Identification of potential biomarkers of genotoxicity and carcinogenicity in L5178Y mouse lymphoma cells by cDNA microarray analysis

In the present study, cDNA microarray analyses were performed with mouse cDNA chips in order to evaluate similarities and differences in the gene expression profiles for compounds differing in their genotoxic and carcinogenic potential. Eight test substances were evaluated, two each from four classes of compounds: genotoxic carcinogens (1,2-dibromoethane and glycidol), genotoxic noncarcinogens (8-hydroxyquinoline and emodin), nongenotoxic carcinogens (methyl carbamate and o-nitrotoluene), and nongenotoxic noncarcinogens (D-mannitol and 1,2-dichlorobenzene). Quadruplicate hybridization experiments were performed in order to identify a set of genes with significant expression changes for these four classes of substances. Twelve genes were consistently altered more than twofold by the genotoxic noncarcinogens while four genes were consistently regulated by the nongenotoxic carcinogens. One gene (Trp63) was identified whose expression was upregulated by all four genotoxic substances regardless of the presence or absence of carcinogenicity; this finding, however, was not confirmed by quantitative real-time RT-PCR. RT-PCR did confirm the change in expression of 9 of 15 genes (60%) identified by microarray analysis. Interestingly, the downregulated genes were least likely to be validated by real-time RT-PCR. Those genes showing more than a twofold change in expression level in response to at least one substance were further analyzed with hierarchical clustering after category assignment of each gene according to its main cellular function. Clustering revealed differences in the gene expression profiles between the genotoxic and nongenotoxic substances for genes involved in cell cycle control, the stress response, and the immune response. However, no clustering specific to all four carcinogenic substances was observed in any of the functional categories. Taken together, these results suggest that gene expression profiling in mouse lymphoma cells can provide valuable information for the evaluation of potential genotoxicity but may have limitations in predicting carcinogenicity.     

PEP-19 overexpression in human uterine leiomyoma

Although uterine leiomyomas represent one of the most common neoplasms in adult women, their pathogenesis remains poorly understood. A cDNA microarray analysis was performed to search for candidate genes expressed to a greater degree in leiomyoma compared with matched myometrium. A total of 15 candidate genes was obtained; neuron-specific protein PEP-19 (Purkinje cell protein 4; PCP 4) exhibited a striking difference in expression between leiomyoma and myometrium. Although PEP-19 expression has been reported exclusively in the central nervous system, the present study demonstrated that PEP-19 is also expressed in other human organs, including prostate, kidney and uterus. To clarify the role of PEP-19 in the pathogenesis of leiomyomas, PEP-19 expression was investigated for a series of human leiomyoma, as well as normal myometrium and leiomyosarcoma. PEP-19 mRNA and protein expression were much stronger in leiomyomas compared with normal myometrium, suggesting that PEP-19 might be involved in leiomyoma pathogenesis.     

Proteomic Evaluation to Identify Biomarkers for Carpal Tunnel Syndrome: A Comparative Serum Analysis

Carpal tunnel syndrome (CTS) is the most common peripheral nerve entrapment, causing pain, impairment, and disability. To identify proteins of CTS comprehensively, a comparative serum analysis of CTS patients and normal control subjects was performed. The two-dimensional electrophoresis patterns of serum obtained from six CTS patients and six normal control subjects were compared. We found 10 proteins that were significantly altered in the serum of CTS patients, among which four were upregulated and six were downregulated. The upregulated spots were identified as Chain A, heat shock 70-kDa protein, 42-kDa ATPase N-terminal domain; glutathione-insulin transhydrogenase (216AA); cAMP-dependent protein kinase inhibitor alpha; and mutant β-globin. The downregulated spots were identified as vitamin D-binding protein (VDBP), fibrinogen gamma chain, apolipoprotein A-IV (ApoA-IV), clusterin, heterogeneous nuclear ribonucleoprotein H1 (hnRNP H1), and one unidentified protein. The information obtained from this proteomic analysis will be very useful in understanding the pathophysiology of CTS and in finding suitable proteins that can serve as new diagnostic biomarkers of CTS.     

应用基因芯片分析妇科恶性肿瘤的基因表达

目的应用基因微矩阵芯片研究妇科恶性肿瘤相关基因表达.方法分别提取癌组织和正常对照组织mRNA,经反转录分别用Cy3-dCTP和Cy5-dCTP荧光标记cDNA,获得两组探针,混合后与基因芯片H40s(基因点数为4096点)杂交,经严格洗片后用GenePix4000B扫描仪进行扫描,获得荧光信号图像,用图像处理软件:GenePix Pro3.0对图像进行处理,获得两种组织中差异表达的基因信息.结果在4种癌组织中同时出现表达差异的基因有35条,占0.85%.其中4种癌组织中都下调表达的基因6条,没有均上调表达的基因,在前3种癌组织中都上调表达而在乳腺癌中却下调表达的基因12条,在前3种癌组织中都下调表达而在乳腺癌中却上调表达的基因12条,其它5条.结论 1.肿瘤的发生过程比我们已了解的要复杂的多,它是多种基因表达失衡的结果.每种肿瘤的每个患病个体其肿瘤的发生和发展都具有自己一系列独特的基因表达谱,即使是同一肿瘤的不同个体之间,基因表达谱可能差异也很大.2.子宫颈癌、乳腺癌、卵巢癌和子宫内膜癌这四种癌组织中具有相同表达行为的基因只有6个,它们是:AB023136(编码人类蛋白 KIAA0919)、AF080158(丝氨酸、苏氨酸K激酶基因)、S79522(蛋白质合成延长因子EF-1基因)、NM_000984(核糖体蛋白基因)、M32110(细胞增殖核抗原蛋白P120基因)、NM_000978(核糖体蛋白RPL23)基因,并且均下调表达.3. 子宫颈癌、子宫内膜癌和卵巢癌基因表达谱的一致性较高,而与乳腺癌基因表达谱的差异很大,说明3种内生殖器肿瘤发生的机理与乳腺癌的发病机理可能完全不同,有12个基因在子宫颈癌、子宫内膜癌和卵巢癌中上调表达而在乳腺癌中下调表达;同时另外12个基因在子宫颈癌、子宫内膜癌和卵巢癌中下调表达而在乳腺癌中上调表达.4.基因芯片是筛查妇科恶性肿瘤相关基因表达的有力工具.     

Ventromedial hypothalamic lesions change the expression of neuron-related genes and immune-related genes in rat liver

There are no reports that hypothalamus can directly affect the expression of neuron-related genes and immune-related genes in liver. We identified genes of which expression profiles showed significant modulation in rat liver after ventromedial hypothalamic (VMH) lesions. Total RNA was extracted, and differences in the gene expression profiles between rats at day 3 after VMH lesioning and sham-VMH lesioned rats were investigated using DNA microarray analysis. The result revealed that VMH lesions regulated the genes that were involved in functions related to neuronal development and immunofunction in the liver. Real-time PCR also confirmed that gene expression of SULT4A1 was upregulated, but expression of ACSL1 and CISH were downregulated at day 3 after VMH lesions. VMH lesions may change the expression of neuron-related genes and immune-related genes in rat liver.     

代谢相关基因在先兆子痫胎盘中的表达情况分析

目的探讨细胞代谢相关基因在先兆子痫胎盘组织中的表达变化及其影响机制。方法使用含12000个与代谢、凋亡、细胞粘附、信号传导、转录因子等有关基因的cDNA表达谱芯片,检测4例重度妊娠高血压疾病子痫前期及正常的胎盘组织的基因表达谱差异,并差异表达的细胞代谢相关基因进行了Northern验证。结果4先兆子痫胎盘中同时有44种基因表达发生了变化,其中糖原磷酸化酶（GP—M）基因、瘦素（1eptin）基因、脂蛋白酯酶（LPL）基因及糖代谢相关基因（Glucose transporter）表达增强,核苷酸代谢基因（CD73）与能量代谢调节基因（Creatine kinase B）表达下降。结论多种基因表达异常与先兆子痫的病理发生有关,细胞代谢相关基因表达异常可能是血管内皮损伤的原因之一。     

Alterations in gene expression profiles and the DNA-damage response in ionizing radiation-exposed TK6 cells

Identifying genes that are differentially expressed in response to DNA damage may help elucidate markers for genetic damage and provide insight into the cellular responses to specific genotoxic agents. We utilized cDNA microarrays to develop gene expression profiles for ionizing radiation-exposed human lymphoblastoid TK6 cells. In order to relate changes in the expression profiles to biological responses, the effects of ionizing radiation on cell viability, cloning efficiency, and micronucleus formation were measured. TK6 cells were exposed to 0.5, 1, 5, 10, and 20 Gy ionizing radiation and cultured for 4 or 24 hr. A significant (P < 0.0001) decrease in cloning efficiency was observed at all doses at 4 and 24 hr after exposure. Flow cytometry revealed significant decreases in cell viability at 24 hr in cells exposed to 5 (P < 0.001), 10 (P < 0.0001), and 20 Gy (P < 0.0001). An increase in micronucleus frequency occurred at both 4 and 24 hr at 0.5 and 1 Gy; however, insufficient binucleated cells were present for analysis at the higher doses. Gene expression profiles were developed from mRNA isolated from cells exposed to 5, 10, and 20 Gy using a 350 gene human cDNA array platform. Overall, more genes were differentially expressed at 24-hr than at the 4-hr time point. The genes upregulated (> 1.5-fold) or downregulated (< 0.67-fold) at 4 hr were those primarily involved in the cessation of the cell cycle, cellular detoxification pathways, DNA repair, and apoptosis. At 24 hr, glutathione-associated genes were induced in addition to genes involved in apoptosis. Genes involved in cell cycle progression and mitosis were downregulated at 24 hr. Real-time quantitative PCR was used to confirm the microarray results and to evaluate expression levels of selected genes at the low doses (0.5 and 1.0 Gy). The expression profiles reflect the cellular and molecular responses to ionizing radiation related to the recognition of DNA damage, a halt in progression through the cell cycle, activation of DNA-repair pathways, and the promotion of apoptosis.     

Giant cell tumors of the bone: molecular profiling and expression analysis of Ephrin A1 receptor, Claudin 7, CD52, FGFR3 and AMFR

Giant cell tumors (GCTs) of the bone are osteolytic neoplasms with variable degrees of aggressiveness. The aim of this study was the molecular characterization of GCT tissue. We established gene expression profiles and discovered a number of genes that have not been described in GCTs before. RNA was prepared from 7 cryopreserved GCTs (primary tumors n = 5, relapses n = 2) and was hybridized to Affymetrix HG U133A microarrays. Paraffin-embedded samples were used for immunohistochemical validation (primary tumors n = 16, relapses n = 6). Gene ontology revealed that the majority of genes, found to be differentially expressed between primary and recurrent GCTs, were associated with receptor tyrosine kinase activity. We selected one upregulated gene (Claudin 7) and four downregulated genes (CD52, Ephrin A1 receptor, autocrine motility factor receptor [AMFR] and fibroblast growth factor receptor 3 [FGFR3] for further analysis using immunohistochemistry. Immunohistochemical analysis of CD52, AMFR, and Ephrin A1 receptor revealed expression profiles concordant with the microarray data, also with regard to differences between primary tumors and relapses.     

Gene expression studies provide clues to the pathogenesis of uterine leiomyoma: new evidence and a systematic review

BACKGROUND: Uterine leiomyomas are extremely common and a major cause of pelvic pain, bleeding, infertility, and the leading indication for hysterectomy. Familial and epidemiological studies provide compelling evidence that genetic alterations play an important role in leiomyoma development. METHODS: Using Affymetrix U133A GeneChip we analysed expression profiles of 22,283 genes in paired samples of leiomyoma and adjacent normal myometrium. We compared our results with previously published data on gene expression in uterine leiomyoma and identified the overlapping gene alterations. RESULTS: We detected 80 genes with average differences of > or = 2-fold and false discovery rates of < 5% (14 overexpressed and 66 underexpressed). A comparative analysis including eight previous gene expression studies revealed eight prominent genes (ADH1, ATF3, CRABP2, CYR61, DPT, GRIA2, IGF2, MEST) identified by at least five different studies, eleven genes (ALDH1, CD24, CTGF, DCX, DUSP1, FOS, GAGEC1, IGFBP6, PTGDS, PTGER3, TYMS) reported by four studies, twelve genes (ABCA, ANXA1, APM2, CCL21, CDKN1A, CRMP1, EMP1, ESR1, FY, MAP3K5, TGFBR2, TIMP3) identified by three studies, and 40 genes reported by two different studies. CONCLUSIONS: Review of gene expression data revealed concordant changes in genes regulating retinoid synthesis, IGF metabolism, TGF-beta signaling and extracellular matrix formation. Gene expression studies provide clues to the relevant pathways of leiomyoma development.     

Profiles of metabolic gene expression in the white adipose tissue,liver and hypothalamus in leptin knockout (LepΔI14/ΔI14 ) rats

Leptin deficiency is principally linked to metabolic disorders. Leptin knockout (LepΔI14/ΔI14) Sprague Dawley rats created by CRISPR/Cas9 is a new model to study metabolic disorders. We used a whole rat genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of the white adipose tissue, liver and hypothalamus in LepΔI14/ΔI14 and wild-type (WT) rats. We found 1,651 differentially expressed (enriched) genes in white adipose tissue, 916 in the liver, and 306 in the hypothalamus in the LepΔI14/ΔI14 rats compared to WT. Gene ontology category and KEGG pathway analysis of the relationships among differentially expressed genes showed that these genes were represented in a variety of functional categories, including fatty acid metabolism, molecular transducers and cellular processes. The reliability of the data obtained from microarray was verified by quantitative real-time PCR on 14 representative genes. These data will contribute to a greater understanding of different metabolic disorders, such as obesity and diabetes.     

先兆子痫胎盘的基因表达谱研究

目的： 利用cDNA芯片分析先兆子痫胎盘中基因表达的变化情况,寻找新的先兆子痫相关基因。方法: 建立含12 000个与代谢、凋亡、细胞黏附、信号转导、转录因子等有关基因的cDNA表达谱芯片,将先兆子痫及正常胎盘mRNA与cDNA芯片进行杂交,得到先兆子痫的基因表达谱;对部分差异表达基因进行Northern验证。结果: 在4例先兆子痫胎盘组织中发现均有差异表达的基因44个,其中表达上调有30个,表达下调有14个,Northern杂交鉴定的结果与芯片结果相符合。结论: 重度妊娠高血压疾病的基因表达谱存在明显差异,差异的基因可能涉及信号转导、细胞代谢、炎性细胞因子等方面,这些基因可能与妊娠高血压病的发病相关。     

Global analysis of differentially expressed genes in early gestational decidua and chorionic villi using a 9600 human cDNA microarray

The global gene expression profiles of the decidua and chorionic villi of early human pregnancies were analysed by using cDNA microarray technology. Decidual and villous placental tissues were obtained from first trimester abortus and mRNA was extracted for cDNA microarray analysis. The human cDNA microarray [9600 clones, including known regulatory genes and expressed sequence tags (EST)] with colorimetric detection was used to identify differentially expressed genes between early gestational decidua and villi. According to cDNA microarray analysis, we have identified 641 genes with highly expressed mRNA in both decidua and villi, 49 genes with higher expressions in decidua, and 75 genes with higher expression in chorionic villi. These differentially expressed genes were further grouped into categories by their putative functions, including: cell growth-related factors, hormones/cytokines, cell adhesion molecules, signal transduction molecules, apoptosis-related factors, cytoskeleton/extracellular matrix proteins, and EST. Immunohistochemical stainings of cathepsin L, leukaemia inhibitory factor-receptor, and proliferative cell nuclear antigen showed results consistent with the microarray data. Identification of the differentially expressed genes between decidua and villi by microarray provide a global profiling of the gene expression pattern. This work adds to our understanding of placentation by reporting the gene expression profiles during first trimester human pregnancies using cDNA microarray.     

Gene expression profiling of oral squamous cell carcinoma using laser microdissection and cDNA microarray

Cancer diagnosis and therapy are performed on the basis of clinical stage and clinicopathological findings; however, sensitivity to therapy and prognosis may not always be the same even when considering similar cancers because it is difficult to recognize adequate biological characteristics of a cancer when determining cancer therapy. To enable personalized medicine for cancer diagnosis and therapy, which may solve this problem, we used laser microdissection and cDNA microarrays to study the gene expression profile of oral squamous cell carcinoma. Moreover, to establish an objective evaluation with this system, we examined which type of gene expression profile corresponded to the biological characteristics of this cancer. We identified several genes that were up- or downregulated in the majority of cases and clarified genes sharing common behavioral profiles between metastasis-positive and metastasis-negative cases. It was suspected that the genes that were commonly up- or downregulated in the majority of cases were important for histogenesis and acquisition of invasion and proliferation capability and that the genes sharing common behavioral profiles between metastasis-positive and metastasis-negative cases played a large role in cancer metastasis. Using the expression profile of these genes, it may be possible to evaluate cellular state and metastatic potential and use them as tumor markers. Alternately, we showed averaged gene expression profiles in cases with or without metastasis; this may reveal a profile that could evaluate metastatic potential, which is an important element in the biological characteristics of cancer. In conclusion, our system using laser microdissection and cDNA microarray may contribute to cancer diagnosis and therapy and improvement in the quality of life of cancer patients.