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Emergence of inflammatory fibroblasts with aging in Hermansky-Pudlak syndrome associated pulmonary fibrosis.
The longitudinal cellular interactions that drive pulmonary fibrosis are not well understood. To investigate the disease underpinnings associated with fibrosis onset and progression, we generated a scRNA-seq atlas of lungs from young and aged mouse models of multiple subtypes of Hermansky-Pudlak syndrome (HPS), a collection of rare autosomal recessive diseases associated with albinism, platelet dysfunction, and pulmonary fibrosis. We have identified an age-dependent increase in SAA3+ inflammatory lung fibroblasts in HPS mice, including in double-mutant HPS1-2 mice which develop spontaneous fibrosis. HPS1 fibroblasts show increased expression of IL-1R1, whereas alveolar type II epithelial cells from HPS2 mice induce the inflammatory gene signature in co-cultured fibroblasts. scRNA-seq of lung tissue from three HPS1 patients similarly shows the presence of inflammatory fibroblasts and increased IL1R1 expression on fibroblasts. These data posit complex interactions between dysfunctional epithelial cells, inflammatory fibroblasts, and recruited immune cells, suggesting potential opportunities for mitigation of the fibrotic cascade.
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Evaluation of Tissue from Patients with Prostate Cancer Identifies B7-H3 as an Androgen-Regulated, Broadly Expressed, Combinatorial Therapeutic Target.
PURPOSE: Advanced prostate cancer management suffers from therapeutic resistance due to naturally transient or androgen receptor (AR)-dependent expression of clinically actionable surface targets. We aimed to identify the most promising clinically relevant prostate cancer targets using RNA and protein expression levels across the prostate cancer continuum-hormone-sensitive, castration-resistant, neuroendocrine, and "double-negative" prostate cancer. EXPERIMENTAL DESIGN: We performed integration of a large single-cell transcriptomics atlas (JHU-PANORAMA, ∼1 million cells and 213 patients) and patient-derived xenograft models for the systematic investigation of the clinically relevant surfaceome, followed by proteomic validation on patient samples and mechanistic investigations on prostate cancer cell lines and patient samples. RESULTS: B7 homolog 3 (B7-H3) was found to be the most uniformly expressed across the entire prostate cancer continuum. JHU-PANORAMA is made available for interactive visualization as an R Shiny web app. Further mitigation of therapeutic resistance is proposed through a systematic framework for bispecific antibody design, in which B7-H3 demonstrates high combinatorial scores with TROP-2, NECTIN1, KLK2, and NECTIN4. B7-H3 was also shown to be negatively regulated by AR and synergistically inhibit tumor growth when combined with androgen inhibition. CONCLUSIONS: B7-H3 demonstrates low interpatient and intratumoral heterogeneity, with significant synergistic effects in combination with AR inhibition. These properties could uniquely position B7-H3 as a broad-spectrum therapeutic target, with the potential to combine B7-H3 based therapeutics with standard androgen deprivation therapy for synergistic effects to overcome therapeutic resistance across the prostate cancer disease continuum. See related article by Makovec et al., p. 3381.
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Single-cell landscape of lymphoid and myeloid heterogeneity across type-stratified craniofacial lesions in polyostotic fibrous dysplasia.
BACKGROUND: Polyostotic fibrous dysplasia (POFD) is a mosaic skeletal disorder driven by somatic GNAS mutations that constitutively activate Gsα-cAMP signaling, producing fibro-osseous craniofacial deformities. POFD lesions are histologically classified into three subtypes-Type I (connective-tissue predominant), Type II (cancellous-bone predominant), and Type III (sclerotic-bone predominant)-yet the immune microenvironment across these categories remains undefined. This study aims to dissect lymphoid and myeloid heterogeneity and inter-cellular communication networks among distinct POFD histological categories. METHODS: We performed single-cell RNA sequencing on maxillary lesion tissues from three age- and sex-matched POFD patients classified as Type I (n=1), Type II (n=1), and Type III (n=1). After stringent quality control, 24,567 cells (median 1,762 genes/cell) were integrated and clustered. Ligand-receptor interactions were inferred using CellChat. RESULTS: Four major lineages were resolved: mesenchyme, lymphoid, myeloid, endovascular. Lymphoid representation differed across subtypes (Type I 1.00%, Type II 5.10%, Type III 10.90%), whereas endovascular fractions showed an inverse pattern (Type I 25.10%, Type II 9.90%, Type III 4.50%). Sub-clustering identified five lymphoid and six myeloid subsets. CD4+ T cells were most abundant in Type I (51.10%) but less represented in Type II (36.50%) and Type III (29.30%). CD8+ T cells constituted 2.10%, 11.90%, and 11.20% across Types I-III, respectively; germinal-center (GC) B cells were undetectable in Type I, minor in Type II (~1.60%), and prominent in Type III (~29.20%). Among myeloid cells, M1 macrophages comprised 9.90% in Type I, 25.70% in Type II, and 15.30% in Type III; osteoclasts were abundant in Type I (35.40%) but scarce in Types II and III (<5%). Dendritic cells (DCs) were absent in Type I yet detectable in Type II (1.90%) and Type III (2.60%). Network-central genes included LTB, TXNIP, FTH1, and PABPC1 for CD4+ and GC B cells, and S100A8/9, CXCL8, CCL2/3/4, and IL1B for M1 macrophages and monocytes. Inter-cellular communication networks differed markedly by subtype: Type I and II displayed relatively simple interactomes, whereas Type III exhibited densely interconnected signaling with strengthened M2 macrophage-monocyte, M2 macrophage-GC B cell (CXCL12-CXCR4, APP-CD74), and GC B cell-monocyte axes, alongside attenuated CD4+ T cell-GC B cell (CLEC2D-KLRB1, ADGRE5-CD55) and M1 macrophage-CD4+ T cell crosstalk. Pathway enrichment revealed subtype-specific activation of oxidative phosphorylation, NF-κB, and antigen-presentation cascades across lymphoid and myeloid compartments. CONCLUSIONS: This study provides the first single-cell immune atlas of POFD, delineating lymphoid and myeloid heterogeneity across three histological subtypes. The identified subtype-specific markers and inter-cellular communication architectures offer candidate biomarkers for diagnostic stratification and reveal potential immunomodulatory targets for this disfiguring bone disorder.
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Interpretable inflammation landscape of circulating immune cells.
Inflammation is a biological phenomenon beneficial for homeostasis, but it is unfavorable if dysregulated. Although major progress has been made in characterizing inflammation in specific diseases, a global, holistic understanding is still elusive. This is particularly intriguing, considering its function for human health and the potential for modern medicine if fully deciphered. In this study, we leveraged advances in single-cell transcriptomics to delineate inflammatory processes of circulating immune cells during infection, immune-mediated inflammatory diseases and cancer. Our single-cell atlas of more than 6.5 million peripheral blood mononuclear cells from 1,047 patients (56% female, 43% male) and 19 diseases allowed us to learn a comprehensive model of inflammation in circulating immune cells. The atlas expands current knowledge of the biology of inflammation of immune-mediated diseases, acute and chronic inflammatory diseases, infections and solid tumors and lays the foundation to develop a disease classification framework using unsupervised as well as explainable machine learning. Beyond a disease-centered analysis, we charted altered activity of inflammatory molecules in peripheral blood cells, depicting discriminative inflammation-related genes to further understand mechanisms of inflammation. We present a rich resource for the community and lay the groundwork for learning a classifier for inflammatory diseases, presenting cells in circulation as living biomarkers.
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CHIT1-positive microglia drive motor neuron ageing in the primate spinal cord.
Ageing is a critical factor in spinal-cord-associated disorders1, yet the ageing-specific mechanisms underlying this relationship remain poorly understood. Here, to address this knowledge gap, we combined single-nucleus RNA-sequencing analysis with behavioural and neurophysiological analysis in non-human primates (NHPs). We identified motor neuron senescence and neuroinflammation with microglial hyperactivation as intertwined hallmarks of spinal cord ageing. As an underlying mechanism, we identified a neurotoxic microglial state demarcated by elevated expression of CHIT1 (a secreted mammalian chitinase) specific to the aged spinal cords in NHP and human biopsies. In the aged spinal cord, CHIT1-positive microglia preferentially localize around motor neurons, and they have the ability to trigger senescence, partly by activating SMAD signalling. We further validated the driving role of secreted CHIT1 on MN senescence using multimodal experiments both in vivo, using the NHP spinal cord as a model, and in vitro, using a sophisticated system modelling the human motor-neuron-microenvironment interplay. Moreover, we demonstrated that ascorbic acid, a geroprotective compound, counteracted the pro-senescent effect of CHIT1 and mitigated motor neuron senescence in aged monkeys. Our findings provide the single-cell resolution cellular and molecular landscape of the aged primate spinal cord and identify a new biomarker and intervention target for spinal cord degeneration.
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Multimodal decoding of human liver regeneration.
The liver has a unique ability to regenerate1,2; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option3-5. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.
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Single-cell integration reveals metaplasia in inflammatory gut diseases.
The gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and barrier immunity. Advances in genomics and a surge in gastrointestinal diseases1,2 has fuelled efforts to catalogue cells constituting gastrointestinal tissues in health and disease3. Here we present systematic integration of 25 single-cell RNA sequencing datasets spanning the entire healthy gastrointestinal tract in development and in adulthood. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated quality control approach (scAutoQC), leading to a healthy reference atlas with approximately 1.1 million cells and 136 fine-grained cell states. We anchor 12 gastrointestinal disease datasets spanning gastrointestinal cancers, coeliac disease, ulcerative colitis and Crohn's disease to this reference. Utilizing this 1.6 million cell resource (gutcellatlas.org), we discover epithelial cell metaplasia originating from stem cells in intestinal inflammatory diseases with transcriptional similarity to cells found in pyloric and Brunner's glands. Although previously linked to mucosal healing4, we now implicate pyloric gland metaplastic cells in inflammation through recruitment of immune cells including T cells and neutrophils. Overall, we describe inflammation-induced changes in stem cells that alter mucosal tissue architecture and promote further inflammation, a concept applicable to other tissues and diseases.
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Integrin αvβ3-dependent pathogenic effect and therapeutic effects of DL-N2 combined with EGFR inhibitors in pancreatic adenocarcinoma.
BACKGROUND: Pancreatic adenocarcinoma (PDAC) remains one of the most lethal malignancies, characterized by aggressive progression, pronounced stromal desmoplasia, and a limited response to targeted therapies. Although epidermal growth factor receptor (EGFR) inhibitors have shown promise in preclinical studies, their clinical efficacy has been modest, suggesting the existence of compensatory signaling networks. METHODS: An integrated analytical framework was employed, combining bulk transcriptomic analyses of TCGA-PDAC and GTEx datasets, DNA methylation profiling, protein–protein interaction (PPI) network analysis, immune infiltration estimation, and single-cell RNA sequencing. Expression patterns and clinical associations of integrin αvβ3 were evaluated using TCGA, GEPIA, UALCAN, and the Human Protein Atlas. Functional validation was performed using in vitro assays in pancreatic cancer cell lines to assess the effects of DL-N2, a tetrac-conjugated nanoparticle targeting integrin αvβ3, alone or in combination with gefitinib. RESULTS: Integrin αvβ3 (ITGAV/ITGB3) was upregulated in PDAC tissues compared with normal pancreatic tissue and was associated with poor prognosis. Single-cell transcriptomic profiling localized αvβ3 expression to malignant ductal cells and stromal fibroblasts. Computational analyses predicted strong associations of αvβ3 with EGFR, MMP2, and MMP9, implicating it in epithelial–mesenchymal transition (EMT), extracellular matrix (ECM) remodeling, and immune regulation. In vitro, experiments showed that DL-N2 suppressed basal and EGF-induced proliferation, decreased the expression of EGFR, PCNA, and CCND1, and reduced angiogenic and invasive mediators, including VEGF-α, bFGF2, and MMP9. Notably, DL-N2 inhibited PD-L1 expression, linking αvβ3 signaling to immune evasion. In addition, both DL-N2 and gefitinib inhibited cell migration, and their combined treatment exerted an additive effect on the suppression of pancreatic cancer cell migration. CONCLUSION: Our findings establish integrin αvβ3 as a multifunctional regulator of pancreatic cancer progression, integrating growth-associated signaling, extracellular matrix regulation, and immune-associated pathways. Targeting αvβ3 with DL-N2 remodels both tumor-intrinsic and microenvironmental pathways, potentially enhancing EGFR inhibition and restoring chemosensitivity. Dual blockade of αvβ3 and EGFR represents a rational therapeutic strategy to overcome drug resistance and improve outcomes in PDAC.
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Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes.
Rheumatoid arthritis is a prototypical autoimmune disease that causes joint inflammation and destruction1. There is currently no cure for rheumatoid arthritis, and the effectiveness of treatments varies across patients, suggesting an undefined pathogenic diversity1,2. Here, to deconstruct the cell states and pathways that characterize this pathogenic heterogeneity, we profiled the full spectrum of cells in inflamed synovium from patients with rheumatoid arthritis. We used multi-modal single-cell RNA-sequencing and surface protein data coupled with histology of synovial tissue from 79 donors to build single-cell atlas of rheumatoid arthritis synovial tissue that includes more than 314,000 cells. We stratified tissues into six groups, referred to as cell-type abundance phenotypes (CTAPs), each characterized by selectively enriched cell states. These CTAPs demonstrate the diversity of synovial inflammation in rheumatoid arthritis, ranging from samples enriched for T and B cells to those largely lacking lymphocytes. Disease-relevant cell states, cytokines, risk genes, histology and serology metrics are associated with particular CTAPs. CTAPs are dynamic and can predict treatment response, highlighting the clinical utility of classifying rheumatoid arthritis synovial phenotypes. This comprehensive atlas and molecular, tissue-based stratification of rheumatoid arthritis synovial tissue reveal new insights into rheumatoid arthritis pathology and heterogeneity that could inform novel targeted treatments.
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Standardization of Single-Cell RNA-Sequencing Analysis Workflow to Study Drosophila Ovary.
Developments in single-cell technology have considerably changed the way we study biology. Significant efforts have been made over the last few years to build comprehensive cell-type-specific transcriptomic atlases for a wide range of tissues in several model organisms in order to discover cell-type-specific markers and drivers of gene expression. One such tissue is the ovary of the fruit-fly Drosophila melanogaster, which is a popular model system with wide-ranging applications in the study of both development and disease. Three independent studies have recently produced comprehensive maps of cell-type-specific gene expression that describe both spatiotemporal regulation of the process of oogenesis and unique transcriptomic profiles of different cell types that constitute the ovary. In this chapter, we outlined the wet-lab protocol that was followed in our recent study for sample preparation and reanalyze the resultant dataset to discuss the benchmarks in data analysis, which are fundamental to comprehensive curation of the single-cell dataset representing the fly ovary.