Detection of differentially expressed genes in HeLa x fibroblast hybrids using subtractive suppression hybridization

To understand genetic differences and similarities between tumorigenic and nontumorigenic HeLa x fibroblast hybrid cells, subtractive suppression hybridization (SSH), based on suppression PCR and a combination of normalization and subtraction in a single procedure, was used. Using the nontumorigenic CGL1 and tumorigenic CGL3, forward (CGL1-CGL3) and reverse (CGL3-CGL1) subtracted libraries were constructed. Among 192 clones, seven were identified as differentially expressed genes specific for either CGL1 or CGL3. All seven were not reported previously as differentially expressed genes in this hybrid system. In the forward subtraction, p16 was isolated, indicating the involvement of the loss of tumorigenic phenotype. Subsequent transfection of wild-type p16 to the tumorigenic CGL3 showed growth suppression in colony formation assay; however, no tumor suppression was observed when the transfectant was inoculated into nude mice. These results indicate that: (a) SSH is a suitable method to identify differentially expressed genes in two types of cells; and (b) although p16 plays some roles in growth suppression, the p16-transfected CGL3 is still capable to proliferate in vivo.     

Analysis of differentially expressed genes in human hepatocellular carcinoma using suppression subtractive hybridization.

The genetic basis of hepatocellular carcinoma (HCC) has not yet been fully understood. Although various methods have been developed to detect differentially expressed genes in malignant diseases, efficient analysis from clinical specimens is generally difficult to perform due to the requirement of a large amount of samples. In the present study, we analysed differentially expressed genes with a small amount of human HCC samples using suppression subtractive hybridization (SSH). Total RNA were obtained from the hepatitis C virus-associated HCC and adjacent non-HCC liver tissues. cDNA was synthesized using modified RT-PCR, and then tester cDNA was ligated with 2 different kinds of adaptors and hybridized with an excess amount of driver cDNA. Tester specific cDNA was obtained by suppression PCR and the final PCR product was subcloned and sequenced. We identified 7 known genes (focal adhesion kinase, deleted in colon cancer, guanine binding inhibitory protein alpha, glutamine synthetase, ornithine aminotransferase, M130, and pepsinogen C) and 2 previously unknown genes as being overexpressed in HCC, and 1 gene (decorin) as suppressed in HCC. Quantitative analysis of gene expression using quantitative RT-PCR demonstrated the differential expression of these genes in the original and other HCC samples. These findings demonstrated that it is possible to identify the previously unknown, differential gene expression from a small amount of clinical samples. Information about such alterations in gene expression could be useful for elucidating the genetic events in HCC pathogenesis, developing the new diagnostic markers, or determining novel therapeutic targets.     

Identification of genes differentially expressed in human hepatocellular carcinoma by a modified suppression subtractive hybridization method

To identify differentially expressed genes in human HCC in China, we applied a modified SSH method for cDNA subtraction. Such modification has made the method more effective for subtraction. We have obtained 36 and 24 differentially expressed cDNA fragments after modified SSH from 4 paired samples of human HCC and non-HCC tissues, respectively. Reverse Northern blotting analysis was performed to further identify the genes differentially expressed in the HCC and non-HCC tissue samples. There were 25 genes really overexpressed in HCC, and their corresponding encoding molecules may reflect the events of cell accelerated metabolism, proliferation, angiogenesis, anti-apoptosis, tumorigenesis (TLH107, TFH9) and the potential for metastasis. Of the 25 genes overexpressed in HCC, 5 were novel and their full-length cDNAs were cloned. These 5 novel genes are functionally associated with the occurrence and development of HCC according to the Database analysis. In the paired non-HCC tissues, there were 15 genes lowly or not expressed in HCC, and their encoding proteins function as tumor suppressors (TFA3, TFA11), acute-phase reactive proteins, and the blood plasma proteins that are mainly or exclusively synthesized in the liver. The distinct profiles of the differentially expressed genes in HCC and the paired non-HCC tissues have partially reflected the genetic alterations during HCC tumorigenesis. The novel HCC-specific gene TLH6 and the CT antigen encoding gene TLH107 may have diagnostic and therapeutic potentials in HCC and/or other solid cancers.     

应用抑制性消减杂交技术克隆人肺鳞癌差异性表达基因

目的 克隆人肺鳞癌肿瘤差异性表达基因。方法 应用抑制性消减杂交技术（suppression subtractive hybridization,SSH)构建人肺鳞癌cDNA消减杂交文库，筛选后挑选阳性克隆进行测序，并在Gen Bank数据库中进行同源性比较，最后经RT－PCR验证。结果 成功克隆10个差异基因片段，其中2个为新基因（GenBank登录号分别为：C20：AF363068；C34：AY032661）。结论 抑制性消减杂交技术是克隆差异表达基因及发现新基因的有效方法。     

Screening and identification of differentially expressed transcripts in circulating cells of prostate cancer patients using suppression subtractive hybridization

Background  

Tumor metastasis and changes in host immunosurveillance are important components in cancer development. Tumor cell invasion into the bloodstream is an essential step for systemic metastasis. Currently, the detection of tumor cells in the circulation is mainly dependent upon the utilization of known epithelial cell markers. However, expression of these molecules is not limited to cancer patients; healthy people also have a small number of epithelial cells in their circulation. Utilizing these markers to detect circulating tumor cells (CTCs) cannot adequately explain the mechanisms of tumor cell survival or their development of metastatic potential in peripheral blood. The immune system can also evolve along with the cancer, actually promoting or selecting the outgrowth of tumor variants. Unfortunately, both metastasis and immunosurveillance remain mysterious and are debatable because we have yet to define the molecules that participate in these processes. We are interested in identifying the existence of expressed genes, or mRNA species, that are specifically associated with circulating cells of cancer-bearing patients using prostate cancer (PCa) as a model.     

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.     

应用抑制消减杂交技术筛选人肾癌差异表达新基因

背景与目的：认识肾癌差异表达基因有助于阐明肾癌发生,发展的分子机制。但至今有关肾癌差异基因尤其肾癌特异相关基因的研究仍不令人满意,本实验应用抑制消减杂交技术筛选入肾癌组织与正常肾组织间差异表达的新基因,以期克隆出新的肾癌特异相关基因。方法：以肾癌组织mRNA为检测对象（Tester)。正常肾组织mRNA为驱赶者（Driver)。构建cDNA消减文库,随机挑取文库克隆进行酶切及测序,所得结果在GenBank中做同源性比对分析。对感兴趣的片段进行电子定位确定其在染色体的位置,用Northern blot,半定量RT-PCR方法检测新基因在肾癌组织与正常肾组织中的差异表达。结果：文库包含414个阳性克隆;随机挑取280个克隆提取质粒并酶切分析,其中265个有插入片段;将其中80个克隆进行测序,初步显示28、158、170、249号4个克隆为新基因片段,电子定位表明上述4个基因分别位于染色体21q^22,4q^15.3,9q^34,22q^11.2。已在GenBank中登录（BM181083,BI784487,BI863835,BI863386）,对其中28、170号克隆用Northern杂交,半定量RT-PCR检测,证实新基因在肾癌组织中表达较正常肾组织显著增高。结论：抑制消减杂交技术是筛选,克隆肾癌差异表达新基因的有效手段;筛选到的新基因片段为进一步克隆其全长,研究基因功能提供了实验基础。     

Analysis of differentially expressed genes in hepatocellular carcinoma with hepatitis C virus by suppression subtractive hybridization

Hepatitis C virus (HCV) infection is associated with pathogenesis of hepatocellular carcinoma (HCC). We carried out suppression subtractive hybridization to identify variable expression of genes linked to HCC with HCV infection. RNA from both tumorous (tester) and nontumorous (driver) liver tissues was isolated. The cDNA clones were subjected to MegaBACE PCR sequencing to identify those that hybridized to the subtracted library with preference. Nucleic acid sequences generated were searched against the human UniGene database. Among 576 clones screened in the tumorous liver tissue, we identified 30 genes and 28 expressed sequence tags (ESTs). Among 30 genes detected, 23 were with known functions and 7 with unknown functions. The known genes identified had diversified functions and could be divided into 10 functional categories. Twenty percent of these genes were previously known to be tumor related and those most frequently appearing were haptoglobin alpha(2FS)-beta precursor, haptoglobin related protein, and alpha-2-macroglobulin. Four out of 30 known genes (immunoglobulin lambda light chain, kappa immunoglobulin, spliceosomal protein, and X-ray repair cross-complementing protein) were related to chromosome translocation and nucleotide repair. These four genes may contribute to carcinogenesis caused by DNA-damaged agents and to the efficiency of anticancer therapy. The genes with unknown function, which were most frequently detected, were PRO2760 and PRO2955; both encode proteins that express in fetal liver. Twenty-one known and six novel genes were discovered in the nontumorous liver tissue. Apparently, these 27 genes were lost in the tumorous liver tissues. Therefore, using suppression subtractive hybridization, we have identified a number of genes associated with HCC with HCV infection. Most of these genes have not been reported in HCC. Further characterization of these differentially expressed known and unknown genes will provide useful information in understanding the genes responsible for the development of HCC.     

Identification of human renal cell carcinoma associated genes by suppression subtractive hybridization.

Renal cell carcinoma (RCC) are frequently chemo- and radiation resistant. Thus, there is a need for identifying biological features of these cells that could serve as alternative therapeutic targets. We performed suppression subtractive hybridization (SSH) on patient-matched normal renal and RCC tissue to identify variably regulated genes. 11 genes were strongly up-regulated or selectively expressed in more than one RCC tissue or cell line. Screening of filters containing cancer-related cDNAs confirmed overexpression of 3 of these genes and 3 additional genes were identified. These 14 differentially expressed genes, only 6 of which have previously been associated with RCC, are related to tumour growth/survival (EGFR, cyclin D1, insulin-like growth factor-binding protein-1 and a MLRQ sub-unit homologue of the NADH:ubiquinone oxidoreductase complex), angiogenesis (vascular endothelial growth factor, endothelial PAS domain protein-1, ceruloplasmin, angiopoietin-related protein 2) and cell adhesion/motility (protocadherin 2, cadherin 6, autotaxin, vimentin, lysyl oxidase and semaphorin G). Since some of these genes were overexpressed in 80-90% of RCC tissues, it is important to evaluate their suitability as therapeutic targets.     

Discovery of over-expressed genes and genetic alterations in breast cancer cells using a combination of suppression subtractive hybridization,multiplex FISH and comparative genomic hybridization

To identify genes that are involved in breast cancer, suppression subtractive hybridization (SSH) was utilized to construct a breast cancer subtracted library. Differential screening of the library isolated 28 genes which by Northern analysis were highly expressed in the breast cancer cell line MDA-MB-231 compared to the normal breast cell line MCF12A. Sequence analysis revealed that 15 clones coded for previously described genes such as SNAP43, Cyr61, Thymosin beta4, tra1, elongation factor 1alpha, BSF-2/IL6, BiP, and GDP/GTP exchange protein. The remaining 13 clones did not match sequences in GenBank/EMBL database, indicating that they may be novel genes. SNAP43, a subunit of the TBP-TAF complex, was expressed 20-fold higher in MDA-MB-231 compared to MCF12A and several breast cancer cell lines, implying that SNAP43 may be involved in tumorigenesis of a specific subset of breast cancers. Amplification of SNAP43 was not found by Southern analysis. However, genetic alterations of MDA-MB-231 included a deletion of chromosome 14 with a reciprocal translocation t(6;14) and two additional translocations [t(12;14) and t(14;15)] as determined by fluorescent in situ hybridization (FISH) with YAC 823G8 located at chromosome 14q23 which contained SNAP43. Because of the numerous alterations observed by FISH in MDA-MB-231, we further explored the genetic abnormalities in this breast cancer cell line using multiplex FISH (M-FISH) and comparative genomic hybridization (CGH). These cells were replete with numerous complex structural rearrangements and had DNA copy-number imbalances involving multiple chromosomes including gains on chromosomes 2p, 2q31-q32, 3p14-pter, 5q, 6p, 7q36-qter, 11, 14q21-q24, 17p11.2-pter, 17q21-qter, 19, 20, Xp11-q13 and losses on chromosomes 4pter-q32, 8p, 9p21-p24, 10q26-qter, 16p13-pter, 18q12-qter, 22, Xp11.3-p22.1, Xq13-qter. In summary, SSH revealed a number of genes that were either novel or previously not associated with breast cancer. In addition, we found that breast cancer cells abounded with abnormalities as observed by M-FISH and CGH. Together, these results may facilitate defining the genetic alterations associated with breast cancer progression.     

Characteristics of normal rat mammary epithelial cells and N-ethyl-N-nitrosourea-induced mammary adenocarcinoma cells grown in culture

The characteristics of normal mammary epithelial cells derived from Lewis and Sprague-Dawley rats and N-Ethyl-N-Nitrosourea (ENU)-induced mammary gland adenocarcinoma cells derived from Sprague-Dawley (CD) and Fisher (CDF) rats and grown in culture were compared. After collagenase treatment, the rat mammary epithelial cell aggregates were placed in a hormone-supplemented medium. The normal mammary epithelial cells (NE) attached to the surface of the dish within 50 hours, whereas the mammary adenocarcinoma cells (MA) attached within 24 hours and grew as cell multilayers. After the colonies of NE and MA cells became confluent, the culture system entered a steady state in which the cells from the upper layer were shed into the medium. The rate of proliferation and squame detachment in confluent cultures was increased by the presence of epidermal growth factor (EGF). Rhodanile blue staining and transmission electron microscopy showed that the shed cells were partially keratinized. In addition, cultured MA (but not normal) cells were able to grow in soft agar and form tumors when inoculated into appropriate hosts. The opposite was true in each case for the mammary adenocarcinoma cells. Karyotypes of normal and neoplastic rat epithelial cells revealed a hypodiploid modal number of chromosomes.     

Characterization of cytokeratins expressed in metastatic rat mammary adenocarcinoma cells

The expression of cytokeratins (CKs) was investigated in cell lines and clones established from the rat 13762NF mammary adenocarcinoma tumor and its spontaneous lymph node and lung metastases. Two-dimensional polyacrylamide gel electrophoresis of intermediate filament-enriched protein fractions from cultured cells revealed that clones established from spontaneous metastases contained three CKs (Mr approximately 54,000, approximately 52,000, and approximately 40,000) characteristic of simple epithelia and two CKs (Mr approximately 51,000 and approximately 47,000) characteristic of stratified epithelia. CK expression varied qualitatively and quantitatively between the different metastasis-derived cell clones. In contrast, cell clones established from the original mammary fat pad tumor expressed low or undetectable levels of CKs. Western blot analyses with a panel of anti-CK antibodies with defined specificities confirmed the observations. One-dimensional polyacrylamide gel electrophoresis of whole-cell lysates and intermediate filament-enriched extracts were transferred and probed with the panel of antibodies. The relative expression of individual CKs varied according to the cell line or clone examined and environmental conditions (low versus high passage and in vitro versus in vivo growth), whereas the amount of total CKs expressed relative to total cell protein varied according to cell line or clone and growth conditions.