Biology subjects

Schwartz, M.

Publications and source records attributed to Schwartz, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A minimal model of a forest after neutral theory

Community ecology seeks the mechanisms underlying biodiversity, and simplified models can reveal them. Neutral ecology exemplifies this approach, but it doesn't distinguish species, limiting its capability for forecasting and prediction. We address this by developing a predictive, minimal model for forest dynamics. We show in a neotropical forest plot that environmental variation couples to the community as a single common effect on all species' growth rates. Life history acts on that variation, forecasting species' gains and losses a decade ahead. Finally, immigration, coupled to competition and life history, allows us to predict long-run species abundances. Simple rules thus govern the dynamics of this forest: competition, immigration, and the effect of the environment on growth. Beyond that, species are set apart by their life histories alone.

ecology↗

bioRxiv2026

One-carbon metabolism sustains effector T cell function through cell-surface glycosylation

Folate is a driver of one-carbon metabolism that is essential in T cells. The cellular consequences of its deprivation in CD8+ T cells and impact on anti-tumor function are unknown. Single cell RNA-seq analysis of primary central nervous system lymphoma (PCNSL) patients' tumor samples revealed exhaustion in T cells with high folate metabolism gene expression signature. Functional genomics, metabolite profiling, and glycomics identified disrupted cell surface glycosylation as a major consequence of folate deprivation in CD8+ T cells. Mechanistically, folate deprivation reduced nucleotide sugar levels, perturbed glycosylation, and triggered the apoptotic unfolded protein response. Overexpressing folate transporters in adoptively transferred CD8+ T cells increased intratumoral T cell numbers and reduced exhaustion. Therefore, our data draw a mechanistic line between one-carbon metabolism, cell-surface glycosylation, and anti-tumor T cell function, and support a hypothesis that increased folate uptake can enhance CD8+ T cell function including ex vivo and in vivo CAR-T cells.

cell biology↗

bioRxiv2026

Disruption of the Brain-Spleen Axis Impairs Monocyte-Microglia Communication and Accelerates Disease Progression in a Model of Amyloidosis

Alzheimers disease (AD) is characterized by a prolonged asymptomatic phase before cognitive decline emerges, yet the mechanisms driving symptom onset remain unclear. Here, we hypothesized that the transition from asymptomatic to symptomatic disease is linked to dysfunction of brain-immune communication. Retrograde neuronal tracing in the 5xFAD mouse model of amyloidosis revealed reduced brain-spleen connectivity at advanced disease stages. To probe the functional role of the brain-spleen axis in coping with disease, we denervated the splenic nerve at an early presymptomatic stage. This intervention accelerated cognitive decline, impaired splenic hematopoiesis, diminished monocyte recruitment to the brain, disrupted monocyte-microglia signaling networks, and reduced the transition of microglia from a homeostatic to the disease-associated (DAM) state. Conversely, enhancing splenic noradrenergic input increased hematopoiesis, restored monocyte homing to the brain, and delayed cognitive impairment. The protective role of splenic monocytes was independently validated in a retinal cytotoxic injury model, in which splenic denervation impaired post-insult retinal ganglion cell survival. Together, these findings identify an active brain-spleen circuit in regulating monocyte recruitment and establish peripheral monocytes as key drivers of microglial state transitions and disease progression.

neuroscience↗

bioRxiv2026

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland

Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles--absent in reference populations--and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

genomics↗

bioRxiv2025

Systemic administration of PD-L1 blocking antibodies leads to removal of senescent microglia

Senescent microglia develop during aging and Alzheimers disease (AD), driving chronic neuroinflammation. Here we hypothesized that the previously observed disease-modifying effects of PD-1/PD-L1 blockade occur through clearance of senescent microglia. Using CyTOF, we found that a single systemic anti-PD-L1 injection leads to rapid elimination of senescent microglia in 5xFAD and aged wild-type mice, independently of Fc effector function, while increasing homeostatic microglia. These findings suggest that immune rejuvenation via PD-L1 blockade promotes disease modification in AD through senescent-microglial elimination.

neuroscience↗

bioRxiv2025

Integrated Metabolic Complex Genetic Interaction 1 Network of Chromosome 4p Loss in Basal Breast Cancer

Basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and exhibits a recurrent large chromosomal deletion in chromosome 4p (chr4p). Chr4p loss is associated with poor survival, evolves early in tumorigenesis and confers on cells a proliferative state. Here, we map the integrated metabolic complex genetic interaction network of chr4p in basal breast cancer to identify targetable vulnerabilities. Differential gene expression analysis of patient derived xenografts and cancer cell models revealed that chr4p loss is associated with changes in cellular energetics and reduction/oxidation balance. Analysis of DepMap pooled genome-wide CRISPR-Cas9 screens identified complex genetic interactions specific to chr4p deletion in basal breast cancer cell models. Functional assays revealed that chr4p loss is associated with disrupted mitochondrial respiratory function and reduced glycolytic capacity, suggesting metabolic rewiring. Increased reactive oxygen species and lipid peroxidation compromised antioxidant defense mechanisms. Ultimately, this study sheds light on targeted therapies for basal breast cancer harboring large chromosomal deletions.

genomics↗

bioRxiv2025

Alzheimer's disease causes bone marrow myelopoiesis dysfunction

Accumulating evidence suggests that both innate and adaptive immunity play crucial roles in combating Alzheimers disease (AD). Specifically, enhancing the homing of monocyte-derived macrophages to the affected brain has been shown to reduce local inflammation, decrease proteinopathy, rescue neurons, and mitigate cognitive decline. However, the factors limiting their spontaneous recruitment remain unclear. Using multi-omics techniques, we identified impaired myelopoiesis and monocyte development in both mice and AD patients. While not the primary cause of the disease, this impairment is associated with disease progression. In the 5xFAD mouse model, monocyte differentiation was found to be disrupted due to a maladaptive bone marrow (BM) response, driven by type I interferon (IFN-I) signaling. A similar phenotype was found in circulating monocytes from AD patients compared to healthy controls. Blocking IFN-I with monoclonal antibodies or using chimeric AD mice with BM from mice lacking the IFN-I receptor (IFNAR1) alleviated myelopoiesis dysfunction, normalized monocyte phenotypes, and reduced cognitive impairment. These improvements in myeloid function were accompanied by an increased homing of monocyte-derived macrophages in the AD brain. Our results reveal an unexpected dysfunction in BM myelopoiesis in the context of neurodegeneration and support the emerging concept that neurodegenerative diseases are not solely brain-centric.

neuroscience↗

bioRxiv2025

A single injection of anti-PD-L1 blocking antibody induces a transient reduction in tau pathology in P301S (PS19) mouse model of tauopathy

Blocking the inhibitory PD-1/PD-L1 immune checkpoint pathway has been shown to arrest cognitive decline and reduce multiple aspects of brain pathology in various mouse models of amyloidosis and tauopathy. In this study, we evaluated whether anti-PD-L1 treatment would be effective in a tauopathy model characterized by rapidly progressing pathology. Using the P301S (PS19) transgenic mouse model, we found that a single injection of anti-PD-L1 antibody significantly attenuated cognitive deficits, with effects detectable 1-month post-treatment, aligned with the kinetics reported in other models. This cognitive benefit was observed irrespective of microglial TREM2 signalling. The effect on brain pathology was transient; phosphorylated tau in the brain, and total tau in the cerebrospinal fluid were significantly reduced 14 days post-treatment but not at 28 days. These findings indicate that PD-L1 blockade is effective across multiple disease models, while emphasizing the importance of carefully monitoring the timing of effect assessments, treatment outcomes, and dosing frequency, especially in models with accelerated disease progression.

immunology↗

bioRxiv2025

Parsing the Functions of Immediate Early Proteins in HCMV Infection Outcome

Human cytomegalovirus (HCMV) is a prevalent pathogen of the herpesvirus family, infecting most of the human population worldwide. Like all herpesviruses, HCMV can establish a latent infection that persists throughout the lifetime of the host. The HCMV immediate early (IE) proteins, IE1 and IE2, are viewed as master regulators of HCMV infection and are commonly assumed to play pivotal roles in regulating the balance between latent and lytic infection, as their repression is a hallmark of latency. However, it is still unclear whether their expression can indeed determine the establishment of productive infection and what functions, either related to viral gene expression or to cellular pathways, are involved in this activity. Using THP1 monocytes, ectopically expressing the HCMV receptor, PDGFR to boost viral entry, we show that overexpression of either IE1 or IE2 significantly enhances productive infection, illustrating their critical role in determining infection outcome. Mechanistically, we show IE2 drives expression of the viral early genes at early stages of infection, whereas IE1 acts more broadly to enhance global viral gene expression. We further show that from the many functions of IE1, its ability to promote lytic infection is mainly linked to the disruption of PML nuclear bodies. Importantly, induction of either IE1 or IE2 expression in latently infected cells enhances viral reactivation, with IE1-mediated PML representing a central mechanism. Taken together, our findings elucidate the distinct and complementary roles of IE1 and IE2 in overcoming barriers to productive infection and reactivation.

microbiology↗

bioRxiv2025

HIV-1 Amplifies IL-8 Response Of Human Stellate Cells To Gram-Positive Microbial Products Via H4K5 Histone Acetylation

BackgroundPatients living with human immunodeficiency virus 1 (PLWH) develop accelerated liver fibrosis, but the exact mechanism remains unknown. Activation of hepatic stellate cells (HSCs)--a cornerstone of fibrosis--is influenced by various factors, including viral infection, hepatocellular injury, chronic immune activation, gut barrier dysfunction, and microbial translocation. The role of gram-positive microbial products in human immunodeficiency virus 1 (HIV-1) infection-associated liver inflammation and fibrosis remains poorly understood. This study investigates the effect of lipoteichoic acid (LTA), a major gram-positive bacterial component, on HSCs in the context of HIV-1 infection. MethodsHuman HSCs were isolated from liver tissues of both HIV-1-infected and uninfected individuals undergoing hepatic resection. Inflammatory responses of HSCs to LTA stimulation were measured ex vivo via ELISA before and after HIV-1BaL exposure. Western blotting, ChIP-qPCR and RNA-seq were used to reveal the mechanisms contributing to the IL-8 response to LTA stimulation and HIV-1BaL exposure in HSCs. ResultsLTA modestly induced interleukin-8/CXCL8 (IL-8) production in HSCs, but this response was significantly heightened following HIV-1 exposure. Increased IL-8 levels were also observed in liver tissues from HIV-1-infected patients. In vitro, IL-8 treatment of HSCs elevated -SMA and COL1A1 expression, implicating IL-8 in fibrosis progression in HIV-1 infection. Transcriptomic analysis pointed to histone acetylation as a key regulator of the IL-8 response of HSCs to LTA during HIV-1 infection. Supporting this, the histone deacetylase (HDAC) inhibitor Trichostatin A (TSA) further enhanced IL-8 expression in HIV-1-exposed HSCs. ChIP-qPCR confirmed that acetylation of histone H4K5 facilitated IL-8 promoter transactivation, sensitizing HSCs to LTA under HIV-1 influence. ConclusionsHIV-1 infection primes HSCs for an exaggerated response to LTA, driven by histone acetylation and resulting in elevated IL-8 production--potentially accelerating liver fibrosis in PLWH. Given the persistence of microbial translocation despite effective antiretroviral therapy, these findings highlight the need for targeted interventions to prevent or mitigate liver fibrosis in PLWH.

immunology↗

bioRxiv2025

MARQO pipeline resolves multiparametric cellular and spatial organization in cancer tissue lesions

Multiplex immunostaining analysis remains fragmented, underperforming, and labor-intensive despite tissue proteomic methodologies achieving ever-increasing marker complexity. Here we propose an open-source, semi-supervised automated pipeline that streamlines start-to-finish, single-cell resolution analysis of whole-slide tissue, named Multiplex-imaging Analysis, Registration, Quantification, and Overlaying (MARQO). We compared and validated MARQO using Multiplex Immunohistochemical Consecutive Staining on a Single Slide (MICSSS) using human tumor and adjacent normal tissue samples. Performance was compared with manually-curated pathologist determinations and quantification of multiple markers. We also optimized MARQO to analyze diverse tissue sizes (whole tissue, biopsy, tissue microarray) and staining approaches (singleplex immunohistochemistry, 20-color multiplex immunofluorescence) to determine marker co-expression patterns in multiple human solid cancer types. Lastly, we validated CD8 T cell enrichment in hepatocellular carcinoma responders to neoadjuvant cemiplimab in a phase II clinical trial, further demonstrating MARQOs ability to provide spatially-resolved in situ mechanisms by providing multiplex whole-slide single-cell resolution data.

immunology↗

bioRxiv2025

A multi-modal whole-slide image processing pipeline for quantitative mapping of tissue architecture, histopathology, and tissue microenvironment

Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for immune microenvironment profiling, and whole-slide histopathology. This approach enables detailed morphological mapping of tissue architecture and cell morphology, while simultaneously linking them to the functional states of individual cells across the entire slide. By analyzing tissue biopsies from patients with ulcerative colitis, we demonstrate the potential of this pipeline for quantitative spatial analysis of molecular markers related to mucosal healing. Open-source and compatible with conventional microscopy systems, this pipeline provides a powerful tool for research and clinical applications through its comprehensive integration of quantitative, high-content, and histological imaging modalities.

bioinformatics↗

bioRxiv2024

PIEZO1 overexpression in hereditary hemorrhagic telangiectasia arteriovenous malformations

BackgroundHereditary hemorrhagic telangiectasia (HHT) is an inherited vascular disorder characterized by arteriovenous malformations (AVMs). Loss-of-function mutations in Activin receptor-like kinase 1 (ALK1) cause type 2 HHT and Alk1 knockout (KO) mice develop AVMs due to overactivation of VEGFR2/PI3K/AKT signaling pathways. However, the full spectrum of signaling alterations in Alk1 mutants remains unknown and means to combat AVM formation in patients are yet to be developed. MethodsSingle-cell RNA sequencing of endothelial-specific Alk1 KO mouse retinas and controls identified a cluster of endothelial cells (ECs) that was unique to Alk1 mutants and that overexpressed fluid shear stress (FSS) signaling signatures including upregulation of the mechanosensitive ion channel PIEZO1. PIEZO1 overexpression was confirmed in human HHT lesions, and genetic and pharmacological PIEZO1 inhibition was tested in Alk1 KO mice, as well as downstream PIEZO1 signaling. ResultsPharmacological PIEZO1 inhibition, and genetic Piezo1 deletion in Alk1-deficient mice effectively mitigated AVM formation. Furthermore, we identified that elevated VEGFR2/AKT, ERK5-p62-KLF4, hypoxia and proliferation signaling were significantly reduced in Alk1-Piezo1 double ECKO mice. ConclusionsPIEZO1 overexpression and signaling is integral to HHT2, and PIEZO1 blockade reduces AVM formation and alleviates cellular and molecular hallmarks of ALK1-deficient cells. This finding provides new insights into the mechanistic underpinnings of ALK1-related vascular diseases and identifies potential therapeutic targets to prevent AVMs.

molecular biology↗

bioRxiv2024

Virus Entry is a Major Determinant of HCMV Latency in Monocytes

Human cytomegalovirus (HCMV) infection can result in either productive or latent infection, the latter enabling life-long viral persistence. Monocytes support latent infection but become permissive to productive infection upon differentiation into macrophages. The molecular basis for these differentiation-driven differences has been largely attributed to chromatin-mediated repression of the viral genome. Using metabolic labeling of newly synthesized RNA during the early stages of infection, we observed markedly lower viral transcription in monocytes compared to macrophages. Unbiased comparison of the two cell types revealed that this difference is partly due to reduced viral entry in monocytes: fewer viruses enter, and correspondingly fewer genomes reach the nucleus. Indeed, ectopic expression of known HCMV entry receptors in monocytes enhanced viral entry and consequently facilitated productive infection, demonstrating that these cells can support full replication if entry is efficient. We further identified integrin {beta}3 as a surface protein upregulated upon differentiation that plays an important role in HCMV entry into macrophages, partially accounting for the observed differences in entry efficiency. Finally, we show that cells receiving fewer viral genomes are the ones that establish latent infection and have the capacity to reactivate. Overall, our findings reveal that entry is a previously unrecognized factor contributing to latent infection in monocytes, adding a critical layer to the paradigm of HCMV latency.

microbiology↗

bioRxiv2024

PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance

Existing genetic classification systems for porcine reproductive and respiratory syndrome virus 2 (PRRSV-2), such as restriction fragment length polymorphisms (RFLPs) and sub-lineages, are unreliable indicators of genetic relatedness or lack sufficient resolution for epidemiological monitoring routinely conducted by veterinarians. Here, we outline a fine-scale classification system for PRRSV-2 genetic variants in the U.S. Based on >25,000 U.S. open-reading-frame 5 (ORF5) sequences, sub-lineages were divided into genetic variants using a clustering algorithm. Through classifying new sequences every three months and systematically identifying new variants across eight years, we demonstrated that prospective implementation of the variant classification system produced robust, reproducible results across time and can dynamically accommodate new genetic diversity arising from virus evolution. From 2015 and 2023, 118 variants were identified, with [~]48 active variants per year, of which 26 were common (detected >50 times). Mean within-variant genetic distance was 2.4% (max: 4.8%). The mean distance to the closest related variant was 4.9%. A routinely updated webtool (https://stemma.shinyapps.io/PRRSLoom-variants/) was developed and is publicly available for end-users to assign newly generated sequences to a variant ID. This classification system relies on U.S. sequences from 2015 onwards; further efforts are required to extend this system to older or international sequences. Finally, we demonstrate how variant classification can better discriminate between previous and new strains on a farm, determine possible sources of new introductions into a farm/system, and track emerging variants regionally. Adoption of this classification system will enhance PRRSV-2 epidemiological monitoring, research, and communication, and improve industry responses to emerging genetic variants. ImportanceThe development and implementation of a fine-scale classification system for PRRSV-2 genetic variants represents a significant advancement for monitoring PRRSV-2 occurrence in the swine industry. Based on systematically-applied criteria for variant identification using national-scale sequence data, this system addresses the shortcomings of existing classification methods by offering higher resolution and adaptability to capture emerging variants. This system provides a stable and reproducible method for classifying PRRSV-2 variants, facilitated by a freely available and regularly updated webtool for use by veterinarians and diagnostic labs. Although currently based on U.S. PRRSV-2 ORF5 sequences, this system can be expanded to include sequences from other countries, paving the way for a standardized global classification system. By enabling accurate and improved discrimination of PRRSV-2 genetic variants, this classification system significantly enhances the ability to monitor, research, and respond to PRRSV-2 outbreaks, ultimately supporting better management and control strategies in the swine industry.

microbiology↗

bioRxiv2024

Essentiality and dynamic expression of the human tRNA pool during viral infection

Human viruses depend on the translation resources of the host cell. A significant translation resource is the tRNA pool of the cell, as human viruses do not encode tRNA genes. Through tRNA sequencing, we inspected the human tRNA pool upon infection of human Cytomegalovirus (HCMV) and SARS-CoV-2. HCMV-induced alterations in tRNA expression were predominantly virus-driven, with minimal influence from the cellular immune response. Notably, specific tRNA post-transcriptional modifications appeared to modulate stability and were susceptible to HCMV manipulation. In contrast, SARS-CoV-2 infection did not significantly impact tRNA expression or modifications. We compared the codon usage of viral genes to the proliferation-differentiation codon-usage signatures of human genes. We found a marked difference between the viruses, with HCMV genes aligning with differentiation codon usage and SARS-CoV-2 genes reflecting proliferation codon usage. We further found that codon usage of structural and gene expression-related viral genes displayed high adaptation to host cell tRNA pools. Through a systematic CRISPR screen targeting human tRNA genes and modification enzymes, we identified specific tRNAs and enzymes that improve or reduce HCMV infectivity and cellular growth. These findings highlight the dynamic interplay between the tRNA pool and viral infection dynamics, shedding light on mechanisms governing host-virus interactions.

genomics↗

bioRxiv2023

A virally encoded high resolution screen of cytomegalovirus host dependencies

Genetic screens have transformed our ability to interrogate cellular factor requirements in infection, yet current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information which is often based on infected cell survival. Here, by engineering human cytomegalovirus to express sgRNA libraries directly from the viral genome, we developed a sensitive, versatile, viral centric approach that allows profiling of different stages along viral infection in a pooled format. Using this approach, which we termed VECOS (Virus Encoded CRISPR-based direct readOut Screening system), we identified hundreds of novel host dependency and restriction factors and quantified their direct effects on viral genome replication, viral particle secretion and infectiousness of secreted particles, providing a multi-dimensional perspective on viral-host interactions. These high resolution measurements reveal that perturbations that alter late stages in HCMV life cycle mostly regulate HCMV particle quality rather than quantity, defining correct virion assembly as a critical stage that is heavily reliant on viral-host interactions. Overall, VECOS facilitates systematic high resolution dissection of human proteins role along the infection cycle, providing a roadmap for in-depth dissection of host-herpesvirus interactions.

microbiology↗

bioRxiv2023

Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring

The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize the evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. TCGA data analysis showed recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a unique panel of 23 primary tumor/patient-derived xenograft basal breast cancers revealed early evolution of chr4p deletion. Mechanistically we show that Chr4p loss is associated with enhanced proliferation. Gene function studies identified an unknown gene, C4orf19, within chr4p, which suppressed proliferation when overexpressed and is a novel member of a PDCD10-GCKIII kinase module, we name as PGCA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames, identified chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner implicating network interactions. Together this sheds light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.

genomics↗