Integration of single-cell transcriptomics and genomic mutation analysis identifies an immunotherapy-resistant tumor subcluster and validates ARNTL2 as a malignant driver in lung adenocarcinoma.

Zhengang Qiu; Hui Zhao; Qiong Lyu; Zhigang Li; Qiujiang Xi; Bingqing Ye; Qianshan Long; Zhengxin Lai; Xiang Cao; Wenjuan Zhong; Yu Zhang; Rongrong Liu

doi:10.1016/j.tranon.2026.102971

PubMed · 42603344

Integration of single-cell transcriptomics and genomic mutation analysis identifies an immunotherapy-resistant tumor subcluster and validates ARNTL2 as a malignant driver in lung adenocarcinoma.

Zhengang Qiu·Hui Zhao·Qiong Lyu·Zhigang Li·Qiujiang Xi·Bingqing Ye·Qianshan Long·Zhengxin Lai·Xiang Cao·Wenjuan Zhong·Yu Zhang·Rongrong Liu

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Abstract

BACKGROUND: Immunotherapy resistance in lung adenocarcinoma (LUAD) remains a critical clinical challenge, and the mechanisms underlying resistance-associated intratumoral heterogeneity are poorly characterized. METHODS: We performed single-cell RNA sequencing of LUAD patients receiving neoadjuvant immunotherapy (responders vs. non-responders), integrating inferCNV, GSVA, and differential expression analyses. Cluster-specific genes were validated across seven independent cohorts (TCGA-LUAD, GSE13213, GSE26939, GSE29016, GSE30219, GSE31210, GSE42127). A multi-algorithm machine learning framework was used to construct a prognostic model, and the immune microenvironment was characterized using TCIA scoring, seven infiltration algorithms, and ESTIMATE. ARNTL2 function was assessed by CCK-8 and Transwell assays in A549 and H1299 cells. RESULTS: Non-responders showed significant enrichment of epithelial cells, depletion of cytotoxic T/NK cells, and elevated copy number variation burden versus responders (p < 0.0001). A resistance-enriched malignant subcluster (Cluster 2) exhibited hyperproliferative and metabolic reprogramming signatures with upregulated KRT17, S100A2, and CST6, which showed tumor-specific overexpression, adverse prognostic value, and genomic amplification across cohorts. CoxBoost combined with survivalSVM achieved optimal predictive performance (C-index = 0.686), yielding robust risk stratification (HR: 2.54-10.51, all p < 0.05). Low-risk patients showed greater immune infiltration and higher TCIA immunophenoscores. ARNTL2 was an independent prognostic factor (HR: 2.07-4.64) strongly correlated with risk score (r = 0.69), and its knockdown suppressed proliferation and invasion in both LUAD cell lines (all p < 0.05). CONCLUSION: This study identifies a resistance-associated malignant subcluster in LUAD, constructs a validated CoxBoost + survivalSVM prognostic model with robust immune stratification, and establishes ARNTL2 as a core oncogenic driver and therapeutic target.

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ARNTL2 Lung adenocarcinoma Prognostic model Single-cell transcriptomics Tumor microenvironment Journal Article

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Zhengang Qiu, Hui Zhao, Qiong Lyu, Zhigang Li, Qiujiang Xi, Bingqing Ye, Qianshan Long, Zhengxin Lai, Xiang Cao, Wenjuan Zhong, Yu Zhang, Rongrong Liu. 2026-08-15. Integration of single-cell transcriptomics and genomic mutation analysis identifies an immunotherapy-resistant tumor subcluster and validates ARNTL2 as a malignant driver in lung adenocarcinoma.. https://doi.org/10.1016/j.tranon.2026.102971

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