Molecular characterization of lung cancer: A two-miRNA prognostic signature based on cancer stem-like cells related genes

Lung cancer is one of the deadliest cancers worldwide. To increase the survival rate of lung cancer, it is necessary to explore specific prognosis markers. More and more evidence finds that noncoding RNA is closely associated with the survival of lung cancer, and cancer stem cells (CSCs) also play a significant role in the progress of lung cancer. The objective of this study is to find CSLCs genes that affect the prognosis of lung cancer. The differential expression of long noncoding RNAs (lncRNAs), microRNAs (miRNAs), messenger RNAs (mRNAs) in the Cancer Genome Atlas (TCGA) database and differential expression data from microarray of CD326⁺ and CD326⁻ A549 cell are intersected to identify stable and consistent expression genes (2 lncRNAs, 15 miRNAs, and 134 mRNAs). The intersection of lncRNAs and miRNAs is analyzed by univariate and multivariate Cox regression to obtained prognostic genes. Two miRNAs (miR-30b-5p and miR-29c-3p) are significantly correlated with the overall survival rate. Then using these two miRNAs to construct a risk score model as a prognosis signature of lung cancer. Subsequently, we analyzed the association between two miRNAs and clinical information of lung cancer patients, of which T stage, Neoplasm cancer and risk score (P < .05) can be used as independent prognostic indicators of lung cancer. Finally, target genes of 2 miRNAs and 134 mRNAs were annotated with Gene Ontology and analyzed with Kyoto Encyclopedia of Genes and Genomes pathway, and verified with the GEO database. In summary, this study illustrates the role of miRNAs in the promotion of lung cancer by CSCs, which is important to find molecular biomarkers of lung cancer.     

Genome-wide analysis of organ-preferential metastasis of human small cell lung cancer in mice

Although a number of molecules have been implicated in the process of cancer metastasis, the organ-selective nature of cancer cells is still poorly understood. To investigate this issue, we established a metastasis model in mice with multiple organ dissemination by i.v. injection of human small cell lung cancer (SBC-5) cells. We analyzed gene-expression profiles of 25 metastatic lesions from four organs (lung, liver, kidney, and bone) using a cDNA microarray representing 23,040 genes and extracted 435 genes that seemed to reflect the organ specificity of the metastatic cells and the cross-talk between cancer cells and microenvironment. Furthermore, we discovered 105 genes that might be involved in the incipient stage of secondary-tumor formation by comparing the gene-expression profiles of metastatic lesions classified according to size (<1 or >2 mm) as either "micrometastases" or "macrometastases." This genome-wide analysis should contribute to a greater understanding of molecular aspects of the metastatic process in different microenvironments, and provide indicators for new strategies to predict and prevent metastasis.     

Lipase member H is a novel secreted protein selectively upregulated in human lung adenocarcinomas and bronchioloalveolar carcinomas

Lung cancer is one of the most frequent causes of cancer-related death worldwide. However, molecular markers for lung cancer have not been well established. To identify novel genes related to lung cancer development, we surveyed publicly available DNA microarray data on lung cancer tissues. We identified lipase member H (LIPH, also known as mPA-PLA1) as one of the significantly upregulated genes in lung adenocarcinoma. LIPH was expressed in several adenocarcinoma cell lines when they were analyzed by quantitative real-time polymerase chain reaction (qPCR), western blotting, and sandwich enzyme-linked immunosorbent assay (ELISA). Immunohistochemical analysis detected LIPH expression in most of the adenocarcinomas and bronchioloalveolar carcinomas tissue sections obtained from lung cancer patients. LIPH expression was also observed less frequently in the squamous lung cancer tissue samples. Furthermore, LIPH protein was upregulated in the serum of early- and late-phase lung cancer patients when they were analyzed by ELISA. Interestingly, high serum level of LIPH was correlated with better survival in early phase lung cancer patients after surgery. Thus, LIPH may be a novel molecular biomarker for lung cancer, especially for adenocarcinoma and bronchioloalveolar carcinoma.     

Towards a genetic-based classification of human lung cancer.

Lung cancer is a highly aggressive neoplasm which is reflected by a multitude of genetic aberrations being detectable on the chromosomal and molecular level. In order to understand this seemingly genetic chaos, we performed Comparative Genomic Hybridisation (CGH) in a large collective of human lung carcinomas investigating different tumor entities as well as multiple individual tumour specimens of single patients. Despite the considerable genetic instability being reflected by the well known morphological heterogeneity of lung cancer the comparison of different tumour groups using custom made computer software revealed recurrent aberration patterns and highlighted chromosomal imbalances that were significantly associated with morphological histotypes and biological phenotypes. Specifically we identified imbalances in NSCLC being associated with metastasis formation which are typically present in SCLC thus explaining why the latter is such an aggressive neoplasm characterized by widespread tumor dissemination. Based on the genetic data a new model for the development of SCLC is presented. It suggests that SCLC evolving from the same stem cell as NSCLC should be differentiated into primary and secondary tumors. Primary SCLC corresponding to the classical type evolved directly from an epithelial precursor cell. In contrast, secondary SCLC correlating with the combined SCLC develops via an NSCLC intermediate. In addition, we established libraries of differentially expressed genes from different human lung cancer types to identify new candidate genes for several of the chromosomal subregions identified by CGH. In this review, we summarise the status of our results aiming at a refined classification of lung cancer based on the pattern of genetic aberrations.     

人类蛋白组学草图的肺癌分子标记物初探

传统的肺癌分子标记物探索通常基于基因组或者转录组研究,而基于蛋白质水平的肺癌分子标记物探索通常局限在低通量水平。质谱技术已经开始产生高通量的全局正常及癌症蛋白组。我们采用开源统计软件R对人类蛋白组学草图数据及已发表的肺癌蛋白质组学数据进行二次分析,筛选出91个潜在的候选肺癌分子标记物。基因注解分析显示候选肺癌基因富集了和代谢、TP53通路以及MicroRNA调控等相关的基因。最后,利用Human Protein Atlas数据库及Pubmed对前20候选标记物进行验证,结果显示大部分候选肺癌基因大多能够得到验证。可见数据挖掘在即将到来的质谱推动的组学大数据时代将发挥重要作用。     

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.     

Study of lung cancer regulatory network that involves erbB4 and tumor marker gene

Our purpose is to screen out serum tumor markers closely correlated to the nature of solitary pulmonary nodule (SPN) and to draw a regulatory network containing genes correlated to lung cancer. Two hundred and sixty cases of SPN patients confirmed through pathological diagnosis were collected as subjects, factors closely correlated to the nature of SPN were screened out from eight tumor markers through Fisher discriminant method, and functional annotation and pathway analysis were conducted on erbB4 as well as its tumor marker genes by GO and KEGG databases. Four key tumor markers: CYFRA21-1, CA125, SCC-Ag and CA153 were successfully screened out and the first three proteins’ corresponding gene were KRT19, MUC16 and SERPINB3 while that of CA153 was not found. GO analysis on erbB4, KRT19, MUC16 and SERPINB3 showed that they covered three domains, cell components, molecular function and biological process; meanwhile, combined with KEGG database and based on signal pathway of erbB4, a regulatory network of lung cancer cells escaping from apoptosis was successfully made. This study indicates that serum tumor marker genes play an important role in the occurrence and development of lung cancer, besides, this study primarily discussed the molecular mechanism of these tumor markers in predicting tumor, which provides a basis for in-depth information about lung cancer.     

Gene therapy for lung cancer

Lung cancer continues to be the largest killer of Americans due to cancer. Although progress has been made, with advances in chemotherapy, the majority of patients diagnosed with lung cancer ultimately succumb to the disease. A better understanding of the molecular pathogenesis of lung cancer is demonstrating how alterations in oncogenes and tumor suppressor genes control lung cancer initiation, growth, and survival. In this article, attempts to target molecular alterations in lung cancer using gene therapy techniques are reviewed. These include introducing suicide genes into tumor cells, replacement of defective tumor suppressor genes, inactivating oncogenes, and immunotherapy-based approaches using gene therapy technology. The major barrier for these techniques continues to be the inability to specifically target tumor cells while sparing normal cells. Nonetheless, these approaches are likely to yield important biologic and clinical data which will further the progress of lung cancer treatment.     

Class discovery analysis of the lung cancer gene expression data

Traditional histological classification of lung cancer subtypes is informative, but incomplete. Recent studies of gene expression suggest that molecular classification can be used for effective diagnostic and prediction of the treatment outcome. We attempt to build a molecular classification based on the public data available from a few independent sources. The data is reanalyzed with a new cluster analysis algorithm. This algorithm allows us to preserve the high dimensionality of data and produce the cluster structure without preliminary selection of significant genes or any other presumption about the relation between different cancer and normal tissue samples. The resulting clusters are generally consistent with the histological classification. However, our analysis reveals many additional details and subtypes of previously defined types of lung cancer. Large histological cancer types can be further divided into subclasses with different patterns of gene expression. These subtypes should be taken into account in diagnostics, drug testing, and treatment development for lung cancer patients.     

New molecular approaches to lung cancer: biological and clinical implications of P53, P16 and K-RAS studies

The most common genetic changes associated with lung cancer involve abnormalities of the genes that regulate the cell cycle. Molecular networking of P53 and P16 tumor suppressor genes and K-RAS oncogene exerts a crucial impact on cell cycle regulation and appears to be of major clinical significance for lung cancer evaluation. The present review article summarizes evaluations of P53, P16 and K-RAS in lung cancer with particular focus on biological and clinical implications, as well as on new molecular approaches to the study of these genes: P53 by yeast functional assay, P16 by methylation specific PCR (MSP) and K-RAS by enriched PCR technique.     

Analysis of dysregulation of immune system in pancreatic cancer based on gene expression profile

The aim of this study was to explore the dysregulated expression of the immune system in pancreatic cancer and clarify the pathogenesis of pancreatic cancer. The Dataset GSE15471 was downloaded from GEO database, Student’s t test was used to screen differentially expressed genes (DEGs) between the pancreatic cancer group and the normal control group. Kyoto Encyclopedia of Genes and Genomes (KEGG) provides functional annotation was employed to explore the significant DEGs involved in biological functions. We got 988 significantly DEGs, including 832 up-regulated genes and 156 down-regulated genes. The ratio of up-regulated genes and down-regulated genes was 5.3. Total 13 biological pathways which were significant enriched with DEGs by KEGG pathway enrichment analysis. Finally, we constructed a overall network of the immune system in pancreatic cancer with these biological pathways information. Our study reveals that dysregulated pathways in pancreatic cancer associated with the immune system. Besides, we also identify some important molecular biomarkers of the pancreatic cancer, including CXCR4 and CD4. Dysfunctional pathways and important molecular biomarkers of pancreatic cancer will provide useful information for potential treatment of pancreatic cancer.     

Molecular chemoprevention by selenium: a genomic approach

Basic research and clinical chemoprevention trials support the protective role of selenium in cancer prevention but the mechanisms based on the molecular level remain to be fully defined. This mini-review focuses only on the elucidation of the molecular mechanisms of cancer prevention by selenium using the genomics approach; target organs discussed here are breast, prostate, colon and lung. The results described here support the utility of microarray technology in delineating the molecular mechanisms of cancer prevention by selenium. These results are based on studies employing human and rodent cell lines and tissues from animal models ranging from normal to frank cancer. The dose and the form of selenium are determining factors in cancer chemoprevention. The results of the microarray analysis reviewed here indicate that selenium, independent of its form and the target organ examined, alters several genes in a manner that can account for cancer prevention. Selenium can up regulate genes related to phase II detoxification enzymes, certain selenium-binding proteins and select apoptotic genes, while down regulating those related to phase I activating enzymes and cell proliferation. Independent of tissue type, selenium arrests cells in G1 phase of cell cycle, inhibits CYCLIN A, CYCLIN D1, CDC25A, CDK4, PCNA and E2F gene expressions while induces the expressions of P19, P21, P53, GST, SOD, NQO1, GADD153 and certain CASPASES. In addition to those described above, genes such as OPN, which is mainly involved in metastasis and recently reported to be down regulated by selenium, should be considered as potential molecular marker in clinical chemoprevention trials. Collectively, literature data indicate that some of these genes that were altered by selenium are also involved in the development of human cancers described in this review. It appears that androgen receptor status may influence the effect of selenium on gene expression profile in prostate cancer; whether estrogen receptor may influence the effect of selenium on gene expression in breast cancer requires further studies. Knowledge from gene array data in combination with proteomics approaches, using homogenous population of cell types with the aid of laser capture microdissection, may provide an individualized dimension of information on cancer risk and potential targets for its prevention. The molecular (genetic) biomarkers presented in this review will provide the foundation for future studies of the chemopreventive properties of structurally varied selenium compounds.     

LncRNA HSPC324 plays role in lung development and tumorigenesis

Lung cancer is a leading cause of cancer-related death in the world. Therefore, identifying the genes and molecular pathways involved in lung development and tumorigenesis can help us improve the therapeutic strategies of lung cancer. Accumulating evidence confirms that long noncoding RNAs, as a novel layer of regulatory RNA molecules, play an important role in various aspects of the cells. Here, using available high throughput gene expression data, we identified an lncRNA (HSPC324) with high expression level in lung tissue that is distinctly expressed in lung tumor tissues relative to normal. Using GO enrichment and KEGG pathway analyses, we further analyzed the functions and pathways involving the HSPC324-correlated genes. Ectopic expression of lncRNA HSPC324 significantly inhibited proliferation, cell cycle and migration; on the other hand, increased apoptosis and ROS production in lung adenocarcinoma cells. Overall, this study introduces HSPC324 as a new player in the development of lung cancer.     

Prediction of potential drivers connecting different dysfunctional levels in lung adenocarcinoma via a protein–protein interaction network

Lung cancer is a serious disease that threatens an affected individual's life. Its pathogenesis has not yet to be fully described, thereby impeding the development of effective treatments and preventive measures. “Cancer driver” theory considers that tumor initiation can be associated with a number of specific mutations in genes called cancer driver genes. Four omics levels, namely, (1) methylation, (2) microRNA, (3) mutation, and (4) mRNA levels, are utilized to cluster cancer driver genes. In this study, the known dysfunctional genes of these four levels were used to identify novel driver genes of lung adenocarcinoma, a subtype of lung cancer. These genes could contribute to the initiation and progression of lung adenocarcinoma in at least two levels. First, random walk with restart algorithm was performed on a protein–protein interaction (PPI) network constructed with PPI information in STRING by using known dysfunctional genes as seed nodes for each level, thereby yielding four groups of possible genes. Second, these genes were further evaluated in a test strategy to exclude false positives and select the most important ones. Finally, after conducting an intersection operation in any two groups of genes, we obtained several inferred driver genes that contributed to the initiation of lung adenocarcinoma in at least two omics levels. Several genes from these groups could be confirmed according to recently published studies. The inferred genes reported in this study were also different from those described in a previous study, suggesting that they can be used as essential supplementary data for investigations on the initiation of lung adenocarcinoma. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.     

Accumulation of genetic alterations and their significance in each primary human cancer and cell line

Analyses of multiple genetic alterations accumulated in each cancer cell is expected to provide useful information to elucidate the molecular mechanisms involved in tumorigenesis. Here, we summarized the results of studies on aberrations of oncogenes and tumor suppressor genes by ourselves and other groups. DNAs analyzed were from particular sets of surgical specimens from human tumors and cancer cell lines derived from non-small cell lung cancers, pancreatic cancers, hepatocellular carcinomas and gliomas. Tumors could be grouped into two types based on the genetic alterations detected. Tumors in group 1 had mutations in genes encoding proteins involved in a limited number of signal transduction cascades such as p16-cyclin D1/CDK4-RB or MDM2-p53-p21, where the aberration of one component seems to be sufficient to cause dysfunction of the cascade. Group 2 contained a subset of tumors in which no alteration was detected in the genes analyzed, even in the advanced stage or established cancer cells, indicating the involvement of completely different oncogenic pathways.     

ERCC1, XPD and RAI mRNA levels in lymphocytes are not associated with lung cancer risk in a prospective study of Danes

Low DNA-repair capacity has been associated with increased risk of several types of cancer. mRNA levels of the nucleotide excision repair genes ERCC1 and XPD have been shown to correlate with the DNA-repair capacity. Likewise, mRNA levels of several DNA-repair genes including ERCC1 have been shown to be lower in lymphocytes from patients with lung cancer and head and neck cancer compared with healthy persons. In these studies, the low DNA-repair gene expression levels could be either a risk factor for disease or a consequence of the same. In this nested case-cohort study, which to our knowledge, is the first prospective study of DNA-repair gene mRNA levels as predictors of lung cancer, we have investigated the occurrence of lung cancer in relation to the mRNA level of the two DNA-repair genes ERCC1 and XPD and the NF kappaB inhibitor RAI in blood samples prior to disease. Among 54,220 members of a Danish prospective cohort study, 265 lung cancer cases were identified and a sub-cohort comprising 272 individuals was used for comparison. The expression levels of the three adjacent genes were found to be highly inter-correlated, to be higher in women compared to men and to be lower in older individuals. The incidence rate ratios for lung cancer in association with one log-unit increase (natural logarithm) in mRNA levels were 1.12 (CI=0.89-1.41) for ERCC1, 1.00 (CI=0.83-1.21) for XPD and 1.25 (0.89-1.74) for RAI. In conclusion, this study indicated no association between mRNA expression of the DNA-repair genes ERCC1 and XPD and risk of subsequent development of lung cancer.