Ion Channel Gene Expression in Lung Adenocarcinoma: Potential Role in Prognosis and Diagnosis

Ion channels are known to regulate cancer processes at all stages. The roles of ion channels in cancer pathology are extremely diverse. We systematically analyzed the expression patterns of ion channel genes in lung adenocarcinoma. First, we compared the expression of ion channel genes between normal and tumor tissues in patients with lung adenocarcinoma. Thirty-seven ion channel genes were identified as being differentially expressed between the two groups. Next, we investigated the prognostic power of ion channel genes in lung adenocarcinoma. We assigned a risk score to each lung adenocarcinoma patient based on the expression of the differentially expressed ion channel genes. We demonstrated that the risk score effectively predicted overall survival and recurrence-free survival in lung adenocarcinoma. We also found that the risk scores for ever-smokers were higher than those for never-smokers. Multivariate analysis indicated that the risk score was a significant prognostic factor for survival, which is independent of patient age, gender, stage, smoking history, Myc level, and EGFR/KRAS/ALK gene mutation status. Finally, we investigated the difference in ion channel gene expression between the two major subtypes of non-small cell lung cancer: adenocarcinoma and squamous-cell carcinoma. Thirty ion channel genes were identified as being differentially expressed between the two groups. We suggest that ion channel gene expression can be used to improve the subtype classification in non-small cell lung cancer at the molecular level. The findings in this study have been validated in several independent lung cancer cohorts.     

Yin Yang Gene Expression Ratio Signature for Lung Cancer Prognosis

Many studies have established gene expression-based prognostic signatures for lung cancer. All of these signatures were built from training data sets by learning the correlation of gene expression with the patients'' survival time. They require all new sample data to be normalized to the training data, ultimately resulting in common problems of low reproducibility and impracticality. To overcome these problems, we propose a new signature model which does not involve data training. We hypothesize that the imbalance of two opposing effects in lung cancer cells, represented by Yin and Yang genes, determines a patient’s prognosis. We selected the Yin and Yang genes by comparing expression data from normal lung and lung cancer tissue samples using both unsupervised clustering and pathways analyses. We calculated the Yin and Yang gene expression mean ratio (YMR) as patient risk scores. Thirty-one Yin and thirty-two Yang genes were identified and selected for the signature development. In normal lung tissues, the YMR is less than 1.0; in lung cancer cases, the YMR is greater than 1.0. The YMR was tested for lung cancer prognosis prediction in four independent data sets and it significantly stratified patients into high- and low-risk survival groups (p = 0.02, HR = 2.72; p = 0.01, HR = 2.70; p = 0.007, HR = 2.73; p = 0.005, HR = 2.63). It also showed prediction of the chemotherapy outcomes for stage II & III. In multivariate analysis, the YMR risk factor was more successful at predicting clinical outcomes than other commonly used clinical factors, with the exception of tumor stage. The YMR can be measured in an individual patient in the clinic independent of gene expression platform. This study provided a novel insight into the biology of lung cancer and shed light on the clinical applicability.     

光神霉素A抑制人肺腺癌A549／DDP细胞MRP1基因表达

该研究旨在探讨Sp1抑制剂光神霉素A（MithramycinA）对人肺腺癌A549／DDP细胞MRPI表达的影响。不同浓度光神霉素A作用A549／DDP细胞48h后,采用MTT法检测细胞存活率,RealtimeRT-PcR检测印,和MRPI基因表达水平,Westernblotg检测NSp1和MRP1蛋白表达水平。结果显示,300nmol／L光神霉素A作用A549／DDP细胞48h后印,和MRP1mRNA表达水平分别降低31．22％和85．44％,Sp1和MRP1蛋白表达水平分别降低53．27％和40．42％。提示光神霉素A能够通过抑制勋,表达,从而抑制MRP1表达。     

野生型P53、P16基因协同对肺腺癌细胞系生长抑制作用的研究

为了探讨野生型P53基因及P16基因在恶性肿瘤基因治疗中的作用,用腺病毒为载体将野生型P53基因转入高、低转移的肺腺癌细胞系Anip973、AGZY83-a和经野生型P16基因质粒转染的高、低转移肺腺癌细胞系Anip973（Anip973P16）、AGZY83-a（AGZY83-aP16）。对各组转染细胞进行生长曲线、MTT生长抑制率、原位末端标记、Western-blotting等技术检测分析。结果发现（1）野生型P53蛋白的过表达对上述肺腺癌细胞系均呈现出较强的生长抑制作用。（2）野生型P53蛋白的过表达对高转移肺癌细胞系Anip973的抑制作用明显高于低转移细胞系AGZY83-a。（3）野生型p53蛋白的过表达对经野生型P16基因转染的高、低转移的肺癌细胞Anip973、AGZY83-a抑制作用明显高于未经P16基因转染的细胞。野生型P53基因可以作为肺腺癌基因治疗的候选基因。肿瘤抑制基因P53、P16的联合转染可能是对肺腺癌进行基因治疗的有效手段。 Abstract：To investigate the suppression effect of tumor suppressor genes in lung adenocarcinoma cell lines,we transferred a pair of lung adenocarcinoma cell lines with different metastasis potential,Anip973(High-metastasis potential cell line) and AGZY83-a (Low-metastasis potential cell line)and this pair of cell lines transfected with P16 gene:AGZY83-a P16 and Anip973 P16 with wild type P53 gene with adenovirus vector.The suppression effects of P53 gene were evaluated by cell growth curve,MTT,western-blotting analysis and TUNEL technique.Overexpression of wild-type P53 gene in AGZY83-a,Anip973,Anip973 P16 and AGZY83-a P16 inhibited the growth of these four kinds of lung cancer cells and induced apoptosis of the cells.The suppression effect of P53 gene in Anip973 and Anip973 P16 was higher than AGZY83-a and AGZY83-a P16 while co-expression of P53 and　P16 in this pair of cell lines inhibited the cells more efficiently comparing with the expression of P53 alone.Wild-type P53 gene might act as a candidate gene in lung adenocarcinoma gene therapy while co-transfection of P53 and P16 genes was a more effective method.     

人肾上腺基因表达谱的建立及其功能的新认识

为深入理解人类肾上腺（AD）的功能,构建了正常人肾上腺cDNA文库,并利用大规模表达序列标签（ESTs）测序和生物信息学技术,研究显示参与基因/蛋白表达的基因类型表达最多,其次为能量代谢类.肾上腺中表达丰度最高的3个基因均为参与类固醇合成的酶类和蛋白.一些重要的基因首次显示在肾上腺表达,包括神经激素和神经肽,如促肾上腺皮质激素释放激素（CRH）,黑色素浓激素（MCH）,urocortin,可卡因和安非他明调节肽（CART）和垂体腺苷酸环化酶激活肽（PACAP）;许多重要介质的受体,如细胞因子、神经肽及神经递质受体;参与胆固醇代谢的基因,如LDL受体、HDL结合蛋白和胆固醇合成酶.研究结果表明在肾上腺表达丰度最高的基因与该器官的功能特异性有关,除类固醇激素外,许多神经肽、细胞因子在肾上腺产生,肾上腺与体内其他重要的系统间存在广泛的应答,而且在人肾上腺局部可能存在一个CRH-ACTH-皮质醇调节网络.     

Erythropoietin Receptor Expression Is a Potential Prognostic Factor in Human Lung Adenocarcinoma

Recombinant human erythropoietins (rHuEPOs) are used to treat cancer-related anemia. Recent preclinical studies and clinical trials, however, have raised concerns about the potential tumor-promoting effects of these drugs. Because the clinical significance of erythropoietin receptor (EPOR) signaling in human non-small cell lung cancer (NSCLC) also remains controversial, our aim was to study whether EPO treatment modifies tumor growth and if EPOR expression has an impact on the clinical behavior of this malignancy. A total of 43 patients with stage III–IV adenocarcinoma (ADC) and complete clinicopathological data were included. EPOR expression in human ADC samples and cell lines was measured by quantitative real-time polymerase chain reaction. Effects of exogenous rHuEPOα were studied on human lung ADC cell lines in vitro. In vivo growth of human ADC xenografts treated with rHuEPOα with or without chemotherapy was also assessed. In vivo tumor and endothelial cell (EC) proliferation was determined by 5-bromo-2’-deoxy-uridine (BrdU) incorporation and immunofluorescent labeling. Although EPOR mRNA was expressed in all of the three investigated ADC cell lines, rHuEPOα treatment (either alone or in combination with gemcitabine) did not alter ADC cell proliferation in vitro. However, rHuEPOα significantly decreased tumor cell proliferation and growth of human H1975 lung ADC xenografts. At the same time, rHuEPOα treatment of H1975 tumors resulted in accelerated tumor endothelial cell proliferation. Moreover, in patients with advanced stage lung ADC, high intratumoral EPOR mRNA levels were associated with significantly increased overall survival. This study reveals high EPOR level as a potential novel positive prognostic marker in human lung ADC.     

外源上皮钙粘着蛋白基因在人肺腺癌细胞中的表达及调节细胞悬浮生长

为了研究上皮钙粘着蛋白（E-cadherin)对人肺腺癌细胞间粘聚和细胞悬浮生长的影响。利用基因重组技术构建了含全长上皮钙粘着蛋白cDNA的真核表达载体。通过脂质体法转染到A549肺腺癌细胞株中,用RT-PCR和Western印迹鉴定并筛选上皮钙粘着蛋白高表达的细胞,株,并观察转染前后肿瘤细胞间粘聚能力的改变以及细胞悬浮培养下的生长状态,结果表明转染细胞间聚集力比对照细胞增强,上皮钙粘着蛋白能够促进细胞悬浮生长的速度。     

MMP11在肺鳞癌和腺癌组织中的表达及与预后的关系

MMP11属于MMPs家族,它与肿瘤的浸润转移密切相关.探讨MMP11在肺鳞癌和腺癌组织中的表达,及其与浸润转移和预后的关系.应用免疫组化检测50例肺鳞癌和38例肺腺癌组织中MMP11蛋白的表达.结果显示,MMP11在肺鳞癌和腺癌组织中的阳性率分别为68.0%(34/50)和73.7%(28/38)(P=0.563).MMP11的阳性率随着肺癌T分期的增加、淋巴结转移和TNM分期的增加而增加(P<0.05).Kaplan-meier单因素生存分析显示,MMP11表达(P=0.001)、T分期(P=0.009)、淋巴结转移(P<0.001)和TNM分期(P<0.001)对生存期的影响有统计学意义.Cox多因素分析显示,只有TNM分期(P=0.028)是肺癌的独立预后危险因素,MMP11(P=0.105)不是肺癌的独立预后危险因素.MMP11的表达与肺癌的浸润、转移及生存期密切相关.     

Gene Expression Profiling in Preterm Infants: New Aspects of Bronchopulmonary Dysplasia Development

Rationale

Bronchopulmonary dysplasia is one of the most serious complications observed in premature infants. Thanks to microarray technique, expression of nearly all human genes can be reliably evaluated.

Objective

To compare whole genome expression in the first month of life in groups of infants with and without bronchopulmonary dysplasia.

Methods

111 newborns were included in the study. The mean birth weight was 1029g (SD:290), and the mean gestational age was 27.8 weeks (SD:2.5). Blood samples were drawn from the study participants on the 5th, 14th and 28th day of life. The mRNA samples were evaluated for gene expression with the use of GeneChip® Human Gene 1.0 ST microarrays. The infants were divided into two groups: bronchopulmonary dysplasia (n=68) and control (n=43).

Results

Overall 2086 genes were differentially expressed on the day 5, only 324 on the day 14 and 3498 on the day 28. Based on pathway enrichment analysis we found that the cell cycle pathway was up-regulated in the bronchopulmonary dysplasia group. The activation of this pathway does not seem to be related with the maturity of the infant. Four pathways related to inflammatory response were continuously on the 5^th, 14^th and 28^th day of life down-regulated in the bronchopulmonary dysplasia group. However, the expression of genes depended on both factors: immaturity and disease severity. The most significantly down-regulated pathway was the T cell receptor signaling pathway.

Conclusion

The results of the whole genome expression study revealed alteration of the expression of nearly 10% of the genome in bronchopulmonary dysplasia patients.     

Impact of Statins on Gene Expression in Human Lung Tissues

Statins are 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors that alter the synthesis of cholesterol. Some studies have shown a significant association of statins with improved respiratory health outcomes of patients with asthma, chronic obstructive pulmonary disease and lung cancer. Here we hypothesize that statins impact gene expression in human lungs and may reveal the pleiotropic effects of statins that are taking place directly in lung tissues. Human lung tissues were obtained from patients who underwent lung resection or transplantation. Gene expression was measured on a custom Affymetrix array in a discovery cohort (n = 408) and two replication sets (n = 341 and 282). Gene expression was evaluated by linear regression between statin users and non-users, adjusting for age, gender, smoking status, and other covariables. The results of each cohort were combined in a meta-analysis and biological pathways were studied using Gene Set Enrichment Analysis. The discovery set included 141 statin users. The lung mRNA expression levels of eighteen and three genes were up-regulated and down-regulated in statin users (FDR < 0.05), respectively. Twelve of the up-regulated genes were replicated in the first replication set, but none in the second (p-value < 0.05). Combining the discovery and replication sets into a meta-analysis improved the significance of the 12 up-regulated genes, which includes genes encoding enzymes and membrane proteins involved in cholesterol biosynthesis. Canonical biological pathways altered by statins in the lung include cholesterol, steroid, and terpenoid backbone biosynthesis. No genes encoding inflammatory, proteases, pro-fibrotic or growth factors were altered by statins, suggesting that the direct effect of statin in the lung do not go beyond its antilipidemic action. Although more studies are needed with specific lung cell types and different classes and doses of statins, the improved health outcomes and survival observed in statin users with chronic lung diseases do not seem to be mediated through direct regulation of gene expression in the lung.     

抑制Hedgehog信号通路改变结肠癌细胞基因表达谱

Hedgehog（Hh）信号通路在机体发育和肿瘤发生中发挥着重要作用。在该研究中,Western blot检测三株结肠癌细胞Hedgehog信号通路组分的表达,结果表明三株结肠癌细胞中HT-29细胞Hedgehog信号通路组分较完整。采用MTT和BrdU法检测Hedgehog信号通路膜受体Smo特异性抑制剂环杷明和末端转录因子Gli1/2的特异性抑制剂GANT61对HT-29细胞的影响,提示这两种抑制剂均显著抑制HT-29细胞生存率和细胞增殖率,且GANT61比环杷明更敏感。表达谱芯片检测阻断Hedgehog信号通路后HT-29细胞基因谱的变化,结合生物信息学分析,揭示HT-29细胞经环杷明和GANT61处理后基因表达呈现抑制特征,其差异基因表达主要以下调为主,其中环杷明主要影响细胞内源刺激等,而GANT61主要影响代谢和类固醇合成,并与MAPK信号通路有关联,两者均能影响细胞免疫及凋亡相关通路。这些结果提示,Hh信号通路有可能作为结肠癌的治疗靶点。     

HCMV感染及C-Jun表达与结直肠腺癌相关性研究

目的:探讨人巨细胞病毒(humancytomegalovirus,HCMV)感染在结直肠癌发生、发展过程中的作用及其可能的作用机制.方法:选择84例结直肠腺癌患者的腺癌组织及自身癌旁正常组织,应用RT-PCR技术检测组织中即刻早期基因2(immediate-early gene2,IE2)mRNA的阳性率来反映HCMV的感染情况,免疫组化技术检测凋亡相关基因C-Jun的表达情况.结果:HCMV IE2基因在结直肠腺癌组织中的阳性率高于癌旁组织(P＜0.01);C-Jun基因在结直肠腺癌组织中表达的阳性率高于癌旁组织(P＜0.01);HCMV感染与C-Jun基因在结直肠腺癌组织内的表达存在关联性.结论:HCMV感染在结直肠癌的发生、发展中具有一定作用,其作用机制可能与C-Jun基因的表达有关.     

Profiling Gene Expression in Germinating Brassica Roots

Based on previously developed solid-phase gene extraction (SPGE) we examined the mRNA profile in primary roots of Brassica rapa seedlings for highly expressed genes like ACT7 (actin7), TUB (tubulin1), UBQ (ubiquitin), and low expressed GLK (glucokinase) during the first day post-germination. The assessment was based on the mRNA load of the SPGE probe of about 2.1 ng. The number of copies of the investigated genes changed spatially along the length of primary roots. The expression level of all genes differed significantly at each sample position. Among the examined genes ACT7 expression was most even along the root. UBQ was highest at the tip and root–shoot junction (RS). TUB and GLK showed a basipetal gradient. The temporal expression of UBQ was highest in the MZ 9 h after primary root emergence and higher than at any other sample position. Expressions of GLK in EZ and RS increased gradually over time. SPGE extraction is the result of oligo-dT and oligo-dA hybridization and the results illustrate that SPGE can be used for gene expression profiling at high spatial and temporal resolution. SPGE needles can be used within two weeks when stored at 4 °C. Our data indicate that gene expression studies that are based on the entire root miss important differences in gene expression that SPGE is able to resolve for example growth adjustments during gravitropism.     

An Expression Profile of Active Genes in Human Lung

An expression profile ofgenes active in the human lung was obtainedby collecting 797 partial sequences from a 3'-directed cDNAlibrary. Three genes were found to produce mRNA each of whichcomprised more than 1% of total mRNA. These three have beenidentified as genes for pulmonary surfactant apoprotein (PSP-A),Clara cells 10-kDa secretory protein, and HLA-E heavy chain.In the remaining 745 clones, 221 were composed of89 speciesthat occurred recurrently, and 524 clones appeared only once.Because the 3'-directed cDNA library faithfully represents themRNA population in the source tissue, these numbers representthe relative activities ofthe gene expression. Altogether 437gene species were novel, and 179 gene species were identifiedin GenBank. A significant portion ofthese genes encode proteinsfound in secretory proteins, cell surface proteins, and componentsin the protein synthesis machinery, representing the functionof the lung.     

基于WGCNA和SVM-RFE算法挖掘肺腺癌诊断和预后基因标志物

目的 肺癌是世界上最常见的癌症之一,在众多肺癌患者中,肺腺癌(lung adenocarcinoma,LUAD)的死亡率最高.基因表达谱的变化与肿瘤的发生和发展过程有关,通过识别与LUAD患者相关的诊断和预后基因标志物,可以为肺腺癌的预防和治疗提供理论依据.方法 本研究以肿瘤基因组图谱(The Cancer Gene ...     

Gene Expression Profiling of Rat Cerebral Cortex Development Using cDNA Microarrays

A large amount of genetic information is devoted to brain development. In this study, the cortical development in rats at eight developmental time points (four embryonic [E15, E16, E18, E20] and four postnatal [P0, P7, P14, P21]) was studied using a rat brain 10K cDNA microarray. Significant differential expression was observed in 467 of the 9,805 genes represented on the microarray. Two major Gene Ontology classes—cell differentiation and cell–cell signaling—were found to be important for cortical development. Genes for ribosomal proteins, heterogeneous nuclear ribonucleoproteins, and tubulin proteins were up-regulated in the embryonic stage, coincidently with extensive proliferation of neural precursor cells as the major component of the cerebral cortex. Genes related to neurogenesis, including neurite regeneration, neuron development, and synaptic transmission, were more active in adulthood, when the cerebral cortex reached maturity. The many developmentally modulated genes identified by this approach will facilitate further studies of cortical functions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.