Reconstructing gene expression atlases for human tissues is challenging due to limited access to healthy samples from live individuals. Neurologically deceased donors often show ischaemic changes, and tissues near diseased regions may have altered gene expression1,2. The liver, with its unique regenerative capacity, allows analysis from live healthy donors. Here, using spatial transcriptomics (Visium, Visium HD3, multiplexed error-robust fluorescence in situ hybridization (MERFISH)4 and PhenoCycler imaging5) and single-nucleus RNA sequencing6, we analysed 16 liver samples: 8 from young live healthy donors and 8 from individuals with liver pathology, sampling ‘adjacent normal’ tissue. Livers from live healthy donors displayed significant gene expression differences compared with the adjacent normal tissues from individuals with liver pathology. Hepatocytes and non-parenchymal cells exhibited marked zonation along the porto–central axis of the liver lobules, with key functions being pericentrally shifted compared to mice and other mammals. Our atlas identified dynamic programmes in early steatotic hepatocytes, including a decline in nuclear-encoded mitochondrial proteins and a compensatory increase in mitochondria-encoded transcripts. This study presents a spatial gene expression reference for the healthy human liver and insights into hepatocyte changes in early steatosis.
