Biology subjects

Gerner, M. Y.

Publications and source records attributed to Gerner, M. Y..

10 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics of pediatric tuberculosis lymph nodes reveals a conserved hypoxia_SPP1 niche

Pediatric tuberculosis (TB) often presents as primary disease involving the mediastinal lymph nodes; however, its granuloma microenvironment remains poorly characterized because these population patient tissues are rarely available for study. Here, we use spatial transcriptomics to profile 60 granulomas from four children aged 4 to 36 months. We identified nine recurrent transcriptional microenvironments shared across granulomas, despite their marked histological heterogeneity. One macrophage-rich microenvironment showed strong hypoxia-associated activity and secreted phosphoprotein 1 (SPP1) enrichment. This microenvironment was present in both non-necrotic and necrotic lesions and overlapped with a Mtb-persistence macrophage signature previously identified in murine TB lymph nodes. Pathway analysis revealed the enrichment of both antimicrobial and regulatory programs within this microenvironment, suggesting partial immune control rather than uniform inflammatory or suppressive activity in this region. SPP1 expression was associated with regions enriched for both M1- and M2-like macrophages, suggesting a macrophage program that extends beyond conventional polarization classifications and may be influenced by the local granuloma microenvironment. We further observed a similar spatial association between hypoxia-associated activity and SPP1 expression in an independent adult TB dataset (pooled Spearman {rho}=0.65) and validated this association at protein level by multiplex immunofluorescence in our pediatric TB granuloma sample. Overall, this study identified a hypoxia-associated SPP1-enriched microenvironment that may contribute to incomplete bacterial clearance and could provide a framework for evaluating host-directed strategies to enhance sterilizing immunity without exacerbating tissue damage.

immunology↗

bioRxiv2026

Lymphatic networks enable diversification of B cell responses to vaccines

Vaccination generates heterogenous B cell responses that collectively provide protective immunity, yet how this diversity is established remains poorly understood. Here, we identify the draining lymphatic network as a spatial organizer of humoral immunity. Vaccine dispersal across interconnected draining lymph nodes (dLNs) establishes gradients of antigen and inflammation that create distinct B cell differentiation and selection environments. dLNs proximal to the vaccination site preferentially support antibody-secreting cells and clonally diverse germinal center (GC) responses. In contrast, distal dLNs impose more stringent selection, favoring clonally restricted GCs enriched for high-affinity B cells. Spatially distinct inflammatory environments further determine antibody isotype, linking LN position to antibody effector class. These spatial biases persist upon recall and can be reprogrammed through vaccine design, including nanoparticle properties and LN-directed targeting. Thus, lymphatic networks diversify B cell fate, repertoire and affinity selection, and antibody isotype, revealing a programmable axis for tuning humoral immunity through vaccine design.

immunology↗

bioRxiv2026

Defects in CD8+ T cell suppression by Foxp3-ΔE2 expressing regulatory T cells

AbstractRegulatory T cells (Tregs) prevent autoimmunity through suppressive functions largely programmed by the transcription factor FOXP3. Healthy humans express approximately equivalent levels of two major alternatively spliced isoforms of FOXP3: a full-length version containing all coding exons (FOXP3-FL) and a version lacking exon 2 (FOXP3-{Delta}E2). However, sole FOXP3-{Delta}E2 expression causes lethal IPEX syndrome, and the FOXP3-{Delta}E2 isoform is elevated in several autoimmune diseases. These observations strongly suggest defects in suppression by FOXP3-{Delta}E2 Tregs which we investigated here using Foxp3-{Delta}E2 mice. In an influenza virus infection model, Foxp3-{Delta}E2 mice had an increased magnitude of the CD8+ T cell response during acute and memory formation phases of infection. Transcriptomic and chromatin accessibility analyses of homeostatic Foxp3-{Delta}E2 Tregs revealed impaired Treg programming, including reduced expression of inhibitory molecules such as Il2ra and chemokine receptors. Decreased cell surface CD25 expression on Foxp3-{Delta}E2 Tregs was associated with reduced IL-2 responsiveness in Foxp3-{Delta}E2 Tregs and, reciprocally, increased IL-2 responsiveness in CD8+ T cells from Foxp3-{Delta}E2 mice. Additionally, altered chemokine receptor expression resulted in diminished localization of Foxp3-{Delta}E2 Tregs to the T cell zone of the inflamed lymph node. Thus, Treg programming by the Foxp3-{Delta}E2 isoform impairs suppressive function, resulting in failure to restrain CD8+ T cells and aberrant immune responses. One Sentence SummaryFoxp3-{Delta}E2 expressing regulatory T cells have altered cellular programming which impairs their IL-2 sink function and co-localization with conventional T cells during priming, enhancing CD8+ T cell responses.

immunology↗

bioRxiv2024

CD4-mediated immunity shapes neutrophil-driven tuberculous pathology

Pulmonary Mycobacterium tuberculosis (Mtb) infection results in highly heterogeneous lesions ranging from granulomas with central necrosis to those primarily comprised of alveolitis. While alveolitis has been associated with prior immunity in human post-mortem studies, the drivers of these distinct pathologic outcomes are poorly understood. Here, we show that these divergent lesion structures can be modeled in C3HeB/FeJ mice and are regulated by prior immunity. Using quantitative imaging, scRNAseq, and flow cytometry, we demonstrate that Mtb infection in the absence of prior immunity elicits dysregulated neutrophil recruitment and necrotic granulomas. In contrast, prior immunity induces rapid recruitment and activation of T cells, local macrophage activation, and diminished late neutrophil responses. Depletion studies at distinct infection stages demonstrated that neutrophils are required for early necrosis initiation and necrosis propagation at chronic stages, whereas early CD4 T cell responses prevent neutrophil feedforward circuits and necrosis. Together, these studies reveal fundamental determinants of tuberculosis lesion structure and pathogenesis, which have important implications for new strategies to prevent or treat tuberculosis.

immunology↗

bioRxiv2023

Prolonged T cell - DC macro-clustering within lymph node microenvironments initiates Th2 cell differentiation in a site specific manner

Formation of T helper 2 (Th2) responses has been attributed to low-grade T cell stimulation, yet how large-scale polyclonal Th2 responses are generated in vivo remains unclear. Here, we used quantitative imaging to investigate early Th2 differentiation within lymph nodes (LNs) following cutaneous allergen administration. Contrary to current models, Th2 differentiation was associated with enhanced T cell activation and extensive integrin-dependent macro-clustering at the T-B border, which also contrasted clustering behavior seen during Th1 differentiation. Unexpectedly, formation of Th2 macro-clusters within LNs was highly dependent on the site of skin sensitization. Differences between sites were driven by divergent activation states of migratory cDC2 from different dermal tissues, with enhanced costimulatory molecule expression by cDC2 in Th2-generating LNs promoting T cell macro-clustering and cytokine sensing. Thus, generation of dedicated priming micro-environments through enhanced costimulatory molecule signaling initiates the generation of Th2 responses in vivo and occurs in a skin site-specific manner.

immunology↗

bioRxiv2021

Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated with Anti-Tumor Immunity

Tumors are populated by a multitude of immune cell types with varied phenotypic and functional properties, which can either promote or inhibit anti-tumor responses. Appropriate localization and function of these cells within tumors is critical for protective immunity, with CD8 T cell infiltration being a biomarker of disease outcome and therapeutic efficacy. Recent multiplexed imaging approaches have revealed highly complex patterns of localization for these immune cell subsets and the generation of distinct tumor microenvironments (TMEs), which can vary among cancer types, individuals, and within individual tumors. While it is recognized that TMEs play a pivotal role in disease progression, a better understanding of their composition, organization, and heterogeneity, as well as how distinct TMEs are reshaped with immunotherapy, is necessary. Here, we performed spatial analysis using multi-parameter confocal imaging, histocytometry, and CytoMAP to study the microanatomical organization of immune cells in two widely used preclinical cancer models, the MC38 colorectal and KPC pancreatic murine tumors engineered to express human carcinoembryonic antigen (CEA). Immune responses were examined in either unperturbed tumors or after immunotherapy with a CEA T cell bispecific (CEA-TCB) surrogate antibody and anti-PD-L1 treatment. CEA-TCB mono and combination immunotherapy markedly enhanced intra-tumoral cellularity of CD8 T cells, dominantly driven by the expansion of TCF1- PD1+ effector T cells and with more minor increases in TCF1+PD1+ resource CD8 T cells. The majority of infiltrating T cells, particularly resource CD8 T cells, were colocalized with dendritic cells (DCs) or activated MHCII+ macrophages, but largely avoided the deeper tumor nest regions composed of cancer cells and non-activated macrophages. These myeloid cell - T cell aggregates were found in close proximity to tumor blood vessels, generating perivascular immune niches. This perivascular TME was present in untreated samples and markedly increased after CEA-TCB therapy, with its relative abundance positively associated with response to therapy. Together, these studies demonstrate the utility of advanced spatial analysis in cancer research by revealing that blood vessels are key organizational hubs of innate and adaptive immune cells within tumors, and suggesting the likely relevance of the perivascular immune TME in disease outcome.

immunology↗

bioRxiv2019

CytoMAP: a spatial analysis toolbox reveals features of myeloid cell organization in lymphoid tissues

Recently developed approaches for highly-multiplexed 2-dimensional (2D) and 3D imaging have revealed complex patterns of cellular positioning and cell-cell interactions with important roles in both cellular and tissue level physiology. However, robust and accessible tools to quantitatively study cellular patterning and tissue architecture are currently lacking. Here, we developed a spatial analysis toolbox, Histo-Cytometric Multidimensional Analysis Pipeline (CytoMAP), which incorporates neural network based data clustering, positional correlation, dimensionality reduction, and 2D/3D region reconstruction to identify localized cellular networks and reveal fundamental features of tissue organization. We apply CytoMAP to study the microanatomy of innate immune subsets in murine lymph nodes (LNs) and reveal mutually exclusive segregation of migratory dendritic cells (DCs), regionalized compartmentalization of SIRPa- dermal DCs, as well as preferential association of resident DCs with select LN vasculature. These studies provide new insights into the organization of myeloid cells in LNs, and demonstrate that CytoMAP is a comprehensive analytics toolbox for revealing fundamental features of tissue organization in quantitative imaging datasets.

immunology↗

bioRxiv2019

TGFβ restricts T cell function and bacterial control within the tuberculous granuloma

Interferon gamma (IFN{gamma}) produced by CD4 T cells is required for immune containment of Mycobacterium tuberculosis (Mtb) infection. Despite this, IFN{gamma} plays a minor role in CD4 T cell-mediated immunity within the lung. In this study, we use a recently-developed murine model of physiologic Mtb infection coupled with advanced quantitative imaging to demonstrate that IFN{gamma} production by Mtb-specific T cells is rapidly extinguished within the granuloma, but not in unaffected areas of the lung. This is mediated via localized immunosuppression through cell-intrinsic TGF{beta} signaling in effector T helper 1 cells within the granuloma, and blockade of TGF{beta} signaling in T cells results in improved immune cell function and decreased pulmonary bacterial burden. These findings uncover a potent immunosuppressive mechanism associated with Mtb infection and provide potential targets for host-directed therapy.

immunology↗

bioRxiv2019

BCG-induced T cells shape Mycobacterium tuberculosis infection before reducing the bacterial burden

Growing evidence suggests the outcome of Mycobacterium tuberculosis (Mtb) infection is established rapidly after exposure, but how the current tuberculosis vaccine, BCG, impacts early immunity is poorly understood. Here we found that murine BCG immunization promotes a dramatic shift in infected cell types. While alveolar macrophages (AM) are the major infected cell for the first two weeks in unimmunized animals, BCG promotes the accelerated recruitment and infection of lung infiltrating phagocytes. Interestingly, this shift is dependent on CD4 T cells, yet does not require intrinsic recognition of antigen presented by infected AM. Mtb-specific T cells are first activated in lung regions devoid of infected cells, and these events precede vaccine-induced reduction of the bacterial burden, which occurs only after the co-localization of T cells and infected cells. Understanding how BCG alters early immune responses to Mtb provides new avenues to improve upon the immunity it confers.

immunology↗

bioRxiv2019

Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues

Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols. Here we present a multi-immersion open-top light-sheet microscope that enables simple mounting of multiple specimens processed with a variety of protocols, which will facilitate wider adoption by preclinical researchers and clinical laboratories. One Sentence SummaryGlaser et al. describe a multi-immersion open-top light-sheet microscope that enables simple and high-throughput imaging of large numbers of preclinical and clinical specimens prepared with a variety of clearing protocols.

bioengineering↗