Biology subjects

Chung, J.

Publications and source records attributed to Chung, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Food perception alone stimulates oviposition through serotonin signaling in Drosophila

Reproduction is strongly shaped by nutrient availability, but whether sensory information about food can regulate reproductive output before nutrients are consumed remains unclear. Here, using Drosophila melanogaster, we show that sensory perception of dietary yeast, a protein-rich food source widely used to stimulate fecundity in the fruit fly, is sufficient to rapidly promote egg laying. Specifically, we found that yeast odor exposure increased the rate of oviposition and the number of eggs laid within hours, independent of yeast intake, and that this response was mediated by olfactory signaling through the odorant receptor co-receptor Orco. We further identified serotonin receptor 2A (5-HT2A), but not 5-HT2B, as necessary for yeast odor-induced egg laying. We then asked whether yeast odor also elicits broader life-history changes and whether its reproductive and longevity effects depend on a shared mechanism. Consistent with previous observations, yeast odor also shortened lifespan. However, this lifespan effect was independent of 5-HT2A signaling, indicating that the reproductive and longevity responses to food perception are separable. Finally, our brain connectomic analyses revealed that yeast-responsive olfactory neurons preferentially influence oviposition descending neurons (OviDNs) compared with other olfactory neurons. OviDNs further connect with endocrine-related circuitry in the corpora allata (CA), and, most interestingly, the interneurons linking OviDNs to CA neurons are enriched for serotonergic and dopaminergic modulation. Taken together, our observations indicate that nutrient acquisition is not a prerequisite for animals to adjust their reproduction to the nutritional environment. Sensory information predicting food availability itself can elicit changes in neural state, likely through olfactory-reproductive circuits, that acutely alter reproductive physiology.

physiology↗

bioRxiv2026

Bacterial RNA polymerase exemplifies a general physical mechanism for accelerating protein-DNA association

Bacterial RNA polymerases (RNAPs) have two flexibly tethered subunit C-terminal domains (-CTDs) that bind DNA. Interaction between -CTDs and some promoter DNA motifs is known to accelerate transcription initiation, but the physical mechanism by which it does so is unclear. We used single-molecule multiwavelength fluorescence microscopy to test how the diffusion-limited binding kinetics of core RNAP to non-promoter DNA differ from those of mutant RNAPs that lack one or both -CTDs. We find that even though -CTDs and their tethers are small compared to the complete RNAP molecule, the presence of two -CTDs accelerates DNA binding by [~]10-fold and [~]55-fold respectively relative to RNAP constructs in which one or both -CTDs are deleted. In contrast, the presence of -CTDs did not have a detectable effect on RNAP-DNA complex lifetimes in the absence of RNA synthesis. We explain how -CTDs achieve the dramatic acceleration of RNAP binding to DNA using a quantitative three-state kinetic model that includes a transient binding intermediate where only the -CTD(s) are bound to DNA, tethering the rest of the RNAP in the vicinity of DNA. The model and assumed parameters are validated using Brownian dynamics simulations of the DNA association reactions for two-, one-, or zero-CTD RNAP constructs. The combination of single-molecule experiments, mathematical theory, and simulations suggests that adding a flexible DNA-binding tether is a general physical mechanism which can accelerate the diffusion-limited binding of a large protein like RNAP to DNA and quantitatively defines the conditions under which this acceleration can occur. Significance StatementLarge enzymes that must associate with DNA to perform their biological functions are expected to bind DNA only slowly because of slow enzyme diffusion. However, some DNA-binding enzymes have one or more additional small DNA-binding domains that can diffuse rapidly but are attached to the enzyme through an unstructured flexible tether. Combining single-molecule experiments, theory, and computation, we present evidence for a general mechanism by which such tethered domains can accelerate enzyme binding to DNA by orders of magnitude, while not significantly changing the duration of the DNA-bound state. We demonstrate this effect for the flexibly-tethered -subunit C-terminal domain of bacterial RNA polymerase. The mechanism may allow the polymerase to rapidly bind DNA while minimizing non-functional sequestration on the genome.

biophysics↗

bioRxiv2026

Activity-dependent lipid droplet biogenesis and turnover regulate synaptic integrity

Lipid droplets (LDs) are conserved organelles that buffer lipid storage and stress, yet their dynamics and functions in neurons remain largely unknown. Here, we report activity-dependent dynamics of neuronal LDs, visualized by a novel, genetically encoded LD reporter (termed LipiDew), in both cultured neurons and mouse motor cortex. Using LipiDew, we found that various paradigms of neuronal activation induced predominant and transient formation of LDs in neurites. Disruption of autophagic LD degradation (lipophagy) resulted in abnormal lipid accumulation in dendritic spines and shafts, promoted recruitment of synaptic scaffolding proteins to LDs, and altered intracellular calcium kinetics in neurons. In addition, mice with neuron-specific genetic impairment of lipophagy showed motor function defects. Together, these findings identify activity-dependent LD formation and lipophagic clearance in neuronal compartments as a crucial regulatory mechanism of synaptic integrity and neuronal function.

neuroscience↗

bioRxiv2026

Landscape-scale navigation unlocks antibody CDR structural logic for AI-guided rescue and therapeutic optimization

While AI offers transformative potential for therapeutic antibody design, the lack of ground-truth data fundamentally constrains our ability to model the epistatic topology of fitness landscapes. Here, we establish a high-throughput workflow to characterize tens of thousands of antibody variants per week with gold-standard biophysical precision. By combinatorially assembling functional variants from deep mutational scanning, we charted antibody fitness landscapes comprising over 17,000 data points, which revealed an extremely rugged, non-navigable epistatic topology. Yet, navigating at this unprecedented scale enabled the discovery of rare peak clusters exhibiting simultaneous enhancements in affinity and productivity. Strikingly, ProteinMPNN predicted the CDR-dependent productivity landscape with remarkable accuracy, suggesting that sequence-structure compatibility within CDRs gates cellular productivity. This insight enabled a structure-guided rescue strategy combining AlphaFold3 and ProteinMPNN, which successfully restored the cellular productivity of high-affinity, low-productivity clones via single amino acid substitutions. Two elite variants drawn directly from peak clusters further demonstrated 20- to 100-fold in vivo efficacy gains in a murine psoriasis model. Our findings establish CDR structural fitness as a fundamental determinant of antibody cellular productivity and validate landscape-scale navigation as a powerful framework for therapeutic antibody optimization.

bioengineering↗

bioRxiv2025

Single-molecule tracking of RNA-DNA hybrid removal enzymes important for lagging-strand replication

The formation of RNA-DNA hybrid (RDH) primers by primase is an essential step in the recruitment of DNA polymerase during replication initiation and for the synthesis of each Okazaki fragment on the lagging strand. In addition to primers, RDHs form through misincorporation of ribonucleotides by DNA polymerase during elongation and by formation of R-loops during transcription. R-loops are three-stranded structures that form when the nascent mRNA anneals to the template DNA strand, displacing the complementary DNA strand. The persistence of RDHs is deleterious to genome stability in all cells because they increase susceptibility to mutations, impaired replication fork progression, DNA double-stranded breaks, and genomic rearrangements. In many bacteria, it is well established that components of the replicative DNA polymerase form a macromolecular complex that can be imaged using single-molecule or ensemble fluorescence approaches. The spatiotemporal regulation of proteins involved in RDH removal during lagging-strand maturation is less clear. Here, we study three proteins that are involved in the removal of RDHs from the lagging strand during DNA replication in the Gram-positive bacterium Bacillus subtilis: DNA polymerase I (Pol I), FenA, and RNase HIII. We characterized the behavior of each PAmCherry-tagged lagging-strand enzyme in living cells using single-particle tracking photactivated localization microscopy. In this work, we find that all three proteins are highly mobile, suggesting residence times at their target substrates are below our temporal resolution. We also find evidence that Pol I activity is modulated through interaction with the replisome, whereas FenA and RNase HIII are regulated through access to the nucleoid. Our results provide new insight into how enzymes are recruited to resolve RDHs during lagging-strand replication in vivo. SignificanceRNA-DNA hybrids (RDHs) are essential, transient intermediates in DNA replication, yet their presence significantly increases the susceptibility of the genome to damage. We characterized the single-molecule behavior of three proteins important for processing RDHs in Okazaki fragments in living bacteria. We find that enzyme activity is modulated by access to the replisome and nucleoid. Specifically, we find that DNA polymerase I is preferentially localized to the replisome, while FenA and RNase HIII dwell times at the replisome are very short and below our detection limit. Our work shows that Pol I, FenA, and RNase HIII turn over rapidly in cells, providing new insight into how lagging-strand replication is coordinated in vivo.

biophysics↗

bioRxiv2025

Dynamics of TFIIH and Spt5 during the transition from transcription initiation to elongation

The transition of RNA polymerase II from initiation to elongation requires the timely exchange of many factors. Some initiation factors and elongation factors contact the same RNA polymerase II surfaces in an apparently mutually exclusive manner. For example, space occupied by the initiation factor TFIIH and elongation factor Spt4/5 (also known as DSIF) are predicted to overlap. To determine whether Spt4/5 actively displaces TFIIH, or binds only after TFIIH dissociates, labeled yeast nuclear extracts were combined with single-molecule fluorescence microscopy to observe their dynamics in real time. TFIIH categorically dissociates before Spt4/5 arrives, with a clear interval in between with neither factor present. Therefore, Spt4/5 binding is not required to dissociate TFIIH from RNA polymerase II.

molecular biology↗

bioRxiv2025

A single extracellular vesicle-based platform supporting both RBD protein and mRNA vaccination against SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syn-drome coronavirus 2 (SARS-CoV-2) has highlighted the need for novel, effective, and safe vaccine platforms. Extracellular vesicles (EVs) facilitate cell-to-cell communication and can modulate immune responses by delivering antigens. Here, we propose a versatile EV-based vaccine plat-form in which immune-stimulating EVs, engineered using acoustic shock waves (SW), are used to deliver either protein or mRNA antigens. Immunostimulatory EVs derived from LPS-activated THP-1 monocytes (aTEVs) were loaded with SARS-CoV-2 receptor-binding domain (RBD) protein or RBD-encoding mRNA via SW post-loading. Both aTEV-RBD-Pro and aTEV-RBD-mRNA elicited robust RBD-specific humoral and cellular immune responses in mice without the need for external adjuvants. Moreover, lyophilized aTEV-RBD-Pro vaccines retained immunogenicity after storage, supporting their chain-independent stability. These results demonstrate that a single EV-based platform can independently support both protein- and mRNA-based vaccination, highlighting its flexibility for next-generation vaccine development.

immunology↗

bioRxiv2025

Sialylated CD43 is a glyco-immune checkpoint for macrophage phagocytosis

Macrophages in the tumor microenvironment exert potent anti-tumorigenic activity through phagocytosis. Yet therapeutics that enhance macrophage phagocytosis have not improved outcomes in clinical trials for patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). To systematically identify regulators of phagocytosis, we performed genome-scale CRISPR knockout screens in human leukemia cells co-cultured with human monocyte-derived macrophages. Surprisingly, we found that whereas the classic "dont eat me" signal CD47 inhibited mouse macrophages, it did not inhibit phagocytosis by human macrophages. In contrast, the O-linked glycosylation and sialylation pathways were strong negative regulators of phagocytosis. In AML, the cell surface O-linked glycoprotein CD43 was the major effector of the O-linked glycosylation and sialylation pathways. Genetic deletion or antibody blockade of CD43 enhanced macrophage phagocytosis. This work highlights the importance of using human platforms to identify immune checkpoints, and nominates CD43 as a glyco-immune regulator of human macrophage phagocytosis.

cancer biology↗

bioRxiv2025

Network Biomarkers of Alzheimer's Disease Risk Derived from Joint Volume and Texture Covariance Patterns in Mouse Models

Alzheimers disease (AD) lacks effective cures and is typically detected after substantial pathological changes have occurred, making intervention challenging. Early detection and understanding of risk factors and their downstream effects are therefore crucial. Animal models provide valuable tools to study these prodromal stages. We investigated various levels of genetic risk for AD using mice expressing the three major human APOE alleles in place of mouse APOE. We leverage these mouse models utilizing high-resolution magnetic resonance diffusion imaging, due to its ability to provide multiple parameters that can be analysed jointly. We examine how APOE genotype interacts with age, sex, diet, and immunity to yield jointly discernable changes in regional brain volume and fractional anisotropy, a sensitive metric for brain water diffusion. Our results demonstrate that genotype strongly influences the caudate putamen, pons, cingulate cortex, and cerebellum, while sex affects the amygdala and piriform cortex bilaterally. Immune status impacts numerous regions, including the parietal association cortices, thalamus, auditory cortex, V1, and bilateral dentate cerebellar nuclei. Risk factor interactions particularly affect the amygdala, thalamus, and pons. APOE2 mice on a regular diet exhibited the fewest temporal changes, suggesting resilience, while APOE3 mice showed minimal effects from a high-fat diet (HFD). HFD amplified aging effects across multiple brain regions. The interaction of AD risk factors, including diet, revealed significant changes in the periaqueductal gray, pons, amygdala, inferior colliculus, M1, and ventral orbital cortex. Future studies should investigate the mechanisms underlying these coordinated changes in volume and texture, potentially by examining network similarities in gene expression and metabolism, and their relationship to structural pathways involved in neurodegenerative disease progression.

neuroscience↗

bioRxiv2024

Early prediction of preeclampsia using the first trimester vaginal microbiome

Preeclampsia is a severe obstetrical syndrome which contributes to 10-15% of all maternal deaths. Although the mechanisms underlying systemic damage in preeclampsia--such as impaired placentation, endothelial dysfunction, and immune dysregulation--are well studied, the initial triggers of the condition remain largely unknown. Furthermore, although the pathogenesis of preeclampsia begins early in pregnancy, there are no early diagnostics for this life-threatening syndrome, which is typically diagnosed much later, after systemic damage has already manifested. Here, we performed deep metagenomic sequencing and multiplex immunoassays of vaginal samples collected during the first trimester from 124 pregnant individuals, including 62 who developed preeclampsia with severe features. We identified multiple significant associations between vaginal immune factors, microbes, clinical factors, and the early pathogenesis of preeclampsia. These associations vary with BMI, and stratification revealed strong associations between preeclampsia and Bifidobacterium spp., Prevotella timonensis, and Sneathia vaginalis. Finally, we developed machine learning models that predict the development of preeclampsia using this first trimester data, collected ~5.7 months prior to clinical diagnosis, with an auROC of 0.78. We validated our models using data from an independent cohort (MOMS-PI), achieving an auROC of 0.80. Our findings highlight robust associations among the vaginal microbiome, local host immunity, and early pathogenic processes of preeclampsia, paving the way for early detection, prevention and intervention for this devastating condition.

microbiology↗

bioRxiv2024

Inhibiting monocyte migration reduces arterial thrombosis and facilitates thrombolysis

BackgroundMonocytes contribute to the initiation and propagation of venous thrombosis. Little is known about the roles monocytes play in arterial thrombosis, the cause of stroke and MI. MethodsWe investigated how chemokine receptor 2 (CCR2) knockout (-/-) affects platelet function, blood coagulation, thrombus volume, and thrombolytic susceptibility in 627 mice with FeCl3-mediated carotid arterial thrombosis: three CX3CR1-GFP mice, 326 C57BL/6 mice, and 288 CCR2-/- mice. We performed i) intravital microscopy imaging of leukocyte recruitment to carotid thrombus, ii) flow cytometry-based quantification of leukocytes in blood vs. thrombus and leukocyte-platelet aggregates in blood, iii) platelet aggregometry, iv) coagulation assays, v) micro-computed tomography (microCT)-based thrombus imaging using gold nanoparticles after tissue plasminogen activator (tPA) therapy with or without either a) CCR2 siRNA pretreatment (for 3 days) or post-treatment or b) clopidogrel pretreatment (for 7 days), and vi) histology including scanning electron microscopy. ResultsIntravital microscopy and flow cytometry showed that both neutrophils and monocytes were recruited to the acute arterial thrombus, as observed 30 minutes post-thrombosis. Platelet function tests demonstrated platelet aggregation to be lower in the whole blood of CCR2-/- mice (vs. C57BL/6 mice) but not in their leukocyte-free platelet rich plasma, suggesting this platelet dysfunction is cell-mediated. Flow cytometry experiments revealed lower numbers of monocyte - platelet aggregates (MPAs), a marker of platelet activity, in the blood of CCR2-/- mice, compared to C57BL/6 mice. Blood levels of FXIII and monocyte levels of FXIII-A were increased after carotid thrombosis in C57BL/6 mice but not CCR2-/- mice. Further, in vivo microCT and histology, respectively, showed that CCR2-/- mice had smaller and more porous thrombi with less fibrin cross-linking, compared with C57BL/6 mice. MicroCT also demonstrated that tPA-mediated thrombolysis was faster in CCR2-/- mice and CCR2 siRNA-treated mice, compared to C57BL/6 mice. In addition, clopidogrel had a greater effect on inducing thrombus formation with smaller sizes after FeCl3 application, while CCR2-/- had a greater effect on dissolving thrombus faster after tPA administration. ConclusionsCCR2 antagonism decreases platelet aggregation and reduces FXIII levels in blood and monocytes, thus driving arterial thrombosis towards the generation of a relatively small, porous, more lysable clot. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIIn venous thrombosis, monocytes cooperate with platelets and neutrophils to promote thrombus formation; however, few studies have investigated the roles of monocytes in arterial thrombosis. C_LIO_LIAn in vitro study using arterial blood samples from patients with acute coronary syndrome showed that P-selectin on activated platelets upregulated monocyte chemokine receptor 2 (CCR2) expression, which was higher in monocyte-platelet aggregates (MPAs) than in monocytes without platelets. C_LIO_LIIn a mouse study using an in vivo model of FeCl3-induced arterial thrombosis, the time to thrombotic occlusion was prolonged in CC chemokine ligand 2 (CCL2) knockout (-/-) mice compared with wild-type mice. C_LI What New Information Does This Article Contribute?O_LIThis study is the first to demonstrate that CCR2-/--mediated monocyte deficiency exerts antithrombotic and tissue plasminogen activator (tPA)-facilitating effects in acute arterial thrombosis. C_LIO_LICCR2-/- mice had a) decreased platelet aggregability, probably due in part to reduced post-thrombosis MPA numbers, and b) lower blood and monocyte levels of Factor XIII (FXIII), compared to those of C57BL/6 mice. C_LIO_LIMicro-computed tomography (microCT) thrombus imaging showed that i) CCR2-/- mice, compared to C57BL/6 mice, had smaller thrombi, with more porosity and less fibrin cross-linking on histology and ii) CCR2-/- or CCR2 siRNA facilitates tPA-mediated thrombolysis. C_LI The majority of ischemic strokes occur due to thromboembolic occlusion of cerebral arteries. Tissue plasminogen activator (tPA), which is the only FDA-approved drug for acute ischemic stroke, has only a moderate efficacy rate regarding early recanalization, which is closely associated with thrombus volume and thrombolytic resistance. Monocytes, in cooperation with platelets and neutrophils, contribute to thrombus formation in venous thrombosis. To date, only a few studies have detailed potential prothrombotic roles for monocytes in arterial thrombosis. In the present study, using a mouse model of FeCl3-mediated carotid artery thrombosis and high-resolution microCT thrombus imaging, we demonstrate that CCR2-/--mediated monocyte deficiency exerts antithrombotic and tPA-facilitating effects. Compared to C57BL/6 mice, CCR2-/- mice exhibited decreased platelet aggregability along with lower numbers of circulating MPAs (a marker of platelet activity) and reduced monocyte recruitment to arterial thrombi. Moreover, CCR2-/- mice had lower levels of both circulating FXIII and monocyte FXIII-A, which are known to strengthen and stabilize thrombi. In line with these findings, i) CCR2-/- mice had smaller, more porous thrombi with less fibrin cross-linking and ii) tPA-mediated thrombolysis was faster in CCR2-/- mice or with CCR2 siRNA.

immunology↗

bioRxiv2024

Inhibition of nitric oxide synthase transforms carotid occlusion-mediated benign oligemia into de novo large cerebral infarction

It remains unclear why unilateral proximal carotid artery occlusion (UCAO) causes benign oligemia, without progressing to cerebral infarction, in mice, yet leads to a wide variety of outcomes (ranging from asymptomatic to death) in humans. We hypothesized that inhibition of NOS both transforms UCAO-mediated oligemia into full infarction and expands pre-existing infarction. In support, intraperitoneal administration of N{omega}-nitro-L-arginine methyl ester (L-NAME) followed by UCAO induced large-arterial infarction in mice, unlike UCAO alone. Six-hour laser-speckle-contrast imaging detected spreading ischemia in mice with infarction as assessed at 24h. In agreement with vasoconstriction/microthrombus formation shown by intravital microscopy, the NO-donor, molsidomine and the endothelial-NOS- activating antiplatelet, cilostazol, attenuated or prevented progression to infarction. Moreover, UCAO without L-NAME caused infarction in mice with hyperglycemia and hyperlipidemia, which, in turn, were associated with greater symmetric dimethylarginine (SDMA) levels. Further, increased levels of glucose and cholesterol associated with significantly larger infarct volumes in 438 consecutive patients with UCAO-mediated infarction. Lastly, Mendelian randomization identified a causative role of NOS inhibition, particularly in elevated SDMA concentration, in ischemic stroke risk. Therefore, NOS activity is a key factor determining the fate of hypoperfused brain following acute carotid occlusion, where SDMA could be a potential risk predictor.

neuroscience↗

bioRxiv2024

Utility of Cellular Measurements of Non-Specific Endocytosis to Assess the Target-Independent Clearance of Monoclonal Antibodies

Past studies have demonstrated higher clearance for monoclonal antibodies possessing increased rates of non-specific endocytosis. However, this metric is oftentimes evaluated indirectly using biophysical techniques or cell surface binding studies that may not provide insight into the specific rates of cellular turnover. Furthermore, few examples evaluating non-specific endocytosis have been reported for a therapeutic antibody that reached clinical assessment. In the current report, we evaluated a therapeutic human immunoglobulin G2 monoclonal antibody targeted against the interleukin-4 receptor alpha chain (IL-4R) that exhibited elevated target independent clearance in previous Phase 1 and 2 studies. We confirmed high non-specific clearance of the anti-IL-4R antibody as compared to a reference antibody during pharmacokinetic assessments in wild type mice where target-mediated disposition was absent. We then developed a cell-based method capable of measuring cellular protein endocytosis and demonstrated the anti-IL-4R antibody exhibited marked non-specific uptake relative to the reference compound. Antibody homology modeling identified the anti-IL-4R antibody possessed positive charge patches whose removal via targeted mutations substantially reduced its non-specific endocytosis. We then expanded the scope of the study by evaluating a panel of consisting of both preclinical and clinical monoclonal antibodies and demonstrate those with the highest rates of non-specific uptake in vitro exhibit elevated target independent clearance, low subcutaneous bioavailability, or both. Our results support the observation that high non-specific endocytosis is a negative attribute in monoclonal antibody development and demonstrate the utility of a generic cell-based screen as a quantitative tool to measure non-specific endocytosis of protein therapeutics at the single-cell level. Highlights- Developed a novel, reproducible cellular assay to directly quantify non-specific endocytosis of therapeutic proteins. - A previous clinical candidate monoclonal antibody with rapid target-independent clearance in mice and humans possessed extensive non-specific endocytosis that was due to exposed positive charge features. - Demonstration of distinct rates of endocytosis into mammalian cells for disparate monoclonal antibodies, even those with common specificity for targets or isoelectric points. - Cell-based assay to quantify the potential impact of non-specific endocytosis on target-independent clearance and/or subcutaneous bioavailability of monoclonal antibodies.

biochemistry↗

bioRxiv2024

Identification of B cell subsets based on antigen receptor sequences using deep learning

B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.

bioinformatics↗

bioRxiv2023

Stereotypic persistent B cell receptor clonotypes in Alzheimer's Disease

We constructed B cell receptor (BCR) repertoires in silico using peripheral blood (PB) samples collected from 44 Alzheimers Disease (AD) patients at baseline and 37 patients at follow-up. For the control group (CG), we used BCR repertoire data from the chronologically collected PB samples of 55 healthy volunteers vaccinated with SARS-CoV-2 mRNA. The AD patients shared 3,983 stereotypic non-naive BCR clonotypes not found in CG, and their degree of overlap between patient pairs were significantly higher than that of CG pairs, even with the SARS-CoV-2 spike protein triggering a concerted BCR response. Twenty stereotypic non-naive AD patient-specific BCR clonotypes co-existed in more than four patients and persisted throughout two sampling points. One of these BCR clonotypes encoded an antibody reactive to the A{beta}42 peptide. Our findings strongly suggest that AD patients are exposed to common (auto)antigens associated with disease pathology, and their BCR repertoires show unique signatures with diagnostic potential.

immunology↗

bioRxiv2023

An single oscillating proto-hypothalamic neuron gates taxis behavior in the primitive chordate Ciona

Ciona larvae display a number of behaviors, including negative phototaxis. In negative phototaxis, the larvae first perform short spontaneous rhythmic casting swims. As larvae cast in a light field, their photoreceptors are directionally shaded by an associated pigment cell, providing a phototactic cue. This then evokes an extended negative taxis swim. We report here that the larval forebrain of Ciona has a previously uncharacterized single slow-oscillating inhibitory neuron (neuron cor-assBVIN78) that projects to the midbrain, where it targets key interneurons of the phototaxis circuit known as the photoreceptor relay neurons. The anatomical location, gene expression and oscillation of cor-assBVIN78 suggest homology to oscillating neurons of the vertebrate hypothalamus. Ablation of cor-assBVIN78 results in larvae showing extended phototaxis-like swims, but which occur in the absence of phototactic cues. These results indicate that cor-assBVIN78 has a gating activity on phototaxis by projecting temporally-oscillating inhibition to the photoreceptor relay neurons. However, in intact larvae the frequency of cor-assBVIN78 oscillation does not match that of the rhythmic spontaneous swims, indicating that the troughs in oscillations do not themselves initiate swims, but rather that cor-assBVIN78 may modulate the phototaxis circuit by filtering out low level inputs while restricting them temporally to the troughs in inhibition.

neuroscience↗

bioRxiv2023

Human Connectomes Are Heritable

A complete understanding of human behavior and disease depends upon our ability to parse genetic and environmental influences in the human brain. The heritability of a trait quantifies the degree of its variability due to genetic influences. Classical approach for quantifying heritability operate on simple traits, and sometimes do not properly control for other potential sources of variation, such as age or sex. We therefore develop Causal Heritability of Networks (CHaiN) to rigorously quantify heritability of human brain networks (i.e., connectomes). We applied CHaiN to 1024 anatomical connectomes derived from the Human Connectome Project. Connectomes appeared to be heritable, but heritability was insignificant once we addressed variability within networks. These results suggest that previous conclusions on connectome heritability may be driven by the shared network structures, and highlights the importance of modeling networks and other sources of variability when studying heritability of connectomes.

neuroscience↗

bioRxiv2023

An ancestral vaccine induces anti-Omicron antibodies by hypermutation

The immune escape of Omicron variants significantly subsides by the third dose of an mRNA vaccine. However, it is unclear how Omicron variant-neutralizing antibodies develop under repeated vaccination. We analyzed blood samples from 41 BNT162b2 vaccinees following the course of three injections and analyzed their B-cell receptor (BCR) repertoires at six time points in total. The concomitant reactivity to both ancestral and Omicron receptor-binding domain (RBD) was achieved by a limited number of BCR clonotypes depending on the accumulation of somatic hypermutation (SHM) after the third dose. Our findings suggest that SHM accumulation in the BCR space to broaden its specificity for unseen antigens is a counter protective mechanism against virus variant immune escape.

bioengineering↗