Expression profiles of SV40‐immortalization‐associated genes upregulated in various human cancers

Immortalization is an early and essential step of human carcinogenesis which is associated with alterations in gene expression and regulation. Suppression subtractive hybridization (SSH) was successfully performed to identify immortalization‐associated genes upregulated in SV40‐immortalized lung fibroblasts. We identified 116 known genes which were related to diverse functions, with 32.8% relevant for cell cycle or proliferation indicating the potential involvement of these genes in immortalization. We chose eight known genes located on the overrepresented chromosomes of non‐small‐cell lung cancers (NSCLCs). ASPM, RFC4, C3orf26, BXDC2, C15orf44, AURKA, C20orf77, and RBMX were upregulated in immortalized cells, cancer cells, and non‐small‐cell lung cancer (NSCLC) tissues. We additionally cloned two novel genes (CHA‐V‐97 and CHA‐V‐165) which showed similar upregulated expression patterns in cells and tissues examined. Identification and further characterization of these genes may provide insights of novel players for immortalization and human carcinogenesis. J. Cell. Biochem. 106: 703–713, 2009. © 2009 Wiley‐Liss, Inc.     

Putative identification of expressed genes associated with attachment of the zebra mussel (Dreissena polymorpha)

Because of its aggressive growth and firm attachment to substrata, the zebra mussel (Dreissena polymorpha) has caused severe economic and ecological problems since its invasion into North America. The nature and details of attachment of this nuisance mollusc remains largely unexplored. Byssus, a special glandular apparatus located at the root of the foot of the mussel produces threads and plates through which firm attachment of the mollusc to underwater objects takes place. In an attempt to better understand the adhesion mechanism of the zebra mussel, the suppression subtractive hybridization (SSH) assay was employed to produce a cDNA library with genes unique to the foot of the mussel. Analysis of the SSH cDNA library revealed the presence of 750 new expressed sequence tags (ESTs) including 304 contigs and 446 singlets. Using BLAST search, 365 zebra mussel ESTs showed homology to other gene sequences with putative functions. The putative functions of the homologues included proteins involved in byssal thread formation in zebra and blue mussels, exocrine gland secretion, host defence, and house keeping. The generated data provide, for the first time, some useful insights into the foot structure of the zebra mussel and its underwater adhesion.     

差异表达基因的分离策略

生命活动的各个进程伴随着不同基因的选择性开启和关闭。如何有效地分离克隆各种差异表达的基因,成为分子生物学研究的一个努力方向,大量差异基因分离策略因之问世。本文扼要介绍了近年来发展的几种主要分离策略,并详细介绍一种新的差异基因分离方法--抑制差减杂交。     

人体肝癌细胞急性低氧及低氧习服差异表达基因分析

本文分析了人体肝癌细胞(HepG2)急性低氧处理以及低氧习服处理后基因表达谱的改变。急性低氧处理为细胞在1％氧气中培养48h,低氧习服处理为细胞在1％氧气中培养24h,常氧培养24h,以此作为一个周期,重复6个周期。联合应用抑制消减杂交技术和cDNA芯片技术,筛选HepG2细胞经急性低氧处理与正常培养细胞相比差异表达的基因,以及经低氧习服处理细胞与正常培养细胞相比差异表达的基因。结果显示,HepG2细胞经急性低氧处理与在常氧条件下培养相比,差异表达的基因有37个,表达水平全部表现为下调,其中包括参与细胞周期、细胞应激、细胞信号转导、细胞骨架形成、转录相关蛋白及细胞代谢相关蛋白的基因,1个未知基因序列、4个EST序列、5个线粒体蛋白基因,另外有功能不明的蛋白质基因12个。低氧习服处理的细胞与常氧条件下培养的细胞相比,差异表达的基因有6个,其中包括两个线粒体蛋白基因、金属蛋白酶1基因、转铁蛋白基因、Thymosin ．beta-4和TPT1基因。其中线粒体蛋白ND4、转铁蛋白、Thymosin.beta-4和TPT1基因的表达呈上调,线粒体NDl及金属蛋白酶1基因的表达水平呈下调。经低氧习服处理后,细胞低氧耐受力提高,低氧习服处理细胞基因的表达与急性低氧处理细胞和正常培养细胞的基因表达不同,这种变化可能与低氧习服细胞低氧耐受力的增强有关。     

链状亚历山大藻生长衰亡相关基因的筛选

采用抑制性消减杂交(Suppression subtractive hybridization,SSH)技术构建了衰亡期的链状亚历山大藻(Alexandriumcatenella)特异表达的cDNA文库。共获得800个克隆,利用巢式引物进行PCR筛选,最终确定阳性克隆556个。利用斑点杂交技术对这些阳性克隆进行差异筛选,获得差异表达克隆160个。测序后得到片段125个,经过归类,获得21种序列,其中6种在NCBI中经Blast,获得功能基因与其匹配,这些功能基因分别是CHK1类似检测点蛋白(checkpoint-like protein)、核酸外切酶复合体、谷氧还蛋白、Na+/K+ATPase、叶绿体中的一个开放阅读框和pG1蛋白,其他blast无同源序列,可能为新基因。推测链状亚历山大藻的衰亡过程可能涉及到DNA损伤、mRNA降解过程、氧化还原状态的变化、离子动态平衡的变化以及叶绿体一些生理状况的变化等过程。     

Mercury-induced genes in Arabidopsis thaliana: identification of induced genes upon long-term mercuric ion exposure

Mercuric‐ion‐induced gene expression was studied in Arabidopsis thaliana Columbia wild type. Rosettes of plants grown for 21 d on agar medium supplemented with 20, 30 and 40 µm HgCl₂ were pooled and used to isolate cDNAs of induced genes by suppression subtractive hybridization. Of the 576 clones isolated initially, 31 turned out to be mercury‐induced by Northern hybridization. However, kinetic studies using cDNA arrays clearly showed that seven genes were exclusively mercuric‐ion‐induced, 14 were induced by mercury but also affected by a diurnal rhythm, and 10 clones were only modulated by the day–night cycle. The expression levels of the metal‐induced genes increased from 1·5‐fold to 10‐fold. Functional classification resulted in genes encoding proteins for the photosynthetic apparatus and for the antioxidative system. In addition, unexpected genes, whose connection to mercury ion stress is not evident, were identified.     

抑制消减杂交技术在肿瘤转移调控研究中的应用

为探讨肿瘤转移发生的分子生物学机制奠定基础,通过使用抑制消减杂交技术从一对同一新本、转移表型不同的人肺巨细胞癌细胞株中分离转移抑制相关基因可核苷酸片段。结果获得５个在低转移肺巨细胞癌中高表达的、均与已知的人类基因片段有很高同源性的核苷酸片段,它们可能在维持肿瘤细胞自身稳定防止转移中起重要作用。     

Identification of differentially expressed genes related to metabolic syndrome induced with high-fat diet in E3 rats

Understanding the genes differentially expressing in aberrant organs of metabolic syndrome (MetS) facilitates the uncovering of molecular mechanisms and the identification of novel therapeutic targets for the disease. This study aimed to identify differentially expressed genes related to MetS in livers of E3 rats with high-fat-diet-induced metabolic syndrome (HFD-MetS). E3 rats were fed with high-fat diet for 24 weeks to induce MetS. Then, suppression subtractive hybridization (SSH) technology was used to identify the genes differentially expressed between HFD-MetS and control E3 rat livers. Twenty positive recombinant clones were chosen randomly from forward subtractive library and sent to sequence. BLAST analysis in GenBank database was used to determine the property of each cDNA fragment. In total, 11 annotated genes, 3 ESTs, and 2 novel gene fragments were identified by SSH technology. The expression of four genes (Alb, Pip4k2a, Scd1, and Tf) known to be associated with MetS and other five genes (Eif1, Rnase4, Rps12, Rup2, and Tmsb4) unknown to be relevant to MetS was significantly up-regulated in the livers of HFD-MetS E3 rats compared with control rats using real-time quantitative PCR (RT-qPCR). By analyzing the correlations between the expression of these nine genes and serum concentrations of TG, Tch, HDL-C, and LDL-C, we found that there were significant positive correlations between TG and the expression of five genes (Alb, Eif1, Pip4k2a, Rps12, and Tmsb4x), Tch and three genes (Rnase4, Scd1, and Tmsb4x), and LDL-C and two genes (Rnase4 and Scd1), as well there were significant negative correlations between HDL-C and the expression of three genes (Rup2, Scd1, and Tf). This study provides important clues for unraveling the molecular mechanisms of MetS.     

以抑制消减杂交法筛选肿瘤耐药相关基因

避开化疗诱导多药耐药性的常规方法,建立烷基磷脂类化合物（十六烷基磷酸胆碱,HePC)诱导人上皮性肿瘤细胞系产生交叉耐药。旨在以新的角度认识肿瘤多药耐药性,揭示新的调控机制。利用抑制消减杂交技术,对库进行克隆分析,在获得的可分析的78个克隆中,27%没有同源基因片段或同源性很低,暂定为“新基因”;14%具有染色体明确定位,认为是化疗敏感肿瘤KB细胞所特有的cDNA片段;19%在人类EST库库MGC和CGAP中出现,可能是肿瘤细胞特有基因;发现与耐药相关的巳知功能基因高达40%。     

Identification of up-regulated genes in human uterine leiomyoma by suppression subtractive hybridization

In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.     

Identification of up-regulated genes in human uterine leiomyoma by sup-pression subtractive hybridization

In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88 genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes were firstly associated with UL. Three genes with notable difference were selected for Northern confirmation. Our results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showed up-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obvious expression in prostate, testis, liver, heart and skeletal muscle.     

AMPK-mTOR-ULK1 axis activation-dependent autophagy promotes hydroxycamptothecin-induced apoptosis in human bladder cancer cells

10-hydroxycamptothecin (HCPT), a natural plant extract, exerts anticancer capacity. HCPT has been reported to induce apoptosis and autophagy in human cancer cells. The interaction between autophagy and apoptosis induced by HCPT and the molecular mechanism in bladder cancer cells were investigated in this study. Our results confirmed that HCPT suppressed cell viability and migration and caused cell-cycle arrest in T24 and 5637. Then, we used Z-VAD(OMe)-FMK to clarify that apoptosis induced by HCPT was mediated by caspase. Moreover, HCPT boosted autophagy through activating the AMPK/mTOR/ULK1 pathway. Blocking autophagy by 3-methyladenine, the adenosine monophosphate-activated protein kinase (AMPK) inhibitor dorsomorphin and siATG7 reversed HCPT-induced cytotoxicity. Conversely, rapamycin and the AMPK activator AICAR enhanced growth inhibition and cell apoptosis, suggesting that autophagy played a proapoptosis role. Taken together, our findings showed that HCPT-induced autophagy mediated by the AMPK pathway in T24 and 5637 cell lines, which reinforced the apoptosis, indicating that HCPT together with autophagy activator would be a novel strategy for clinical treatment in bladder cancer.     

Identification of sheep ovary genes potentially associated with off-season reproduction

Off-season reproduction is a favorable economic trait for sheep industry.Hu sheep,an indigenous Chinese sheep breed,demonstrates a higher productivity of lambs and displays year-around oestrous behavior under proper nutrition and environment.The genetic basis behind these traits,however,is not well understood.In order to identify genes associated with the off-season reproduction,we constructed a suppression subtractive hybridization(SSH) cDNA library using pooled ovary mRNAs of 6 oestrous Hu females as a tester and the pooled ovary mRNAs of 6 non-oestrous Chinese Merino females as a driver.A total of 382 resulting positive clones were obtained after the SSH.We identified 114 differentially up-regulated genes in oestrous Hu sheep by using subsequent screening and DNA sequencing,of which 8 were previously known,93 were reported for the first time in sheep,and 13 were novel with no significant homology to any sequence in the DNA databases.Functions of the genes identified are related to cell division,signal transduction,structure,metabolism,or cell defense.To validate the results of SSH,6 genes(Ntrk2,Ppap2b,Htra1,Nid1,Serpine2 and Foxola) were selected for conformational analysis using quantitative real-time PCR(qRT-PCR),and two of them(Htral and Foxola) were verified by Northern blot.All of the 6 genes were differentially up-regulated in the ovary of oestrous Hu.It is obvious that off-season reproduction is a complex trait involving multiple genes in multiple organs.This study helps to provide a foundation for the final identification of functional genes involved in the sheep ovary.     

Differential gene expression profiling of human epidermal growth factor receptor 2-overexpressing mammary tumor

Human epidermal growth factor receptor 2 (HER2) is highly expressed in approximately 30% of breast cancer patients, and substantial evidence supports the relationship between HER2 overexpression and poor overall survival. However, the biological function of HER2 signal transduction pathways is not entirely clear. To investigate gene activation within the pathways, we screened differentially expressed genes in HER2-positive mouse mammary tumor using two-directional suppression subtractive hybridization combined with reverse dot-blotting analysis. Forty genes and expressed sequence tags related to transduction, cell proliferation/growth/apoptosis and secreted/extracellular matrix proteins were differentially expressed in HER2-positive mammary tumor tissue. Among these, 19 were already reported to be differentially expressed in mammary tumor, 11 were first identified to be differentially expressed in mammary tumor in this study but were already reported in other tumors, and 10 correlated with other cancers. These genes can facilitate the understanding of the role of HER2 signaling in breast cancer.     

Identification of signature genes associated with 5-fluorouracil-resistance in human gastric cancer cells

A comparative cDNA microarray analysis was carried out using human gastric cancer cells and their derivative cells made resistant to 5-fluorouracil. Three genes, SRP72, DNA primase, and caspase-6, were identified that were transiently induced by 5-fluorouracil and also overexpressed in 5-fluorouracil-resistant gastric cancer cells.     

抑制性消减杂交在生物基因克隆中的应用

抑制性消减杂交(SSH)是抑制PCR与消减杂交技术相结合,能对未知序列差异表达基因克隆的一种方法。该方法具有速度快、效率高、假阳性率低、目的序列富集程度高、实验结果复杂程度低等特点。本主要介绍其基本原理、操作过程、优缺点、在生物基因克隆中的应用,并对其应用前景进行了分析。