Methylation Status Of CpG Islands Research Articles

Abstract 4410: The CpG island methylator phenotype is closely associated with prognosis in patients with oral squamous cell carcinomas

Abstract Few abnormalities are known to be closely associated with prognosis in OSCC cases. In this study, genomic abnormalities of cancer-related genes and epigenomic abnormalities of genes methylation-silenced in OSCCs were analyzed to identify abnormalities associated with prognosis. Thirty-nine OSCC cases and their surgical materials were analyzed for the presence of mutations using next-generation sequencing. Methylation status of promoter CpG islands of five genes was analyzed by methylation-specific PCR. Mutations in CRG, TP53 and PIK3CA were observed in 64.1%, 38.5%, and 33.3%, respectively, of the cases. However, no significant association between mutation status and overall survival (OS) was observed. Aberrant methylation of CMTM3, NKX2-3, RBP4, EGFLAM, and MAP6 were observed in 51.3%, 41.0%, 66.7%, 38.5%, and 41.0%, respectively. Methylation of NKX2-3, EGFLAM, and MAP6 were significantly associated with OS in OSCC cases (p=0.006, 0.006, and 0.012, respectively). Cases with methylation of CMTM3 and RBP4 showed a trend toward poor prognosis (p=0.052 and 0.059, respectively). Methylation profiles of the five genes indicated the presence of the CpG island methylator phenotype (CIMP), and the CIMP-positive cases showed poor prognosis (HR=20.5, p<0.001). In conclusion, CIMP was closely associated with the prognosis of OSCC cases. Citation Format: Masanobu Abe, Satoshi Yamashita, Toshikazu Ushijima, Kazuto Hoshi. The CpG island methylator phenotype is closely associated with prognosis in patients with oral squamous cell carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4410.

The impact of SLC10A3 on prognosis and immune microenvironment in colorectal adenocarcinoma

BackgroundSLC10A3, a gene upregulated in pan-cancer, lacks full understanding regarding its prognostic implications and association with immune infiltration in colorectal cancer (CRC). This study comprehensively analyzed SLC10A3 in CRC, evaluating its prognostic significance and influence on the tumor's immune microenvironment.MethodsTranscriptomic data from TCGA were obtained to compare SLC10A3 expression in both colorectal cancer (CRC) and normal tissues. Prognostic value was assessed for overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). DNA methylation patterns of SLC10A3 and correlation with DNA mismatch repair (MMR) were explored. Genetic alterations in SLC10A3 were scrutinized. The study also delved into the influence of SLC10A3 on the immune microenvironment of CRC, including immune cell infiltration and chemokines. Involvement of cancer-associated fibroblasts (CAFs) was explored. Methylation status of specific CpG islands in the SLC10A3 gene correlated with CRC patient prognosis. CRC tissue microarray was performed to verify the expression of SLC10A3 and its relationship with prognosis.ResultsThe research revealed that SLC10A3 is significantly upregulated in CRC and holds promise as a potential diagnostic marker. Elevated SLC10A3 expression was linked to poorer OS, DSS, and PFI. Methylation patterns of SLC10A3 displayed prognostic relevance, and genetic alterations in the gene were identified. SLC10A3 was shown to impact the immune microenvironment, with significant correlations observed between its expression and various immune cell types, chemokines, and markers associated with CAFs. Furthermore, an inverse relationship between SLC10A3 and MMR molecules was established. Methylation status of specific CpG islands within the SLC10A3 gene was associated with CRC patient prognosis. Tissue microarray showed that SLC10A3 was highly expressed in CRC and significantly correlated with poor prognosis.ConclusionThe study underscores the importance of elevated SLC10A3 in CRC, associating it with decreased survival and immune infiltration, proposing it as a diagnostic biomarker and appealing immunotherapy target, given its significant overexpression and influence on the immune microenvironment and prognosis through methylation patterns.Graphical

Retraction: Zinc sulfate contributes to promote telomere length extension via increasing telomerase gene expression, telomerase activity and change in the TERT gene promoter CpG island methylation status of human adipose-derived mesenchymal stem cells.

Retraction: Zinc sulfate contributes to promote telomere length extension via increasing telomerase gene expression, telomerase activity and change in the TERT gene promoter CpG island methylation status of human adipose-derived mesenchymal stem cells.

Significance of O6-methyl guanine methyltransferase promoter methylation in high grade glioma patients: optimal cutoff point, CpG locus, and genetic assay.

To evaluate O6-methyl guanine methyltransferase (MGMT) promoter methylation status in high grade glioma patients and to identify the best cutoff point as well as the most predictive CpG loci for patients survival. Consecutive high grade glioma patients treated with surgical gross total resection followed by concomitant radiochemotherapy and adjuvant chemotherapy were included in this retrospective observational study. Methylation status of MGMT promoter CpG island of resected tumor tissue were evaluated using next generation sequencing assay. The outcomes were grouped as CpG 70-78, CpG 79-83, CpG 84-87, CpG 70-87, and whole promoter. Quantitative analyses were dichotomized as methylated or unmethylated based on the cutoff points set to %10, and methylation was further graded as <%10 unmethylated, %10-30 low-methylated, and %30-100 high-methylated. Total of 95 patients with the mean age of 51.50 ± 12.36 years were included in the study. Overall survival (OS) and progression free survival (PFS) were 14.53 ± 1.92 (95% CI 10.77-18.30) and 10.90 ± 2.05 (95% CI 6.89-14.92) months, respectively. MGMT promoter was methylated in 38.2% of cases and high-methylated in 10.5% of cases. Methylation status of MGMT promoter was recognized as a very powerful predictor of OS and PFS. In particular, high-methylation of CpG 79-83 and CpG 84-87 islands at promoter region were strongly associated with better survival outcomes (p < 0.05). Our outcomes support the prognostic value of MGMT promoter methylation in patients with high grade glioma. Sequencing of whole promoter CpG islands demonstrated that methylation of particular CpG sites might predict clinical outcomes more precisely.

Quantitative Evaluation of NOD2 Promoter Methylation Profiling in Colon Biopsy Samples from Ulcerative Colitis Patients and Non-Colitis Controls

Background: Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with evidence addressing the role of epigenetic changes. The intention of this study was to detect the association of DNA methylation levels of NOD2 gene with UC and to evaluate whether any of these changes might be a useful biomarker for detecting patients with UC.&#x0D; Methods: The methylation status of the promoter CpG islands (CGIs) of NOD2 gene was examined in the colonic mucosae of 15 cancer-free patients with UC and 15 age- and sex-matched healthy controls by the real-time quantitative multiplex-methylation specific PCR (QM-MSP) assay. Methylation-specific melting curve analysis (MS-MCA) were used to analyze the data.&#x0D; Results: The median unmethylated DNA index was significantly higher in cases compared to controls, and hypormethylation of NOD2 gene was significantly correlated with UC (Unmethylated DNA in UC vs. HC; 0.102±0.055 vs. 0.025±0.016, P = 0.000).&#x0D; Conclusion: The NOD2 gene that was differentially methylated in UC patients, providing new insights into the pathogenesis of UC, with a view to making steps toward the development of accurate biomarkers for diagnostic tools in UC.

Integrated analysis of diagnostic, prognostic value and potential drug treatment of GSDME in head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSC) poses a global health challenge. Effective biomarkers for early detection are necessary to improve the survival rate of HNSC patient. The purpose of this study was using integrated bioinformatic analysis to investigate the potential biological roles of GSDME in HNSC. The Gene Expression Omnibus (GEO) and Cancer Gnome Atlas (TCGA) databases were used to analyze the expression of GSDME in different cancer types. The correlation between GSDME expression and immune cell infiltration or immune checkpoint genes was examined by Spearman correlation analysis. DNA methylation analysis of the GSDME gene was conducted using the MethSurv database. Kaplan-Meier (K-M) survival curves, diagnostic receiver operating characteristic (ROC) curves, nomogram model, and Cox regression analysis were chosen to evaluate the diagnostic and prognostic predictive value of GSDME. Connectivity Map (Cmap) online platform, Protein Data Bank (PDB) database and Chem3D, AutoDock Tool and PyMol software were used to predict and visualize potential molecular drugs aimed for GSDME. GSDME expression level in HNSC was significantly higher than in the controls (p < 0.001). Differentially expressed genes (DEGs) correlation with GSDME were enriched in the GO pathways, such as protein activation cascade, complement activation and classical pathway (p < 0.05). According to GSEA, GSDME-associated differentially expressed genes were significantly enriched in KRAS signaling pathway and cytokine signaling molecule (p < 0.05). There is a significant relation between GSDME expression and immune cell infiltration in HNSC tissues, as well as immune checkpoint genes expression (p < 0.001). DNA methylation status of cg17790129 CpG islands of GSDME gene is correlated with HNSC prognosis (p < 0.05). Based on Cox regression analysis of HNSC patients, GSDME as a potential risk gene has high correlation with overall survival (OS) and disease specific survival (DSS) (p < 0.05). In a ROC curve analysis, HNSC tissues were differentiated from adjacent peritumoral tissues based on GSDME expression levels (AUC = 0.928). Totally six potential drugs targeted for GSDME were screened and the molecular docking tests between GSDME protein and candidate drugs were conducted. GSDME is a promising therapeutic target as well as a potential clinical biomarker in HNSC patients.

A CpG methylation-powered dynamic three-dimensional-DNAzyme walker for single-molecule monitoring of multiple cytosine-C5 methyltransferases

Cytosine-C5 methyltransferases (MTases) maintain methylation status in CpG islands (CpGIs), and their abnormal activities are implicated in various diseases and cancers. Simultaneous monitoring of multiple cytosine-C5 MTases has remained challenging due to diversity of DNA substrates and scarcity of methylation-independent restriction endonucleases (MIREs). Herein, we construct a CpG methylation-powered dynamic three-dimensional-DNAzyme walker for single-molecule monitoring of multiple cytosine-C5 MTases. The presence of M.SssI and M.CviPI catalyzes cytosines-C5 methylation in hairpin probes to form catalytic substrates of GlaI. Then GlaI specifically cleaves 5-mCs to yield two metal-specific DNAzymes. Upon the addition of substrate probes (SP1/SP2)-functionalized AuNPs, two DNAzymes selectively bind with SP1 and SP2, and autonomously complete 3D-DNAzymes walking with assistance of cofactors Mg2+ and Zn2+, inducing cyclic cleavage of substrate probes and dissociation of abundant Cy5 and Cy3 from AuNPs. Cy5 and Cy3 are simply measured through single-molecule imaging, with Cy5 indicating M.SssI and Cy3 indicating M.CviPI. This nanosensor achieves a limit of detection (LOD) of 3.944 × 10-9 U/μL for M.SssI and 5.046 × 10-9 U/μL for M.CviPI. It can discriminate cytosine-C5 MTases members, screen potential inhibitors, and quantify multiple cytosine-C5 MTases in human serum and diverse cell lysates, providing a powerful platform for biomedical research and clinical diagnostics.

The CpG Island Methylation Status and mRNA Expression Level of CTLA4 in Childhood Hashimoto’s Thyroiditis

The CpG Island Methylation Status and mRNA Expression Level of CTLA4 in Childhood Hashimoto’s Thyroiditis

Consequences of aberrated DNA methylation in Colon Adenocarcinoma: a bioinformatic-based multi-approach

IntroductionThe biology of colorectal cancer (CRC) is remained to be elucidated. Numerous genetic and epigenetic modifications are in concert to create and progress CRC. DNA methylation as a principal epigenetic factor has gained increased attention and could be utilized for biological studies. This study aims to find novel methylated and downregulated genes with a focus on HAND2 in CRC and decipher the biological consequences.Material and methodData on DNA methylation from GEO and SMART databases and the expression GEPIA2 database were downloaded. Afterward, a set of hypermethylated and downregulated genes in CRC was chosen by overlapping genes. Consequently, HAND2 was selected as a key gene for further investigation and confirmed with cell lines methylation and expression data. The functions of HAND2 were further analyzed using gene ontology analyses and the protein–protein interaction network.ResultsThe methylation (p < 0.01) and expression (p < 0.01) of HAND2 are significantly varied in CRC compared to normal control. The correlation analysis (Pearson's correlation coefficient = -0.44, p = 6.6e-14) conveys that HAND2 significantly downregulated and has a reverse correlation with the methylation status of CpG islands. The biological process analysis of HAND2 target genes conveyed that disruption in HAND2 expression could dysregulate ERK1 and ERK2 signaling pathways.ConclusionTogether, the findings showed that DNA hypermethylation of HAND2 was critical evidence in CRC. Further validation and prospective studies are needed to utilize HAND2 methylation as a promising biomarker.

Acute Hypoxia Stress-Induced Apoptosis in Gill of Japanese Flounder (Paralichthys olivaceus) by Modulating the Epas1/Bad Pathway.

The physiological responses and molecular mechanisms of apoptosis in Japanese flounder under hypoxic stress remain unclear. In the present study, we performed acute hypoxia stress on Japanese flounder (2.39 ± 0.84 mg/L) and detected gills responses in histomorphology and molecular mechanisms. The results showed that the volume of the interlamellar cell mass decreased and the gill lamellae prolonged, indicating the expansion of the respiratory surface area. Additionally, the fluorescence signal of apoptosis increased under hypoxic stress. In addition, the expression of two genes (EPAS1 and Bad) related to apoptosis increased about four-fold and two-fold, respectively, at 6 h of hypoxia. Meanwhile, the result of the dual-luciferase reporter assay showed that EPAS1 is a transcription factor, which could regulate (p &lt; 0.05) the expression of the Bad gene, and we identified the binding site of EPAS1 was the AATGGAAAC sequence located near -766. DNA methylation assay showed that hypoxia affected the methylation status of CpG islands of EPAS1 and Bad genes. All results indicated that hypoxia could activate the EPAS1/Bad signal pathway to induce gill apoptosis of Japanese flounder. Our study provides new light on understanding the molecular mechanism of hypoxia-induced apoptosis in Japanese flounder.

Impact of G-Quadruplex Structures on Methylation of Model Substrates by DNA Methyltransferase Dnmt3a.

In mammals, de novo methylation of cytosines in DNA CpG sites is performed by DNA methyltransferase Dnmt3a. Changes in the methylation status of CpG islands are critical for gene regulation and for the progression of some cancers. Recently, the potential involvement of DNA G-quadruplexes (G4s) in methylation control has been found. Here, we provide evidence for a link between G4 formation and the function of murine DNA methyltransferase Dnmt3a and its individual domains. As DNA models, we used (i) an isolated G4 formed by oligonucleotide capable of folding into parallel quadruplex and (ii) the same G4 inserted into a double-stranded DNA bearing several CpG sites. Using electrophoretic mobility shift and fluorescence polarization assays, we showed that the Dnmt3a catalytic domain (Dnmt3a-CD), in contrast to regulatory PWWP domain, effectively binds the G4 structure formed in both DNA models. The G4-forming oligonucleotide displaced the DNA substrate from its complex with Dnmt3a-CD, resulting in a dramatic suppression of the enzyme activity. In addition, a direct impact of G4 inserted into the DNA duplex on the methylation of a specific CpG site was revealed. Possible mechanisms of G4-mediated epigenetic regulation may include Dnmt3a sequestration at G4 and/or disruption of Dnmt3a oligomerization on the DNA surface.

Sequential evaluation of MUC promoter methylation using next-generation sequencing-based custom-made panels in liquid-based cytology specimens of pancreatic cancer.

As liquid-based cytology (LBC) specimens preserve high-quality DNA, clinical sequencing of LBC specimens using next-generation sequencing (NGS) is becoming a common strategy. This study aimed to evaluate the feasibility of NGS-based custom-made panels for evaluating MUC promoter methylation in LBC specimens. Thirty-one patients with pancreatic cancer were enrolled in the study. Cancer tissue samples were obtained using endoscopic ultrasound-guided fine-needle aspiration/biopsy (EUS-FNA/FNB). LBC, formalin-fixed paraffin-embedded (FFPE), and fresh frozen specimens were prepared for DNA extraction after pathological diagnosis. These specimens were then subjected to NGS analysis using custom-made cancer gene screening and methylation panels comprising 28 cancer-related genes and 13 gene promoter regions, including MUC1, MUC2, and MUC4. The success rate of NGS using the cancer gene panel was comparable among the LBC, FFPE, and frozen specimens, and the presence of cancer cell-derived somatic mutations in each specimen was confirmed. The specimens were then tested using a methylation panel that revealed the sequential methylation status of CpG islands located in the promoter regions of MUC genes. The methylation status results obtained from LBC specimens were almost comparable with those from FFPE and frozen specimens. MUC and other gene methylation analyses using an NGS-based panel were successfully performed in residual LBC specimens obtained by EUS-FNA/FNB. Therefore, this approach provides an alternative source of molecular tests for gene mutations and methylation, especially in the pancreatic cancers, which are often unresectable and unsuitable for obtaining FFPE specimens.

Epigenteic Alteration of DOK7 Gene CpG Island in Blood Leukocyte of Patients with Gastric Cancer and Intestinal Methaplasia.

Intestinal metaplasia (IM) is a benign lesion with no serious concern for patients' health. On the other hand, gastric cancer (GC) is a malignant lesion that has to be differentially diagnosed from benign intestinal metaplasia. Epigenetic modifications have been suggested to play an important role in cancer initiation and development, and they have been investigated as a reliable biomarker tool even for early cancer diagnosis. Whole blood leucocytes (WBC) are potentially the most accessible tissue for cancer early diagnosis, especially for GC, which is hard to diagnose in the early stage. This study aims to investigate the methylation status of DOK7 gene CpG island in blood leukocytes of patients with IM and GC compared to normal control groups. DNA was extracted from the whole blood of 30 IM patients, 30 GC patients, and 34 normal controls samples, and MSRE-PCR was utilized to evaluate the loci methylation status. Significant hypermethylation of DOK7 gene CpG has been observed in GC 88.1 % (p < 0.001) and IM 66.0 % (p = 0.03) in comparison to the normal control group 56.8%. A cutoff upper than 84.5 % of hypermethylation is considered as a presence of gastric cancer malignant lesions. This is the first reported on hypermethylation in DOK7 CPG in blood leukocytes of patients with GC and IM and establishing a laboratory blood based test that may be useful as a novel biomarker test in the early diagnosis and screaning of GC and IM.

Global DNA methylation profiles of\xa0buffalo (Bubalus bubalis)\xa0preimplantation embryos produced by handmade cloning and in vitro fertilization

Somatic cell nuclear transfer technique (SCNT) has proved to be an outstanding method of multiplication of elite animals but accompanied with low efficiency and live birth rate of cloned animals. Epigenetic alterations of DNA has been one of the culprits behind this issue. Cloned embryos are found to deviate slightly from regular pattern of demethylation and re-methylation at the time of nuclear reprogramming and embryonic development when compared with embryos produced by in vitro fertilization (IVF). Thus, the present study was aimed at evaluating global DNA methylation profiles of cloned embryos at 2-cell, 8-cell and blastocyst stages and compare it with corresponding stages of embryos produced by IVF by using MeDIP-Sequencing on Illumina-based platform. We found out that cloned embryos exhibited significantly different DNA methylation pattern as compared to IVF embryos with respect to distribution of differentially methylated regions in different components of genome, CpG islands distribution and methylation status, gene ontological profiles and pathways affected throughout the developmental stages. The data generated from MeDIP-Seq was validated at blastocyst stage cloned and IVF embryos by bisulfite-sequencing PCR on five randomly selected gene regions.

Development of a Standard Control for qMSP to Analyze the Methylation Status of LINE-1

Cancer screening is an important aspect of comprehensive health care, making a significant contribution to reducing the risk of death and the cost of treating patients. Finding new tumor markers with high sensitivity and specificity is a trend in the research activities in Vietnam as well as all over the world. Long interspersed element-1 (LINE-1), a large proportion of repeating DNA, is transposable to different positions in the genome. LINE-1 activity is controlled through DNA methylation (the CpG is attached with CH3), whereby LINE-1 is highly methylated in normal cells. However, in some types of cancer such as lung, breast, stomach, liver, rectum... changes in the methylation status LINE-1 have been noticed. To study the methylation status of the LINE-1 sequence, we used a quantitative methyl-specific PCR technique. This method requires a standard calibrator to quantify the rate of methylation. From the commercial methylated DNA (CpG Methylated Human Genomic DNA, Promega), we cloned two regions of the LINE-1 promoter corresponding to a reference sequence and an investigated one (target sequence) which are bisulfite transformed. As a result, we have created two recombinant plasmids, pRef-LINE1 and pMe-LINE1. The plasmids were mixed at 10% of methylation and could be used as a standard control for analyzing the DNA methylation of specimens from patients.&#x0D; Keywords: DNA methylation, DNA repeating sequence, LINE-1, quantitative methyl-specific-PCR (qMSP), tumor markers.&#x0D; References&#x0D; [1] A. P. Feinberg, Phenotypic Plasticity and the Epigenetics of Human Disease, Nature, Vol. 447, No. 7143, 2007, pp. 433-40, https://doi.org/10.1038/nature05919.[2] A. H. Ting, K. M. McGarvey, S. B. Baylin, The cancer Epigenome-Components and Functional Correlates, Genes Dev, Vol. 20, No. 23, 2006, pp. 3215-31, https://doi.org/10.1101/gad.1464906.[3] A. E. Teschendorff et al., DNA Methylation Outliers in Normal Breast Tissue Identify Field Defects that are Enriched in Cancer, Nat Commun, Vol. 7, No., 2016, pp. 10478, https://doi.org/10.1038/ncomms10478.[4] C. Leygo et al., DNA Methylation as a Noninvasive Epigenetic Biomarker for the Detection of Cancer, Dis Markers, Vol. 2017, No., 2017, pp. 3726595, https://doi.org/10.1155/2017/3726595.[5] X. Hao et al., DNA Methylation Markers for Diagnosis and Prognosis of Common Cancers, Proc Natl Acad Sci U S A, Vol. 114, No. 28, 2017, pp. 7414-7419, https://doi.org/10.1073/pnas.1703577114.[6] N. Kitkumthorn, A. Mutirangura, Long Interspersed Nuclear Element-1 Hypomethylation in Cancer: Biology and Clinical Applications, Clin Epigenetics, Vol. 2, No. 2, 2011, pp. 315-30, https://doi.org/10.1007/s13148-011-0032-8.[7] M. A. Kerachian, M. Kerachian, Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Colorectal Cancer, Clin Chim Acta, Vol. 488, No., 2019, pp. 209-214, https://doi.org/10.1016/j.cca.2018.11.018.[8] M. Barchitta et al., LINE-1 Hypermethylation in White Blood Cell DNA Is Associated with High-Grade Cervical Intraepithelial Neoplasia, BMC Cancer, Vol. 17, No. 1, 2017, pp. 601, https://doi.org/10.1186/s12885-017-3582-0.[9] Y. Baba et al., Long Interspersed Element-1 Methylation Level as a Prognostic Biomarker in Gastrointestinal Cancers, Digestion, Vol. 97, No. 1, 2018, pp. 26-30, https://doi.org/10.1159/000484104.[10] J. G. Herman et al., Methylation-specific PCR: a Novel PCR Assay for Methylation Status of Cpg Islands, Proc Natl Acad Sci U S A, Vol. 93, No. 18, 1996, pp. 9821-9826, https://doi.org/10.1073/pnas.93.18.9821.[11] K. Hattermann et al., A Methylation-Specific And SYBR-Green-Based Quantitative Polymerase Chain Reaction Technique for O6-Methylguanine DNA Methyltransferase Promoter Methylation Analysis, Anal Biochem, Vol. 377, No. 1, 2008, pp. 62-71, https://doi.org/10.1016/j.ab.2008.03.014. [12] K. J. Livak, T. D. Schmittgen, Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2(-Delta Delta C(T)) Method, Methods, Vol. 25, No. 4, 2001, pp. 402-408, https://doi.org/10.1006/meth.2001.1262.[13] Y. Hou et al., Serious Overestimation In Quantitative PCR By Circular (Supercoiled) Plasmid Standard: Microalgal Pcna As The Model Gene, PLoS One, Vol. 5, No. 3, 2010, pp. e9545, https://doi.org/10.1371/journal.pone.0009545.[14] G. Johnson, T. Nolan, S. A. Bustin, Real-time Quantitative PCR, Pathogen Detection and MIQE, Methods Mol Biol, Vol. 943, 2013, pp. 1-16, https://doi.org/10.1007/978-1-60327-353-4_1.&#x0D;

Loss of EphA7 Expression in Basal Cell Carcinoma by Hypermethylation of CpG Islands in the Promoter Region.

Basal cell carcinoma (BCC) is the most common malignancy worldwide, with increasing incidence. BCCs present low mortality but high morbidity, and its pathogenesis remains unclear. Eph receptors have been implicated in tumorigenesis. EphA7 plays a role as a tumor suppressor in certain cancers. We checked EphA7 expression levels and methylation status in a set of BCCs, benign skin diseases, and compound nevus tissue samples using immunohistochemistry. EphA7 protein was positively expressed in normal basal cells, benign skin diseases, and compound nevus cells, but lost in areas of BCC tissues. We detected hypermethylation in BCC tissue samples with reduced expression of EphA7. There is a significant relationship between the expression level of EphA7 receptor protein and the methylation status of CpG islands in the EphA7 promoter region (P < 0.001). To our knowledge, this is the first study to report the EphA7 expression profile and hypermethylation of EphA7 in BCC. The role of the EphA7 gene and the status of hypermethylation in tumorigenesis and treatment of BCC warrant further investigation.

Prognostic Utility of CpG Island Hypermethylated Phenotype in Early-Stage Invasive Primary Melanomas

In their article in the Journal of Investigative Dermatology, Conway etal. (2021) show the significance of the CpG island methylator phenotype (CIMP) subclass in early-stage invasive primary melanomas, particularly in the lentigo maligna melanoma histological subtype. CIMP melanomas had reduced melanoma-specific survival compared with intermediate and low methylation subtypes. This study emphasizes the importance of epigenomic changes in early-stage primary tumors that are associated with poor prognosis.

Genomic imprinting of the IGF2R/AIR locus is conserved between bovines and mice

Genomic imprinting is an epigenetic phenomenon that leads to genes monoallelically expressed in a parent-of-origin-specific manner and plays an important role in the embryonic development and postnatal growth of mammals. Imprinted genes usually occur in clusters in a chromosomal region and are regulated by a cis-acting imprinting control region that involves differential DNA methylation modification. Igf2r, Slc22a2 and Slc22a3 are three maternally expressed genes on mouse chromosome 17. The paternally expressed long noncoding RNA (lncRNA) Air and the nonimprinted gene Slc22a1 are also located in the imprinted region. Comparative characterization of imprinted clusters between species is useful for us to understand the biological significance and epigenetic regulating mechanism of genomic imprinting. The aim of this study was to analyze the allelic expression pattern of AIR and SLC22A1-3 genes in cattle and to determine the role of DNA methylation in regulating gene expression. Allelic expression analysis was performed in bovine adult tissues and term placenta using an SNP-based approach. We found that IGF2R, AIR and SLC22A3 were monoallelically expressed in all detected bovine somatic tissues, including heart, liver, spleen, lung, kidney, muscle, fat and brain. In bovine placenta, IGF2R and SLC22A3 are maternally expressed; however, the AIR gene is paternally expressed. Tissue-specific monoallelic expression of SLC22A2 is detected in bovines, with monoallelic expression in the spleen and brain but biallelic expression in kidney tissues. SLC22A1 is only detected in bovine liver and kidney tissues and is biallelicly expressed, which is consistent with the imprint expression in mice. To determine the possible role of DNA methylation in regulating the monoallelic/imprinted expression of bovine IGF2R, AIR, SLC22A2, and SLC22A3 genes, we analyzed the DNA methylation status of CpG islands in the first exon of SLC22A2, the promoter region of SLC22A3 and region 2 in the second intron of the IGF2R gene by bisulfite sequencing. Two differentially methylated regions (DMRs) were detected in the first exon of bovine SLC22A3 and the common regions of IGF2R and AIR. This suggests that DNA methylation is involved in the regulation of monoallelic/imprinted expression of IGF2R, AIR and SLC22A3 genes in cattle.

Метилирование генов BCL-2, CDKN1A и ATM у лиц, подвергшихся хроническому облучению

DNA methylation is the most common epigenetic modification, caused by ionizing radiation. There may be both hypermethylation, which suppresses transcription of gene promoter regions, and hypomethylation, resulting in gene activation. Both mechanisms may be involved in carcinogenesis. The study was aimed to assess methylation status of CpG islands in the protective system BCL-2, CDKN1A and ATM gene promoters in the peripheral blood cells of the chronically exposed individuals, living in the villages, located along the Techa River, over a long-term period. Methylation of BCL-2, CDKN1A and ATM gene promoter regions in 68 residents of the villages, located along the Techa River (Chelyabinsk region), was assessed by the real-time methylation-specific PCR. The group of exposed individuals included 54 people with accumulated dose to red bone marrow within the range of 0.09–3.51 Gy. The comparison group included 14 people, living in similar economic and social environment, with the dose to red bone marrow, accumulated during the whole life, not exceeding 70 mGy. The pilot study of exposed individuals over a long period of time after chronic low-dose radiation exposure revealed no significant changes in methylation levels of CpG islands in the CDKN1A, BCL-2, ATM gene promoter regions compared to the comparison group. None were revealed in the dose subgroups “87–994 mGy” and “over 1000 mGy”.

HIST2H2BF Potentiates the Propagation of Cancer Stem Cells via Notch Signaling to Promote Malignancy and Liver Metastasis in Colorectal Carcinoma.

BackgroundGrowing evidence demonstrates that the initiation and progression of colorectal carcinoma (CRC) is related to the presence of cancer stem cells (CSCs). However, the mechanism through which the stem cell features of CRC cells are maintained is poorly understood. In this study, we identified the oncogenic histone cluster 2 H2B family member F (HIST2H2BF) and aimed to investigate the function of upregulated HIST2H2BF expression in maintaining the stem cell features of CRC cells, which accelerate the progression of CRC.MethodsHIST2H2BF expression was quantified using real-time polymerase chain reaction, immunohistochemistry, and western blotting. The correlation between CpG island methylation status and HIST2H2BF re-expression was assessed through bisulfite sequencing polymerase chain reaction, methylation-specific polymerase chain reaction, and 5-Aza-dC treatment. Functional assays were performed on CRC cells and mice to investigate the HIST2H2BF-induced stem cell-like and cancer properties of CRC. Using the Notch pathway inhibitor FLI-06, the regulatory effect of HIST2H2BF on downstream Notch signaling was confirmed.ResultsHIST2H2BF was highly expressed in CRC tissues and cell lines. The reactivation of HIST2H2BF in CRC stems at least in part from the hypomethylated CpG islands. CRC patients with high HIST2H2BF expression have poor survival outcomes. Functional studies have shown that HIST2H2BF promotes CSC phenotype, malignancy, and liver metastasis through the activation of Notch signaling in CRC. Blockage of the Notch pathway reduced the stem cell-like and cancer properties.ConclusionOur study suggests that HIST2H2BF upregulation enhances the CSC phenotype, malignancy, and liver metastasis through the activation of Notch signaling in CRC. These results identified a new perspective on the mechanism by which the stem cell features of CRC cells are maintained and highlighted the potential novel therapeutic targets for CRC.