Spatial Transcriptomics of Immune Cell Distribution in Non-Small Cell Lung Cancer Identifies Tertiary Lymphoid Structures and Its Density and Area Fraction Were Associated with Neoadjuvant Therapy Response

Background: Non-small cell lung cancer (NSCLC) remains one of the leading causes of cancer-related mortality worldwide over the past decade. Single-cell sequencing loses spatial location information and potential cell–cell interactions, making it difficult to interpret molecular features or biological phenomena. Tertiary lymphoid structures (TLSs) inherently require such spatial immune cell distribution information. Although associations between TLS and response to immune checkpoint inhibitors (ICIs) or chemotherapy have been reported, the relationship between TLS and neoadjuvant therapy (ICI combined with chemotherapy) remains unclear. Methods: We performed spatial transcriptomics on NSCLC samples (including one lung squamous cell carcinoma (LUSC) and one lung adenocarcinoma (LUAD)). Multiplex immunohistochemistry (mIHC) was used to identify the TLS, while immunohistochemistry staining (IHC) was used to identify the TLS status and cell characteristics. We evaluated the associations between (mature) TLS density, area proportion and patients’ responses in 66 patients. Results: Heterogeneity of immune cells in NSCLC was found. Gene ontology analysis and cell score comparison identified TLS with activated B and T cells inside, while plasma cells and macrophages were mainly distributed outside TLS. Four genes from antigen-presenting machinery (TAP1, TAP2, B2M, TAPBP) were more highly expressed inside TLS than outside them. Also, TLS exhibited heterogeneity, with both mature and immature TLS. Mature TLS showed an average area of 62,387.43 μm2, while the immature TLS showed 51,189.90 μm2. The Spearman correlation coefficient of B-cell number and mTLS area showed r = 0.900. TLS density and mature TLS (mTLS) density in the tumor bed were 1.95 ± 0.95 TLS/10 mm2 (mean ± SD, n = 34) and 1.13 ± 0.77 mTLS/10 mm2, significantly higher than that in the non-responder group (1.18 ± 1.15 TLS/10 mm2, 0.70 ± 0.90 mTLS/10 mm2, mean ± SD, n = 32) separately. B cells belonging to TLS had a significantly higher density (71.32 ± 55.71 cells/mm2, mean ± SD, n = 34) in the responder group than the non-responder group (61.33 ± 111.95 cells/mm2, mean ± SD, n = 32) normalized to the tumor bed area. Conclusions: Spatial transcriptomics reveals immune cell heterogeneity and distribution patterns in the NSCLC tumor bed, with activated B and T cells localized inside and plasma cells/macrophages outside. Antigen-presenting machinery (APM)-related genes were highly expressed in TLS accompanied by a high expression of upstream and downstream genes of MHC class I. mTLS have a larger area by mainly containing more B cells. The responder group had a significantly higher (mature) TLS density and larger (mature) TLS area proportion compared with the non-responder group, suggesting their potential function in anti-tumor effect in neoadjuvant treatment.