Final Report Summary - LIVHET (Single cell heterogeneity in the mammalian liver)
The liver is a highly heterogeneous organ. Hepatocytes operate in repeating anatomical units called lobules that are polarized by blood flow, creating gradients of oxygen, nutrients and hormones. This graded microenvironment gives rise to division of labor among hepatocytes residing in different lobule coordinates, a phenomenon termed 'liver zonation'. In our project we sought to obtain a global quantitative description of liver zonation. To this end we developed advanced tools, ranging from single molecule transcript imaging in the intact liver through single cell RNA sequencing of thousands of hepatocytes, to paired-cell sequencing of hepatocytes and non-parenchymal liver cells that interact with them. These tools, combined with algorithms for spatial inference of sequenced cell positions, enabled a comprehensive global reconstruction of the spatial expression patterns of all hepatocyte genes, as well as all liver endothelial cell genes. These liver tissue maps revealed prominent design principles governing division of labor, such as allocation of energetically demanding tasks to lobule layers with higher oxygen levels and 'production line' patterns, whereby sequential enzymes in a metabolic cascade are expressed in sequential lobule layers. Our single molecule transcript imaging tools further revealed an intriguing phenomenon of 'bursty' transcription in the liver, whereby mRNA is produced in intermittent stochastic production bursts. Such bursts can potentially generate unwanted variability in expression among hepatocytes residing in the same lobule zone. We identified diverse mechanisms hepatocytes apply to buffer the burst-associated noise, including hepatocyte polyploidy and nuclear retention of mRNA.