Decoding the role of macrophage LAP3 in lung cancer – integration of single-cell technologies and machine learning reveals an orchestrating immunometabolic circuit at the tumor-epithelial interface

TL;DR

This study explores how the LAP3 protein in lung cancer connects metabolism and immune responses, suggesting it could help guide new treatments.

Contribution

The study identifies LAP3 as a novel immunometabolic hub linking amino acid metabolism to immune signaling in lung cancer.

Findings

LAP3 is enriched in tumor epithelium and a specific macrophage subset at tumor-epithelial interfaces.

LAP3 overexpression reduces tumor cell proliferation, motility, and invasiveness in vitro and in vivo.

LAP3 functions as a signaling hub, secreting chemokines, cytokines, and ECM components.

Abstract

Amino acid metabolism plays a crucial role in shaping tumor–immune crosstalk in non–small cell lung cancer (NSCLC). However, the key cellular mediators that translate metabolic states into intercellular signals remain poorly defined.

We integrated single-cell RNA-seq with spatial transcriptomics to map immunometabolic architecture. Transcriptional co-variation was decomposed into amino-acid metabolic programs using Non-negative Matrix Factorization (NMF); spatial deconvolution localized programs and cell types in tissue. Myeloid populations were subclustered to resolve macrophage states. Functional assays tested LAP3 overexpression (OE-LAP3) in A549/PC9 cells (qRT-PCR, Western blot, CCK-8, colony formation, wound-healing, Transwell) and a nude-mouse subcutaneous mouse model.

Integrative single-cell and spatial transcriptomic analyses revealed that tumor epithelial and myeloid cells dominate the NSCLC microenvironment and exhibit lineage-specific activation of amino acid metabolic programs. Notably, LAP3 was selectively enriched in both tumor epithelium and a distinct macrophage subset. Spatial mapping localized this LAP3-high macrophage state to epithelial–myeloid interfaces, where it functions as a signaling hub, actively secreting chemokines, cytokines, adhesion molecules, and extracellular matrix (ECM) components. To test whether LAP3 plays a causal role in tumor behavior, we established stable LAP3-overexpressing A549 and PC9 cell lines, confirming robust upregulation at both mRNA and protein levels. Functionally, LAP3 overexpression significantly suppressed proliferation—evident in CCK-8 time-course and colony formation assays—and impaired motility and invasiveness, as shown by delayed wound healing and reduced cell migration/invasion in Transwell assays. Most importantly, these effects translated in vivo: LAP3-overexpressing xenografts formed markedly smaller tumors in nude mice.

LAP3 appears to functionally link amino acid catabolism to immune communication in NSCLC, defining an epithelial–macrophage immunometabolic niche where metabolic activity may shape the immune contexture. Its overexpression is associated with attenuated malignant phenotypes and heightened immune engagement, suggesting a potential dual role in restraining tumor aggressiveness and fostering an immune-responsive microenvironment. While these findings support LAP3 as a candidate biomarker for patient stratification and provide a rationale for combining metabolic modulation with immunotherapy, further mechanistic and clinical validation remains necessary.

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