Identification And Mechamism Of Key Regulators Of Cell Proliferation In Liver Regeneration And Liver Cancer Formation

Liver cancer is one of the most common cancers in the world and ranks second in cancer deaths.The liver has an amazing ability to regenerate.After injury or partial hepatectomy,hepatocytes in the resting phase will rapidly enter into the cell cycle and then proliferate.However,when the residual liver arrives to the number of cells in the original liver,the cells enter the G0 phase from the cell cycle.Obviously,cell proliferation is essential in liver cancer formation and liver regeneration,but the proliferation of the former will continue,and the cell proliferation in latter is strictly regulated.Therefore,the difference in gene function between liver regeneration and liver cancer is worth studying.In this study,a series of bioinformatics methods,including time series analysis,weight gene co-expression network analysis(WGCNA),physiological function enrichment,and spatial analysis of functional enrichment(SAFE)were used to analyze the gene expression profile in the regenerative liver after 2/3 hepatectomy and liver cancer caused by hepatitis C.The purpose is to find out the similarities and differences of key genes in liver regeneration and liver cancer formation,and to explore the ways of causing the difference between them.This will shed light on revealing molecular mechanisms that regulate normal cell proliferation and abnormal cell proliferation.The research results of this paper include:1.In the study of liver regeneration,the key genes that determine the proliferation of hepatocytes and their mechanisms of action have been identified.(1)Both the gene co-expression network and the protein-protein interaction network show that the blue module represented by cell proliferation plays a dominant role in liver regeneration.At the same time,the protein interaction network also shows the important role of cyan module,magenta module,green and greenyellow modules in liver regeneration.Through the localization of known genes related to liver regeneration in protein interaction networks,they are mainly mapped to the above modules.In addition,hub-bottlenecks genes are also distributed in the above modules.(2)A ternary regression analysis of gene expression data at 10 time points after liver resection in rats revealed that there is an important turning point in liver regeneration at approximately 45 hours.After hepatectomy in rats,cell proliferation was completed before 72 hours after hepatectomy.Then,the genes related to reconstruction of the extracellular matrix,angiogenesis and lipid metabolism upregulated,which is directly realated to the large demand for energy and cellular components.(3)Mouse phenotypic enrichment analysis of differentially expressed genes revealed that rat liver regeneration was accompanied by brain atrophy and dysplastic organ development,which may be due to redistribution of energy after liver resection.(4)Unreported key genes in liver regeneration were identified,which include Fyn?Polr2c?Impdh2?Cav1?Ran?Cdk2?Hsp90aa1?Rrm1?Insr1?Cdc45?Vim?Nrp1.They regulate the resting hepatocytes enter the cell cycle after hepatectomy by regulating the G1/S checkpoint.(5)The transcription factors including PU1,ELK1,E2F1,E2F4,NRF1,and KTGGYRSGAA_UNKOWNUSF were selected based on the assumption that genes with similar expression patterns are likely to be involved in the same physiological pathway or regulated by the same transcription factorIn the research of hepatocarcinogenesis,key genes which determine the abnormal proliferation of hepatocytes were identified.2.In the study of hepatocarcinogenesis,the key genes that determine the abnormal proliferation of hepatocytes were identified and the mechanism of action was explored.(1)Time-sequence analysis of gene expression profile data of six pathological stages in liver cancer formation revealed that the most significant change in gene expression was dysplasia of nodules to the early stage of liver cancer,that is,the onset of canceration.(2)The genes in brown_c56 module which represented by cell proliferation changed significantly in the formation of hepatocarcinogenesis,followed by the brown_c12 module and the red module.Known liver disease related genes(including cirrhosis,hepatic dysplasia,liver cancer infiltration and metastasis)are mainly concentrated in the above modules.The hubbottlenecks genes were distributed in the cell proliferation module,suggesting that the occurrence and development of liver cancer is most closely related to cell proliferation.(3)At the tumor state,the expression profile of the genes related to fatty acid ?-oxidation and the tricarboxylic acid cycle down-regeulated and suggested that the supply of cellular energy has changed.This may be because the rapid proliferation of tumor cells requires a rapid energy supply or oxygen deficiency caused by rapid proliferation.(4)Unreported key genes in liver caner were identified,which include Unreported key genes in liver regeneration were identified,which include Fyn?Polr2c?Impdh2?Cav1?Ran?Cdk2?Hsp90aa1?Rrm1?Insr1?Cdc45?Vim?Nrp1.They regulate cell cycle by activating G2/M checkpoint.(5)The transcription factors including USF ? MAX ? E2F1,4 ? NRF1 ? YY1 and KTGGYRSGAA_UNKOWN were selected based on the assumption that genes with similar expression patterns are likely to be involved in the same physiological pathway or regulated by the same transcription factor.3.In the study of differences in cell proliferation behavior in liver regeneration and liver cancer,the key genes were identified which regulate the normal proliferation and abnormal proliferation.(1)Comparing the homologous matching results of differential genes in liver regeneration in rat and hepatocarcinogenesis in human by the biomaRt package,it was found that 849 differential genes in rat liver regeneration matched the human homologous genes.During the formation of liver cancer,1047 differential genes matched to 892 homologous genes in rat.There were 104 common genes and 25 human race-specific genes.(2)The overall change trend of differential genes screened during liver regeneration and liver cancer formation is different.In liver regeneration,the transcriptional expression of DEGs returns to the starting point,whereas in liver cancer,it deviates from the starting point.This microcosmic change in expression profile and macroscopic phenotypic changes(hepatic regeneration back to the starting point of liver resection,and the end-stage metastasis of liver cancer)are very consistent.(3)Cell proliferation is the most significant dysregulated process shared by liver regeneration and liver cancer.The pattern of cell proliferation-related gene expression in progression stage during liver regeneration is similar to the transition process from dysplasia to early stage of liver cancer.(4)The proliferation-related key genes in liver regeneration and liver cancer control regulate cell proliferation through different cell cycle checkpoints.In liver regeneration,key genes such as CDC45,CDK2,HSP90AA1,MCM2-3,MCM5-7,NCAPD2,POLD1,RAN,RPA2,RRM1-2,and SUGT1 enable quiescent hepatocytes to re-enter the cell cycle after hepatectomy in rats by regulating G1/S checkpoints.During the liver cancer formation,key genes such as AURKA,BIRC5,CCNA2,CCNB2,CDK1,CENPF,and FOXM1 regulate whether cells enter the mitosis phase by regulating the G2/M checkpoint.(5)Through the comparative analysis of key genes in liver regeneration and hepatocarcinogenesis,key genes such as FYN,XPO1,FOXM1,EZH2,and CENPF were screened out.Among them,FYN is a gene that expresses the opposite expression pattern in liver regeneration(upregulation)and hepatic cancer proliferation(downregulation).It may regulate the process of cell proliferation and apoptosis by combining different upstream factors RTKs and TSP1/CD36 respectively in liver regeneration and liver cancer.The above results indicate that the key regulation point for cell proliferation in liver regeneration is the G1/S checkpoint of the cell cycle.The genes that play a key role are CDC45,CDK2,HSP90AA1,MCM2-3,MCM5-7,NCAPD2,POLD1,RAN,RPA2,RRM1-2,SUGT1,etc.The key regulatory point for cell proliferation in liver cancer formation is the G2/M checkpoint of the cell cycle.The genes that play a key role are AURKA,BIRC5,CCNA2,CCNB2,CDK1,CENPF,FOXM1 and so on.Furthermore,it is speculated that relatively few key genes such as FYN,XPO1,FOXM1,EZH2,CENPF regulate the two different cell proliferation processes in liver regeneration and liver cancer.