Federica Sotgia, Diana Whitaker-Menezes, et al.
Cell Cycle
Clonal evolution of a tumor ecosystem depends on different selection pressures that are principally immune and treatment mediated. We integrate RNA-seq, DNA sequencing, TCR-seq and SNP array data across multiple regions of liver cancer specimens to map spatio-temporal interactions between cancer and immune cells. We investigate how these interactions reflect intra-tumor heterogeneity (ITH) by correlating regional neo-epitope and viral antigen burden with the regional adaptive immune response. Regional expression of passenger mutations dominantly recruits adaptive responses as opposed to hepatitis B virus and cancer-testis antigens. We detect different clonal expansion of the adaptive immune system in distant regions of the same tumor. An ITH-based gene signature improves single-biopsy patient survival predictions and an expression survey of 38,553 single cells across 7 regions of 2 patients further reveals heterogeneity in liver cancer. These data quantify transcriptomic ITH and how the different components of the HCC ecosystem interact during cancer evolution.
Federica Sotgia, Diana Whitaker-Menezes, et al.
Cell Cycle
Matteo Manica, Loic Kwate Dassi, et al.
ISGC 2022
Riselda Kodra, Hadjer Benmeziane, et al.
ICLR 2025
Xu Han, Dongliang Zhang, et al.
Nature Communications