Epigenetic Silencing of DKK3 in medulloblastoma.

Medulloblastoma (MB) is a malignant pediatric brain tumor arising in the cerebellum consisting of four distinct subgroups: WNT, SHH, Group 3 and Group 4, which exhibit different molecular phenotypes. We studied the expression of Dickkopf (DKK) 1-4 family genes, inhibitors of the Wnt signaling cascade, in MB by screening 355 expression profiles derived from four independent datasets. Upregulation of DKK1, DKK2 and DKK4 mRNA was observed in the WNT subgroup, whereas DKK3 was downregulated in 80% MBs across subgroups with respect to the normal cerebellum (p < 0.001). Since copy number aberrations targeting the DKK3 locus (11p15.3) are rare events, we hypothesized that epigenetic factors could play a role in DKK3 regulation. Accordingly, we studied 77 miRNAs predicting to repress DKK3; however, no significant inverse correlation between miRNA/mRNA expression was observed. Moreover, the low methylation levels in the DKK3 promoters (median: 3%, 5% and 5% for promoter 1, 2 and 3, respectively) excluded the downregulation of gene expression by methylation. On the other hand, the treatment of MB cells with Trichostatin A (TSA), a potent inhibitor of histone deacetylases (HDAC), was able to restore both DKK3 mRNA and protein. In conclusion, DKK3 downregulation across all MB subgroups may be due to epigenetic mechanisms, in particular, through chromatin condensation.

HOXA7, 9, and 10 are methylation targets associated with aggressive behavior in meningiomas.

Meningioma is one of the most common intracranial tumors and is graded according to the World Health Organization (WHO) classification system. Although these tumors are often surgically curable, a malignant behavior also may occur in meningiomas with benign histologic profiles (WHO I). Thus, it is mandatory to identify biomolecular parameters useful to improve the classification of these tumors. HOXA genes belong to the HOX gene family that encodes homeodomain-containing transcription factors known to be key regulators of embryonic development, involved in cell growth and differentiation and in the development of the central nervous system. Moreover, altered HOXA gene methylation and expression have prognostic value in many tumors. The purpose of this study was to determine whether the level of HOXA3, 7, 9, and 10 methylation in meningioma could be a biomarker linked to the pathologic characteristics of the tumor. We found that methylation levels of HOXA7, 9, and 10 in 131 meningioma samples were significantly higher in WHO II/III tumors compared with WHO I tumors. Moreover, in newly diagnosed WHO I meningiomas, HOXA7, 9, and 10 methylation was significantly lower than in WHO I samples derived from recurring tumors, and multiple meningiomas presented significantly higher HOXA 10 methylation with respect to solitary meningiomas. This study demonstrates that HOXA7, 9, and 10 are methylation targets in meningioma, associated with histopathology and clinical aggressiveness parameters. Our findings suggest the possibility of detecting the malignancy potential of meningioma by assessing the HOXA methylation level and identifying patients at higher risk who could benefit from closer follow-up or postoperative adjuvant treatments.

Quantitative methylation analysis of HOXA3, 7, 9, and 10 genes in glioma: association with tumor WHO grade and clinical outcome.

PURPOSE: The purpose of this study was to determine whether specific HOXA epigenetic signatures could differentiate glioma with distinct biological, pathological, and clinical characteristics. METHODS: We evaluated HOXA3, 7, 9, and 10 methylation in 63 glioma samples by MassARRAY and pyrosequencing. RESULTS: We demonstrated the direct statistical correlation between the level of methylation of all HOXA genes examined and WHO grading. Moreover, in glioblastoma patients, higher level of HOXA9 and HOXA10 methylation significantly correlated with increased survival probability (HOXA9-HR: 0.36, P = 0.007; HOXA10-HR: 0.46, P = 0.045; combined HOXA9 and 10-HR 0.28, P = 0.004). CONCLUSIONS: This study identifies HOXA3, 7, 9, and 10 as methylation targets mainly in high-grade glioma and hypermethylation of the HOXA9 and 10 as prognostic factor in glioblastoma patients. Our data indicate that these epigenetic changes may be biomarkers of clinically different subgroups of glioma patients that could eventually benefit from personalized therapeutic strategies.

A pyrosequencing assay for the quantitative methylation analysis of the PCDHB gene cluster, the major factor in neuroblastoma methylator phenotype.

Epigenetic alterations are hallmarks of cancer and powerful biomarkers, whose clinical utilization is made difficult by the absence of standardization and of common methods of data interpretation. The coordinate methylation of many loci in cancer is defined as 'CpG island methylator phenotype' (CIMP) and identifies clinically distinct groups of patients. In neuroblastoma (NB), CIMP is defined by a methylation signature, which includes different loci, but its predictive power on outcome is entirely recapitulated by the PCDHB cluster only. We have developed a robust and cost-effective pyrosequencing-based assay that could facilitate the clinical application of CIMP in NB. This assay permits the unbiased simultaneous amplification and sequencing of 17 out of 19 genes of the PCDHB cluster for quantitative methylation analysis, taking into account all the sequence variations. As some of these variations were at CpG doublets, we bypassed the data interpretation conducted by the methylation analysis software to assign the corrected methylation value at these sites. The final result of the assay is the mean methylation level of 17 gene fragments in the protocadherin B cluster (PCDHB) cluster. We have utilized this assay to compare the methylation levels of the PCDHB cluster between high-risk and very low-risk NB patients, confirming the predictive value of CIMP. Our results demonstrate that the pyrosequencing-based assay herein described is a powerful instrument for the analysis of this gene cluster that may simplify the data comparison between different laboratories and, in perspective, could facilitate its clinical application. Furthermore, our results demonstrate that, in principle, pyrosequencing can be efficiently utilized for the methylation analysis of gene clusters with high internal homologies.

Epigenetic mechanisms regulate ΔNP73 promoter function in human tonsil B cells.

ΔNp73 is an anti-apoptotic product of the TP73 gene whose function in the immune system has not been extensively studied. We analyzed human tonsil B cell subpopulations physically subdivided into resting or activated fractions and found ΔNp73 gene expression essentially in cells bearing features of activation. Moreover, and accordingly, both these fractions proved to be sensitive to treatment in culture with the polyclonal activator TPA that caused substantial increase in ΔNp73 mRNA and protein expression. We also analyzed the TP73 oncogenic-relevant internal promoter 2 (P2) and identified epigenetics as its major regulatory factor since active DNA and histone configurations strictly correlated with ΔNp73 expression upon activation by agents capable of loosening chromatin compaction. Finally, in line with the known TPA pathway, we found that nuclear proteins could bind a sequence corresponding to a unique AP1 site on promoter 2 selectively in the activated cell fraction. Our results suggest a ΔNp73 function in B cell immunity, indicate epigenetics as master TP73 P2 regulator, and point to AP1 site occupancy as playing an putative mechanistic role in this process.

Toward an epigenetic view of our musical mind.

We are transient beings, in a world of constantly changing culture. At home in the fields of Art and Science, seemingly capable of magnificent abstractions, humans have an intense need to externalize their insights. Music is an art and a highly transmissible cultural product, but we still have an incomplete understanding of how our musical experience shapes and is vividly retained within our brain, and how it affects our behavior. However, the developing field of social epigenetics is now helping us to describe how communication and emotion, prime hallmarks of music, can be linked to a transmissible, biochemical change.

Circulating Tumor Nucleic Acids: Perspective in Breast Cancer.

In 1940, it was demonstrated that free DNA could be identified in the bloodstream. It was later shown that circulating nucleic acids (CNA), both DNA and RNA, are present in several neoplastic and non-neoplastic diseases, and that in cancer they originate mostly from the tumor. In this review, we discuss the potential application of CNA as a breast cancer biomarker for early diagnosis and patient evaluation. Most of the initial studies on CNA compared the levels of CNA in cancer patients and healthy individuals. To increase sensitivity and specificity, cancer-specific molecular alterations were then utilized. In this respect, epigenetic alterations and microRNA offer considerable advantages over mutations because of their easiness of detection. Epigenetic signatures, being early events of carcinogenesis, may also be valuable markers for screening purposes. Monitoring the follow-up of the patients is one of the most interesting applications of CNA-based assays, and it is reasonable to hypothesize that CNA may become a surrogate marker for circulating cancer cells in the prediction of patient outcome. Transferring these findings to the clinical practice is the next effort, and this will be possible when a 'common language' is defined to allow proper validation of these new markers.

Outcome prediction and risk assessment by quantitative pyrosequencing methylation analysis of the SFN gene in advanced stage, high-risk, neuroblastic tumor patients.

The aim of our study was to identify threshold levels of DNA methylation predictive of the outcome to better define the risk group of stage 4 neuroblastic tumor patients. Quantitative pyrosequencing analysis was applied to a training set of 50 stage 4, high risk patients and to a validation cohort of 72 consecutive patients. Stage 4 patients at lower risk and ganglioneuroma patients were included as control groups. Predictive thresholds of methylation were identified by ROC curve analysis. The prognostic end points of the study were the overall and progression-free survival at 60 months. Data were analyzed with the Cox proportional hazard model. In a multivariate model the methylation threshold identified for the SFN gene (14.3.3sigma) distinguished the patients presenting favorable outcome from those with progressing disease, independently from all known predictors (Training set: Overall Survival HR 8.53, p = 0.001; Validation set: HR 4.07, p = 0.008). The level of methylation in the tumors of high-risk patients surviving more than 60 months was comparable to that of tumors derived from lower risk patients and to that of benign ganglioneuroma. Methylation above the threshold level was associated with reduced SFN expression in comparison with samples below the threshold. Quantitative methylation is a promising tool to predict survival in neuroblastic tumor patients. Our results lead to the hypothesis that a subset of patients considered at high risk-but displaying low levels of methylation-could be assigned at a lower risk group.

Inflammation, HIF-1, and the epigenetics that follows.

We summarize recent findings linking inflammatory hypoxia to chromatin modifications, in particular to repressive histone signatures. We focus on the role of Hypoxia-Induced Factor-1 in promoting the activity of specific histone demethylases thus deeply modifying chromatin configuration. The consequences of these changes are depicted in terms of gene expression and cellular phenotypes. We finally integrate available data to introduce novel speculations on the relationship between inflammation, histones, and DNA function and integrity.

Angiostatin anti-angiogenesis requires IL-12: the innate immune system as a key target.

BACKGROUND: Angiostatin, an endogenous angiogenesis inhibitor, is a fragment of plasminogen. Its anti-angiogenic activity was discovered with functional assays in vivo, however, its direct action on endothelial cells is moderate and identification of definitive mechanisms of action has been elusive to date. We had previously demonstrated that innate immune cells are key targets of angiostatin, however the pathway involved in this immune-related angiogenesis inhibition was not known. Here we present evidence that IL-12, a principal TH1 cytokine with potent anti-angiogenic activity, is the mediator of angiostatin's activity. METHODS: Function blocking antibodies and gene-targeted animals were employed or in vivo studies using the subcutaneous matrigel model of angiogenesis. Quantitative real-time PCR were used to assess modulation of cytokine production in vitro. RESULTS: Angiostatin inhibts angiogenesis induced by VEGF-TNFalpha or supernatants of Kaposi's Sarcoma cells (a highly angiogenic and inflammation-associated tumor). We found that function-blocking antibodies to IL-12 reverted angiostatin induced angiogenesis inhibition. The use of KO animal models revealed that angiostatin is unable to exert angiogenesis inhibition in mice with gene-targeted deletions of either the IL-12 specific receptor subunit IL-12Rbeta2 or the IL-12 p40 subunit. Angiostatin induces IL-12 mRNA synthesis by human macrophages in vitro, suggesting that these innate immunity cells produce IL-12 upon angiostatin stimulation and could be a major cellular mediator. CONCLUSION: Our data demonstrate that an endogenous angiogenesis inhibitor such as angiostatin act on innate immune cells as key targets in inflammatory angiogenesis. Angiostatin proves to be anti-angiogenic as an immune modulator rather than a direct anti-vascular agent. This article is dedicated to the memory of Prof Judah Folkman for his leadership and for encouragement of these studies.

Different intracellular compartmentalization of TA and DeltaNp73 in non-small cell lung cancer.

The p53 homologue p73 is overexpressed in many tumors, including lung cancer. We have evaluated the differential expression and subcellular localization of the functionally distinct apoptotic (TA) and anti-apoptotic (DeltaN) isoforms of p73 in non-small cell lung cancer (NSCLC), their possible association with p53 expression and determined the methylation status of the two p73 gene promoters (P1 and P2) in this tumor type. Immunohistochemical analysis showed that both isoforms are expressed in the majority of cases. However, the oncogenic DeltaN variant, derived from the transcripts DeltaN'p73 (from P1) and/or DeltaNp73 (from P2), is localized mainly in the nucleus, while the anti-oncogenic TAp73 isoform (derived from a P1 transcript) is sequestered in the cytoplasm in almost all cases analyzed. Significant correlation was found between p53 and DeltaNp73 expression (p=0.041). Methylation analysis conducted on 41 tumor samples showed that the P1 promoter is almost invariably unmethylated (39/41 cases) whereas P2 was found completely methylated in 17 cases and partially or totally unmethylated in 24 samples. No correlation was found between the methylation status of P1 and P2 and p73 expression. Our results demonstrate that both isoforms contribute to p73 overexpression in NSCLC and suggest that their different intracellular localization may reflect an alteration of the functional p53-p73 network that might contribute to lung cancer development.

The "chemoinvasion assay": a tool to study tumor and endothelial cell invasion of basement membranes.

Several genetic and epigenetic factors, both in the cell and in the host, contribute to the progression of tumors towards metastases. The escape of cancer cells from a primary, localized tumor to distant organs transforms a relatively curable pathology to an almost untreatable one. Metastatic lesions are often resistant to cancer therapy because of the progressive phenotypic changes that they have undergone. In this article we will give a bird's eye view on the features of metastatic cells and potential therapeutic targets. In particular, the invasion of basement membranes represents a fundamental step for cell dispersion. Over seventeen years ago we established the Matrigel "chemoinvasion" assay, a useful tool for studying the mechanisms involved in tumor and endothelial cell invasion of basement membranes and for the screening of anti-invasive agents. We will describe the assay and review some of the major results it enabled to obtain.

DLX genes as targets of ALL-1: DLX 2,3,4 down-regulation in t(4;11) acute lymphoblastic leukemias.

Dlx genes constitute a gene family thought to be essential in morphogenesis and development. We show here that in vertebrate cells, Dlx genes appear to be part of a regulatory cascade initiated by acute lymphoblastic leukemia (ALL)-1, a master regulator gene whose disruption is implicated in several human acute leukemias. The expression of Dlx2, Dlx3, Dlx5, Dlx6, and Dlx7 was absent in All-1 -/- mouse embryonic stem cells and reduced in All-1 +/- cells. In leukemic patients affected by the t(4;11)(q21;q23) chromosomal abnormality, the expression of DLX2, DLX3, and DLX4 was virtually abrogated. Our data indicate that Dlx genes are downstream targets of ALL-1 and could be considered as important tools for the study of the early leukemic cell phenotype.

Induction of apoptosis by fenretinide in tumor cell lines correlates with DLX2, DLX3 and DLX4 gene expression.

We investigated a possible relationship between apoptosis induction by fenretinide (4HPR) and the expression of a group of genes thought to be essential in morphogenesis and development, the DLX genes. We analyzed their expression under normal conditions or upon 4HPR stimulation in several tumor cell lines. We show that DLX2, DLX3 and DLX4 were expressed at higher levels in cell lines which where more sensitive to apoptotic induction, whereas DLX 5 and 6 appeared to segregate in a distinct functional compartment. Our data support the notion that DLX2, 3, 4 genes could participate in the control of 4HPR-mediated apoptosis, making them important molecules for the monitoring of therapy efficacy in cancer patients.

HIV Tat, its TARgets and the control of viral gene expression.

The human immunodeficiency virus (HIV-1) (transactivator of transcription (Tat)) protein is a pleiotropic factor that induces a broad range of biological effects in numerous cell types. At the HIV promoter, Tat is a powerful transactivator of gene expression, which acts by both inducing chromatin remodeling and by recruiting elongation-competent transcriptional complexes onto the viral LTR. Besides these transcriptional activities, Tat is released outside the cells and interacts with different cell membrane-associated receptors. Finally, extracellular Tat can be internalized by cells through an active endocytosis process. Here we discuss some of the molecular mechanisms involved in intracellular and extracellular Tat function.

Angiostatin inhibits extracellular HIV-Tat-induced inflammatory angiogenesis.

The HIV-Tat protein can be released extracellularly where it is able to recruit leukocytes and induce angiogenesis. These activities are mediated by the direct interaction of Tat with VEGFR2 on endothelial cells and chemokine receptors on leukocytes. We have recently shown that angiostatin, an anti-angiogenic peptide fragment of plasminogen, is able to inhibit the recruitment of neutrophils induced by bacterial fMLP and alpha chemokines both in vitro and in vivo. In vivo this was associated with an inhibition of the angiogenic response by angiostatin. These observations suggested that angiostatin could be a suitable inhibitor of Tat-induced angiogenesis, as it acts on both endothelial and neutrophil at the same time. In vitro, chemotaxis assays demonstrated that angiostatin inhibited Tat-induced chemotaxis of neutrophils with an inverse bell shaped profile. In vivo the injection of matrigel plugs containing Tat or its chemokine-like peptide (CysL24-51) caused the infiltration of neutrophils and a strong angiogenic response. Angiostatin completely blocked this inflammatory response, inhibiting the recruitment of inflammatory and endothelial cells inside the implant. Taken together, these results indicate that angiostatin can act as an inhibitor of both endothelial and neutrophil recruitment. As these cell types are also the targets of extracellularly released Tat, angiostatin could be used to contrast Tat-associated vasculopathies.

Tumors and inflammatory infiltrates: friends or foes?

The recognition of a role for inflammation in the natural history of a tumor has a long record, stretching from the mid-19th century. From the times of Virkow, who postulated that cancer originates from inflamed tissues, to Metchnikoff and many others, this field has continued to excite (and divide) the scientific community. The question as to whether the inflammatory infiltrate helps or hinders tumors is still open. In a sense, modern molecular biology has, if anything, worsened this dualism, and the literature on this issue shows a plethora of conflicting reports. We would like to provide another contribution to this topic, which was the subject of a recent brilliant review (Balkwill F and Mantovani A. Lancet 2001; 357: 539-45), by focussing more specifically to the relation between inflammation and tumor invasion and how this could drive rational therapeutic approaches.