Degree Of DNA Methylation Research Articles

Assessment of the Degree Of DNA Methylation in Lymphocytes аfter а Single Blood Irradiation in vitro

DNA methylation is one of the processes of epigenetic regulation of the genome, which is sensitive to the influence of endogenous and exogenous factors. The effect of ionizing radiation on the genome is accompanied by a change in the degree of DNA methylation, which can be dose-dependent and persist for a long time after radiation exposure. The objective of the study was to assess the degree of DNA methylation of blood lymphocytes after a single exposure to gamma radiation at a dose of 1.5 Gy using wide-genome bisulfite sequencing. The study included 10 conditionally healthy male employees of the ionizing radiation facility who were not exposed to radiation and did not suffer from chronic diseases. The material was whole blood: 0 Gy (control samples) and 1.5 Gy (experimental samples irradiated with gamma radiation). After irradiation with subsequent cultivation of whole blood, DNA isolation and bisulfite sequencing of limited sets of genomic loci (Reduced representation bisulfite sequencing) was performed using XmaI restriction enzyme (XmaI-RRBS). 41 genes were identified, including 26 genes (HOXD4, PADI2, FOXK1, FTCD, PRDM16, TOM1, PPP1R14A, FLNB, OR1F1, RARA, CRTAC1, AP5B1, ARL5C, NOC2L, MAMDC4, FGFRL1, PPFIA3, CUX2, ANKRD20A19P, FAM83H-AS1, CBFA2T3, POLN, MIR4458HG, FNBP1, SPIRE2, and ZSCAN10) have a tendency to hypomethylation DNA, and another 15 genes (CHRNA4, SEPTIN9, ZNF174, ELK3, NFAM1, ALG10, SOX8, KLHL30, URI1, HBZ, KLF14, MYO16, MYEOV, DMKN, and PAX7) tend to have hypermethylated state detected in at least 50٪ of the experimental samples. Thus, the genes identified in this study can be promising markers of radiation exposure and, in the future, be used to develop a new type of biological dosimetry – epigenomic dosimetry of personnel in contact with ionizing radiation sources in the course of their professional activities.

Role of genetics and epigenetics in Graves' orbitopathy.

Objectives The pathogenesis of Graves' orbitopathy (GO) remains to be fully elucidated. Here we reviewed the role of genetics and epigenetics. Design We conducted a PubMed search with the following key words: Graves' orbitopathy, thyroid eye disease; or Graves' ophthalmopathy; or thyroid-associated ophthalmopathy; and: genetic, or epigenetic, or gene expression, or gene mutation, or gene variant, or gene polymorphism, or DNA methylation, or DNA acetylation. Articles in which whole DNA and/or RNA sequencing, proteome and methylome analysis were performed were chosen. Results The different prevalence of GO in the two sexes as well as racial differences suggest that genetics play a role in GO pathogenesis. In addition, the long-lasting phenotype of GO and of patient-derived orbital fibroblasts suggest a genetic or epigenetic mechanism. Although no genes have been found to confer a specific risk for GO, differential gene expression has been reported in orbital fibroblasts from GO patients vs control fibroblasts, suggesting that an epigenetic mechanism may be involved. In this regard, a different degree of DNA methylation, which affects gene expression, has been found between GO and control fibroblasts, which was confirmed by whole methylome analysis. Histone acetylation and deacetylation, which also affect gene expression, remain to be investigated. Conclusions Although pathogenetic gene variants have not been reported, epigenetic mechanisms elicited by an initial autoimmune insult seem to be needed for differential gene expression to occur and, thus, for GO to develop and persist over time.

LncRNA HOTTIP promotes LPS-induced lung epithelial cell injury by recruiting DNMT1 to epigenetically regulate SP-C.

The objective of this study was to elucidate the involvement of the long noncoding RNA (lncRNA) HOTTIP in acute lung injury and understand the underlying mechanisms. Relevant expression of mRNAs and proteins were assessed by qRT-PCR and western blot assays. Cell viability was determined by employing the CCK-8 assay, and apoptosis was quantified through TUNEL staining. The concentration of inflammatory factors was measured by ELISA. The degree of DNA methylation was quantified through MSP assay. The interaction between HOTTIP and DNA methyltransferase 1 (DNMT1) was examined by RIP assay. LPS upregulated HOTTIP, whereas downregulated SP-C level in AEC II cells. HOTTIP knockdown inhibited LPS-induced apoptosis and the secretion of inflammatory cytokines (TNF-α, IL-1β and IL-6) in AEC II cells. Mechanistically, HOTTIP recruited DNMT1 to the SP-C promoter, thereby facilitating DNA methylation of SP-C and suppressing its expression. Additionally, inhibitory of SP-C reversed the effects of HOTTIP or DNMT1 knockdown on apoptosis and inflammation in AEC II cells induced by LPS. HOTTIP recruited DNMT1 to epigenetically inhibit SP-C expression, leading to the promotion of lung epithelial cell injury caused by LPS, suggesting that targeting HOTTIP may be an effective strategy for the therapy of lung epithelial cell injury.

Prenatal exposure to Di(2-ethylhexyl) phthalate and high-fat diet synergistically disrupts gonadal function in male mice†.

Prenatal exposure to Di (2-ethylhexyl) phthalate (DEHP) impairs the reproductive system and causes fertility defects in male offspring. Additionally, high-fat (HF) diet is a risk factor for reproductive disorders in males. In this study, we tested the hypothesis that prenatal exposure to a physiologically relevant dose of DEHP in conjunction with HF diet synergistically impacts reproductive function and fertility in male offspring. Female mice were fed a control or HF diet 7days prior to mating and until their litters were weaned on postnatal day 21. Pregnant dams were exposed to DEHP or vehicle from gestational day 10.5 until birth. The male offspring's gross phenotype, sperm quality, serum hormonal levels, testicular histopathology, and testicular gene expression pattern were analyzed. Male mice born to dams exposed to DEHP + HF had smaller testes, epididymides, and shorter anogenital distance compared with those exposed to HF or DEHP alone. DEHP + HF mice had lower sperm concentration and motility compared with DEHP mice. Moreover, DEHP + HF mice had more apoptotic germ cells, fewer Leydig cells, and lower serum testosterone levels than DEHP mice. Furthermore, testicular mRNA expression of Dnmt1 and Dnmt3a was two to eight-fold higher than in DEHP mice by qPCR, suggesting that maternal HF diet and prenatal DEHP exposure additively impact gonadal function by altering the degree of DNA methylation in the testis. These results suggest that the combined exposure to DEHP and high-fat synergistically impairs reproductive function in male offspring, greater than exposure to DEHP or HF dietalone.

Quantification of DNA Methylation by ELISA in Epigenetic Studies in Plant Tissue Culture: A Theoretical-Practical Guide.

This chapter describes a step-by-step protocol for rapid serological quantification of global DNA methylation by enzyme-linked immunosorbent assay (ELISA) in plant tissue culture specimens. As a case study model, we used the coconut palm (Cocos nucifera), from which plumules were subjected to somatic embryogenesis followed by embryogenic calli multiplication. DNA methylation is one of the most common epigenetic markers in the regulation of gene expression. DNA methylation is generally associated with non-expressed genes, that is, gene silencing under certain conditions, and the degree of DNA methylation can be used as a marker of various physiological processes, both in plants and in animal cells. Methylation consists of adding a methyl radical to carbon 5 of the DNA cytosine base. Herein, the global DNA methylation was quantified by ELISA with antibodies against methylated cytosines using a commercial kit (Zymo-Research™). The method allowed the detection of methylation in total DNA extracts from coconut palm embryogenic calli (arising from somatic embryogenesis) cultivated in liquid or solid media by using antibodies against methylated cytosines and enzymatic development with a colorimetric substrate. Control samplesof commercially provided Escherichia coli bacterial DNA with previously known methylation percentages were included in the ELISA testto construct an experimental methylation standard curve. The logarithmic regression of this E. coli standard curve allowed methylation quantification in coconut palm samples. The present ELISA methodology, applied to coconut palm tissue culture specimens, is promising for use in other plant species and botanical families. This chapter is presented in a suitable format for use as a step-by-step laboratory procedure manual, with theoretical introduction information, which makes it easy to apply the protocol in samples of any biological nature to evaluate DNA global methylation associated with any physiological process.

DNA Methylation-Regulated HOXC8's Role in HER2-Positive Breast Cancer Function and its Contribution to Herceptin Resistance.

The epidermal growth factor receptor 2 (HER2) is overexpressed in 30% of breast cancers, and this overexpression is strongly correlated with a poor prognosis. Herceptin is a common treatment for HER2-positive breast cancer; however, cancer cells tend to adapt gradually to the drug, rendering it ineffective. The study revealed an association between the methylation status of the Homeobox C8 (HOXC8) gene and tumor development. Therefore, it is of paramount importance to delve into the interaction between HOXC8 and HER2-positive breast cancer, along with its molecular mechanisms. This exploration holds significant implications for a deeper understanding of the pathophysiological processes underlying HER2-positive breast cancer. Tumor tissue and pathological data from patients with HER2-positive breast cancer were systematically collected. Additionally, the human HER2-positive breast cancer cell line, SKBR3, was cultured in vitro to assess both the expression level of HOXC8 and the degree of DNA methylation. The study aimed to explore the relationship between the relative expression of HOXC8 and the clinical characteristics of breast cancer patients. The expression level of HOXC8 and the promoter methylation of HOXC8 were verified by methylation treatment of SKBR3 breast cancer cells. The regulation of HOXC8 was meticulously carried out, leading to the division of the cells into distinct groups. The study further analyzed the expression levels and biological capabilities within each group. Finally, the in vitro and in vivo sensitivity of the cells to Herceptin, a common treatment for HER2-positive breast cancer, was measured to assess the efficacy of the drug. In HER2-positive breast cancer cases characterized by poor methylation, there was an up-regulation of HOXC8. Its expression was found to be correlated with key clinical factors such as tumor size, lymph node status, clinical tumor, node, metastasis (cTNM) staging, and Herceptin resistance (p < 0.05). Upon methylation of breast cancer cells, there was a significant decrease in HOXC8 expression (p < 0.05). The study revealed that overexpression of HOXC8 resulted in increased proliferation, cloning, and metastasis of HER2-positive breast cancer cells, along with a reduced apoptosis rate (p < 0.05). Conversely, interference with HOXC8 expression reversed this scenario (p < 0.05). A Herceptin-resistant substrain, POOL2, was established using SKBR3 cells. Animal studies demonstrated that overexpressing HOXC8 accelerated tumor development and enhanced POOL2 cells' resistance to Herceptin (p < 0.05). However, following interference with HOXC8, POOL2 cells exhibited increased responsiveness to Herceptin, leading to a gradual reduction in tumor size (p < 0.05). In HER2-positive breast cancer, the expression of HOXC8 is elevated in a manner dependent on DNA methylation, and this elevated expression is closely linked to the pathology of the patient. Interfering with HOXC8 expression demonstrates the potential to partially inhibit the development and spread of breast cancer, as well as to alleviate resistance to Herceptin.

Age-related promoter-switch regulates Runx1 expression in adult rat hearts

BackgroundRunt-related transcription factor-1 (RUNX1), a key member of the core-binding factor family of transcription factors, has emerged as a novel therapeutic target for cardiovascular disease. There is an urgent need to fully understand the expression pattern of Runx1 in the heart and the mechanisms by which it is controlled under normal conditions and in response to disease. The expression of Runx1 is regulated at the transcriptional level by two promoters designated P1 and P2. Alternative usage of these two promoters creates differential mRNA transcripts diversified in distribution and translational potential. While the significance of P1/P2 promoter-switch in the transcriptional control of Runx1 has been highlighted in the embryogenic process, very little is known about the level of P1- and P2-specific transcripts in adult hearts, and the underlying mechanisms controlling the promoter-switch.MethodsTo amplify P1/P2 specific sequences in the heart, we used two different sense primers complementary to either P1 or P2 5'-regions to monitor the expression of P1/P2 transcripts. DNA methylation levels were assessed at the Runx1 promoter regions. Rats were grouped by age.ResultsThe expression levels of both P1- and P2-derived Runx1 transcripts were decreased in older rats when compared with that in young adults, paralleled with an age-dependent decline in Runx1 protein level. Furthermore, older rats demonstrated a higher degree of DNA methylation at Runx1 promoter regions. Alternative promoter usage was observed in hearts with increased age, as reflected by altered P1:P2 mRNA ratio.ConclusionOur data demonstrate that the expression of Runx1 in the heart is age-dependent and underscore the importance of gene methylation in the promoter-mediated transcriptional control of Runx1, thereby providing new insights to the role of epigenetic regulation in the heart.

Assessing the Association of the Degree of DNA Methylation and the Frequency of Chromosomal Aberrations in Human Lymphocytes in a Single Irradiation of Blood &lt;i&gt;in vitro&lt;/i&gt;

The most sensitive biomolecule under radiation exposure is DNA, whose damage manifests itself in the form of chromosomal aberrations (CA). The processes of DNA methylation, which are involved in the regulation of gene expression, replication, DNA repair, etc., are also affected by gamma radiation. The aim of the study was to evaluate the relationship between the degree of DNA methylation and the frequency of CA after acute in vitro irradiation of human blood lymphocytes with gamma radiation. The study involved 10 conditionally healthy workers of the Siberian Chemical Combine, in whose blood lymphocytes the degree of methylation of CpG-dinucleotides (wide-genome bisulfite sequencing, XmaI-Reduced representation bisulfite sequencing – XmaI-RRBS) and the frequency of CA (cytogenetic study) after acute in vitro blood irradiation with doses of 0 and 1.5 Gy were evaluated. After acute exposure to gamma radiation in lymphocytes, the frequency of aberrant cells, dicentric chromosomes, chromatid and chromosomal fragments increased. Correlation analysis of the status of CpG-dinucleotide methylation and the frequency of CA revealed changes in the degree of methylation of 97 genes, which strongly correlated positively (56 genes) or negatively (41 genes) with an increased frequency of CA. A primary genome-wide screening of genes whose methylation is correlates with a high frequency of CA was carried out. Many of the identified genes are promising as potential markers of radiation exposure and to study the mechanisms of formation of radiosensitivity of the body and radioresistance of tumors during radiation therapy.

Assessing the Association of the Degree of DNA Methylation and the Frequency of Chromosomal Aberrations in Human Lymphocytes in a Single Irradiation of Blood In Vitro

Assessing the Association of the Degree of DNA Methylation and the Frequency of Chromosomal Aberrations in Human Lymphocytes in a Single Irradiation of Blood In Vitro

Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.)

BackgroundHeterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages.ResultsTranscriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid.ConclusionsThese multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.

Posterior fossa ependymomas in children and adolescents - the state of the art

Central nervous system tumors in pediatric patients represent the most frequent solid tumor type in this age group, especially ependymomas, which comprise 5% of childhood intracranial tumors, and occur mainly in the posterior fossa. The MEDLINE and ClinicalTrials databases were searched for studies on posterior fossa ependymomas, 64 studies met the search criteria. &#x0D; Symptoms include ataxia, vertigo, headache, vomiting, cranial nerve palsies, or papilledema, resulting from intracranial hypertension due to obstruction of CSF circulation. Imaging examination often reveals posterior fossa ependymomas in the fourth ventricle or cerebellopontine angle; they may extend through the foramina of Luschka, Magendie, and/or magnum. These tumors cause a significant mass effect, displacing rather than invading the hidbrain, and may involve vessels or cranial nerves, making surgical resection difficult. Various radiological features have been studied to distinguish between ependymomas and other histological types, as well as between ependymoma subtypes. &#x0D; The 2021 WHO classification of central nervous system tumors classifies ependymomas by location. Three types occur in the posterior fossa: subependymomas, PF-A, and PF-B. These are differentiated by the degree of DNA methylation and CpG islands, which can be assessed by immunohistochemical analysis with H3K27me3. &#x0D; The consensus on the treatment of posterior fossa ependymomas in children advocates the maximum possible surgical resection, followed by radiotherapy in patients &gt;1 year. Chemotherapy remains controversial, with no survival gain. Recent studies suggest molecular subgroups as an independent prognostic factor in posterior fossa ependymomas. The therapeutic challenge of ependymomas requires new treatment options, based on new technologies and molecular discoveries.

Learning models for classifying Raman spectra of genomic DNA from tumor subtypes

An early and accurate detection of different subtypes of tumors is crucial for an effective guidance to personalized therapy and in predicting the ability of tumor to metastasize. Here we exploit the Surface Enhanced Raman Scattering (SERS) platform, based on disordered silver coated silicon nanowires (Ag/SiNWs), to efficiently discriminate genomic DNA of different subtypes of melanoma and colon tumors. The diagnostic information is obtained by performing label free Raman maps of the dried drops of DNA solutions onto the Ag/NWs mat and leveraging the classification ability of learning models to reveal the specific and distinct physico-chemical interaction of tumor DNA molecules with the Ag/NW, here supposed to be partly caused by a different DNA methylation degree.

Genome-wide DNA methylation analysis reveals different methylation patterns in Chinese indigenous sheep with different type of tail.

The study was aimed to analyze the difference of genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which the typical breeds with different type tails, as to screen the differentially methylated genes (DMGs) that affect the type of tails. In this study, three Lanzhou Large-tailed sheep, three Altay sheep and three Tibetan sheep were detected by whole genome bisulfite sequencing (WGBS). The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed. The candidate genes affecting the tail type of sheep were identified by GO and KEGG pathway enrichment analysis of DMGs. we identified 68,603 different methylated regions (DMCs) and 75 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in biological process, cellular component and molecular function, Some of the genes in these pathways are involved in fat metabolism: NFATC4, LPIN2, MGAT2 and MAT2B. Our results may help to further understand the epigenetic regulation mechanisms of deposition of fat in the tail of sheep and provide new basic data for the study of local sheep.

DSTN Hypomethylation Promotes Radiotherapy Resistance of Rectal Cancer by Activating the Wnt/β-Catenin Signaling Pathway

Although surgical resection combined with neoadjuvant radiation therapy can reduce the local recurrence rate of rectal cancer, not all patients benefit from neoadjuvant radiation therapy. Therefore, screening for patients with rectal cancer who are sensitive or resistant to radiation therapy has great clinical significance. Patients with rectal cancer were selected according to postoperative tumor regression grade, and tumor samples were taken for detection. Differential genes between radiation-resistant and radiation-sensitive tissues were screened and validated by Illumina Infinium MethylationEPIC BeadChip, proteomics, Agena MassARRAY methylation, reverse transcription quantitative real-time polymerase chain reaction, and immunohistochemistry. In vitro and in vivo functional experiments verified the role of DSTN. Protein coimmunoprecipitation, western blot, and immunofluorescence were used to investigate the mechanisms of DSTN-related radiation resistance. DSTN was found to be highly expressed (P < .05) and hypomethylated (P < .01) in rectal cancer tissues resistant to neoadjuvant radiation therapy. Follow-up data confirmed that patients with high expression of DSTN in neoadjuvant radiation therapy-resistant rectal cancer tissues had shorter disease-free survival (P < .05). DSTN expression increased after methyltransferase inhibitor inhibition of DNA methylation in colorectal cancer cells (P < .05). In vitro and in vivo experiments showed that knockdown of DSTN promoted the sensitivity of colorectal cancer cells to radiation therapy, and overexpression of DSTN promoted the resistance of colorectal cancer cells to radiation (P < .05). The Wnt/β-catenin signaling pathway was activated in colorectal cancer cells overexpressing DSTN. β-catenin was highly expressed in radiation therapy-resistant tissues, and there was a linear correlation between the expression of DSTN and β-catenin (P < .0001). Further studies showed that DSTN can bind to β-catenin and increase its stability. The degree of DNA methylation and the expression level of DSTN can be used as biomarkers to predict the sensitivity of neoadjuvant radiation therapy for rectal cancer. DSTN and β-catenin are also expected to become a reference for the selection of neoadjuvant radiation therapy.

Epigenetic modification of gene expression in cancer cells by terahertz demethylation

Terahertz (THz) radiation can affect the degree of DNA methylation, the spectral characteristics of which exist in the terahertz region. DNA methylation is an epigenetic modification in which a methyl (CH3) group is attached to cytosine, a nucleobase in human DNA. Appropriately controlled DNA methylation leads to proper regulation of gene expression. However, abnormal gene expression that departs from controlled genetic transcription through aberrant DNA methylation may occur in cancer or other diseases. In this study, we demonstrate the modification of gene expression in cells by THz demethylation using resonant THz radiation. Using an enzyme-linked immunosorbent assay, we observed changes in the degree of global DNA methylation in the SK-MEL-3 melanoma cell line under irradiation with 1.6-THz radiation with limited spectral bandwidth. Resonant THz radiation demethylated living melanoma cells by 19%, with no significant occurrence of apurinic/apyrimidinic sites, and the demethylation ratio was linearly proportional to the power of THz radiation. THz demethylation downregulates FOS, JUN, and CXCL8 genes, which are involved in cancer and apoptosis pathways. Our results show that THz demethylation has the potential to be a gene expression modifier with promising applications in cancer treatment.

Genome-wide analysis of DNA methylation reveals significant impact of two typical high temperature stress on biological functions in Apostichopus japonicus

Sea cucumber Apostichopus japonicus, an important marine benthic animal, is particularly sensitive to environmental temperature stress, which affected the growth, metabolism, and reproduction even survival. In this study, we used whole genome bisulfite sequencing (WGBS) to perform a comprehensive comparative analysis of the DNA methylation profiles of A. japonicus at three temperatures: normal (20 °C), aestivation (26 °C), and lethal (32 °C). The results showed that the total methylation level was highest in group T26 and lowest in group T32. Most of the DNA methylation occurred on the C bases of the CG type, and the degree of DNA methylation on the CG-type C bases was 13.32–14.99%, reflecting a moderate level of DNA methylation. Comparison of differentially methylated regions (DMRs) in the CG sequence context, we identified 17,174 DMRs in group T26_vs_T20 and 16,216 DMRs in group T32_vs_T26. There were more hypermethylated regions than hypomethylated regions, and this difference was more obvious in group T32_vs_T26. DMRs analysis of the promoter regions and the gene body regions identified more DMR-related genes in the gene body region than in the promoter region in both comparison groups (T26_vs_T20 and T32_vs_T26). GO and KEGG analysis showed that pathways such as protein processing in the endoplasmic reticulum, ubiquitin mediated proteolysis, and endocytosis, etc., were highly enriched in the DMR-related genes in the comparison groups. Some of these pathways that were significantly enriched in the hypermethylated genes in group T26_vs_T20 but were enriched in the hypomethylated genes in group T32_vs_T26. Enrichment analysis of genes both differentially methylated and differentially expressed showed that downregulated genes in group T32_vs_T26 that were also hypomethylated in the gene body region were significantly enriched in the metabolic and the antioxidant-related glutathione metabolism pathway. Our results suggested that DNA methylation develop a lot of variation in the regulation of the response of A. japonicus to two levels of heat stress: at aestivation temperature and at lethal temperature, and there are many differences between the two. The results of this study provide important insights into the epigenetic mechanisms underlying the response of A. japonicus to the pressure of environmental temperature.

No strong association among epigenetic modifications by DNA methylation, telomere length, and physical fitness in biological aging

Cellular senescence is greatly accelerated by telomere shortening, and the steps forward in human aging are strongly influenced by environmental and lifestyle factors, whether DNA methylation (DNAm) is affected by exercise training, remains unclear. In the present study, we investigated the relationships between physiological functions, maximal oxygen uptake (VO2max), vertical jump, working memory, telomere length (TL) assessed by RT-PCR, DNA methylation-based estimation of TL (DNAmTL), and DNA methylation-based biomarkers of aging of master rowers (N = 146) and sedentary subjects (N = 95), aged between 37 and 85 years. It was found that the TL inversely correlated with chronological age. We could not detect an association between telomere length and VO2max, vertical jump, and working memory by RT-PCR method, while these physiological test results showed a correlation with DNAmTL. DNAmGrimAge and DNAmPhenoAge acceleration were inversely associated with telomere length assessed by both methods. It appears that there are no strong beneficial effects of exercise or physiological fitness on telomere shortening, however, the degree of DNA methylation is associated with telomere length.

Abstract A081: Epigenetic regulation of SPDEF gene in RCC7/T cells, a line of malignant African-American prostate epithelial cells

Abstract Background: Prostate cancer (PCa) in African American (AA) men has an earlier onset, more aggressiveness with higher metastasis and mortality rate than in Caucasian men. SAM-pointed domain-containing Ets-like factor (SPDEF) has been identified as a possible suppressor of metastasis in castration-resistant prostate cancer (CRPC) in earlier investigations. Ongoing studies in our lab are focused on deciphering the role of SPDEF in PCa progression and metastasis with special emphasis on PCa in AA men. We discovered that SPDEF expression is lost in RCC7/T cells, and re-expression of SPDEF limits metastatic properties of these cells, however, the regulatory mechanisms underlying the loss of SPDEF have not been elucidated. In the current study, we investigated the role of epigenetic modulators (DNA methylation and histone modifications) in driving the loss of SPDEF. Methods: We analyzed publicly available data sets from TCGA (GDC TCGA Prostate Cancer, and TCGA Prostate Cancer (PRAD) for DNA methylation using Xena UCSC genome browser (https://xena.ucsc.edu/). We also analyzed histone ChIP-seq data from PCa cell lines using cistrome project (http://cistrome.org/db/#/). RCC7/T cells were grown in DMEM and maintained at 37°C in a humidified incubator. We used bisulfite sequencing (BSP) to examine DNA methylation in SPDEF gene in SPDEF proficient (LNCaP) and deficient (RCC7/T) cells. We also employed the ChIP-qPCR to reveal the active and repressive key histone marks (H3K4me3, H3K27ac, and H3K27me3) across the SPDEF gene. Results: In the clinical cohorts, SPDEF expression showed an inverse correlation with the degree of DNA methylation and expression of the epigenetic writer enzymes such as DNMT1 and EZH2. Our results revealed that the CpG islands in SPDEF gene are hyper-methylated in RCC7/T cells compared to LNCaP cells. Our analysis of the data from the cistrome project revealed an elevated enhancer repressive mark H3K27me3 (marked by EZH2) and a decreased promoter active mark, H3K4me3, in PC3 cells as compared with less metastatic LNCaP cells. Our results from ChIP-qPCR confirmed these findings. Moreover, we observed the methylation profiles in RCC7/T cells were similar to those of PC3 cells. Additionally, combination treatment with 5-aza-2-deoxycytidine (DNMT inhibitor) and GSK-126 (EZH2 inhibitor) increased the PDEF expressions levels and also restricted colony formation, migration and invasion in RCC7/T cells. Conclusion: Overall, these findings reveal an inverse correlation between expression of epigenetic writers (DNMT1 and EZH2) and SPDEF expression in PCa. Our results also suggest that SPDEF expression in PCa is regulated in part by epigenetic modifications, and that combined inhibition of DNMT1 and EZH2 may offer a therapeutic benefit in subsets of PCa patients including in AA men. Acknowledgements: These studies were funded in part by NIH/NCI-7R01CA242839 (HK) and unrestricted funds from the LSU-LCMC Cancer Center, School of Medicine -LSUHSC, New Orleans (HK). Grateful to LCU-LCMC Genomics core for DNA sequencing Citation Format: Mousa Vatanmakanian, Sweaty Koul, Thangavel Chellappagounder, Hari K. Koul. Epigenetic regulation of SPDEF gene in RCC7/T cells, a line of malignant African-American prostate epithelial cells [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A081.

Transcriptomic Network Regulation of Rat Tooth Germ from Bell Differentiation Stage to Secretory Stage: MAPK Signaling Pathway Is Crucial to Extracellular Matrix Remodeling.

Hard tissues make up the vast majority of teeth and are mineralized from the surrounding matrix. If the development of tooth germ is affected during mineralization, hypoplasia of the tooth tissue can occur. To better understand the mechanisms mediating hypoplasia, we need to first study normal development. Using a rodent model, we highlight the transcriptomic changes that occur from the differentiation to secretion stages of mandibular molar germs. The tooth germ was dissected from rats at postnatal day 1.5 or 3.5 for high-throughput sequencing. Combining transcriptome analysis and DNA methylation, we identified 590 differentially expressed genes (436 upregulated and 154 downregulated) and 551 differentially expressed lncRNAs (long noncoding RNA; 369 upregulated and 182 downregulated) which were linked to the biological processes of odontogenesis, amelogenesis, tooth mineralization, and the alteration of extracellular matrix (ECM), especially matrix metalloproteinases (MMPs) and elastin. We found DNA methylation changes in 32 selected fragments involved in 5 chromosomes, 26 targets, and 2 haplotypes. Finally, three novel genes were identified: MMP20, Tgfb3, and Dusp1. Further analysis revealed that MMP20 has a role in odontogenesis and amelogenesis by influencing Slc24a4 and DSPP; Tgfb3 is involved in epithelial cell proliferation, cellular component disassembly process, ECM cellular component, and decomposition of cell components. But lncRNA expression could affect DNA methylation and mRNA expression. Moreover, the degree of DNA methylation could also affect the transcriptome level. Thus, Tgfb3 had no difference in DNA methylation, and Dusp1 conferred no difference at the transcriptome level. These three genes were all enriched in the MAPK pathway and played an important role in ECM remodeling. These data suggest that during the period of the bell differentiation stage to the secretory stage, along with enamel/dentin matrix secretion and hard tissue occurrence, the ECM is remodeled via MAPK signaling.

Plasma EBV DNA Methylation: Evidence of EBV Lytic Infection in HIV(+) EBV(+) Plasmablastic Lymphoma

Background: Among people living with HIV, plasmablastic lymphoma (PBL) and classical Hodgkin lymphoma (HL) are almost uniformly associated with Epstein-Barr virus (EBV). Immunohistochemical studies have demonstrated high levels of lytic gene expression in PL,1 whereas EBV(+) HL shows exclusively latent viral gene expression. EBV virion DNA is never CpG methylated, but tumor-derived plasma EBV is CpG methylated as previously shown by our group in EBV(+) HL and nasopharyngeal carcinoma (NPC).2 Others have also presented evidence that patterns of CpG methylation of plasma EBV DNA varies between people with NPC and non-malignant EBV(+) conditions.3 To better characterize the nature of plasma EBV in patients with lymphoma, we investigated EBV DNA copy number and EBV DNA methylation in HIV-associated PBL and HL. Methods: With appropriate approvals from the Human Research Ethics Committee of the University of the Witwatersrand and the Johns Hopkins Institutional Review Boards, we collected plasma from newly diagnosed untreated patients with HIV and PBL or HL in Johannesburg, South Africa. Diagnostic biopsy specimens were reviewed in Baltimore by a hematopathologist to confirm the diagnosis and Epstein-Barr encoding region (EBER) in situ hybridization was performed to determine EBV association. Plasma EBV copies were measured by standard qPCR targeting the BamW repeats. qPCR using the same primers was also performed after capture with methyl-DNA binding protein 2 (MBD2) magnetic beads, where the captured fraction represents methylated DNA and the flow-through represents unmethylated DNA. Results: We studied plasma from 7 patients with PBL and 12 patients with HL. Four of five PBL tumors were EBV (+) and eight of 10 HL tumors were EBV (+) by tissue EBER in situ hybridization. Analysis of plasma EBV DNA copy number showed overlapping levels of EBV DNA (median 2.7 Log10 copy/mL in PBL and 3.2 Log10 copy/mL in HL) (Fig. 1). Patients with at least 1.5 Log10 copy/mL of EBV underwent CpG methylation evaluation, which showed very different EBV CpG methylation indices. The EBV methylation index was highly variable in PBL (median of 51%) and was uniformly high in HL (median of 97%). Conclusions: Although plasma from plasmablastic lymphoma patients show high EBV copy number, the characteristic of that EBV DNA is very different from the plasma EBV detected in Hodgkin lymphoma patients. This difference is hypothesized to be related to evidence of viral lytic gene expression seen in PBL. The degree of plasma EBV DNA methylation may have broad implications for lymphoma diagnosis and subtyping.