Single-cell atlas reveals inflammatory monocyte state tied to WTAP in healthy lungs and COPD

Researchers in China have built a high-resolution single-cell RNA sequencing atlas of the human respiratory system and uncovered a previously underappreciated feature of healthy lungs: a population of monocytes that carries a fully armed inflammatory transcriptional program even in the absence of disease. The team, led by Guoping Chen of the Department of Respiratory and Critical Care Medicine at Binhai County People’s Hospital, affiliated with Yangzhou University Medical College, published the findings in Frontiers in Cellular and Infection Microbiology on 27 October 2026. Their analysis identifies a monocyte state marked by the gene HSPA1B, links it to the RNA-modifying protein WTAP, and shows that this same program is more prominently represented in the lungs of patients with chronic obstructive pulmonary disease, or COPD.

COPD is one of the world’s most burdensome chronic illnesses, affecting an estimated 384 million people and ranking as the third leading cause of death globally. It is defined by persistent airflow limitation, chronic respiratory symptoms, and progressive structural remodeling of lung tissue, driven largely by chronic inflammation. Existing therapies, including bronchodilators and anti-inflammatory drugs, mainly manage symptoms rather than modify disease course, a limitation the authors attribute to an incomplete understanding of the cellular and molecular mechanisms that sustain pulmonary inflammation. Monocytes and their macrophage descendants have long been recognized as central players in this process, but how their functional states are organized in healthy lung tissue has remained unclear.

To address this gap, the researchers assembled publicly available single-cell transcriptomic datasets from the CELLxGENE Discover platform and the Gene Expression Omnibus, covering lung parenchyma, respiratory airways, and nasal tissue from healthy donors. They combined this healthy reference atlas with COPD lung tissue datasets, bronchoalveolar lavage fluid samples generated in the laboratory of Reyad Shaykhiev at Weill Cornell Medical College, and peripheral blood mononuclear cell profiles from COPD patients and healthy individuals. After standard quality control, normalization, batch correction with Harmony, and clustering in Seurat, they annotated nine major cell populations in the healthy respiratory atlas, including epithelial cells, endothelial cells, fibroblasts, macrophages, monocytes, dendritic cells, T and NK cells, B and plasma cells, and other immune cells.

The atlas revealed striking regional specialization. Nasal mucosa and airways were dominated by epithelial cells, consistent with their role as frontline barriers against environmental stimuli, while the lung parenchyma hosted a far more complex landscape in which macrophages were the most abundant population, followed by epithelial cells, T and NK cells, endothelial cells, monocytes, and fibroblasts. When the team scored each cell type for inflammatory gene expression, monocytes stood out with the strongest inflammatory activity of any population, even in healthy tissue. This finding suggests that respiratory monocytes maintain a state of inflammatory preparedness under physiological conditions, potentially priming them for rapid responses to environmental challenges.

High-resolution reclustering of the monocyte compartment identified five transcriptionally distinct subpopulations, designated Mono_1 through Mono_5. The Mono_4 cluster emerged as the most distinctive: it expressed high levels of CD14, the hallmark of classical monocytes, carried the strongest inflammatory signature of any subset, and preferentially expressed inflammatory mediators including TNF, CCL5, CXCL8, CCL3, CCL4, CCL20, and IL6. Screening for markers specific to this cluster singled out HSPA1B, a gene encoding a heat shock protein, whose expression was largely restricted to Mono_4. The researchers accordingly named this population the HSPA1B-positive inflammatory monocyte state. By contrast, the Mono_5 cluster showed non-classical monocyte features and elevated antigen-presentation signatures, while Mono_3 displayed enhanced interferon-response characteristics.

Gene Ontology enrichment analysis deepened the functional portrait of the HSPA1B-positive state. Genes upregulated in Mono_4 were enriched not only in inflammatory response pathways but also in cytoplasmic translation, protein biosynthesis, and ribosome-related components, alongside extracellular vesicle and secretory granule terms. Molecular function categories included chemokine receptor binding, chemokine activity, cytokine activity, and CCR-related ligand-receptor interactions. Pseudotime trajectory analysis with Monocle2 placed the monocyte subsets along a continuous transcriptional spectrum rather than as isolated clusters, with one branch linking inflammatory classical states and another extending toward non-classical, antigen-presenting states. The authors caution that pseudotime ordering does not establish definitive lineage relationships, so the HSPA1B-positive state should be viewed as one position within a continuum rather than an obligate differentiation endpoint.

Cell-cell communication analysis using CellChat mapped the signaling ecosystem of the healthy lung. Fibroblasts dominated outgoing extracellular matrix signaling through COLLAGEN, LAMININ, and FN1 pathways, while macrophages and monocyte subsets formed a myeloid-centered immune communication module built on MIF, CXCL, ANNEXIN, and GALECTIN signaling. Within this network, HSPA1B-positive inflammatory monocytes acted as active communication nodes with strong bidirectional signaling. They received MIF signals through CD74-CD44 and CD74-CXCR4 receptor pairs, along with extracellular matrix and adhesion inputs such as collagen-CD44, LAMA-CD44, THBS1-CD36, and ITGB2-ICAM1 interactions. Outgoing signals included CXCL8, CXCL3, and CXCL2 engaging ACKR1 on vascular-associated cells, suggesting a role in coordinating immune cell trafficking across the endothelium. MIF signaling carried the highest overall information flow of any pathway in the healthy lung network.

The pivotal disease comparison came when the team integrated COPD lung tissue datasets. COPD lungs showed marked remodeling of the cellular ecosystem, with increased proportions of monocytes, macrophages, mast cells, and epithelial cells and reduced proportions of T and NK cells and fibroblasts. Reclustering COPD monocytes yielded six subsets, among which the Mo_2 cluster carried the strongest inflammatory and interferon-response signatures. When the researchers projected the healthy HSPA1B-positive inflammatory monocyte signature onto the COPD data, it was most strongly enriched in Mo_2, indicating that the COPD-associated inflammatory monocytes closely resemble the state already present in healthy tissue rather than representing an entirely novel pathological population. The authors describe a trend toward greater representation of this Mo_2-like state in COPD lungs, framing chronic pulmonary inflammation as potentially involving amplification and remodeling of existing physiological immune programs.

The study’s second major thread concerns epitranscriptomics, specifically N6-methyladenosine, or m6A, the most abundant internal modification of mammalian messenger RNA. Unsupervised clustering showed that expression of m6A regulatory genes alone could distinguish monocyte functional states with discriminatory power comparable to whole-transcriptome profiles. Among the writers, erasers, and readers analyzed, WTAP, a scaffold component of the METTL3-METTL14 methyltransferase complex, showed the strongest association with inflammatory characteristics: its expression correlated positively with inflammation scores and inversely with interferon-response and antigen-presentation signatures. WTAP-high monocytes were enriched for inflammatory response, lipopolysaccharide response, and NF-kappaB signaling programs, along with secretory granule, lysosomal, and endosomal membrane components and chemokine-related functions.

Functional experiments supported this association. In THP-1 human monocytes stimulated with lipopolysaccharide and interferon-gamma to induce an inflammatory state, silencing WTAP with siRNA reduced WTAP-positive cell fractions while keeping viability above 90 percent, and it lowered HSPA1B expression along with the inflammatory genes IL1B, TNF, CXCL8, and IL6. At the same time, WTAP depletion increased expression of interferon-responsive genes including ISG15, IFIT1, IFIT3, MX1, OAS1, and RSAD2, and of antigen-presentation genes including HLA-DRA, HLA-DRB1, CD74, CIITA, HLA-DPA1, and CTSS. The same pattern was reproduced in primary human monocytes isolated from commercially obtained peripheral blood. In COPD bronchoalveolar lavage fluid, the monocyte subset enriched for the HSPA1B-positive signature showed elevated WTAP expression, whereas peripheral blood monocytes from both healthy donors and COPD patients showed limited enrichment of the signature and low WTAP levels, suggesting the inflammatory state is preferentially established within the lung environment rather than expanded in circulation.

The authors are careful about the limits of their conclusions. The cross-sectional nature of the datasets cannot establish whether monocyte remodeling precedes or follows COPD progression, and because direct m6A modification was not measured, the findings do not demonstrate a direct WTAP-m6A regulatory mechanism; WTAP is presented as a factor associated with the inflammatory program, not a proven driver. Trajectory inferences require lineage tracing, and whether targeting WTAP-associated pathways could modulate pulmonary inflammation in vivo remains untested. Even so, the work offers a compelling reframing of COPD immunology: chronic inflammation may arise not from wholly new pathogenic cell types but from the expansion and transcriptional retuning of inflammatory states that already exist in healthy lungs, with WTAP-linked epitranscriptomic regulation emerging as a candidate lever for future investigation.

Subject of Research: A single-cell transcriptomic atlas of the human respiratory system identifying an HSPA1B-positive inflammatory monocyte state associated with the m6A regulator WTAP in health and COPD

Article Title: A single-cell atlas of the human respiratory system identifies a monocyte-centered HSPA1B+ inflammatory primed state associated with WTAP

Article References: Wang, Y., Zhu, L., Zhu, Y., & Chen, G. (2026). A single-cell atlas of the human respiratory system identifies a monocyte-centered HSPA1B+ inflammatory primed state associated with WTAP. Frontiers in Cellular and Infection Microbiology, 16, 1950659. https://doi.org/10.3389/fcimb.2026.1950659

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1950659

Keywords: single-cell RNA sequencing, monocytes, COPD, HSPA1B, WTAP, m6A methylation, lung atlas, inflammation, cell-cell communication, bronchoalveolar lavage, epitranscriptomics, THP-1