spatial-neighborhood-construction-niches-connectomics-for

Spatial Neighborhood Construction and NICHES Connectomics for Differential Ligand-Receptor Analysis in Fibrotic Human Lung

Spatial transcriptomics enables measurement of gene expression within intact tissue architecture, yet most analytical workflows emphasize cell-type ...

Yale School of Medicine

Yale University

Tissue homeostasis is controlled by cellular circuits governing cell growth, organization, and differentation. In this study we identify previously undescribed cell-to-cell communication that mediates information flow from mechanosensitive pleural mesothelial cells to alveolar-resident stem-like tuft cells in the lung. We find mesothelial cells to express a combination of mechanotransduction genes and lineage-restricted ligands which makes them uniquely capable of responding to tissue tension and producing paracrine cues acting on parenchymal populations. In parallel, we describe a large population of stem-like alveolar tuft cells that express the endodermal stem cell markers Sox9 and Lgr5 and a receptor profile making them uniquely sensitive to cues produced by pleural Mesothelium. We hypothesized that crosstalk from mesothelial cells to alveolar tuft cells might be central to the regulation of post-penumonectomy lung regeneration. Following pneumonectomy, we find that mesothelial cells display radically altered phenotype and ligand expression, in a pattern that closely tracks with parenchymal epithelial proliferation and alveolar tissue growth. During an initial pro-inflammatory stage of tissue regeneration, Mesothelium promotes epithelial proliferation via WNT ligand secretion, orchestrates an increase in microvascular permeability, and encourages immune extravasation via chemokine secretion. This stage is followed first by a tissue remodeling period, characterized by angiogenesis and BMP pathway sensitization, and then a stable return to homeostasis. Coupled with key changes in parenchymal structure and matrix production, the cumulative effect is a now larger organ including newly-grown, fully-functional tissue parenchyma. This study paints Mesothelial cells as a key orchestrating cell type that defines the boundary of the lung and exerts critical influence over the tissue-level signaling state regulating resident stem cell populations. The cellular circuits unearthed here suggest that human lung regeneration might be inducible through well-engineered approaches targeting the induction of tissue regeneration and safe return to homeostasis.

Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration.

To date, few studies have detailed the tumor microenvironment (TME) of Ewing sarcoma (EwS). The TME has a vital role in cancer survival and progression with implications in drug resistance and immune escape. By performing spatially resolved transcriptomic analysis of primary treatment-naïve EwS samples, we discovered greater stromal enrichment in localized EwS tumors compared to metastatic EwS tumors. Through spatial ligand-receptor analysis, we show that the stromal enriched regions harbor unique extracellular matrix related cytokines, immune recruitment and proinflammatory microenvironmental signals, implying EwS stroma may play an anti-tumorigenic role by acting as an immune recruitment center. All EwS tumors expressed pro-tumorigenic MIF-CD74 immune signaling, suggesting a potential immune-evasive mechanism and immunotherapy target. Our findings provide insight into tumor cell/stromal cell interactions in EwS and serve as a valuable resource for further investigations in the tumor immune microenvironment of EwS.

Tumor-associated stroma shapes the spatial tumor immune microenvironment of primary Ewing sarcomas.

The tumor microenvironment (TME) plays a vital role in cancer survival and progression and may play roles in drug resistance and immune escape. To date, few studies have detailed the TME of Ewing sarcoma.

Spatial Profiling Identifies Tumor-Associated Stroma Enrichment and MIF as Potential Immunotherapy Targets in Primary Ewing Sarcomas.

Congenital diaphragmatic hernia (CDH) lungs are characterized by pulmonary hypertension and lung hypoplasia. We have used single cell RNA sequencing (scRNA-seq) to show that mesenchyme is perturbed in CDH, leading to disrupted epithelial-mesenchymal transition (EMT) dynamics and inflammatory signaling.

Altered Epithelial-Mesenchymal Progenitor States Lead to Matrix Deposition, Tissue Inflammation, and Transitional Epithelial State in Congenital Diaphragmatic Hernia.

Recent research has emphasized the critical role of cell state transitions in tissue homeostasis. In lung biology, transitional cells are recognized as a feature of tissue-scale processes during both normal physiology and disease. The precise way that transitional cell states emerge and are regulated remains to be determined. Engineered tissues, built in a laboratory through bioengineering approaches, allow detailed study of cellular states that are not commonly found in native biology, and allow opportunities to directly induce and manipulate cellular transitions. The following study explores and characterizes epithelial cell states that emerge via cellular reprogramming in a tissue engineering context.

Epithelial Reprogramming and Transition during Pulmonary Bioengineering.

Aberrant epithelial regeneration and immune remodeling are hallmarks of chronic lung diseases such as idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease. How cellular context shapes these trajectories remains unresolved. We present a lung organoid model that varies immune, epithelial, and mesenchymal inputs to reveal how composition dictates epithelial plasticity and macrophage polarization. We observed condition-dependent emergence of transitional cell states, including   stressed progenitors, RAS-like intermediates, and hillock-like cells, alongside macrophage activation profiles. In mesenchyme-rich contexts, epithelial-immune-mesenchymal crosstalk reinforced inflammatory signaling and stabilized transitional cells, while immune-dominant inputs favored ATI-like repair and squamous remodeling. Hillock-like cells displayed context-dependent activation and expressed immune-regulatory genes, suggesting a role as epithelial orchestrators calibrating inflammatory response during regeneration. Regenerative outcomes were associated with multicellular signaling networks integrating stress sensing, immune coordination, and epithelial resilience. This platform facilitates modeling of milieu-specific regenerative mechanisms and informs strategies to redirect epithelial fate in chronic lung disease.

Article	Year
Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration. bioRxiv : the preprint server for biology\| PubMed ID: 38260691	2024
Tumor-associated stroma shapes the spatial tumor immune microenvironment of primary Ewing sarcomas. bioRxiv : the preprint server for biology\| PubMed ID: 39975230	2025
Spatial Profiling Identifies Tumor-Associated Stroma Enrichment and MIF as Potential Immunotherapy Targets in Primary Ewing Sarcomas. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 40986513	2025
Altered Epithelial-Mesenchymal Progenitor States Lead to Matrix Deposition, Tissue Inflammation, and Transitional Epithelial State in Congenital Diaphragmatic Hernia. Fetal and pediatric pathology\| PubMed ID: 41246903	2025
Epithelial Reprogramming and Transition during Pulmonary Bioengineering. bioRxiv : the preprint server for biology\| PubMed ID: 41659587	2026
Pulmonary organoid models demonstrate compositionally driven epithelial plasticity and immune polarization. iScience\| PubMed ID: 41940331	2026

Nuoya Wang

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