Lung cancer genotype-based therapy and predictive biomarkers: present and future

Mechanisms and clinical implications of tumor heterogeneity and convergence on recurrent phenotypes

Tumor heterogeneity has been identified at various -omic levels. The tumor genome, transcriptome, proteome, and phenome can vary widely across cells in patient tumors and are influenced by tumor cell interactions with heterogeneous physical conditions and cellular components of the tumor microenvironment. Here, we explore the concept that while variation exists at multiple -omic levels, changes at each of these levels converge on the same pathways and lead to convergent phenotypes in tumors that can provide common drug targets. These phenotypes include cellular growth and proliferation, sustained oncogenic signaling, and immune avoidance, among others. Tumor heterogeneity complicates treatment of patient cancers as it leads to varied response to therapies. Identification of convergent cellular phenotypes arising in patient cancers and targeted therapies that reverse them has the potential to transform the way clinicians treat these cancers and to improve patient outcome.

Exome sequencing deciphers a germline MET mutation in familial epidermal growth factor receptor-mutant lung cancer

Lung cancer accompanied by somatic activating mutations in the epidermal growth factor receptor (EGFR) gene, which is associated with a significant clinical response to the targeted therapy, is frequently found in never-smoking Asian women with adenocarcinoma. Although this implies genetic factors underlying the carcinogenesis, the etiology remains unclear. To gain insight into the pathogenic mechanisms, we sequenced the exomes in the peripheral-blood DNA from six siblings, four affected and two unaffected siblings, of a family with familial EGFR-mutant lung adenocarcinoma. We identified a heterozygous missense mutation in MET proto-oncogene, p.Asn375Lys, in all four affected siblings. Combined with somatic loss of heterozygosity for MET, the higher allele frequency in a Japanese sequencing database supports a causative role of the MET mutation in EGFR-mutant lung cancer. Functional assays showed that the mutation reduces the binding affinity of MET for its ligand, hepatocyte growth factor, and damages the subsequent cellular processes, including proliferation, clonogenicity, motility and tumorigenicity. The MET mutation was further observed to abrogate the ERBB3-mediated AKT signal transduction, which is shared downstream by EGFR. These findings provide an etiological view that the MET mutation is involved in the pathogenesis of EGFR-mutant lung cancer because it generates oncogenic stress that induces compensatory EGFR activation. The identification of MET in a family with familial EGFR-mutant lung cancer is insightful to explore the pathogenic mechanism of not only familial, but also sporadic EGFR-mutant lung cancer by underscoring MET-related signaling molecules.

Selective expression of transthyretin in subtypes of lung cancer

Transthyretin (TTR) is expressed primarily in liver, choroid plexus of brain and pancreatic islet A and B cells. It is also synthesized in some endocrine tumors. In the present study, the protein expression of TTR in lung cancer tissues and cell lines was investigated by western blot. The mRNA expression of TTR in 24 pairs of frozen lung cancer tissues was examined by RT-PCR. The specific expression and cellular distribution of TTR were also evaluated in 104 paraffin-embedded lung cancer samples and 3 normal lung tissues by immunohistochemistry. Similarly, the subcellular localization and expression of TTR were further analyzed in lung cancer cell lines. With the exception of mucinous adenocarcinoma, the expression of TTR protein was observed in all tested subtypes of lung carcinoma. Adenocarcinoma displayed the highest positive expression rate of TTR, accounting for 84.4 %, and the positive expression rate of TTR was up to 85.7 % at stages III and IV. The secretory bubbles with strong TTR staining were observed in luminal cells of lung cancer. Furthermore, the localization of TTR in the cytoplasm of lung cancer cells and the secretion of TTR into extracellular milieu were also confirmed. Taken together, TTR is selectively synthesized in lung cancer cells and can be secreted extracellularly.

DKK1 is a potential novel mediator of cisplatin-refractoriness in non-small cell lung cancer cell lines

Background

Platinum compounds are the mainstay of chemotherapy for lung cancer. Unfortunately treatment failure remains a critical issue since about 60 % of all non-small cell lung cancer (NSCLC) patients display intrinsic platinum resistance.

Methods

We analyzed global gene expression profiles of NSCLC clones surviving a pulse treatment with cisplatin and mapped deregulated signaling networks in silico by Ingenuity Pathway Analysis (IPA). Further validation was done using siRNA.

Results

The pooled cisplatin-surviving NSCLC clones from each of the biological replicates demonstrated heterogeneous gene expression patterns both in terms of the number and the identity of the altered genes. Genes involved in Wnt signaling pathway (Dickkopf-1, DKK1), DNA repair machinery (XRCC2) and cell-cell/cell-matrix interaction (FMN1, LGALS9) were among the top deregulated genes by microarray in these replicates and were validated by q-RT-PCR. We focused on DKK1 which previously was reported to be overexpressed in NSCLC patients. IPA network analysis revealed coordinate up-regulation of several DKK1 transcriptional regulators (TCF4, EZH2, DNAJB6 and HDAC2) in cisplatin-surviving clones from that biological replicate. Knockdown of DKK1 by siRNA sensitized for cisplatin in two different NSCLC cell lines and in ovarian A2780 cells, but not in the A2780 cis subline made resistant to cisplatin by chronic exposure, suggesting a role of DKK1 in intrinsic but not acquired platinum refractoriness.

Conclusions

We identified DKK1 as a possible marker of a cisplatin-refractory phenotype and as a potential novel therapeutic target to improve platinum response of NSCLC cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-015-1635-9) contains supplementary material, which is available to authorized users.

RBMMMDA: predicting multiple types of disease-microRNA associations

Accumulating evidences have shown that plenty of miRNAs play fundamental and important roles in various biological processes and the deregulations of miRNAs are associated with a broad range of human diseases. However, the mechanisms underlying the dysregulations of miRNAs still have not been fully understood yet. All the previous computational approaches can only predict binary associations between diseases and miRNAs. Predicting multiple types of disease-miRNA associations can further broaden our understanding about the molecular basis of diseases in the level of miRNAs. In this study, the model of Restricted Boltzmann machine for multiple types of miRNA-disease association prediction (RBMMMDA) was developed to predict four different types of miRNA-disease associations. Based on this model, we could obtain not only new miRNA-disease associations, but also corresponding association types. To our knowledge, RBMMMDA is the first model which could computationally infer association types of miRNA-disease pairs. Leave-one-out cross validation was implemented for RBMMMDA and the AUC of 0.8606 demonstrated the reliable and effective performance of RBMMMDA. In the case studies about lung cancer, breast cancer, and global prediction for all the diseases simultaneously, 50, 42, and 45 out of top 100 predicted miRNA-disease association types were confirmed by recent biological experimental literatures, respectively.

Integrative analysis reveals enhanced regulatory effects of human long intergenic non-coding RNAs in lung adenocarcinoma

Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs (lincRNAs) play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed "regulatory lincRNAs", representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GAS5, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.

Mining featured micro ribonucleic acids associated with lung cancer based on bioinformatics

Background

Few genetic markers useful for the screening of lung cancer risk exist. Although related research has shown that certain expression profiles of micro ribonucleic acids (miRNAs) are different in lung cancer versus the normal lung, such as miR-29a and miR-29s, the precise molecular mechanism of lung cancer remains obscure. In order to get a better understanding of the pathogenetic mechanism of lung cancer, we analyzed the differentially expressed genes (DEGs) and identified featured miRNAs in lung cancer tissues.

Methods

We used the gene expression profile GSE10072, including 49 gene chips of non-tumor tissues and 58 gene chips of lung tumor specimens. The DEGs between these two groups were identified by Limma package in R language. The TarBase database was used to construct the networks of miRNA regulating DEGs related to lung cancer. After ordering miRNAs regulating DEGs, we further screened featured miRNAs combined with the miR2Disease database.

Results

A total of 5572 DEGs were obtained between lung cancer and control specimens. After constructing a miRNA regulatory network, a total of 398 regulations between 57 miRNAs and 321 target genes existed. By intergrating the miR2Disease database and using a sorting algorithm, a total of six featured miRNAs related to lung cancer were identified, including miR-520h, miR-133a, miR-34, miR-103, miR-370, and miR-148. They might be involved in lung cancer progression by regulating ABCG2, PKM2, VAMP2, GPD1, MAP3K8, and DNMT3B, respectively.

Conclusion

The top 10 significant miRNAs, such as miR-520h, miR-133a, miR-34, and miR-103 may be potential therapeutic targets for lung cancer.

Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity

Increasing evidence has indicated that plenty of lncRNAs play important roles in many critical biological processes. Developing powerful computational models to construct lncRNA functional similarity network based on heterogeneous biological datasets is one of the most important and popular topics in the fields of both lncRNAs and complex diseases. Functional similarity network consturction could benefit the model development for both lncRNA function inference and lncRNA-disease association identification. However, little effort has been attempted to analysis and calculate lncRNA functional similarity on a large scale. In this study, based on the assumption that functionally similar lncRNAs tend to be associated with similar diseases, we developed two novel lncRNA functional similarity calculation models (LNCSIM). LNCSIM was evaluated by introducing similarity scores into the model of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) for lncRNA-disease association prediction. As a result, new predictive models improved the performance of LRLSLDA in the leave-one-out cross validation of various known lncRNA-disease associations datasets. Furthermore, some of the predictive results for colorectal cancer and lung cancer were verified by independent biological experimental studies. It is anticipated that LNCSIM could be a useful and important biological tool for human disease diagnosis, treatment, and prevention.

Medical care costs incurred by patients with smoking-related non-small cell lung cancer treated at the National Cancer Institute of Mexico

BACKGROUND

Smoking is a public health problem in Mexico and worldwide; its economic impact on developing countries has not been well documented. The aim of this study was to assess the direct medical costs attributable to smoking incurred by lung cancer patients treated at the National Cancer Institute of Mexico (INCan).

METHODS

The study was conducted at INCan in 2009. We carried out a cost of illness (COI) methodology, using data derived from an expert panel consensus and from medical chart review. A panel of experts developed a diagnostic-therapeutic guide that combined the hospital patient pathways and the infrastructure, human resources, technology, and services provided by the medical units at INCan. Cost estimates in Mexican pesos were adjusted by inflation and converted into US Dollars using the 2013 FIX exchange rate for foreign transactions (1 USD = 13.06 Mexican pesos).

RESULTS

A 297 incident cases diagnosed with any type of lung cancer were analyzed. According to clinical stage, the costs per patient were 13,456; 35,648; 106,186; and 144,555 USD, for lung cancer stages I, II, III, and IV respectively. The weighted average annual cost/patient was and 139,801 USD and the average annual cost/patient that was attributable to smoking was 92,269 USD. This cost was independent of the clinical stage, with stage IV representing 96% of the annual cost. The total annual cost of smoking-related lung cancer at INCan was 19,969,781 USD.

CONCLUSIONS

The medical care costs of lung cancer attributable to smoking represent a high cost both for INCan and the Mexican health sector. These costs could be reduced if all provisions established in the Framework Convention of Tobacco Control of the World Health Organization were implemented in Mexico.

CUL4A overexpression enhances lung tumor growth and sensitizes lung cancer cells to erlotinib via transcriptional regulation of EGFR

Background

CUL4A has been proposed as oncogene in several types of human cancer, but its clinical significance and functional role in human non-small cell lung cancer (NSCLC) remain unclear.

Methods

Expression level of CUL4A was examined by RT-PCR and Western blot. Forced expression of CUL4A was mediated by retroviruses, and CUL4A silencing by shRNAs expressing lentiviruses. Growth capacity of lung cancer cells was measured by MTT in vitro and tumorigenesis in vivo, respectively.

Results

We found that CUL4A was highly expressed in human lung cancer tissues and lung cancer cell lines, and this elevated expression positively correlated with disease progression and prognosis. Overexpression of CUL4A in human lung cancer cell lines increased cell proliferation, inhibited apoptosis, and subsequently conferred resistance to chemotherapy. On other hand, silencing CUL4A expression in NSCLC cells reduced proliferation, promoted apoptosis and resulted in tumor growth inhibition in cancer xenograft model. Mechanistically, we revealed CUL4A regulated EGFR transcriptional expression and activation, and subsequently activated AKT. Targeted inhibition of EGFR activity blocked these CUL4A induced oncogenic activities.

Conclusions

Our results highlight the significance of CUL4A in NSCLC and suggest that CUL4A could be a promising therapy target and a potential biomarker for prognosis and EGFR target therapy in NSCLC patients.

Electronic supplementary material

The online version of this article (doi:10.1186/1476-4598-13-252) contains supplementary material, which is available to authorized users.

[Immunohistochemical detections of EGFR mutations in NSCLC]

近些年来，人们越来越认识到，存在表皮生长因子受体（epidermal growth factor receptor, EGFR）突变的非小细胞肺癌（non-small cell lung cancer, NSCLC）患者对靶向药物EGFR酪氨酸激酶抑制剂（EGFR-tyrosine kinase inhibitor, EGFR-TKI）的治疗有良好反应。目前，检测EGFR突变应用最多且较为可靠的是以DNA分子为基础的检测（如DNA测序）方法，但此法操作繁琐，耗时长，花费高，对样本要求严格。相比之下，免疫组织化学法（immunohistochemistry, IHC）则充分弥补了上述缺陷，可作为EGFR突变筛查的辅助手段。但影响其结果的因素较多，如不同的免疫组化染色方法、不同抗原修复液的选择及不同的结果评判标准等，因此此法尚未广泛应用于临床，仅处于研究阶段。本文通过检索不同研究者应用免疫组化法对NSCLC患者进行EGFR突变检测的相关文献，进一步讨论如何合理应用免疫组化法检测EGFR突变可发挥其临床应用的最大价值。

Spongionella secondary metabolites protect mitochondrial function in cortical neurons against oxidative stress

The marine habitat provides a large number of structurally-diverse bioactive compounds for drug development. Marine sponges have been studied over many years and are found to be a rich source of these bioactive chemicals. This study is focused on the evaluation of the activity of six diterpene derivatives isolated from Spongionella sp. on mitochondrial function using an oxidative in vitro stress model. The test compounds include the Gracilins (A, H, K, J and L) and tetrahydroaplysulphurin-1. Compounds were co-incubated with hydrogen peroxide for 12 hours to determine their protective capacities and their effect on markers of apoptosis and Nrf2/ARE pathways was evaluated. Results conclude that Gracilins preserve neurons against oxidative damage, and that in particular, tetrahydroaplysulphurin-1 shows a complete neuroprotective activity. Oxidative stress is linked to mitochondrial dysfunction and consequently to neurodegenerative disorders like Parkinson and Alzheimer diseases, Friedreich ataxia or Amyotrophic lateral sclerosis. This neuroprotection against oxidation conditions suggest that these metabolites could be interesting lead candidates in drug development for neurodegenerative diseases.

Clinicopathological and immunohistochemical profile of non-small cell lung carcinoma in a tertiary care medical centre in South India

BACKGROUND

Lung cancer is a highly aggressive malignancy causing high morbidity and mortality. An increasing incidence of lung cancer has been observed in India. Currently, the classification of lung carcinoma has gone beyond small cell lung carcinoma and non-small cell lung carcinoma (NSCLC). Precise subtyping of poorly differentiated NSCLC into adenocarcinoma and squamous cell carcinoma has a direct impact on patient management and prognosis. With this background, many molecules are under study for developing targeted therapies. Epidermal growth factor receptor (EGFR) is one such biomarker considered to be useful in targeted therapy for adenocarcinoma.

OBJECTIVE

The aim of this study was to subtype poorly differentiated NSCLC based on the expression of thyroid transcription factor-1 (TTF-1) and p-63 and to evaluate EGFR expression in adenocarcinomas.

MATERIALS AND METHODS

A retrospective analysis of 84 cases of poorly differentiated carcinomas of the lung was performed. Paraffin sections were immunostained with TTF-1 and p-63 and the tumors were subtyped. EGFR expression was assessed in adenocarcinomas by immunohistochemistry.

RESULTS

Fifty-five percent of the NSCLC were adenocarcinoma, with a peak incidence between 61 and 70 years of age and a male predominance. EGFR was expressed in 89% of the adenocarcinomas.

CONCLUSIONS

Poorly differentiated non-small cell carcinoma can be subtyped by immunohistochemical markers and hence has a direct impact on the current therapeutic strategies.

Lung Cancer Biomarkers: Present Status and Future Developments

The publication of the “Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology” has now provided a guideline for biomarker testing for first-generation lung cancer tyrosine kinase inhibitors. Biomarker testing has forever altered the role of pathologists in the management of patients with lung cancer. Current, unresolved issues in the precision medicine of lung cancer will be addressed by the development of new biomarker tests, new drugs, and new test technologies and by improvement in the cost to benefit ratio of biomarker testing.

EGFR mutations in US Hispanic versus non-Hispanic white patients with lung adenocarcinoma

CONTEXT

Lung cancer is the leading cause of cancer deaths worldwide. First-generation tyrosine kinase inhibitors improve progression-free survival in lung cancers with epidermal growth factor receptor (EGFR) mutations. EGFR mutations occur predominantly in exons 19 and 21 in lung adenocarcinomas of Asians (∼30%), whites (∼15%), and African Americans (∼19%). However, minimal information exists on the prevalence or type of genetic changes that occur in lung cancers in US Hispanic patients. We investigated the EGFR mutation frequency in primary lung adenocarcinomas in US Hispanics compared with non-Hispanic whites.

OBJECTIVE

To evaluate EGFR mutations in lung adenocarcinomas from US Hispanic patients compared with those from non-Hispanic white patients.

DESIGN

DNA samples were extracted from paraffin-embedded tissue of consecutive lung adenocarcinomas from 83 patients. Samples were collected from 40 Hispanics and 43 non-Hispanic whites. Mutations in EGFR were analyzed using a custom assay. Results.-Fourteen of 83 patients (16.9%) had EGFR mutations in their tumor DNA, including 6 of 40 Hispanics (15.0%) and 8 of 43 non-Hispanic whites (18.6%). No association with age, sex, or tumor stage was identified. Smoking history could not be obtained for most of the 83 patients, although 8 of the 11 patients with EGFR mutations for whom smoking history was obtained were nonsmokers. Most of the tumors with EGFR mutations (12 of 14; 85.7%) were acinar with lepidic or papillary subtypes. EGFR mutations occurred in exon 19 (42.8%), exon 18 (28.6%), exon 20 (28.6%), and exon 21 (14.3%). Two cases had 2 mutations identified in different exons.

CONCLUSION

The frequency of EGFR mutations is similar in US Hispanics compared with non-Hispanic whites.

Lung adenocarcinoma biomarker incidence in Hispanic versus non-Hispanic white patients

CONTEXT

Lung cancer is the leading cause of cancer deaths in the United States and worldwide. Biomarker testing is critical to personalized therapy in lung adenocarcinoma and has been extensively investigated in non-Hispanic whites, Asians, and African Americans. However, little information addresses the underlying genetic changes in lung adenocarcinoma among Hispanic patients in the United States.

OBJECTIVE

To identify targetable biomarkers other than EGFR and EML4-ALK in Hispanic patients with lung adenocarcinoma.

DESIGN

We tested DNA extracted from 85 lung adenocarcinoma specimens collected from 40 Hispanic and 43 non-Hispanic white patients for previously reported mutations in KRAS, MET, BRAF, mTOR, STAT3, JAK2, PIK3CA, AKT1 through AKT3, and PTEN with a custom Sequenom massARRAY assay (Sequenom, San Diego, California).

RESULTS

Mutations in KRAS were identified in 11 cases (13%; 6 Hispanic [7%], 5 non-Hispanic white [6%]) and had no correlation with sex, age, or smoking history. Mutations in PIK3CA were identified in 2 of the 40 Hispanic patients (5%), including one patient (2.5%) with a concurrent KRAS mutation. The tumors were wild type for all other genes tested.

CONCLUSIONS

Targetable biomarkers other than EGFR and EML4-ALK were identified in 7 of the 40 Hispanic patients (18%) and 5 of the 43 non-Hispanic white patients (12%), suggesting a similar mutational frequency. Our highly multiplexed genotyping assay detected actionable mutations in 14% (12 of 83) more patients than would have been identified by EGFR and EML4-ALK testing alone.

Lysine acetyltransferase GCN5 potentiates the growth of non-small cell lung cancer via promotion of E2F1, cyclin D1, and cyclin E1 expression

The lysine acetyltransferases play crucial but complex roles in cancer development. GCN5 is a lysine acetyltransferase that generally regulates gene expression, but its role in cancer development remains largely unknown. In this study, we report that GCN5 is highly expressed in non-small cell lung cancer tissues and that its expression correlates with tumor size. We found that the expression of GCN5 promotes cell growth and the G1/S phase transition in multiple lung cancer cell lines. Further study revealed that GCN5 regulates the expression of E2F1, cyclin D1, and cyclin E1. Our reporter assays indicated that the expression of GCN5 enhances the activities of the E2F1, cyclin D1, and cyclin E1 promoters. ChIP experiments suggested that GCN5 binds directly to these promoters and increases the extent of histone acetylation within these regions. Mechanistic studies suggested that GCN5 interacts with E2F1 and is recruited by E2F1 to the E2F1, cyclin D1, and cyclin E1 promoters. The function of GCN5 in lung cancer cells is abrogated by the knockdown of E2F1. Finally, we confirmed that GCN5 regulates the expression of E2F1, cyclin D1, and cyclin E1 and potentiates lung cancer cell growth in a mouse tumor model. Taken together, our results demonstrate that GCN5 specifically potentiates lung cancer growth by directly promoting the expression of E2F1, cyclin D1, and cyclin E1 in an E2F1-dependent manner. Our study identifies a specific and novel function of GCN5 in lung cancer development and suggests that the GCN5-E2F1 interaction represents a potential target for lung cancer treatment.