Presence of onco-fetal neighborhoods in hepatocellular carcinoma is associated with relapse and response to immunotherapy

The HCC01 and HCC03 Stereo-seq data have been deposited in the China National GeneBank Sequence Archive (CNSA) under accession code CNP0004497. The M311 and M316 Stereo-seq data have been deposited in the Sequence Read Archive (SRA) under accession code PRJNA1005053. The CoxMx data have been deposited in the under accession code. The original data used to construct the HCC atlas are available with accession codes GSE156337, GSE149614, GSE151530, GSE212046 (GEO), HRA000069 (Genome Sequence Archive) and CNP0000650 (CNSA). The original data of PLANET cohort and GO30140 and IMbrave150 trials are available with accession codes EGAS00001003813 and EGAS00001005503 (European Genome-phenome Archive). The TCGA LIHC datasets were downloaded from UCSC Xena (http://xena.ucsc.edu/). All processed expression data have been uploaded to figshare, which can be visited through the following private links: HCC Atlas, https://doi.org/10.6084/m9.figshare.22332568; Onco-fetal CAF Identification, https://doi.org/ 10.6084/m9.figshare.22332655; HCC01 and HCC03 Stereo-seq Data, https://doi.org/10.6084/m9.figshare.22332223; Nanostring CosMx Data, https://doi.org/10.6084/m9.figshare.23972991; PLANET corhort Data, https://doi.org/10.6084/m9.figshare.23732370; HCC and Fetal Liver Nanostring DSP Data, https://doi.org/10.6084/m9.figshare.22332397; HCC Immunotherapy Stereo-seq Data, https://doi.org/10.6084/m9.figshare.22332352. Source data for Fig. 1-8 and Extended Data Fig. 1-10 have been provided as Source Data files. All other data supporting the findings of this study are available from the corresponding author upon reasonable request.