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![HOXD gene cluster at chromosome 2 shows hypomethylation processes. M-value graphical representation. Blue intensity reflects unmethylation, while red shows methylation. Control nerves are bounded by a green box, while nonvestibular schwannomas are above (red box). Vestibular samples are not highlighted. The miRNA-10b, present at the cluster, also had the same alteration. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]](profile/Rommel-Burbano/publication/270000225/figure/fig3/AS:282619540459542@1444393157872/HOXD-gene-cluster-at-chromosome-2-shows-hypomethylation-processes-M-value-graphical.png)
HOXD gene cluster at chromosome 2 shows hypomethylation processes. M-value graphical representation. Blue intensity reflects unmethylation, while red shows methylation. Control nerves are bounded by a green box, while nonvestibular schwannomas are above (red box). Vestibular samples are not highlighted. The miRNA-10b, present at the cluster, also had the same alteration. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]
Source publication
Schwannomas are tumors that develop from Schwann cells in the peripheral nerves and commonly arise from the vestibular nerve. Vestibular schwannomas can present unilaterally and sporadically or bilaterally when the tumor is associated with neurofibromatosis Type 2 (NF2) syndrome. The molecular hallmark of the disease is biallelic inactivation of th...
Contexts in source publication
Context 1
... et al., 2008). After importing the iDAT files, we obtained a MethyLumiM class object. First, a background correction was performed with the bgAdjust method, and color bias was adjusted by the quantile method. Color bias adjustment was performed because the differences between the red and green channels were very pronounced (Supporting Information Fig. 1). Normalization was performed using simple scaling normalization. M-values were used instead of B-values due to the severe heteroscedasticity of the data when they were not in the middle of the methylation range ( Du et al., 2010); M-values were, therefore, more statistically valid. After processing the data, the methyAnalysis package ...
Context 2
... HOX genes, which participate in body plan development, showed a differential methylation pattern, in most cases hypomethyla- tion in schwannomas. The HOXD cluster, located at chromosome 2q, showed HOXD1, HOXD3, HOXD4, HOXD8, and HOXD9 to be clearly hypo- methylated in 35 probes, as shown in Figure 1. The HOXA cluster, located at chromosome 7p, also had this pattern in a total of 27 probes in HOXA3, HOXA4, and HOXA6. ...
Context 3
... HOX genes, which participate in body plan development, showed a differential methylation pattern, in most cases hypomethyla- tion in schwannomas. The HOXD cluster, located at chromosome 2q, showed HOXD1, HOXD3, HOXD4, HOXD8, and HOXD9 to be clearly hypo- methylated in 35 probes, as shown in Figure 1. The HOXA cluster, located at chromosome 7p, also had this pattern in a total of 27 probes in HOXA3, HOXA4, and HOXA6. ...
Citations
... [46] Previous studies demonstrated the link between methylation of homeobox genes (HOX) and several malignancies, including leukemia and breast cancer. [47,48] Genome-wide methylation analysis in VS demonstrated global hypomethylation at the HOX gene cluster [49]. Other epigenetic modifications pertaining to VS formation are post-transcriptional changes of NF2, alterations in lysine acetylation, and dysregulation of miRNA expression [50][51][52][53]. ...
Neurofibromatosis type 2 (NF2) is a genetic condition marked by the development of multiple benign tumors in the nervous system. The most common tumors associated with NF2 are bilateral vestibular schwannoma, meningioma, and ependymoma. The clinical manifestations of NF2 depend on the site of involvement. Vestibular schwannoma can present with hearing loss, dizziness, and tinnitus, while spinal tumor leads to debilitating pain, muscle weakness, or paresthesias. Clinical diagnosis of NF2 is based on the Manchester criteria, which have been updated in the last decade. NF2 is caused by loss-of-function mutations in the NF2 gene on chromosome 22, leading the merlin protein to malfunction. Over half of NF2 patients have de novo mutations, and half of this group are mosaic. NF2 can be managed by surgery, stereotactic radiosurgery, monoclonal antibody bevacizumab, and close observation. However, the nature of multiple tumors and the necessity of multiple surgeries over the lifetime, inoperable tumors like meningiomatosis with infiltration of the sinus or in the area of the lower cranial nerves, the complications caused by the operation, the malignancies induced by radiotherapy, and inefficiency of cytotoxic chemotherapy due to the benign nature of NF-related tumors have led a march toward exploring targeted therapies. Recent advances in genetics and molecular biology have allowed identifying and targeting of underlying pathways in the pathogenesis of NF2. In this review, we explain the clinicopathological characteristics of NF2, its genetic and molecular background, and the current knowledge and challenges of implementing genetics to develop efficient therapies.
... GSE39645 includes 31 VS samples and 9 normal nerve samples. GSE56597 contains 31 VS samples and 9 normal nerve samples (7)(8)(9). ...
The aim of the present study is to identify novel promising marks and targets of diagnosis, therapy and prognosis for patients with vestibular schwannoma at the molecular level. The gene expression profiles of GSE54934, GSE39645 and GSE56597 datasets were obtained respectively from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified by comparing between gene expression profiles of the vestibular schwannoma tissues and normal tissues. Subsequently, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and protein-protein interaction (PPI) network analysis were performed. The function and pathway enrichment analysis were performed for DEGs with DAVID. Reverse transcription-quantitative PCR were conducted to confirm the expression of BCL2, AGT, IL6 and ITGA2 in human Schwann cells and vestibular schwannoma cells. A total of 4,025, 1,1291 and 1,513 DEGs were identified from GSE54934, GSE56597 and GSE39645 datasets, respectively. GO and KEGG analysis showed that the mutual upregulated genes were mainly enriched in cell division, mitotic nuclear division, and transition of mitotic cell cycle, whilst mutual downregulated genes were enriched in chemical synaptic transmission, neurotransmitter transport, and synaptic vesicle membrane. Subsequently, 20 genes, including BCL2, AGT, IL6 and ITGA2 were selected as hub genes with high degrees after PPI network analysis. The significant differential expression of those genes were detected among vestibular schwannoma tissues compared with normal nerve tissues. In conclusion, BCL2, AGT, IL6 and ITGA2 are significantly higher expressed in vestibular schwannoma tissues compared with human Schwann tissues. The DEGs identified in the present study provide novel targets for the diagnosis and treatment of vestibular schwannoma.
... In line with our findings, we saw most of our hypermethylated miRs described as downregulated in several tumor types including CRC, and to play a role as potential tumor and/or metastasis suppressors. Similarly, in case of hypomethylated miR genes found in this study, most studies supported an oncogenic and/or pro-metastatic role while being more highly expressed in diverse solid cancers, including CRC. hsa-miR-548F5 -Hypermethylated -Schwannomas - [70] Abbreviations ...
MiRs are important players in cancer and primarily genetic/transcriptional means of regulating their gene expression are known. However, epigenetic changes modify gene expression significantly. Here, we evaluated genome-wide methylation changes focusing on miR genes from primary CRC and corresponding normal tissues. Differentially methylated CpGs spanning CpG islands, open seas, and north and south shore regions were evaluated, with the largest number of changes observed within open seas and islands. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed several of these miRs to act in important cancer-related pathways, including phosphatidylinositol 3-kinase (PI3K)–protein kinase B (Akt) and mitogen-activated protein kinase (MAPK) pathways. We found 18 miR genes to be significantly differentially methylated, with MIR124-2, MIR124-3, MIR129-2, MIR137, MIR34B, MIR34C, MIR548G, MIR762, and MIR9-3 hypermethylated and MIR1204, MIR17, MIR17HG, MIR18A, MIR19A, MIR19B1, MIR20A, MIR548F5, and MIR548I4 hypomethylated in CRC tumor compared with normal tissue, most of these miRs having been shown to regulate steps of metastasis. Generally, methylation changes were distributed evenly across all chromosomes with predominance for chromosomes 1/2 and protein-coding genes. Interestingly, chromosomes abundantly affected by methylation changes globally were rarely affected by methylation changes within miR genes. Our findings support additional mechanisms of methylation changes affecting (miR) genes that orchestrate CRC progression and metastasis.
... PMP2, the peripheral myelin protein, was the most highly down-regulated protein. However, this protein was found to be overexpressed in dermal and vestibular schwannomas [14,15]. A possible explanation for the conflicting results is the variable expression patterns of PMP2 in schwannomas of different nerve origin. ...
Facial nerve schwannomas (FNS) represents one of the more difficult treatment paradigms in neurotology. The aim of this study is to investigate the molecular alterations of FNS, thus providing potential targets treatable in the tumour. We for the first time suggest that the deficiency of merlin (the product of NF2 tumour suppressor) is probably one of the key mechanisms underlying FNS tumourigenesis, although no disease-causing NF2 mutations were demonstrated in tumour samples. TMT-labeled spectrometry analysis was used to identify the proteome of FNS relative to nerve controls. Eighty-four significantly deregulated proteins were identified, among which the PML tumour suppressor showed the most significantly increased expression. The PML protein was distributed in the nucleoplasm of non-tumorous Schwann cells, whereas it was preferentially confined to the cytoplasm of FNS cultures. Overexpression of PML and p53, partner proteins positively regulating each other to trigger apoptosis, was further confirmed in FNS tissues/cultures, and this correlated with a significant decrease in the proliferation of FNS cultures in comparison to Schwann cells. It is therefore probable that PML-p53 overexpression may occur as part of protective cellular mechanisms in response to the proliferation signal mediated by loss of merlin in FNS, in accordance with the fact that the tumour is benign slow-growing. This hypothesis was supported by the finding that the p53 activator nutlin-3 could exert dose-dependent inhibitory effects on FNS cultures via a cooperative induction of PML-p53 levels. Thus, the current study may present a potential treatment target directed on the molecular mechanisms of this disease.
... The molecular alterations of VS include NF2 gene mutation/loss/mitotic recombination [5-7], abnormal gene expression [8], involvement of immunological factors [9,10], deoxyribonucleic acid (DNA) methylation [11,12] and change in growth factors [13][14][15]. ...
... CpG dinucleotides show higher density than other parts of the genome and CpG are normally unmethylated [34]. Methylation is a process to inhibit gene transcription at the transcriptional start site and 5 -UTR regions [11]. Methylation has been widely reported to be associated with VS. ...
Vestibular schwannoma (VS) is a benign primary brain tumor that occurs sporadic or as part of a genetic syndrome. The most common cause is the mutation of the NF2 tumor suppressor gene that is involved in the production of the protein merlin. Merlin plays a role in cell growth and cell adhesion. In patients with NF2, the VSs arise bilaterally and coincide with other brain tumors. In sporadic VS, the tumor is typically unilateral and does not coincide in combination with other tumors. MRI is the standard imaging technique and can be used to assess the size and aspect of the tumor as well as the progression of disease. The preferred management of large VS in both VS types is surgery with or without adjuvant radiation. The management for the medium- or small-sized VS includes wait and scan, radiotherapy and/or surgery. This choice depends on the preference of the patient and institutional protocols. The outcomes of surgical and radiotherapy treatments are improving due to progress in surgical equipment/approaches, advances in radiation delivery techniques and dose optimizations protocols. The main purpose of the management of VS is preserving function as long as possible in combination with tumor control.
... (59) In this study, 14 of 23 VS tumors examined were found to have methylation in 3 CpG sites of the NF2 promoter region, which was associated with reduced mRNA expression of the NF2 gene. However, other studies have suggested that methylation of the NF2 gene and its promoter is actually rare and may not be a primary mechanism for formation of VS. (60)(61)(62) A study by Kullar et al. showed that while hypermethylation of the NF2 gene is rare in sporadic VS, other genes, particularly THBS1, MGMT, TIMP3, and P73, were frequently found to be aberrantly hypermethylated in schwannomas.(63) Methylation of these genes has been shown to be tumor specific. ...
... (82,85,86) Methylation analysis in the tumor tissue using bisulfite sequencing of the NF2 gene or broader assessments may also identify methylation patterns that lead to NF2 phenotypes. (62,85) ...
Objectives:
In this review, we discuss current knowledge about the genetics and epigenetics of vestibular schwannoma (VS) in relation to hearing loss. A multistep and sequential genetic algorithm suitable for the identification of Neurofibromatosis Type 2 (NF2) constitutional and somatic mutations is discussed.
Data sources, study selection:
A review was performed of the English literature from 1990 to 2019 using PubMed regarding genetics and epigenetics of vestibular schwannoma and NF2.
Conclusion:
NF2 is a genetic disorder characterized by NF2 mutations that affect the function of a tumor suppressor called merlin. In particular, individuals with NF2 develop bilateral VS that can lead to hearing loss and even deafness. Recent advances in genetic and epigenetic studies have improved our understanding of the genotype-phenotype relationships that affect hearing in NF2 patients. Specific constitutional NF2 mutations including particular truncating, deletion, and missense mutations have been associated with poorer hearing outcomes and more severe clinical manifestations. Epigenetic events, such as DNA methylation and histone modifications, also contribute to the development and progression of hearing loss in NF2 patients. Furthermore, the accumulation of multiple NF2 and non-NF2 genetic and epigenetic abnormalities at the level of the tumor may contribute to worse hearing outcomes. Understanding genetic and epigenetic signatures in individual NF2 patients and particularly in each VS will allow us to develop novel gene therapies and precision medicine algorithms to preserve hearing in NF2 individuals.
... Significant hypomethylation of the Hox gene cluster was identified as a commonly occurring alteration but this study did not identify any NF2 promoter hypermethylation, unlike previously (Feber et al., 2011;Torres-Martín et al., 2015). ...
DNA methylation is one of many epigenetic marks, which directly modifies base residues, usually cytosines, in a multiple‐step cycle. It has been linked to the regulation of gene expression and alternative splicing in several cell types, including during cell lineage specification and differentiation processes. DNA methylation changes have also been observed during aging, and aberrant methylation patterns have been reported in several neurological diseases. We here review the role of DNA methylation in Schwann cells and oligodendrocytes, the myelin‐forming glia of the peripheral and central nervous systems, respectively. We first address how methylation and demethylation are regulating myelinating cells' differentiation during development and repair. We then mention how DNA methylation dysregulation in diseases and cancers could explain their pathogenesis by directly influencing myelinating cells' proliferation and differentiation capacities. DNA methylation regulates Schwann cells and oligodendrocytes differentiation. DNA modifications are necessary for myelination or remyelinating events in the central nervous system (CNS). DNA methylation is dysregulated in myelinating glia in aging, in neurodegenerative diseases, and in Schwannomas and CNS gliomas.
... Lassaletta et al. investigated the methylation status of 16 genes in 22 sporadic VSs and related it to clinical and radiological findings (57), the connection observed between TP73 aberrant methylation and deafness being important [Pure Tone Average (PTA) = 43 and 17 dB for patients with methylated and unmethylated TP73 genes, respectively]. A genome-wide methylation analysis in VS also showed a trend toward hypomethylation in several miRNAs and coding genes, including alternative transcripts, opening a window to possible therapeutic targets (64). ...
Vestibular schwannomas (VSs) are benign tumors composed of differentiated neoplastic Schwann cells. They can be classified into two groups: sporadic VS and those associated with neurofibromatosis type 2 (NF2). VSs usually grow slowly, initially causing unilateral sensorineural hearing loss (HL) and tinnitus. These tumors cause HL both due to compression of the auditory nerve or the labyrinthine artery and due to the secretion of different substances potentially toxic to the inner ear or the cochlear nerve. As more and more patients are diagnosed and need to be managed, we are more than ever in need of searching for biomarkers associated with these tumors. Owing to an unknown toxic substance generated by the tumor, HL in VS may be linked to a high protein amount of perilymph. Previous studies have identified perilymph proteins correlated with tumor-associated HL, including μ-Crystallin (CRYM), low density lipoprotein receptor-related protein 2 (LRP2), immunoglobulin (Ig) γ-4 chain C region, Ig κ-chain C region, complement C3, and immunoglobulin heavy constant γ 3. Besides, the presence of specific subtypes of heat shock protein 70 has been suggested to be associated with preservation of residual hearing. It has been recently demonstrated that chemokine receptor-4 (CXCR4) is overexpressed in sporadic VS as well as in NF2 tumors and that hearing disability and CXCR4 expression may be correlated. Further, the genetic profile of VS and its relationship with poor hearing has also been studied, including DNA methylation, deregulated genes, growth factors, and NF2 gene mutations. The knowledge of biomarkers associated with VS would be of significant value to maximize outcomes of hearing preservation in these patients.
... 83 Most CHARGE syndrome cases are caused by haploinsufficiency of the CHD7 gene, which encodes an ATP-dependent chromatin-remodeling protein involved in the epigenetic regulation of gene expression. 85 There are many epigenetic alterations associated with the pathophysiology of different types of ataxia, multiple sclerosis, and migraine, although they do not explain the origin of vertigo ( ...
Vertigo is a complex and heterogeneous entity that can be categorized as vestibular or central. Alterations in the vestibular system cause an illusory sensation of tilting, floating, or spinning. Most cases have a genetic background, so deep phenotyping might be necessary to complete an accurate diagnosis. Epigenetic mechanisms are involved in hair cell regeneration, and alterations may cause vertigo-associated disorders. There are reports of genetic mutations and epigenetic changes in Ménière disease, neurofibromatosis, different types of ataxia, and other syndromes. Treatment of vertigo varies depending on its type, characteristics, and sequels. Pharmacological treatments include corticosteroids, anticonvulsants, anticholinergics, calcium channel blockers, antihistamines, diuretics, benzodiazepines, and other drugs. Most of the drugs involved in vertigo metabolize through CYP group enzymes that can be present in central structures and can be affected by epigenetic factors that also affect interindividual variability in drug response. There are different receptor genes involved in vestibular functioning that may be useful for the development of new treatments. These receptors may also be modified epigenetically, and their epigenetic status can affect patient response to therapy. Multiple lines of pharmacological and nonpharmacological treatments may induce epigenetic changes, diminishing or increasing gene expression. Drugs can induce epigenetic modifications, and there are several reports showing effectiveness when using epigenetic treatments, such as in vestibular schwannoma, Friedreich ataxia, or inner ear disorders.
... Several studies have reported that hypomethylation of miRNA clusters is associated with re-activation of corresponding miRNA expression [24,25,29]. However, we could not conclude that tumor-specific hypomethylation was simply associated with tumor-specific expression (see Additional file 3: Figure S2A and Fig. 3c, d). ...
Background
While hepatitis B and C viral infection have been suppressed, non-B non-C hepatocellular carcinoma (NBNC-HCC) is considered to be rising in incidence terms in some developed countries where prevalence of those viral infections among HCC patients had been very high (such as Japan, Korea, and Italy). To elucidate critical molecular changes in NBNC-HCC, we integrated three large datasets relating to comprehensive array-based analysis of genome-wide DNA methylation (N = 43 pairs) and mRNA/miRNA expression (N = 15, and 24 pairs, respectively) via statistical modeling.
Results
Hierarchical clustering of DNA methylation in miRNA coding regions clearly distinguished NBNC-HCC tissue samples from relevant background tissues, revealing a remarkable tumor-specific hypomethylation cluster. In addition, miRNA clusters were extremely hypomethylated in tumor samples (median methylation change for non-clustered miRNAs: -2.3%, clustered miRNAs: -24.6%). The proportion of CpGs hypomethylated in more than 90% of the samples was 55.9% of all CpGs within miRNA clusters, and the peak methylation level was drastically shifted from 84% to 39%. Following statistical adjustment, the difference in methylation levels within miRNA coding regions was positively associated with their expression change. Receiver operating characteristic (ROC) analysis revealed a great discriminatory ability in respect to cluster-miRNA methylation. Moreover, miRNA methylation change was negatively correlated with corresponding target gene expression amongst conserved and highly matched miRNA sites.
Conclusions
We observed a drastic negative shift of methylation levels in miRNA cluster regions. Changes in methylation status of miRNAs were more indicative of target gene expression and pathological diagnosis than respective miRNA expression changes, suggesting the importance of genome-wide miRNA methylation for tumor development. Our study dynamically summarized global miRNA hypomethylation and its genome-wide scale consequence in NBNC-HCC.
Electronic supplementary material
The online version of this article (doi:10.1186/s12943-016-0514-6) contains supplementary material, which is available to authorized users.
