抗Thy-1肾炎模型基因表达谱和蛋白质表达谱研究
|
摘要
背景与目的：
系膜增殖是慢性肾小球肾炎常见的病理表现,由于发病机制不清,缺乏有效的治疗措施。抗Thy-1肾炎模型是经典的系膜增殖性肾炎模型,主要表现为可逆的系膜细胞增殖。本研究通过分析抗Thy-1肾炎模型不同时间点肾脏的基因表达谱和蛋白质表达谱,筛选与系膜增殖相关的基因和蛋白质,为系膜增殖性肾炎的发病机制及其干预措施的研究提供候选基因和干预靶点。
材料和方法：
1、模型的制备：200g健康雄性Wistar大鼠,随机分为对照组(6只)和模型组(30只)。对照组尾静脉注射生理盐水,模型组一次性尾静脉注射抗Thy-1抗体(2.5mg/kg),制备抗Thy-1肾炎模型,分别于0d(对照组)、3d、5d、7d、10d、14d(均为模型组,分别代表抗体注射后第3、5、7、10、14天)处死大鼠。
2、基因表达谱分析：提取肾脏皮质RNA,利用Affymetrix U230 2.0芯片(包含31000个探针位点,代表28000个大鼠基因),分析各时间点大鼠的基因表达谱。利用SAM软件进行数据处理,得到模型组各时间点与对照组比较的差异表达基因；利用Cluster3.0软件对差异表达基因和其中的转录相关基因进行系统聚类分析；利用Gominer软件和MAS系统分别进行基因的生物进程和分子功能分析；利用KEGG数据库分析分子通路变化；用定量PCR对TIMP-1、CCL2、S100A4、KLF15、MXI1进行验证。
3、蛋白质组学分析：提取大鼠肾小球蛋白质,采用Cy2、Cy3、Cy5分别标记各样本。24cm pH3-11 NL strip和12.5%聚丙烯酰胺凝胶进行双相分离,利用Decyder软件进行数据处理和统计学分析；从制备胶中切取差异表达蛋白质点,利用飞行时间质谱和液质联用方法鉴定差异表达蛋白质,然后进行系统聚类分析。Western blot验证FHL2、NIT2蛋白质的表达。
结果：
1、抗Thy-1肾炎模型的病理改变和血、尿检测：(1)大鼠肾组织病理改变：模型肾脏在3d时出现系膜溶解,5d时出现系膜增殖,7d时出现重度的系膜细胞增殖和细胞外基质积聚,10d系膜增殖开始消退,14d系膜增殖显著消退。(2)24hr尿蛋白定量：模型组大鼠3d、5d、7d、10d尿蛋白定量显著高于对照组,其中3d是高峰；(3)血肌酐和尿素氮：模型组大鼠5d和7d血肌酐和尿素氮显著高于对照组,其中7d是高峰。
2、抗Thy-1肾炎模型肾脏基因表达谱分析：(1)SAM软件分析结果显示,与对照组比较,模型组3d、5d、7d、10d、14d的差异表达基因数量分别是30、952、494、154、861个。(2)系统聚类分析结果显示,模型组差异表达基因的变化趋势可以分为5种类型：第1类变化趋势：在5d和／或7d表达上调至高峰,10d和／或14d下调；第2类变化趋势：在5d和／或7d表达下调至低点,10d和／或14d上调；第3类变化趋势：在5d和／或7d表达下调,10d上调,14d下调；第4类变化趋势,在5d和／或7d表达开始下调,10d和／或14d下调至最低点；第5类变化趋势,在5d和／或7d表达开始上调,10d和／或14d上调至最高峰。在各个类型中,都有增殖和凋亡相关的基因差异表达。(3)GO分析结果显示,模型组各时间点的差异表达基因主要参与代谢、生物调节、信号转导、应激等生物进程和催化活性、分子结合等分子功能。(4)转录相关基因系统聚类分析结果显示,转录相关基因表达变化趋势主要集中在以下2类：一类在5d和／或7d上调至峰值,10d和／或14d表达下调,以促凋亡基因和抑增殖基因为主；另一类在5d和／或7d开始下调,14d下调至最低值,以促凋亡基因为主。(5)分子通路分析结果显示,模型组5d、7d、10d、14d发生变化的分子通路数量分别是28、24、9、22条。与细胞增殖相关的分子通路主要包括局部粘附、缝隙连接、紧密连接、细胞骨架调节、p53信号通路、细胞周期、细胞因子与受体相互作用、细胞粘附分子、MAPK信号途径等。在系膜增殖期,这些通路被激活；在系膜增殖恢复期,局部粘附、缝隙连接、细胞周期等通路被抑制。(6)定量PCR检测TIMP-1、CCL2、S100A4、KLF15、MXI1基因表达表达趋势与芯片中的结果基本一致。
3、抗Thy-1肾炎模型蛋白质组学分析：(1)利用Decyder软件分析,在模型组中共发现了108个差异表达蛋白质。利用Maldi-Tof-MS和LTQ技术进行鉴定,共鉴定出了40个差异表达蛋白质,这些差异表达蛋白质主要参与代谢、应激、生物调节等生物进程和催化活性、分子结合等分子功能。(2)系统聚类分析结果显示：差异表达蛋白质的变化趋势主要集中在以下2类：类是10d和／或14d表达下调,包括促增殖和抑增殖蛋白质；另一类是10d和／或14d表达上调,以抑增殖蛋白质为主。(3)验证：用Western blotting验证了FHL2和NIT2蛋白质表达,检测结果与蛋白质组学检测结果一致。
结论：
无论是抗Thy-1肾炎的系膜增殖期还是增殖恢复期,都有增殖和凋亡相关的基因差异表达,其中包括相关的转录基因。各时间点差异表达基因和蛋白质主要参与代谢、生物调节、信号转导等生物进程和催化活性、分子结合等分子功能。细胞粘附、细胞连接、细胞骨架调节、p53信号通路和细胞周期等分子通路及其相互作用在系膜增殖过程中被激活；而局部粘附、缝隙连接、细胞周期等分子通路在系膜增殖恢复期被抑制。这些结果提示系膜增殖与恢复涉及多个分子网络的复杂作用,在系膜增殖期抑制过度激活的分子通路可能有利于增殖的恢复。
Background and purpose:Mesangial proliferation is a common pathological phenomenon in chronic glomerular nephritis, which lacks effective therapy due to unclear pathogenesis. Anti-Thy-1 nephritis, as a traditional model of mesangial proliferation and matrix expansion, is wildly used in mesangial proliferation research. In this study we screen the genes and proteins related with mesangial proliferation by analyzing the gene and protein expression profiles to reveal the molecular pathogenesis of mesangial cells proliferation.
Materials and methods:
1.200g male Wistar rats were randomly allocated to either control or model group. Model group were induced with intravenous injection of anti-Thy-1 antibody at a dose of 2.5mg/kg. Control group were injected with same volume of isotonic saline. Anti-Thy-1 treated animals were sacrificed at 3d,5d, 7d, 10d and 14d. Control group were sacrificed at Od.
2. Cortical regions of the kidney from each group were collected for RNA isolation. Affymetrix U230 2.0 chips (31000 probe sets,28000 well-substantiated rat genes.) were applied for microarray analysis. SAM (Significant Analysis of Microarray) software was performed to analyze significantly changed genes in every timepoint during anti-Thy-1 nephrites (vs. 0d); Gominer and MAS system (KEGG database) were performed to analyze GO (gene ontology) and pathway (KEGG) separately; Hierarchical clustering analysis (Spearman rank correlation) was performed by cluster 3.0; Quantitative PCR was performed for detecting the mRNA expression of TIMP-1, CCL2, S100A4, KLF15, MXI.
3. Proteins labeled by Cy2, Cy3, or Cy5 were separated in the pH3-11 range 24cm Non-linear strips in the first dimension and 12.5% SDS-polyacrylamide gel in the second dimension. Decyder software was performed for data processing and statistic analysis; The protein spots from preparation gel were identified by MALDI-TOF MS (Matrix-assisted laser desorption inoization-time of flight mass spectrometry) or LTQ (Linear trap quadrupole). Hierarchical clustering analysis (Spearman rank correlation) was performed by cluster 3.0. Western blot was performed to detect the expression of FHL2 and NIT2 protein.
Results:
1. (1)The histological injury in anti-thyl nephritis began with an initial complement-dependent mesangiolysis at 3d, followed by mesangial cell proliferation at 5d. Mesangial cell proliferation peaked at 7d with mesangial matrix expansion and began to recover at 10d. Mesangial cell proliferation was decreased significantly at 14d. (2)The level of 24hr urine protein was increased significantly at 3d,5d,7d, 10d and peaked at 3d during anti-Thy-1 nephritis. Scr and BUN was increased significantly at 5d,7d and peaked at 7d during anti-Thy-1 nephritis.
2. (1) 30,952,494,154,861 differential genes were identified at 3d,5d,7d, 10d, 14d respectively. (2)Differential genes in anti-Thy-1 nephritis were divided into five clusters (cluster 1:gene expression was upregulated at 5d and/or 7d, recovered at 10d and/or 14d; cluster 2:gene expression was downregulated at 5d and/or 7d, and recovered at 10d and/or 14d; cluster 3:gene expression was downregulated at 5d and/or 7d, upregulated at 10d, then downregulated at 14d; cluster 4:gene expression began to decrease at 5d and/or 7d, and reached the lowest value at 10d and/or 14d; cluster 5 gene expression was upregulated at 5d and/or 7d and peaked at 10d and/or 14d). There exited genes related with cell proliferation or apoptosis in every cluster. (3) Differential genes in anti-Thy-1 model were mainly involved in biological process such as metabolic process, biological regulation, signaling, response to stimulus and molecular function such as catalytic activity, binding. (4) Transcription genes were mainly assigned to cluster 1 and cluster 3. Cluster 1, in which gene expression was upregulated at 5d and/or 7d, and recovered at 10d and/or 14d, included genes inducing apoptosis and genes inhibiting cell proliferation. Clulster3, in which gene expression began to decrease at 5d and/or 7d, and reached the lowest value at 10d and/or 14d, included genes inducing apoptosis. (5) 328,24,9,22 pathways were affected at 3d,5d,7d, 10d,14d, respectively. Cell proliferation related pathways including focal adhesion, tight junction, gap junction, regulation of actin cytoskeleton, p53 signaling pathway, cell cycle, MAPK signaling pathway et al were activated in the phase of mesangial proliferation. Focal adhesion, gap junction and cell cycle were inhibited in the recovery phase of mesangial proliferation. (6) The mRNA expression trends of TIMP-1, CCL2, S100A4, MXI1, KLF15 detected by QPCR were consistent with the data in gene chip.
3. (1) 40 differential proteins identified by Maldi-Tof-MS or LTQ were involved in biological process such as metabolic process, biological regulation, response to stimulus, signaling and molecular function such as catalytic activity, binding. (2) Differential proteins were assigned to two clusters:one cluster, in which genes expression was downregulated at lOd and/or 14d, included both genes promoting cell proliferation and genes inhibiting proliferation; The another one cluster, in which genes expression was upregulated at 10d and/or 14d, included genes inhibiting cell proliferation. (3) Protein expression trends of FHL2, NIT2 detected by western blot were consistent with the data in DIGE.
Conclusion:Genes related with cell proliferation and apoptosis (including interrelated transcription genes) are regulated during the whole process of anti-Thy-1 model. Differential genes and proteins are mainly involved in metabolic process, biological regulation, signaling, response to stimulus, catalytic activity and binding in anti-Thy-1 nephritis. Pathway networks played a crucial role in regulating mesangial cell proliferation. Inhibiting the activation of pathways that can promote cell proliferation may suppress the mesangial cell proliferation, which may be the new therapy strategy for mesangial proliferation nephritis.
系膜增殖是慢性肾小球肾炎常见的病理表现,由于发病机制不清,缺乏有效的治疗措施。抗Thy-1肾炎模型是经典的系膜增殖性肾炎模型,主要表现为可逆的系膜细胞增殖。本研究通过分析抗Thy-1肾炎模型不同时间点肾脏的基因表达谱和蛋白质表达谱,筛选与系膜增殖相关的基因和蛋白质,为系膜增殖性肾炎的发病机制及其干预措施的研究提供候选基因和干预靶点。
材料和方法：
1、模型的制备：200g健康雄性Wistar大鼠,随机分为对照组(6只)和模型组(30只)。对照组尾静脉注射生理盐水,模型组一次性尾静脉注射抗Thy-1抗体(2.5mg/kg),制备抗Thy-1肾炎模型,分别于0d(对照组)、3d、5d、7d、10d、14d(均为模型组,分别代表抗体注射后第3、5、7、10、14天)处死大鼠。
2、基因表达谱分析：提取肾脏皮质RNA,利用Affymetrix U230 2.0芯片(包含31000个探针位点,代表28000个大鼠基因),分析各时间点大鼠的基因表达谱。利用SAM软件进行数据处理,得到模型组各时间点与对照组比较的差异表达基因；利用Cluster3.0软件对差异表达基因和其中的转录相关基因进行系统聚类分析；利用Gominer软件和MAS系统分别进行基因的生物进程和分子功能分析；利用KEGG数据库分析分子通路变化；用定量PCR对TIMP-1、CCL2、S100A4、KLF15、MXI1进行验证。
3、蛋白质组学分析：提取大鼠肾小球蛋白质,采用Cy2、Cy3、Cy5分别标记各样本。24cm pH3-11 NL strip和12.5%聚丙烯酰胺凝胶进行双相分离,利用Decyder软件进行数据处理和统计学分析；从制备胶中切取差异表达蛋白质点,利用飞行时间质谱和液质联用方法鉴定差异表达蛋白质,然后进行系统聚类分析。Western blot验证FHL2、NIT2蛋白质的表达。
结果：
1、抗Thy-1肾炎模型的病理改变和血、尿检测：(1)大鼠肾组织病理改变：模型肾脏在3d时出现系膜溶解,5d时出现系膜增殖,7d时出现重度的系膜细胞增殖和细胞外基质积聚,10d系膜增殖开始消退,14d系膜增殖显著消退。(2)24hr尿蛋白定量：模型组大鼠3d、5d、7d、10d尿蛋白定量显著高于对照组,其中3d是高峰；(3)血肌酐和尿素氮：模型组大鼠5d和7d血肌酐和尿素氮显著高于对照组,其中7d是高峰。
2、抗Thy-1肾炎模型肾脏基因表达谱分析：(1)SAM软件分析结果显示,与对照组比较,模型组3d、5d、7d、10d、14d的差异表达基因数量分别是30、952、494、154、861个。(2)系统聚类分析结果显示,模型组差异表达基因的变化趋势可以分为5种类型：第1类变化趋势：在5d和／或7d表达上调至高峰,10d和／或14d下调；第2类变化趋势：在5d和／或7d表达下调至低点,10d和／或14d上调；第3类变化趋势：在5d和／或7d表达下调,10d上调,14d下调；第4类变化趋势,在5d和／或7d表达开始下调,10d和／或14d下调至最低点；第5类变化趋势,在5d和／或7d表达开始上调,10d和／或14d上调至最高峰。在各个类型中,都有增殖和凋亡相关的基因差异表达。(3)GO分析结果显示,模型组各时间点的差异表达基因主要参与代谢、生物调节、信号转导、应激等生物进程和催化活性、分子结合等分子功能。(4)转录相关基因系统聚类分析结果显示,转录相关基因表达变化趋势主要集中在以下2类：一类在5d和／或7d上调至峰值,10d和／或14d表达下调,以促凋亡基因和抑增殖基因为主；另一类在5d和／或7d开始下调,14d下调至最低值,以促凋亡基因为主。(5)分子通路分析结果显示,模型组5d、7d、10d、14d发生变化的分子通路数量分别是28、24、9、22条。与细胞增殖相关的分子通路主要包括局部粘附、缝隙连接、紧密连接、细胞骨架调节、p53信号通路、细胞周期、细胞因子与受体相互作用、细胞粘附分子、MAPK信号途径等。在系膜增殖期,这些通路被激活；在系膜增殖恢复期,局部粘附、缝隙连接、细胞周期等通路被抑制。(6)定量PCR检测TIMP-1、CCL2、S100A4、KLF15、MXI1基因表达表达趋势与芯片中的结果基本一致。
3、抗Thy-1肾炎模型蛋白质组学分析：(1)利用Decyder软件分析,在模型组中共发现了108个差异表达蛋白质。利用Maldi-Tof-MS和LTQ技术进行鉴定,共鉴定出了40个差异表达蛋白质,这些差异表达蛋白质主要参与代谢、应激、生物调节等生物进程和催化活性、分子结合等分子功能。(2)系统聚类分析结果显示：差异表达蛋白质的变化趋势主要集中在以下2类：类是10d和／或14d表达下调,包括促增殖和抑增殖蛋白质；另一类是10d和／或14d表达上调,以抑增殖蛋白质为主。(3)验证：用Western blotting验证了FHL2和NIT2蛋白质表达,检测结果与蛋白质组学检测结果一致。
结论：
无论是抗Thy-1肾炎的系膜增殖期还是增殖恢复期,都有增殖和凋亡相关的基因差异表达,其中包括相关的转录基因。各时间点差异表达基因和蛋白质主要参与代谢、生物调节、信号转导等生物进程和催化活性、分子结合等分子功能。细胞粘附、细胞连接、细胞骨架调节、p53信号通路和细胞周期等分子通路及其相互作用在系膜增殖过程中被激活；而局部粘附、缝隙连接、细胞周期等分子通路在系膜增殖恢复期被抑制。这些结果提示系膜增殖与恢复涉及多个分子网络的复杂作用,在系膜增殖期抑制过度激活的分子通路可能有利于增殖的恢复。
Background and purpose:Mesangial proliferation is a common pathological phenomenon in chronic glomerular nephritis, which lacks effective therapy due to unclear pathogenesis. Anti-Thy-1 nephritis, as a traditional model of mesangial proliferation and matrix expansion, is wildly used in mesangial proliferation research. In this study we screen the genes and proteins related with mesangial proliferation by analyzing the gene and protein expression profiles to reveal the molecular pathogenesis of mesangial cells proliferation.
Materials and methods:
1.200g male Wistar rats were randomly allocated to either control or model group. Model group were induced with intravenous injection of anti-Thy-1 antibody at a dose of 2.5mg/kg. Control group were injected with same volume of isotonic saline. Anti-Thy-1 treated animals were sacrificed at 3d,5d, 7d, 10d and 14d. Control group were sacrificed at Od.
2. Cortical regions of the kidney from each group were collected for RNA isolation. Affymetrix U230 2.0 chips (31000 probe sets,28000 well-substantiated rat genes.) were applied for microarray analysis. SAM (Significant Analysis of Microarray) software was performed to analyze significantly changed genes in every timepoint during anti-Thy-1 nephrites (vs. 0d); Gominer and MAS system (KEGG database) were performed to analyze GO (gene ontology) and pathway (KEGG) separately; Hierarchical clustering analysis (Spearman rank correlation) was performed by cluster 3.0; Quantitative PCR was performed for detecting the mRNA expression of TIMP-1, CCL2, S100A4, KLF15, MXI.
3. Proteins labeled by Cy2, Cy3, or Cy5 were separated in the pH3-11 range 24cm Non-linear strips in the first dimension and 12.5% SDS-polyacrylamide gel in the second dimension. Decyder software was performed for data processing and statistic analysis; The protein spots from preparation gel were identified by MALDI-TOF MS (Matrix-assisted laser desorption inoization-time of flight mass spectrometry) or LTQ (Linear trap quadrupole). Hierarchical clustering analysis (Spearman rank correlation) was performed by cluster 3.0. Western blot was performed to detect the expression of FHL2 and NIT2 protein.
Results:
1. (1)The histological injury in anti-thyl nephritis began with an initial complement-dependent mesangiolysis at 3d, followed by mesangial cell proliferation at 5d. Mesangial cell proliferation peaked at 7d with mesangial matrix expansion and began to recover at 10d. Mesangial cell proliferation was decreased significantly at 14d. (2)The level of 24hr urine protein was increased significantly at 3d,5d,7d, 10d and peaked at 3d during anti-Thy-1 nephritis. Scr and BUN was increased significantly at 5d,7d and peaked at 7d during anti-Thy-1 nephritis.
2. (1) 30,952,494,154,861 differential genes were identified at 3d,5d,7d, 10d, 14d respectively. (2)Differential genes in anti-Thy-1 nephritis were divided into five clusters (cluster 1:gene expression was upregulated at 5d and/or 7d, recovered at 10d and/or 14d; cluster 2:gene expression was downregulated at 5d and/or 7d, and recovered at 10d and/or 14d; cluster 3:gene expression was downregulated at 5d and/or 7d, upregulated at 10d, then downregulated at 14d; cluster 4:gene expression began to decrease at 5d and/or 7d, and reached the lowest value at 10d and/or 14d; cluster 5 gene expression was upregulated at 5d and/or 7d and peaked at 10d and/or 14d). There exited genes related with cell proliferation or apoptosis in every cluster. (3) Differential genes in anti-Thy-1 model were mainly involved in biological process such as metabolic process, biological regulation, signaling, response to stimulus and molecular function such as catalytic activity, binding. (4) Transcription genes were mainly assigned to cluster 1 and cluster 3. Cluster 1, in which gene expression was upregulated at 5d and/or 7d, and recovered at 10d and/or 14d, included genes inducing apoptosis and genes inhibiting cell proliferation. Clulster3, in which gene expression began to decrease at 5d and/or 7d, and reached the lowest value at 10d and/or 14d, included genes inducing apoptosis. (5) 328,24,9,22 pathways were affected at 3d,5d,7d, 10d,14d, respectively. Cell proliferation related pathways including focal adhesion, tight junction, gap junction, regulation of actin cytoskeleton, p53 signaling pathway, cell cycle, MAPK signaling pathway et al were activated in the phase of mesangial proliferation. Focal adhesion, gap junction and cell cycle were inhibited in the recovery phase of mesangial proliferation. (6) The mRNA expression trends of TIMP-1, CCL2, S100A4, MXI1, KLF15 detected by QPCR were consistent with the data in gene chip.
3. (1) 40 differential proteins identified by Maldi-Tof-MS or LTQ were involved in biological process such as metabolic process, biological regulation, response to stimulus, signaling and molecular function such as catalytic activity, binding. (2) Differential proteins were assigned to two clusters:one cluster, in which genes expression was downregulated at lOd and/or 14d, included both genes promoting cell proliferation and genes inhibiting proliferation; The another one cluster, in which genes expression was upregulated at 10d and/or 14d, included genes inhibiting cell proliferation. (3) Protein expression trends of FHL2, NIT2 detected by western blot were consistent with the data in DIGE.
Conclusion:Genes related with cell proliferation and apoptosis (including interrelated transcription genes) are regulated during the whole process of anti-Thy-1 model. Differential genes and proteins are mainly involved in metabolic process, biological regulation, signaling, response to stimulus, catalytic activity and binding in anti-Thy-1 nephritis. Pathway networks played a crucial role in regulating mesangial cell proliferation. Inhibiting the activation of pathways that can promote cell proliferation may suppress the mesangial cell proliferation, which may be the new therapy strategy for mesangial proliferation nephritis.
引文
1. Ono T, Liu N, Makino T, Nogaki F, Muso E, Honda G, Kita T: Suppressive mechanisms of Sairei-to on mesangial matrix expansion in rat mesangioproliferative glomerulonephritis. Nephron Exp Nephrol 2005, 100(3):e132-142.
2. Kriz W, Hahnel B, Hosser H, Ostendorf T, Gaertner S, Kranzlin B, Gretz N, Shimizu F, Floege J:Pathways to recovery and loss of nephrons in anti-Thy-1 nephritis. J Am Soc Nephrol 2003,14(7):1904-1926.
3. Wang Y, He Q, Qin H, Xu J, Tong J, Gao L:The complement C5b-9 complexes induced injury of glomerular mesangial cells in rats with Thy-1 nephritis by increasing nitric oxide synthesis. Life Sci 2006, 79(2):182-192.
4. Wan Y, Gu L, Suzuki K, Karasawa T, Fujioka Y, Han GD, Koike H, Kawachi H, Shimizu F:Multi-glycoside of Tripterygium wilfordii Hook f. ameliorates proteinuria and acute mesangial injury induced by anti-Thy1.1 monoclonal antibody. Nephron Exp Nephrol 2005,99(4):e121-129.
5. Majidi J, Baradaran B, Hassan ZM, Mostafaie A:Production and characterization of monoclonal antibodies against human IgG in Balb/c mouse. Hum Antibodies 2005,14(1-2):1-5.
6. Kummer U, Haunschild J, Reisbach G, Delecluse HJ, Thierfelder S: Mitogenicity of anti-Thy-1 monoclonal antibodies attributable to an Fc-dependent mechanism. Eur J Immunol 1993,23(10):2649-2654.
7. D'Agostino B, Bellofiore P, De Martino T, Punzo C, Rivieccio V, Verdoliva A:Affinity purification of IgG monoclonal antibodies using the D-PAM synthetic ligand:chromatographic comparison with protein A and thermodynamic investigation of the D-PAM/IgG interaction. J Immunol Methods 2008,333(1-2):126-138.
8. Gaza-Bulseco G, Faldu S, Hurkmans K, Chumsae C, Liu H:Effect of methionine oxidation of a recombinant monoclonal antibody on the binding affinity to protein A and protein G. J Chromatogr B Analyt Technol Biomed Life Sci 2008,870(1):55-62.
9. Jefferson JA, Johnson RJ:Experimental mesangial proliferative glomerulonephritis (the anti-Thy-1.1 model). J Nephrol 1999, 12(5):297-307.
1. Izumi Y, Izumiya Y, Shiota M, Yukimura T, Shiojima S, Yamada M, Kadowaki T, Katsuma S, Hirasawa A, Tsujimoto G et al: Gene expression profile in experimental mesangial proliferative glomerulonephritis. J Pharmacol Sci 2004,96(1):91-94.
2. Sadlier DM, Ouyang X, McMahon B, Mu W, Ohashi R, Rodgers K, Murray D, Nakagawa T, Godson C, Doran P et al: Microarray and bioinformatic detection of novel and established genes expressed in experimental anti-Thyl nephritis. Kidney Int 2005,68(6):2542-2561.
3. Xu JH, Qiu W, Wang YW, Xu J, Tong JX, Gao LJ, Xu WH, Wu YQ: Gene expression profile and overexpression of apoptosis-related genes (NGFI-B and Gadd 45 gamma) in early phase of Thy-1 nephritis model. Cell Tissue Res 2006,326(1):159-168.
4. Ahn JD, Morishita R, Kaneda Y, Kim HJ, Kim YD, Lee HJ, Lee KU, Park JY, Kim YH, Park KK et al: Transcription factor decoy for AP-1 reduces mesangial cell proliferation and extracellular matrix production in vitro and in vivo. Gene Ther 2004,11(11):916-923.
5. Tomita N, Kim JY, Gibbons GH, Zhang L, Kaneda Y, Stahl RA, Ogborn M, Venderville B, Morishita R, Baran D et al: Gene therapy with an E2F transcription factor decoy inhibits cell cycle progression in rat anti-Thy 1 glomerulonephritis. Int J Mol Med 2004,13(5):629-636.
6. Bokemeyer D, Ostendorf T, Kunter U, Lindemann M, Kramer HJ, Floege
J:Differential activation of mitogen-activated protein kinases in experimental mesangioproliferative glomerulonephritis. J Am Soc Nephrol 2000,11(2):232-240.
7. Moyes KM, Drackley JK, Morin DE, Bionaz M, Rodriguez-Zas SL, Everts RE, Lewin HA, Loor JJ:Gene network and pathway analysis of bovine mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPARgamma signaling as potential mechanism for the negative relationships between immune response and lipid metabolism. BMC Genomics 2009,10:542.
8. Li ZD, Hu XW, Wang YT, Fang J:Apigenin inhibits proliferation of ovarian cancer A2780 cells through Idl. FEBS Lett 2009, 583(12):1999-2003.
9. Jiang X, Zhang J, Xia M, Qiu W, Wang H, Zhao D, Wang Y:Role of activating transcription factor 3 (ATF3) in sublytic C5b-9-induced glomerular mesangial cell apoptosis. Cell Mol Immunol,7(2):143-151.
10. Huang X, Li X, Guo B:KLF6 induces apoptosis in prostate cancer cells through up-regulation of ATF3. J Biol Chem 2008,283(44):29795-29801.
11. Liu J, Du T, Yuan Y, He Y, Tan Z, Liu Z:KLF6 inhibits estrogen receptor-mediated cell growth in breast cancer via a c-Src-mediated pathway. Mol Cell Biochem,335(1-2):29-35.
12. Unoki M, Nakamura Y:EGR2 induces apoptosis in various cancer cell lines by direct transactivation of BNIP3L and BAK. Oncogene 2003, 22(14):2172-2185.
13. Wu Q, Jin H, Yang Z, Luo G, Lu Y, Li K, Ren G, Su T, Pan Y, Feng B et al: MiR-150 promotes gastric cancer proliferation by negatively regulating the pro-apoptotic gene EGR2. Biochem Biophys Res Commun, 392(3):340-345.
14. Li D, Das S, Yamada T, Samuels HH:The NRIF3 family of transcriptional coregulators induces rapid and profound apoptosis in breast cancer cells. Mol Cell Biol 2004,24(9):3838-3848.
15. Tinnikov AA, Yeung KT, Das S, Samuels HH:Identification of a novel pathway that selectively modulates apoptosis of breast cancer cells. Cancer Res 2009,69(4):1375-1382.
16. Zhang L, Huang H, Wu K, Wang M, Wu B:Impact of BTG2 expression on proliferation and invasion of gastric cancer cells in vitro. Mol Biol Rep 2009.
17. Romieu-Mourez R, Solis M, Nardin A, Goubau D, Baron-Bodo V, Lin R, Massie B, Salcedo M, Hiscott J:Distinct roles for IFN regulatory factor (IRF)-3 and IRF-7 in the activation of antitumor properties of human macrophages. Cancer Res 2006,66(21):10576-10585.
18. Li Q, Tang L, Roberts PC, Kraniak JM, Fridman AL, Kulaeva OI, Tehrani OS, Tainsky MA:Interferon regulatory factors IRF5 and IRF7 inhibit growth and induce senescence in immortal Li-Fraumeni fibroblasts. Mol Cancer Res 2008,6(5):770-784.
19. Burchert A, Cai D, Hofbauer LC, Samuelsson MK, Slater EP, Duyster J, Ritter M, Hochhaus A, Muller R, Eilers M et al: Interferon consensus sequence binding protein (ICSBP; IRF-8) antagonizes BCR/ABL and down-regulates bcl-2. Blood 2004,103(9):3480-3489.
20. Takaoka A, Hayakawa S, Yanai H, Stoiber D, Negishi H, Kikuchi H, Sasaki S, Imai K, Shibue T, Honda K et al: Integration of interferon-alpha/beta signalling to p53 responses in tumour suppression and antiviral defence. Nature 2003,424(6948):516-523.
21. Kasof GM, Goyal L, White E:Btf, a novel death-promoting transcriptional repressor that interacts with Bcl-2-related proteins. Mol Cell Biol 1999, 19(6):4390-4404.
22. Linggi MS, Burke TL, Williams BB, Harrington A, Kraemer R, Hempstead BL, Yoon SO, Carter BD:Neurotrophin receptor interacting factor (NRIF) is an essential mediator of apoptotic signaling by the p75 neurotrophin receptor. J Biol Chem 2005,280(14):13801-13808.
23. Bai L, Merchant JL:ZBP-89 promotes growth arrest through stabilization of p53. Mol Cell Biol 2001,21(14):4670-4683.
24. Inoue K, Roussel MF, Sherr CJ:Induction of ARF tumor suppressor gene expression and cell cycle arrest by transcription factor DMP1. Proc Natl Acad Sci USA 1999,96(7):3993-3998.
25. Hayashi K, Yokozaki H, Naka K, Yasui W, Lotan R, Tahara E: Overexpression of retinoic acid receptor beta induces growth arrest and apoptosis in oral cancer cell lines. Jpn J Cancer Res 2001,92(1):42-50.
26. Yang Q, Shan L, Yoshimura G, Nakamura M, Nakamura Y, Suzuma T, Umemura T, Mori I, Sakurai T, Kakudo K:5-aza-2'-deoxycytidine induces retinoic acid receptor beta 2 demethylation, cell cycle arrest and growth inhibition in breast carcinoma cells. Anticancer Res 2002, 22(5):2753-2756.
27. Oda A, Katayose Y, Yabuuchi S, Yamamoto K, Mizuma M, Shirasou S, Onogawa T, Ohtsuka H, Yoshida H, Hayashi H et al: Clock gene mouse period2 overexpression inhibits growth of human pancreatic cancer cells and has synergistic effect with cisplatin. Anticancer Res 2009, 29(4):1201-1209.
28. Peng S, Wu H, Mo YY, Watabe K, Pauza ME:c-Maf increases apoptosis in peripheral CD8 cells by transactivating Caspase 6. Immunology 2009, 127(2):267-278.
29. Camacho CP, Latini FR, Oler G, Hojaij FC, Maciel RM, Riggins GJ, Cerutti JM:Down-regulation of NR4A1 in follicular thyroid carcinomas is restored following lithium treatment. Clin Endocrinol (Oxf) 2009, 70(3):475-483.
30. Paulson KE, Rieger-Christ K, McDevitt MA, Kuperwasser C, Kim J, Unanue VE, Zhang X, Hu M, Ruthazer R, Berasi SP et al: Alterations of the HBP1 transcriptional repressor are associated with invasive breast cancer. Cancer Res 2007,67(13):6136-6145.
31. Kikuchi K, Kawahara K, Biswas KK, Ito T, Tancharoen S, Morimoto Y, Matsuda F, Oyama Y, Takenouchi K, Miura N et al:Minocycline attenuates both OGD-induced HMGB1 release and HMGB1-induced cell death in ischemic neuronal injury in PC 12 cells. Biochem Biophys Res Commun 2009,385(2):132-136.
32. Carey JP, Asirvatham AJ, Galm O, Ghogomu TA, Chaudhary J:Inhibitor of differentiation 4 (Id4) is a potential tumor suppressor in prostate cancer. BMC Cancer 2009,9:173.
33. Wechsler DS, Shelly CA, Petroff CA, Dang CV:MXI1, a putative tumor suppressor gene, suppresses growth of human glioblastoma cells. Cancer 1997,57(21):4905-4912.
34. De Gottardi A, Dumonceau JM, Bruttin F, Vonlaufen A, Morard I, Spahr L, Rubbia-Brandt L, Frossard JL, Dinjens WN, Rabinovitch PS et al: Expression of the bile acid receptor FXR in Barrett's esophagus and enhancement of apoptosis by guggulsterone in vitro. Mol Cancer 2006, 5:48.
35. Maran RR, Thomas A, Roth M, Sheng Z, Esterly N, Pinson D, Gao X, Zhang Y, Ganapathy V, Gonzalez FJ et al: Farnesoid X receptor deficiency in mice leads to increased intestinal epithelial cell proliferation and tumor development. J Pharmacol Exp Ther 2009,328(2):469-477.
36. Zhang XL, Simmen FA, Michel FJ, Simmen RC:Increased expression of the Zn-finger transcription factor BTEB1 in human endometrial cells is correlated with distinct cell phenotype, gene expression patterns, and proliferative responsiveness to serum and TGF-betal. Mol Cell Endocrinol 2001,181(1-2):81-96.
37. Wu JT, Han BM, Yu SQ, Wang HP, Xia SJ:Androgen Receptor Is a Potential Therapeutic Target for Bladder Cancer. Urology.
38. Yu SQ, Han BM, Shao Y, Wu JT, Zhao FJ, Liu HT, Sun XW, Tang YQ, Xia SJ:Androgen receptor functioned as a suppressor in the prostate cancer cell line PC3 in vitro and in vivo. Chin Med J (Engl) 2009, 122(22):2779-2783.
39. Cortes-Wanstreet MM, Giedzinski E, Limoli CL, Luderer U: Overexpression of glutamate-cysteine ligase protects human COV434 granulosa tumour cells against oxidative and gamma-radiation-induced cell death. Mutagenesis 2009,24(3):211-224.
40. Okouchi M, Okayama N, Alexander JS, Aw TY:NRF2-dependent glutamate-L-cysteine ligase catalytic subunit expression mediates insulin protection against hyperglycemia-induced brain endothelial cell apoptosis. Curr Neurovasc Res 2006,3(4):249-261.
41. Bokemeyer D, Panek D, Kramer HJ, Lindemann M, Kitahara M, Boor P, Kerjaschki D, Trzaskos JM, Floege J, Ostendorf T:In vivo identification of the mitogen-activated protein kinase cascade as a central pathogenic pathway in experimental mesangioproliferative glomerulonephritis. J Am Soc Nephrol 2002,13(6):1473-1480.
42. Kanegae K, Tamura M, Kabashima N, Serino R, Tokunaga M, Oikawa S, Nakashima Y:Synergistic induction of monocyte chemoattractant protein-1 by integrins and platelet-derived growth factor via focal adhesion kinase in mesangial cells. Nephrol Dial Transplant 2005, 20(10):2080-2088.
43. Harper L, Kashiwagi Y, Pusey CD, Hendry BM, Domin J:Platelet-derived growth factor reorganizes the actin cytoskeleton through 3-phosphoinositide-dependent and 3-phosphoinositide-independent mechanisms in human mesangial cells. Nephron Physiol 2007, 107(2):p45-56.
44. Khwaja A, Sharpe CC, Noor M, Hendry BM:The role of geranylgeranylated proteins in human mesangial cell proliferation. Kidney Int 2006,70(7):1296-1304.
45. Marti HP:The role of matrix metalloproteinases in the activation of mesangial cells. Transpl Immunol 2002,9(2-4):97-100.
46. Han SY, Chang EJ, Choi HJ, Kwak CS, Park SB, Kim HC, Mun KC: Apoptosis by cyclosporine in mesangial cells. Transplant Proc 2006, 38(7):2244-2246.
1. Yoshida Y, Miyazaki K, Kamiie J, Sato M, Okuizumi S, Kenmochi A, Kamijo K, Nabetani T, Tsugita A, Xu B et al: Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics 2005,5(4):1083-1096.
2. Park MR, Wang EH, Jin DC, Cha JH, Lee KH, Yang CW, Kang CS, Choi YJ:Establishment of a 2-D human urinary proteomic map in IgA nephropathy. Proteomics 2006,6(3):1066-1076.
3. Haubitz M, Wittke S, Weissinger EM, Walden M, Rupprecht HD, Floege J, Haller H, Mischak H:Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 2005,67(6):2313-2320.
4. Julian BA, Wittke S, Novak J, Good DM, Coon JJ, Kellmann M, Zurbig P, Schiffer E, Haubitz M, Moldoveanu Z et al: Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis 2007,28(23):4469-4483.
5. Hoorn EJ, Hoffert JD, Knepper MA:The application of DIGE-based proteomics to renal physiology. Nephron Physiol 2006,104(1):p61-72.
6. Nazeer K, Janech MG, Lin JJ, Ryan KJ, Arthur JM, Budisavljevic MN: Changes in protein profiles during course of experimental glomerulonephritis. Am JPhysiol Renal Physiol 2009,296(1):F186-193.
7. Perluigi M, Sultana R, Cenini G, Di Domenico F, Memo M, Pierce WM, Coccia R, Butterfield DA:Redox proteomics identification of 4-hydroxynonenal-modified brain proteins in Alzheimer's disease:Role of lipid peroxidation in Alzheimer's disease pathogenesis. Proteomics Clin Appl 2009,3(6):682-693.
8. Nilo R, Saffie C, Lilley K, Baeza-Yates R, Cambiazo V, Campos-Vargas R, Gonzalez M, Meisel LA, Retamales J, Silva H et al: Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics 2010,11:43.
9. Chang TS, Cho CS, Park S, Yu S, Kang SW, Rhee SG:Peroxiredoxin Ⅲ, a mitochondrion-specific peroxidase, regulates apoptotic signaling by mitochondria. JBiol Chem 2004,279(40):41975-41984.
10. Walsh B, Pearl A, Suchy S, Tartaglio J, Visco K, Phelan SA: Overexpression of Prdx6 and resistance to peroxide-induced death in Hepal-6 cells:Prdx suppression increases apoptosis. Redox Rep 2009, 14(6):275-284.
11. Sasazawa Y, Futamura Y, Tashiro E, Imoto M:Vacuolar H+-ATPase inhibitors overcome Bcl-xL-mediated chemoresistance through restoration of a caspase-independent apoptotic pathway. Cancer Sci 2009, 100(8):1460-1467.
12. Rousalova I, Krepela E, Prochazka J, Cermak J, Benkova K:Expression of proteinase inhibitor-9/serpinB9 in non-small cell lung carcinoma cells and tissues. Int J Oncol 2010,36(1):275-283.
13. Su YR, Dove DE, Major AS, Hasty AH, Boone B, Linton MF, Fazio S: Reduced ABCA1-mediated cholesterol efflux and accelerated atherosclerosis in apolipoprotein E-deficient mice lacking macrophage-derived ACAT1. Circulation 2005,111(18):2373-2381.
14. Kim SC, Stice JP, Chen L, Jung JS, Gupta S, Wang Y, Baumgarten G, Trial J, Knowlton AA:Extracellular heat shock protein 60, cardiac myocytes, and apoptosis. Circ Res 2009,105(12):1186-1195.
15. Salama SA, Kamel MW, Botting S, Salih SM, Borahay MA, Hamed AA, Kilic GS, Saeed M, Williams MY, Diaz-Arrastia CR: Catechol-o-methyltransferase expression and 2-methoxyestradiol affect microtubule dynamics and modify steroid receptor signaling in leiomyoma cells. PLoS One 2009,4(10):e7356.
16. Vichalkovski A, Gresko E, Cornils H, Hergovich A, Schmitz D, Hemmings BA:NDR kinase is activated by RASSF1A/MST1 in response to Fas receptor stimulation and promotes apoptosis. Curr Biol 2008, 18(23):1889-1895.
17. Tang SJ, Ho MY, Cho HC, Lin YC, Sun GH, Chi KH, Wang YS, Jhou RS, Yang W, Sun KH:Phosphoglycerate kinase 1-overexpressing lung cancer cells reduce cyclooxygenase 2 expression and promote anti-tumor immunity in vivo. Int J Cancer 2008,123(12):2840-2848.
18. Lin CH, Chung MY, Chen WB, Chien CH:Growth inhibitory effect of the human NIT2 gene and its allelic imbalance in cancers. FEBS J 2007, 274(11):2946-2956.
19. Yu W, Ding X, Chen F, Liu M, Shen S, Gu X, Yu L:The phosphorylation of SEPT2 on Ser218 by casein kinase 2 is important to hepatoma carcinoma cell proliferation. Mol Cell Biochem 2009,325(1-2):61-67.
20. Ding L, Wang Z, Yan J, Yang X, Liu A, Qiu W, Zhu J, Han J, Zhang H, Lin J et al: Human four-and-a-half LIM family members suppress tumor cell growth through a TGF-beta-like signaling pathway. J Clin Invest 2009, 119(2):349-361.
21. Qian Z, Mao L, Fernald AA, Yu H, Luo R, Jiang Y, Anastasi J, Valk PJ, Delwel R, Le Beau MM:Enhanced expression of FHL2 leads to abnormal myelopoiesis in vivo. Leukemia 2009,23(9):1650-1657.
22. Wear MA, Cooper JA:Capping protein binding to S100B:implications for the tentacle model for capping the actin filament barbed end. J Biol Chem 2004,279(14):14382-14390.
23. Wright NT, Cannon BR, Wilder PT, Morgan MT, Varney KM, Zimmer DB, Weber DJ:Solution structure of S100A1 bound to the CapZ peptide (TRTK12). JMol Biol 2009,386(5):1265-1277.
24. Tsoporis JN, Mohammadzadeh F, Parker TG:S100B:a multifunctional role in cardiovascular pathophysiology. Amino Acids 2010.
1. O'Farrell PH:High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975,250(10):4007-4021.
2. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M:Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001,1(3):377-396.
3. Han DK, Eng J, Zhou H, Aebersold R:Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 2001,19(10):946-951.
4. Sethuraman M, McComb ME, Heibeck T, Costello CE, Cohen RA: Isotope-coded affinity tag approach to identify and quantify oxidant-sensitive protein thiols. Mol Cell Proteomics 2004,3(3):273-278.
5. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S et al: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004,3(12):1154-1169.
6. Levin Y, Schwarz E, Wang L, Leweke FM, Bahn S:Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples. J Sep Sci 2007,30(14):2198-2203.
7. Cutillas PR, Vanhaesebroeck B:Quantitative profile of five murine core proteomes using label-free functional proteomics. Mol Cell Proteomics 2007,6(9):1560-1573.
8. Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW:Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002,48(8):1296-1304.
9. Dai S, Wang X, Liu L, Liu J, Wu S, Huang L, Xiao X, He D:Discovery and identification of Serum Amyloid A protein elevated in lung cancer serum. Sci China C Life Sci 2007,50(3):305-311.
10. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS:Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999,20(18):3551-3567.
11. Zhang W, Chait BT:ProFound:an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 2000, 72(11):2482-2489.
12. Marshall T, Williams KM:Two-dimensional electrophoresis of human urine and cerebrospinal fluid following protein concentration by dye precipitation. Biochem Soc Trans 1997,25(4):S657.
13. Heine G, Raida M, Forssmann WG:Mapping of peptides and protein fragments in human urine using liquid chromatography-mass spectrometry. J Chromatogr A 1997,776(1):117-124.
14. Thongboonkerd V, McLeish KR, Arthur JM, Klein JB:Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 2002,62(4):1461-1469.
15. Schaub S, Wilkins J, Weiler T, Sangster K, Rush D, Nickerson P:Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004,65(1):323-332.
16. Wittke S, Fliser D, Haubitz M, Bartel S, Krebs R, Hausadel F, Hillmann M, Golovko I, Koester P, Haller H et al: Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A 2003,1013(1-2):173-181.
17. Zurbig P, Schiffer E, Mischak H:Capillary electrophoresis coupled to mass spectrometry for proteomic profiling of human urine and biomarker discovery. Methods Mol Biol 2009,564:105-121.
18. Haubitz M, Wittke S, Weissinger EM, Walden M, Rupprecht HD, Floege J, Haller H, Mischak H:Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 2005,67(6):2313-2320.
19. Park MR, Wang EH, Jin DC, Cha JH, Lee KH, Yang CW, Kang CS, Choi YJ:Establishment of a 2-D human urinary proteomic map in IgA nephropathy. Proteomics 2006,6(3):1066-1076.
20. Yokota H, Hiramoto M, Okada H, Kanno Y, Yuri M, Morita S, Naitou M, Ichikawa A, Katoh M, Suzuki H:Absence of increased alpha1-microglobulin in IgA nephropathy proteinuria. Mol Cell Proteomics 2007,6(4):738-744.
21. Jiang H, Guan G, Zhang R, Liu G, Cheng J, Hou X, Cui Y:Identification of urinary soluble E-cadherin as a novel biomarker for diabetic nephropathy. Diabetes Metab Res Rev 2009,25(3):232-241.
22. Rossing K, Mischak H, Dakna M, Zurbig P, Novak J, Julian BA, Good DM, Coon JJ, Tarnow L, Rossing P:Urinary proteomics in diabetes and CKD. JAm Soc Nephrol 2008,19(7):1283-1290.
23. Otu HH, Can H, Spentzos D, Nelson RG, Hanson RL, Looker HC, Knowler WC, Monroy M, Libermann TA, Karumanchi SA et al; Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy. Diabetes Care 2007, 30(3):638-643.
24. Zhang X, Jin M, Wu H, Nadasdy T, Nadasdy G, Harris N, Green-Church K, Nagaraja H, Birmingham DJ, Yu CY et al: Biomarkers of lupus nephritis determined by serial urine proteomics. Kidney Int 2008, 74(6):799-807.
25. Mosley K, Tam FW, Edwards RJ, Crozier J, Pusey CD, Lightstone L Urinary proteomic profiles distinguish between active and inactive lupus nephritis. Rheumatology (Oxford) 2006,45(12):1497-1504.
26. Ngai HH, Sit WH, Jiang PP, Xu RJ, Wan JM, Thongboonkerd V:Serial changes in urinary proteome profile of membranous nephropathy: implications for pathophysiology and biomarker discovery. J Proteome Res 2006,5(11):3038-3047.
27. Yoshida Y, Miyazaki K, Kamiie J, Sato M, Okuizumi S, Kenmochi A, Kamijo K, Nabetani T, Tsugita A, Xu B et al: Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics 2005,5(4):1083-1096.
28. Miyamoto M, Yoshida Y, Taguchi I, Nagasaka Y, Tasaki M, Zhang Y, Xu B, Nameta M, Sezaki H, Cuellar LM et al: In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J Proteome Res 2007,6(9):3680-3690.
29. Nazeer K, Janech MG, Lin JJ, Ryan KJ, Arthur JM, Budisavljevic MN: Changes in protein profiles during course of experimental glomerulonephritis. Am J Physiol Renal Physiol 2009,296(1):F 186-193.
30. Xu BJ, Shyr Y, Liang X, Ma LJ, Donnert EM, Roberts JD, Zhang X, Kon V, Brown NJ, Caprioli RM et al: Proteomic patterns and prediction of glomerulosclerosis and its mechanisms. J Am Soc Nephrol 2005, 16(10):2967-2975.
31. Sitek B, Potthoff S, Schulenborg T, Stegbauer J, Vinke T, Rump LC, Meyer HE, Vonend O, Stuhler K:Novel approaches to analyse glomerular proteins from smallest scale murine and human samples using DIGE saturation labelling. Proteomics 2006,6(15):4337-4345.
32. Jiang XS, Tang LY, Cao XJ, Zhou H, Xia QC, Wu JR, Zeng R: Two-dimensional gel electrophoresis maps of the proteome and phosphoproteome of primitively cultured rat mesangial cells. Electrophoresis 2005,26(23):4540-4562.
33. Ramachandra Rao SP, Wassell R, Shaw MA, Sharma K:Profiling of human mesangial cell subproteomes reveals a role for calmodulin in glucose uptake. Am J Physiol Renal Physiol 2007,292(4):F1182-1189.
34. Viney RL, Morrison AA, van den Heuvel LP, Ni L, Mathieson PW, Saleem MA, Ladomery MR:A proteomic investigation of glomerular podocytes from a Denys-Drash syndrome patient with a mutation in the Wilms tumour suppressor gene WT1. Proteomics 2007,7(5):804-815.
2. Kriz W, Hahnel B, Hosser H, Ostendorf T, Gaertner S, Kranzlin B, Gretz N, Shimizu F, Floege J:Pathways to recovery and loss of nephrons in anti-Thy-1 nephritis. J Am Soc Nephrol 2003,14(7):1904-1926.
3. Wang Y, He Q, Qin H, Xu J, Tong J, Gao L:The complement C5b-9 complexes induced injury of glomerular mesangial cells in rats with Thy-1 nephritis by increasing nitric oxide synthesis. Life Sci 2006, 79(2):182-192.
4. Wan Y, Gu L, Suzuki K, Karasawa T, Fujioka Y, Han GD, Koike H, Kawachi H, Shimizu F:Multi-glycoside of Tripterygium wilfordii Hook f. ameliorates proteinuria and acute mesangial injury induced by anti-Thy1.1 monoclonal antibody. Nephron Exp Nephrol 2005,99(4):e121-129.
5. Majidi J, Baradaran B, Hassan ZM, Mostafaie A:Production and characterization of monoclonal antibodies against human IgG in Balb/c mouse. Hum Antibodies 2005,14(1-2):1-5.
6. Kummer U, Haunschild J, Reisbach G, Delecluse HJ, Thierfelder S: Mitogenicity of anti-Thy-1 monoclonal antibodies attributable to an Fc-dependent mechanism. Eur J Immunol 1993,23(10):2649-2654.
7. D'Agostino B, Bellofiore P, De Martino T, Punzo C, Rivieccio V, Verdoliva A:Affinity purification of IgG monoclonal antibodies using the D-PAM synthetic ligand:chromatographic comparison with protein A and thermodynamic investigation of the D-PAM/IgG interaction. J Immunol Methods 2008,333(1-2):126-138.
8. Gaza-Bulseco G, Faldu S, Hurkmans K, Chumsae C, Liu H:Effect of methionine oxidation of a recombinant monoclonal antibody on the binding affinity to protein A and protein G. J Chromatogr B Analyt Technol Biomed Life Sci 2008,870(1):55-62.
9. Jefferson JA, Johnson RJ:Experimental mesangial proliferative glomerulonephritis (the anti-Thy-1.1 model). J Nephrol 1999, 12(5):297-307.
1. Izumi Y, Izumiya Y, Shiota M, Yukimura T, Shiojima S, Yamada M, Kadowaki T, Katsuma S, Hirasawa A, Tsujimoto G et al: Gene expression profile in experimental mesangial proliferative glomerulonephritis. J Pharmacol Sci 2004,96(1):91-94.
2. Sadlier DM, Ouyang X, McMahon B, Mu W, Ohashi R, Rodgers K, Murray D, Nakagawa T, Godson C, Doran P et al: Microarray and bioinformatic detection of novel and established genes expressed in experimental anti-Thyl nephritis. Kidney Int 2005,68(6):2542-2561.
3. Xu JH, Qiu W, Wang YW, Xu J, Tong JX, Gao LJ, Xu WH, Wu YQ: Gene expression profile and overexpression of apoptosis-related genes (NGFI-B and Gadd 45 gamma) in early phase of Thy-1 nephritis model. Cell Tissue Res 2006,326(1):159-168.
4. Ahn JD, Morishita R, Kaneda Y, Kim HJ, Kim YD, Lee HJ, Lee KU, Park JY, Kim YH, Park KK et al: Transcription factor decoy for AP-1 reduces mesangial cell proliferation and extracellular matrix production in vitro and in vivo. Gene Ther 2004,11(11):916-923.
5. Tomita N, Kim JY, Gibbons GH, Zhang L, Kaneda Y, Stahl RA, Ogborn M, Venderville B, Morishita R, Baran D et al: Gene therapy with an E2F transcription factor decoy inhibits cell cycle progression in rat anti-Thy 1 glomerulonephritis. Int J Mol Med 2004,13(5):629-636.
6. Bokemeyer D, Ostendorf T, Kunter U, Lindemann M, Kramer HJ, Floege
J:Differential activation of mitogen-activated protein kinases in experimental mesangioproliferative glomerulonephritis. J Am Soc Nephrol 2000,11(2):232-240.
7. Moyes KM, Drackley JK, Morin DE, Bionaz M, Rodriguez-Zas SL, Everts RE, Lewin HA, Loor JJ:Gene network and pathway analysis of bovine mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPARgamma signaling as potential mechanism for the negative relationships between immune response and lipid metabolism. BMC Genomics 2009,10:542.
8. Li ZD, Hu XW, Wang YT, Fang J:Apigenin inhibits proliferation of ovarian cancer A2780 cells through Idl. FEBS Lett 2009, 583(12):1999-2003.
9. Jiang X, Zhang J, Xia M, Qiu W, Wang H, Zhao D, Wang Y:Role of activating transcription factor 3 (ATF3) in sublytic C5b-9-induced glomerular mesangial cell apoptosis. Cell Mol Immunol,7(2):143-151.
10. Huang X, Li X, Guo B:KLF6 induces apoptosis in prostate cancer cells through up-regulation of ATF3. J Biol Chem 2008,283(44):29795-29801.
11. Liu J, Du T, Yuan Y, He Y, Tan Z, Liu Z:KLF6 inhibits estrogen receptor-mediated cell growth in breast cancer via a c-Src-mediated pathway. Mol Cell Biochem,335(1-2):29-35.
12. Unoki M, Nakamura Y:EGR2 induces apoptosis in various cancer cell lines by direct transactivation of BNIP3L and BAK. Oncogene 2003, 22(14):2172-2185.
13. Wu Q, Jin H, Yang Z, Luo G, Lu Y, Li K, Ren G, Su T, Pan Y, Feng B et al: MiR-150 promotes gastric cancer proliferation by negatively regulating the pro-apoptotic gene EGR2. Biochem Biophys Res Commun, 392(3):340-345.
14. Li D, Das S, Yamada T, Samuels HH:The NRIF3 family of transcriptional coregulators induces rapid and profound apoptosis in breast cancer cells. Mol Cell Biol 2004,24(9):3838-3848.
15. Tinnikov AA, Yeung KT, Das S, Samuels HH:Identification of a novel pathway that selectively modulates apoptosis of breast cancer cells. Cancer Res 2009,69(4):1375-1382.
16. Zhang L, Huang H, Wu K, Wang M, Wu B:Impact of BTG2 expression on proliferation and invasion of gastric cancer cells in vitro. Mol Biol Rep 2009.
17. Romieu-Mourez R, Solis M, Nardin A, Goubau D, Baron-Bodo V, Lin R, Massie B, Salcedo M, Hiscott J:Distinct roles for IFN regulatory factor (IRF)-3 and IRF-7 in the activation of antitumor properties of human macrophages. Cancer Res 2006,66(21):10576-10585.
18. Li Q, Tang L, Roberts PC, Kraniak JM, Fridman AL, Kulaeva OI, Tehrani OS, Tainsky MA:Interferon regulatory factors IRF5 and IRF7 inhibit growth and induce senescence in immortal Li-Fraumeni fibroblasts. Mol Cancer Res 2008,6(5):770-784.
19. Burchert A, Cai D, Hofbauer LC, Samuelsson MK, Slater EP, Duyster J, Ritter M, Hochhaus A, Muller R, Eilers M et al: Interferon consensus sequence binding protein (ICSBP; IRF-8) antagonizes BCR/ABL and down-regulates bcl-2. Blood 2004,103(9):3480-3489.
20. Takaoka A, Hayakawa S, Yanai H, Stoiber D, Negishi H, Kikuchi H, Sasaki S, Imai K, Shibue T, Honda K et al: Integration of interferon-alpha/beta signalling to p53 responses in tumour suppression and antiviral defence. Nature 2003,424(6948):516-523.
21. Kasof GM, Goyal L, White E:Btf, a novel death-promoting transcriptional repressor that interacts with Bcl-2-related proteins. Mol Cell Biol 1999, 19(6):4390-4404.
22. Linggi MS, Burke TL, Williams BB, Harrington A, Kraemer R, Hempstead BL, Yoon SO, Carter BD:Neurotrophin receptor interacting factor (NRIF) is an essential mediator of apoptotic signaling by the p75 neurotrophin receptor. J Biol Chem 2005,280(14):13801-13808.
23. Bai L, Merchant JL:ZBP-89 promotes growth arrest through stabilization of p53. Mol Cell Biol 2001,21(14):4670-4683.
24. Inoue K, Roussel MF, Sherr CJ:Induction of ARF tumor suppressor gene expression and cell cycle arrest by transcription factor DMP1. Proc Natl Acad Sci USA 1999,96(7):3993-3998.
25. Hayashi K, Yokozaki H, Naka K, Yasui W, Lotan R, Tahara E: Overexpression of retinoic acid receptor beta induces growth arrest and apoptosis in oral cancer cell lines. Jpn J Cancer Res 2001,92(1):42-50.
26. Yang Q, Shan L, Yoshimura G, Nakamura M, Nakamura Y, Suzuma T, Umemura T, Mori I, Sakurai T, Kakudo K:5-aza-2'-deoxycytidine induces retinoic acid receptor beta 2 demethylation, cell cycle arrest and growth inhibition in breast carcinoma cells. Anticancer Res 2002, 22(5):2753-2756.
27. Oda A, Katayose Y, Yabuuchi S, Yamamoto K, Mizuma M, Shirasou S, Onogawa T, Ohtsuka H, Yoshida H, Hayashi H et al: Clock gene mouse period2 overexpression inhibits growth of human pancreatic cancer cells and has synergistic effect with cisplatin. Anticancer Res 2009, 29(4):1201-1209.
28. Peng S, Wu H, Mo YY, Watabe K, Pauza ME:c-Maf increases apoptosis in peripheral CD8 cells by transactivating Caspase 6. Immunology 2009, 127(2):267-278.
29. Camacho CP, Latini FR, Oler G, Hojaij FC, Maciel RM, Riggins GJ, Cerutti JM:Down-regulation of NR4A1 in follicular thyroid carcinomas is restored following lithium treatment. Clin Endocrinol (Oxf) 2009, 70(3):475-483.
30. Paulson KE, Rieger-Christ K, McDevitt MA, Kuperwasser C, Kim J, Unanue VE, Zhang X, Hu M, Ruthazer R, Berasi SP et al: Alterations of the HBP1 transcriptional repressor are associated with invasive breast cancer. Cancer Res 2007,67(13):6136-6145.
31. Kikuchi K, Kawahara K, Biswas KK, Ito T, Tancharoen S, Morimoto Y, Matsuda F, Oyama Y, Takenouchi K, Miura N et al:Minocycline attenuates both OGD-induced HMGB1 release and HMGB1-induced cell death in ischemic neuronal injury in PC 12 cells. Biochem Biophys Res Commun 2009,385(2):132-136.
32. Carey JP, Asirvatham AJ, Galm O, Ghogomu TA, Chaudhary J:Inhibitor of differentiation 4 (Id4) is a potential tumor suppressor in prostate cancer. BMC Cancer 2009,9:173.
33. Wechsler DS, Shelly CA, Petroff CA, Dang CV:MXI1, a putative tumor suppressor gene, suppresses growth of human glioblastoma cells. Cancer 1997,57(21):4905-4912.
34. De Gottardi A, Dumonceau JM, Bruttin F, Vonlaufen A, Morard I, Spahr L, Rubbia-Brandt L, Frossard JL, Dinjens WN, Rabinovitch PS et al: Expression of the bile acid receptor FXR in Barrett's esophagus and enhancement of apoptosis by guggulsterone in vitro. Mol Cancer 2006, 5:48.
35. Maran RR, Thomas A, Roth M, Sheng Z, Esterly N, Pinson D, Gao X, Zhang Y, Ganapathy V, Gonzalez FJ et al: Farnesoid X receptor deficiency in mice leads to increased intestinal epithelial cell proliferation and tumor development. J Pharmacol Exp Ther 2009,328(2):469-477.
36. Zhang XL, Simmen FA, Michel FJ, Simmen RC:Increased expression of the Zn-finger transcription factor BTEB1 in human endometrial cells is correlated with distinct cell phenotype, gene expression patterns, and proliferative responsiveness to serum and TGF-betal. Mol Cell Endocrinol 2001,181(1-2):81-96.
37. Wu JT, Han BM, Yu SQ, Wang HP, Xia SJ:Androgen Receptor Is a Potential Therapeutic Target for Bladder Cancer. Urology.
38. Yu SQ, Han BM, Shao Y, Wu JT, Zhao FJ, Liu HT, Sun XW, Tang YQ, Xia SJ:Androgen receptor functioned as a suppressor in the prostate cancer cell line PC3 in vitro and in vivo. Chin Med J (Engl) 2009, 122(22):2779-2783.
39. Cortes-Wanstreet MM, Giedzinski E, Limoli CL, Luderer U: Overexpression of glutamate-cysteine ligase protects human COV434 granulosa tumour cells against oxidative and gamma-radiation-induced cell death. Mutagenesis 2009,24(3):211-224.
40. Okouchi M, Okayama N, Alexander JS, Aw TY:NRF2-dependent glutamate-L-cysteine ligase catalytic subunit expression mediates insulin protection against hyperglycemia-induced brain endothelial cell apoptosis. Curr Neurovasc Res 2006,3(4):249-261.
41. Bokemeyer D, Panek D, Kramer HJ, Lindemann M, Kitahara M, Boor P, Kerjaschki D, Trzaskos JM, Floege J, Ostendorf T:In vivo identification of the mitogen-activated protein kinase cascade as a central pathogenic pathway in experimental mesangioproliferative glomerulonephritis. J Am Soc Nephrol 2002,13(6):1473-1480.
42. Kanegae K, Tamura M, Kabashima N, Serino R, Tokunaga M, Oikawa S, Nakashima Y:Synergistic induction of monocyte chemoattractant protein-1 by integrins and platelet-derived growth factor via focal adhesion kinase in mesangial cells. Nephrol Dial Transplant 2005, 20(10):2080-2088.
43. Harper L, Kashiwagi Y, Pusey CD, Hendry BM, Domin J:Platelet-derived growth factor reorganizes the actin cytoskeleton through 3-phosphoinositide-dependent and 3-phosphoinositide-independent mechanisms in human mesangial cells. Nephron Physiol 2007, 107(2):p45-56.
44. Khwaja A, Sharpe CC, Noor M, Hendry BM:The role of geranylgeranylated proteins in human mesangial cell proliferation. Kidney Int 2006,70(7):1296-1304.
45. Marti HP:The role of matrix metalloproteinases in the activation of mesangial cells. Transpl Immunol 2002,9(2-4):97-100.
46. Han SY, Chang EJ, Choi HJ, Kwak CS, Park SB, Kim HC, Mun KC: Apoptosis by cyclosporine in mesangial cells. Transplant Proc 2006, 38(7):2244-2246.
1. Yoshida Y, Miyazaki K, Kamiie J, Sato M, Okuizumi S, Kenmochi A, Kamijo K, Nabetani T, Tsugita A, Xu B et al: Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics 2005,5(4):1083-1096.
2. Park MR, Wang EH, Jin DC, Cha JH, Lee KH, Yang CW, Kang CS, Choi YJ:Establishment of a 2-D human urinary proteomic map in IgA nephropathy. Proteomics 2006,6(3):1066-1076.
3. Haubitz M, Wittke S, Weissinger EM, Walden M, Rupprecht HD, Floege J, Haller H, Mischak H:Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 2005,67(6):2313-2320.
4. Julian BA, Wittke S, Novak J, Good DM, Coon JJ, Kellmann M, Zurbig P, Schiffer E, Haubitz M, Moldoveanu Z et al: Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis 2007,28(23):4469-4483.
5. Hoorn EJ, Hoffert JD, Knepper MA:The application of DIGE-based proteomics to renal physiology. Nephron Physiol 2006,104(1):p61-72.
6. Nazeer K, Janech MG, Lin JJ, Ryan KJ, Arthur JM, Budisavljevic MN: Changes in protein profiles during course of experimental glomerulonephritis. Am JPhysiol Renal Physiol 2009,296(1):F186-193.
7. Perluigi M, Sultana R, Cenini G, Di Domenico F, Memo M, Pierce WM, Coccia R, Butterfield DA:Redox proteomics identification of 4-hydroxynonenal-modified brain proteins in Alzheimer's disease:Role of lipid peroxidation in Alzheimer's disease pathogenesis. Proteomics Clin Appl 2009,3(6):682-693.
8. Nilo R, Saffie C, Lilley K, Baeza-Yates R, Cambiazo V, Campos-Vargas R, Gonzalez M, Meisel LA, Retamales J, Silva H et al: Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics 2010,11:43.
9. Chang TS, Cho CS, Park S, Yu S, Kang SW, Rhee SG:Peroxiredoxin Ⅲ, a mitochondrion-specific peroxidase, regulates apoptotic signaling by mitochondria. JBiol Chem 2004,279(40):41975-41984.
10. Walsh B, Pearl A, Suchy S, Tartaglio J, Visco K, Phelan SA: Overexpression of Prdx6 and resistance to peroxide-induced death in Hepal-6 cells:Prdx suppression increases apoptosis. Redox Rep 2009, 14(6):275-284.
11. Sasazawa Y, Futamura Y, Tashiro E, Imoto M:Vacuolar H+-ATPase inhibitors overcome Bcl-xL-mediated chemoresistance through restoration of a caspase-independent apoptotic pathway. Cancer Sci 2009, 100(8):1460-1467.
12. Rousalova I, Krepela E, Prochazka J, Cermak J, Benkova K:Expression of proteinase inhibitor-9/serpinB9 in non-small cell lung carcinoma cells and tissues. Int J Oncol 2010,36(1):275-283.
13. Su YR, Dove DE, Major AS, Hasty AH, Boone B, Linton MF, Fazio S: Reduced ABCA1-mediated cholesterol efflux and accelerated atherosclerosis in apolipoprotein E-deficient mice lacking macrophage-derived ACAT1. Circulation 2005,111(18):2373-2381.
14. Kim SC, Stice JP, Chen L, Jung JS, Gupta S, Wang Y, Baumgarten G, Trial J, Knowlton AA:Extracellular heat shock protein 60, cardiac myocytes, and apoptosis. Circ Res 2009,105(12):1186-1195.
15. Salama SA, Kamel MW, Botting S, Salih SM, Borahay MA, Hamed AA, Kilic GS, Saeed M, Williams MY, Diaz-Arrastia CR: Catechol-o-methyltransferase expression and 2-methoxyestradiol affect microtubule dynamics and modify steroid receptor signaling in leiomyoma cells. PLoS One 2009,4(10):e7356.
16. Vichalkovski A, Gresko E, Cornils H, Hergovich A, Schmitz D, Hemmings BA:NDR kinase is activated by RASSF1A/MST1 in response to Fas receptor stimulation and promotes apoptosis. Curr Biol 2008, 18(23):1889-1895.
17. Tang SJ, Ho MY, Cho HC, Lin YC, Sun GH, Chi KH, Wang YS, Jhou RS, Yang W, Sun KH:Phosphoglycerate kinase 1-overexpressing lung cancer cells reduce cyclooxygenase 2 expression and promote anti-tumor immunity in vivo. Int J Cancer 2008,123(12):2840-2848.
18. Lin CH, Chung MY, Chen WB, Chien CH:Growth inhibitory effect of the human NIT2 gene and its allelic imbalance in cancers. FEBS J 2007, 274(11):2946-2956.
19. Yu W, Ding X, Chen F, Liu M, Shen S, Gu X, Yu L:The phosphorylation of SEPT2 on Ser218 by casein kinase 2 is important to hepatoma carcinoma cell proliferation. Mol Cell Biochem 2009,325(1-2):61-67.
20. Ding L, Wang Z, Yan J, Yang X, Liu A, Qiu W, Zhu J, Han J, Zhang H, Lin J et al: Human four-and-a-half LIM family members suppress tumor cell growth through a TGF-beta-like signaling pathway. J Clin Invest 2009, 119(2):349-361.
21. Qian Z, Mao L, Fernald AA, Yu H, Luo R, Jiang Y, Anastasi J, Valk PJ, Delwel R, Le Beau MM:Enhanced expression of FHL2 leads to abnormal myelopoiesis in vivo. Leukemia 2009,23(9):1650-1657.
22. Wear MA, Cooper JA:Capping protein binding to S100B:implications for the tentacle model for capping the actin filament barbed end. J Biol Chem 2004,279(14):14382-14390.
23. Wright NT, Cannon BR, Wilder PT, Morgan MT, Varney KM, Zimmer DB, Weber DJ:Solution structure of S100A1 bound to the CapZ peptide (TRTK12). JMol Biol 2009,386(5):1265-1277.
24. Tsoporis JN, Mohammadzadeh F, Parker TG:S100B:a multifunctional role in cardiovascular pathophysiology. Amino Acids 2010.
1. O'Farrell PH:High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975,250(10):4007-4021.
2. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M:Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001,1(3):377-396.
3. Han DK, Eng J, Zhou H, Aebersold R:Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 2001,19(10):946-951.
4. Sethuraman M, McComb ME, Heibeck T, Costello CE, Cohen RA: Isotope-coded affinity tag approach to identify and quantify oxidant-sensitive protein thiols. Mol Cell Proteomics 2004,3(3):273-278.
5. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S et al: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004,3(12):1154-1169.
6. Levin Y, Schwarz E, Wang L, Leweke FM, Bahn S:Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples. J Sep Sci 2007,30(14):2198-2203.
7. Cutillas PR, Vanhaesebroeck B:Quantitative profile of five murine core proteomes using label-free functional proteomics. Mol Cell Proteomics 2007,6(9):1560-1573.
8. Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW:Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002,48(8):1296-1304.
9. Dai S, Wang X, Liu L, Liu J, Wu S, Huang L, Xiao X, He D:Discovery and identification of Serum Amyloid A protein elevated in lung cancer serum. Sci China C Life Sci 2007,50(3):305-311.
10. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS:Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999,20(18):3551-3567.
11. Zhang W, Chait BT:ProFound:an expert system for protein identification using mass spectrometric peptide mapping information. Anal Chem 2000, 72(11):2482-2489.
12. Marshall T, Williams KM:Two-dimensional electrophoresis of human urine and cerebrospinal fluid following protein concentration by dye precipitation. Biochem Soc Trans 1997,25(4):S657.
13. Heine G, Raida M, Forssmann WG:Mapping of peptides and protein fragments in human urine using liquid chromatography-mass spectrometry. J Chromatogr A 1997,776(1):117-124.
14. Thongboonkerd V, McLeish KR, Arthur JM, Klein JB:Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 2002,62(4):1461-1469.
15. Schaub S, Wilkins J, Weiler T, Sangster K, Rush D, Nickerson P:Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004,65(1):323-332.
16. Wittke S, Fliser D, Haubitz M, Bartel S, Krebs R, Hausadel F, Hillmann M, Golovko I, Koester P, Haller H et al: Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A 2003,1013(1-2):173-181.
17. Zurbig P, Schiffer E, Mischak H:Capillary electrophoresis coupled to mass spectrometry for proteomic profiling of human urine and biomarker discovery. Methods Mol Biol 2009,564:105-121.
18. Haubitz M, Wittke S, Weissinger EM, Walden M, Rupprecht HD, Floege J, Haller H, Mischak H:Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 2005,67(6):2313-2320.
19. Park MR, Wang EH, Jin DC, Cha JH, Lee KH, Yang CW, Kang CS, Choi YJ:Establishment of a 2-D human urinary proteomic map in IgA nephropathy. Proteomics 2006,6(3):1066-1076.
20. Yokota H, Hiramoto M, Okada H, Kanno Y, Yuri M, Morita S, Naitou M, Ichikawa A, Katoh M, Suzuki H:Absence of increased alpha1-microglobulin in IgA nephropathy proteinuria. Mol Cell Proteomics 2007,6(4):738-744.
21. Jiang H, Guan G, Zhang R, Liu G, Cheng J, Hou X, Cui Y:Identification of urinary soluble E-cadherin as a novel biomarker for diabetic nephropathy. Diabetes Metab Res Rev 2009,25(3):232-241.
22. Rossing K, Mischak H, Dakna M, Zurbig P, Novak J, Julian BA, Good DM, Coon JJ, Tarnow L, Rossing P:Urinary proteomics in diabetes and CKD. JAm Soc Nephrol 2008,19(7):1283-1290.
23. Otu HH, Can H, Spentzos D, Nelson RG, Hanson RL, Looker HC, Knowler WC, Monroy M, Libermann TA, Karumanchi SA et al; Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy. Diabetes Care 2007, 30(3):638-643.
24. Zhang X, Jin M, Wu H, Nadasdy T, Nadasdy G, Harris N, Green-Church K, Nagaraja H, Birmingham DJ, Yu CY et al: Biomarkers of lupus nephritis determined by serial urine proteomics. Kidney Int 2008, 74(6):799-807.
25. Mosley K, Tam FW, Edwards RJ, Crozier J, Pusey CD, Lightstone L Urinary proteomic profiles distinguish between active and inactive lupus nephritis. Rheumatology (Oxford) 2006,45(12):1497-1504.
26. Ngai HH, Sit WH, Jiang PP, Xu RJ, Wan JM, Thongboonkerd V:Serial changes in urinary proteome profile of membranous nephropathy: implications for pathophysiology and biomarker discovery. J Proteome Res 2006,5(11):3038-3047.
27. Yoshida Y, Miyazaki K, Kamiie J, Sato M, Okuizumi S, Kenmochi A, Kamijo K, Nabetani T, Tsugita A, Xu B et al: Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics 2005,5(4):1083-1096.
28. Miyamoto M, Yoshida Y, Taguchi I, Nagasaka Y, Tasaki M, Zhang Y, Xu B, Nameta M, Sezaki H, Cuellar LM et al: In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J Proteome Res 2007,6(9):3680-3690.
29. Nazeer K, Janech MG, Lin JJ, Ryan KJ, Arthur JM, Budisavljevic MN: Changes in protein profiles during course of experimental glomerulonephritis. Am J Physiol Renal Physiol 2009,296(1):F 186-193.
30. Xu BJ, Shyr Y, Liang X, Ma LJ, Donnert EM, Roberts JD, Zhang X, Kon V, Brown NJ, Caprioli RM et al: Proteomic patterns and prediction of glomerulosclerosis and its mechanisms. J Am Soc Nephrol 2005, 16(10):2967-2975.
31. Sitek B, Potthoff S, Schulenborg T, Stegbauer J, Vinke T, Rump LC, Meyer HE, Vonend O, Stuhler K:Novel approaches to analyse glomerular proteins from smallest scale murine and human samples using DIGE saturation labelling. Proteomics 2006,6(15):4337-4345.
32. Jiang XS, Tang LY, Cao XJ, Zhou H, Xia QC, Wu JR, Zeng R: Two-dimensional gel electrophoresis maps of the proteome and phosphoproteome of primitively cultured rat mesangial cells. Electrophoresis 2005,26(23):4540-4562.
33. Ramachandra Rao SP, Wassell R, Shaw MA, Sharma K:Profiling of human mesangial cell subproteomes reveals a role for calmodulin in glucose uptake. Am J Physiol Renal Physiol 2007,292(4):F1182-1189.
34. Viney RL, Morrison AA, van den Heuvel LP, Ni L, Mathieson PW, Saleem MA, Ladomery MR:A proteomic investigation of glomerular podocytes from a Denys-Drash syndrome patient with a mutation in the Wilms tumour suppressor gene WT1. Proteomics 2007,7(5):804-815.