The relation between c-myc expression and interferon sensitivity in uveal melanoma

Identification of Prognostic Fatty Acid Metabolism lncRNAs and Potential Molecular Targeting Drugs in Uveal Melanoma

Background

The aim of this study was to identify prognostic fatty acid metabolism lncRNAs and potential molecular targeting drugs in uveal melanoma through integrated bioinformatics analysis.

Methods

In the present study, we obtained the expression matrix of 309 FAM-mRNAs and identified 225 FAM-lncRNAs by coexpression network analysis. We then performed univariate Cox analysis, LASSO regression analysis, and cross-validation and finally obtained an optimized UVM prognosis prediction model composed of four PFAM-lncRNAs (AC104129.1, SOS1-IT1, IDI2-AS1, and DLGAP1-AS2).

Results

The survival curves showed that the survival time of UVM patients in the high-risk group was significantly lower than that in the low-risk group in the train cohort, test cohort, and all patients in the prognostic prediction model (P < 0.05). We further performed risk prognostic assessment, and the results showed that the risk scores of the high-risk group in the train cohort, test cohort, and all patients were significantly higher than those of the low-risk group (P < 0.05), patient survival decreased and the number of deaths increased with increasing risk scores, and AC104129.1, SOS1-IT1, and DLGAP1-AS2 were high-risk PFAM-lncRNAs, while IDI2-AS1 were low-risk PFAM-lncRNAs. Afterwards, we further verified the accuracy and the prognostic value of our model in predicting prognosis by PCA analysis and ROC curves.

Conclusion

We identified 24 potential molecularly targeted drugs with significant sensitivity differences between high- and low-risk UVM patients, of which 13 may be potential targeted drugs for high-risk patients. Our findings have important implications for early prediction and early clinical intervention in high-risk UVM patients.

Using Flow Cytometry to Study Myc's Role in Shaping the Tumor Immune Microenvironment

Myc is deregulated in most-if not all-cancers, and it not only promotes tumor progression by inducing cell proliferation but is also responsible for tumor immune evasion. In a nutshell, MYC promotes the development of tumor-associated macrophages, impairs the cellular response to interferons, induces the expression of immunosuppressive molecules, and excludes tumor infiltrating lymphocytes (TILs) from the tumor site. Based on the insights into the role of MYC in promoting and regulating immune evasion by cancer cells, it is of special interest to study the different immune cell populations infiltrating the tumors. MYC inhibition has emerged as a potential new strategy for the treatment of cancer, directly inhibiting tumor progression while also counteracting the immunosuppressive tumor microenvironment, allowing an optimal anti-tumor immune response. Hence, this chapter describes a flow cytometry-based method to study the different immune cell subsets infiltrating the tumor by combining surface, cytoplasmic, and nuclear multicolor protein stainings.

Knockdown of DEAD-box RNA helicase 52 (DDX52) suppresses the proliferation of melanoma cells in vitro and of nude mouse xenografts by targeting c-Myc

The ATP-dependent protein DEAD-box RNA helicase 52 (DDX52) is an important regulator in RNA biology and has been implicated in the development of prostate and lung cancer. However, its biological functions and clinical importance in malignant melanoma (MM) are still unclear. Understanding the potential mechanism underlying the regulation of MM progression by DDX52 might lead to novel therapeutic strategies. The aim of the present study was to investigate the role of DDX52 in the regulation of MM progression and its clinical relevance. DDX52 expression in normal and MM tissues was evaluated by GEO analysis and immunohistochemistry. The effects of DDX52 on cell growth were evaluated in MM cells with downregulated DDX52 expression. In this study, we found that DDX52 was markedly overexpressed in MM tissues compared with nontumor tissues and was associated with shorter overall survival in patients; therefore, DDX52 might be a prognostic marker in MM. Downregulation of DDX52 expression in the MM cell lines A2058 and MV3 markedly inhibited cell proliferation and colony formation. Additionally, knockdown of DDX52 in MM cells caused significant regression of established tumors in nude mice and delayed the onset time. Moreover, downregulation of DDX52 markedly suppressed c-Myc mRNA and protein expression, and an RNA immunoprecipitation assay confirmed the association between DDX52 and c-Myc. Restoration of c-Myc expression partly rescued the effects of DDX52 deficiency in MM cells. In conclusion, our study found that DDX52 mediated oncogenesis by promoting the transcriptional activity of c-Myc and could be a therapeutic target in MM.

N-Myc expression enhances the oncolytic effects of vesicular stomatitis virus in human neuroblastoma cells

N-myc oncogene amplification is associated but not present in all cases of high-risk neuroblastoma (NB). Since oncogene expression could often modulate sensitivity to oncolytic viruses, we wanted to examine if N-myc expression status would determine virotherapy efficacy to high-risk NB. We showed that induction of exogenous N-myc in a non-N-myc-amplified cell line background (TET-21N) increased susceptibility to oncolytic vesicular stomatitis virus (mutant VSVΔM51) and alleviated the type I IFN-induced antiviral state. Cells with basal N-myc, on the other hand, were less susceptible to virus-induced oncolysis and established a robust IFN-mediated antiviral state. The same effects were also observed in NB cell lines with and without N-myc amplification. Microarray analysis showed that N-myc overexpression in TET-21N cells downregulated IFN-stimulated genes (ISGs) with known antiviral functions. Furthermore, virus infection caused significant changes in global gene expression in TET-21N cells overexpressing N-myc. Such changes involved ISGs with various functions. Therefore, the present study showed that augmented susceptibility to VSVΔM51 by N-myc at least involves downregulation of ISGs with antiviral functions and alleviation of the IFN-stimulated antiviral state. Our studies suggest the potential utility of N-myc amplification/overexpression as a predictive biomarker of virotherapy response for high-risk NB using IFN-sensitive oncolytic viruses.

Cystathionase mediates senescence evasion in melanocytes and melanoma cells

The development of malignant melanoma is a highly complex process, which is still poorly understood. A majority of human melanomas are found to express a few oncogenic proteins, such as mutant RAS and BRAF variants. However, these oncogenes are also found in nevi, and it is now a well-accepted fact that their expression alone leads to senescence. This renders the understanding of senescence escape mechanisms an important point to understand tumor development. Here, we approached the question of senescence evasion by expressing the transcription factor v-myc myelocytomatosis viral oncogene homolog (c-MYC), which is known to act synergistically with many oncogenes, in melanocytes. We observed that MYC drives the evasion of reactive-oxygen stress-induced melanocyte senescence, caused by activated receptor tyrosine kinase signaling. Conversely, MIZ1, the growth suppressing interaction partner of MYC, is involved in mediating melanocyte senescence. Both, MYC overexpression and Miz1 knockdown led to a strong reduction of endogenous reactive-oxygen species (ROS), DNA damage and senescence. We identified the cystathionase (CTH) gene product as mediator of the ROS-related MYC and MIZ1 effects. Blocking CTH enzymatic activity in MYC-overexpressing and Miz1 knockdown cells increased intracellular stress and senescence. Importantly, pharmacological inhibition of CTH in human melanoma cells also reconstituted senescence in the majority of cell lines, and CTH knockdown reduced tumorigenic effects such as proliferation, H2O2 resistance and soft agar growth. Thus, we identified CTH as new MYC target gene with an important function in senescence evasion.

Sequence analysis, expression patterns and transcriptional regulation of mouse Ifrg15 during preimplantation embryonic development

Ifrg15 is a newly identified interferon alpha responsive gene and is implicated in a wide variety of physiological roles in mammals. In the present study, multiple alignments of the deduced amino acids of 10 eutherian mammalian IFRG15/Ifrg15s isolated from open genomic database revealed that they were highly conserved. Real-time PCR showed that mouse Ifrg15 mRNA was expressed in MII stage oocytes and preimplantation embryos, and its highest value peaked at the stage of mouse blastocysts. To understand the effect of three development-related genes on the promoter activity of mouse Ifrg15, promoter analysis using luciferase assays in COS-7 cells were performed. The results showed that the transcription of mouse Ifrg15 was suppressed by Oct4 and Nanog when transfected with the longest Ifrg15 promoter reporter gene. After the relatively shorter promoters were co-transfected with Oct4, c-Myc and Nanog, the relative luciferase activities of Ifrg15 were gradually increased. These in vitro results data and expression profiles of Ifrg15 as revealed by real-time PCR partly indicated that Ifrg15 transcription might be either potentially regulated or dependent on the post-transcriptional effects of IFN-α mediated by the three genes indirectly. Our data suggested that the mouse Ifrg15 might interact with these key development-related genes and play significant roles on the mouse preimplantation embryos development, especially for the development of mouse blastocysts.

Acetaminophen modulates the transcriptional response to recombinant interferon-beta

Background

Recombinant interferon treatment can result in several common side effects including fever and injection-site pain. Patients are often advised to use acetaminophen or other over-the-counter pain medications as needed. Little is known regarding the transcriptional changes induced by such co-administration.

Methodology/Principal Findings

We tested whether the administration of acetaminophen causes a change in the response normally induced by interferon-β treatment. CD-1 mice were administered acetaminophen (APAP), interferon-β (IFN-β) or a combination of IFN-β+APAP and liver and serum samples were collected for analysis. Differential gene expression was determined using an Agilent 22 k whole mouse genome microarray. Data were analyzed by several methods including Gene Ontology term clustering and Gene Set Enrichment Analysis. We observed a significant change in the transcription profile of hepatic cells when APAP was co-administered with IFN-β. These transcriptional changes included a marked up-regulation of genes involved in signal transduction and cell differentiation and down-regulation of genes involved in cellular metabolism, trafficking and the IκBK/NF-κB cascade. Additionally, we observed a large decrease in the expression of several IFN-induced genes including Ifit-3, Isg-15, Oasl1, Zbp1 and predicted gene EG634650 at both early and late time points.

Conclusions/Significance

A significant change in the transcriptional response was observed following co-administration of IFN-β+APAP relative to IFN-β treatment alone. These results suggest that administration of acetaminophen has the potential to modify the efficacy of IFN-β treatment.

c-MYC impairs immunogenicity of human B cells

Deregulation of c-myc expression through chromosomal translocation is essential in the pathogenesis of Burkitt's lymphoma (BL). A characteristic feature of BL cells, compared to Epstein-Barr Virus (EBV)-immortalized B cells, is their lack of immunogenicity. To study the contribution of EBV genes and of the c-MYC protein to this phenotype, we have generated a conditional B cell system in which the viral proliferation program and expression of c-myc can be regulated independently of each other. In cells proliferating due to exogenous c-myc overexpression, the cell surface phenotype, the pattern of proliferation in single cell suspension, and the immunological characteristics of BL cells could be completely recapitulated. Yet, it had remained open whether nonimmunogenicity is the default phenotype when EBNA2 and LMP1 are switched off, or whether c-MYC actively contributes to immunosuppression. We provide evidence also for the latter by showing that c-MYC down-regulates genes of the NF-kappaB and interferon pathway in a dose-dependent fashion. c-MYC acts at at least two different levels, the level of interferon induction as well as at the level of action of type I and type II interferons on their respective target promoters. c-MYC does not block the interferon pathway completely, it shifts the balance and increases the threshold of interferon induction and action.

Epigenetics of cutaneous melanoma

Tumorigenesis is traditionally thought to be caused by the imbalance between oncogenes and tumor-suppressor genes. Epigenetics is a recently described phenomenon that uses an alternative mechanism to explain the transcriptional inactivation of tumor-suppressor genes predominantly by hypermethylation of the promoter regions. Hypermethylation of these regions has been described extensively in many neoplasms, including cutaneous melanoma. Histone modification, primarily by acetylation and deacetylation, is a current potential target for melanoma therapy, but more research is required to understand the mechanisms involved and the therapeutic effectiveness of regimens involving these agents. These mechanisms not only are important for understanding the origin and progression of neoplasms but also have important potential therapeutic implications. Understanding the epigenetic mechanisms involved in melanoma can provide valuable information with significant implications in diagnosis, treatment, and prevention.

The sodium pump alpha1 sub-unit: a disease progression-related target for metastatic melanoma treatment

Melanomas remain associated with dismal prognosis because they are naturally resistant to apoptosis and they markedly metastasize. Up-regulated expression of sodium pump α sub-units has previously been demonstrated when comparing metastatic to non-metastatic melanomas. Our previous data revealed that impairing sodium pump α1 activity by means of selective ligands, that are cardiotonic steroids, markedly impairs cell migration and kills apoptosis-resistant cancer cells. The objective of this study was to determine the expression levels of sodium pump α sub-units in melanoma clinical samples and cell lines and also to characterize the role of α1 sub-units in melanoma cell biology. Quantitative RT-PCR, Western blotting and immunohistochemistry were used to determine the expression levels of sodium pump α sub-units. In vitro cytotoxicity of various cardenolides and of an anti-α1 siRNA was evaluated by means of MTT assay, quantitative videomicroscopy and through apoptosis assays. The in vivo activity of a novel cardenolide UNBS1450 was evaluated in a melanoma brain metastasis model. Our data show that all investigated human melanoma cell lines expressed high levels of the α1 sub-unit, and 33% of human melanomas displayed significant α1 sub-unit expression in correlation with the Breslow index. Furthermore, cardenolides (notably UNBS1450; currently in Phase I clinical trials) displayed marked anti-tumour effects against melanomas in vitro. This activity was closely paralleled by decreases in cMyc expression and by increases in apoptotic features. UNBS1450 also displayed marked anti-tumour activity in the aggressive human metastatic brain melanoma model in vivo. The α1 sodium pump sub-unit could represent a potential novel target for combating melanoma.

Epigenetic events in malignant melanoma

Irreversible changes in the DNA sequence, including chromosomal deletions or amplification, activating or inactivating mutations in genes, have been implicated in the development and progression of melanoma. However, increasing attention is being turned towards the participation of 'epigenetic' events in melanoma progression that do not affect DNA sequence, but which nevertheless may lead to stable inherited changes in gene expression. Epigenetic events including histone modifications and DNA methylation play a key role in normal development and are crucial to establishing the correct program of gene expression. In contrast, mistargeting of such epigenetic modifications can lead to aberrant patterns of gene expression and loss of anti-cancer checkpoints. Thus, to date at least 50 genes have been reported to be dysregulated in melanoma by aberrant DNA methylation and accumulating evidence also suggests that mistargetting of histone modifications and altered chromatin remodeling activities will play a key role in melanoma. This review gives an overview of the many different types of epigenetic modifications and their involvement in cancer and especially in melanoma development and progression.

Combined immunologic and anti-angiogenic therapy reduces hepatic micrometastases in a murine ocular melanoma model

PURPOSE

To evaluate the combined effect of neoadjuvant intracameral interferon alpha -2b and adjuvant low-dose angiostatin in reducing the number of hepatic micrometastases in a murine model of ocular melanoma.

METHODS

The posterior compartments of the right eyes of C57BL6 mice were inoculated with 5 x 10(5) cells/2.5 microl of cells from the Queens, B16F10, or B16LS9 melanoma cell lines. The right eyes were enucleated at 7 days, and the mice were sacrificed at 28 days postinoculation, respectively. Hepatic micrometastases were counted. There were four treatment groups (n = 15 each) for each cell line as follows: group 1, intraperitoneal injections of 20 KIU interferon alpha -2b for 4 days prior to enucleation; group 2, intramuscular injections of 100 microl 0.1 microg/microl murine angiostatin every day for 14 days starting on day 1 after enucleation; group 3, treatment of group 1 and group 2 combined; group 4, intraperitoneal and intramuscular injections of equal volumes of phosphate-buffered saline (PBS) (control group).

RESULTS

Results showed decreased micrometastases for groups 1 through 3 compared with group 4, with the greatest reduction in group 3 (p < 0.006).

CONCLUSIONS

This study suggests that combined neoadjuvant interferon alpha -2b and adjuvant low-dose angiostatin therapy act synergistically to decrease hepatic micrometastases in a murine ocular melanoma model.

Defining the mechanism by which IFN-β dowregulates c-myc expression in human melanoma cells: pivotal role for human polynucleotide phosphorylase (hPNPaseold-35)

Type I interferons (IFN-alpha/-beta) are capable of suppressing c-myc mRNA expression by modulating post-transcriptional processing. However, the molecular mechanism of this phenomenon is poorly understood. We previously established that human polynucleotide phosphorylase (hPNPase(old-35)), a type I IFN-inducible 3',5' exoribonuclease involved in mRNA degradation, induces G1 cell cycle arrest and eventually apoptosis by specifically degrading c-myc mRNA. We now demonstrate a close association between IFN-beta-induced hPNPase(old-35) upregulation and c-myc downregulation in human melanoma cells. Employing stable melanoma cell clones expressing hPNPase(old-35) small inhibitory RNA, we demonstrate that hPNPase(old-35) is a key molecule coupled with IFN-beta-mediated downregulation of c-myc mRNA. Inhibition of hPNPase(old-35) or overexpression of c-myc protects melanoma cells from IFN-beta-mediated growth inhibition, emphasizing the importance of hPNPase(old-35) upregulation and consequent c-myc downregulation in IFN-beta-induced growth inhibition and apoptosis induction. In these contexts, targeted overexpression of hPNPase(old-35) might be a novel therapeutic strategy for c-myc-overexpressing and IFN-resistant tumors, such as melanomas.

Proteome analysis of a human uveal melanoma primary cell culture by 2-DE and MS

We present here the first proteomics analysis of uveal melanoma (UM) cells. These cells represent a good model for the identification of polypeptide markers, which could be developed as diagnostic tools. UM is the most common primary intraocular tumour in adults. In contrast to other cancers, the survival rate of patients with this malignancy has changed little over the past few decades; a better understanding of the molecular biology of UM oncogenesis and metastasis is needed to build the basis for the identification of novel drug targets. In the study presented here, proteins from a UM primary cell culture were separated by 2-DE using a pI 3-10 gradient; 270 spots were analysed by LC-MS/MS, identifying 683 proteins derived from 393 different genes. Of those, 69 (18%) are related to cancer processes involving cell division, proliferation, invasion, metastasis, oncogenesis, drug resistance and others. To our knowledge, 96% of the proteins identified, including 16 hypothetical proteins, have never been reported in UM before. This study represents the first step towards the establishment of a UM protein database as a valuable resource for the study of this malignancy.