Polyploidisation pleiotropically buffers ageing in hepatocytes

• Published in: Journal of hepatology Vol. 81; no. 2; pp. 289 - 302
• Main Authors: Yin, Kelvin, Büttner, Maren, Deligiannis, Ioannis K., Strzelecki, Mateusz, Zhang, Liwei, Talavera-López, Carlos, Theis, Fabian, Odom, Duncan T., Martinez-Jimenez, Celia P.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2024
• Subjects: ageing; Aging - genetics; Aging - physiology; Animals; BaseScope; CCAAT-Enhancer-Binding Proteins - genetics; CCAAT-Enhancer-Binding Proteins - metabolism; Cellular Senescence - genetics; Cellular Senescence - physiology; epigenetic clock; Fatty Liver - genetics; Fatty Liver - pathology; Gene Regulatory Networks; Haploinsufficiency; Hepatocyte Nuclear Factor 4 - genetics; Hepatocyte Nuclear Factor 4 - metabolism; Hepatocytes - metabolism; Hepatocytes - physiology; Liver; Liver - metabolism; Male; Mice; Mice, Inbred C57BL; Polyploidy; single-nucleus RNA-seq; ageing; haploinsufficiency; polyploidy; Liver; single-nucleus RNA-seq; BaseScope; epigenetic clock
• ISSN: 0168-8278; 1600-0641; 1600-0641
• DOI: 10.1016/j.jhep.2024.03.043

Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. We performed single-nucleus RNA sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent strains that were haploinsufficient for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. We observed that ageing in wild-type mice results in nuclei polyploidy and a marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in the CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A-haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbations. Our results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome. The functional role of hepatocyte polyploidisation during ageing is poorly understood. Using single-nucleus RNA sequencing and BaseScope approaches, we have studied ploidy dynamics during ageing in murine livers with non-deleterious genetic perturbations. We have identified that hepatocytes present different cellular states and the ability to buffer ageing-associated dysfunctions. Tetraploid nuclei exhibit robust transcriptional networks and are better adapted to genomically overcome perturbations. Novel therapeutic interventions aimed at attenuating age-related changes in tissue function could be exploited by manipulation of ploidy dynamics during chronic liver conditions. [Display omitted] •In hepatocytes, an increase in nuclear ploidy is a fundamental cellular state that preserves tissue function.•Tetraploid hepatocyte nuclei, carrying multiple copies of the genome, attenuate age-related transcriptomic changes.•Early accumulation of tetraploid nuclei in hepatocytes reduces age-related steatosis.•The impact of gene haploinsufficiency is modulated in tetraploid hepatocyte nuclei.•The protective phenotype from polyploidisation relies on non-random selection of wild-type alleles during ageing.