Abstract 113: An atlas of epithelial cell states and plasticity in lung adenocarcinoma
Authors: Han Guangchun , Sinjab Ansam , Treekitkarnmongkol Warapen , Rahal Zahraa , Liu Yuejiang , Serrano Alejandra G. , Feng Jiping , Liang Ke , Khan Khaja , Lu Wei , Hernandez Sharia , Cao Xuanye , Dai Enyu , Liu Yunhe , Pei Guangsheng , Hu Jian , Bolanos Lorena I. Gomez , Parra Edwin R. , Cascone Tina , Sepesi Boris , Moghaddam Seyed Javad , Scheet Paul , Negrao Marcelo V. , Heymach John V. , Li Mingyao , Chen Jichao , Dubinett Steven M. , Fujimoto Junya , Solis Luisa M. , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Wang Linghua , Kadara Humam 
Published: April 2023

Abstract
Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. While most if not all single-cell RNA sequencing (scRNA-seq) studies of lung cancer provided details on immune and stromal states, little insight is drawn to epithelial cells given their paucity (~4%) when performing unbiased scRNA-seq analysis without prior enrichment. Here, we performed in-depth scRNA-seq of enriched (by sorting for EPCAM+) epithelial cell subsets from 16 early-stage LUADs and 47 matching normal lung (NL) tissues. We also studied tissues from the same LUADs and adjacent NL by whole exome sequencing and a subset by high-resolution spatial protein and transcriptome analysis. We also performed scRNA-seq analysis of murine lungs from a human-relevant model of LUAD development following exposure to tobacco carcinogen, including strains with an alveolar type II (AT2) cell-specific lineage reporter. After extensive quality control, we retained 246,102 high quality human epithelial cells which comprised diverse normal alveolar and airway lineages as well as cancer cell populations. Diversity among cancer cells was strongly linked to LUAD oncogenic drivers. KRAS-mutant cancer cells were unique in their transcriptional features, strikingly reduced differentiation, low levels of copy number changes, and increased variability amongst the cells themselves. The local epithelial niche of LUADs, relative to that of NL, was enriched with intermediary cells in lung alveolar differentiation. A subset of these cells displayed elevated KRT8 expression (KRT8+ alveolar cells; KACs), increased plasticity and frequency of KRASG12D mutations, and its gene expression profiles were enriched in lung precancer and LUAD and signified poor survival. Notably, KACs harboring KRAS mutations were only found in the ecosystem of KRAS-mutant LUADs. Murine KACs were evident in lungs of tobacco carcinogen-exposed mice that develop KRAS-mutant LUADs but not in the saline-treated control group. While murine KACs emerged prior to tumor onset, they persisted for months after carcinogen cessation, and like their human counterparts, acquired driver Kras mutations, were poorly differentiated, and harbored KRAS-specific transcriptional programs. Spatial transcriptomics analysis showed that KAC and KRAS signatures were elevated in both murine and human tumors as well as in KACs that were in the local spatial vicinity of the LUADs. Organoids derived from lungs of tumor-bearing reporter mice were markedly enriched with KACs and were conspicuously sensitive to targeted inhibition of KRAS-G12D. This study provides new insights into the landscape of normal epithelial and malignant cells in LUAD, the role of alveolar intermediate subsets in development of the malignancy, particularly that driven by mutant KRAS, and, thus, potential targets for early interception.
Citation Format: Guangchun Han, Ansam Sinjab, Warapen Treekitkarnmongkol, Zahraa Rahal, Yuejiang Liu, Alejandra G. Serrano, Jiping Feng, Ke Liang, Khaja Khan, Wei Lu, Sharia Hernandez, Xuanye Cao, Enyu Dai, Yunhe Liu, Guangsheng Pei, Jian Hu, Lorena I. Gomez Bolanos, Edwin R. Parra, Tina Cascone, Boris Sepesi, Seyed Javad Moghaddam, Paul Scheet, Marcelo V. Negrao, John V. Heymach, Mingyao Li, Jichao Chen, Steven M. Dubinett, Junya Fujimoto, Luisa M. Solis, Ignacio I. Wistuba, Christopher S. Stevenson, Avrum Spira, Linghua Wang, Humam Kadara. An atlas of epithelial cell states and plasticity in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 113.