Personalized targeted therapy for lung cancer

Targeted Therapy for Cancers: From Ongoing Clinical Trials to FDA-Approved Drugs

The development of targeted therapies has revolutionized cancer treatment, offering improved efficacy with reduced side effects compared with traditional chemotherapy. This review highlights the current landscape of targeted therapy in lung cancer, colorectal cancer, and prostate cancer, focusing on key molecular targets. Moreover, it aligns with US Food and Drug Administration (FDA)-approved drugs and drug candidates. In lung cancer, mutations in the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) gene rearrangements have emerged as significant targets. FDA-approved drugs like osimertinib and crizotinib specifically inhibit these aberrant pathways, providing remarkable benefits in patients with EGFR-mutated or ALK-positive lung cancer. Colorectal cancer treatment has been shaped by targeting the vascular endothelial growth factor (VEGF) and EGFR. Bevacizumab and cetuximab are prominent FDA-approved agents that hinder VEGF and EGFR signaling, significantly enhancing outcomes in metastatic colorectal cancer patients. In prostate cancer, androgen receptor (AR) targeting is pivotal. Drugs like enzalutamide, apalutamide, and darolutamide effectively inhibit AR signaling, demonstrating efficacy in castration-resistant prostate cancer. This review further highlights promising targets like mesenchymal-epithelial transition (MET), ROS1, BRAF, and poly(ADP-ribose) polymeras (PARP) in specific cancer subsets, along with ongoing clinical trials that continue to shape the future of targeted therapy.

A novel prognostic model related to oxidative stress for treatment prediction in lung adenocarcinoma

Background

The prognostic model based on oxidative stress for lung adenocarcinoma (LUAD) remains unclear.

Methods

The information of LUAD patients were acquired from TCGA dataset. We also collected two external datasets from GEO for verification. Oxidative stress-related genes (ORGs) were extracted from Genecards. We performed machine learning algorithms, including Univariate Cox regression, Random Survival Forest, and Least Absolute Shrinkage and Selection Operator (Lasso) analyses on the ORGs to build the OS-score and OS-signature. We drew the Kaplan-Meier and time-dependent receiver operating characteristic curve (ROC) to evaluate the efficacy of the OS-signature in predicting the prognosis of LUAD. We used GISTIC 2.0 and maftool algorithms to explore Genomic mutation of OS-signature. To analyze characteristic of tumor infiltrating immune cells, ESTIMATE, TIMER2.0, MCPcounter and ssGSEA algorithms were applied, thus evaluating the immunotherapeutic strategies. Chemotherapeutics sensitivity analysis was based on pRRophetic package. Finally, PCR assays was also used to detect the expression values of related genes in the OS-signature in cell lines.

Results

Ten ORGs with prognostic value and the OS-signature containing three prognostic ORGs were identified. The significantly better prognosis of LUAD patients was observed in LUAD patients. The efficiency and accuracy of OS-signature in predicting prognosis for LUAD patients was confirmed by survival ROC curves and two external validation data sets. It was clearly observed that patients with high OS-scores had lower immunomodulators levels (with a few exceptions), stromal score, immune score, ESTIMATE score and infiltrating immune cell populations. On the contrary, patients with higher OS-scores were more likely to have higher tumor purity. PCR assays showed that, MRPL44 and CYCS were significantly higher expressed in LUAD cell lines, while CAT was significantly lower expressed.

Conclusion

The novel oxidative stress-related model we identified could be used for prognosis and treatment prediction in lung adenocarcinoma.

Targeted Therapy and Personalized Medicine

Targeted therapy and personalized medicine are novel emerging disciplines of cancer research intended for treatment and prevention. One of the most significant advancements in modern oncology is the shift from an organ-centric strategy to a personalized strategy guided by deep molecular analysis. This shift in view, which focuses on the tumour's precise molecular changes, has paved the way for individualized treatment. Researchers and clinicians are using targeted therapies to select the best treatment available based on the molecular characterization of malignant cancer. In the treatment of a cancer, personalized medicine entails the use of genetic, immunological, and proteomic profiling to provide therapeutic alternatives as well as prognostic information about cancer. In this book, targeted therapies and personalized medicine have been covered for specific malignancies, including latest FDA-approved targeted therapies and it also sheds light on effective anti-cancer regimens and drug resistance. This will help to enhance our ability to conduct individualized health planning, make early diagnoses, and choose optimal medications for each cancer patient with predictable side effects and outcomes in a quickly evolving era. Various applications and tools' capacity have been improved for early diagnosis of cancer and the growing number of clinical trials that choose specific molecular targets reflects this predicament. Nevertheless, there are several limitations that must need to be addressed. Hence, in this chapter, we will discuss recent advancements, challenges, and opportunities in personalized medicine for various cancers, with a specific emphasis on target therapies in diagnostics and therapeutics.

Correlation between oncogene integrator complex subunit 7 and a poor prognosis in lung adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is one of the most common types of cancer worldwide with high incidence and mortality rates. The integrator complex subunit 7 (INTS7) encodes a subunit of the integrator complex that mediates small-nuclear ribonucleic acid (RNA) processing and has been shown to be associated with RNA polymerase II. However, the clinical significance of INTS7 in LUAD is still not clear and needs to be investigated.

Methods

The single-cell sequencing of a publicly available data set was conducted to compare the expression levels and percentages of INTS7 in lung malignant cells at different classifications and stages. Further, 33 cancer types from The Cancer Genome Atlas (TCGA) database were analyzed, protein-protein interaction (PPI) networks were constructed, and functional annotations were undertaken for the INTS7 gene. INTS7 small-interfering RNAs were transfected into LUAD cell lines, and cell biological behaviors, such as migration, invasion, apoptosis and proliferation capacity, were then examined.

Results

We found that the expression of INTS7 was significantly more upregulated in the LUAD tissues than the adjacent normal tissues. Increased INTS7 messenger RNA expression was correlated with TNM (tumor node metastasis classification) stage and gender in LUAD patients. Further, the Kaplan-Meier survival analysis indicated that LUAD patients with high INTS7 expression levels had a worse prognosis than those with low INTS7 expression levels. Finally, we found that silencing INTS7 inhibited LUAD cell viability and invasion in vitro.

Conclusions

These results suggest that INTS7 can be used as a potential therapy target and prognostic marker for LUAD. Further, INTS7 may aggravate migration and invasion, induce the proliferation, and attenuate the apoptosis capacity of cells in LUAD.

AIM2 upregulation promotes metastatic progression and PD-L1 expression in lung adenocarcinoma

Cancer metastasis leading to the dysfunction of invaded organs is the main cause of the reduced survival rates in lung cancer patients. However, the molecular mechanism for lung cancer metastasis remains unclear. Recently, the increased activity of inflammasome appeared to correlate with the metastatic progression and immunosuppressive ability of various cancer types. Our results showed that the mRNA levels of absence in melanoma 2 (AIM2), one of the inflammasome members, are extensively upregulated in primary tumors compared with normal tissues derived from the TCGA lung adenocarcinoma (LUAD) database. Moreover, Kaplan-Meier analysis demonstrated that a higher mRNA level of AIM2 refers to a poor prognosis in LUAD patients. Particularly, AIM2 upregulation is closely correlated with smoking history and the absence of EGFR/KRAS/ALK mutations in LUAD. We further showed that the endogenous mRNA levels of AIM2 are causally associated with the metastatic potentials of the tested LUAD cell lines. AIM2 knockdown suppressed but overexpression promoted the migration ability and lung colony-forming ability of tested LUAD cells. In addition, we found that AIM2 upregulation is closely associated with an increased level of immune checkpoint gene set, as well as programmed cell death-ligand 1 (PD-L1) transcript, in TCGA LUAD samples. AIM2 knockdown predominantly repressed but overexpression enhanced PD-L1 expression via altering the activity of PD-L1 transcriptional regulators NF-κB/STAT1 in LUAD cells. Our results not only provide a possible mechanism underlying the AIM2-promoted metastatic progression and immune evasion of LUAD but also offer a new strategy for combating metastatic/immunosuppressive LUAD via targeting AIM2 activity.

Elevated air quality index and fine particulate matter levels contribute to the poor prognosis and progression of nonsmall-cell lung cancer: A cohort study combined with external validation

Background

Poor air quality can result in a variety of respiratory disorders. However, the air quality index (AQI) and the level of fine particulate matter (PM2.5) on the progression and prognosis of nonsmall‐cell lung cancer (NSCLC) are unclear.

Methods

We launched a cohort study focused on the relationship between air quality and overall survival as well as progression, incorporating data from 590 patients with NSCLC in our medical center between November 1, 2013 and March 1, 2016. Forty‐nine patients from Sichuan Cancer Hospital were used for validation.

Results

Cases with poorer AQI 6 months before NSCLC diagnosis were more likely to progress to stage III to IV NSCLC than controls (OR = 2.61, 95% CI 1.35–5.24, p = 0.005). Similarly, if exposed to high levels of PM2.5 during these 6 months, overall survival was poor (HR [95% CI] = 1.53 [1.13, 2.07], p = 0.006). According to multivariate analysis, age, gender, KPS, PM2.5, hyperlipemia, and NSCLC stage were independent risk factors of overall survival. A predictive model developed by these factors above yielded a favorable agreement (C‐index = 0.758) on the calibration curve. External validation was conducted by 46 patients from Sichuan Cancer Hospital displaying an AUC of 0.724 (0.684–0.763).

Conclusions

PM2.5 and AQI levels affect disease progression and long‐term survival in NSCLC patients. An overall survival prediction model based on the PM2.5 level can help clinicians predict the risk of death in NSCLC.

Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma

Background

AU-rich elements (ARE) are vital cis-acting short sequences in the 3’UTR affecting mRNA stability and translation. The deregulation of ARE-mediated pathways can contribute to tumorigenesis and development. Consequently, ARE-genes are promising to predict prognosis of lung adenocarcinoma (LUAD) patients.

Methods

Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature. The genetic signature was combined with clinicopathological features to establish a prognostic model. LUAD patients were divided into high- and low-risk groups by the model. Kaplan–Meier curve, Harrell’s concordance index (C-index), calibration curves and decision curve analyses (DCA) were used to assess the model. Function enrichment analysis, immunity and tumor mutation analyses were performed to further explore the underlying molecular mechanisms. GEO data were used for external validation.

Results

Twelve prognostic genes were identified. The gene riskScore, age and stage were independent prognostic factors. The high-risk group had worse overall survival and was less sensitive to chemotherapy and radiotherapy (P < 0.01). C-index and calibration curves showed good performance on survival prediction in both TCGA (1, 3, 5-year ROC: 0.788, 0.776, 0.766) and the GSE13213 validation cohort (1, 3, 5-year ROC: 0.781, 0.811, 0.734). DCA showed the model had notable clinical net benefit. Furthermore, the high-risk group were enriched in cell cycle, DNA damage response, multiple oncological pathways and associated with higher PD-L1 expression, M1 macrophage infiltration. There was no significant difference in tumor mutation burden (TMB) between high- and low-risk groups.

Conclusion

ARE-genes can reliably predict prognosis of LUAD and may become new therapeutic targets for LUAD.

Expression Status and Prognostic Value of m6A RNA Methylation Regulators in Lung Adenocarcinoma

N⁶-methyladenosine (m⁶A) RNA modification is the most abundant modification method in mRNA, and it plays an important role in the occurrence and development of many cancers. This paper mainly discusses the role of m⁶A RNA methylation regulators in lung adenocarcinoma (LUAD) to identify novel prognostic biomarkers. The gene expression data of 19 m⁶A methylation regulators in LUAD patients and its relevant clinical parameters were extracted from The Cancer Genome Atlas (TCGA) database. We selected three significantly differentially expressed m⁶A regulators in LUAD to construct the risk signature, and evaluated its prognostic prediction efficiency using the receiver operating characteristic (ROC) curve. Kaplan–Meier survival analysis and Cox regression analysis were used to identify the independent prognostic significance of the risk signature. The ROC curve indicated that the area under the curve (AUC) was 0.659, which means that the risk signature had a good prediction efficiency. The results of the Kaplan–Meier survival analysis and Cox regression analysis showed that the risk score can be used as an independent prognostic factor for LUAD. In addition, we explored the differential signaling pathways and cellular processes related to m⁶A methylation regulators in LUAD.

Knockdown of HSDL2 inhibits lung adenocarcinoma progression via down-regulating AKT2 expression

The aims of the present study are to investigate the role of hydroxysteroid dehydrogenase-like 2 (HSDL2) in the progression of lung adenocarcinoma and illuminate the underlying molecular mechanisms. ShRNA targeting HSDL2 gene (siHSDL2) was utilized to knockdown (KD) HSDL2 expression. In vitro and in vivo experiments were carried out to investigate the effect of siHSDL2 on the progression of lung adenocarcinoma. Microarray hybridization and gene expression analysis were used to investigate effect of siHSDL2 on mRNA expression profile in lung cancer cell line H1299. Our data demonstrated that HSDL2 was up-regulated in lung adenocarcinoma tissue samples (P<0.001). Patients with high HSDL2 expression in cancer tissues had a worse overall survival (P<0.001). HSDL2 KD not only inhibited the proliferation, cell cycle, apoptosis, clone-formation, invasion and migration of lung adenocarcinoma cells in vitro (P<0.05), but also suppressed the growth and metastasis in vivo (P<0.05). HSDL2 KD resulted in up-regulation of 681 genes and down-regulation of 276 genes. HSDL2 KD down-regulated the protein expression and phosphorylation of protein kinase B β (AKT2) (P<0.001 and P<0.001, respectively) and protein expression of baculoviral IAP repeat-containing 3 (BIRC3; P=0.001), and up-regulated the phosphorylation of ERK (P<0.001). Rescue experiments showed that AKT2 overexpression reversed the suppression effect of siHSDL2 on cell proliferation (P<0.001), invasion (P<0.001) and migration (P<0.001) significantly. HSDL2 functions as an oncogene to promote the growth and metastasis of lung adenocarcinoma via promoting the expression of AKT2.

circRNA hsa_circ_0018414 inhibits the progression of LUAD by sponging miR-6807-3p and upregulating DKK1

Lung adenocarcinoma (LUAD) is a subtype of lung cancer with a high incidence and mortality all over the world. In recent years, circular RNAs (circRNAs) have been verified to be a novel subtype of noncoding RNAs that exert vital functions in various cancers. Our research was designed to investigate the role of circ_0018414 in LUAD. We first observed that circ_0018414 was downregulated in LUAD tissues and cells. Also, low expression of circ_0018414 predicted unfavorable prognosis of LUAD patients. Then, upregulation of circ_0018414 repressed cell proliferation and stemness, while promoting cell apoptosis, in LUAD. Moreover, circ_0018414 overexpression enhanced the expression of its host gene, dickkopf WNT signaling pathway inhibitor 1 (DKK1), therefore inactivating the Wnt/β-catenin pathway. Additionally, circ_0018414 could sponge miR-6807-3p to protect DKK1 mRNA from miR-6807-3p-induced silencing, leading to DKK1 upregulation in LUAD cells. Finally, rescue assays proved that circ_0018414 inhibited the progression of LUAD via the miR-6807-3p/DKK1 axis-inactivated Wnt/β-catenin pathway. The findings in our work indicated circ_0018414 as a tumor inhibitor in LUAD, which might provide a new perspective for LUAD treatment.

Development and validation of a nomogram with an epigenetic signature for predicting survival in patients with lung adenocarcinoma

Epigenetic factors play crucial roles in carcinogenesis by modifying chromatin architecture. Here, we established an epigenetic biosignature-based model for examining survival in patients with lung adenocarcinoma (LUAD). We retrieved gene-expression profiles and clinical data from The Cancer Genome Atlas and Gene Expression Omnibus and clustered the data into training (n = 490) and Validation (n = 226) datasets, respectively. To establish an epigenetic model, we identified prognostic epigenetic regulation-related genes by LASSO and Cox regression analyses, and established a novel 11-gene signature, including EPC1, GADD45A, HCFC2, RCOR1, SMARCAL1, TLE2, TRIM28, and ZNF516, for predicting LUAD overall survival (OS). The biosignature performed optimally in both the training and validation sets according to receiver operating characteristic and calibration plots. Moreover, the biosignature classified patients into high- and low-risk clusters with distinct survival times, with Cox regression analysis revealing the biosignature as an independent LUAD prognostic index. Furthermore, the generated nomogram integrating the prognostic gene biosignature and clinical indices predicted LUAD OS with high efficiency and outperformed tumor-node-metastasis staging in LUAD survival prediction. These results demonstrated the efficacy of the epigenetic signature prognostic nomogram for reliably predicting LUAD OS and its potential application for informing clinical decision making and individualized treatment.

Circular RNAs and cancer: Opportunities and challenges

Circular RNAs (circRNAs) are covalently circularized RNA moieties that despite being relatively abundant were only recently identified and have only begun to be investigated within the last couple of years. Even though there are many thousands of genes that appear capable of producing circRNAs, and the fact that many circRNAs appear to be highly evolutionarily conserved, the function of all but a few remain to be fully explored. What has been determined, however, is that circRNAs play key regulatory roles in many aspects of biology with focus being given to their function in cancer. Most of the studies to date have found that circRNAs act as master regulator of gene expression most often than not acting to regulate levels though sequestration or "sponging" of other gene expression regulators, particularly miRNAs. They can also function directly modulating transcription, or by interfering with splicing mechanisms. Some circRNAs can also be translated into functional proteins or peptides. A combination of tissue and developmental stage specific expression along with an innate resistance to RNAse activity means that circRNAs show perhaps their greatest potential as novel biomarkers of cancer. In this chapter we consider the current state of knowledge regarding these molecules, their synthesis, function, and association with cancer. We also consider some of the challenges that remain to be overcome to allow this emerging class of RNAs to fulfill their potential in clinical practice.

Impaired AKT signaling and lung tumorigenesis by PIERCE1 ablation in KRAS-mutant non-small cell lung cancer

KRAS-mutant non-small cell lung cancer (NSCLC) is a major lung cancer subtype that leads to many cancer-related deaths worldwide. Although numerous studies on KRAS-mutant type NSCLC have been conducted, new oncogenic or tumor suppressive genes need to be detected because a large proportion of NSCLC patients does not respond to currently used therapeutics. Here, we show the tumor-promoting function of a cell cycle-related protein, PIERCE1, in KRAS-mutant NSCLC. Mechanistically, PIERCE1 depletion inhibits cell growth and AKT phosphorylation (pAKT) at S473, which is particularly observed in KRAS-mutant lung cancers. Analyses of AKT-related genes using microarray, immunoblotting, and real-time quantitative PCR indicated that PIERCE1 negatively regulates the gene expression of the AKT suppressor, TRIB3, through the CHOP pathway, which is a key regulatory pathway for TRIB3 expression. Similarly, in vivo analyses of PIERCE1 depletion in the KRAS mutation-related lung cancer mouse models revealed the suppressive effect of PIERCE1 knockout in urethane- and KRAS^G12D-induced lung tumorigenesis with decreased pAKT levels observed in the tumors. Tissue microarrays of human lung cancers indicated the expression of PIERCE1 in 83% of lung cancers and its correlation with pAKT expression. Thus, we illustrate how PIERCE1 depletion may serve as a therapeutic strategy against KRAS-mutant NSCLC and propose the clinical benefit of PIERCE1.

GALNT6 promotes invasion and metastasis of human lung adenocarcinoma cells through O-glycosylating chaperone protein GRP78

Lung adenocarcinoma remains a threat to human health due to its high rate of recurrence and distant metastasis. However, the molecular mechanism underlying lung adenocarcinoma metastasis remains yet incompletely understood. Here, we show that upregulated expression of polypeptide N-acetylgalactosaminyltransferase6 (GALNT6) in lung adenocarcinoma is associated with lymph node metastasis and poor prognosis. In lung adenocarcinoma cells, GALNT6 over-expression promoted epithelial-mesenchymal transition (EMT), wound healing, and invasion which could be significantly reversed by GALNT6 silencing. GALNT6 silencing also mitigated the metastasis of lung adenocarcinoma and prolonged the survival of xenograft tumor-bearing mice. Furthermore, GALNT6 directly interacted with, and O-glycosylated chaperone protein GRP78, which promoted EMT by enhancing the MEK1/2/ERK1/2 signaling in lung cancer cells. Therefore, GALNT6 is emerging as novel positive regulator for the malignancy of human lung adenocarcinoma. Targeting GALNT6-GRP78-MEK1/2/ERK1/2 may thus represent a new avenue to develop therapeutics against lung cancer metastasis.

The Targeted Therapies Era Beyond the Surgical Point of View: What Spine Surgeons Should Know Before Approaching Spinal Metastases

In the last few years, the treatment of spinal metastases has significantly changed. This is due to the advancements in surgical technique, radiotherapy, and chemotherapy which have enriched the multidisciplinary management. Above all, the field of molecular biology of tumors is in continuous and prosperous evolution. In this review, the molecular markers and new approaches that have radically modified the chemotherapeutic strategy of the most common metastatic neoplasms will be examined together with clinical and surgical implications. The experience and skills of several different medical professionals are mandatory: an interdisciplinary oncology team represents the winning strategy in the treatment of patients with spinal metastases

Establishment and Evaluation of a 6-Gene Survival Risk Assessment Model Related to Lung Adenocarcinoma Microenvironment

Objective

A survival risk assessment model associated with a lung adenocarcinoma (LUAD) microenvironment was established and evaluated to identify effective independent prognostic factors for LUAD.

Methods

The public data were downloaded from the TCGA database, and ESTIMATE prediction software was used to score immune cells and stromal cells for tumor purity prediction. The samples were divided into the high-score group and the low-score group by the median value of the immune score (or stromal score). The Wilcoxon test was used for differential analysis. GO and KEGG enrichment analysis of differentially expressed genes (DEGs) was performed using “clusterProfiler” of R package. Meanwhile, univariate and multivariate regression analysis was performed on DEGs to construct a multivariate Cox risk regression model with variable gene expression levels as independent prognostic factors affecting a tumor microenvironment (TME) and tumor immunity.

Results

This study found that LUAD patients with high immune cell (stromal cell) infiltration had better prognosis and were in earlier staging. Functional enrichment analysis revealed that most DEGs were related to the proliferation and activation of immune cells or stromal cells. A survival prediction model composed of 6 TME-related genes (CLEC17A, TAGAP, ABCC8, BCAN, FLT3, and CCR2) was established, and finally, the 6 feature genes closely related to the prognosis of LUAD were proved. The AUC value of the ROC curve in this model was 0.7, indicating that the model was reliable.

Conclusion

Six genes related to the LUAD microenvironment have a predictive prognostic value in LUAD.

A novel circular RNA, hsa-circ-0000211, promotes lung adenocarcinoma migration and invasion through sponging of hsa-miR-622 and modulating HIF1-α expression

Recently, several studies have evaluated the role of circular RNAs in the metastasis and development of multiple cancers. In our earlier microarray-based study, we had reported the aberrant expression of a novel circular RNA, hsa-circ-0000211 in lung adenocarcinoma (LAC) tissues. However, the roles of hsa-circ-0000211 in LAC have not been studied. Here hsa-circ-0000211 expression in the LAC tissues and cell lines was determined by quantitative real-time PCR (qRT-PCR). The function of hsa-circ-0000211 was evaluated by transwell assay and wound healing. Mechanisms of hsa-circ-0000211 was measured by luciferase reporter assay and western blot. Results revealed the expression of hsa-circ-0000211 in the human LAC tissues and LAC cell lines was higher than that in normal tissue and human lung normal epithelial cells, respectively. The knockdown of hsa-circ-0000211 could inhibit the migration and invasion properties of LAC. Furthermore, hsa-circ-0000211 promoted the migration and invasion of LAC by sponging miR-622. Moreover, hsa-circ-0000211 upregulated the HIF1-α expression by targeting miR-622. hsa-circ-0000211 promoted LAC cell migration and invasion by modulating the miR-622/HIF1-α network. Our study demonstrated that hsa-circ-0000211 can be a potential novel therapeutic target for LAC.

Competitive endogenous RNA network identifies four long non-coding RNA signature as a candidate prognostic biomarker for lung adenocarcinoma

BACKGROUND

Lung adenocarcinoma (LUAD) is the most commonly histological subtype of lung cancer (LC) and the prognoses of the majority of LUAD patients are still very poor. The present study aimed at integrating long non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression data to construct lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network and identify importantly potential lncRNA signature in ceRNA network as a candidate prognostic biomarker for LUAD patients.

METHODS

lncRNA, miRNA and mRNA expression data as well as clinical characteristics of LUAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs) and differentially expressed miRNA (DEmiRNA) between LUAD and normal lung tissues samples were analyzed. A lncRNA-miRNA-mRNA ceRNA network was constructed and the biological functions of DEmRNAs in ceRNA network were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Univariate and multivariate Cox regression analyses of DElncRNAs in ceRNA network were implemented to predict the overall survival (OS) in LUAD patients. The receiver operating characteristic (ROC) analysis was used to evaluate the performance of multivariate Cox regression model.

RESULTS

A total of 1,664 DElncRNAs, 120 DEmiRNAs and 2,503 DEmRNAs was identified between LUAD and normal lung tissues samples. A lncRNA-miRNA-mRNA ceRNA network including 140 DElncRNAs, 33 DEmiRNAs and 57 DEmRNAs was established. Kaplan-Meier (KM) [Log-rank (LR) test] and univariate regression analysis of those 140 DElncRNAs revealed that 7 DElncRNAs (LINC00518, UCA1, NAV2-AS2, MED4-AS1, SYNPR-AS1, AC011483.1, AP002478.1) were simultaneously identified to be associated with OS of LUAD patients. A multivariate Cox regression analysis of those 7 DElncRNAs showed that a group of 4 DElncRNAs including AP002478.1 (Cox P=4.66E-03), LINC00518 (Cox P=2.34E-04), MED4-AS1 (Cox P=6.42E-03) and NAV2-AS2 (Cox P=6.66E-02) had significantly prognostic value in OS of LUAD patients. The cumulative risk score indicated that the 4-lncRNA signature was significantly associated with OS of LUAD patients (P=0). The area under the curve (AUC) of the 4-lncRNA signature related with 3-year survival was 0.669.

CONCLUSIONS

The present study provides novel insights into the lncRNA-related regulatory mechanisms in LUAD, and identifying 4-lncRNA signature may serve as a candidate prognostic biomarker in predicting the OS of LUAD patients.

CRISPR/Cas9 - An evolving biological tool kit for cancer biology and oncology

The development of genetic engineering in the 1970s marked a new frontier in genome-editing technology. Gene-editing technologies have provided a plethora of benefits to the life sciences. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/ Cas9) system is a versatile technology that provides the ability to add or remove DNA in the genome in a sequence-specific manner. Serious efforts are underway to improve the efficiency of CRISPR/Cas9 targeting and thus reduce off-target effects. Currently, various applications of CRISPR/Cas9 are used in cancer biology and oncology to perform robust site-specific gene editing, thereby becoming more useful for biological and clinical applications. Many variants and applications of CRISPR/Cas9 are being rapidly developed. Experimental approaches that are based on CRISPR technology have created a very promising tool that is inexpensive and simple for developing effective cancer therapeutics. This review discusses diverse applications of CRISPR-based gene-editing tools in oncology and potential future cancer therapies.

Development of a miRNA-seq based prognostic signature in lung adenocarcinoma

Background

We utilized miRNAs expression and clinical data to develop a prognostic signature for patients with lung adenocarcinoma, with respect to their overall survival, to identify high-risk subjects based on their miRNA genomic profile.

Methods

MiRNA expressions based on miRNA sequencing and clinical data of lung adenocarcinoma patients (n = 479) from the Cancer Genome Atlas were randomly partitioned into non-overlapping Model (n = 320) and Test (n = 159) sets, respectively, for model estimation and validation.

Results

Among the ten miRNAs identified using the univariate Cox analysis, six from miR-8, miR-181, miR-326, miR-375, miR-99a, and miR-10, families showed improvement of the overall survival chance, while two miRNAs from miR-582 and miR-584 families showed a worsening of survival chances. The final prognostic signature was developed with five miRNAs—miR-375, miR-582-3p, miR-326, miR-181c-5p, and miR-99a-5p—utilizing a stepwise variable selection procedure. Using the KEGG pathway analysis, we found potential evidence supporting their significance in multiple cancer pathways, including non-small cell lung cancer. We defined two risk groups with a score calculated using the Cox regression coefficients. The five-year survival rates for the low-risk group was approximately 48.76% (95% CI = (36.15, 63.93)); however, it was as low as 7.50% (95% CI = (2.34, 24.01)) for the high-risk group. Furthermore, we demonstrated the effect of the genomic profile using the miRNA signature, quantifying survival rates for hypothetical subjects in different pathological stages of cancer.

Conclusions

The proposed prognostic signature can be used as a reliable tool for identifying high-risk subjects regarding survival based on their miRNA genomic profile.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-5206-8) contains supplementary material, which is available to authorized users.

CircABCB10 promotes nonsmall cell lung cancer cell proliferation and migration by regulating the miR-1252/FOXR2 axis

Circular RNA (circRNA) is a key regulator in the development and progression of human cancers. Previous studies confirmed circRNA‐0008717 (circABCB10) as an oncogene in osteosarcoma, but the regulatory effect of circABCB10 in nonsmall cell lung cancer (NSCLC) is still unclear. In the current study, we examined the expression of circABCB10 in different NSCLC cell lines. Bioinformatics analysis, Cell Counting Kit‐8 assays, Transwell migration, fluorescein reporting experiments, and xenografts in mice were used to detect the effect of circABCB10 on NSCLC cell proliferation and migration in vitro and tumor growth in vivo. The results showed that the expression of circABCB10 in NSCLC cell lines was increased. Downregulation of circABCB10 suppressed NSCLC cell proliferation and migration by promoting microRNA miR‐1252 expression and suppressing Forkhead box 2 (FOXR2). Fluorescein reporting experiments confirmed that circABCB10 expression increased FOXR2 levels by sponging miR‐1252, and in vivo experiments found that knockdown of circABCB10 decreased tumor growth. These data suggested that circABCB10 acted as a tumor promoter through a novel miR‐1252/FOXR2 axis, providing potential biomarkers and therapeutic targets for the management of NSCLC.

CRISPR therapeutic tools for complex genetic disorders and cancer (Review)

One of the fundamental discoveries in the field of biology is the ability to modulate the genome and to monitor the functional outputs derived from genomic alterations. In order to unravel new therapeutic options, scientists had initially focused on inducing genetic alterations in primary cells, in established cancer cell lines and mouse models using either RNA interference or cDNA overexpression or various programmable nucleases [zinc finger nucleases (ZNF), transcription activator-like effector nucleases (TALEN)]. Even though a huge volume of data was produced, its use was neither cheap nor accurate. Therefore, the clustered regularly interspaced short palindromic repeats (CRISPR) system was evidenced to be the next step in genome engineering tools. CRISPR-associated protein 9 (Cas9)-mediated genetic perturbation is simple, precise and highly efficient, empowering researchers to apply this method to immortalized cancerous cell lines, primary cells derived from mouse and human origins, xenografts, induced pluripotent stem cells, organoid cultures, as well as the generation of genetically engineered animal models. In this review, we assess the development of the CRISPR system and its therapeutic applications to a wide range of complex diseases (particularly distinct tumors), aiming at personalized therapy. Special emphasis is given to organoids and CRISPR screens in the design of innovative therapeutic approaches. Overall, the CRISPR system is regarded as an eminent genome engineering tool in therapeutics. We envision a new era in cancer biology during which the CRISPR-based genome engineering toolbox will serve as the fundamental conduit between the bench and the bedside; nonetheless, certain obstacles need to be addressed, such as the eradication of side-effects, maximization of efficiency, the assurance of delivery and the elimination of immunogenicity.

NK Cells Mediate Synergistic Antitumor Effects of Combined Inhibition of HDAC6 and BET in a SCLC Preclinical Model

Small-cell lung cancer (SCLC) has the highest malignancy among all lung cancers, exhibiting aggressive growth and early metastasis to distant sites. For 30 years, treatment options for SCLC have been limited to chemotherapy, warranting the need for more effective treatments. Frequent inactivation of TP53 and RB1 as well as histone dysmodifications in SCLC suggest that transcriptional and epigenetic regulations play a major role in SCLC disease evolution. Here we performed a synthetic lethal screen using the BET inhibitor JQ1 and an shRNA library targeting 550 epigenetic genes in treatment-refractory SCLC xenograft models and identified HDAC6 as a synthetic lethal target in combination with JQ1. Combined treatment of human and mouse SCLC cell line-derived xenograft tumors with the HDAC6 inhibitor ricolinostat (ACY-1215) and JQ1 demonstrated significant inhibition of tumor growth; this effect was abolished upon depletion of NK cells, suggesting that these innate immune lymphoid cells play a role in SCLC tumor treatment response. Collectively, these findings suggest a potential new treatment for recurrent SCLC.Significance: These findings identify a novel therapeutic strategy for SCLC using a combination of HDAC6 and BET inhibitors. Cancer Res; 78(13); 3709-17. ©2018 AACR.

MutScan: fast detection and visualization of target mutations by scanning FASTQ data

Background

Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering, which may cause miss-detection of key mutations with low frequencies. Variant validation is also indicated for key mutations detected by bioinformatics pipelines. Typically, this process can be executed using alignment visualization tools such as IGV or GenomeBrowse. However, these tools are too heavy and therefore unsuitable for validating mutations in ultra-deep sequencing data.

Result

We developed MutScan to address problems of sensitive detection and efficient validation for target mutations. MutScan involves highly optimized string-searching algorithms, which can scan input FASTQ files to grab all reads that support target mutations. The collected supporting reads for each target mutation will be piled up and visualized using web technologies such as HTML and JavaScript. Algorithms such as rolling hash and bloom filter are applied to accelerate scanning and make MutScan applicable to detect or visualize target mutations in a very fast way.

Conclusion

MutScan is a tool for the detection and visualization of target mutations by only scanning FASTQ raw data directly. Compared to conventional pipelines, this offers a very high performance, executing about 20 times faster, and offering maximal sensitivity since it can grab mutations with even one single supporting read. MutScan visualizes detected mutations by generating interactive pile-ups using web technologies. These can serve to validate target mutations, thus avoiding false positives. Furthermore, MutScan can visualize all mutation records in a VCF file to HTML pages for cloud-friendly VCF validation. MutScan is an open source tool available at GitHub: https://github.com/OpenGene/MutScan

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2024-6) contains supplementary material, which is available to authorized users.

Emerging Role of Circular RNAs as Potential Biomarkers for the Diagnosis of Human Diseases

In the eukaryotic transcriptome, the evolutionary conserved circular RNAs naturally occur from the family of noncoding RNAs. Circular RNAs possess a unique feature to interact with nucleic acids and ribonucleoproteins and are establishing themselves as an obligatory composition for the regulatory messages which are encoded by the genome. The back-splicing mechanism leads to the formation of circularized RNA, and because of this they become resistant to exonuclease-mediated degradation. The differential and aberrant expression of circular RNAs can be detected with the help of various profiling methods by using serum, plasma, and tissue samples. In this chapter, we have highlighted the role of circular RNAs as putative biomarker for the detection of various human diseases along with its profiling methods. Here we have discussed the differentially expressed circular RNAs in neurological disorders and infectious diseases along with cancer diseases. For instance, in case of pulmonary tuberculosis, hsa_circRNA_001937 was upregulated, while hsa_circRNA_102101 got downregulated; Hsa_circ_000178 was depicted to get upregulated in breast cancer which is associated with disease progression. Furthermore, it has been observed that circRNAs are abundantly present within the mammalian brain tissues. In epileptic condition, Circ-EFCAB2 was observed to get notably upregulated within patients. Taking the above conditions into consideration, circular RNAs have proven themselves as promising noninvasive biomarker for the detection of human diseases.

Modes of Cell Death Induced by Photodynamic Therapy Using Zinc Phthalocyanine in Lung Cancer Cells Grown as a Monolayer and Three-Dimensional Multicellular Spheroids

Photodynamic therapy (PDT) involves interaction of a photosensitizer, light, and molecular oxygen which produces singlet oxygen and subsequent tumour eradication. The development of second generation photosensitizers, such as phthalocyanines, has improved this technology. Customary monolayer cell culture techniques are, unfortunately, too simple to replicate treatment effects in vivo. Multicellular tumour spheroids may provide a better alternative since they mimic aspects of the human tumour environment. This study aimed to profile 84 genes involved in apoptosis following treatment with PDT on lung cancer cells (A549) grown in a monolayer versus three-dimensional multicellular tumour spheroids (250 and 500 μm). Gene expression profiling was performed 24 h post irradiation (680 nm; 5 J/cm²) with zinc sulfophthalocyanine (ZnPcSmix) to determine the genes involved in apoptotic cell death. In the monolayer cells, eight pro-apoptotic genes were upregulated, and two were downregulated. In the multicellular tumour spheroids (250 µm) there was upregulation of only 1 gene while there was downregulation of 56 genes. Apoptosis in the monolayer cultured cells was induced via both the intrinsic and extrinsic apoptotic pathways. However, in the multicellular tumour spheroids (250 and 500 µm) the apoptotic pathway that was followed was not conclusive.

ALK rearrangement in specific subtypes of lung adenocarcinoma: immunophenotypic and morphological features

Lung adenocarcinomas are characterized by a variety of genetic and epigenetic changes that lead to activation of specific signaling pathways. This allowed the classification of lung adenocarcinomas according to genetic alterations and the clinical development of novel anticancer agents that affect the activity of specific oncoproteins. In such a context, chromosomal rearrangements that cause constitutive activation of ALK gene define a category of lung adenocarcinomas that is amenable to targeted therapy with ALK inhibitors. Thus, a major issue of current research is to define the morphological and immunophenotypic features of lung ALK-rearranged adenocarcinomas to improve the selection of tumors suitable for molecular genotyping. ALK status was determined, by immunohistochemistry and fluorescence in situ hybridization, in 94 surgically resected lung adenocarcinomas and correlated with histomorphological parameters. Indeed, ALK rearrangement was observed in 10/94 (11%) lung adenocarcinomas and enriched in tumors with a predominant mucinous (46%; p < 0.05) and solid (29%; p < 0.05) pattern. By contrast, it was lacking or sporadically observed in lung adenocarcinomas with predominant acinar, papillary or lepidic pattern. Moreover, the presence of signet-ring cells was predominantly observed in ALK-rearranged tumors (47%; p < 0.05). These data suggest that ALK rearrangement is associated with specific and distinct clinical-pathological characters compared to other genotypes. Thus, the knowledge of these characteristics can improve the diagnostic accuracy and lead to a better understanding of the behavior of ALK-rearranged NSCLC.

Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search

In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation. Signaling is initiated by binding the ligand protein EGF to the membrane-bound receptor EGFR so as to trigger a reactions path which have several linked elements through the cell from the membrane till the nucleus. We present two different types of search for analyzing the EGF/proliferation system with the help of Pathway Logic tool, which provides a knowledge-based development environment to carry out the modeling of the signaling. The first one is a standard (forward) search. The second one is a novel approach based on narrowing, which allows us to trace backwards the causes of a given final state. The analysis allows the identification of critical elements that have to be activated to provoke proliferation.

Targeting roles of inflammatory microenvironment in lung cancer and metastasis

Inflammatory cells and mediators are essential components in tumor microenvironment and play decisive roles in the initiation, proliferation, survival, promotion, invasion, or metastasis of lung cancer. Clinical and epidemiologic studies suggested a strong association between inflammation and lung cancer and an influence of immune surveillances and tumor responses to chemotherapeutic drugs, although roles of inflammation in lung cancer remain unclear. The present review outlined roles of inflammation in lung cancer, with particular focus on inflammatory components, types, biomarkers, or principal mechanisms by which the inflammation contributes to the development of lung cancer. The cancer-associated inflammatory cells (CICs) should be furthermore defined and include cancer-specific and interacted cells with inflammatory or inflammation-like characteristics, e.g., innate or adaptive immune cells and cancer tissue cells. We also discuss targeting potentials of inflammation in the prevention and treatment of lung cancer. The diversity of cancer-related inflammatory microenvironment is instrumental to design novel therapeutic approaches for lung cancer.

Molecular Markers and Targeted Therapeutics in Metastatic Tumors of the Spine: Changing the Treatment Paradigms

STUDY TYPE

A review of the literature.

OBJECTIVE

The aim of this study was to discuss the evolution of molecular signatures and the history and development of targeted therapeutics in metastatic tumor types affecting the spinal column.

SUMMARY OF BACKGROUND DATA

Molecular characterization of metastatic spine tumors is expected to usher in a revolution in diagnostic and treatment paradigms. Molecular characterization will provide critical information that can be used for initial diagnosis, prognosticating the ideal treatment strategy, assessment of treatment efficacy, surveillance and monitoring recurrence, and predicting complications, clinical outcome, and overall survival in patients diagnosed with metastatic cancers to the spinal column.

METHODS

A review of the literature was performed focusing on illustrative examples of the role that molecular-based therapeutics have played in clinical outcomes for patients diagnosed with metastatic tumor types affecting the spinal column.

RESULTS

The impact of molecular therapeutics including receptor tyrosine kinases and immune checkpoint inhibitors and the ability of molecular signatures to provide prognostic information are discussed in metastatic breast cancer, lung cancer, prostate cancer, melanoma, and renal cell cancer affecting the spinal column.

CONCLUSION

For the providers who will ultimately counsel patients diagnosed with metastases to the spinal column, molecular advancements will radically alter the management/surgical paradigms utilized. Ultimately, the translation of these molecular advancements into routine clinical care will greatly improve the quality and quantity of life for patients diagnosed with spinal malignancies and provide better overall outcomes and counseling for treating physicians.

LEVEL OF EVIDENCE

N/A.

Tanshinones suppress AURKA through up-regulation of miR-32 expression in non-small cell lung cancer

Tanshinone is the liposoluble constituent of Salia miltiorrhiza, a root used in traditional herbal medicine which is known to possess certain health benefits. Although it is known that tanshinones, including tanshinone I (T1), tanshinone IIA (T2A), and cryptotanshinone (CT), can inhibit the growth of lung cancer cells in vitro, the mechanism under which they act is still unclear. AURKA, an oncogene, encodes a serine-threonine kinase which regulates mitotic processes in mammalian cells. Here, we reported that tanshinones mediate AURKA suppression partly through up-regulating the expression of miR-32. We found that tanshinones could inhibit cell proliferation, promote apoptosis, and impede cell-cycle progression, thus performing an antineoplastic function in non-small cell lung cancer (NSCLC). Additionally, we demonstrated that tanshinones attained these effects in part by down-regulating AURKA, corroborating previous reports. Our results showed that in NSCLC, similar effects were obtained with knock-down of the AURKA gene by siRNA. We also verified that AURKA was the direct target of miR-32. Collectively, our results demonstrated that tanshinones could inhibit NSCLC by suppressing AURKA via up-regulating the expressions of miR-32 and other related miRNAs.

Pingyangmycin and Bleomycin Share the Same Cytotoxicity Pathway

Pingyangmycin is an anticancer drug known as bleomycin A5 (A5), discovered in the Pingyang County of Zhejiang Province of China. Bleomycin (BLM) is a mixture of mainly two compounds (A2 and B2), which is on the World Health Organization’s list of essential medicines. Both BLM and A5 are hydrophilic molecules that depend on transporters or endocytosis receptors to get inside of cells. Once inside, the anticancer activities rely on their abilities to produce DNA breaks, thus leading to cell death. Interestingly, the half maximal inhibitory concentration (IC₅₀) of BLMs in different cancer cell lines varies from nM to μM ranges. Different cellular uptake, DNA repair rate, and/or increased drug detoxification might be some of the reasons; however, the molecules and signaling pathways responsible for these processes are largely unknown. In the current study, we purified the A2 and B2 from the BLM and tested the cytotoxicities and the molecular mechanisms of each individual compound or in combination with six different cell lines, including a Chinese hamster ovary (CHO) cell line defective in glycosaminoglycan biosynthesis. Our data suggested that glycosaminoglycans might be involved in the cellular uptake of BLMs. Moreover, both BLM and A5 shared similar signaling pathways and are involved in cell cycle and apoptosis in different cancer cell lines.

Basigin-2 upregulated by receptor activator of NF-κB ligand enhances lung cancer-induced osteolytic lesions

BACKGROUND

Lung cancer bone metastasis causes poor prognosis. Basigin-2, a novel cancer-associated biomarker, is upregulated in lung cancer and has been linked with tumor progression. But little is known about the role of basigin-2 in lung cancer bone metastasis and osteolytic lesion.

METHODS

Basigin-2 expression was evaluated in biopsy tissue specimens of 20 lung cancer patients with bone metastases via immunohistochemistry. Invasion assay and MTT proliferation assay were performed to test the invasion and proliferation of lung cancer cell after modulated basigin-2 expression. The osteoclastic activity of basigin-2 was detected in tibia cancer model by injected of lung cancer cells. The regulation role of receptor activator of NF-κB ligand (RANKL) on basigin-2 and its downstream molecules were measured by real-time quantitative RT-PCR, gelatin zymography and western blot analysis.

RESULTS

We found that basigin-2 was highly expressed in lung cancer bone metastases. Then, we demonstrated that basigin-2 could promote lung cancer cells invasion, metastasis and proliferation through upregulating metalloproteinases-2 (MMP-2), MMP-9 and vascular endothelial growth factor (VEGF) expression. The lung cancer cells overexpressing basigin-2 strongly induced the osteolytic lesions in immunodeficient mice, which were reduced by treatment with basigin-2 blocking antibody. Furthermore, we explored the enhanced basigin-2 molecular mechanism in lung cancer bone metastasis. Our results indicated the RANKL, pivotal for the control of bone resorption, could increase basigin-2 and its downstream molecules MMP-2, MMP-9 and VEGF expression in vitro.

CONCLUSIONS

Basigin-2 upregulated by RANKL induces MMPs and VEGF, which may increase lung cancer cell metastasis ability and support osteoclastic activity. Thus, our data suggest important roles for basigin-2 in lung cancer-induced osteolytic lesion and implicate this protein potential application as a target for lung cancer bone metastasis therapy.

Chromogenic Assay for Lung Cancer-Related EGFR Exon 19 Hotspot Deletion Mutations

BACKGROUND

Epidermal growth factor receptor (EGFR) deletion mutations are associated with the development of nonsmall-cell lung cancer (NSCLC) and can serve as useful biomarkers.

AIM

In the present study, a novel assay for the detection of EGFR hotspot mutations was designed to be highly sensitive and practically false-positive-free to harness the potential of detecting such mutations as biomarkers early in the diagnosis of NSCLC. The new assay draws from the polymerase chain reaction (PCR) for amplification, blue-white screening for initial allele discrimination, and Sanger sequencing for mutation confirmation.

RESULTS

Mutant plasmids were mixed with wild-type DNA in ratios from 1:10 to 1:1000, followed by PCR amplification, blue-white screening, and sequencing. Mutants were successfully sequence confirmed for mixtures at ratios of 1:300 and 1:1000, highlighting the assay's high sensitivity and low risk of false-positives due to confirmation by Sanger sequencing.

CONCLUSION

With high sensitivity and low false positives, the present assay is appealing as an aid in the early diagnosis of NSCLC through liquid biopsy. The highly customizable nature of the assay provides the possibility of applications in the early diagnosis of other cancer-related genes through nonsense-transformable mutations.

Tyr1068-phosphorylated epidermal growth factor receptor (EGFR) predicts cancer stem cell targeting by erlotinib in preclinical models of wild-type EGFR lung cancer

Tyrosine kinase inhibitors (TKIs) have shown strong activity against non-small-cell lung cancer (NSCLC) patients harboring activating epidermal growth factor receptor (EGFR) mutations. However, a fraction of EGFR wild-type (WT) patients may have an improvement in terms of response rate and progression-free survival when treated with erlotinib, suggesting that factors other than EGFR mutation may lead to TKI sensitivity. However, at present, no sufficiently robust clinical or biological parameters have been defined to identify WT-EGFR patients with greater chances of response. Therapeutics validation has necessarily to focus on lung cancer stem cells (LCSCs) as they are more difficult to eradicate and represent the tumor-maintaining cell population. Here, we investigated erlotinib response of lung CSCs with WT-EGFR and identified EGFR phosphorylation at tyrosine1068 (EGFRtyr1068) as a powerful biomarker associated with erlotinib sensitivity both in vitro and in preclinical CSC-generated xenografts. In contrast to the preferential cytotoxicity of chemotherapy against the more differentiated cells, in EGFRtyr1068 cells, erlotinib was even more active against the LCSCs compared with their differentiated counterpart, acquiring potential value as CSC-directed therapeutics in the context of WT-EGFR lung cancer. Although tumor growth was inhibited to a similar extent during erlotinib or chemotherapy administration to responsive tumors, erlotinib proved superior to chemotherapy in terms of higher tolerability and reduced tumor aggressiveness after treatment suspension, substantiating the possibility of preferential LCSC targeting, both in adenocarcinoma (ADC) and squamous cell carcinoma (SCC) tumors. We conclude that EGFRtyr1068 may represent a potential candidate biomarker predicting erlotinib response at CSC-level in EGFR-WT lung cancer patients. Finally, besides its invariable association with erlotinib sensitivity in EGFR-WT lung CSCs, EGFRtyr1068 was associated with EGFR-sensitizing mutations in cell lines and patient tumors, with relevant diagnostic, clinical and therapeutic implications.

Post-trial access to treatment for patients participating in clinical trials

Clinical trials are the mainstay for bringing out newer and better drugs to serve the mankind. By virtue of participating in a clinical trial, a patient receives access to the newer drugs/therapies, but nothing is generally being offered to them once their participation in the study comes to an end. Though the issue of post-trial access to treatment by patients participating in a clinical trial is debatable, there is no compelling justification either for or against it. We examined a case study in order to evaluate the applicability of post-trial access to treatment for patients participating in clinical trials. The provision of post-trial access to treatment should also keep into consideration the compassionate use of drugs on humanitarian grounds, especially in cases of trial drugs that have offered significant benefit to the trial patients and whose termination would lead to deterioration in patient's overall condition. In the present era of personalized medicine, the incorporation of genetic testing into clinical practice further authenticates the rationale of compassionate use of drugs and post-trial access to treatment.

Wnt signaling regulates the stemness of lung cancer stem cells and its inhibitors exert anticancer effect on lung cancer SPC-A1 cells

Wnt signaling plays an important role in regulating the activity of cancer stem cells (CSCs) in a variety of cancers. In this study, we explored the role of Wnt signaling in the lung cancer stem cells (LCSCs). LCSCs were obtained by sphere culture, for which human lung adenocarcinoma cell line SPC-A1 was treated with IGF, EGF and FGF-10. The stemness of LCSCs was confirmed by immunofluorescence, and pathway analysis was performed by functional genome screening and RT-PCR. The relationship between the identified signaling pathway and the expression of the stemness genes was explored by agonist/antagonist assay. Moreover, the effects of different signaling molecule inhibitors on sphere formation, cell viability and colony formation were also analyzed. The results showed that LCSCs were successfully generated as they expressed pluripotent stem cell markers Nanog and Oct 4, and lung distal epithelial markers CCSP and SP-C, by which the phenotype characterization of stem cells can be confirmed. The involvement of Wnt pathway in LCSCs was identified by functional genome screening and verified by RT-PCR. The expression of Wnt signaling components was closely related to the expression of the Nanog and Oct 4. Furthermore, targeting Wnt signaling pathway by using different signaling molecule inhibitors can exert anticancer effects. In conclusion, Wnt signaling pathway is involved in the stemness regulation of LCSCs and might be considered as a potential therapeutic target in lung adenocarcinoma.

Molecular markers to predict clinical outcome and radiation induced toxicity in lung cancer

The elucidation of driver mutations involved in the molecular pathogenesis of cancer has led to a surge in the application of novel targeted therapeutics in lung cancer. Novel oncologic research continues to lead investigators towards targeting personalized tumor characteristics rather than applying targeted therapy to broad patient populations. Several driver genes, in particular epidermal growth factor receptor (EGFR) and ALK fusions, are the earliest to have made their way into clinical trials. The avant-garde role of genomic profiling has led to important clinical challenges when adapting current standard treatments to personalized oncologic care. This new frontier of medicine requires newer biomarkers for toxicity that will identify patients at risk, as well as, new molecular markers to predict and assess clinical outcomes. Thus far, several signature genes have been developed to predict outcome as well as genetic factors related to inflammation to predict toxicity.

[Next-generation sequencing for lung cancer]

肺癌在生物学上具有侵袭性，并且是癌症相关死亡的主要原因。根据临床特征、预后、对治疗的反应和耐受性，每一例肺癌患者的进展均是独特的。传统上基于毛细管的单基因测序的第一代技术（如Sanger测序法）已被允许大量平行测序且成本更低、通量更高的下一代测序技术（next-generation sequencing, NGS）所替代。与传统方法相比，NGS技术取得显著进步。我们希望这些方法可全面地解释癌症全球图谱，并提供更多信息以满足个体化用药的需求。本综述包括对不同NGS技术的简要说明，NGS在肺癌研究进展中的应用和重要发现的总结，包括对已知靶基因（EGFR、ALK和KRAS）的进一步探索、其它肺癌突变的鉴定和癌症基因组研究的全局协调。

Next-generation sequencing for lung cancer

Lung cancer is biologically aggressive and is the leading cause of cancer-related deaths. The development of lung cancer is unique in each patient according to clinical characterizations, prognosis, response and tolerance to treatment. Traditional capillary-based single-gene sequencing by a first-generation technique (known as Sanger sequencing) has been replaced by next-generation sequencing (NGS) since it allows massive parallel sequencing with lower cost and higher throughput. The NGS approach has made remarkable advances compared with traditional methods. We expect these methodologies to comprehensively interpret the global landscape of cancer and provide more information to fulfill the needs of personalized medicine. This review covers a brief introduction and summary on various NGS technologies, applications and important findings by NGS in lung cancer advances, including further discoveries in previously known target genes (EGFR, ALK and KRAS), the identification of additional lung cancer mutations and the global coordination of cancer genome studies.

Network-based inference framework for identifying cancer genes from gene expression data

Great efforts have been devoted to alleviate uncertainty of detected cancer genes as accurate identification of oncogenes is of tremendous significance and helps unravel the biological behavior of tumors. In this paper, we present a differential network-based framework to detect biologically meaningful cancer-related genes. Firstly, a gene regulatory network construction algorithm is proposed, in which a boosting regression based on likelihood score and informative prior is employed for improving accuracy of identification. Secondly, with the algorithm, two gene regulatory networks are constructed from case and control samples independently. Thirdly, by subtracting the two networks, a differential-network model is obtained and then used to rank differentially expressed hub genes for identification of cancer biomarkers. Compared with two existing gene-based methods (t-test and lasso), the method has a significant improvement in accuracy both on synthetic datasets and two real breast cancer datasets. Furthermore, identified six genes (TSPYL5, CD55, CCNE2, DCK, BBC3, and MUC1) susceptible to breast cancer were verified through the literature mining, GO analysis, and pathway functional enrichment analysis. Among these oncogenes, TSPYL5 and CCNE2 have been already known as prognostic biomarkers in breast cancer, CD55 has been suspected of playing an important role in breast cancer prognosis from literature evidence, and other three genes are newly discovered breast cancer biomarkers. More generally, the differential-network schema can be extended to other complex diseases for detection of disease associated-genes.

[Molecular pathology of the lungs. New perspectives by next generation sequencing]

Lung cancer is one of the most frequent malignancies in the western world. Its frequent association with a wide spectrum of mutations in genes encoding various signal transducers that are often linked to therapy response, emphasizes the obvious need for improved, fast and highly efficient approaches in molecular pathology. Comprehensive analyses of the mutation status of progression and therapy relevant genes can be performed by the novel sequencing forms named next generation sequencing (NGS) providing extremely high capacities for ultra-deep sequence analyses. The 454 pyrosequencing method, the sequencing by synthesis and the semiconductor sequencing platform are now available for parallel sequencing approaches of multitudinous target genes linked to multiple tumor DNA applications. The "one molecule, one clone, one read" principle by the NGS approaches supplies not only information on allele frequencies and mutation rates but also has the advantage of a very sensitive detection of low frequency variants.

Cancer stem cells in lung cancer: Evidence and controversies

The cancer stem cell (CSC) model is based on a myriad of experimental and clinical observations suggesting that the malignant phenotype is sustained by a subset of cells characterized by the capacity for self-renewal, differentiation and innate resistance to chemotherapy and radiation. CSC may be responsible for disease recurrence after definitive therapy and may therefore be functionally synonymous with minimal residual disease. Similar to other solid tumours, several putative surface markers for lung CSC have been identified, including CD133 and CD44. In addition, expression and/or activity of the cytoplasmic enzyme aldehyde dehydrogenase ALDH and capacity of cells to exclude membrane permeable dyes (known as the 'side population') correlate with stem-like function in vitro and in vivo. Embryonic stem cell pathways such as Hedgehog, Notch and WNT may also be active in lung cancers stem cells and therefore may be therapeutically targetable for maintenance therapy in patients achieving a complete response to surgery, radiotherapy or chemotherapy. This paper will review the evidence regarding the existence and function of lung CSC in the context of the experimental and clinical evidence and discuss some ongoing controversies regarding this model.

Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

Non-small-cell lung cancer (NSCLC) is the most common cause of premature death among the malignant diseases worldwide. The current staging criteria do not fully capture the complexity of this disease. Molecular biology techniques, particularly gene expression microarrays, proteomics, and next-generation sequencing, have recently been developed to facilitate effectively its molecular classification. The underlying etiology, pathogenesis, therapeutics, and prognosis of NSCLC based on an improved molecular classification scheme may promote individualized treatment and improve clinical outcomes. This review focuses on the molecular classification of NSCLC based on gene expression microarray technology reported during the past decade, as well as their applications for improving the diagnosis, staging and treatment of NSCLC, including the discovery of prognostic markers or potential therapeutic targets. We highlight some of the recent studies that may refine the identification of NSCLC subtypes using novel techniques such as epigenetics, proteomics, or deep sequencing.

Erlotinib resistance in lung cancer: current progress and future perspectives

Lung cancer is the most common cancer in the world. Despite modern advancements in surgeries, chemotherapies, and radiotherapies over the past few years, lung cancer still remains a very difficult disease to treat. This has left the death rate from lung cancer victims largely unchanged throughout the past few decades. A key cause for the high mortality rate is the drug resistance that builds up for patients being currently treated with the chemotherapeutic agents. Although certain chemotherapeutic agents may initially effectively treat lung cancer patients, there is a high probability that there will be a reoccurrence of the cancer after the patient develops resistance to the drug. Erlotinib, the epidermal growth factor receptor (EGFR)-targeting tyrosine kinase inhibitor, has been approved for localized as well as metastatic non-small cell lung cancer where it seems to be more effective in patients with EGFR mutations. Resistance to erlotinib is a common observation in clinics and this review details our current knowledge on the subject. We discuss the causes of such resistance as well as innovative research to overcome it. Evidently, new chemotherapy strategies are desperately needed in order to better treat lung cancer patients. Current research is investigating alternative treatment plans to enhance the chemotherapy that is already offered. Better insight into the molecular mechanisms behind combination therapy pathways and even single molecular pathways may help improve the efficacy of the current treatment options.