Genomic copy number alterations associated with the early brain metastasis of non-small cell lung cancer

Actin Alpha 2, Smooth Muscle (ACTA2) Is Involved in the Migratory Potential of Malignant Gliomas, and Its Increased Expression at Recurrence Is a Significant Adverse Prognostic Factor

Malignant glioma is a highly invasive tumor, and elucidating the glioma invasion mechanism is essential for developing novel therapies. We aimed to highlight actin alpha 2, smooth muscle (ACTA2) as potential biomarkers of brain invasion and distant recurrence in malignant gliomas. Using the human malignant glioma cell line, U251MG, we generated ACTA2 knockdown (KD) cells treated with small interfering RNA, and the cell motility and proliferation of the ACTA2 KD group were analyzed. Furthermore, tumor samples from 12 glioma patients who underwent reoperation at the time of tumor recurrence were utilized to measure ACTA2 expression in the tumors before and after recurrence. Thereafter, we examined how ACTA2 expression correlates with the time to tumor recurrence and the mode of recurrence. The results showed that the ACTA2 KD group demonstrated a decline in the mean motion distance and proliferative capacity compared to the control group. In the clinical glioma samples, ACTA2 expression was remarkably increased in recurrent samples compared to the primary samples from the same patients, and the higher the change in ACTCA2 expression from the start to relapse, the shorter the progression-free survival. In conclusion, ACTA2 may be involved in distant recurrence in clinical gliomas.

Mutational and Transcriptional Characterization Establishes Prognostic Models for Resectable Lung Squamous Cell Carcinoma

Background

The prognosis of non-small cell lung cancer (NSCLC) patients has been comprehensively studied. However, the prognosis of resectable (stage I-IIIA) lung squamous cell carcinoma (LUSC) has not been thoroughly investigated at genomic and transcriptional levels.

Methods

Data of genomic alterations and transcriptional-level changes of 355 stage I-IIIA LUSC patients were downloaded from The Cancer Genome Atlas (TCGA) database, together with the clinicopathological information (training cohort). A validation cohort of 91 patients was retrospectively recruited. Data were analyzed and figures were plotted using the R software.

Results

Training cohort was established with 355 patients. TP53 (78%), TTN (68%), CSMD3 (39%), MUT16 (36%) and RYR2 (36%) were genes with the highest mutational frequency. BRINP3, COL11A1, GRIN2B, MUC5B, NLRP3 and TENM3 exhibited significant higher mutational frequency in stage III (P < 0.05). Patients with stage III also exhibited significantly higher tumor mutational burden (TMB) than those with stage I (P < 0.01). The mutational status of 10 genes were found to have significant stratification on patient prognosis. TMB at threshold of 25 percentile (TMB = 2.39 muts/Mb) also significantly stratified the patient prognosis (P = 0.0003). Univariate and multivariate analyses revealed TTN, ADGRB3, MYH7 and MYH15 mutational status and TMB as independent risk factors. Further analysis of transcriptional profile revealed many significantly up- and down-regulated genes, and multivariate analysis found the transcriptional levels of seven genes as independent risk factors. Significant factors from the multivariate analyses were used to establish a Nomogram model to quantify the risk in prognosis of individual LUSC patients. The model was validated with a cohort containing 91 patients, which showed good predicting efficacy and consistency.

Conclusion

The influencing factors of prognosis of stage I-III LUSC patients have been revealed. Risk factors including gender, T stage, cancer location, and the mutational and transcriptional status of several genes were used to establish a Nomogram model to assess the patient prognosis. Subsequent validation proved its effectiveness.

Characterizing and Targeting Genes Regulated by Transcription Factor MYBL2 in Lung Adenocarcinoma Cells

Overexpression of MYBL2 is associated with poor survival of lung adenocarcinoma patients, but the molecular mechanism by which it regulates transcription and carcinogenesis has not yet been elucidated. In this study, we performed ChIP-seq using an MYBL2-targeted antibody and discovered that MYBL2 primarily binds to the promoters of highly expressed genes in lung adenocarcinoma cells. Using a knockdown experiment of MYBL2 and global transcriptome profiling, we identified that over a thousand genes are dysregulated by MYBL2, and MYBL2 acts as a transcriptional activator in lung adenocarcinoma cells. Moreover, we revealed that the binding sites of FOXM1 are largely shared with MYBL2 binding sites, and genes involved in cell cycle phase transitions are regulated by these transcription factors. We furthermore investigated the effect of a previously reported FOXM1 inhibitor, FDI-6, in lung adenocarcinoma cells. We demonstrated that FDI-6 decreases the proliferation of lung adenocarcinoma cells and inhibits the activities of FOXM1 as well as MYBL2. Moreover, we found that genes involved in cell death and cell cycle are inhibited by FDI-6. Overall, our findings suggest that MYBL2 and FOXM1 activate cell cycle genes together, acting as oncogenic transcription factors in lung adenocarcinoma cells, and they are potential treatment targets for the disease.

Systemic treatment of brain metastases in non-small cell lung cancer

Brain metastases (BrMs) are associated with significant morbidity and are found in up to 50% of patients with advanced non-small cell lung cancer (NSCLC). Most of the literature focuses on symptomatic BrMs, with a lack of baseline brain imaging in asymptomatic patients. Unfortunately, much of the data on local treatments with or without systemic treatment is retrospective. Clinical trials of systemic treatments largely exclude patients with BrMs. Chemotherapy is an active treatment for BrM with response rates in the brain similar to other sites of disease. Targeted systemic treatments in patients with driver mutations (EGFR and ALK-MET to date) have impressive central nervous system (CNS) penetrance and response rates. Unfortunately, no prospective data can currently guide the timings or modality of local therapies with systemic treatments in these patients who have a high incidence of CNS disease, but retrospective data suggest that early local therapies may give better intracranial progression-free survival (ICPFS). Recent immunotherapy trials have included patients with BrMs. These patients have largely been pre-treated with local therapies and are asymptomatic. Thus, the current standard is becoming, early local therapies before or in conjunction with immunotherapy agents. The approach seems to be safe. Prospective studies are needed in NSCLC BrMs patients to make sure any benefit from local therapies on the ICPFS and quality of life is not overlooked. Here we report what we think are reasonable conclusions from the available data and make suggestions for future clinical trials in the management of NSCLC BrMs.

Potential Molecular Signatures Predictive of Lung Cancer Brain Metastasis

Brain metastases are the most common tumors of the central nervous system (CNS). Incidence rates vary according to primary tumor origin, whereas the majority of the cerebral metastases arise from primary tumors in the lung (40-50%). Brain metastases from lung cancer can occur concurrently or within months after lung cancer diagnosis. Survival rates after lung cancer brain metastasis diagnosis remain poor, to an utmost of 10 months. Therefore, prevention of brain metastasis is a critical concern in order to improve survival among cancer patients. Although several studies have been made in order to disclose the genetic and molecular mechanisms associated with CNS metastasis, the precise mechanisms that govern the CNS metastasis from lung cancer are yet to be clarified. The ability to forecast, which patients have a higher risk of brain metastasis occurrence, would aid cancer management approaches to diminish or prevent the development of brain metastasis and improve the clinical outcome for such patients. In this work, we revise genetic and molecular targets suitable for prediction of lung cancer CNS disease.

Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes

In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels.

To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples.

We identified 85 “paradoxical” genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes.

Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status.

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response

We used next-generation sequencing to identify somatic alterations in multiple metastatic sites from an “exceptional responder” lung adenocarcinoma patient during his 7-yr course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ∼1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies showed increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy because of L869R mutation and increased migration because of ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a subclone metastasized early from the primary site and evolved independently in lymph nodes.

Phosphoglycerate mutase 1 promotes cancer cell migration independent of its metabolic activity

Phosphoglycerate mutase 1 (PGAM1) is a glycolytic enzyme that coordinates glycolysis and biosynthesis to promote cancer growth via its metabolic activity. Here, we report the discovery of a non-metabolic function of PGAM1 in promoting cancer metastasis. A proteomic study identified α-smooth muscle actin (ACTA2) as a PGAM1-associated protein. PGAM1 modulated actin filaments assembly, cell motility and cancer cell migration via directly interacting with ACTA2, which was independent of its metabolic activity. The enzymatically inactive H186R mutant retained its association with ACTA2, whereas 201-210 amino acids deleted PGAM1 mutant lost the interaction with ACTA2 regardless of intact metabolic activity. Importantly, PGAM1 knockdown decreased metastatic potential of breast cancer cells in vivo and PGAM1 and ACTA2 were jointly associated with the prognosis of breast cancer patients. Together, this study provided the first evidence revealing a non-metabolic function of PGAM1 in promoting cell migration, and gained new insights into the role of PGAM1 in cancer progression.

Advances in decoding breast cancer brain metastasis

The past decade has witnessed impressive advances in cancer treatment ushered in by targeted and immunotherapies. However, with significantly prolonged survival, upon recurrence, more patients become inflicted by brain metastasis, which is mostly refractory to all currently available therapeutic regimens. Historically, brain metastasis is an understudied area in cancer research, partly due to the dearth of appropriate experimental models that closely simulate the special biological features of metastasis in the unique brain environment and to the sophistication of techniques required to perform in-depth studies of the extremely complex and challenging brain metastasis. Yet, with increasing clinical demand for more effective treatment options, brain metastasis research has rapidly advanced in recent years. The present review spotlights the recent major progresses in basic and translational studies of brain metastasis with focuses on new animal models, novel imaging technologies, omics "big data" resources, and some new and exciting biological insights on brain metastasis.

The Current and Future Treatment of Brain Metastases

Brain metastases are the most common intracranial malignancy, accounting for significant morbidity and mortality in oncology patients. The current treatment paradigm for brain metastasis depends on the patient’s overall health status, the primary tumor pathology, and the number and location of brain lesions. Herein, we review the modern management options for these tumors, including surgical resection, radiotherapy, and chemotherapy. Recent operative advances, such as fluorescence, confocal microscopy, and brachytherapy, are highlighted. With an increased understanding of the pathophysiology of brain metastasis come increased future therapeutic options. Therapy targeted to specific tumor molecular pathways, such as those involved in blood–brain barrier transgression, cell–cell adhesion, and angiogenesis, are also reviewed. A personalized plan for each patient, based on molecular characterizations of the tumor that are used to better target radiotherapy and chemotherapy, is undoubtedly the future of brain metastasis treatment.

Number of cerebral lesions predicts freedom from new brain metastases after radiosurgery alone in lung cancer patients

Numerous patients with few brain metastases receive radiosurgery, either alone or in combination with whole-brain irradiation. The addition of whole-brain irradiation to radiosurgery reduces the rate of intracerebral failures, particularly the development of new cerebral lesions distant from those treated with radiosurgery. Less intracerebral failures mean less neurocognitive deficits. However, whole-brain irradiation itself may lead to a decline in neurocognitive functions. Therefore, a number of physicians have reservations with regard to adding whole-brain irradiation to radiosurgery. Prognostic factors that allow an estimation of the risk of developing new cerebral metastases can facilitate the decision regarding additional whole-brain irradiation. Since primary tumors show a different biology and clinical course, prognostic factors should be identified separately for each primary tumor leading to brain metastasis. The present study investigated 10 characteristics in a series of 98 patients receiving radiosurgery alone for 1-2 cerebral metastases from lung cancer, the most common primary tumor associated with brain metastasis. These characteristics included radiosurgery dose, age, gender, performance status, histology, number of cerebral lesions, maximum total diameter of cerebral lesions, main location of cerebral lesions, extracranial spread and interval from first diagnosis of lung cancer to administration of radiosurgery. On univariate analysis, the number of cerebral lesions prior to radiosurgery (1 vs. 2 lesions) was the only characteristic significantly associated with freedom from new brain metastases (P=0.002). In cases of 2 lesions, 73% of patients developed new cerebral lesions within 1 year. On multivariate analysis, the number of brain metastases remained significant (risk ratio, 2.46; 95% confidence interval, 1.34-4.58; P=0.004). Given the high rates of new cerebral lesions in patients with 2 brain metastases, these patients should be strongly considered for additional whole-brain irradiation.

Concomitant expression of far upstream element (FUSE) binding protein (FBP) interacting repressor (FIR) and its splice variants induce migration and invasion of non-small cell lung cancer (NSCLC) cells

Transcription factors integrate a variety of oncogenic input information, facilitate tumour growth and cell dissemination, and therefore represent promising therapeutic target structures. Because over-expression of DNA-interacting far upstream element binding protein (FBP) supports non-small cell lung cancer (NSCLC) migration, we asked whether its repressor, FBP-interacting repressor (FIR) is functionally inactivated and how FIR might affect NSCLC cell biology. Different FIR splice variants were highly expressed in the majority of NSCLCs, with the highest levels in tumours carrying genomic gains of chromosome 8q24.3, which contained the FIR gene locus. Nuclear FIR expression was significantly enriched at the invasion front of primary NSCLCs, but this did not correlate with tumour cell proliferation. FIR accumulation was associated with worse patient survival and tumour recurrence; in addition, FIR over-expression significantly correlated with lymph node metastasis in squamous cell carcinomas (SCCs). In vitro, we applied newly developed methods and modelling approaches for the quantitative and time-resolved description of the pro-migratory and pro-invasive capacities of SCC cells. siRNA-mediated silencing of all FIR variants significantly reduced the speed and directional movement of tumour cells in all phases of migration. Furthermore, sprouting efficiency and single cell invasiveness were diminished following FIR inhibition. Interestingly, the silencing of FIR isoforms lacking exon 2 (FIR(Δexon2)) alone was sufficient to reduce lateral migration and invasion. In summary, by using scale-spanning data derived from primary human tissues, quantitative cellular analyses and mathematical modelling, we have demonstrated that concomitant over-expression of FIR and its splice variants drives NSCLC migration and dissemination.

Estimation of the Survival of Patients With Lung Squamous Cell Carcinoma Using Genomic Copy Number Aberrations

BACKGROUND

Estimation of the survival of patients with lung squamous cell carcinoma (SCC) on the basis of histopathology is inadequate. The aim of this study was to identify genomic regions with potential value for estimating the prognosis of these patients.

PATIENTS AND METHODS

Depending on their survival time, 100 patients with primary lung SCC were separated into high- or low-risk prognostic groups, and their copy number aberrations (CNAs) were analyzed using array-comparative genomic hybridization (array-CGH).

RESULTS

We identified 123 CNA regions that were significantly associated with survival. Among these regions, some have been reported previously (eg, amplifications of 8p12, 3q27.1, and loss of 9p21.3 and 13q34) but others have never been reported. For example, gains of 3q27.1, 5p13.2, and 5p13.3 were found to be associated with a favorable prognosis, but patients harboring gains of 11q23.3, 11q13.1, and 14q32.3, and deletions of 3p21.3 and 9p21.3 tended to have poor survival. Among the 123 CNA regions, 41 were further selected to construct a survival estimation model that could effectively separate SCC patients into high- or low-risk groups with an accuracy of 92%, sensitivity of 90%, and specificity of 94%. The results of the array-CGH were further validated in an independent cohort of 45 formalin-fixed, paraffin-embedded specimens using real-time polymerase chain reaction.

CONCLUSION

A number of CNA regions were found to be associated with the survival of SCC patients, and we were able to construct a model to estimate prognosis on the basis of these regions. Assessment of these CNAs could potentially assist in clinical decision-making regarding adjuvant therapy after surgery.

Acquirement of DNA copy number variations in non-small cell lung cancer metastasis to the brain

Brain metastasis is a major complication of non-small cell lung cancer (NSCLC) and leads to most of the mortality of this disease. However, the biological mechanisms and molecular features in brain metastasis of NSCLC are poorly understood. In the present study, we compared whole-genome copy number variations (CNVs) between a primary lung adenocarcinoma and secondary metastatic brain lesion from the same patient using array comparative genomic hybridization (aCGH). The number of CNV regions was markedly higher in the secondary metastatic tumor than the primary tumor in the lung. In detail, the common CNVs in both tumors included gains of 7p22, 7p12-p11, 7q11, 7q22, 21q22, and 19q13; gains of 1p33-p34, 1q22, 5p13 and 14q11 whereas losses of 3p, 4q31, 5q, 11p15, Xp21-p22 and Xq21 were identified only in the secondary lesion. Gene Ontology enrichment analysis revealed that the genes with amplified copy numbers in both tumors were related to such processes as DNA replication and mismatch repair. Genes only amplified in the metastatic tumor were enriched in processes that include leukocyte migration and organ development, and genes with a lower copy number in the secondary tumor included the processes of proteolysis regulation, negative regulation of cell proliferation and cell adhesion. These findings provided new insight into the genomic mechanism of the spread of lung adenocarcinoma to the brain, and the candidate genes identified serve as novel indicators or putative targets in NSCLC brain metastasis.

affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

Background

The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies.

Results

We illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling.

Conclusion

Both examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0608-y) contains supplementary material, which is available to authorized users.

Molecular determinants of lung cancer metastasis to the central nervous system

Lung cancer remains the leading cause of cancer-related mortality worldwide. The propensity for metastasis to the central nervous system (CNS) is a major clinical hurdle contributing to the low five-year survival rate of advanced disease. CNS metastases significantly outnumber primary brain tumors and carry a dismal prognosis in part due to the inability of therapeutic agents to cross the blood brain barrier. Standard treatment using radiation has been largely ineffective in improving mortality, suggesting the need for new agents targeting the critical metastatic drivers. The genetic and molecular events governing CNS metastasis from the lung are poorly understood at this time. This review highlights genetic events associated with CNS dissemination from the lung and molecular mechanisms associated with CNS metastasis. In vivo model systems that faithfully recapitulate escape from the lung and colonization of the CNS are described as tools for understanding the metastatic phenotype and for testing new therapeutic agents. A deeper understanding of the mechanisms of lung cancer metastasis to the CNS is needed to elucidate novel therapeutic avenues towards the improvement of the mortality associated with advanced stage lung cancer.

Value of oncogenes for the prediction of brain metastases at initial diagnosis: a review of published data

Identifying cancer patients who are at high risk of developing brain metastases at initial diagnosis and applying effective intervention or monitoring strategies is of vital importance. Recent advances in the biology of brain metastases revealed that some oncogenes from primary tumors may be potential markers for identifying cancer patients likely to metastasize to the brain. We here summarize data on the mechanisms of brain metastases supporting the involvement of oncogene changes in the brain metastatic evolution. We also review the available evidence on clinical studies of oncogenes in the prediction of cancer patients with high incidence of brain metastases.

Alpha-smooth muscle actin (ACTA2) is required for metastatic potential of human lung adenocarcinoma

PURPOSE

Metastatic relapse of primary lung cancer leads to therapeutic resistance and unfavorable clinical prognosis; therefore, identification of key molecules associated with metastatic conversion has significant clinical implications. We previously identified a link between early brain metastasis of lung adenocarcinoma and amplification of the α-smooth muscle actin (ACTA2) gene. The aim of present study was to investigate the prognostic and functional significance of ACTA2 expression in cancer cells for the metastatic potential of lung adenocarcinomas.

EXPERIMENTAL DESIGN

ACTA2 expression was analyzed in tumor cells from 263 patients with primary lung adenocarcinomas by immunohistochemistry, and was correlated with clinicopathologic parameters. The expression of ACTA2 in human lung adenocarcinoma cells was modulated with short hairpin RNAs (shRNA) and siRNAs specifically targeting ACTA2.

RESULTS

The patients with lung adenocarcinomas with high ACTA2 expression in tumor cells showed significantly enhanced distant metastasis and unfavorable prognosis. ACTA2 downregulation remarkably impaired in vitro migration, invasion, clonogenicity, and transendothelial penetration of lung adenocarcinoma cells without affecting proliferation. Consistent with the in vitro results, depletion of ACTA2 in human lung adenocarcinoma PC14PE6 cells significantly reduced their metastatic potential without altering their tumorigenic potential. Expression of c-MET and FAK in lung adenocarcinoma cells was also reduced by ACTA2-targeting siRNAs and shRNAs, and was accompanied by a loss of mesenchymal characteristics.

CONCLUSIONS

These findings indicate that ACTA2 regulates c-MET and FAK expression in lung adenocarcinoma cells, which positively and selectively influence metastatic potential. Therefore, ACTA2 could be a promising prognostic biomarker and/or therapeutic target for metastatic lung adenocarcinoma.

The role of astrocytes in CNS tumors: pre-clinical models and novel imaging approaches

Brain metastasis is a significant clinical problem, yet the mechanisms governing tumor cell extravasation across the blood-brain barrier (BBB) and CNS colonization are unclear. Astrocytes are increasingly implicated in the pathogenesis of brain metastasis but in vitro work suggests both tumoricidal and tumor-promoting roles for astrocyte-derived molecules. Also, the involvement of astrogliosis in primary brain tumor progression is under much investigation. However, translation of in vitro findings into in vivo and clinical settings has not been realized. Increasingly sophisticated resources, such as transgenic models and imaging technologies aimed at astrocyte-specific markers, will enable better characterization of astrocyte function in CNS tumors. Techniques such as bioluminescence and in vivo fluorescent cell labeling have potential for understanding the real-time responses of astrocytes to tumor burden. Transgenic models targeting signaling pathways involved in the astrocytic response also hold great promise, allowing translation of in vitro mechanistic findings into pre-clinical models. The challenging nature of in vivo CNS work has slowed progress in this area. Nonetheless, there has been a surge of interest in generating pre-clinical models, yielding insights into cell extravasation across the BBB, as well as immune cell recruitment to the parenchyma. While the function of astrocytes in the tumor microenvironment is still unknown, the relationship between astrogliosis and tumor growth is evident. Here, we review the role of astrogliosis in both primary and secondary brain tumors and outline the potential for the use of novel imaging modalities in research and clinical settings. These imaging approaches have the potential to enhance our understanding of the local host response to tumor progression in the brain, as well as providing new, more sensitive diagnostic imaging methods.

Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value

We performed a genome wide analysis of 164 urothelial carcinoma samples and 27 bladder cancer cell lines to identify copy number changes associated with disease characteristics, and examined the association of amplification events with stage and grade of disease. Multiplex inversion probe (MIP) analysis, a recently developed genomic technique, was used to study 80 urothelial carcinomas to identify mutations and copy number changes. Selected amplification events were then analyzed in a validation cohort of 84 bladder cancers by multiplex ligation-dependent probe assay (MLPA). In the MIP analysis, 44 regions of significant copy number change were identified using GISTIC. Nine gene-containing regions of amplification were selected for validation in the second cohort by MLPA. Amplification events at these 9 genomic regions were found to correlate strongly with stage, being seen in only 2 of 23 (9%) Ta grade 1 or 1–2 cancers, in contrast to 31 of 61 (51%) Ta grade 3 and T2 grade 2 cancers, p<0.001. These observations suggest that analysis of genomic amplification of these 9 regions might help distinguish non-invasive from invasive urothelial carcinoma, although further study is required. Both MIP and MLPA methods perform well on formalin-fixed paraffin-embedded DNA, enhancing their potential clinical use. Furthermore several of the amplified genes identified here (ERBB2, MDM2, CCND1) are potential therapeutic targets.