Biology subjects

Pezoldt, J.

Publications and source records attributed to Pezoldt, J..

9 recordsLinked to original sources

bioRxiv2026

Epithelial innate immune sensing of pneumococci is inherently restricted to a small cellular minority across species and infection niches

Streptococcus pneumoniae colonises the nasopharynx asymptomatically yet causes life-threatening invasive disease. How it navigates early epithelial immune surveillance to cause disease remains unclear. Conventional innate immune models predict coordinated, population-wide epithelial responses to bacterial infection. Using single-cell RNA sequencing, RNA fluorescence in situ hybridization and in vivo mouse and zebrafish models, pneumococcal infection is instead shown to activate innate immune genes including chemokine, NF-{kappa}B regulatory, and prostaglandin pathway genes, in only 1-4% of lung epithelial cells. This restriction is seemingly pneumococcal-specific as Escherichia coli triggers responses in over 40% of the same cells. Strikingly, nasopharyngeal epithelial cells show complete immune silence to pneumococci while responding robustly to E. coli and Staphylococcus aureus, suggesting niche-specific immune evasion. Additionally, pharmacological inhibition of COX-2 significantly increased mortality in a zebrafish meningitis model, identifying prostaglandin signalling as a protective host response during invasive disease. Competence-associated surface remodelling contributes modestly and incrementally to immune restriction, while the predominant dampening is competence-independent. These findings challenge canonical epithelial immunity models against bacterial infection and provide a cellular framework for understanding pneumococcal commensalism and pathogenesis. Significance statementClassical innate immune models predict that bacterial infection triggers coordinated, population-wide transcriptional responses across the epithelium. Using single-cell RNA sequencing, RNA fluorescence in situ hybridization, and in vivo zebrafish and mouse models, we show that Streptococcus pneumoniae, responsible for over one million deaths annually, activates innate immune genes in only 1-4% of lung epithelial cells. Escherichia coli triggers responses in over 40% of the same cells, demonstrating this restriction is pneumococcal-specific. Nasopharyngeal epithelial cells, the bacteriums primary colonization niche, show complete immune silence to pneumococci, suggesting niche-specific evolutionary adaptation. The prostaglandin pathway is identified as a protective host response during invasive disease. These findings challenge canonical models of epithelial immunity and provide a cellular framework for pneumococcal commensalism and pathogenesis.

microbiology↗

bioRxiv2026

Generative modeling reveals the connection between cellular morphology and gene expression

The understanding of how transcriptional programs give rise to cellular morphology, and how morphological features reflect and influence cell identity and function remains limited. This is due in part to the lack of large-scale datasets pairing the two modalities as well as the absence of computational frameworks capable of modeling their cross-modal structure. Here, we introduce COSMIC, a bidirectional generative framework that enables quantitative decomposition of transcriptional variance reflected in morphology and morphological variance explained by gene expression. COSMIC builds on a foundation model trained on over 21 million segmented nuclei and couples it with existing transcriptomic embeddings. To enable cross-modal learning, we leveraged a newly generated multimodal dataset acquired using IRIS, a technology that captures high-resolution images and transcriptomes from the same single cells at scale. COSMIC accurately modeled cell type identity, as well as continuous dynamics such as cell-cycle progression, establishing a quantitative link between morphological phenotypes and underlying gene expression. In prostate cancer cells, COSMIC identified morphological and transcriptomic differences between chemotherapy drug treatment-responsive and -resistant cells, and revealed morphology-associated genes linked to tumor state. Together, these results demonstrate that generative modeling powered by paired single-cell measurements can capture the bidirectional flow of information between cellular form and gene expression, opening new avenues for mechanistic discovery and predictive modeling in both basic and translational cell biology.

bioinformatics↗

bioRxiv2025

Single-cell phenomics through integrated imaging and molecular profiling

Single-cell technologies such as transcriptomics, microscopy, and flow cytometry have revolutionized the study of cellular identity and function. While each of these technologies is powerful on its own, their full potential lies in their integration, enabling multimodal profiling of the same cell and revealing how distinct modalities influence one another. Here, we introduce IRIS (Interconnected Robotic Imaging and Single cell transcriptomics), a deterministic single-cell platform technology that seamlessly couples high-resolution microscopy with droplet-based single-cell RNA sequencing. IRIS enables precise cell positioning, multimode imaging across brightfield and fluorescent channels, and subsequent molecular capture from the same cell, directly linking high-resolution morphological features to matched transcriptomes. We validate IRIS by recovering cell cycle progression states and transcriptional programmes associated with canonical morphologies and demonstrate its discovery power by molecularly resolving two nuclear-ER architectures within naive CD8+ T cells, each defined by distinct gene expression profiles and functional markers. IRIS establishes an integrative single-cell phenomics framework, opening new avenues for dissecting how cellular form relates to molecular state and function.

immunology↗

bioRxiv2025

Secondary lymphoid organ endothelial cells prime alloreactive CD4+ T cells to trigger acute graft-versus-host disease

Donor CD4 T cell priming is a pivotal determinant of acute graft-versus-host disease (aGvHD) after allogeneic hematopoietic cell transplantation (allo-HCT). While professional hematopoietic antigen-presenting cells (APCs) have long been implicated in the pathogenesis of aGvHD, the contribution of non-hematopoietic APCs has remained unclear. Here, we show that naive alloreactive CD4 T cells initially localize and activate specifically within secondary lymphoid organs (SLOs) before infiltrating target tissues. Using genetic models to selectively ablate MHC class II on endothelial cells (ECs) or hematopoietic cells, we demonstrate that blood endothelial cells (BECs) in SLOs function as APCs, efficiently processing and presenting antigen to prime donor CD4 T cells. Deletion of MHC class II (MHCII) specifically in ECs substantially attenuates T cell activation and protects mice from lethal aGvHD, whereas selective deletion of MHCII in lymphatic ECs has no effect. Likewise, selective deletion of MHCII in hematopoietic cells also protects mice against aGvHD, suggesting that both cell types contribute to pathogenic allogeneic T cells activation after allo-HCT. Mechanistically, IL-12/IFN{gamma} signaling upregulates MHC class II expression on BECs. These findings identify BECs in SLOs as initiators of alloreactive CD4 T cell responses and highlight a potential target for preventing aGvHD. HighlightsO_LIBlood endothelial cells in secondary lymphoid organs prime naive CD4 T cells to trigger acute GvHD. C_LIO_LIT cell activation occurs exclusively in secondary lymphoid organs before tissue infiltration. C_LIO_LIExpression of MHC class II only on endothelial cells is sufficient to drive lethal GvHD, independent of other antigen presenting cells. C_LIO_LIRegulation of MHC class II expression in blood endothelial cells by IL-12/IFN{gamma} offers the potential for new therapeutic targets and corroborates findings for existing therapeutics. C_LI

immunology↗

bioRxiv2023

A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion

Adipose tissue plasticity is orchestrated by molecularly and functionally diverse cells within the stromal vascular fraction (SVF). While several mouse and human adipose SVF cellular subpopulations have now been identified, we still lack an understanding of the cellular and functional variability of adipose stem and progenitor cell (ASPC) populations across human fat depots. To address this, we performed single-cell and bulk RNA-seq analyses of >30 Lin-SVF samples across four human adipose depots, revealing two ubiquitous hASPC subpopulations with distinct proliferative and adipogenic properties but also depot- and BMI-dependent proportions. Furthermore, we identified an omental-specific, high IGFBP2- expressing stromal population that transitions between mesothelial and mesenchymal cell states and inhibits hASPC adipogenesis through IGFBP2 secretion. Our analyses highlight the molecular and cellular uniqueness of different adipose niches while our discovery of an anti-adipogenic IGFBP2+ omental-specific population provides a new rationale for the biomedically relevant, limited adipogenic capacity of omental hASPCs.

cell biology↗

bioRxiv2022

Pseudomonas aeruginosa contracts mucus to rapidly form biofilms in tissue-engineered human airways

The opportunistic pathogen Pseudomonas aeruginosa causes antibiotic-recalcitrant pneumonia by forming biofilms in the respiratory tract. Despite extensive in vitro experimentation, how P. aeruginosa forms biofilms at the airway mucosa is unresolved. To investigate the process of biofilm formation in realistic conditions, we developed AirGels: 3D, optically-accessible tissue-engineered human lung models that emulate the airway mucosal environment. AirGels recapitulate important factors that mediate host-pathogen interactions including mucus secretion, flow and air-liquid interface, while accommodating high resolution live microscopy. With AirGels, we investigated the contributions of mucus to P. aeruginosa biofilm biogenesis in in vivo-like conditions. We found that P. aeruginosa forms mucus-associated biofilms within hours by contracting luminal mucus early during colonization. Mucus contractions facilitates aggregation, thereby nucleating biofilms. We show that P. aeruginosa actively contracts mucus using retractile filaments called type IV pili. Our results therefore suggest that, while protecting epithelia, mucus constitutes a breeding ground for biofilms.

microbiology↗

bioRxiv2021

Postnatal lymph node expansion of stromal progenitors towards reticular and CD34+ stromal cell subsets is determined by distinct transcriptional programs

Gut-draining mesenteric lymph nodes (mLN) provide the framework and microenvironment to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in composition and immuno-modulatory function of SCs. Here, we dissect the tissue-specific epigenomic DNA accessibility and CpG methylation landscape of LN non-endothelial SCs and identify a microbiota-independent core epigenomic signature of LN SCs. By combined analysis of transcription factor (TF) binding sites together with the gene expression profiles of non-endothelial SCs, we delineated TFs poising skin-draining peripheral LN (pLN) SCs for pro-inflammatory responses. Furthermore, using scRNA-seq, we dissected the developmental trajectory of mLN SCs derived from postnatal to aged mice, identifying two distinct putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid postnatal LN expansion. Finally, we identified Irf3 as a key differentiation TF inferred from the epigenomic signature of mLN SCs that is dynamically expressed along the differentiation trajectories of FRCs, and validated Irf3 as a regulator of Cxcl9+ FRC differentiation. Together, our data constitute a comprehensive transcriptional and epigenomic map of mLN development and dissect location-specific, microbiota-independent properties of mLN non-endothelial SCs. As such, our findings represent a valuable resource to identify core transcriptional regulators that impinge on the developing mLN early in life, thereby shaping long-lasting intestinal adaptive immune responses.

immunology↗

bioRxiv2020

Deterministic scRNA-seq of individual intestinal organoids reveals new subtypes and coexisting distinct stem cell pools

Single-cell RNA-sequencing (scRNA-seq) has transformed our ability to resolve cellular properties across systems. However, current scRNA-seq platforms are one-size-fits-all approaches that are tailored toward large cell inputs (> 1,000 cells), rendering them inefficient and costly when processing small, individual tissue samples. This important drawback tends to be resolved by loading bulk samples, but this yields confounded mosaic cell population read-outs. To overcome these technological limitations, we developed a deterministic, mRNA-capture bead and cell co-encapsulation dropleting system, DisCo. We demonstrate that DisCo enables precise particle and cell positioning and droplet sorting control through combined machine-vision and multilayer microfluidics. In comparison to other microfluidics systems, the active flow control driving DisCo, enables continuous operation and processing of low-input samples (< 100 cells) at high capture efficiency (> 70%). To underscore the unique capabilities of our approach, we analyzed intestinal organoid development by "DisCo-ing" 31 individual organoids at varying developmental stages. This revealed extensive organoid heterogeneity, identifying distinct subtypes including a regenerative fetal-like Ly6a+ stem cell population which persists as symmetrical cysts even under differentiation conditions. Furthermore, we uncovered a so far uncharacterized "gobloid" subtype consisting predominantly of precursor and mature (Muc2+) goblet cells. These findings demonstrate the unique power of DisCo in providing high-resolution snapshots of cellular heterogeneity among small, individual tissues.

bioengineering↗

bioRxiv2020

Disparate temperature-dependent virus - host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Since its emergence in December 2019, SARS-CoV-2 has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human respiratory tract have been shown to affect the replication kinetics of several viruses, as well as host immune response dynamics, we investigated the impact of temperatures during SARS-CoV-2 and SARS-CoV infection in the human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated more efficiently at temperatures encountered in the upper respiratory tract, and displayed higher sensitivity to type I and type III IFNs. Time-resolved transcriptome analysis highlighted a temperature-dependent and virus-specific induction of the IFN-mediated antiviral response. These data reflect clinical features of SARS-CoV-2 and SARS-CoV, as well as their associated transmission efficiencies, and provide crucial insight on pivotal virus - host interaction dynamics.

microbiology↗