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Campos, J.

Publications and source records attributed to Campos, J..

At least 19 recordsLinked to original sources
bioRxiv2026

Human Neocortical Glutamatergic Neurons Revealed Through Multimodal Profiling

The human neocortex underlies higher cognition and is the engine of complex thought. Yet our understanding of its neuronal diversity is limited by sparse access to tissue, inconsistent sampling across studies, and a lack of multiple modality data. Although single-cell transcriptomic taxonomies are an important framework for characterizing cell type diversity, transcriptomic information alone cannot reveal the cellular properties that define neuronal computations. To address this, we performed Patch-seq, a method for collecting Morphology, Electrophysiology, and Transcriptomic data from a single neuron. We focused on glutamatergic, neocortical, excitatory neurons, the principal long-range projecting neurons of the cortex, and systematically integrated their morphoelectric features with transcriptomic identity. In combination with spatial transcriptomic data, we interrogated 39 of 42 transcriptomically-defined neuron types with a layer-centric perspective. Morphoelectric properties, such as cortical depth, apical dendrite structure, and excitability clearly distinguish transcriptomic subclasses and support many finer transcriptomic types. Morphoelectric properties are influenced by spatial location in supragranular layers, while deeper layers exhibit greater heterogeneity. Cross-species comparisons reveal conserved subclass organization but pronounced differences in apical dendrite arborization between mouse and human, and surprising similarities between human and macaque. Together, these datasets provide a unified multimodal reference that advances our understanding of human cortical circuitry and establishes a foundation for experimental and computational studies of human brain function and disease.

neuroscience↗
bioRxiv2025

A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

The basal ganglia are interconnected subcortical nuclei with complex topographical organization that orchestrate goal-directed behaviors and are implicated in neurodegenerative movement disorders. We generated a cellular-resolution, spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, sampling over one million cells in each species. By integrating spatial data with a cross-species, consensus snRNA-seq cell type taxonomy, this atlas reveals conserved principles of molecular organization within and across structures. The cellular architecture is complex but highly stereotyped, with gene expression gradients superimposed onto discrete compartments. Extensive spatial sampling illuminates 3D gradients of molecular organization in the striatum and reveals cell type-specific core and shell compartments in the primate internal globus pallidus, which is conserved with mouse. This unified, cross-species spatial transcriptomic atlas will be a foundational resource for characterizing the molecular and functional organization of the basal ganglia and their roles in health and disease.

neuroscience↗
bioRxiv2025

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

Mammalian brain cell identity is shaped by intrinsic factors and external context. We present a spatially resolved transcriptomic and gene regulatory atlas of cell types across all subcortical regions in a primate, the common marmoset. Dense sampling and cross-species integration revealed spatially precise neuronal assemblies, including in complex midbrain and diencephalic structures. Chromatin accessibility and transcriptional identity are spatially tuned within and across subcortical structures; spatial gradients within hippocampal subfields are orchestrated by graded transcription factors acting through graded enhancers. The primate-expanded thalamic GABAergic population shares transcriptional and regulatory syntax with conserved midbrain populations, reflecting an evolutionary adaptation compared with rodents. Similar regional expression across cell types can arise by distinct regulatory architectures, as for telencephalic astrocytes and neurons. Conversely, distant cell types can share regulatory programs despite divergent identities: striatal GABAergic medium spiny neurons and telencephalic glutamatergic neurons share a postsynaptic regulatory program despite divergent lineage, region, and neurotransmitter identity.

neuroscience↗
bioRxiv2025

Multi-omics Profiling of the Lateral Ventricle Choroid Plexus Reveals Developmental Cellular Remodeling, Early Immune Gene Activation, and a Novel Epithelial Subtype

Healthy brain development and function highly depend on the choroid plexus. Temporal alterations in the cellular landscape and gene expression of choroid plexus cells can alter immune cell trafficking in the brain and cerebrospinal fluid composition, ultimately impacting brain dynamics. Here, we performed a comprehensive multi-omics analysis--including bulk and single-cell transcriptomics and epigenomics--of the lateral ventricle choroid plexus across early postnatal and adult stages in mice and rats. We uncovered striking changes in the choroid plexus cellular composition from neonatal to adult stages, accompanied by transcriptional remodeling of all main cell types. Immune cells were markedly increased in adulthood and immune cell profiling revealed an altered cell-type diversity through time. Surprisingly, we observed an early gene activation of host-defense genes in all choroid plexus main cell types, beginning in the neonatal period and progressively increasing into young adulthood. Moreover, some genes induced in epithelial cells in response to inflammation were found to be epigenetically primed, despite not being transcriptionally active. Epithelial cells exhibited subtype diversity and plasticity, with distinct gene expression programs and chromatin accessibility profiles emerging over time. Notably, we identified a novel epithelial cell subtype with unique gene markers suggesting a specialized function potentially linked to neuro-signaling. Ligand-receptor interaction analysis revealed a progressive remodeling of cellular crosstalk networks during choroid plexus maturation, suggesting dynamic intercellular signaling as the tissue develops. Our study offers a comprehensive atlas of transcriptional activity and chromatin accessibility in choroid plexus cells, providing a valuable resource to guide future efforts in targeting gene expression at the choroid plexus for therapeutical purposes.

neuroscience↗
bioRxiv2025

Utilizing combined spatial transcriptomics to elucidate localized immune responses within human coronary arteries throughout the progression of atherosclerosis

Atherosclerosis is a complex inflammatory disease characterized by the accumulation of lipids and immune cells in the arterial wall, leading to the narrowing and stiffening of blood vessels. The involvement of both innate and adaptive immunity in the pathogenesis of human atherosclerosis is increasingly recognised. However, the spatial organization and specific roles of immune cells during the various stages of disease progression remain poorly understood, underscoring the necessity for additional research to elucidate their functions throughout the disease course. A better understanding of the immune responses contribution to atherosclerosis progression could unveil novel therapeutic targets to mitigate plaque development and rupture, ultimately reducing the burden of cardiovascular events. In this study, we utilised NanoString GeoMx(R) and CosMx technologies to analyse serial sections of human coronary arteries from patients with varying degrees of atherosclerotic lesion severity. Our work consists of a series of investigations, and integrated findings from both the GeoMx(R) and CosMx datasets, including pathway analyses, cell typing, and neighbourhood analysis. This workflow underscores the power of combining these spatial transcriptomics platforms to elucidate biological processes at the single-cell level, hence unbiasedly providing molecules and pathways of relevance to aid in the understanding of disease pathogenesis and assessing the opportunity of novel therapies.

immunology↗
bioRxiv2024

Genomic Characterisation of Group B Streptococcus from Argentina: Insights into Prophage Diversity, Virulence Factors and Antibiotic Resistance Genes

Group B Streptococcus (GBS) is a commensal bacterium that can cause severe infections in infants and adults with comorbidities. Resistance and reduced susceptibility to antibiotics is continually on the rise, and vaccines remain in-development. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on prophage contribution to the epidemiology of GBS isolates from humans in South America. In the context of an Argentinian multicentric study, we had previously phenotypically characterised 365 human GBS isolates from invasive disease, urinary infections and maternal colonisation. These isolates had been whole genome sequenced and their prophage presence bioinformatically determined. In this study, we genomically characterised the isolates and analysed the prophage content in the context of the epidemiological data. The phylogenetic analysis of the 365 genomes with 103 GBS from public databases revealed that Argentinian GBS were related to isolates from around the world. The most prevalent lineages, independently of the isolate source, were CC23/Ia and CC12/Ib. Genes encoding virulence factors involved in immune response evasion, tissue damage and adherence to host tissues and invasion were found in all of the genomes in accordance with previously described lineage distribution. According to the prevalent capsular types and the distribution of specific virulence factors in Argentinian GBS, over 95% coverage would be expected from the vaccines currently under development. Antibiotic resistance determinants (ARDs) to at least one antibiotic class were found in 90% of the genomes, including novel mutations in pbp2x, while more than 15% carried ARDs to 3 or more classes. GBS collected from urinary infections carried a significantly higher proportion of ARDs to multiple antibiotic classes than the rest of the isolates. A total of 454 prophages were found among the 468 genomes analysed, which were classified into 23 prophage types. Prophage presence exhibited variations based on GBS clonal complex and capsular type. A possible association between an increased GBS pathogenicity and the carriage of prophages with integrase type GBSInt8 and/or the presence of genes that encode the Phox Homology domain has been observed. The highest prevalence of prophages per genome was found in lineages CC17/III and CC19/III, while the lowest amount was observed in CC12/Ib. Overall, the highest density of prophages, virulence factors and ARDs determinants was found in CC19 isolates, mostly of capsular type III, independently of the isolates source. This is the first analysis of the human-associated GBS population in South America based on whole genome sequencing data, which will make a significant contribution to future studies on the global GBS population structure. Data summarySupplementary results and figures can be found in Supplementary Material 1. Supplementary tables can be found in Supplementary Material 2. All datasets analysed in this study are detailed in the Supplementary Materials. Metadata about the genomes analysed can be found in the microreact project created for this study: https://microreact.org/project/gbs-pangenomic-analysis. Impact statementIn Latin America studies on the epidemiology of Group B Streptococcus (GBS) are scarce, especially those describing clonal complex and serotype distribution, and the role of prophages in GBS epidemiology has not been studied. This article addresses the first genomic characterisation of the human-isolated GBS population in Latin America based on whole genome sequencing data, with special focus on the analysis of prophage content. We determine the clonal complex and serotype distribution of 365 GBS isolates collected from clinical samples in an Argentinian multicenter study and analyse the presence of prophages and virulence and antibiotic resistance determinants in the context of the epidemiological data. Through these analyses, we were able to determine how GBS population structure in Argentina differs from other parts of the world and to predict the potential coverage of the in-development GBS vaccines. We also found a possible association between the carriage of certain types of prophages and an increased GBS pathogenicity. In the context of increased global efforts to develop new strategies to prevent GBS infections through vaccine development, this study makes a significant contribution to our understanding of the global GBS population structure.

bioinformatics↗
bioRxiv2024

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimensional datasets and several open-source software packages are available to facilitate analysis and visualization. The outputs of spatial transcriptomics platforms are typically imperfect. For example, local variations in transcript detection probability are common. Software tools to characterize imperfections and their impact on downstream analyses are lacking so the data quality is assessed manually, a laborious and often a subjective process. Here we describe imperfections in a dataset of 641 fresh-frozen adult mouse brain sections collected using the Vizgen MERSCOPE. Common imperfections included the local loss of tissue from the section, tissue outside the imaging volume due to detachment from the coverslip, transcripts missing due to dropped images, varying detection probability through space, and differences in transcript detection probability between experiments. We describe the incidence of each imperfection and the likely impact on the accuracy of cell type labels. We develop MerQuaCo, open-source code that detects and quantifies imperfections without user input, facilitating the selection of sections for further analysis with existing packages. Together, our results and MerQuaCo facilitate rigorous, objective assessment of the quality of spatial transcriptomics results.

bioinformatics↗
bioRxiv2024

Liprin-α/RIM complex regulates the dynamic assembly of presynaptic active zones via liquid-liquid phase separation

Presynaptic scaffold proteins, including liprin-, RIM, and ELKS, are pivotal to the assembly of the active zone and regulating the coupling of calcium signals and neurotransmitter release, yet the underlying mechanism remains poorly understood. Here, we determined the crystal structure of the liprin-2/RIM1 complex, revealing a multifaceted intermolecular interaction that drives the liprin-/RIM assembly. Neurodevelopmental disease-associated mutations block the formation of the complex. Disrupting this interaction in neurons impairs synaptic transmission and reduces the readily releasable pool of synaptic vesicles. Super-resolution imaging analysis supports a role for liprin- in recruiting RIM1 to the active zone, presumably by promoting the liquid-liquid phase separation (LLPS) of RIM1. Strikingly, the liprin-/RIM interaction modulates the competitive distribution of ELKS1 and voltage-gated calcium channels (VGCCs) in RIM1 condensates. Disrupting the liprin-/RIM interaction significantly decreased VGCC accumulation in the condensed phase and rendered release more sensitive to the slow calcium buffer EGTA, suggesting an increased physical distance between VGCC and vesicular calcium sensors. Together, our findings provide a plausible mechanism of the liprin-/RIM complex in regulating the coupling of calcium channels and primed synaptic vesicles via LLPS for efficient synaptic transmission and uncover the pathological implication of liprin- mutations in neurodevelopmental disorders.

neuroscience↗
bioRxiv2024

Revisiting typing systems for group B Streptococcus (GBS) prophages: an application in prophage detection and classification in GBS isolates from Argentina

Group B Streptococcus (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out in silico) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorised with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with 10 new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including 2 novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing. Author summaryBacteriophages, which are viruses that infect bacteria, exert a profound influence on microbial evolution when integrated into the bacterial genome, a state in which they are called prophages. It has been proposed that prophage acquisition played a role in the emergence of Streptococcus agalactiae (GBS) as a human pathogen in European countries. Further study and characterization of prophages of GBS from around the world would provide valuable insights into the mechanisms underlying GBS adaptation, evolution and epidemiology. Unfortunately, existing tools for prophage screening exhibit limitations in the detection and classification of all prophages present in GBS genomes. To address this issue, in this work we propose a new prophage typing system that allows the detection and classification of GBS prophages based on both their phylogenetic lineage and integration site within the bacterial genome. Using this methodology we were able to identify 29 prophage types in 615 GBS isolated globally. We further characterised these prophages and found that they carried genes that could give an evolutionary advantage to their host and that different lineages of GBS carried different prophage types. Comprehensive exploration and characterization of prophages represent an indispensable endeavour, providing critical insights into microbial evolution, epidemiology, and potential therapeutic interventions.

bioinformatics↗
bioRxiv2024

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.

bioinformatics↗
bioRxiv2024

Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing

Glioblastomas are invasive brain tumors with high therapeutic resistance. Neuron-to-glioma synapses have been shown to promote glioblastoma progression. However, a characterization of tumor-connected neurons has been hampered by a lack of technologies. Here, we adapted retrograde tracing using rabies viruses to investigate and manipulate neuron-tumor networks. Glioblastoma rapidly integrated into neural circuits across the brain engaging in widespread functional communication, with acetylcholinergic neurons driving glioblastoma invasion. We uncovered patient-specific and tumor cell state-dependent differences in synaptogenic gene expression associated with neuron-tumor connectivity and subsequent invasivity. Importantly, radiotherapy enhanced neuron-tumor connectivity by increased neuronal activity. In turn, simultaneous neuronal activity inhibition and radiotherapy showed increased therapeutic effects, indicative of a role for neuron-to-glioma synapses in contributing to therapeutic resistance. Lastly, rabies-mediated genetic ablation of tumor-connected neurons halted glioblastoma progression, offering a viral strategy to tackle glioblastoma. Together, this study provides a framework to comprehensively characterize neuron-tumor networks and target glioblastoma.

cancer biology↗
bioRxiv2024

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling

The detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development of a number of different bioinformatic AMR prediction tools. Although many may implement similar principles, these tools differ significantly in their supported inputs, search algorithms, parameterisation, and underlying reference databases. Each of these tools generates a report of detected AMR genes or variants in a distinct, non-standard, format. This presents a huge barrier to the comparison of results and to the modularity of tools for AMR gene prediction within bioinformatic workflows. In collaboration with 17 public health laboratories across 10 countries, the Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) data structures working group has developed and piloted a standardized output specification for the bioinformatic detection of AMR from microbial genomes. In this report, we discuss hAMRonization, a python package and command-line utility, which implements PHA4GEs AMR specification to combine the outputs of disparate antimicrobial resistance gene detection tools into a single unified format. hAMRonization can be easily extended and currently supports 18 different tools (both species-agnostic and species-specific) for the detection of genes and/or variants conferring AMR. The harmonized reports are available in tabular form, JSON format or through an interactive HTML file (e.g., https://maguire-lab.github.io/assets/interactive_report_demo.html) that can be opened within the browser for navigable data exploration. As of 2024-03-07 hAMRonization has been downloaded [~]12,500 times, incorporated into >9 public bioinformatic tools and workflows, and been internally adopted by several national and international public health groups. The hAMRonization tool and underlying specification are open-source and freely available through PyPI, conda and GitHub (https://github.com/pha4ge/hAMRonization).

bioinformatics↗
bioRxiv2024

CXCR3-expressing myeloid cells recruited to the hypothalamus protect against diet-induced body mass gain and metabolic dysfunction

Microgliosis is an important component of diet-induced hypothalamic inflammation in obesity. A few hours after the introduction of a high-fat diet, the mediobasal hypothalamus resident microglia undergo morphological and functional changes toward an inflammatory phenotype. If the consumption of large amounts of dietary fats persists for long periods, bone marrow- derived myeloid cells are recruited and integrated into a new landscape of hypothalamic microglia. However, it is currently unknown what are the transcriptional signatures and specific functions exerted by either resident or recruited subsets of hypothalamic microglia. Here, the elucidation of the transcriptional signatures revealed that resident microglia undergo only minor changes in response to dietary fats; however, under the consumption of a high-fat diet, there are major transcriptional differences between resident and recruited immune cells with major impact on chemotaxis. In addition, in CCR2+ recruited peripheral immune cells, there are major transcriptional differences between females and males with important impact on transcripts involved in neurodegeneration and thermogenesis. The chemokine receptor CXCR3 emerged as one of the components of chemotaxis with the greatest difference between recruited and resident microglia, and thus, was elected for further intervention. The hypothalamic immunoneutralization of CXCL10, one of the ligands for CXCR3, resulted in increased body mass gain and reduced energy expenditure, particularly in females. Furthermore, the chemical inhibition of CXCR3 resulted in a much greater change in phenotype with increased body mass gain, reduced energy expenditure, increased blood leptin, glucose intolerance, and reduced insulin. Thus, this study has elucidated the transcriptional differences between resident microglia and recruited immune cells in diet-induced obesity, identifying chemokines as a relevant subset of genes undergoing regulation. In addition, we showed that a subset of recruited immune cells expressing CXCR3 has a protective, rather than a detrimental role in the metabolic outcomes promoted by the consumption of a high-fat diet, thus, establishing a new concept in obesity-associated hypothalamic inflammation.

neuroscience↗
bioRxiv2023

Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have also revealed substantial diversity of glial cells, particularly astrocytes. To better understand glial cell types and their roles in neurobiology, we built a new suite of adeno-associated viral (AAV)-based genetic tools to enable genetic access to astrocytes and oligodendrocytes. These oligodendrocyte and astrocyte enhancer-AAVs are highly specific (usually > 95% cell type specificity) with variable expression levels, and the astrocyte enhancer-AAVs show multiple distinct expression patterns reflecting the spatial distribution of astrocyte cell types. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity across transgenes and in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs.

neuroscience↗
bioRxiv2023

SCD inhibition eradicates AML displaying high de novo fatty acid desaturation and synergizes with chemotherapy

Identification of specific and therapeutically actionable vulnerabilities in acute myeloid leukaemia (AML) is needed to improve patients outcome. These features should be ideally present in many patients independently of mutational background. Here we identify de novo fatty acid (FA) desaturation, specifically stearoyl-CoA desaturase (SCD) inhibition, as a therapeutic vulnerability across multiple AML models in vitro and in vivo. We use the novel clinical grade SCD inhibitor SSI-4 to show that SCD inhibition induces AML cell death via pleiotropic effects, and sensitivity is based on their dependency on FA desaturation regardless of mutational profile. SSI-4 efficacy is enhanced by driving FA biosynthesis in vitro while stroma confers protective effects that extend to in vivo models. SCD inhibition increases DNA damage and its combination with standard DNA damage-inducing chemotherapy prolongs survival in aggressive murine AML models. Our work supports developing FA desaturase inhibitors in AML while stressing the importance of identifying predictive biomarkers of response and biologically validated combination therapies to realize their therapeutic potential. One Sentence SummarySCD inhibition is toxic to AML cells with high rates of fatty acid desaturation and in combination with chemotherapy prolongs survival in murine AML models.

cancer biology↗
bioRxiv2023

ACE2 mimetic antibody potently neutralizes all SARS-CoV-2 variants and fully protects in XBB.1.5 challenged monkeys

The rapid evolution of SARS-CoV-2 to variants with improved transmission efficiency and reduced sensitivity to vaccine-induced humoral immunity has abolished the protective effect of licensed therapeutic human monoclonal antibodies (mAbs). To fill this unmet medical need and protect vulnerable patient populations, we isolated the P4J15 mAb from a previously infected, vaccinated donor, with <20 ng/ml neutralizing activity against all Omicron variants including the latest XBB.2.3 and EG.1 sub-lineages. Structural studies of P4J15 in complex with Omicron XBB.1 Spike show that the P4J15 epitope shares [~]93% of its buried surface area with the ACE2 contact region, consistent with an ACE2 mimetic antibody. Although SARS-CoV-2 mutants escaping neutralization by P4J15 were selected in vitro, these displayed lower infectivity, poor binding to ACE2, and the corresponding escape mutations are accordingly rare in public sequence databases. Using a SARS-CoV-2 XBB.1.5 monkey challenge model, we show that P4J15 confers complete prophylactic protection. We conclude that the P4J15 mAb has potential as a broad-spectrum anti-SARS-CoV-2 drug.

microbiology↗
bioRxiv2023

Integrated multimodal cell atlas of Alzheimer's disease

Alzheimers disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms driving AD progression and vulnerable cell populations affected by disease remain coarsely understood. The current study harnesses single cell and spatial genomics tools and knowledge from the BRAIN Initiative Cell Census Network to understand the impact of disease progression on middle temporal gyrus cell types. We used image-based quantitative neuropathology to place 84 donors spanning the spectrum of AD pathology along a continuous disease pseudoprogression score and multiomic technologies to profile single nuclei from each donor, mapping their transcriptomes, epigenomes, and spatial coordinates to a common cell type reference with unprecedented resolution. Pseudo-progression analysis showed two major epochs corresponding with a slow early increase in pathology and a later exponential increase that correlated with cognitive decline. The early phase included inflammatory microglial and reactive astrocyte component, as well as a selective loss of Sst+ inhibitory neuron types in superficial cortical layers, loss of myelinating oligodendrocytes, and up-regulation of a re-myelination program by OPCs. The later phase involved loss of excitatory neurons and Pvalb and Vip neuron subtypes also predominantly in superficial layers. These cell vulnerabilities were also seen in prefrontal cortex and replicated by other independent studies when integrated with the BRAIN Initiative reference. Study data and exploratory tools are freely available to accelerate progress in AD research at SEA-AD.org.

genomics↗
bioRxiv2023

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single- cell RNA-sequencing (scRNA-seq) dataset of [~]7 million cells profiled, and a spatially resolved transcriptomic dataset of [~]4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.

neuroscience↗