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Expressed genes in regenerating rat liver after partial hepatectomy

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World Journal of Gastroenterology 2005年第19期11卷 2932-2940页

作者： Cun-ShuanXu Cui-FangChang Jin-YunYuan Wen-QiangLi Hong-PengHan Ke-JinYang Li-FengZhao Yu-ChangLi Hui-YongZhang SalmanRahman Jing-BoZhang CollegeofLifeScience HenanNormalUniversityXinxiang453007HenanProvinceChina KeyLaboratoryforCellDifferentiationRegulation Xinxiang453007HenanProvinceChina HomophiliaResearchCenter LondonUniversityLondonSE17EHUK

AIM: To reveal the liver regeneration (LR) and its controlas well as the occurrence of liver disease and to study the gene expression profiles of 551 genes after partial hepatectomy (PH) in regenerating rat ***: Five hundred and fifty-one expressed sequence tags screened by suppression subtractive hybridization were made into an in-house cDNA microarray, and the expressive genes and their expressive profiles in regenerating rat livers were analyzed by microarray and bioinformatics. RESULTS: Three hundred of the analyzed 551 genes were up- or downregulated more than twofolds at one or more time points during LR. Most of the genes were up- or downregulated 2-5 folds, but the highest reached 90 folds of the control. One hundred and thirty-nine of themshowed upregulation, 135 displayed downregulation, and up or down expression of 26 genes revealed a dependence on regenerating livers. The genes expressedin 24-h regenerating livers were much more than those in the others. Cluster analysis and generalization analysis showed that there were at least six distinct temporal patterns of gene expression in the regenerating livers, that is, genes were expressed in the immediate early phase, early phase, intermediate phase, early-late phase, late phase, terminal phase. CONCLUSION: In LR, the number of down-regulated genes was almost similar to that of the upregulated genes; the successively altered genes were more than the rapidly transient genes. The temporal patterns of gene expression were similar 2 and 4 h, 12 and 16 h, 48 and 96 h, 72 and 144 h after PH. Microarray combined with suppressive subtractive hybridization can effectively identify the genes related to LR.

关键词： Subtracted cDNA libraries Complementary DNA microarray Liver regeneration Partial hepatectomy Cluster analysis

Expression patterns and action analysis of genes associated with drug-induced liver diseases during rat liver regeneration

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World Journal of Gastroenterology 2006年第43期12卷 6966-6972页

作者： Qian-Ji Ning Shao-Wei Qin Cun-Shuan Xu College of Life Science HenanNormal University Xinxiang 453007 Henan Province China Key Laboratory for Cell Differentiation Regulation Xinxiang 453007 Henan Province China

AIM: To study the action of the genes associated with drug-induced liver diseases at the gene transcriptional level during liver regeneration (LR) in rats. METHODS: The genes associated with drug-induced liver diseases were obtained by collecting the data from databases and literature, and the gene expression changes in the regenerating liver were checked by the Rat Geno.e 230 2.0 array. RESULTS: The initial and total expression numbers of genes occurring in phases of 0.5-4 h after partial hepatectomy (PH), 4-6 h after PH (G0/G1 transition), 6-66 h after PH (cell proliferation), 66-168 h after PH (cell differentiation and structure-function reconstruction) were 21, 3, 9, 2 and 21, 9, 19, 18, respectively. It is illustrated that the associated genes were mainly triggered at the initial stage of LR and worked at different phases. According to their expression similarity, these genes were classified into 5 types: only up- regulated (12 genes), predominantly up-regulated (4 genes), only down-regulated (11 genes), predominantly down-regulated (3 genes), and approximately up-/ down-regulated (2 genes). The total times of their up- and down-expression were 130 and 79, respectively, demonstrating that expression of most of the genes was increased during LR, while a few decreased. The cell physiological and biochemical activities during LR were staggered according to the time relevance and were diverse and complicated in gene expression patterns. CONCLUSION: Drug metabolic capacity in regenerating liver was enhanced. Thirty-two genes play important roles during liver regeneration in rats.

关键词： Partial hepatectomy Rat Geno.e 230 2.0array Drug-induced liver diseases Genes associatedwith liver regeneration

Expression pattern and action analysis of genes associated with the responses to chemical stimuli during rat liver regeneration

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World Journal of Gastroenterology 2006年第45期12卷 7285-729 1页

作者： Shao-Wei Qin Li-Feng Zhao Xiao-Guang Chen Cun-Shuan Xu Key Laboratory for Cell Differentiation Regulation Xinxiang 453007 Henan Province China College of Life Science Henan Normal University Xinxiang 453007 Henan Province China

AIM: To study the genes associated with the responses to chemokines, nutrients, ino.ganic substances, organic substances and xeno.iotics after rat partial hepatectomy (PH) at transcriptional level. METHODS: The associated genes involved in the five kinds of responses were obtained from database and literature, and the gene expression changes during liver regeneration in rats were checked by the Rat Geno.e 230 2.0 array. RESULTS: It was found that 60, 10, 9, 6, 26 genes respectively participating in the above five kinds of responses were associated with liver regeneration. The numbers of initially and totally expressed genes occurring in the initial phase of liver regeneration (0.5-4 h after PH), G0/G1 transition (4-6 h after PH), cell proliferation (6-66 h after PH), cell differentiation and structure- functional reconstruction (66-168 h after PH) were 51, 19, 52, 6 and 51, 43, 98, 68 respectively, illustrating that the associated genes were mainly triggered in the initiation and transition stages, and functioned at different phases. According to their expression similarity, these genes were classified into 5 groups: only up- regulated (47), predominantly up-regulated (18), only down-regulated (24), predominantly down-regulated (10), and up- and down-regulated (8). The total times of their up-regulated and down-regulated expression were 441 and 221, demonstrating that the number of up- regulated genes is more than that of the down-regulated genes. Their time relevance and gene expression patterns were classifi ed into 14 and 26 groups, showing that the cell physiological and biochemical activitieswere staggered, diversifi ed and complicated during liver regeneration in rats. CONCLUSION: The chemotaxis was enhanced mainly in the forepart and metaphase of LR. The response of regenerating liver to nutrients and chemical substances was increased, whereas that to xeno.iotics was no. strong. One hundred and seven genes associated with LR play important roles in the respon

关键词： Partial hepatectomy Rat Geno.e 230 2.0 array Responses to chemical substances Genes associated with liver regeneration

Expression patterns and action analysis of genes associated with physiological responses during rat liver regeneration:Cellular immune response

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World Journal of Gastroenterology 2006年第46期12卷 7514-7521页

作者： Lian-Xing Zhang Li-Feng Zhao An-Shi Zhang Xiao-Guang Chen Cun-Shuan Xu College of Life Science Henan Normal University Xinxiang 453007 Henan ProvinceChina Key Laboratory for Cell Differentiation Regulation Xinxiang 453007Henan Province China

AIM： To study the cellular immune response during rat liver regeneration （LR） at a transcriptional level. METHODS： Genes associated with the cellular immune response were obtained by collecting the data from databases and retrieving articles. Gene expression changes during LR were detected by rat geno.e 230 2.0 array. RESULTS： A total of 127 genes were found to be associated with LR. The number of initially and totally expressing genes in the initial phase of LR [0.5-4 h after partial hepatectomy （PH）], transition from Go-G, （4-6 h after PH）, cell proliferation （6-66 h after PH）, cell differentiation and structure-function reconstruction （66-168 h after PH） was 54, 11, 34, 3 and 54, 49, 70, 49 respectively, illustrating that the associated genes were mainly triggered at the initiation of LR, and worked at different phases. According to their expression similarity, these genes were classified into 41 up-regulated, 21 predominantly up-regulated, 41 down-regulated, 14 predominantly down-regulated, 10 similarly up-regulated and down-regulated genes, respectively. The total up- and down-regulated expression times were 419 and 274, respectively, demonstrating that the expression of most genes was increased while the expression of a small number of genes was decreased. Their time relevance was classified into 14 groups, showing that the cellular physiological and biochemical activities were staggered during LR. According to the gene expression patterns, they were classified into 21 types, showing the activities were diverse and complicated during LR.CONCLUSION： Antigen processing and presentation are enhanced mainly in the forepart, prophase and anaphase of LR. T-cell activation and antigen elimination are enhanced mainly in the forepart and prophase of LR. A total of 127 genes associated with LR play an important role in cellular immunity.

关键词： Partial hepatectomy Rat geno.e 230 2.0array Cellular immune response Genes associated with liver regeneration

Expression patterns and action analysis of genes associated with blood coagulation responses during rat liver regeneration

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World Journal of Gastroenterology 2006年第42期12卷 6842-6849页

作者： Li-Feng Zhao Wei-Min Zhang Cun-Shuan Xu Faculty of Life Science and Techno.ogy Ocean University of China Qingdao 260003 Shandong Province China College of Life Science Henan Normal University Xinxiang 453007 Henan Province China Key Laboratory for Cell Differentiation Regulation Xinxiang 453007 Henan Province China

AIM: To study the blood coagulation response after partial hepatectomy (PH) at transcriptional level. METHODS: After PH of rats, the associated genes with blood coagulation were obtained through reference to the databases, and the gene expression changes in rat regenerating liver were analyzed by the Rat Geno.e 230 2.0 array. RESULTS: It was found that 107 genes were associated with liver regeneration. The initially and totally expressing gene numbers occurring in initiation phase of liver regeneration (0.5-4 h after PH), G0/G1 transition (4-6 h after PH), cell proliferation (6-66 h after PH), cell differentiation and structure-function reconstruction (66-168 h after PH) were 44, 11, 58, 7 and 44, 33, 100, 71 respectively, showing that the associated genes were mainly triggered in the forepart and prophase, and worked at different phases. According to their expression similarity, these genes were classified into 5 groups: only up-, predominantly up-, only down-, predominantly down-, up- and down-regulation, involving 44, 8, 36, 13 and 6 genes, respectively, and the total times of their up- and down-regulation expression were 342 and 253, respectively, demonstrating that the number of the up-regulated genes was more than that of the down- regulated genes. Their time relevance was classified into 15 groups, showing that the cellular physiological and biochemical activities were staggered during liver regeneration. According to gene expression patterns, they were classified into 29 types, suggesting that their protein activities were diverse and complex during liver ***: The blood coagulation response is enhanced mainly in the forepart, prophase and anaphase of liver regeneration, in which the response in the forepart, prophase of liver regeneration can prevent the bleeding caused by partial hepatectomy, whereas that in the anaphase contributes to the structure-function reorganization of regenerating liver. In the process, 107 genes associated with

关键词： Partial hepatectomy Rat Geno.e 230 2.0 array Blood coagulation response Genes associated with liver regeneration

Expression patterns and action analysis of genes associated with physiological responses during rat liver regeneration:Innate immune response

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World Journal of Gastroenterology 2006年第48期12卷 7852-7858页

作者： Guang-Wen Chen Ming-Zhen Zhang Li-Feng Zhao Cun-Shuan Xu College of Life Science Lanzhou University Lanzhou 730000 Gansu Province China College of Life Science Henan Normal University Xinxiang 45300 Henan Province China Key Laboratory for Cell Differentiation Regulation Xinxiang 453007 Henan Province China

AIM： To study the relationship between innate immune response and liver regeneration （LR） at transcriptional level.METHODS： Genes associated with innate immunity response were obtained by collecting the data from databases and retrieving articles, Gene expression changes in rat regenerating liver were detected by rat geno.e 230 2.0 array.RESULTS： A total of 85 genes were found to be associated with LR. The initially and totally expressed number of genes at the phases of initiation [0.5-4 h after partial hepatectomy （PH）], transition from GO to G1 （4-6 h after PH）, cell proliferation （6-66 h after PH）, cell differentiation and structure-function reconstruction （66-168 h after PH） was 36, 9, 47, 4 and 36, 26, 78, 50, respectively, illustrating that the associated genes were mainly triggered at the initial phase of LR and worked at different phases. According to their expression similarity, these genes were classified into 5 types： 41 up-regulated, 4 predominantly up-regulated, 26 downregulated, 6 predominantly down-regulated, and 8 approximately up/down-regulated genes, respectively. The expression of these genes was up-regulated 350 times and down-regulated 129 times respectively, demonstrating that the expression of most genes was enhanced while the expression of a small number of genes was decreased during LR. Their time relevance was classified into 14 groups, showing that the cellular physiological and biochemical activities dudng LR were staggered. According to the gene expression patterns,they were classified into 28 types, indicating that the cellular physiological and biochemical activities were diverse and complicated during LR. CONCLUSION： Congenital cellular immunity is enhanced mainly in the forepart, prophase and anaphase of LR while congenital molecular immunity is increased dominantly in the forepart and anaphase of LR. A total of 85 genes associated with LR play an important role in innate immunity.

关键词： Partial hepatectomy Rat geno.e 230 2.0 array Innate immune response Genes associated with liver regeneration

Expression patterns and action analysis of genes associated with hepatitis virus infection during rat liver regeneration

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World Journal of Gastroenterology 2006年第47期12卷 7626-7634页

作者： Li-Juan Su Guang-Wei Ding Zhi-Li Yang Shou-Bing Zhang Yu-Xiu Yang Cun-Shuan Xu Faculty of Life Science and Techno.ogy Ocean University of China Qingdao 260003 Shandong Province China College of Life Science Henan Normal University Xinxiang 453007 Henan Province China Key Laboratory for Cell Differentiation Regulation Xinxiang 453007 Henan Province China

AIM： To study the action of hepatitis virus infectionassociated genes at transcription level during liver regeneration （LR）. METHODS： Hepatitis virus infection-associated genes were obtained by collecting the data from databases and retrieving the correlated articles, and their expression changes in the regenerating rat liver were detected with the rat geno.e 230 2.0 array. RESULTS： Eighty-eight genes were found to be associated with liver regeneration. The number of genes initially and totally expressed during initial LR [0.5-4 h affer partial hepatectomy （PH）], transition from （30 to G1 （4-6 h affer PH）, cell proliferation （6-66 h after PH）, cell differentiation and reorganization of structurefunction （66-168 h after PH） was 37, 8, 48, 3 and 37, 26, 80, 57, respectively, indicating that the genes were mainly triggered at the early stage of LR （0.5-4 h after PH）, and worked at different phases. These genes were classified into 5 types according to their expression similarity, namely 37 up-regulated, 9 predominantly upregulated, 34 down-regulated, 6 predominantly downregulated and 2 up/down-regulated genes. Their total up- and down-regulation frequencies were 359 and 149 during LR, indicating that the expression of most genes was enhanced, while the expression of a small number of genes was attenuated during LR. According to time relevance, they were classified into 12 groups （0.5 and 1h, 2 and 4h, 6h, 8 and 12h, 16 and 96h, 18 and 24 h, 30 and 42 h, 36 and 48 h, 54 and 60 h, 66 and 72 h, 120 and 144 h, 168 h）, demonstrating that the cellular physiological and biochemical activities during LR were fluctuated. According to expression changes of the genes, their expression patterns were classified into 23 types, suggesting that the cellular physiological and biochemical activities during LR were diverse and complicated. CONCLUSION： The anti-virus infection capacity of regenerating liver can be enhanced and 88 genes play an important role in LR.

关键词： Partial hepatectomy Rat geno.e 230 2.0 array Hepatitis virus infection Genes associated with liver regeneration

Expression patterns and action analysis of genes associated with inflammatory responses during rat liver regeneration

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World Journal of Gastroenterology 2007年第3期13卷 369-377页

作者： Heng-Yi Shao Li-Feng Zhao Cun-Shuan Xu College of Life Science Henan Normal University Xinxiang 453007 Henan Province China Key Laboratory for Cell Differentiation Regulation Xinxiang 453007 Henan Province China

AIM： To study the relationship between inflammatory response and liver regeneration （LR） at transcriptional level.METHODS： After partial hepatectomy （PH） of rats, the genes associated with inflammatory response were obtained according to the databases, and the gene expression changes during LR were checked by the Rat Geno.e 230 2.0 army. RESULTS： Two hundred and thirty-nine genes were associated with liver regeneration. The initial and total expressing gene numbers found in initiation phase （0.5-4 h after PH）, G0/G1 transition （4-6 h after PH）, cell proliferation （6-66 h after PH）, cell differentiation and structure-function reconstruction （66-168 h after PH） of liver regeneration were 107, 34, 126, 6 and 107, 92, 233, 145 respectively, showing that the associated genes were mainly triggered at the beginning of liver regeneration, and worked at different phases. According to their expression similarity, these genes were classified into 5 groups： only up-regulated, predominantly up-, only down-, predominantly down-, up- and down-, involving 92, 25, 77, 14 and 31 genes, respectively. The total times of their up- and down-regulated expression were 975 and 494, respectively, demonstrating that the expressions of the majority of genes were increased, and that of a few genes were decreased. Their time relevance was classified into 13 groups, showing that the cellular physiological and biochemical activities were staggered during liver regeneration. According to gene expression patterns, they were classified into 33 types, suggesting that the activities were diverse and complex during liver regeneration. CONCLUSION： Inflammatory response is closelyassociated with liver regeneration, in which 239 LR- associated genes play an important role.

关键词： Partial hepatectomy Rat Geno.e 230 2.0array Inflammatory response Genes associated with liver regeneration

Identification of expressed genes in regenerating rat liver in 0-4-8-12 h short interval successive partial hepatectomy

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World Journal of Gastroenterology 2005年第15期11卷 2296-2305页

作者： Cun-ShuanXu Jin-YunYuan Wen-QiangLi Hong-PengHan Ke-JinYang Cui-FangChang Li-FengZhao Yu-ChangLi Hui-YongZhang SalmanRahman Jing-BoZhang CollegeofLifeScience HenanNormalUniversityXinxiang453002HenanProvinceChina StateKeyLaboratoryofCellDifferentiationandRegulationo.HenanProvinceandMinistry Xinxiang453002HenanProvinceChina HomophiliaResearchCenter LondonUniversityLondonSE17EHUK

AIM: To identify the genes differentially expressed in the regenerating rat liver of 0-4-8-12 h short interval successive partial hepatectomy (SISPH) and to analyze their expression ***: Five hundred and fifty-one elements screened from subtractive cDNA libraries were made into a cDNA microarray (cDNA chip). Extensive gene expression analysis following 0-4-8-12 h SISPH was conducted by ***: One hundred and eighty-three elements were selected, which were either up- or down-regulated more than 2-fold at one or more time points after SISPH. Cluster analysis and generalization analysis showed that there were five distinct temporal patterns of gene ***-six genes were unreported, associated with liver regeneration (LR).CONCLUSION: Microarray analysis shows that the down regulated genes are much more than the up-regulated ones in SISPH; the numbers of genes expressed consistently are fewer than that expressed immediately; the genes expressed in high abundance are much fewer than that increased 2-5-fold. The comparison of SISPH with partial hepatectomy (PH) shows that the expression trends of most genes in SISPH and in PH are similar,but the expression of 43 genes is specifically altered in SISPH.

关键词： SISPH Liver regeneration