Multi-omic profiling of pleural effusions: a reservoir-incubator for non-invasive insights into tumor heterogeneity

Abstract Pleural effusions (PEs) are common in advanced cancer and are routinely sampled for cytological evaluation; however, their full potential as a source of tumor and immune information remains underexplored. Although malignant PEs (MPEs) are increasingly used for liquid biopsy, their cellular complex interactions have not been resolved at high resolution. Here, we present the first comprehensive single-cell and multi-omic atlas of PEs, integrating scRNA-seq, TCR-seq and whole-exome sequencing with lung, breast, or ovarian cancer, as well as non-malignant heart failure controls. We profiled over 200,000 cells and identified more than 30 immune, stromal, and tumor subpopulations across disease contexts. The tumor cell signature in MPEs recapitulates the genomic and transcriptomic features of matched primary tumors, supporting their use for non-invasive tumor profiling. In contrast, immune landscapes varied by disease: lung cancer MPEs were enriched in exhausted CD8⁺ T cells, breast MPEs showed CD4⁺ T helper cell dominance, and ovarian and heart failure PEs harbored tissue-resident myeloid cell populations. These data reveal that PEs are dynamic, disease-specific ecosystems shaped by tumor-driven immune remodeling. By leveraging their cellular diversity, we position MPEs as a powerful platform for studying metastatic adaptation and immune responses in vivo, with direct implications for diagnostics, immune monitoring, and precision oncology. Competing Interest Statement HH is a co-founder and shareholder of Omniscope, a scientific advisory board member of NanoString and MiRXES and a consultant to Moderna and Singularity. JCN is a scientific consultant for Omniscope. The remaining authors declare that the research was carried out without any commercial or financial relationships that could potentially create a conflict of interest. Footnotes ↵# shared last authors