Cell-Free DNA-Derived Immune Cell Ratios Uncover Cancer-Associated Systemic Changes

Genome-wide coverage patterns of plasma cell-free DNA (cfDNA) fragments reflect nucleosome positioning in the cells of origin, enabling noninvasive inference of cell type contributions and transcriptional activity. Whereas the majority of cfDNA originates from hematopoietic cells, the diagnostic and biological relevance of this fraction remains underexplored. In this study, we performed cfDNA-based deconvolution of blood cell types by integrating transcription start site (TSS) coverage profiles from plasma whole-genome sequencing with single-cell transcriptomic reference data. By correlating cfDNA TSS coverage with gene expression across 457 blood cell types, we ranked their relative contributions to the cfDNA pool. We analyzed 788 pretreatment and longitudinal plasma samples from patients with localized colorectal cancer, muscle-invasive bladder cancer (MIBC), as well as 30 samples from healthy controls. In healthy individuals, cfDNA TSS coverage profiles reflected blood gene expression, and the inferred cell type contributions recapitulated the known hematopoietic composition. In patients with cancer, we observed a significant increase in cfDNA contributions from lymphocytes, including T cells and plasma cells, and decreased contributions from monocytes and granulocytes. These immune-derived signatures distinguished patients with colorectal cancer (AUC = 0.793) and MIBC (AUC = 0.745) from healthy controls. Longitudinal analysis of immune cell type contributions revealed treatment-associated changes in the relative abundance of classic monocytes and plasma cells, although these temporal dynamics were not predictive of relapse or outcome. Together, these findings suggest that cfDNA-derived immune signatures may capture aspects of systemic immune remodeling in cancer, potentially providing a complementary noninvasive biomarker in liquid biopsies beyond tumor-derived signals.

There is limited understanding of how plasma cfDNA reflects systemic immune changes in cancer. We show that cfDNA coverage profiles reflect blood cell gene expression and can be used to infer blood cell ranks that recapitulate known cell compositions. These cfDNA-derived ranks reveal cancer-associated immune alterations that distinguish patients with cancer from healthy controls. Our findings highlight cfDNA as a minimally invasive biomarker of systemic immune remodeling in cancer.