Epigenetic remodeling is increasingly recognized as a driver of immune dysregulation in pulmonary tuberculosis, yet the mechanisms by which it shapes the granuloma immune microenvironment remain insufficiently defined. In particular, how chronic inflammation elicits long-term epigenetic reprogramming to establish a suppressive network and promote disease progression warrants investigation. Integrated single-cell RNA sequencing, spatial transcriptomics, bulk transcriptomics, and bisulfite sequencing were used to profile human tuberculosis lesions. Multiplex immunofluorescence validated spatial cellular interactions in both human and mouse tissues. Mycobacterium tuberculosis–infected macrophage–T-cell co-cultures, pharmacological inhibition, gene knockdown/overexpression, and myeloid-specific Dnmt3a knockout mice were employed for mechanistic and functional validation. Multi-omics revealed a DNA methylation–chemokine coupling signature in pulmonary tuberculosis. DNMT3A was predominantly upregulated in lesion macrophages and enriched within CCL5⁺ macrophages, a population concentrated in inflammation-active granulomatous regions and inversely associated with T-cell and NK-cell infiltration. Mechanistically, DNMT3A was linked to PPARGC1B hypermethylation, suppression of PPARγ, activation of NF-κB, and increased CCL5 expression. Functionally, DNMT3A inhibition or knockdown reduced intracellular bacterial burden, while exogenous CCL5 rescued this antibacterial effect. Critically, CCL5⁺ macrophages promoted M2-like polarization and T-cell exhaustion-like phenotype through CCL5–CCR5 autocrine signaling; CCR5 blockade reversed CCL5-driven PD-1⁺TIM-3⁺ T-cell exhaustion-like phenotype and counteracted the increase in CD206⁺CD68⁺ macrophages. CCL5⁺ macrophages further formed an immunosuppressive interaction network involving APOE–TREM2 and HLA-E–CD94/NKG2A signaling. DNMT3A promotes pulmonary tuberculosis progression by driving CCL5⁺ macrophage-mediated immunosuppression through the PPARγ/NF-κB axis and the CCL5–CCR5 autocrine loop. Importantly, long-term inflammation–associated epigenetic reprogramming may be a key determinant of immune homeostasis imbalance and the establishment of a suppressive microenvironment that favors T-cell exhaustion. Targeting this epigenetic pathway and the CCL5–CCR5 axis may represent a promising host-directed therapeutic strategy for pulmonary tuberculosis.
Lymphangioleiomyomatosis (LAM) is a metastatic cystic lung disease characterized by cysts lined with nodules exhibiting cellular heterogeneity. These nodules contain smooth muscle–like LAM cells with melanosomal features (e.g., Pmel17) and mutations in the tuberous sclerosis complex (TSC) genes, TSC1 and/or TSC2. Loss of TSC function leads to hyperactivation of the mechanistic target of rapamycin (mTOR) pathway, and sirolimus, an mTOR inhibitor, is used to slow disease progression. Proteins involved in melanosome structure are regulated by the microphthalmia-associated transcription factor (MITF). Because vitamin A plays a critical role in lung development and deficiency leads to lung destruction, and because MITF is regulated by vitamin A metabolites, we hypothesized that vitamin A influences LAM disease progression. Serum vitamin A (retinol) levels were measured in 653 patients with LAM over 4,502 clinical visits. Clinical phenotyping and pulmonary function testing were performed longitudinally. The effects of retinol metabolites on cultured lung-derived and circulating LAM cells were evaluated. Gene expression profiling was conducted on laser-capture microdissected (LCM) LAM nodules. Circulating LAM cells were characterized phenotypically and genotypically. Higher blood retinol levels were associated with higher percent-predicted FEV₁ and DLCO (both P < 0.001) in multivariate analyses adjusting for baseline pulmonary function, TSC status, mTOR inhibitor use, and time of visit. Patients with higher retinol levels exhibited a significantly slower annual decline in percent-predicted FEV₁ compared with those with lower levels (P = 0.003). Approximately 80
Cadherin-16 (Cdh16) is transiently expressed during lung development, while its functional role remains unclear. Herein, we identified Cdh16 as a marker for a dynamic population of alveolar epithelial progenitors. Spatiotemporal and lineage tracing analysis in mice demonstrated that Cdh16-positive (Cdh16Pos) cells prevalent in distal buds during pesudoglandular stage, contributing to both AT2 and AT1 cell lineages, while its expression decreased subsequently and maintained a very low level postnatally. Single-cell RNA sequencing confirms that these cells represent a transient intermediate state during the differentiation from AT2 to AT1 cells. Functional ablation of the Cdh16Pos lineage in vivo disrupts alveolar morphogenesis, impairing epithelial differentiation. Additionally, Cdh16 is both necessary and sufficient for alveolar progenitor differentiation and alveolar organoid maturation. In the adult lung, the quiescent Cdh16Pos population is rapidly activated following lipopolysaccharide-induced injury, expands, and differentiates along the AT2-to-AT1 axis to contribute to alveolar repair. Depletion of this lineage compromises regeneration, leading to persistent structural defects. Our findings establish Cdh16Pos cells as a crucial source of alveolar epithelial progenitors essential for lung development and injury-induced regeneration, our work indicate that Cdh16 is a key regulator of alveolar lineage specification.
Traumatic brain injury (TBI) represents a devastating public health problem frequently complicated by secondary acute lung injury (ALI), which severely worsens clinical outcomes. However, the underlying mechanisms linking the brain-lung axis remain poorly defined. Here, we performed integrated transcriptomic, metabolomic, and 16 S rRNA microbiome analyses in patients with TBI-ALI before and after emergency treatment, and identified neuronal nitric oxide synthase (NOS1) as a key regulator associated with calcium signaling and cGMP-PKG pathway disorders. Functional validation in LPS-stimulated MLE-12 cells and a mouse TBI model demonstrated that NOS1 was markedly upregulated under pathological conditions, accompanied by excessive inflammation, oxidative stress, disrupted calcium homeostasis, and suppressed PKG1 signaling. NOS1 knockdown significantly reduced pro-inflammatory cytokine secretion, pathological NO production, and oxidative stress, while restoring cGMP levels, PKG1 activation, calcium homeostasis, and Nrf2/HO-1 antioxidant signaling, thereby reducing apoptosis and alleviating lung and brain tissue damage. Pharmacological inhibition of PKG1 with KT5823 markedly attenuated these protective effects, accompanied by reduced VASP phosphorylation and renewed calcium dysregulation, confirming the critical role of PKG1 signaling. Neurological assessment further showed that NOS1 silencing improved TBI-induced neurological deficits, whereas PKG1 inhibition partially reversed this benefit. In conclusion, our study demonstrates that NOS1 knockdown alleviates TBI-ALI, at least in part, by modulating the NO-cGMP-PKG1 signaling axis, which promotes antioxidant defense and restores calcium homeostasis. This study provides mechanistic insight into brain-lung axis injury and identifies the NOS1-PKG1 signaling axis as a potential therapeutic target.
The primary cilium is a solitary, non-motile, microtubule-based structure that projects from the surface of most mammalian cells. Once regarded as an evolutionary relic, the primary cilium is now recognized as a vital signaling hub coordinating key cellular processes including cell cycle progression, differentiation, and the maintenance of tissue homeostasis. In the lung, primary cilia exhibit dynamic spatiotemporal patterns: they are abundant during early lung development and show cell type- and context-dependent changes in mature tissues, with altered ciliogenesis observed during injury and repair. This review summarizes the dynamic functions of primary cilia in lung development and their associations with major signaling and sensory pathways, including Hedgehog, transforming growth factor-β/bone morphogenetic protein (TGF-β/BMP), Notch, Wnt, platelet-derived growth factor (PDGF) signaling, and mechanosensitive pathways. We also focus on the growing evidence linking primary ciliary dysfunction to major respiratory diseases including asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, pulmonary arterial hypertension and lung cancer. Understanding the biology of primary cilia not only provides critical insights into the development of respiratory diseases but also holds significant promise for identifying novel therapeutic targets.
