations sampled across 12 degrees of latitude. We found that populations with higher heat tolerance (southern) showed lower plasticity (measured as increased survival at higher temperatures after a prior exposure to sub-lethal temperature). Our comparative transcriptomic analyses revealed that higher heat tolerance was associated with maintaining elevated expression of genes coding for peptidases even in absence of heat shock and higher plasticity of heat tolerance was associated with an increase in gene expression plasticity of genes coding for chitin and extracellular matrix (ECM). Our results highlight ontology-specific patterns associated with changes in the trait means and plasticity of heat tolerance across populations. These findings improve our mechanistic knowledge of thermotolerance as a trait and our ability to predict which populations are most vulnerable to extinction based on the trade-off between fixed thermal limits and plastic responses.

evolutionary biology↗

bioRxiv2026

Repeated mild traumatic brain injury does not affect sleep or epileptiform activity one-month post-injury in a knock-in mouse model of Alzheimer's disease

Traumatic brain injuries (TBIs) are associated with increased risk of neurodegenerative disease, including Alzheimers disease (AD); however, the mechanisms by which TBI promotes AD pathogenesis remain poorly understood. It also remains unclear whether post-TBI sequelae, including sleep disturbances and seizures, play a role in driving disease progression. To investigate these relationships, we employed a translational approach using the Closed-Head Injury Model of Engineered Rotational Acceleration (CHIMERA) of repeated mild TBI (rmTBI) and an AD knock-in mouse model to assess sleep, power spectral density, epileptiform activity, and A{beta} pathology one month post-injury. RmTBI caused elevated neurofilament-light and glial fibrillary acidic protein, markers of neuronal damage. Sex differences were observed in acute injury outcomes, sleep measures, and A{beta} plaque size. Specifically, females exhibited longer recovery post-injury, higher mortality, decreased non-rapid eye movement sleep duration, and larger average plaque size than males at equivalent impact energy. These findings highlight the importance of including both sexes when establishing injury severity thresholds. Future studies should incorporate validated TBI biomarkers of neural injury to define equivalent injury parameters across sexes and examine the chronic effects of rmTBI on sleep, epileptiform activity and AD pathology.

neuroscience↗

bioRxiv2026

Evolutionary biomechanics of maximum running speed in spiders (Araneae)

BackgroundMaximum running speed is a central performance trait, linking morphology, physiology and behaviour to fitness. It is shaped by physical capacity and ecological selection but may also be constrained by ancestry. To examine how these forces interact across macroevolutionary timescales, we conducted an allometric study in a hyper-diverse arthropod taxon--spiders (Araneae). ResultsDrawing on running performance data for 258 species from 64 of the 139 extant spider families, we integrated phylogenetic comparative methods and biomechanical modelling to disentangle the effects of body size, ancestry, leg morphology, ecological guild and preferred locomotor orientation. Maximum running speed varied substantially, both across body mass and among species of similar body mass. By accounting for body mass with a recent biomechanical model, we show that size-specific performance carries a strong phylogenetic signal, and that high-performing runners first evolved within the derived infraorder Araneomorphae.Strong running performance, after accounting for both body size and shared ancestry, was associated with relatively longer legs and, to a lesser extent, ecological guild, but not with leg slenderness or a preference for inverted versus upright locomotion. ConclusionsMacroevolutionary patterns of running performance thus reflect not only variation in body size, but also size-specific leg morphology, ecological differentiation and phylogenetic history. We hope this study contributes to the development of formal evolutionary biomechanics--one that seeks to explain patterns of diversity through the explicit integration of large-scale comparative data, natural history and quantitative models derived from first principles.

zoology↗

bioRxiv2026

Critical flicker fusion thresholds predict attentional blink magnitude

The critical flicker fusion (CFF) threshold is a psychophysical measure used to quantify the temporal resolution of the visual system and is known to vary across individuals. However, it is unclear if this measure is stimulus-specific, or if it may represent a more fundamental processing rate for visual perception in general. Here, we assess if individual variation in CFF is predictive of two features of visual processing that are dependent on temporal perception: the attentional blink and global motion sensitivity. In a non-clinical sample of 84 individuals, flicker fusion thresholds were predictive of the magnitude of the attentional blink. In contrast, we found no link between flicker fusion and global motion sensitivity in a sample of 79 individuals. Our results suggest that CFF reflects a visual processing rate that impacts other, more complex perceptual tasks.

neuroscience↗

bioRxiv2026

HIV broadly neutralizing antibodies with enhanced Fc-CD16 affinity increase NK cell ADCC even with limited envelope binding

The persistence of latent HIV-1 reservoirs remains the primary barrier to a cure. Shock and kill strategies aim to reactivate these reservoirs and eliminate them via effector cells, such as Natural Killer (NK) cells. However, chronic infection leaves NK cells exhausted. In this study, we investigated the interplay between cytokine-mediated NK cell activation and antibody-dependent cellular cytotoxicity (ADCC) across diverse HIV-1 subtypes. We demonstrated that while cytokine stimulation enhanced natural cytotoxicity, it simultaneously induces shedding of the Fc receptor CD16 via the metalloproteinase enzyme ADAM17. However, restoring CD16 expression through ADAM17 inhibition (TAPI-1) did not improve ADCC, suggesting that CD16 surface levels in NK cells is not the only limiting factor. On the other hand, Fc-engineered broadly neutralizing antibodies (bNAbs) with increased CD16 affinity, in particular LPLIL and GASDALIE, significantly enhance ADCC across the six different HIV-1 subtypes, regardless of NK cells activation, CD16 downregulation or limited surface Envelope expression in CD4T cells. These findings suggest that enhancing receptor affinity of bNAbs can bypass viral immune evasion and NK cell exhaustion, supporting their potential incorporation into HIV cure strategies. ImportanceEradicating latent HIV reservoirs remains a global health priority, as it would liberate millions of people living with HIV (PLWH) from the economic and physiological burdens of lifelong antiretroviral therapy (ART). By utilizing a primary human cell model that resembles in vivo conditions across diverse viral strains, we identified that simply preventing CD16 receptor shedding from NK cells is insufficient to improve HIV-1 clearance. Instead, we demonstrated that enhancing the binding of antibodies to the CD16 receptor enables NK cells to overcome viral immune evasion and the loss of CD16 expression. This allows for potent elimination of infected cells through antibody-dependent cellular cytotoxicity (ADCC). These findings provide a clear strategy for designing more effective "kill" components in future therapeutic strategies.

immunology↗

bioRxiv2026

Genomic history and selection in Roman and early medieval Britain

Leading biomedical resources rely on genome variation in Britain1-3, but the historical processes that shaped present-day fine-scale diversity remain debated4-13. Here we sequenced 1039 ancient shotgun genomes from Britain (median 1.4-fold coverage), primarily dating to the first millennium CE. We imputed [~]660 million variants in the UK Biobank14-16 and employed genealogy-based ancestry reconstruction. We found an association between Iron Age consanguinity and matrilineal burial practices17, later disrupted following the Roman Conquest. Despite this societal impact, only 20% of Roman-period individuals carried detectable ancestry from outside Britain. In contrast, from the 6th century CE we detect widespread influx of ancestry in over 70% of individuals in southernAnglo-Saxon Britain, with limited local admixture. We find previously underappreciated heterogeneity, with ancestries associated with Central and Southern Europe rising in prevalence from the 7th century CE. We demonstrate distinct Scandinavian-related ancestry in many Viking-associated contexts, but show that the population-level impact of the Viking Age in Britain was limited. Finally, we detect pre-medieval selection on variants linked with key immunity genes TLR10-TLR1 and IRF8. These results identify population-level and selective processes that shape variation and disease risk in Britain today.

genomics↗

bioRxiv2026

Age-Related Upregulation and Strong Expression Correlation of the Proinflammatory Cytokines IL-1β and IL-6 Across Multiple Segments of the Mouse Eye

Emerging evidence suggests that ocular inflammation increases with age and is associated with various disease states. That said, the majority of studies suffer from a significant limitation--they only focus on a single segment of the eye. This represents a limitation because age-related increases in neuroinflammatory markers are not necessarily uniform within an organ, and other age-related changes in the eye are known to occur in a segment-specific manner. The present study aims to address this gap by comparting/contrasting age-related changes in the proinflammatory cytokines IL-6 and IL-1{beta} across multiple mouse ocular segments: the (i) anterior segment (i.e., cornea, ciliary body and muscle, and zonules), (ii) retina, and (iii) posterior segment (i.e., sclera, choroid, Bruchs membrane, retinal pigmented epithelium, and parts of the optic nerve). IL-6 and IL-1{beta} were selected as targets since they exhibit differential regional patterns of age-related increases within the brain. Eyes were collected on postnatal days (P) P28, P56, P98, P200 and P500 and processed by Western blot. Both IL-6 and IL-1{beta} protein levels increased across the lifespan in all three eye segments. Interestingly, correlational analyses revealed that IL-1{beta} and IL-6 expression correlated with each other not only within individual eye segments, but also across segments. In old mice, IL-1{beta} and IL-6 levels also correlated with expression of phosphodiesterase 11A (PDE11A), an enzyme known to regulate neuroinflammation. Together, these findings suggest that inflammaging in the eye is broadly controlled by a systemic governor, unlike the brain that shows region-specific changes in cytokines with age.

neuroscience↗

bioRxiv2025

Functional Characterization of 123 Genes from Mycobacteriophage LeBron Uncovers Cytotoxic Gene Families in Cluster L1

Bacteriophages represent a vast reservoir of genetic diversity however, functional annotation remains a major challenge, as most predicted gene products lack detectable similarity to characterized gene families. Experimental approaches such as systematic overexpression screens provide an avenue for identifying phage genes that influence bacterial physiology. Here, we report an overexpression screen of all 123 predicted protein-coding genes from Cluster L1 mycobacteriophage LeBron, the first representative of this cluster to undergo genome-wide functional analysis. Expression assays in Mycobacterium smegmatis revealed that 39 genes (32%) impaired host growth, with nineteen of these toxic genes (49%) assigned no known function. The proportion of cytotoxic genes observed in LeBron is comparable to findings from Clusters K and F, despite minimal sequence conservation across clusters. Interestingly, a subset of LeBrons toxic genes appear to be functionally analogous to previously identified toxic genes in other clusters, suggesting conserved biological activities carried out by non-homologous proteins. Additionally, this analysis uncovered several novel gene families that elicit strong cytotoxic effects, expanding the known catalog of phage-derived bacterial growth inhibitors. These results provide new insights into phage gene functions and demonstrate the value of genome-wide expression screening for uncovering conserved and cluster-specific interactions between bacteriophages and their hosts.

microbiology↗

bioRxiv2025

Genetic assimilation and accommodation shape adaptation to heat stress in a splash pool copepod

Understanding how organisms respond to variable environments is becoming increasingly important in our rapidly changing world. Beyond genetic adaptation, plastic responses to the environment can alter phenotypes and fitness, ultimately driving evolution. However, the interaction between plasticity and adaptation during environmental change is complex and hard to measure in natural systems. Here, we used two populations of Tigriopus californicus copepods, a thermally tolerant southern population and a thermally sensitive northern population, to conduct a fully factorial split brood experiment where we exposed animals as larvae and adults to either a sublethal heat stress or control (no heat treatment) before measuring heat tolerance and gene expression patterns. We found that increased thermal tolerance across populations came at the expense of physiological plasticity and evolved through higher baseline expression of heat stress response genes across environmental contexts as well as increased gene expression plasticity in response to heat stress. In the thermally sensitive northern population, developmental exposure to heat stress led to higher adult tolerance and lower physiological plasticity underpinned by higher gene expression plasticity. Importantly, we found that the same set of genes were largely responsible for both the evolved higher tolerance in the southern population and the developmentally induced tolerance in the northern population suggesting that in this system, a shared molecular response contributes to acclimation and adaptation across both populations. These results link existing physiological plasticity with long-term evolutionary responses providing insight into how these populations will adapt and respond to future environmental change. SIGNIFICANCEUnderstanding plastic and evolutionary responses to dynamic environments is critical to anticipating species vulnerability to climate change. In this study, we compared gene expression and physiological responses to heat stress across two populations of a marine copepod that differ in thermal tolerance to investigate mechanisms of adaptation. We found evidence for plasticity-led evolution in this system, with the same set of genes contributing to long-term evolutionary changes across populations and to short-term physiological adjustments within populations. Our results suggest that populations with a reservoir of plasticity have a greater potential to evolve as the climate continues to warm, but that there may be a limit to this adaptive capacity.

evolutionary biology↗

bioRxiv2025

Translating clinical gene sequencing into a foundational representation of tumor subtype

While gene sequencing is routine in cancer care, translating sequences into treatment decisions remains a challenge. Here we introduce MutationProjector, an AI foundation model that transforms tumor mutation profiles into a compact representation of cancer subtype, with broad implications for diagnosis and therapy. MutationProjector is pre-trained by integrating genomic alterations from >30,000 tumors with extensive molecular knowledge, yielding a model that accurately reconstructs held-out genetic profiles (demonstrating strong generalization) and determines subtype representations from altered molecular pathways (enabling model interpretability). We evaluate MutationProjector in independent tasks related to prediction of immunotherapy response, prediction of chemotherapy response, and classification of metastasis, recording leading performance in all areas. Each task identifies key biomarkers of interest, including KMT2A and KRAS-STK11 alterations which govern immunotherapy response.

systems biology↗

bioRxiv2025

Thermogenic adipocytes alleviate hepatic steatosis and insulin resistance via macrophage cytokine secretion in obese mice

The Nrip1 gene encodes the protein Rip140, which suppresses nuclear receptors that regulate energy metabolism. Here we show adipocyte-selective deficiency of Nrip1 (AdNrip1KO) in mice causes a striking expansion of alternatively activated, M2-like macrophages within subcutaneous inguinal adipose tissue (iWAT) in addition to the appearance of thermogenic adipocytes expressing uncoupling protein 1 (UCP1). AdNrip1KO mice are less cold sensitive but showed no differences in whole body energy expenditure or food intake compared to control mice at 22 {degrees}C. Strikingly, AdNrip1KO mice on HFD display markedly attenuated hepatic steatosis and insulin resistance compared to control mice on HFD. Secreted factors that might mediate this crosstalk from adipose tissue to liver were searched for by iWAT RNAseq. Unexpectedly, upregulation of genes associated with cytokines and cytokine receptor signaling were the most highly correlated with adipocyte-selective Nrip1 loss in obese mice. Furthermore, the top upregulated genes that encode secreted proteins in AdNrip1KO iWAT are most highly expressed in macrophages, not adipocytes. This list included the IL-1b antagonist IL-1rn, known to attenuate hepatic steatosis and insulin resistance. Indeed, the IL-1rn protein in AdNrip1KO mice was found to circulate at levels we previously reported strongly attenuates hepatic steatosis and glucose tolerance in obese mice. Taken together, these results suggest a paradigm for metabolic crosstalk from thermogenic adipose tissue to liver that is mediated by IL-1rn and potentially other factors secreted from M2-like macrophages within beige adipose tissues. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/667482v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@15fb086org.highwire.dtl.DTLVardef@13e6689org.highwire.dtl.DTLVardef@1bde77borg.highwire.dtl.DTLVardef@a83f2e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAdipocyte Nrip1 deficiency (AdNrip1KO) strongly promotes adipose browning C_LIO_LIMouse AdNrip1KO polarizes adipose tissue macrophages towards M2-like C_LIO_LIAdNrip1KO reduces the hepatic fat and insulin resistance of obese mice C_LIO_LIAdNrip1KO adipose tissue macrophages secrete IL-1rn, known to mitigate hepatic fat and insulin resistance C_LI

physiology↗

bioRxiv2025

Dual Role of Glycosylation in Resistance to CD4-binding Site Broadly Neutralizing Antibodies

Broadly neutralizing antibodies (bNAbs) provide a useful tool for HIV cure strategies because of their ability to target conserved regions on the envelope (Env) protein in the context of both virions and infected cells. One of the most well studied bNAbs is the CD4 binding site (CD4bs) antibody, VRC01 and others in its class. A major obstacle to effective cure strategies with bNAbs is viral immune escape. A deeper understanding of escape pathways from VRC01-class antibodies in genetically diverse samples is needed. Using an in vitro viral escape assay where infected CD4+ T cells were cultured in the presence of increasing VRC01 concentrations, complete resistance to VRC01 was detected in Env 246.F3 by day 42. We determined that resistance was due to a mutation at position N276 that resulted in elimination of the glycan-attachment site. As the loss of a glycan at this site is known to increase virus sensitivity to CD4bs antibodies, we explored this finding further. Specifically, we introduced N276D mutation into the 12-virus global Env panel and measured neutralization susceptibility to a panel of CD4bs bNAbs. This N276D mutation increased resistance or sensitivity depending on the Env and bNAb in question, emphasizing a dual role of glycan N276 in VRC01-class bNAb neutralization. The role of this glycan in escape was demonstrated to be dependent on the context of the Env, the bNAb and the glycosylation complexity of the virus due to producer cells. These findings underscore the complexity of glycosylation in genetically diverse HIV escape from antibodies. ImportanceDespite decades of research, an HIV cure remains elusive, largely due to the viruss immense genetic variability and ability to evade immune clearance. While antiretroviral therapy (ART) suppresses viral replication, it does not eradicate the virus and presents long-term challenges related to toxicity, access, and adherence. Broadly neutralizing antibodies (bNAbs), particularly those targeting the conserved CD4 binding site such as VRC01 and others in its class, offer promise for durable control or cure by targeting both circulating virus and infected cells. However, viral escape from bNAbs remains a critical hurdle. In this study, we demonstrate that glycan-mediated escape from VRC01-class bNAbs is highly context-dependent--shaped by Env, bNAb, and the glycosylation patterns introduced by the producer cell. These findings emphasize the dual role of glycans in affecting antibody sensitivity and underscore the importance of viral and host factors in shaping effective bNAb-based cure strategies across diverse HIV-1 strains.

immunology↗

bioRxiv2025

Repetitive mild traumatic brain injury causes neuronal damage in the APP/PS1 mouse model of Alzheimer's disease without an enduring impact on amyloid pathology, sleep, or epileptiform activity

Traumatic Brain Injury (TBI) is a known risk factor for Alzheimers disease and related neurodegenerative diseases. Sleep disturbances and epileptiform abnormalities can appear after TBI and may contribute to the development of neuropathology. In this study, we characterized sleep, epileptiform activity, and neuropathology after repetitive mild traumatic brain injury (rmTBI) in a mouse model of Alzheimers disease. We used the Closed Head Impact Model of Engineered Rotational Acceleration (CHIMERA) to deliver rmTBI or sham (control) treatment to 6-month-old APP/PS1 mice (N=19). One month post-injury, we implanted electroencephalogram (EEG) and electromyographic (EMG) electrodes, recorded for 72 hours, and then collected brain tissue and blood plasma. Our assessment of sleep architecture showed that time spent in vigilance state was not affected by the rmTBI one month post-injury; however, power spectra analysis showed a shift towards higher frequencies in the rmTBI group during non-rapid eye movement (NREM) sleep. Epileptiform activity did not differ between sham and rmTBI. Compared to sham controls, the rmTBI group showed higher neurofilament light (NF-L), but not glial-fibrillary acidic protein (GFAP) in blood plasma and no change in A{beta} pathology. These results indicate sustained neurological injury in the APP/PS1 mice one month after rmTBI without affecting amyloid deposition in the brain. Our study suggests that rmTBI can induce neural injury without causing enduring sleep disruption, seizures, and exacerbation of amyloidosis in the APP/PS1 mouse model.

neuroscience↗