Identification of genes differentially expressed in breast cancer cell line SKBR3: potential identification of new prognostic biomarkers

The identification of differentially expressed genes in tumour cells should have important implications in understanding carcinogenesis and developing new therapeutic and prognostic biomarkers. We have combined PCR-based cDNA subtraction and Northern blotting to identify truly differentially expressed genes in breast cancer cell line SKBR3 as compared to normal human mammary epithelial cells (HMEC). Hybridizing probe molecules were rescued from the Hybond N+ membranes and then PCR reamplified. The PCR reamplification is possible due to the fact that all probe molecules contain the same pair of adapter sequences on both ends. After cloning and sequencing three known genes, ribosomal protein L19 (RPL19), ADP/ATP carrier protein and ErbB-2 with high-elevated mRNA levels in SKBR3 were identified. In addition, two overexpressed genes with unknown functions, CXYorf1-related protein and hypothetical protein PRO2605, were found. High-titer andibodies against the recombinant RPL19 were detected in 5 patients out of 50 patients investigated. Thus, the present novel strategy based on the combination of PCR-based cDNA subtraction and Northern blotting should facilitate the identification of truly differentially expressed biomarkers, which may offer the potential to determine the proper drug for an individual patient at a given stage of disease or treatment.     

Identification of differentially expressed genes in a renal cell carcinoma tumor model after endostatin-treatment

Endostatin is a cleavage product of collagen XVIII that has shown to inhibit tumor-angiogenesis in experimental tumor models. At present, the exact molecular mechanism of action of endostatin is not completely elucidated. In this study, we wanted to identify specific target genes of endostatin. For this purpose, the human renal cell carcinoma RC-9 was subcutaneously implanted in nude mice and treated with endostatin. Tumor growth was inhibited by endostatin after 4 days of treatment. Using immunohistochemistry and the hypoxia marker pimonidazole, we demonstrate disintegration of blood vessels and hypoxia and anoxia as a result of the treatment. Hereafter, we applied the polymerase chain reaction (PCR)-based subtractive suppression hybridization (SSH) method, together with the mirror orientation selection (MOS) technique to identify specifically induced and suppressed genes after endostatin-treatment. We found eight genes to be specifically induced and 11 to be suppressed by the endostatin-treatment. Among other genes, core binding factor a-1/osteoblast-specific factor-2 (cbfa1/osf2) was found to be specifically suppressed by endostatin. Unexpectedly, cbfa1/osf2 was found to be specifically expressed in granulocytes in the tumor, not only in the experimental RC-9 tumor model, but in sections of human breast cancer as well. Since an effect of antiangiogenic therapy on granulocytes has been reported before, this might lead to new insights in the role of granulocytes in antiangiogenic therapy in general. In conclusion, the SSH-PCR implemented with the MOS-technique is a powerful tool to identify differentially expressed genes. Using these techniques, we have identified several target genes of endostatin, of which cbfa1/osf2 was found to be specifically expressed in granulocytes in the tumor.     

放射治疗后宫颈癌组织内差异表达基因鉴定

目的 研究放射治疗对宫颈癌组织基因表达的影响,探讨差异表达基因对放射治疗敏感及在抗拒中的作用.方法 患者接受相同的放疗模式:全盆腔外照射总剂量45戈瑞(Gy),共25次(45 Gy/25 f),腔内近距离内照射每次剂量5～6 Gy,共治疗5～6次.分别在近距离放射治疗前、近距离放射治疗中、近距离放射治疗结束时留取标本....     

乳腺癌个体中差异表达lncRNA的研究

目的 识别乳腺癌个体中差异表达长链非编码RNA (long non-coding RNA,lncRNA).方法 应用LncRIndiv方法识别乳腺癌个体中差异表达lncRNA,并使用超几何检验进行亚型分析和Log-rank检验进行预后分析.结果 lncRNA差异判断的平均准确率高于96％.分别识别出1 81个、32个、15个和72个basal-like、HER2-enriched、luminal A、luminal B 亚型特异的lncRNAs(False discovery rate＜0.05,超几何检验).LncRNA ZNF582-ASl差异下调的乳腺癌患者生存差(TCGA,P=0.038;GSE42568,P=0.026,Log-rank检验),是潜在的预后标志.结论 LncRIndiv方法识别个体中差异表达lncRNA准确性高.乳腺癌个体差异表达lncRNA可用来识别亚型特异的lncRNA和预后标志.     

Suppression of the tumorigenic phenotype by chromosome 18 transfer into pancreatic cancer cell lines

A number of lines of evidence have suggested that the long arm of chromosome 18 apart from SMAD4 may carry a tumor-suppressor gene(s) that plays a role in the early stage of pancreatic ductal carcinogenesis. Thus, adenovirus-mediated introduction of SMAD4 does not suppress in vitro growth in cells with completely inactivated SMAD4, and frequent loss of 18q at the SMAD4 locus is observed in pancreatic cancers but no abnormalities of the normal SMAD4 homolog have been detected. In this study, we introduced a normal copy of chromosome 18 into some pancreatic ductal carcinoma cells with and without a complete inactivation of SMAD4. Both anchorage-dependent and -independent proliferation as well as invasiveness were significantly suppressed in the hybrid clones compared with that of their parental cells. Moreover, significant suppression of tumorigenesis was observed after inoculation in nude mice, irrespective of the SMAD4 status. Our present study provides the first functional evidence of the existence of an additional tumor-suppressor gene(s), other than SMAD4 and DCC, that is responsible for the pathogenesis in the early stage of pancreatic ductal carcinogenesis.     

乳腺癌17号染色体多体的临床病理意义

目的 探讨乳腺癌17号染色体多体异常的临床病理学意义.方法 回顾性分析200例乳腺癌荧光原位杂交结果,并分析17号染色体多体与年龄、核异型性、淋巴结转移以及HER2基因扩增、HER2蛋白表达的关系.结果 200例乳腺癌患者中表现为17号染色体多体异常的52例(26.0%),均为浸润性导管癌;占180例浸润性导管癌的52.8%.17号染色体多体与HER2基因扩增和HER2蛋白表达有关(均P=0.000),并且多体伴HER2基因扩增时也与HER2蛋白表达有关(P=0.001).多体和(或)多体伴HER2基因扩增都与乳腺癌癌细胞的高度异型性(P=0.010或P=0.012)及淋巴结转移有关(P=0.009或P=0.002).17号染色体多体或多体伴HER2基因扩增与乳腺癌患者的年龄无关(P=0.415或P=1.000).结论 17号染色体多体可能与乳腺癌患者的预后不良有关.     

Retroviral transfer of HSV1-TK gene into human lung cancer cell line

We used a recombinant retrovirus as one of the potential vectors for human gene therapy to transfer a drug sensitivity gene into human lung cancer cells. The gene encoding the thymidine kinase (TK) of herpes simplex virus type 1 (HSV1) was used as the drug sensitivity gene. The antiherpes drugs acyclovir (ACV) and ganciclovir (GCV) were chosen to test the HSV1-TK activity transferred into the human lung cancer cell lines. The rationale for this approach was that ACV and GCV are nucleoside analogs specifically converted by HSV1-TK to a toxic form capable of inhibiting DNA synthesis or disrupting cellular DNA replication. The results obtained from our experiments demonstrate that the retroviral vector-mediated HSV1-TK gene transfer leads to ACV- and GCV-dependent cytotoxicity in human lung cancer cell lines, including both small-cell carcinoma and nonsmall-cell carcinoma. Although the gene transfer of HSV1-TK gene into tumor cells would be one model for gene therapy to control lung cancer, further investigations are necessary for the proper choice of the therapeutic gene and vector targeting such as tumor cell specific delivery of the gene or tumor cell specific expression of the transduced gene.Abbreviations ACV Acyclovir - GCV Ganciclovir - HSV1 Herpes simplex virus type 1 - LTR Long terminal repeat - TK Thymidine kinase     

GABRP基因在基底样三阴乳腺癌中的差异表达

目的:探索GABRP基因在基底样三阴乳腺癌(basal-like Triple negative breast cancer,BLTNBC)中的表达,为临床提供预后诊断分子标志物.方法:通过生物信息学分析比较GABRP基因的表达;采用定量PCR方法检测GABRP基因在乳腺癌细胞系及104例乳腺癌石蜡样本中的差异表达,并采用相关性分析、卡方检验及Fisher精确概率法分析GABRP基因与细胞增殖、淋巴结转移、ER及HER-2基因表达的相关性.结果:生物信息学分析和定量PCR结果显示GABRP基因在三阴性乳腺癌(triple negative breast cancer,TNBC)及BLTNBC中显著性高表达(p＜0.05);在non-TNBC,TNBC,BLTNBC中,其表达与细胞增殖、HER-2表达无明显相关性(P＞0.05),而在BLTNBC中与淋巴结转移状态有明显相关性(P＜0.05),在non-TNBC巾与ER表达有明显相关性(P＜0.05).结论:GABRP基因可作为BLTNBC的有潜力的预后诊断分子标志物.     

RNA-Seq筛选脊髓损伤后的差异基因及部分基因功能分析

目的应用RNA-Seq技术分析脊髓损伤后不同阶段基因表达差异情况。方法使用IH脊髓打击仪制备脊髓损伤模型,SD大鼠48只随机分成两组,假手术组和实验组,实验组分别于损伤后1d、4d和7d取材。运用RNA-Seq技术筛选脊髓损伤后不同时间点的差异表达基因,对差异基因进行表达模式分析,功能注释,通路分析等,筛选出血红素氧化酶1(Hmox1)等感兴趣基因进行mRNA和蛋白水平的验证及功能分析。结果 RNA-Seq结果表明,与假手术组相比,脊髓损伤后1d、4d和7d发生显著变化的基因分别有944、1362和1421个。上述差异基因在损伤后不同时间点的变化趋势大致可分为8种形式。Real-time PCR结果显示,Hmox1、尿激酶型纤溶酶原激活剂(Plau)、纤溶酶原激活物抑制剂(Serpine1)和中性粒细胞胞质因子(Ncf2)的表达变化与RNA-Seq测序结果基本一致。Western blotting结果显示,脊髓损伤后Hmox1的蛋白表达变化趋势与核酸水平一致;免疫组织化学结果显示,损伤之后Hmox1主要表达于脊髓组织的神经元中。结论 RNA-Seq技术能高效分析脊髓损伤后的差异基因,从大量差异基因中筛选出感兴趣基因的验证和功能分析为阐述脊髓损伤的分子机制提供了部分资料。     

Rejoining of DNA double-strand breaks after the introduction of chromosome 11 into a radiosensitive bladder carcinoma cell line

Insertion of a normal chromosome 11 into tumour cell lines can protect against a sensitivity to irradiation and oxidative stress. A possible mechanism underlying this effect is that there is a correction of a defect in the rejoining of double-strand breaks (dsb) by the chromosome insertion. In order to explore this hypothesis, three cell lines were evaluated for their ability to rejoin dsb: (1) a bladder carcinoma cell line (`parent') previously shown to be sensitive to irradiation and radical generating species; (2) a derivative of this cell line into which a normal chromosome 11 had been inserted by microcell fusion (`hybrid') showing corrected radiosensitivity; and (3) a `revertant' cell line that had spontaneously lost the insert and reverted to the radiosensitive phenotype. Nuclear extracts from the 3 lines were isolated and evaluated for their capacity to rejoin plasmid (pUC18) DNA broken at defined restriction sites (SalI, EcoRI, KpnI, SmaI) in the lacZ gene. The extent of rejoining was determined by gel electrophoresis and the fidelity of rejoining determined by expression of the lacZ gene in E. coli DH5α bacteria. Results suggest there is no difference between the `parent', `hybrid' and `revertant' nuclear extracts in the fidelity and the total extent of rejoining, regardless of the type of break. However, there is an alteration in the distribution of rejoined products. Nuclear extracts from `hybrid' cells tend to rejoin linear DNA into circular monomers with a greater efficiency than extracts from both `parent' and `revertant' cells. This alteration in distribution is observed when 3′- or 5′-protruding ends are rejoined but not in the rejoining of blunt ends. The results suggest that loci on chromosome 11 are involved in the rejoining of dsb, affecting the relative amount of the different rejoined products. Whether this alteration plays a role in the `parent' cell's radiosensitivity is yet to be determined.     

Cloning and identification of genes differentially expressed in metastatic and non-metastatic rat rhabdomyosarcoma cell lines

The objective of this study was to identify genes involved in invasion and metastasis using a rat rhabdomyosarcoma model (SMF-A and RMS-B cell lines). The SMF-A cell line was established from a metastatic nodule of an induced rhabdomyosarcoma in syngeneic F344 rats. Two cell lines with defined metastatic potentials, SMF-Ai and SMF-Da, were cloned from the SMF-A line. The cell line SMF-Ai is tumorigenic, highly invasive and highly metastatic. On the other hand, the revertant line SMF-Da is less tumorigenic, non-invasive and non-metastatic. We have isolated from a SMF-Ai cDNA library eight cDNA clones which are differentially expressed by the metastatic SMF-Ai and the non-metastatic SMF-Da cell line using Northern blot analysis. Five of these clones, smf-4, smf-6, smf-41, smf-42 and smf-44, are overexpressed in the SMF-Da cell line and have homology with beta-2-microglobulin, lactate dehydrogenase, ribosomal protein L38, ribosomal protein S4 and acidic ribosomal phosphoprotein P1, respectively. The three other clones, smf-7, smf-40 and smf-61, are overexpressed in SMF-Ai. Clones smf-40 and smf-61 show significant homology with the human TB3-1 gene and the human fus gene respectively. The clone smf-7 has no significant homology with known sequences. We also analyzed the expression of these clones in other rat rhabdomyosarcoma cell lines (RMS-B and their clones) and in tumors obtained by injection of these cell lines into rats or nude mice. Smf-61 and smf-7 were the only clones with a differential expression pattern associated with the invasive or metastatic potential of all cell lines examined. A preliminary study of the expression of smf-7 and smf-61 in other cancer cell lines also showed mRNA expression in two human rhabdomyosarcomas and a human epidermoid carcinoma suggesting the existence of genes homologous to smf-7 and smf-61 clones in human cancers. Our findings suggest an association between the expression of smf-7 and smf-61 and invasive or metastatic potential of rhabdomyosarcoma cells.     

Genetic events during the transformation of a tamoxifen-sensitive human breast cancer cell line into a drug-resistant clone

Tamoxifen resistance is a serious clinical problem commonly encountered in the management of patients with breast cancer. The mechanisms leading to its development are unclear. Tamoxifen acts via multiple pathways and has diverse effects. Hence transformation from a tamoxifen-sensitive to a resistant phenotype could involve multiple genetic events. Knowledge of the genetic pathways leading to resistance may facilitate the development of novel therapeutic strategies. In this study, a variation of conventional comparative genomic hybridization (CGH) has been employed to detect genetic alterations associated with tamoxifen resistance. MCF-7, a tamoxifen-sensitive human breast cancer cells line, and its tamoxifen-resistant clone, CL-9 were used. Both cell lines showed extensive areas of concordance but consistent differences were seen with the acquisition of tamoxifen resistance. These differences included the amplification of 2p16.3p23.2, 2q21q34, 3p12.3p14.1, 3p22p26, 3q, 12q13.2q22, 13q12q14, 17q21.3q23, 20q11.2q13.1 and 21q11.2q21 as well as the deletion of 6p21.1, 6p23p25, 7q11.1q31, 7q35q36, 11p15, 11q24, 13q33, 17p, 18q12q21.1, 19p, 19q13.3, 22q13.1q13.2. These findings were supported by conventional cytogenetics and chromosome painting. The regions identified by CGH potentially harbor genes that could be important in the development of tamoxifen resistance.     

Multiple forms of BRMS1 are differentially expressed in the MCF10 isogenic breast cancer progression model

Clinical studies evaluating the mRNA expression level of the BRMS1 metastasis suppressor in the progression of breast cancer have not been consistent. The purpose of this study was to characterize endogenous BRMS1 mRNA and protein in a model of the progression of breast cancer. BRMS1 protein expression was evaluated in the genetically related MCF10 cell lines representing ‘normal’ breast epithelial cells (MCF10A), pre-malignant breast disease (MCF10AT), comedo ductal carcinoma in situ (MCF10DCIS.com), and metastatic carcinoma (MCF10CAa.1 and MCF10CAd.1α) with two antibodies that recognize distinct epitopes in the BRMS1 protein. Nuclear expression of the characteristic ~35 kDa BRMS1 protein was detected in all cell lines. Because BRMS1 was expressed in the metastatic MCF10 variants, the BRMS1 exons were sequenced to scan for possible genetic mutations. BRMS1 was wild-type with the exception of a synonymous T/C transition in exon 7. However, alternatively spliced variants were detected by RT-PCR. Two variants, BRMS1.v2 and BRMS1.v4 were only detected in the MCF10A and AT cell lines, while BRMS1 and BRMS1.v3 were detected in all lines. These results demonstrate that expression of the characteristic ~35 kDa BRMS1 protein is not sufficient to prevent metastasis. The differential expression of alternative splice variants suggests caution should be taken when evaluating BRMS1 mRNA in clinical samples.     

Intersecting batteries of differentially expressed genes in the early sea urchin embryo

We determined the distribution of cis-regulatory sites, previously identified in the control domain of the CyIIIa gene, in three other genes displaying diverse spatial patterns of expression in the sea urchin embryo. Competitive gel-shift reactions were carried out using probes from the CyIIIa gene, with competitor fragments isolated from the previously defined control domains of the other genes. CyIIIa is expressed only in aboral ectoderm lineages; the other genes studied were Spec1, also expressed in aboral ectoderm; CyI, expressed in many different cell types; and SM50, expressed only in skeletogenic mesenchyme. All four genes are activated at about the same time in late cleavage. Where competitive interactions indicated a functionally comparable binding site (in vitro), a sequence homology was sought, and in most cases could be identified. An interesting pattern of putative regulatory site usage emerges: Of 10 CyIIIa interactions tested, three only were unique to the CyIIIa gene with respect to the set of four genes tested; one believed on previous evidence to be a temporal regulator was shared by all four genes, and the remainder were shared in various subsets of the four genes.     

激素耐药型与激素敏感型肾病综合征差异表达基因分析

分析;定量PCR验证芯片的基因差异表达结果.结果 与正常对照组相比较,与SRNS组和SSNS组相关的差异基因共157条;聚类分析显示SSNS组与对照组基因表达差异较小,SRNS组与前两者差异明显;功能分析发现与SRNS组相关的差异表达基因主要参与细胞核内生物学活动和细胞信号转导.结论 不同临床和病理类型原发性肾病综合征涉及多个不同的差异基因和生物学途径,其中HLA-DRB4和CLNS1A基因可能在不同类型原发性肾病综合征发病机制中发挥重要作用.     

Transfer of chromosome 8 into two breast cancer cell lines: total exclusion of three regions indicates location of putative in vitro growth suppressor genes

Loss of heterozygosity (LOH) of the short arm of chromosome 8 occurs frequently in breast tumors. Fine mapping of the smallest regions of overlap of the deletions indicates that multiple tumor suppressor genes may be located in this region. We have performed microcell-mediated chromosome transfer of chromosome 8 into two breast cancer cell lines, 21MT-1 and T-47D. Twenty-two of the resulting hybrids were characterized extensively with chromosome 8 microsatellite markers and a subset were assayed for growth in vitro and soft agar clonicity. There was no evidence in any of the hybrids for suppression of growth or clonicity that could be attributed to the presence of particular regions of chromosome 8; however, none of the 22 hybrids examined had taken up all of the donor chromosome 8, and in fact there were three regions that contained only one allele of the markers genotyped in all 22 hybrids. These results are consistent with the presence of suppressor genes on the short arm of chromosome 8 causing strong growth suppression that is incompatible with growth in vitro; that is, multiple suppressor genes may exist on the short arm of chromosome 8.