Biology subjects

Nelson, B.

Publications and source records attributed to Nelson, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Higher-order metabolic interactions among oral commensals gate pathobiont expansion through succinate-driven pH modulation

Despite advances in defining microbiome shifts associated with inflammatory mucosal diseases, the ecological interactions that constrain or facilitate pathobiont expansion remain poorly understood. Using a six-species synthetic oral microbial community and factorial interaction screening, we identified a higher-order interaction governing the growth of the periodontal pathobiont Porphyromonas gingivalis. The core community member Veillonella parvula was the strongest positive determinant of P. gingivalis growth, but this effect was substantially reduced by the health-associated commensal Actinomyces oris. A. oris-mediated antagonism resulted from extracellular acidification and was enhanced under anaerobic conditions. Genetic dissection of A. oris fermentation revealed that lactate dehydrogenase (ldh1) contributes to anaerobic lactate production, but ldh1 deletion only partially relieved P. gingivalis inhibition. Instead, succinate, produced through a succinate dehydrogenase/fumarate reductase pathway (sdh2), emerged as the principal driver of acidification and P. gingivalis suppression. At high cell densities, however, V. parvula consumed both lactate and succinate, reversing acidification and restoring conditions permissive for P. gingivalis growth. To assess the relevance of these interactions in vivo, we analyzed subgingival microbiome from 1,355 adults, including 555 with detectable P. gingivalis. Among these individuals, P. gingivalis abundance was negatively associated with Actinomyces abundance after adjustment for periodontitis severity, whereas this association was attenuated at high V. parvula abundance, consistent with the interaction observed in vitro. Together, these findings identify succinate as a previously unrecognized mediator of interbacterial antagonism and reveal how higher-order metabolic interactions among oral commensals regulate pathobiont expansion through pH modulation, with protective effects shaped by oxygen availability and metabolic cross-feeding.

microbiology↗

bioRxiv2026

RORγ Inverse Agonism Redirects Tumour-Conditioned Emergency Myelopoiesis and Attenuates Established Tumour Progression

Systemic inflammation is associated with poor outcomes in gastroesophageal adenocarcinoma (GEA), but how it contributes to disease progression remains unclear. We investigated retinoic acid receptor-related orphan receptor gamma (ROR{gamma}) as a regulator of tumour-conditioned myeloid responses. In treatment-naive GEA patients, elevated circulating neutrophil-to-lymphocyte ratio (cNLR) tracked with circulating ROR{gamma} positive neutrophils and tumoural spatial organization of ROR{gamma} positive myeloid cells, rather than neutrophil abundance. In syngeneic tumour models, pharmacologic ROR{gamma} inverse agonism altered marrow progenitor composition before tumour-growth divergence and remodeled myeloid organization across bone marrow, tumour and lung despite no endpoint change in circulating neutrophil proportions, which did not capture the earlier marrow response or subsequent tumour trajectory. ROR{gamma} perturbation enhanced longitudinal tumour control with PD-L1 blockade, whereas effects on metastatic establishment depended on tumour conditioning and treatment timing. These findings identify ROR{gamma} associated myeloid programming as a therapeutically tractable, context-dependent regulator linking systemic inflammation, hematopoiesis, tissue immune organization, and cancer progression.

cancer biology↗

bioRxiv2026

Longitudinal White Matter Microstructure and Transition to Psychosis in Individuals at Clinical High Risk

Altered white matter microstructure, commonly indexed by fractional anisotropy (FA), has been reported in individuals at clinical high-risk of psychosis (CHR-P) across multiple white matter tracts. However, the relationship between these alterations and later transition to psychosis remains unclear. To address this gap, we investigated whether baseline and longitudinally updated FA measurements were associated with risk of transition to psychosis in a large cohort of individuals at CHR-P. We analysed diffusion tensor imaging data from N = 205 participants at CHR-P, 23 of whom developed psychosis within 3 years of follow-up. Data were collected at baseline, 6 months, and 12 months. Associations between global and tract-specific FA and transition risk were examined using Cox proportional hazards models of baseline data and longitudinally updated data. Point estimates were directionally consistent, with hazard ratios <1 for FA across all white matter tracts in both baseline and longitudinal models. Associations reached nominal significance in the hippocampal cingulum, anterior thalamic radiation, and forceps minor, but none of these remained significant after correcting for multiple comparisons (pcorr > .05). The directionally consistent estimates are compatible with small, distributed effects across multiple white matter pathways being associated with transition to psychosis, although this requires replication. Longitudinally updated FA measurements did not yield stronger associations than were available from baseline imaging data alone. Studies at an even larger scale are needed to establish whether these associations are robust and clinically meaningful.

neuroscience↗

bioRxiv2026

Soft-Robotic Magnetic Microfluidic Catheter for Delivery of Aqueous-Based Dual-Component Embolic Formulations

Transcatheter embolization requires materials that can be steered through tortuous vessels, solidify rapidly in situ, remain clearly visible under fluoroscopy, and, ideally, carry therapeutic cargo without harming tissue. To meet these requirements, we present a fully water-based, two-component PEI-PEG hydrogel delivered through a soft-robotic, microfluidic catheter that keeps the precursors separate until they meet in a millimetre-scale mixing chamber at the tip. Fast amide cross-linking converts the liquid pair into a self-supporting gel within seconds, eliminating organic solvents and preventing catheter blockage. By adjusting precursor ratio and flow regime, the gel's stiffness and viscosity can be tuned over orders of magnitude, with the same chemistry allowing to occlude both high-flow arteries and fragile micro-vessels. The platform was validated in three escalating models. First, in ex-vivo perfused human placenta, the hydrogel filled targeted branches without reflux or fragmentation, demonstrating controlled delivery in clinically relevant vasculature. Next, in three porcine embolizations, splenic, hepatic and ascending pharyngeal arteries, the material achieved stable, selective occlusion with no migration, vasospasm or recanalization, showing seamless compatibility with standard interventional workflows. Finally, in rats bearing orthotopic liver tumours, drug-loaded hydrogel delivered through the hepatic artery concentrated doxorubicin inside tumours while sparing healthy tissue, confirming its potential for precision chemoembolization. These results position the PEI-PEG hydrogel and microfluidic catheter as a unified, image-guided platform that couples robust mechanical occlusion with site-specific drug delivery, offering a biocompatible alternative to current liquid embolics and expanding the therapeutic reach of minimally invasive embolization procedures.

bioengineering↗

bioRxiv2026

Preserved implicit metacognitive sensitivity distinguishes psychosis risk from first-episode psychosis: A cross-sectional virtual reality-based study

Relatively preserved insight distinguishes individuals at risk for psychosis from those with full-blown psychosis. Metacognitive processes thought to support insight and uncertainty monitoring may therefore serve as early markers of illness progression. Yet findings have been inconsistent, perhaps partly due to reliance on explicit confidence ratings that introduce reflection and response biases. To address these limitations, we used a novel implicit confidence measure derived from post-decision gaze in a virtual-reality probabilistic learning task. Gaze-based confidence quantifies the alignment between spatial predictions and gaze direction. We assessed first-order learning and gaze-based metacognition in four groups: clinical high-risk for psychosis (CHR-P), first episode psychosis (FEP), help-seeking controls (HSC), and healthy controls (HC). We tested whether implicit metacognition differentiates psychosis risk from psychosis. Learning accuracy was reduced in both CHR-P and FEP compared to control groups. At the metacognitive level, CHR-P confidence levels were approximately commensurate with their reduced first-order performance, indicating preserved confidence calibration, along with preserved metacognitive sensitivity--the ability to distinguish correct from incorrect decisions. In contrast, FEP showed impaired confidence calibration and reduced metacognitive sensitivity. Metacognitive calibration and sensitivity distinguished CHR-P from FEP and provided predictive value in distinguishing CHR-P from FEP, whereas learning accuracy did not. These findings reveal a dissociation between first-order cognitive processes and distinct aspects of implicit metacognition, including confidence calibration and metacognitive sensitivity, across the psychosis continuum. This dissociation may refine early clinical characterization and improve identification of preserved insight-related mechanisms in psychosis risk.

neuroscience↗

bioRxiv2026

Longitudinal White Matter Trajectories in Clinical High Risk and First-Episode Psychosis: Findings from the Multi-Centre PSYSCAN Study

Psychosis has been linked to changes in diffusion-derived fractional anisotropy (FA) across multiple white matter tracts, yet most evidence is cross-sectional. Longitudinal findings are inconsistent, and the clinical relevance of white matter changes over time remains unclear. To address this gap, we investigated longitudinal white matter changes and their clinical correlates in early psychosis in a large, multi-centre diffusion-tensor imaging study. Across 18 sites, 407 participants (healthy controls: n = 97, 59.8% men, mean age 23.9{+/-}4.6 years; clinical high risk of psychosis: n = 158, 53.5% men, mean age 23.0{+/-}4.9 years; first-episode psychosis: n = 152, 71.1% men, mean age 25.1{+/-}5.4 years) were scanned at up to three time points over 12 months. FA was assessed in the cingulum bundle, the superior longitudinal fasciculus, the inferior fronto-occipital fasciculus, and at the whole brain level. FA trajectories were analysed using linear mixed-effects models to test effects of group, social and occupational functioning, and (attenuated) psychotic symptoms, while controlling for demographic and socioeconomic covariates. No significant group differences in FA were observed, either globally or within tracts (p > .05). Longitudinal FA trajectories were not associated with changes in (attenuated) psychotic symptoms or functioning (p > .05). In contrast, higher baseline antipsychotic medication dose was significantly associated with lower FA (pcorr < .05). Overall, these findings indicate that white matter microstructure is relatively stable during the clinical-high-risk and first-episode phases of psychosis, and that it is not clearly associated with variation in symptom severity or functional outcomes over time.

neuroscience↗

bioRxiv2026

SPaCeD: Spatial Point Process Distances for Pairing the Heavy and Light Chains of B Cell Receptors from Spatial BCR-seq

B cells mediate anti-tumor immunity through B cell receptors (BCRs) composed of paired heavy and light chains. Leveraging spatial transcriptomics, we introduce SPaCeD, a framework that infers heavy-light chain pairs by integrating expression matrices with spatial distances between point patterns derived via optimal transport. Applied to ovarian and breast cancer datasets and simulation scenarios, SPaCeD improves pairing accuracy and stability compared with existing methodology (Repair), particularly for pairs with lower spatial expression.

bioinformatics↗

bioRxiv2025

A Cross-Species Generative Cell Atlas Across 1.5 Billion Years ofEvolution: The TranscriptFormer Single-cell Model

Single-cell transcriptomics has revolutionized our understanding of cellular diversity, yet our understanding of the transcriptional programs across the tree of life remains limited. Here we present TranscriptFormer, a family of generative foundation models trained on up to 112 million cells spanning 1.53 billion years of evolution across 12 species. By jointly modeling gene identities and expression levels using a novel generative architecture, TranscriptFormer encodes multi-scale biological structure, functioning as a queryable virtual cell atlas. We demonstrate state-of-the-art performance on both in-distribution and out-of-distribution cell type classification, with robust performance even for species separated by over 685 million years of evolution. TranscriptFormer can also perform zero-shot disease state identification in human cells and accurately transfers cell state annotations across species boundaries. As a generative model, TranscriptFormer can be prompted to predict cell type-specific transcription factors and gene-gene interactions that align with independent experimental observations. Developmental trajectories, phylogenetic relationships and cellular hierarchies emerge naturally in TranscriptFormers representations without any explicit training on these annotations. This work establishes a powerful framework for quantitative single-cell analysis, and comparative cellular biology, thus demonstrating that universal principles of cellular organization can be learned and predicted across the tree of life.

systems biology↗

bioRxiv2025

Inhibition of adenylyl cyclase 1 (AC1) and exchange protein directly activated by cAMP (EPAC) restores ATP-sensitive potassium (KATP) channel activity after chronic opioid exposure

Prolonged exposure to Gi/o receptor agonists such as opioids can lead to a sensitization of adenylyl cyclases (ACs), resulting in heterologous sensitization or cyclic AMP (cAMP) overshoot. The molecular consequences of cAMP overshoot are not well understood, but this adaptive response is suggested to play a critical role in the development of opioid tolerance and withdrawal. We found that genetic reduction of AC1 and simultaneous upregulation of ATP-sensitive potassium (KATP) channel subunits, SUR1 or Kir6.2, significantly attenuated morphine tolerance and reduced naloxone-precipitated withdrawal. In vitro models utilized an EPAC2-GFP-cAMP biosensor to investigate sensitization of adenylyl cyclase in SH-SY5Y neuroblastoma cells and HEK{Delta}AC3/6 knockout cells. Acute application of DAMGO significantly decreased the cAMP signal from the EPAC2-GFP-cAMP biosensor, while chronic DAMGO administration resulted in enhanced cAMP production following AC stimulation. Inhibition of cAMP overshoot was observed with naloxone (NAL), pertussis toxin (PTX), and the neddylation inhibitor, MLN4924 (Pevonedistat), as well as co-expression of {beta}-adrenergic receptor kinase C-terminus ({beta}ARK-CT). After establishment of the AC1-EPAC sensitization in the in vitro models, we found that inhibition of AC1 or EPAC enhanced potassium channel activity after chronic morphine treatment, using a thallium-based assay in SH-SY5Y cells. Similar data were obtained in mouse dorsal root ganglia (DRG) after chronic morphine treatment. This study presents evidence for investigating further AC1 signaling as a target for opioid tolerance and withdrawal, by increasing EPAC activity and affecting potassium channels downstream of opioid receptors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/636278v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@185bb82org.highwire.dtl.DTLVardef@d97ea4org.highwire.dtl.DTLVardef@1097addorg.highwire.dtl.DTLVardef@1616fcf_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

neuroscience↗

bioRxiv2024

Characterization of A Bronchoscopically Induced Transgenic Lung Cancer Pig Model for Human Translatability

BackgroundThere remains a need for animal models with human translatability in lung cancer (LC) research. Findings in pigs have high impact on humans due to similar anatomy and physiology. We present the characterization of a bronchoscopically-induced LC model in Oncopigs carrying inducible KRASG12D and TP53R167H mutations. MethodsTwelve Oncopigs underwent 29 injections via flexible bronchoscopy. Eighteen Adenovirus-Cre recombinase gene (AdCre) inductions were performed endobronchially (n=6) and transbronchially with a needle (n=12). Eleven control injections were performed without AdCre. Oncopigs underwent serial contrast-enhanced chest CT with clinical follow-up for 29 weeks. Following autopsy, lung and organ tissues underwent histopathology, immunohistochemistry, and RNA-sequencing with comparative analysis with The Cancer Genome Atlas (TCGA) human LC data. ResultsAll 18 sites of AdCre injections had lung consolidations on CT imaging. Transbronchial injections led to histopathologic invasive cancer and/or carcinoma in situ (CIS) in 11/12 (91.7%), and invasive cancer (excluding CIS) in 8/12 (66.6%). Endobronchial inductions led to invasive cancer in 3/6 (50%). A soft tissue metastasis was observed in one Oncopig. Immunohistochemistry confirmed expression of Pan-CK+/epithelial cancer cells, with macrophages and T cells infiltration in the tumor microenvironment. Transcriptome comparison showed 54.3% overlap with human LC (TCGA), in contrast to 29.88% overlap of KRAS-mutant mouse LC with human LC. ConclusionsThe transgenic and immunocompetent Oncopig model has a high rate of LC following bronchoscopic transbronchial induction. Overlap of the Oncopig LC transcriptome with human LC transcriptome was noted. This pig model is expected to have high clinical translatability to the human LC patient.

cancer biology↗

bioRxiv2023

Normative modeling of brain morphometry in Clinical High-Risk for Psychosis

ImportanceThe lack of robust neuroanatomical markers of psychosis risk has been traditionally attributed to heterogeneity. A complementary hypothesis is that variation in neuroanatomical measures in the majority of individuals at psychosis risk may be nested within the range observed in healthy individuals. ObjectiveTo quantify deviations from the normative range of neuroanatomical variation in individuals at clinical high-risk for psychosis (CHR-P) and evaluate their overlap with healthy variation and their association with positive symptoms, cognition, and conversion to a psychotic disorder. Design, Setting, and ParticipantsClinical, IQ and FreeSurfer-derived regional measures of cortical thickness (CT), cortical surface area (SA), and subcortical volume (SV) from 1,340 CHR-P individuals [47.09% female; mean age: 20.75 (4.74) years] and 1,237 healthy individuals [44.70% female; mean age: 22.32 (4.95) years] from 29 international sites participating in the ENIGMA Clinical High Risk for Psychosis Working Group. Main Outcomes and MeasuresFor each regional morphometric measure, z-scores were computed that index the degree of deviation from the normative means of that measure in a healthy reference population (N=37,407). Average deviation scores (ADS) for CT, SA, SV, and globally across all measures (G) were generated by averaging the respective regional z-scores. Regression analyses were used to quantify the association of deviation scores with clinical severity and cognition and two-proportion z-tests to identify case-control differences in the proportion of individuals with infranormal (z<-1.96) or supranormal (z>1.96) scores. ResultsCHR-P and healthy individuals overlapped in the distributions of the observed values, regional z-scores, and all ADS vales. The proportion of CHR-P individuals with infranormal or supranormal values in any metric was low (<12%) and similar to that of healthy individuals. CHR-P individuals who converted to psychosis compared to those who did not convert had a higher percentage of infranormal values in temporal regions (5-7% vs 0.9-1.4%). In the CHR-P group, only the ADSSA showed significant but weak associations (|{beta}|<0.09; PFDR<0.05) with positive symptoms and IQ. Conclusions and RelevanceThe study findings challenge the usefulness of macroscale neuromorphometric measures as diagnostic biomarkers of psychosis risk and suggest that such measures do not provide an adequate explanation for psychosis risk. Key pointsO_ST_ABSQuestionC_ST_ABSIs the risk of psychosis associated with brain morphometric changes that deviate significantly from healthy variation? FindingsIn this study of 1340 individuals high-risk for psychosis (CHR-P) and 1237 healthy participants, individual-level variation in macroscale neuromorphometric measures of the CHR-P group was largely nested within healthy variation and was not associated with the severity of positive psychotic symptoms or conversion to a psychotic disorder. MeaningThe findings suggest the macroscale neuromorphometric measures have limited utility as diagnostic biomarkers of psychosis risk.

neuroscience↗

bioRxiv2022

Bursting Translation on Single mRNAs in Live Cells

Stochasticity has emerged as a mechanism to control gene expression. Much of this so-called "noise" has been attributed to bursting transcription. However, the stochasticity of translation has not similarly been investigated due to a lack of enabling imaging technologies. We developed techniques to track single mRNAs and their translation in live cells for hours, allowing measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics. Like transcription, translation is not a constitutive process but instead cycles between inactive and active states or "bursts". But unlike transcription, which is largely frequency modulated, complex structure in the 5-untranslated region alters burst amplitude. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single molecule imaging with stochastic modeling to deduce the fundamental kinetic parameters of translational bursting, a new dimension of translational control. HighlightsO_LILong-term tracking of single mRNAs reveals multi-state, bursting translation C_LIO_LIStructure in the 5-untranslated region modulates translational burst amplitude C_LIO_LI5-cap proximal sequences modulate translational burst frequency C_LIO_LImTOR signaling adjusts translation bursting to respond to environmental cues C_LI

molecular biology↗

bioRxiv2022

Detection of bifenthrin, bifenazate, etoxazole resistance in Tetranychus urticae collected from mint fields and hop yards using targeted sequencing and TaqMan approaches

Tetranychus urticae (Koch) is an economically important pest of many agricultural commodities in the Pacific Northwest. Multiple miticides are currently registered for control including abamectin, bifenazate, bifenthrin, and extoxazole. However, populations of Tetranychus urticae have developed miticide resistance through multiple mechanisms, in many different growing regions. Producers of agricultural commodities where Tetranychus urticae infestations are problematic rely on integrated pest management tools to determine optimal control methods. Within this species multiple single nucleotide polymorphisms have been documented in different genes which are associated with miticide resistance phenotypes. The detection of these mutations through TaqMan qPCR has been suggested as a practical, quick, and reliable tool to inform agricultural producers of miticide resistance phenotypes present within their fields and have potential utility for making appropriate miticide application and integrated pest management decisions. Within this investigation we examined the use of a TaqMan qPCR-based approach to determine miticide resistance genotypes in field-collected populations of Tetranychus urticae from mint fields and hop yards in the Pacific Northwest of the United States and confirmed the results with a multiplex targeted sequencing. The results suggest the TaqMan approach accurately genotypes Tetranychus urticae populations collected from agricultural fields. The interpretation of the results, however, provide additional challenges for integrated pest management practitioners, including making miticide application recommendations where populations of Tetranychus urticae are a mix of resistant and wildtype individuals.

ecology↗

bioRxiv2022

Examining historical rates of leafcutting bee cell pathogens to establish baseline infectivity rates for alfalfa seed growers

The alfalfa leafcutting bee (Megachile rotundata) is one of the primary pollinators for the alfalfa seed industry. The alfalfa leafcutting bee is a solitary cavity nesting bee. Female Megachile rotundata bees will construct and provision individual brood cells lined with cut leaves (cocoon) and will gather nectar and pollen to place within the constructed cocoon. The female bee will lay a single egg within the constructed cocoon and leave the egg to undergo larval stage development and pupation into the adult stage. During this time multiple pathogens and parasitoids can prey on the developing larvae, resulting in the loss of the future adult bee. A major concern for commercial alfalfa seed growers is the presence of invertebrate pests and fugal pathogens. In the present study, we used historical data from the Parma Cocoon Diagnostic Laboratory to determine baseline rates of pathogen and parasite infection of Megachile rotundata cells and used this analysis to determine historical infection rates and cutoffs for management practices. Additionally, using a Faxitron (X-ray) analysis for Megachile rotundata cell obtained in 2020, we compared the presence of chalkbrood, pathogens, and parasitoids in samples collected from both growers stocks and newly purchased Canada bees. The results of the investigation demonstrate historical averages of the presence of chalkbrood, pathogens, and parasitoids. We also show a significant increase in chalkbrood and predators in 2007-2011 and a significant difference in chalkbrood and predators between bee samples obtained from Canada and grower stocks.

ecology↗

bioRxiv2022

Multiplex PCR reveals unique trends in pathogen and parasitoid infestations of alfalfa leafcutting brood cells.

The alfalfa leafcutting bee Megachile rotundata Fabricius (HYMENOPTERA: Megachilidae) is an important pollinator for multiple agricultural seed commodities in the United States. Megachile rotundata is a solitary bee that forms brood cocoons where its larvae can develop. During the developmental stages of growth, broods can be preyed upon by multiple different fungal and bacterial pathogens and insect predators and parasitoids, resulting in the loss of the developing larvae. Larval loss is a major concern for alfalfa (Medicago sativa L.) seed producers because they rely on pollinator services provided by Megachile rotundata and reduced pollination rates result in lower yields and increased production costs. In the present study, we examined the taxonomic composition of organisms found within M. rotundata brood cells using a multiplex PCR assay which was developed for the detection of the most common bacterial, fungal, and invertebrate pests and pathogens of M. rotundata larvae. Known pests of M. rotundata were detected, including members of the fungal genus Ascosphaera, the causative agent of chalkbrood. Co-infection of single brood cells by multiple Ascosphaera species was confirmed, with potential implications for chalkbrood disease management. The multiplex assay also identified DNA from more than 2,400 total species including multiple new predators and pathogenetic species not previously documented in associated with M. rotundata brood cells.

ecology↗

bioRxiv2021

Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617

COVID-19 pathogen SARS-CoV-2 has infected hundreds of millions and caused over 5 million deaths to date. Although multiple vaccines are available, breakthrough infections occur especially by emerging variants. Effective therapeutic options such as monoclonal antibodies (mAbs) are still critical. Here, we report the development, cryo-EM structures, and functional analyses of mAbs that potently neutralize SARS-CoV-2 variants of concern. By high-throughput single cell sequencing of B cells from spike receptor binding domain (RBD) immunized animals, we identified two highly potent SARS-CoV-2 neutralizing mAb clones that have single-digit nanomolar affinity and low-picomolar avidity, and generated a bispecific antibody. Lead antibodies showed strong inhibitory activity against historical SARS-CoV-2 and several emerging variants of concern. We solved several cryo-EM structures at [~]3 [A] resolution of these neutralizing antibodies in complex with prefusion spike trimer ectodomain, and revealed distinct epitopes, binding patterns, and conformations. The lead clones also showed potent efficacy in vivo against authentic SARS-CoV-2 in both prophylactic and therapeutic settings. We also generated and characterized a humanized antibody to facilitate translation and drug development. The humanized clone also has strong potency against both the original virus and the B.1.617.2 Delta variant. These mAbs expand the repertoire of therapeutics against SARS-CoV-2 and emerging variants.

immunology↗

bioRxiv2021

Endothelial Unc5B controls blood-brain barrier integrity

Blood-brain barrier (BBB) integrity is critical for proper function of the central nervous system (CNS). Here, we showed that the endothelial Netrin1 receptor Unc5B controls BBB integrity by maintaining Wnt/{beta}-catenin signaling. Inducible endothelial-specific deletion of Unc5B in adult mice led to region and size-selective BBB opening. Loss of Unc5B decreased BBB Wnt/{beta}-catenin signaling, and {beta}-catenin overexpression rescued Unc5B mutant BBB defects. Mechanistically, Netrin1 enhanced Unc5B interaction with the Wnt co-receptor LRP6, induced its phosphorylation and activated Wnt/{beta}-catenin downstream signaling. Intravenous delivery of antibodies blocking Netrin1 binding to Unc5B caused a transient disruption of Wnt signaling and BBB breakdown, followed by neurovascular barrier resealing. These data identify Netrin-Unc5B signaling as a novel regulator of BBB integrity with potential therapeutic utility for CNS diseases.

cell biology↗

bioRxiv2020

Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data

We introduce SpatialDecon, an algorithm for quantifying cell populations defined by single cell RNA sequencing within the regions of spatially-resolved gene expression studies. It obtains cell abundance estimates that are spatially-resolved, granular, and paired with highly multiplexed gene expression data. SpatialDecon incorporates several advancements in the field of gene expression deconvolution. We propose an algorithm based in log-normal regression, attaining sometimes dramatic performance improvements over classical least-squares methods. We compile cell profile matrices for 27 tissue types. We identify genes whose minimal expression by cancer cells makes them suitable for immune deconvolution in tumors. And we provide a lung tumor dataset for benchmarking immune deconvolution methods. In a lung tumor GeoMx DSP experiment, we observe a spatially heterogeneous immune response in intricate detail and identify 7 distinct phenotypes of the localized immune response. We then demonstrate how cell abundance estimates give crucial context for interpreting gene expression results.

bioinformatics↗