Expression profiles of the genes associated with metabolism and transport of amino acids and their derivatives in rat liver regeneration

Summary. Amino acids (AA) are components of protein and precursors of many important biological molecules. To address effects of the genes associated with metabolism and transport of AA and their derivatives during rat liver regeneration (LR), we firstly obtained the above genes by collecting databases data and retrieving related thesis, and then analyzed their expression profiles during LR using Rat Genome 230 2.0 array. The LR-associated genes were identified by comparing the gene expression difference between partial hepatectomy (PH) and sham-operation (SO) rat livers. It was approved that 134 genes associated with metabolism of AA and their derivatives and 26 genes involved in transport of them were LR-associated. The initially and totally expressing number of these genes occurring in initial phase of LR (0.5–4 h after PH), G0/G1 (4–6 h after PH), cell proliferation (6–66 h after PH), cell differentiation and structure-function reconstruction of liver tissue (72–168 h after PH) were respectively 76, 17, 79, 5 and 162, 89, 564, 195, illustrating that these LR-associated genes were initially expressed mainly in initial stage, and functioned in different phases. Frequencies of up-regulation and down-regulation of them being separately 564 and 357 demonstrated that genes up-regulated outnumbered those down-regulated. Categorization of their expression patterns into 22 types implied the diversity of cell physiological and biochemical activities. According to expression changes and patterns of the above-mentioned genes in LR, it was presumed that histidine biosynthesis in the metaphase and anaphase, valine metabolism in the anaphase, and metabolism of glutamate, glutamine, asparate, asparagine, methionine, alanine, leucine and aromatic amino acid almost were enhanced in the whole LR; as for amino acid derivatives, transport of neutral amino acids, urea, γ-aminobutyric acid, betaine and taurine, metabolism of dopamine, heme, S-adenosylmethionine, thyroxine, and biosynthesis of hydroxyproline, nitric oxide, orinithine, polyamine, carnitine, selenocysteine were augmented during the entire liver restoration. Above results showed that metabolism and transport of AA and their derivates were necessary in liver regeneration. Authors’ address: Prof. Dr. C. S. Xu, College of Life Science, No. 46, Jianshe RD, Henan, Xinxiang 453007, China     

Identification and characterization of 177 unreported genes associated with liver regeneration

The mammalian liver has a very strong regeneration capacity after partial hepatectomy (PH). To further learn the genes participating in the liver regeneration (LR), 551 cDNAs selected from subtracted cDNA libraries of the regenerating rat liver were screened by microarray, and their expression profiles were studied by cluster and generalization analyses. Among them, 177 genes were identified unreported and up-or down-regulated more than twofold at one or more time points after PH, of which 62 genes were down-regulated to less than 0.5; 99 genes were up-regulated to 2-10 folds, and 16 genes were either up- or down-regulated at different time points during LR. By using BLAST and GENSCAN, these genes were located on responsible chromosomes with 131 genes on the long arms of the chromosomes. The cluster and generalization analyses showed that the gene expression profiles are similar in 2 and 4, 12 and 16, 96 and 144 h respectively after PH, suggesting that the actions of the genes expressed in the same profiles are similar, and those expressed in different profiles have less similarity. However, the types,characteristics and functions of the 177 genes remain to be further studied.     

Large scale of identification of differentially expressed genes in the regenerating rat liver after SISPH

Extensive gene expression analysis was carried out after a 0, 4, 36, 72, 96 h short interval successive partial hepatectomy (SISPH) was performed. A total of 185 elements were identified as differing by more than two-fold in their expression levels at one or more time points. Of these 185 elements, 103 were up-regulated, 82 were down-regulated and 86 elements were unreported genes. Quite a few genes were previously unknown to be involved in liver regeneration (LR). Using cluster and general analysis, we found that the genes at five time points of the SISPH share eight different types of different expression profiles and eight distinct temporal induction or suppression patterns. A comparison of the gene expression in SISPH with that after PH found that 41 genes were specifically altered in SISPH, and 144 genes were simultaneously up-regulated or down-regulated in SISPH and after PH, but they were present in different amounts at the different time points. The conclusions are that (i) microarrays combined with suppressive subtractive hybridization (SSH) can effectively identify genes involved in LR on a large scale; (ii) more genes were up-regulated than down-regulated; (iii) there are fewer abundantly expressed genes than those with increased levels of 2–5 fold.     

Gene expression profiling reveals the mechanism and pathophysiology of mouse liver regeneration

Comprehensive analysis of the changes in gene expression during liver regeneration was carried out by using an in-house microarray composed of 2,304 distinct mouse liver cDNA clones. Mice were subjected to partial two-thirds hepatectomy, and changes in mRNA levels were monitored up to 48 h. Of the 2,304 genes analyzed, 496 genes showed expression levels measurable at all time points after the partial hepatectomy. 317 genes were up- or down-regulated 2-fold or more at least at one time point during liver regeneration and were classified into eight clusters based on their expression patterns. With a more stringent cut-off value of +/-2 S.D., 68 genes were listed and were classified into five clusters. In these two analyses with different clustering criteria, functionally categorized genes showed similar cluster distributions. Genes involved in protein synthesis and posttranslational processing were significantly enriched in the cluster characterized by rapid gene activation and subsequent persistence. This suggests the importance of modulating the efficiency of protein supply and/or altering the composition of protein population from the early phase of hepatocyte proliferation. Genes for two major liver functions, i.e. plasma protein secretion and intermediate metabolism were enriched in distinct clusters exhibiting the features of gradual gene activation and sustained repression, respectively. Therefore, these genes are differentially regulated during the regeneration, possibly leading to changes in the flow of amino acids and energy from enzyme proteins to plasma proteins in their synthesis. Thus, clustering analysis of expression patterns of functionally classified genes gave insights into mechanism and pathophysiology of liver regeneration.     

Large scale of identification of differentially expressed genes in the regenerating rat liver after SISPH

After partial hepatectomy (PH), the remnant paren-chyma can completely recover lost liver mass and function in about one week[1,2]. Although adult hepa-tocytes are normally quiescent, they are readily primed to pass from G0 to G1 phase within 2―6 h after PH. The first peak of DNA synthesis appears 24 h after PH, while cell division peaks at 36 h. The liver cells then enter a second cell cycle, and redifferentiation and reconstruction of structure and function[3―6] take place. A great nu…     

Rat Hepatocytes Weighted Gene Co-Expression Network Analysis Identifies Specific Modules and Hub Genes Related to Liver Regeneration after Partial Hepatectomy

The recovery of liver mass is mainly mediated by proliferation of hepatocytes after 2/3 partial hepatectomy (PH) in rats. Studying the gene expression profiles of hepatocytes after 2/3 PH will be helpful to investigate the molecular mechanisms of liver regeneration (LR). We report here the first application of weighted gene co-expression network analysis (WGCNA) to analyze the biological implications of gene expression changes associated with LR. WGCNA identifies 12 specific gene modules and some hub genes from hepatocytes genome-scale microarray data in rat LR. The results suggest that upregulated MCM5 may promote hepatocytes proliferation during LR; BCL3 may play an important role by activating or inhibiting NF-kB pathway; MAPK9 may play a permissible role in DNA replication by p38 MAPK inactivation in hepatocytes proliferation stage. Thus, WGCNA can provide novel insight into understanding the molecular mechanisms of LR.     

Comparative analysis of gene expression profiles of acute hepatic failure and that of liver regeneration in rat

To explore the relevance of rat liver regeneration (LR) to acute hepatic failure (AHF), Rat Genome 230 2.0 Array was used to detect their gene expression profiles in this study, and the reliability of the detection results was confirmed by real-time-PCR. 1012 genes were found to be significantly changed in AHF occurrence and 948 genes in LR. Hierarchical clustering analysis showed that physiological activities of AHF and those of LR had no time correlation. Hierarchical clustering analysis (which is performed to group genes based on the similarity of expression patterns) showed that physiological activities of AHF and those of LR had no time correlation. K-means clustering analysis (which is used to check the difference in the relevant predictor variables between different groups is significant or not) demonstrated that gene expression trend of C1 group (genes relate to categories of stimulus–response and cell apoptosis, etc.) in AHF and in LR was extremely similar, that those of their C2 group (categories of regulation of homeostasis and hormone stimulation, etc.) were contrary, and that those of their C3 (material and energy metabolism and oxidation reduction, etc.), C4 (Cell cycle-related genes) and C5 (cell proliferation-related genes) groups were also similar with the gene expression changes of LR more abundant. GO classifications and functional clustering analysis (which was used to statistics the numbers or composition of proteins or genes at a function level) revealed that cellular processes including immune response, inflammatory reaction, cell migration and adhesion, etc. were increased both in AHF and in LR, whereas material and energy metabolism were decreased. Of them, stimulus response, inflammatory reaction and regulation of apoptosis, etc. were stronger in AHF occurrence than in LR, but ion homeostasis, hormonal response, regulation of cell division and proliferation, etc. were weaker in AHF occurrence. Gene expression changes and physiological activities of AHF and those of LR not only have similarities but also differences.     

脂肪细胞分化相关基因在大鼠再生肝中表达变化

肝脏由多种细胞构成,肝再生与细胞分化密切相关,细胞分化受基因转录水平调控。为在基因转录水平了解脂肪细胞分化基因在大鼠肝再生中作用,本文用搜集网站资料和查阅相关论文等方法获得上述基因,用Rat Genome2302.0芯片检测它们在大鼠肝再生(liver regeneration,LR)中表达情况,将三次检验结果相同或相似、在肝再生中表达变化2倍以上、真手术组和假手术组相比差异显著的基因视为肝再生相关基因。初步证实上述基因中75个基因与肝再生相关。肝再生启动(PH后0.5-4h)、G0/G1过渡(PH后4-6h)、细胞增殖(PH后6-66h)、细胞分化和组织结构功能重建(PH后72-168h)等四个阶段起始表达的基因数为44、13、30和1;基因的总表达次数为88、58、302和90。表明相关基因主要在肝再生启动阶段起始表达,在不同阶段发挥作用。它们共表达上调313次、下调167次,分为43种表达方式。表明肝再生中脂肪细胞发生和分化相关基因活动多样和复杂。根据本文研究结果推测,上述基因不仅调节脂肪细胞分化,而且参与肝再生的生理生化活动。     

蛋白质代谢、折叠、运输、定位、装配相关基因在大鼠肝再生中表达变化

为在基因转录水平了解蛋白质代谢、折叠、运输、定位、装配相关基因在大鼠肝再生中表达情况和作用,本文用搜集网站资料和查阅相关论文等方法获得上述基因,用Rat Genome 2302.0芯片检测它们在大鼠再生肝中表达情况,用真、假手术比较方法确定肝再生相关基因。初步证实上述基因中1147个基因与肝再生相关。其中,参与蛋白质代谢、折叠、运输、定位和装配的基因以上调表达为主;参与蛋白质代谢的基因主要在部分肝切除（partial hepatectomy,PH）后0.5-1h和16-30h起始表达;0.5-12h表达的促进蛋白降解基因数多于促进蛋白积累基因数,而16-48h表达的促进蛋白质积累基因数显著多于促进蛋白质降解基因数;蛋白质合成相关基因在肝再生的16、24、42和66h表达上调较多,在42h最多;几乎在整个肝再生中蛋白质降解相关基因表达上调,在早、前期较多,在后期较少;蛋白质折叠相关基因在2、16-24、42、66、72和168h表达上调较多,在66h最多;蛋白质运输和定位相关基因在整个肝再生中表达上调,在66h表达上调最多;蛋白质装配相关基因在96h前均表达上调,其中,12h表达上调基因最多。根据上述结果推测,在肝再生中期蛋白质合成旺盛,几乎整个肝再生中蛋白质降解、折叠、运输定位和装配活动活跃。     

细胞外基质相关基因在大鼠肝再生中表达模式分析

细胞外基质具有维持细胞极性、调节细胞粘附、增殖、组织器官形态、发生、分化等功能。为了进一步在基因转录水平了解细胞外基质在大鼠肝再生中变化和作用, 用搜集网站资料和查阅相关论文等方法获得细胞外基质基因, 用Rat Genome 230 2.0芯片检测它们在大鼠再生肝中表达情况, 用真、假手术比较方法确定肝再生相关基因。初步证实上述97个基因与肝再生相关。其中, 肝再生启动(部分肝切除(parital hepatectomy, PH)后0.5~4 h)、G0/G1过渡(PH后4~6 h)、细胞增殖(PH后6~66 h)、细胞分化和组织结构功能重建(PH后72~168 h)等4个阶段起始表达的基因数为49、19、73、5, 基因总表达的次数为84、51、369、144, 表明相关基因主要在肝再生启动阶段起始表达, 在不同阶段发挥作用。它们表达的相似性分为均上调、上调占优势、均下调、下调占优势、上调和下调相近等5类, 涉及38、21、21、10和7个基因, 共上调411次, 下调186次, 分为24种表达模式, 表明肝再生中细胞生理生化活动具有阶段性、多样性和复杂性。根据细胞外基质相关基因在肝再生中表达变化推测, 肝再生前期纤粘连蛋白形成相关基因表达增强, 肝再生中期胶原形成相关基因表达增强。