Abstract 763: Multimodal spatial-omics atlas of lung premalignancy and adenocarcinoma reveals tumor initiating interplay between alveolar progenitors and inflammation

Abstract Background: The events mediating the transition of normal-appearing tissue (NAT) to adenomatous premalignant lesions (aPMLs) and minimally or locally invasive lung adenocarcinoma (LUAD) are very poorly narrated. Methods: We analyzed matching NATs, aPMLs, and LUADs from 25 patients using integrative approaches including spatial transcriptomics (ST, n=56 tissues), single-cell RNA-sequencing of fixed cells (scFFPE-seq) from matched uninvolved NAT, aPMLs and LUADs (n = 75 tissues), and whole exome sequencing (WES, n=79). A subset of tissues was also analyzed by sequential immunofluorescence (seqIF, COMET) and subcellular spatial gene expression (Xenium, n=41). Results: We performed multimodal spatial omics analysis of lung tissues along the NAT-aPML-LUAD continuum. After quality control, we retained and analyzed 477, 283 spots by ST, 401, 636 cells by scFFPE-seq, and more than 1.75 million cells by Xenium. Paired aPMLs and LUADs showed distinct spatial transcriptional patterns, lineage plasticity, and cell states. We derived nine metaprograms using scFFPE-seq data of epithelial cells, which showed robust alignment with sub-cell type and states from the ST data. Integrative analysis of ST and scFFPE-seq demarked metaprograms that denote alveolar type 1 (AT1) and type 2 (AT2), alveolar intermediate cell (AIC), and tumor cells in the cellular path to aPML and LUAD. Both LUAD and aPML regions highly expressed signatures of KRT8+ AICs (KACs), which denoted transitionary states between NATs and aPMLs or LUADs. Trajectory analysis demonstrated two alveolar transition paths, namely AT2-AIC-AT1 and AT2-KAC-lung tumors. In contrast to LUADs, early aPMLs and KAC-rich NAT expressed proinflammatory metaprograms, suggesting that interplay between KAC and inflammation is contextual and likely involved in tumor initiation in the peripheral lung. Spatial single-cell neighborhood analysis by Xenium platform concordantly showed that KACs were proximal to proinflammatory macrophages and cancer-associated fibroblasts (CAFs). Specifically, IL-1B+ proinflammatory macrophages and inflammatory CAFs were observed to be enriched in the neighborhood of tumor cells in aPMLs. Multimodal analysis of a tobacco lung carcinogenesis mouse model showed that KACs displayed increased NF-kB signaling and expression of the Il1b receptor Il1r1. Importantly, treatment with IL-1b or macrophage co-culture enhanced growth of KAC-enriched organoids, and IL-1b neutralization in vivo led to KAC regression. Conclusions: We generated a multimodal spatial and single-cell atlas of the transition of normal tissue to aPML and LUAD. This comprehensive atlas uncovered critical interactions between tumor progenitors and inflammation that inspire initiation of lung lesions and inform of unique and targetable cellular states for early detection and interception of LUAD. Citation Format: Fuduan Peng, Ansam Sinjab, Sujuan Yang, Yibo Dai, Minyue Chen, Warapen Treekitkarnmongkol, Tieling Zhou, Alejandra G. Serrano, Jianlong Liao, GuangSheng Pei, Yunhe Liu, Yang Liu, Jiahui Jiang, Kyung Serk Cho, Yanshuo Chu, Kai Yu, Ruiping Wang, Jiping Feng, Zahraa Rahal, Lorena I. Gomez Bolanos, Guangchun Han, Naoe Jimbo, Takuo Hayashi, Satsuki Kishikawa, Kazuya Takamochi, Akshay Basi, Avrum Spira, Steven Dubinett, Tomokazu Itoh, Takashi Yao, Kenji Suzuki, Luisa M. Solis, Stephen Swisher, Mingyao Li, Junya Fujimoto, Ignacio I. Wistuba, Jared Burks, Kadir Akdemir, Jeffrey Myers, Linghua Wang, Humam Kadara. Multimodal spatial-omics atlas of lung premalignancy and adenocarcinoma reveals tumor initiating interplay between alveolar progenitors and inflammation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 763.