Biology subjects

Johnson, A.

Publications and source records attributed to Johnson, A..

At least 19 recordsLinked to original sources

bioRxiv2026

A clinically identified Kirrel3 variant disrupts trans-synaptic circuit assembly

Trans-synaptic adhesion molecules guide selective connections between neurons to establish circuit specificity. Yet, there are gaps in the understanding of how many synaptic adhesion molecules function in vivo and if clinically identified variants perturb their function. Using cell-type-specific deletion in the mouse hippocampus, we show that Kirrel3 is required in both pre-synaptic DG neurons and post-synaptic GABA neurons to form DG-to-GABA excitatory synapses that drive a feed-forward inhibitory connection to CA3. These data provide in vivo, genetic evidence for a homophilic trans-synaptic Kirrel3 interaction driving synapse formation. Moderately increasing or decreasing wildtype Kirrel3 expression did not detectably alter synapse formation or CA3 neuron activity. In contrast, expression of a Kirrel3 missense variant identified in an individual with autism dominantly disrupts synapse formation and CA3 activity in vivo, providing a mechanism by which a single missense allele could disrupt circuit assembly and contribute to disease.

neuroscience↗

bioRxiv2026

An RNase Toxin Hijacks Elongation Factor-Tu to Cleave the Ribosomal Sarcin-Ricin Loop

Ribosome-targeting toxins typically recognize and attack their substrates directly. Here, we provide the functional characterization of SRLase1, a widespread member of a recently identified RNase superfamily, and show that it cleaves the sarcin-ricin loop (SRL) of 23S rRNA. Unlike previously described ribosome-targeting toxins, SRLase1 requires the host elongation factor Tu (EF-Tu) for activity. EF-Tu normally engages the ribosome as part of the aminoacyl-tRNA delivery cycle, but SRLase1 instead exploits this factor through a mechanism incompatible with canonical ternary-complex formation. This host-factor-assisted mechanism reveals a distinct strategy for translation inhibition, in which a toxin repurposes a conserved component of the elongation machinery to access a vulnerable ribosomal target. Homologs of SRLase1 are widespread across bacterial phyla and are frequently encoded in conflict-associated genomic loci. Together, these findings define a widespread family of SRL-targeting toxins, expand the mechanistic repertoire of ribosomal antibacterial toxins, and demonstrate how conserved components of the host translation machinery can be co-opted to promote toxin activity.

microbiology↗

bioRxiv2026

A single cooperative experience increases corticolimbic synaptic density and prosocial behavior

Cooperation is typically studied as an output of the social brain, as opposed to an experience that shapes it. Here, we developed a task in rats that permits interaction while requiring joint action for reward. Cooperation depended on dyad familiarity and visual access. Anterior cingulate cortex (ACC) to basolateral amygdala (BLA) projections were activated during cooperation with a familiar partner, whereas ACC to anterior insula (AI) projections were simultaneously suppressed regardless of familiarity. A single 90 min cooperative experience increased presynaptic marker SV2A, detected by positron emission tomography (PET), in the amygdala and insula one day later. Concurrently, rodents demonstrated heightened attention toward a distressed conspecific. Cooperation is thus an experience that recruits dissociable corticolimbic pathways and changes brain and behavior beyond the encounter itself.

neuroscience↗

bioRxiv2026

Maternal diet and genetics shape the human milk metabolome

Human milk contains a diverse array of metabolites that contribute to infant nutrition, immune development, and microbial colonization. The maternal factors shaping the milk metabolome, and the relative contribution of genetics or diet vs. other factors, remain poorly understood. Here, we profiled 458 milk metabolites in 349 one-month postpartum human milk samples and integrated metabolomic data with maternal diet, clinical, transcriptomic, and genomic measurements. Maternal diet was broadly associated with milk metabolite composition, with significant correlations identified between dietary features and 323 metabolites. Coffee consumption strongly predicted milk quinic acid and 1,3-dimethyluric acid abundance, while high-fiber dietary patterns were associated with metabolites including proline-betaine and N-acetylornithine. Integration of milk transcriptomic and metabolomic data via machine learning identified biologically plausible gene-metabolite pairs, including associations between QPRT expression and quinolinic acid, and DPEP1 and cysteine-glycine dipeptide. Genome-wide association analyses identified nine study-wide significant metabolite quantitative trait loci, including novel milk-specific associations near PDE6A affecting purine metabolites and near GNE affecting free sialic acid. Comparison with plasma metabolite studies demonstrated both shared and milk-specific genetic regulation of metabolites. Finally, we found that of all tested maternal features, diet explained the largest proportion of variation in the milk metabolome. Together, these findings demonstrate that the human milk metabolome reflects both maternal exposures and mammary gland-specific biology. This work establishes a framework for understanding how genetic and environmental factors shape milk composition.

genomics↗

bioRxiv2026

In vivo cellular localisation and nanoscale organisation of NLRP3 inflammasomes

The NLRP3 inflammasome is a critical regulator of inflammation, yet the localisation, organisation, and cellular sources of endogenous NLRP3 inflammasomes remain incompletely understood. Here, we generated NLRP3-mScarlet-I endogenous reporter mice enabling visualisation of NLRP3 at physiological levels in primary cells and in vivo. We show that activated NLRP3 associated with PI4P-positive membranes from multiple organelles, supporting a model where diverse membrane platforms act as a scaffold to nucleate inflammasome assembly. Super-resolution imaging revealed that NLRP3 and ASC occupy distinct nanoscale architectures within the inflammasome, with NLRP3 displaying marked structural heterogeneity and stimulus-dependent organisation. Unexpectedly, circulating monocytes and neutrophils, rather than tissue-resident populations, emerged as the dominant NLRP3-expressing cells in vivo which rapidly infiltrated tissues following systemic inflammation, highlighting an underappreciated cellular source of rapid inflammasome-driven responses. These findings reveal previously unrecognised insights into inflammasome organisation and localisation, establishing a powerful resource for investigating endogenous NLRP3 biology in health and disease.

immunology↗

bioRxiv2026

Sequential HIV-1 fusion protein gates control the initiation of host cell entry

HIV-1 fusion with host cells is initiated upon engagement of the viral envelope (Env) protein by its receptors and co-receptors. Receptor-induced conformational changes in the Env ectodomain expose the fusion machinery and position the HIV-1 fusion peptide for release and transit to the host membrane. However, no allosteric rearrangements in the envelope receptor/co-receptor binding domain that could induce fusion peptide release have been identified, and the trigger for the structural cascade that brings the viral and host membranes together remains unknown. Here, we identified two sequential conformational gates that control fusion peptide release, thereby facilitating its transition to the host membrane. We show that destabilizing a clasp holding the fusion peptide proximal motif enhances fusion peptide release, and that a coupled downstream gate controls the release of the receptor-binding gp120 subunit. Single-particle cryo-EM structures, biased and unbiased atomistic simulations, and functional experiments reveal that this process is controlled by shifts in the angular orientation of the gp120 subunits, induced by the geometries required for receptor and co-receptor binding. These results show how HIV-1 senses contact with the host cell to initiate fusion, thereby permitting viral entry.

molecular biology↗

bioRxiv2026

Conservation of declining Florida ecosystems is critical for an at-risk butterfly

Assessing the availability of protected habitats for at-risk species is needed to determine how the spatial distribution of land cover and land use shapes conservation outcomes. The Loammi skipper (Atrytonopsis loammi) is a nonmigratory, prairie-associated butterfly that has experienced a significant reduction in its formerly widespread southeastern United States distribution over the past several decades. Observations in recent years have been limited to a small number of isolated Florida populations, and it is unclear how much suitable habitat remains and what proportion of that habitat is protected. Here we used publicly available community science data and collected specimens to identify the predominant land cover types occupied by A. loammi. We then quantified the extent to which each of these land cover types overlap with protected areas to estimate the proportion of the butterflys current distribution that occurs on managed conservation lands. Our findings show that A. loammi relies heavily on protected lands, with over half of the total area of the most strongly associated habitats located within protected areas. Given the continued expansion of human-modified landscapes in Florida and the reliance of A. loammi on protected lands, the long-term persistence of A. loammi will likely depend on the conservation and effective management of its remaining suitable habitat. Implications for insect conservationOur results highlight the critical role of protected areas in sustaining at-risk insect populations, particularly for species with limited dispersal and shrinking ranges. More broadly, they suggest that conserving and restoring protected habitats while maintaining connectivity are essential strategies for effective insect conservation in rapidly developing regions.

ecology↗

bioRxiv2026

Sustained GnRH Agonism Alters Endocrine Dynamics and Pubertal Progression in Juvenile Rats

PurposeGonadotropin releasing hormone (GnRH) agonists are clinically used to delay pubertal progression by suppressing the hypothalamic-pituitary-gonadal (HPG) axis. While GnRH agonists have long been used clinically, the developmental characterization of HPG axis suppression during puberty remains incompletely understood. Thus, we examined the effects of GnRH receptor agonism in juvenile rats. HypothesisSustained GnRH receptor agonism will result in lower gonadal mass, blunt peripheral pubertal landmarks, and alter hormonal signaling dynamics within the HPG axis. MethodsAnimals received a single injection of extended-release leuprolide acetate depot (LA) or vehicle control on postnatal day (PND) 23. Animals were assessed for body mass and peripheral markers of puberty. On PND 44, animals were euthanized and tissues were evaluated to assess additional markers of pubertal maturation, pituitary gene transcript levels, and hormone concentrations in serum and gonads. ResultsIn females, LA treatment resulted in a smaller gonad size, increased body mass, and less vaginal openings. In males, LA treatment resulted in smaller gonads but did not significantly alter body mass or preputial separation. In the pituitary, LA-treated rats had lower Gnrhr, Fshb, and Lhb transcript levels regardless of sex, while females exhibited higher Cga and Nr5a1. Serum FSH and ACTH were lower in LA-treated animals, and treated females also had lower progestins and androstenedione, and higher LH. ConclusionsLA treatment reduced aspects of pubertal maturation and HPG axis output, with sex specific outcomes. These findings highlight the need for integrated, multi-level approaches to understand how altered GnRH signaling impacts pubertal and long-term physiology.

Developmental Biology↗

bioRxiv2026

A strain-specific metabolic role for the UDP-glucose 4-epimerase Uge3 in Aspergillus fumigatus virulence

Expression of a fungal-specific sub-telomeric gene, hrmA, in Aspergillus fumigatus is important for a colony biofilm morphology termed H-MORPH, increased hypoxic fitness, and virulence in a murine model of invasive pulmonary aspergillosis (IPA). How expression of hrmA contributes to virulence and worse disease progression is ill-defined. Increased hrmA expression results in reduced attachment of the extracellular matrix (ECM) to the fungal cell wall resulting in decreased strain adherence. Fungal strains that are less adherent in vitro are typically less virulent as the ECM heteropolysaccharide galactosaminogalactan (GAG) aids in adhesion to host cells and confers protection from host responses. Here we report that the UDP-glucose 4-epimerase encoding gene required for GAG biosynthesis, uge3, is necessary for full virulence of the H-MORPH strain, hrmAREV (AF293::hrmAD304G). In contrast, loss of uge3 in the reference strain AF293 did not significantly impact virulence in the tested IPA murine model. Phenotypic, transcriptomic, and metabolic analyses of uge3 loss in the respective strain backgrounds revealed a key role for Uge3 in central carbon metabolism in a strain specific context that promotes disease progression. These results complement the known role of Uge3 in GAG biosynthesis and highlight strain specific metabolic differences in pathogenic A. fumigatus strains. IMPORTANCEAspergillus fumigatus forms adherent biofilms that contribute to its ability to persist and cause disease. However, significant strain diversity exists with regard to the morphology of A. fumigatus biofilms. A distinct colony morphotype associated with increased disease progression and low oxygen fitness, termed H-MORPH, was recently described. An additional defining feature of the H-MORPH biofilm morphotype is reduced in vitro adherence to surfaces. While reduced fungal strain adherence is most commonly associated with reductions in virulence, H-MORPH strains exhibit increased virulence relative to the well-studied N-MORPH reference strain AF293. Here we discover that the UDP-glucose 4-epimerase, Uge3, plays an important role in H-MORPH central carbon metabolism complementary to its role in production of the extracellular matrix polysaccharide galactosaminogalactan (GAG). In H-MORPH strains, this metabolic role for Uge3 becomes central to virulence. These data highlight A. fumigatus strain specific mechanisms of fungal carbon metabolism related to biofilm matrix production and fungal virulence.

microbiology↗

bioRxiv2026

Reh1 is Required for Nonfunctional 25S RNA Decay

25S nonfunctional RNA decay (NRD) eliminates 60S ribosomal subunits carrying inactivating mutations in the RNA. However, how cells identify defective subunits has not been described. We recently showed that the zinc-finger protein Reh1 is the last assembly factor to be released from a nascent 60S subunit. We now show that in yeast Reh1 is required for the degradation of 25S NRD substrates. 25S rRNAs carrying mutations in the catalytic center, A2820G or U2954A (A2451 and U2585, respectively in E coli numbering), are unstable in wildtype cells but are fully stabilized when REH1 is deleted. However, not all 25S rRNA mutations are recognized by Reh1. Ribosomes with a truncated L1 stalk engage in translation but cannot support viability. These ribosomes display a half-life indistinguishable from wild-type rRNA, suggesting that yeast does not have a robust surveillance system for such mutant ribosomes. Deletion of REH1 also has no impact on the levels of defective 18S rRNA. These results indicate that Reh1 and 25S NRD are specific for mutations in or near the catalytic center of the ribosome.

molecular biology↗

bioRxiv2026

Contact dependent suppression of Clostridioides difficile sporulation by enterococci requires the endocarditis and biofilm pilus

Clostridioides difficile is a healthcare-associated infection that arises when broad-spectrum antibiotic treatment disrupts the gut microbiota and is transmitted by highly resistant spores. Vancomycin-resistant Enterococcus faecium (VRE) is an opportunistic pathogen frequently co-isolated from C. difficile patients. We found that C. difficile sporulation is significantly reduced in VRE-C. difficile co-culture. Physical separation of C. difficile and VRE in transwell co-culture restored sporulation. Mixed macrocolony culture assays on solid agar confirmed physical contact is necessary for sporulation inhibition. We screened a panel of enterococci and found that most strains reduce sporulation, except Enterococcus saccharolyticus, which lacks predicted surface displayed virulence factors in its genome. We performed a candidate gene screen using an Enterococcus faecalis OG1RF transposon library and found that an insertion in the major pilin ebpC partially restored C. difficile sporulation in co-culture. These data were confirmed with in-frame deletions in the ebpABC pilus operon and a clinical isolate of E. feacalis lacking ebpABC. These findings suggest enterococci modulate C. difficile sporulation through a contact-dependent mechanism involving the Ebp pilus. ImportanceA characteristic of C. difficile infection is multiple episodes of acute disease. Spores are the transmission vector of C. difficile and are necessary for recurrence in models of disease. Our research demonstrates that C. difficile spore production is significantly reduced in the presence of enterococci, a common group of beneficial and pathogenic bacteria present in the gut microbiota. Physical contact with enterococci reduces C. difficile spore production. We attribute this effect to a protein structure on the surface of enterococci. This finding suggests a potential role for enterococci and the gut microbiota in general to uncover regulators of C. difficile spore formation. This may provide an avenue for innovative treatment strategies that reduce spore formation.

microbiology↗

bioRxiv2026

APOE is a presynaptic protein that accumulates with age and modulates neurotransmitter release

The synaptic vesicle (SV) cycle is the fastest membrane trafficking and protein sorting process in biology. It underlies neuronal communication and cognition, yet synaptic function declines during normal aging, increasing vulnerability to neurologic disease. How the SV cycle is maintained across the lifespan of a complex organism remains unclear. Here, we used wild-type mice (C57BL/6J) to define the age- and sex-stratified molecular landscape of SVs and identified apolipoprotein E (APOE) as an abundant presynaptic protein further enriched in aged female samples. Super-resolution imaging, cell-type selective expression, and protease protection assays demonstrate that APOE originates from astroglia and associates with the cytosolic face of SVs. Using iGluSnFR and pHluorin optophysiology, we find that both decreased and increased APOE levels impair neurotransmission during stimulus trains. Together, these findings place APOE at the synapse and establish it as a cell-nonautonomous regulator of the SV cycle.

neuroscience↗

bioRxiv2026

Rei1 and Reh1 facilitate the loading of eL24

The correct assembly of ribosomes is essential for viability and faithful gene expression. In eukaryotic cells, the pre-40S and pre-60S ribosomal subunits are largely pre-assembled in the nucleolus before they are exported to the cytoplasm for final maturation. Although most ribosomal proteins of the large subunit are loaded onto pre-60S particles in the early nucleolar steps, a few, including eL24, are loaded in the cytoplasm. eL24 is thought to recruit the zinc-finger protein Rei1 (ZNF622 in humans). In yeast, Rei1 has a paralog, Reh1. While we and others have previously shown that Rei1 facilitates the removal of Arx1, Rei1 and Reh1 appear to have an additional unknown function. To identify this function, we first examined the protein composition of pre-60S subunits isolated from rei1{Delta} reh1{Delta} mutant cells and found that these subunits were specifically defective for eL24. However, the absence of eL24 did not impair Rei1 binding to pre-60S. Moreover, overexpression of eL24 suppressed the growth defect of the double mutant. As an alternative approach to understanding the function of Rei1 and Reh1, we screened for bypass suppressors of the growth defect of rei1{Delta} reh1{Delta} cells. We identified mutations in the genes coding for ribosomal protein uL3, the GTPase Lsg1 and the protein phosphatase Ppq1. Importantly, these suppressors all partially reversed the eL24 loading defect of rei1{Delta} reh1{Delta} cells. Based on these results, we propose a revised order of cytoplasmic assembly events where Rei1 and Reh1 facilitate the recruitment of eL24 to the pre-60S particle.

genetics↗

bioRxiv2026

Multiparametric Classification of Pure-tone Responses Distinguishes Neurons in Inferior Colliculus Subdivisions

The inferior colliculus (IC) integrates ascending auditory and descending multimodal inputs within distinct subdivisions, the central nucleus (CNIC) and cortex (CtxIC). Despite differences in connectivity, auditory responses in these subdivisions are similar, complicating localization during in-vivo recordings. Here, we tested whether recordings can be assigned to CNIC or CtxIC using only response properties in awake and anesthetized mice. We constructed frequency response areas (FRAs) from pure tone responses and extracted tuning and firing metrics. Individual FRA features could not reliably localize recordings. In contrast, a random forest classifier combining FRA-derived features accurately localized recordings to CNIC or CtxIC across states. These findings demonstrate that while IC subdivisions differ only subtly along individual response parameters, appropriate multiparametric approaches can enable robust classification. More broadly, our results illustrate how biologically meaningful distinctions may be revealed by combining weakly informative features, an approach that can be applied across diverse brain regions and modalities.

neuroscience↗

bioRxiv2026

Epithelial sensing of vitamin A shapes intestinal antimicrobial defense

Vitamin A is a central regulator of intestinal adaptive immunity, but its role in innate immunity is less defined. Antimicrobial proteins form a chemical barrier that protects the intestinal epithelium from microbial invasion. Among these, REG3 family lectins are induced by the microbiota, yet how nutritional cues intersect with microbial signals to control their expression remains unclear. Here, we show that dietary vitamin A promotes expression of REG3 antimicrobial lectins, including REG3G, in intestinal epithelial cells from both mice and humans. This induction is mediated by retinoic acid and requires retinoic acid receptor (RAR) signaling. Mechanistically, RARs bind directly to the Reg3g promoter adjacent to a STAT3 binding site. As STAT3 mediates microbiota-induced IL-22 signaling in epithelial cells, this arrangement provides a molecular framework for integrating nutritional and microbial inputs at the level of REG3G transcription. Extending these findings, we demonstrate that vitamin A-retinoic acid signaling similarly promotes expression of -defensin antimicrobial proteins. Together, these findings define a transcriptional mechanism by which vitamin A enhances epithelial antimicrobial defenses and strengthens mucosal innate immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/710399v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@18dd8aforg.highwire.dtl.DTLVardef@18cf2fdorg.highwire.dtl.DTLVardef@a4dc89org.highwire.dtl.DTLVardef@18aa9c7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVitamin A promotes epithelial expression of REG3 antimicrobial proteins in the intestine C_LIO_LIRetinoic acid receptors (RARs) directly activate mouse Reg3g and human REG3G transcription C_LIO_LIRARs bind the Reg3g promoter adjacent to STAT3, integrating nutritional and microbial signals C_LIO_LIVitamin A-RAR signaling broadly regulates epithelial antimicrobial programs, including -defensins C_LI

immunology↗

bioRxiv2026

Starve-Feed Cycles Direct Quiescence to Proliferation Transitions in Drosophila Follicle Stem Cells via Transcriptional Regulation

Stem cell quiescence is a reversible state in which cells temporarily exit the cell cycle but remain poised to reenter, on cue. Robust protection of the balance between stem cell quiescence and proliferation (Q->P) is critical for long-term tissue health. Proliferation without proper resources drives disease states including cancer or birth defects. Conversely, extended periods of quiescence can lead to irreversible senescence, causing stem cell loss, aging symptoms, and vulnerability to oncogenic transformation. Diet is a central regulator of Q->P. Tissue stem cells are particularly impacted, entering periods of quiescence during nutrient restriction, with rapid induction of proliferation upon feeding. We demonstrated previously that the Hedgehog (Hh) signaling pathway is necessary and sufficient for controlling Q->P responses to dietary changes in epithelial Follicle Stem Cells (FSCs) in the fly ovary. The Hh effector, Cubitus Interruptus (Ci), is a transcriptional regulator that mediates the feeding response. To identify Ci-induced Q->P regulators, we labeled transcripts that are induced in FSCs during the 6-hour Q->P timecourse using thiouracil tagging (TU-tagging), and sequenced TU-tagged messages versus Input to prioritize candidates. Unexpectedly, cell cycle regulators were not induced, suggesting that other mechanisms control Q->P in FSCs. We describe a sequential screening approach that uncovered seven novel, feeding-dependent Q->P regulators, including a cholesterol transporter and, surprisingly, glial and neuronal regulators. Our results highlight the importance of dynamic regulation of gene expression for translation of dietary signals by stem cells, uncovering new pathways for mechanistic investigation.

genetics↗

bioRxiv2025

A non-canonical role for the ATAD2 ortholog BDF7 in nucleolar ribosome maturation and amastigote survival in Leishmania mexicana.

ATAD2 is a widely conserved, homohexameric ATPase that, in humans, features a bromodomain tier. It plays a role in chromatin remodelling in embryonic stem and germ cells but is frequently upregulated in many cancers, making its bromodomain an attractive drug target. While ATAD2-like proteins generally modulate nucleosome density to control genome compartmentalization and gene expression across eukaryotes, their precise molecular functions vary. We investigated LmxBDF7, the ATAD2 ortholog in the important human pathogen Leishmania mexicana, the causative agent of cutaneous leishmaniasis. Unlike its human counterpart, the LmxBDF7 bromodomain is predicted to be occluded and non-canonical. BDF7 null mutants were unable to develop into infectious amastigote forms and could not infect macrophages, demonstrating it is essential for lifecycle progression. Chromatin Immunoprecipitation sequencing (ChIP-seq) suggested low affinity for chromatin, aligning with its atypical bromodomain. Instead, Proximity-Biotinylation (XL-BioID) suggested a role in ribosome maturation within the nucleolus. RNA-sequencing (RNA-seq) of the {Delta}bdf7 mutant revealed widespread disruption of gene expression during growth and differentiation. Crucially, key genes required for amastigote survival, such as ribosomal protein genes and glutamine synthetase, were downregulated. This downregulation was spatially biased, preferentially affecting genes on Chromosome 23. Our combined data suggest that while BDF7 is essential, its functions have diverged from other ATAD2-like factors found in opisthokonts. Author SummaryATAD2 is a protein that helps cells balance the number of nucleosomes bound to DNA in the nucleus of a cell. Occurring at important sites or times this provides a helper function that ensures other protein complexes can operate on chromatin effectively. In some cancers ATAD2 is disrupted and therefore is being explored as target for new medicines. Orthologues of ATAD2 have been characterised in mammals and several species of yeast. We have sought to identify if an ATAD2-like protein can be found in the important human pathogen, Leishmania mexicana - which is evolutionary distant from humans and yeast. Indeed, we were able to find an ATAD2-like protein called BDF7. Interestingly, BDF7 has a bromodomain which is predicted to be non-functional in terms of being able to bind histones. We were able to make strains of Leishmania mexicana that lacked BDF7 which were viable, but unable to complete the differentiation step required for infecting macrophages. Intriguingly we found BDF7 had a poor association with chromatin and inhabited a protein neighbourhood defined by factors which facilitate ribosome biogenesis. Lastly, RNA-seq analysis of the cells revealed that those lacking BDF7 were potentially depleted for glutamine synthetase which would prevent them developing into fully functional amastigotes.

molecular biology↗

bioRxiv2025

Temporal single-cell profiling uncovers age-associated delays in immune resolution to respiratory viral infection

Aging is a major risk factor for increased morbidity and mortality following acute respiratory virus infections. To elucidate the immune determinants underlying viral pathogenesis and delayed lung repair in the aged lung, a comprehensive time-course study was conducted. Single-cell RNA sequencing (scRNAseq) and high-dimensional flow cytometry were utilized to compare lungs from young and aged mice infected with influenza A virus (IAV). Aged hosts displayed diminished alveolar macrophage (AM) and dendritic cell (DC) but elevated monocyte-derived macrophage (MoM) and interstitial macrophage (IM) presence following infection. Additionally, enhanced accumulation of adaptive immune cells, including CD4+ tissue-resident helper (TRH) cells, CD8+ tissue-resident memory (TRM) cells, and a B cell subset resembling age-associated B cells, was observed in the memory phase. Pathway analysis revealed that elevated type I and II interferon (IFN/{gamma}) signaling, especially in MoM/IM subsets, distinguished the aged hosts from the young. Inhibition of IFN/{gamma} signaling after viral clearance improved long-term respiratory outcomes and reduced both IM and TRH populations in aged mice. These findings highlight the pivotal role of IFN/{gamma} signaling, likely within MoM/IM subsets, in driving the exuberant persistence of adaptive immune cells and chronic immunopathology in the aged lung following acute viral infection.

immunology↗