LuCaS+: A Clinically-Anchored Single-Cell Atlas of Lung Cancer

LuCaS+ (Lung Cancer Single-nucleus Atlas) is a comprehensive, clinically anchored single-nucleus RNA sequencing (snRNA-seq) dataset comprising over 2.5 million nuclei derived from formalin-fixed paraffin-embedded (FFPE)samples of 454 patients diagnosed with non-small cell lung cancer (NSCLC). Patients included in LuCaS+ underwent surgical resection between 2007 and 2022 at three German university hospitals (Charité - Universitätsmedizin Berlin, University Hospital Cologne, and LMU Munich). Sample Processing & Sequencing: Archived FFPE blocks were processed using the 10x Flex Gene Expression protocol and sequenced on an Illumina NovaSeq XP instrument. Data Preprocessing & Cell Type Annotation: Initial dimensionality reduction employed a contrastive learning algorithm (VICreg) for robust representation learning. Hierarchical clustering identified approximately 500 distinct cell clusters, annotated via marker-gene expression patterns and inferred copy-number variation to distinguish malignant from non-malignant populations. Non-malignant populations were further annotated into detailed subtypes including immune, stromal, vascular, and epithelial cells.