Identification of differentially expressed genes in human prostate cancer using subtraction and microarray

We have identified human prostate cancer- and tissue-specific genes using cDNA library subtraction in conjunction with high throughput microarray screening. Subtracted cDNA libraries of prostate tumors and normal prostate tissue were generated. Characterization of subtracted libraries showed enrichment of both cancer- and tissue-specific genes. Highly redundant clones were eliminated by colony hybridization. The remaining clones were selected for microarray to determine gene expression levels in a variety of tumor and normal tissues. Clones showing overexpression in prostate tumors and/or normal prostate tissues were selected and sequenced. Here we report the identification of two genes, P503S and P504S, from subtracted libraries and a third gene, P510S, by subtraction followed by microarray screening. Their expression profiles were further confirmed by Northern blot, real-time PCR (TaqMan), and immunohistochemistry to be overexpressed in prostate tissues and/or prostate tumors. Full-length cDNA sequences were cloned, and their subcellular locations were predicted by a bioinformatic algorithm, PSORT, to be plasma membrane proteins. The genes identified through these approaches are potential candidates for cancer diagnosis and therapy.     

Elevated Expression of Ferritin H-Chain mRNA in Metastatic Ovarian Tumor

To identify genes associated with tumor metastasis, we prepared 5 cDNA libraries using mRNA from normal ovaries, paired primary and metastatic ovarian tumors, as well as paired cultured ovarian tumor cells. By differential screening, we identified 12 clones, which can be divided into 3 classes based on hybridization to various probes. Class 1 clones showed no reaction with the normal probe, slight or no reaction with the primary probe, but high reaction with the metastatic probe. Class 2 clones showed some reaction with normal and primary probes, but showed stronger reaction with the metastatic probe. Class 3 clones showed strong hybridization to the normal probe, slight or no reaction with the primary probe, and did not hybridize with the metastatic clone. These clones were further analyzed by determination of DNA sequence. One of the class 1 clones (clone I) was identified as ferritin heavy chain. Northern blot analysis showed higher expression of ferritin H-chain in metastatic samples compared to primary tumor in 16/23 pairs of samples analyzed so far.     

Parallel overexpression of seven kallikrein genes in ovarian cancer

Recent evidence suggests that many members of the human kallikrein (KLK) gene family are differentially regulated in ovarian cancer and have potential as diagnostic and/or prognostic markers. We used the serial analysis of gene expression and expressed sequence tag databases of the Cancer Genome Anatomy Project to perform in silico analyses of the expression pattern of the 15 human KLK genes in normal and cancerous ovarian tissues and cell lines. We found that seven KLK genes (KLK5, KLK6, KLK7, KLK8, KLK10, KLK11, and KLK14) are up-regulated in ovarian cancer. Probing 2 normal and 10 ovarian cancer serial analysis of gene expression libraries with gene-specific tags for each KLK indicated that whereas no expression was detected in any normal libraries (with the exception of KLK10 and KLK11), these KLKs were found to be expressed with moderate densities (103-408 tags per million) in 40-60% of the ovarian cancer libraries analyzed. These data were verified by screening the expressed sequence tag databases, where 78 of 79 mRNA clones isolated for these genes were from ovarian cancer libraries. X-profiler comparison of the pools of normal and cancerous ovaries identified a significant difference in expression levels for six of the seven KLKs. We experimentally verified the overexpression of six KLK proteins in cancer versus normal or benign tissues with highly sensitive and specific immunofluorometric assays. A statistically significant stepwise increase in protein levels was found among normal, benign, and cancerous ovarian tissues. The expression of five KLKs showed a strong degree of correlation at the protein level, suggesting the existence of a common mechanism or pathway that controls the expression of this group of adjacent genes during ovarian cancer progression.     

Selective identification of secreted and transmembrane breast cancer markers using Escherichia coli ampicillin secretion trap

Secreted and cell surface proteins play important roles in cancer and are potential drug targets and tumor markers. Here, we describe a large-scale analysis of the genes encoding secreted and cell surface proteins in breast cancer. To identify these genes, we developed a novel signal sequence trap method called Escherichia coli ampicillin secretion trap (CAST). For CAST, we constructed a plasmid in which the signal sequence of beta-lactamase was deleted such that it does not confer ampicillin resistance. Eukaryotic cDNA libraries cloned into pCAST produced tens of thousands of ampicillin-resistant clones, 80% of which contained cDNA fragments encoding secreted and membrane spanning proteins. We identified 2,708 unique sequences from cDNA libraries made from surgical breast cancer specimens. We analyzed the expression of 1,287 of the 2,708 genes and found that 166 were overexpressed in breast cancers relative to normal breast tissues. Eighty-five percent of these genes had not been previously identified as markers of breast cancer. Twenty-three of the 166 genes (14%) were relatively tissue restricted, suggesting use as cancer-specific targets. We also identified several new markers of ovarian cancer. Our results indicate that CAST is a robust, rapid, and low cost method to identify cell surface and secreted proteins and is applicable to a variety of relevant biological questions.     

Study of the Gene Expression Profile of Human Ovarian Carcinoma by a Gene Chip

OBJECTIVE To study the difference in gene expression between human ovarian carcinoma and normal ovarian tissues, and screen the novel associated genes by cDNA microarrays.METHODS Total RNA from 10 cases of ovarian cancer and from normal ovarian tissues were extracted by a single step method. The cDNA was retro-transcribed from an equal quantity of mRNA derived from the 10 cases of ovarian carcinoma and normal ovarian tissues, followed by labeling the cDNA strands with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with BiostarH 8464 dot human somatic cell genes.Fluorescence signals were assessed by a ScanArray 4000 laser scanner and the images analyzed by Gene Pix Pro 3.0 software with a digital computer.RESULTS By applying the cDNA microarray we found a total of 185 genes for which expression levels differed more than 5 times comparing human ovarian carcinoma with normal ovarian epithelium. Among these genes 86 were up-regulated ＞5 times and 99 were down regulated ＜0.2.CONCLUSION The cDNA microarray technique is effective in screening the differential gene expression between human ovarian cancers and normal ovarian epithelium. It is suggested that these genes identified are related to the genesis and development of ovarian carcinoma.     

Serologic analysis of ovarian tumor antigens reveals a bias toward antigens encoded on 17q

We utilized SEREX immunoscreening to identify a set of novel tumor antigens that are associated with human serous ovarian cancer and may prove useful for the early detection and treatment of this disease. Extensive screening with a panel of sera from 25 late-stage ovarian cancer patients against 3 independent cDNA libraries identified a set of 9 antigens that were immunogenic in more than 1 patient and not in a panel of 20-45 normal female serum donors. These antigens include p53, NY-ESO-1, UBQLN1, HOXB6, TOP2A, putative helicase-RUVBL (RUVBL), HMBA-inducible (HEXIM1), DDX5 and HDCMA. Ten of 25 ovarian cancer patients (40%) expressed serum IgG to at least 1 of these antigens, while 14% (4/25) had antibodies to 2 or more antigens. Unexpectedly, 4 antigens identified in this screen, DDX5, HEXIM1, TOP2A and HOXB6, are encoded within a region of 17q that also includes the genes for HER2/neu, Homeobox-B7 and BRCA1. Real-time RT-PCR analysis showed that mRNA for HER2/neu and 3 SEREX-defined antigens, TOP2A, HOXB6 and DDX5, was more abundant in ovarian tumors than most normal tissues, including normal and benign ovarian tissues, suggesting that elevated expression of genes encoded within this region of chromosome 17 is a common event in ovarian tumors. Thus, these abnormal expression patterns combined with the endogenous immune response suggests that these antigens represent potential targets for immunotherapy.     

高低转移人卵巢癌细胞系基因表达谱差异

目的 用基因芯片技术研究高低转移人卵巢癌细胞系（HO－8910PM和HO－8910）基因表达谱差异,筛选与转移相关的基因。方法 分别抽提高低转移人卵巢癌细胞和对照正常卵巢上皮的总RNA并纯化mRNA;分别将等量的mRNA逆转录合成以图像,用软件对扫描图像进行数字化处理和分析。结果 HO－8910细胞与正常卵巢上皮比较差异3倍以上共有355个基因;HO－8910PM细胞与正常卵巢上皮比较差异3倍以上共有323个基因。HO－8910PM与母系HO－8910比较差异2倍以上共有163个基因,差异3倍以上共有21个基因。结论 两株人卵巢癌细胞与正常卵巢上皮细胞基因表达谱存在差异,提示这些基因与卵巢癌的发生和发展有关;HO－8910PM与HO－8910比较存在差异的基因可能与高转移特性相关。     

Differential gene expression in chemically induced mouse lung adenomas

Because of similarities in histopathology and tumor progression stages between mouse and human lung adenocarcinomas, the mouse lung tumor model with lung adenomas as the endpoint has been used extensively to evaluate the efficacy of putative lung cancer chemopreventive agents. In this study, a competitive cDNA library screening (CCLS) was employed to determine changes in the expression of mRNA in chemically induced lung adenomas compared with paired normal lung tissues. A total of 2555 clones having altered expression in tumors were observed following competitive hybridization between normal lung and lung adenomas after primary screening of over 160,000 clones from a mouse lung cDNA library. Among the 755 clones confirmed by dot blot hybridization, 240 clones were underexpressed, whereas 515 clones were overexpressed in tumors. Sixty-five clones with the most frequently altered expression in six individual tumors were confirmed by semiquantitative RT-PCR. When examining the 58 known genes, 39 clones had increased expression and 19 had decreased expression, whereas the 7 novel genes showed overexpression. A high percentage (>60%) of overexpressed or underexpressed genes was observed in at least two or three of the lesions. Reproducibly overexpressed genes included ERK-1, JAK-1, surfactant proteins A, B, and C, NFAT1, alpha-1 protease inhibitor, helix-loop-helix ubiquitous kinase (CHUK), alpha-adaptin, alpha-1 PI2, thioether S-methyltransferase, and CYP2C40. Reproducibly underexpressed genes included paroxanase, ALDH II, CC10, von Ebner salivary gland protein, and alpha- and beta-globin. In addition, CCLS identified several novel genes or genes not previously associated with lung carcinogenesis, including a hypothetical protein (FLJ11240) and a guanine nucleotide exchange factor homologue. This study shows the efficacy of this methodology for identifying genes with altered expression. These genes may prove to be helpful in our understanding of the genetic basis of lung carcinogenesis and in developing biomarkers for lung cancer chemoprevention studies in mice.     

Alteration of gene expression in rat mammary tumors induced by N-methyl-N-nitrosourea

Rodents are susceptible to the effects of chemical carcinogens and have been widely used in the study of mammary-gland carcinogenesis. However, little information is available regarding specific phenotypic changes that occur during mammary-gland carcinogenesis. In this study, subtraction hybridization was used to identify specific genes whose expression in N-methyl-N-nitrosourea (MNU)-induced rat mammary tumors had been altered. mRNA isolated from normal rat mammary tissue and tumors induced by treatment of 50-d-old female rats with MNU (50 mg/kg) was used to produce normal and tumor cDNA libraries. Total inserts prepared from each cDNA library were used to produce a subtracted tumor-normal probe. Differential screening of the tumor library with the subtracted probe and normal cDNA yielded 20 clones that appeared to be differentially expressed. Northern analysis of mRNA isolated from normal mammary tissue and tumor tissue confirmed that four of these clones were differentially expressed. The expression of clones 4 and 15 was greatly increased (13-fold and tenfold, respectively) in most MNU-induced mammary tumors, whereas the expression of clones 10 and 27 was decreased (13-fold and fourfold, respectively). Sequence analysis revealed that clones 15 and 27 were highly homologous to calcyclin and a cDNA isolated from HL-60 cells, respectively. The differential expression of clones 4 and 10 was due to the presence within these clones of retroviral sequences and a fragment of transferrin, respectively. These clones may represent markers useful for studying the development of MNU-induced mammary-gland neoplasias. © 1996 Wiley-Liss, Inc.     

Identification of genes over-expressed in small cell lung carcinoma using suppression subtractive hybridization and cDNA microarray expression analysis

To identify genes that are differentially over-expressed in Small Cell Lung Carcinoma (SCLC) we have used a combination of suppression subtractive hybridization and cDNA microarray to analyse the expression profiles of 2400 cDNAs clones. Genes that are over-expressed in SCLC were identified using 32 pairs of fluorescence-labeled cDNA samples representing various lung tumors and normal tissues. This comprehensive approach has resulted in the identification of 209 genes that are differentially over-expressed in SCLC. Quantitative real-time PCR was used to further validate the expression of 43 genes in SCLC tumors and various normal tissues. Discussed in this report are nine genes, which showed the most promising SCLC tumor to normal tissue differential expression profiles, including seven known and two novel genes. The large number of differentially expressed genes identified from this analysis and the characterization of these genes will provide valuable information in better understanding the biology of SCLC and help us in developing these gene products as potential targets for diagnostic as well as therapeutic usage.     

联合应用SSH和cDNA Microarray筛选肺癌相关基因

目的 利用抑制消减杂交(suppression subtractive hybridization，SSH)和cDNA Microarray 筛选肺癌组织、肺癌旁组织和其它肿瘤组织中相互差异表达的基因。方法 将利用SSH构建的BEP2D细胞永生化阶段、恶性转化前阶段和恶性转化阶段三个cDNA文库中的克隆制作在一张芯片上，筛选了15例肺癌组织、5例肺癌旁组织和其他癌组织24例(肝癌、胃癌、食管癌、乳腺癌、白血病、子宫内膜癌、脑神经胶质瘤和结肠癌各3例)中mRNA的表达差异。结果 获得肺癌组织高于肺癌旁组织表达的cDNA26个，肺癌旁组织高于肺癌组织表达的31个。二者高于其它8种癌组织的分别为：肺癌旁组织中63个，肺癌组织中87个。结论 联合应用SSH和cDNA Microarray是筛选和鉴定不同样本中差异表达基因的快速和有效的方法；肺癌旁组织和肺癌组织中差异表达的基因，以及这二者与其它组织差异表达的基因．不仅可能是肺癌发生发展机制中的重要基因，而且可能是用于肺癌诊断的候选基因。     

人垂体肿瘤转化基因1在卵巢癌组织中的表达及其意义

背景与目的:人垂体肿瘤转化基因1(humanpituitarytumortransforminggene1,hPTTG1)是新近发现的一个癌基因。我们用基因表达谱芯片对晚期卵巢低分化浆液性癌进行卵巢癌相关基因的筛查,发现该基因在这种卵巢癌中明显高表达。本研究对不同临床分期、不同病理类型及不同组织学分级的上皮性卵巢癌组织hPTTG1的表达进行检测,探讨该基因在卵巢癌发生发展中的作用。方法:用非竞争性RT-PCR方法半定量检测27例卵巢癌及4例正常卵巢组织中hPTTG1mRNA的表达,用免疫组化方法检测该27例卵巢癌及18例正常卵巢组织中hPTTG1蛋白的表达。结果:在正常卵巢组织中hPTTG1mRNA有低水平的表达,而卵巢癌组织hPTTG1mRNA表达高于正常,两者之间有显著性差异(P<0.01),卵巢癌组织较正常卵巢组织表达倍增1.1～4.8,中位倍增2.4。进一步分析卵巢癌组织中hPTTG1mRNA表达水平与临床分期及病理分级的关系,未发现hPTTG1mRNA表达水平的高低与临床分期具有相关性,但发现hPTTG1mRNA倍增与肿瘤分化程度密切相关(r=0.686,P<0.05)。hPTTG1蛋白在所有卵巢癌组织中表达,而在正常卵巢组织中未检测到hPTTG1蛋白的表达。结论:hPTTG1表达在早期卵巢癌即发生改变,其表达可能与不良分化有关;hPTTG1在卵巢癌组织中高表达,可能是卵巢癌的一个分子标志。     

Identification of breast cancer-restricted antigens by antibody screening of SKBR3 cDNA library using a preselected patient's serum

Screening of a breast cancer cDNA library from SKBR3 human breast cancer cells by SEREX (serological analysis of cDNA expression library) using a preselected serum from a breast cancer patient revealed 13 genes, two of which, INT-MI-1 and INT-MI-2, encode novel gene products, while the remaining 11 genes and their products are identical with or highly homologous to known GenBank entries. Immunoscreening of the 13 clones using 20 allogeneic sera from breast cancer patients and 20 samples from age- and gender-matched healthy donors showed that lactate dehydrogenase-A (LDH-A), lactate dehydrogenase-B (LDH-B), fibulin-1, and thyroid hormone-binding protein (THBP) were recognized principally by the breast cancer patient sera, indicating the immunogenicity of these molecules in vivo. The other antigens were similarly recognized by normal and patients sera, and thus not tumor-restricted immunologically. RT-PCR analysis revealed strong expression of fibulin-1 in tumor cell lines and surgical specimen whereas in the same experimental conditions, normal tissues scored negative. Also THBP expression was found in various tumors whereas in normal tissues, its expression is restricted to the testis and, at lower levels, in ovary, liver, and spleen. In contrast, LDH-A and LDH-B were ubiquitously expressed in normal and tumor tissues, with LDH-B levels considerably lower and heterogeneous in normal samples compared to those expressed in tumor cell lines. The differential expression of fibulin-1 between the normal tissues and breast carcinoma cell lines (5/6) and surgical specimens (5/6) suggests the possible involvement of the overexpression of this extracellular matrix-associated glycoprotein in the pathogenesis of this neoplasm.