Regulation of Regeneration and Clonal Fitness in Normal and Diseased Liver

The potent regenerative capabilities of planaria, newts, and zebrafish are largely absent in mammals. In humans, impaired regeneration contributes to poor outcomes after acute trauma, tissue damage, or organ transplant, as well as in chronic diseases such as liver cirrhosis, inflammatory bowel disease, and diabetes. A central goal of my thesis is to identify unexpected pathways in tissue repair by establishing and exploiting in vivo forward genetic screening approaches, and two key questions were tackled with these platforms. The first goal was to identify druggable chromatin regulators of regeneration. To facilitate the discovery process, direct in vivo CRISPR knockout and CRISPR activation screening platforms in mouse livers were developed. Among 164 epigenetic regulators, both gain- and loss-of-function screens identified imitation-SWI (ISWI) chromatin remodeling components BAZ2A and BAZ2B. In vivo sgRNA, siRNA, and knockout mouse experiments against either paralog confirmed increased liver regeneration. Two distinct BAZ2 bromodomain inhibitors GSK2801 and BAZ2-ICR also resulted in accelerated liver healing after diverse injuries. Mechanistically, BAZ2 inhibition resulted in an increase in ribosomal biogenesis and protein synthesis by directly regulating the expressions of ribosomal proteins, resulting in an expanded reservoir of ribosomes, which allowed a more rapid cell cycle entry. The second part of the thesis was to understand the functional impact of somatic mutations on tissue regeneration in the context of tissue damage. Through exome and ultra-deep sequencing of 82 human cirrhotic liver samples, functional mutations in PKD1, KMT2D, and ARID1A were identified. Heterozygous deletion of these genes in mice promoted regeneration after liver injuries. The key concept from this work is that chronic injury, and perhaps aging, can select for mutations that promote adaptive or regenerative phenotypes rather than carcinogenesis. Together, these discoveries have established new methods for gene discovery in mammalian tissues, identified new targets for regenerative medicine, and uncovered adaptive mechanisms in chronic tissue injury that do not necessarily drive cancer.