Identification of Transcriptional Networks during Liver Regeneration

Abstract

The molecular analysis of mammalian cellular proliferation in vivo is limited in most organ systems by the low turnover and/or the asynchronous nature of cell cycle progression. A notable exception is the partial hepatectomy model, in which quiescent hepatocytes reenter the cell cycle and progress in a synchronous fashion. Here we have exploited this model to identify regulatory networks operative in the mammalian cell cycle. We performed microarray-based expression profiling on livers 0 -40 h post-hepatectomy corresponding to G 0 , G 1 , and S phases. Differentially expressed genes were identified using the statistical analysis program PaGE (Patterns from Gene Expression), which was highly accurate as confirmed by quantitative reverse transcription-PCR of randomly selected targets. A shift in the transcriptional program from genes involved in lipid and hormone biosynthesis in the quiescent liver to those contributing to cytoskeleton assembly and DNA synthesis in the proliferating liver was demonstrated by biological theme analysis. In a novel approach, we employed computational pathway analysis tools to identify specific regulatory networks operative at various stages of the cell cycle. This allowed us to identify a large cluster of genes controlling mitotic spindle assembly and checkpoint control at the 40-h time point as regulated at the mRNA level in vivo.

Liver growth in the embryo and during liver regeneration in zebrafish requires the cell cycle regulator, uhrf1

“…Ccne expression peaks at 24 h in zebrafish regenerating livers and at 40 h in mice. Transcription of TOP2A is directly regulated by UHRF1 (23,28), and Top2a is up-regulated during mouse liver regeneration (38) with the same kinetics that we observe for Uhrf1. To determine whether heterozygous mutation of uhrf1 hinders its capacity to activate top2a during liver regeneration, we used Q-PCR to compare its expression in livers from uhrf1 ϩ/ϩ and uhrf1 ϩ/Ϫ zebrafish at the peak time of uhrf1 expression after PH (36 h).…”

“…UHRF1 directly activates TOP2A transcription in vitro (25,27,28), and Top2a up-regulation after PH has been reported in mice (38,44) and, shown here, in zebrafish. Interestingly, top2a expression after PH in zebrafish requires uhrf1, providing an in vivo example of this relationship and suggests a mechanism by which uhrf1 mutation hampers liver regeneration.…”

Overexpression of regenerating islet-derived 1 alpha and 3 alpha genes in human primary liver tumors with β-catenin mutations

“…Indeed, it has been reported that the overexpression of the mouse ortholog of REG1A under the rat glucagon promoter led to the development of rare tumors, including HCCs, in transgenic mice consistent with tumor-promoting activity (Yamaoka et al, 2000). Furthermore, REG1A and REG3A have recently been found overexpressed during rodent liver regeneration after hepatectomy (White et al, 2005). The REG proteins are associated with inflammation and regenerative processes and therefore we searched for an association between REG expression and clinicopathological features, chronic viral infection or alcohol abuse, but no statistically significant correlation was found.…”

Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation

“…Genes such as Igfbp1, LCN2, and Saa2 are upregulated, whereas Car3, Serpina6, and Cyp2f2 are down-regulated ( Fig. 1C,D ;Togo et al 2004;White et al 2005).…”

“…These programs include hormone biosynthesis, lipid and amino acid metabolisms, and nucleotide biosynthesis. The transcription network revealed by microarray expression profiling during hepatocyte regeneration indicated that Igfbp1, LCN2, and Saa2 increase but, in contrast, Car3, Serpina6 (also called CBG; corticosteroid-binding globulin), and Cyp2f2 are manifestly decreased ∼12 h after hepatectomy (Togo et al 2004;White et al 2005). These genes are also important for hepatic regeneration, in terms of homeostasis and hepatic metabolism.…”