Effects of all-trans retinoic acid on metabolic gene expression in the glioma cell line SHG-44

BACKGROUND： Genetic abnormalities and changes in gene expression have been shown in various grades of glioma. However, the relationship between gene expression patterns and pathways related to malignant transformation of glioma remains poorly understood. OBJECTIVE： To screen differentially expressed genes between normal and all-trans retinoic acid-treated glioma cell line SHG-44 cells with a complementary DNA （cDNA） microarray. DESIGN, TIME AND SETTING： The genomics, in vitro study was performed at the Laboratory of Neurobiology, Third Military Medical University of Chinese PLA, China from January to October 2007. MATERIALS： The glioma cell line SHG-44 was provided by the Third Military Medical University of Chinese PLA. AII-trans retinoic acid was purchased from Sigma, USA. cDNA microarray was purchased from City University of Hong Kong. METHODS： The glioma cell line SHG-44 was treated with 10 μmol/L all-trans retinoic acid for 3 days Differentiation-related genes were determined using cDNA microarray. MAIN OUTCOME MEASURES： Gene expression patterns were compared between normal and all-trans retinoic acid-treated SHG-44 cells. Differentially expressed genes were randomly selected and determined by Northern blot analysis. RESULTS： Northern blot analysis revealed downregulated RPL 13 gene expression and upregulated SOD2 gene expression, which was identical to cDNA microarray results. Five differentially expressed genes （TPI1, BPGM, ALDOA, LDHA, and RRM1） were shown to be involved in cell metabolism, in six metabolic pathways. Four differentially expressed genes （TPI1, BPGM, ALDOA, and LDHA） were associated with carbohydrate metabolism, such as fructose metabolism, pyruvic acid metabolism, pentose phosphate pathway, glycolysis, and gluconeogenesis. One differentially expressed gene （RRM1） was correlated with purine and pyrimidine metabolism. CONCLUSION： Five metabolic genes （TPI1, BPGM, ALDOA, LDHA, and RRM1）, which participate in cell carbohydrate and nucleotide metabolism, were shown to closely correlate with glioma development.     

Gene expression in retinoic acid-induced neural tube defects

BACKGROUND： Neural tube defects can be induced by abnormal factors in vivo or in vitro during development. However, the molecular mechanisms of neural tube defect induction, and the related gene expression and regulation are still unknown. OBJECTIVE： To compare the differences in gene expression between normal embryos and those with neural tube defects. DESIGN, TIME AND SETTING： A neural development study was performed at the Department of Neurobiology, Third Military Medical University of Chinese PLA between January 2006 and October 2007. MATERIALS： Among 120 adult Kunming mice, 60 pregnant mice were randomly and evenly divided into a retinoic acid group （n = 30） and a normal control group （n =30）. The retinoic acid was produced by Sigma, USA, the gene microarray by the Amersham Pharmacia Company, Hong Kong, and the gene sequence was provided by the Incyte database, USA. METHODS： Retinoic acid was administered to prepare models of neural tube defects, and corn oil was similarly administered to the normal control group. Total RNA was extracted from embryonic tissue of the two groups using a Trizol kit, and a cDNA microarray containing 1 100 known genes was used to compare differences in gene expression between the normal control group and the retinoic acid group on embryonic （E） day 10.5 and 11.5. Several differentially expressed genes were randomly selected from the two groups for Northern blotting, to verify the results of the cDNA microarray. MAIN OUTCOME MEASURES： Morphological changes and differential gene expression between the normal control group and the retinoic acid group. RESULTS： Anatomical microscopy demonstrated that an intact closure of the brain was formed in the normal mouse embryos by days E10.5 and E11.5. The cerebral appearance was full and smooth, and the surface of the spine was intact. However, in the retinoic acid group on days E10.5 and E11.5, there were more dead embryos. Morphological malformations typically included non-closure at the top of the cranium and abnormal changes of the metencephalon and face. cDNA microarray analysis suggested that the changes in expression of seven different genes were similar on both days E10.5 and E11.5. These were downregulation of NekT, Igfbp5, Zw10, Csf3r, Psmc6 and Rb 1, and upregulation of Apoa-4. This study also indicated that Cdk5 expression was downregulated in the retinoic acid group on day E11.5. The results of the cDNA microarray analysis were partly confirmed by Northern blotting. CONCLUSION： Cdk5, Nek7, Igfbp5, Zw10, Csf3r, Psmc6, Rb1 and Apoa-4 may be key factors in retinoic acid-induced neural tube defects.     

Gene expression in retinoic acid-induced neural tube defects A cDNA microarray analysis

BACKGROUND:Neural tube defects can be induced by abnormal factors in vivo or in vitro during development.However,the molecular mechanisms of neural tube defect induction,and the related gene expression and regulation are still unknown. OBJECTIVE:To compare the differences in gene expression between normal embryos and those with neural tube defects. DESIGN,TIME AND SETTING:A neural development study was performed at the Department of Neurobiology,Third Military Medical University of Chinese PLA between Ja...     

Differential gene and protein expression between rat tibial nerve and common peroneal nerve during wallerian degeneration

Wallerian degeneration and nerve regeneration after injury are complex processes involving many genes, proteins and cytokines. After different peripheral nerve injuries the regeneration rate can differ. Whether this is caused by differential expression of genes and proteins during Wallerian degeneration remains unclear. The right tibial nerve and the common peroneal nerve of the same rat were exposed and completely cut through and then sutured in the same horizontal plane. On days 1, 7, 14, and 21 after surgery, 1–2 cm of nerve tissue distal to the suture site was dissected out from the tibial and common peroneal nerves. The differences in gene and protein expression during Wallerian degeneration of the injured nerves were then studied by RNA sequencing and proteomic techniques. In the tibial and common peroneal nerves, there were 1718, 1374, 1187, and 2195 differentially expressed genes, and 477, 447, 619, and 495 differentially expressed proteins on days 1, 7, 14, and 21 after surgery, respectively. Forty-seven pathways were activated during Wallerian degeneration. Three genes showing significant differential expression by RNA sequencing(Hoxd4, Lpcat4 and Tbx1) were assayed by real-time quantitative polymerase chain reaction. RNA sequencing and real-time quantitative polymerase chain reaction results were consistent. Our findings showed that expression of genes and proteins in injured tibial and the common peroneal nerves were significantly different during Wallerian degeneration at different time points. This suggests that the biological processes during Wallerian degeneration are different in different peripheral nerves after injury. The procedure was approved by the Animal Experimental Ethics Committee of the Second Military Medical University, China(approval No. CZ20160218) on February 18, 2016.     

人脑胶质瘤CXCL12基因的甲基化分析研究

Objective To detect the methylation status of CXCL12 gene and the mRNA expression of CXCL12, CXCR4 and DNA methyhransferases (DNMTs) in glioma, and to analyze the methylation regulation and mechanism of CXCL12/CXCR4 signaling axis in the malignant progress of glioma. Methods The mRNA expression of CXCL12, CXCR4, DNMT1, DNMT3A and DNMT3B was detected by the semi - quantitative RT - PCR and real - time PCR in 76 gliomas and 10 normal brain tissues. The methylation status of CXCL12 in glioma was also studied by the methylation specific PCR. Results ( 1 ) The mRNA expression of CXCR4 in glioma increased with WHO grades. (2) Methylation of CXCL12 was detected in 34. 2% ( 26/76 ) of gliomas, but the methylation rate decreased with WHO grades. ( 3 ) Epigenetic inactivation of CXCL12 mainly happened in low- grade gliomas, and the CXCL12 mRNA levels were closely related to its methylation status. (4) The expression levels of these three DNMT genes were significantly higher in the CXCL12 - methylated gliomas than in the CXCL12 - unmethylated ones. Conclusion The CXCR4 gene may be a marker of aggressive biological behavior of glioma. The CXCL12 promoter hypermethylation is detected mainly in low - grade gliomas. And the methylaiton of CXCL12 gene cause the down - regulation of its mRNA levels in low - grade gliomas. The high expressions of DNMT1、DNMT3A and DNMT3B may be the potential mechanism of CXCL12 methylation.     

人脑胶质瘤CXCL12基因的甲基化分析研究

Objective To detect the methylation status of CXCL12 gene and the mRNA expression of CXCL12, CXCR4 and DNA methyhransferases (DNMTs) in glioma, and to analyze the methylation regulation and mechanism of CXCL12/CXCR4 signaling axis in the malignant progress of glioma. Methods The mRNA expression of CXCL12, CXCR4, DNMT1, DNMT3A and DNMT3B was detected by the semi - quantitative RT - PCR and real - time PCR in 76 gliomas and 10 normal brain tissues. The methylation status of CXCL12 in glioma was also studied by the methylation specific PCR. Results ( 1 ) The mRNA expression of CXCR4 in glioma increased with WHO grades. (2) Methylation of CXCL12 was detected in 34. 2% ( 26/76 ) of gliomas, but the methylation rate decreased with WHO grades. ( 3 ) Epigenetic inactivation of CXCL12 mainly happened in low- grade gliomas, and the CXCL12 mRNA levels were closely related to its methylation status. (4) The expression levels of these three DNMT genes were significantly higher in the CXCL12 - methylated gliomas than in the CXCL12 - unmethylated ones. Conclusion The CXCR4 gene may be a marker of aggressive biological behavior of glioma. The CXCL12 promoter hypermethylation is detected mainly in low - grade gliomas. And the methylaiton of CXCL12 gene cause the down - regulation of its mRNA levels in low - grade gliomas. The high expressions of DNMT1、DNMT3A and DNMT3B may be the potential mechanism of CXCL12 methylation.     

人脑胶质瘤CXCL12基因的甲基化分析研究

Objective To detect the methylation status of CXCL12 gene and the mRNA expression of CXCL12, CXCR4 and DNA methyhransferases (DNMTs) in glioma, and to analyze the methylation regulation and mechanism of CXCL12/CXCR4 signaling axis in the malignant progress of glioma. Methods The mRNA expression of CXCL12, CXCR4, DNMT1, DNMT3A and DNMT3B was detected by the semi - quantitative RT - PCR and real - time PCR in 76 gliomas and 10 normal brain tissues. The methylation status of CXCL12 in glioma was also studied by the methylation specific PCR. Results ( 1 ) The mRNA expression of CXCR4 in glioma increased with WHO grades. (2) Methylation of CXCL12 was detected in 34. 2% ( 26/76 ) of gliomas, but the methylation rate decreased with WHO grades. ( 3 ) Epigenetic inactivation of CXCL12 mainly happened in low- grade gliomas, and the CXCL12 mRNA levels were closely related to its methylation status. (4) The expression levels of these three DNMT genes were significantly higher in the CXCL12 - methylated gliomas than in the CXCL12 - unmethylated ones. Conclusion The CXCR4 gene may be a marker of aggressive biological behavior of glioma. The CXCL12 promoter hypermethylation is detected mainly in low - grade gliomas. And the methylaiton of CXCL12 gene cause the down - regulation of its mRNA levels in low - grade gliomas. The high expressions of DNMT1、DNMT3A and DNMT3B may be the potential mechanism of CXCL12 methylation.     

人脑胶质瘤CXCL12基因的甲基化分析研究

Objective To detect the methylation status of CXCL12 gene and the mRNA expression of CXCL12, CXCR4 and DNA methyhransferases (DNMTs) in glioma, and to analyze the methylation regulation and mechanism of CXCL12/CXCR4 signaling axis in the malignant progress of glioma. Methods The mRNA expression of CXCL12, CXCR4, DNMT1, DNMT3A and DNMT3B was detected by the semi - quantitative RT - PCR and real - time PCR in 76 gliomas and 10 normal brain tissues. The methylation status of CXCL12 in glioma was also studied by the methylation specific PCR. Results ( 1 ) The mRNA expression of CXCR4 in glioma increased with WHO grades. (2) Methylation of CXCL12 was detected in 34. 2% ( 26/76 ) of gliomas, but the methylation rate decreased with WHO grades. ( 3 ) Epigenetic inactivation of CXCL12 mainly happened in low- grade gliomas, and the CXCL12 mRNA levels were closely related to its methylation status. (4) The expression levels of these three DNMT genes were significantly higher in the CXCL12 - methylated gliomas than in the CXCL12 - unmethylated ones. Conclusion The CXCR4 gene may be a marker of aggressive biological behavior of glioma. The CXCL12 promoter hypermethylation is detected mainly in low - grade gliomas. And the methylaiton of CXCL12 gene cause the down - regulation of its mRNA levels in low - grade gliomas. The high expressions of DNMT1、DNMT3A and DNMT3B may be the potential mechanism of CXCL12 methylation.     

Identification of tumor invasion-related differentially expressed genes in different grades and all-trans retinoic acid-treated astrocytoma cell lines

BACKGROUND:Although several genetic aberrations and gene expressional changes have been shown to exist in tumors and different grades of astrocytomas,as well as in normal tissues,the gene profiling and ge-netic pathways associated with malignant transformation and progression remain unclear. OBJECTIVE: To identify differentially expressed genes related to tumor invasion from various grades and all-trans retinoic acid (ATRA)-treated astrocytoma cell lines by cDNA microarray. DESIGN,TIME AND SETTING: In vitro...     

全反式维甲酸抑制MDM2基因在胶质瘤细胞SHG-44中的表达

目的 探讨全反式维甲酸对胶质瘤细胞SHG-44中MDM2基因表达的影响,为进一步研究脑胶质瘤的进展机制及基因治疗提供依据.方法 分别利用cDNA微阵列与Western blot技术分析在10μmol/L全反式维甲酸(all-transretinoic acid,ATRA)处理前后的胶质瘤SHG-44细胞MDM2基因和蛋白的差异表达应用免疫组化链霉菌抗生物素蛋白-过氧化酶(Streptavidin-Peroxidase,SP)法检测Ⅱ级与Ⅳ级胶质瘤标本MDM2蛋白的表达.随机选择数个差异基因进行Northern杂交实验,以验证cDNA微阵列的结果.结果 应用cDNA微阵列检测发现,MDM2基因在ATRA处理与未处理的SHG-44细胞之间表达量的比值为0.37,提示ATRA可抑制MDM2基因在SHG-44中的表达.该结果进一步得Northern杂交实验结果的支持.Western blot分析结果显示10μmol/L ATRA处理前后胶质瘤SHG-44细胞之间MDM2蛋白的相对表达量分别为21.40±0.58和14.02±0.35(t=24.728,P=0.000),提示MDM2蛋白在SHG-44中的表达受到ATRA抑制.Ⅱ级和Ⅳ级胶质瘤标本MDM2蛋白的阳性表达率分别为24.00%(6/25)和56.52%(13/23)(X2=5.298,P=0.021),MDM2蛋白的表达随胶质瘤恶性程度的增高而增加.结论 ATRA可抑制SHG-44胶质瘤细胞中MDM2基因的表达,MDM2基因的表达水平与胶质瘤的演进有关.     

Differentially expressed genes from the glioblastoma cell line SHG-44 treated with all-trans retinoic acid in vitro

Morphology, immunocytochemistry, growth curve assay, and flow cytometry were used to investigate the effects of all-trans retinoic acid (RA) on cell proliferation, cell cycle progression and differentiation of the astrocytoma cell line SHG-44 from glioblastoma multiforme (World Health Organization grade IV). The differentially expressed genes from RA-treated and normal SHG-44 were identified by cDNA microarray after the cell line SHG-44 was treated with 10 μM RA for 3 days. Validation of some differentially expressed genes was performed by Northern Blot analysis. The expression of glial fibrillary acidic protein (GFAP) was markedly increased in RA-treated SHG-44 cells. Other changes included a short shuttle shape, small nucleus, decreased karyoplasm proportion, the formation of increased thin cytoplasmic processes, reduced cell growth and a 15% increase in G0/G1 phase cell populations. In addition, 42 known genes were identified with altered expression in our cDNA microarray. There was stable down-regulation of MDM2 and UGB as well as overexpression of SOD2, CSTB, and G3BP when RA-treated SHG-44 was compared with normal SHG-44. RA simultaneously suppressed the proliferation of SHG-44 cells significantly as well as induced differentiation and altered gene expression.     

人脑胶质瘤干细胞增殖和分化过程中NOTCH-1信号通路的调控

背景：研究发现NOTCH-1信号通路在神经干细胞或神经前体细胞的自我更新、增殖及分化中起重要作用。 目的：探讨NOTCH-1信号通路在人脑胶质瘤干细胞增殖和分化过程中的调控作用。 设计、时间及地点：开放性实验,于2005-01/2007-03在解放军第三军医大学新桥医院完成。 材料：人脑胶质瘤组织、正常成人脑组织由解放军第三军医大学新桥医院神经外科提供。U251胶质瘤细胞株由解放军第三军医大学新桥医院神经外科吕胜青副教授惠赠;CHG-5胶质瘤细胞株由解放军第三军医大学西南医院病理研究所卞修武教授、姚晓红博士惠赠。 方法：取人脑胶质瘤组织、正常成人脑组织、U251及CHG-5胶质瘤细胞株,采用免疫磁珠法分选获得CD133+脑胶质瘤干细胞,加入DMEM/F12无血清培养基进行增殖培养,形成细胞克隆后,加入含体积分数为10%胎牛血清的培养液,2 h后行抗CD133和抗巢蛋白免疫荧光双标染色。 主要观察指标：人脑胶质瘤干细胞的生长和鉴定,采用WST-8法、免疫组化实验、流式细胞仪、免疫荧光双标实验检测NOTCH-1信号通路蛋白的表达。 结果：在无血清培养基中,细胞呈悬浮生长,培养24~48 h可见单个细胞开始分裂生长,形成肿瘤球,将肿瘤球转入含胎牛血清的培养基后,4 h周边细胞伸出突起并逐渐分化,24 h后肿瘤球迁移出的细胞增多,形成单细胞层。肿瘤球能同时表达干细胞标志物CD133和巢蛋白,CD133+脑胶质瘤干细胞核浆比例达2/3~3/4,突起少,胞浆中线粒体等细胞器较少,核糖体丰富,未见胶质丝等分化结构,符合干细胞超微结构特点。NOTCH-1蛋白在人脑胶质瘤组织中的表达明显强于正常成人脑组织（P < 0.01）,在CD133+ U251及CHG-5胶质瘤细胞中有很强的表达,在GFAP+和MAP2+ U251及CHG-5胶质瘤细胞中的表达强弱不等,在MBP+ U251及CHG-5胶质瘤细胞中呈弱表达或不表达。在脑胶质瘤干细胞增殖过程中能检测到较强的NOTCH-1信号通路关键基因NOTCH-1,CBF-1,HES-1 mRNA及NOTCH-1,HES-1蛋白表达;而在细胞分化时NOTCH-1信号通路关键基因NOTCH-1,CBF-1,HES-1 mRNA和HES-1蛋白表达逐渐减弱。 结论：NOTCH-1信号通路的关键蛋白分子NOTCH-1在人脑胶质瘤组织和胶质瘤细胞株中均有表达,而在正常成人脑组织中仅微弱表达。NOTCH-1信号通路关键基因NOTCH-1和HES-1的表达强弱可能参与了胶质瘤干细胞增殖和分化的调控。     

Gene expression in retinoic acid-induced neural tube defects A cDNA mieroarray analysis

BACKGROUND: Neural tube defects can be induced by abnormal factors in vivo or in vitro during development. However, the molecular mechanisms of neural tube defect induction, and the related gene expression and regulation are still unknown.OBJECTIVE: To compare the differences in gene expression between normal embryos and those with neural tube defects.DESIGN, TIME AND SETTING: A neural development study was performed at the Department of Neurobiology, Third Military Medical University of Chinese PLA between January 2006 and October 2007.MATERIALS: Among 120 adult Kunming mice, 60 pregnant mice were randomly and evenly divided into a retinoic acid group (n = 30) and a normal control group (n =30). The retinoic acid was produced by Sigma, USA, the gene microarray by the Amersham Pharmacia Company, Hong Kong, and the gene sequence was provided by the Incyte database, USA.METHODS: Retinoic acid was administered to prepare models of neural tube defects, and corn oil was similady administered to the normal control group. Total RNA was extracted from embryonic tissue of the two groups using a Trizol kit, and a cDNA microarray containing 1 100 known genes was used to compare differences in gene expression between the normal control group and the retinoic acid group on embryonic (E) clay 10.5 and 11.5. Several differentially expressed genes were randomly selected from the two groups for Northern blotting, to verify the results of the cDNA microarray.MAIN OUTCOME MEASURES: Morphological changes and differential gene expression between the normal control group and the retinoic acid group.RESULTS: Anatomical microscopy demonstrated that an intact closure of the brain was formed in the normal mouse embryos by days E10.5 and E11.5. The cerebral appearance was full and smooth, and the surface of the spine was intact. However, in the retinoic acid group on days E10.5 and E11.5, there were more dead embryos. Morphological malformations typically included non-closure at the top of the cranium and abnormal changes of the metencephalon and face.cDNA microarray analysis suggested that the changes in expression of seven different genes were similar on both days E10.5 and E11.5. These were downregulation of NekT, Igfbp5, Zw10,Csf3r, Psmc6 and Rbl, and upregulation of Apoa-4. This study also indicated that Cdk5 expression was downregulated in the retinoic acid group on day E11.5. The results of the cDNA microarray analysis were partly confirmed by Northern blotting.CONCLUSION: Cdk5, NekT, Igfbp5, ZwlO, Csf3r, Psmc6, Rb 1 and Apoa-4 may be key factors in retinoic acid-induced neural tube defects.     

Growth and radiosensitivity of irradiated human glioma cell progeny

BACKGROUND： Progenitors of the immortalized human glioma cell line, SHG-44, are significantly less sensitive to irradiation. Two hypotheses regarding the mechanism of this effect exist： several studies have suggested that there is a subgroup with different radiosensitivities in identical cell group, and the progenitors of irradiate is a adaptive response subgroup, so its radiosensitivity is descend. A second hypothesis suggests that irradiated glioma progeny have a stronger ability to repair DNA damage. This would suggest that when progeny are continuously irradiated, resistance to irradiation-induced DNA increases, and radiosensitivity decreases. OBJECTIVE： To investigate radiosensitivity and growth features after irradiation to progeny of the human glioma cell line SHG-44. DESIGN, TIME AND SETTING： A randomized, controlled experiment, which was performed at the Department of Radiology Laboratory, the First Hospital Affiliated to Soochow University, between September 2004 and January 2006. MATERIALS： The glioma cell line SHG-44 was provided by the Institute of Neuroscience, First Affiliated Hospital of Suzhou University. Propidium iodide reagent was provided by Coulter Corporation. A linear accelerator, KD-2 type, was provided by Siemens, Germany. The flow cytometer EPICS-XL was provided by Coulter Corporation. METHODS： Brain glioma SHG-44 cells were divided into four groups： SHG-44, SHG-44-2, SHG-44-6, and SHG-44-10 . The SHG-44-2, SHG-44-6, and SHG-44-10 cells were vertically irradiated with varying doses of 2, 6 and 10 Gy by a linear accelerator （6 MVX）. The cells were passaged for 15 generations and cultured in RPMI-1640 culture media. MAIN OUTCOME MEASURES： Community re-double time, mean lethal dose （D0）, extrapolation number （N）, fraction surviving fraction irradiated by 2 Gy dose （SF2）, quasi-threshold dose （Dq）, and cell cycle. RESULTS： The Population doubling time （PDT） of SHG-44-2, SHG-44-6, and SHG-44-10 cell groups was not significant （P = 0.052）. Compare     

Altered expression of immune defense genes in pilocytic astrocytomas

Pilocytic astrocytoma (WHO grade I) is a circumscribed, slowly growing, benign astrocytoma that most frequently develops in the cerebellar hemispheres and in midline structures and occurs predominantly in childhood and adolescence. In contrast to diffusely infiltrating gliomas in adults (e.g. grade II astrocytomas, oligodendrogliomas), survival of patients with pilocytic astrocytoma is excellent after surgical intervention. To search for potential molecular mechanisms underlying its benign biologic behavior, we compared gene expression profiles of pilocytic astrocytomas (8 cases) with those of normal cerebellum (4 cases), low-grade astrocytomas (WHO grade II; 15 cases), and oligodendrogliomas (WHO grade II; 17 cases) by cDNA array analysis. A number of immune system-related genes such as HLA-DRalpha, HLA-DPB1, HLA-DQB1, IgG3, IgGK, FCER1G, A2M, FCRN, IFI-56K, and DAP12 were upregulated in pilocytic astrocytomas relative to normal cerebellum, grade II astrocytomas, and oligodendrogliomas. Genes expressed at higher levels in pilocytic astrocytomas than in grade II astrocytomas and oligodendrogliomas include HLA-DRalpha, HLA-DPA1, HLA-DPB1, HLA-DQB1, A2M, TIMP1, TIMP2, CDKN1A, and SOCS3 and those expressed at lower levels include EGFR and PDGFRA. Hierarchical clustering analysis using the entire set of 1176 genes distinguished pilocytic astrocytomas from grade II astrocytomas and oligodendrogliomas. Clustering analysis using selected subgroups of genes based on their molecular functions revealed that immune system-related genes (75 genes) or cell adhesion, migration, and angiogenesis-related genes (69 genes) showed similar power to the entire gene set for separation of pilocytic astrocytomas from diffusely infiltrating low-grade gliomas. Immunohistochemistry revealed that HLA-DRalpha is expressed diffusely in neoplastic cells in pilocytic astrocytomas, whereas in oligodendrogliomas, expression was limited to scattered reactive astrocytes. These results suggest that gene expression profiles of pilocytic astrocytomas differ significantly from those of diffusely infiltrating low-grade gliomas and that their benign biologic behavior may be related to upregulation of immune defense-associated genes.