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As a treasure trove of natural products (NPs), various fungal species possess great potential as cell factories for valuable NPs bioproduction. However, they have many silent biosynthetic gene clusters (BGCs), and activation of BGCs expression is critical to the discovery of their indetectable NPs, especially secondary metabolites, in which epigenetic regulation plays a significant role. Thanks to the development of sequencing technologies, more and more epigenetic regulators have been characterized and adopted for boosting fungal NPs production. In this review, at first we summarize various kinds of epigenetic regulation and relevant strategies for triggering fungal NPs biosynthesis. Then, we discuss the limitations of the current strategies, and propose future trends in the discovery of fungi derived NPs by manipulating epigenetics. • Epigenetic regulation plays a significant role in discovery of the undetectable natural products from fungal species. • Manipulating histone-modifying proteins is a novel manner to activate the expression of biosynthetic gene clusters. • This work provides a systematical view on triggering fungal natural products biosynthesis by epigenetic regulation. [ABSTRACT FROM AUTHOR]

METTL3-mediated N6-methyladenosine (m6A) modification is critical for gametogenesis and early embryonic development. However, the function of METTL3-mediated m6A modification in the early development of somatic nuclear transfer embryos (SCNT) remains unclear. Here, we found that METTL3 mRNA and protein levels exhibit dynamic changes during the early development of porcine SCNT embryos. The levels of METTL3 mRNA and protein in SCNT embryos at specific developmental stages differ from those in parthenogenetic activation (PA) counterparts. SiRNA injection effectively reduced the levels of METTL3 mRNA and protein in 4-cell embryos and blastocysts. METTL3 knockdown significantly reduced the cleavage and blastocyst rates of SCNT embryos. METTL3 knockdown significantly reduced the number of total cells and trophectoderm (TE) cells in the resulting blastocysts and perturbed cell lineage allocation. In addition, METTL3 knockdown reduced the levels of m6A modification in 4-cell embryos and blastocysts. Importantly, METTL3 knockdown decreased the expression levels of CDX2 , GATA3 , NANOG and YAP , and increased the expression levels of SOX2 and OCT4. Taken together, these results demonstrate that METTL3-mediated m6A modification regulates early development and lineage differentiation of porcine SCNT embryos. [ABSTRACT FROM AUTHOR]

The presence of abundant tumor stroma is a prominent characteristic of pancreatic ductal adenocarcinomas (PDAC) that potentially influences disease progression and therapy response. This study aims to investigate immune cell infiltration and epigenetic profiles in tumor cell enriched ("Tumor") and stroma cell enriched ("Stroma") regions within human PDAC tissue samples. By comparing those regions, we identified 25,410 differentially methylated positions (DMPs) distributed across 6,963 unique genes. Pathway enrichment analysis using the top 2,000 DMPs that were either hyper- or hypomethylated indicated that immune response pathways and the estrogen receptor pathway are epigenetically dysregulated in Tumor and Stroma regions, respectively. In terms of immune cell infiltration, we observed overall low levels of T cells in both regions. In Tumor regions however, occurrence of tumor-associated macrophages (TAMs) was higher than in Stroma regions (p = 0.02) concomitant with a dualistic distribution that stratifies PDAC patients into those with high and low TAM infiltration. By categorizing TAM levels into quartiles, our analysis revealed that PDAC patients with more than 1,515 TAMs per mm² exhibited significantly shorter overall survival (p = 0.036). Our data suggest that variations in inflammatory characteristics between the Tumor and Stroma defined compartments of PDAC may primarily stem from the presence of macrophages rather than lymphocytes. The abundance of TAMs within regions enriched with tumor cells correlates with patient survival, underscoring the potential significance of exploring therapeutic interventions targeting TAMs. Furthermore, directing attention towards the estrogen receptor pathway may represent a promising strategy to address the stroma cell component within the PDAC tumor microenvironment. [ABSTRACT FROM AUTHOR]

Early life adversity is a risk factor for psychopathology and is associated with epigenetic alterations in the 5-HT 1A receptor gene promoter. The 5-HT 1A receptor mediates neurotrophic effects, which could affect brain structure and function. We examined relationships between self-reported early childhood abuse, 5-HT 1A receptor promoter DNA methylation, and gray matter volume (GMV) in Major Depressive Disorder (MDD). Peripheral DNA methylation of 5-HT 1A receptor promoter CpG sites −681 and −1007 was assayed in 50 individuals with MDD, including 18 with a history of childhood abuse. T1-weighted structural magnetic resonance imaging (MRI) was performed. Voxel-based morphometry (VBM) was quantified in amygdala, hippocampus, insula, occipital lobe, orbitofrontal cortex, temporal lobe, parietal lobe, and at the voxel level. No relationship was observed between DNA methylation and history of childhood abuse. We observed regional heterogeneity comparing −681 CpG site methylation and GMV (p = 0.014), with a positive relationship to GMV in orbitofrontal cortex (p = 0.035). Childhood abuse history was associated with higher GMV considering all ROIs simultaneously (p < 0.01). In whole-brain analyses, childhood abuse history was positively correlated with GMV in multiple clusters, including insula and orbitofrontal cortex (p FWE = 0.005), and negatively in intracalcarine cortex (p FWE = 0.001). Small sample size, childhood trauma assessment instrument used, and assay of peripheral, rather than CNS, methylation. These cross-sectional findings support hypotheses of 5-HT 1A receptor-related neurotrophic effects, and of increased regional GMV as a potential regulatory mechanism in the setting of childhood abuse. Orbitofrontal cortex was uniquely associated with both childhood abuse history and 5-HT 1A receptor methylation. • Methylation positively correlated with orbitofrontal cortex gray matter volume • Supports neurotrophic effects of serotonin 1A receptors in major depressive disorder • Orbitofrontal cortex may be susceptible to stress-associated epigenetic changes • History of childhood abuse associated with higher gray matter volume • May be compensatory response after childhood adversity [ABSTRACT FROM AUTHOR]

In an unmodified state, positively charged histone N-terminal tails engage nucleosomal DNA in a manner which restricts access to not only the underlying DNA but also key tail residues subject to binding and/or modification. Charge-neutralizing modifications, such as histone acetylation, serve to disrupt this DNA–tail interaction, facilitating access to such residues. We previously showed that a polyacetylation-mediated chromatin “switch” governs the read-write capability of H3K4me3 by the MLL1 methyltransferase complex. Here, we discern the relative contributions of site-specific acetylation states along the H3 tail and extend our interrogation to other chromatin modifiers. We show that the contributions of H3 tail acetylation to H3K4 methylation by MLL1 are highly variable, with H3K18 and H3K23 acetylation exhibiting robust stimulatory effects and that this extends to the related H3K4 methyltransferase complex, MLL4. We show that H3K4me1 and H3K4me3 are found preferentially co-enriched with H3 Nterminal tail proteoforms bearing dual H3K18 and H3K23 acetylation (H3{K18acK23ac}). We further show that this effect is specific to H3K4 methylation, while methyltransferases targeting other H3 tail residues (H3K9, H3K27, & H3K36), a methyltransferase targeting the nucleosome core (H3K79), and a kinase targeting a residue directly adjacent to H3K4 (H3T3) are insensitive to tail acetylation. Together, these findings indicate a unique and robust stimulation of H3K4 methylation by H3K18 and H3K23 acetylation and provide key insight into why H3K4 methylation is often associated with histone acetylation in the context of active gene expression. [ABSTRACT FROM AUTHOR]

[Display omitted] Penicillium expansum is a harmful plant fungal pathogen that causes blue mold disease and produces mycotoxin patulin, leading to huge economic losses and food safety hazard. Set1 associated complex Set1/COMPASS deposits the methylation at lysine 4 of histone H3, which is associated with gene expression in diverse biological processes of fungi. However, the function and underlying mechanisms of Set1/COMPASS are poorly defined in P. expansum. The study aimed to identify Set1/COMPASS and investigate its regulation mechanisms on growth, pathogenicity, and patulin biosynthesis of P. expansum. Analyses of phylogenetic relationship, conserved structural domain, and gene deletion were used to identify components of Set1/COMPASS. Phenotype analysis and stress tolerance test of gene deletion mutants were conducted to analyze the function of these components. Yeast two-hybrid, Co-Immunoprecipitation (Co-IP), and point mutation were performed to verify the protein interaction. Western blot was conducted for detection of H3K4 methylation levels. P. expansum owns six components of Set1/COMPASS besides PeSet1. Absence of each component resulted in reduction of H3K4 methylation levels and impaired growth, pathogenicity, and patulin biosynthesis, as well as altered stress responses of P. expansum. One component PeBre2p was found to interact with the conserved global regulator PeVelB (Ve lvet L ike protein B) at Asp294 of PeBre2p. This interaction affected fungal growth and utilization of fructose, lactose, glycine, and proline in P. expansum. This study revealed the important roles of Set1/COMPASS in P. expansum and clarified for the first time the combined regulation of PeBre2p and PeVelB in fungal growth and nutrition utilization. These results will provide potential targets for the control of blue mold disease. [ABSTRACT FROM AUTHOR]

Diabetes and other metabolic and inflammatory comorbidities are highly associated with osteoarthritis (OA). However, whether early-life hyperglycemia exposure affects susceptibility to long-term OA is still unknown. The purpose of this study was to explore the fetal origins of OA and provide insights into early-life safeguarding for individual health. This study utilized streptozotocin to induce intrauterine hyperglycemia and performed destabilization of the medial meniscus surgery on the knee joints of the offspring mice to induce accelerated OA. Cartilage degeneration-related markers, as well as the expression levels of mitochondrial respiratory chain complexes and mitophagy genes in the adult offspring mice, were investigated. In vitro, mitochondrial function and mitophagy of chondrocyte C28/I2 cells stimulated under high glucose conditions were also evaluated. The methylation levels of the sirt3 gene promoter region in the articular cartilage of intrauterine hyperglycemia-exposed offspring mice were further analyzed. In this study, we found that the intrauterine hyperglycemic environment could lead to an increase in individual susceptibility to OA in late adulthood, mainly due to persistently low levels of Sirt3 expression. Downregulation of Sirt3 causes impaired mitophagy in chondrocytes and abnormal mitochondrial respiratory function due to a failure to clear aged and damaged mitochondria in a timely manner. Overexpressing Sirt3 at the cellular level or using Sirt3 agonists like Honokiol in mouse models can partially rescue mitophagy disorders caused by the hyperglycemic environment and thus alleviate the progression of OA. Our study revealed a significantly increased susceptibility to OA in the gestational diabetes mellitus offspring, which is partly attributed to exposure to adverse factors in utero and ultimately to the onset of disease via epigenetic modulation. [ABSTRACT FROM AUTHOR]

NDRG1, the first member of the NDRG family, is a multifunctional protein associated with carcinogenesis. Its function in human cancer is currently poorly understood. The aim of this study was to explore the importance of NDRG1 in tumor immune cell infiltration and epithelial–mesenchymal transition (EMT) in hepatocellular carcinoma. NDRG1 expression in various cancers was analyzed using TIMER 2.0, the Human Protein Atlas (HPA), UALCAN and PrognoScan. Wound healing, Transwell, MTT and colony formation assays were performed to confirm the effects of NDRG1 on the metastasis and proliferation of HCC cells. Western blotting was used to study the effect of NDRG1 on the expression of EMT-related proteins. Signaling networks were constructed using LinkedOmics and Metascape. TIMER2.0 and TISIDB were used for comprehensive analysis of tumor-infiltrating immune cells and tumor-infiltrating lymphocytes (TILs). NDRG1 expression was higher in HCC tissue than in normal liver tissue at both the mRNA and protein levels. Overexpression of NDRG1 is associated with poor prognosis in HCC patients. Genomic analysis suggests that NDRG1 promoter hypermethylation leads to enhanced transcription, which may be one mechanism for NDRG1 upregulation in HCC. The overexpression of NDRG1 promotes the invasion, migration, and proliferation of HCC cells and induces the expression of EMT-related proteins. Immunoinfiltration analysis suggests that NDRG1 is involved in the recruitment of immune cells. The present study showed that NDRG1 may induce metastasis and invasion through EMT and immune cell infiltration. NDRG1 could be used as a biomarker for the diagnosis and prognosis of HCC and could be a potential therapeutic target in HCC. [ABSTRACT FROM AUTHOR]

Pancreatic ductal adenocarcinoma (PDAC) is the digestive malignancy with poor prognosis, and there is still a lack of effective diagnostic biomarkers. We aimed to explore the diagnostic efficiency of DNA methylation in peripheral blood monocytes (PBMCs) in PDAC. 850K BeadChips were used to detect genome-wide methylation of PBMCs. For the selected sites, MethylTarget assays was used for further verification. The support vector machine was used to establish the combined panel. A total of 167 PDAC patients and 113 healthy controls were included in this study and were divided into three sets. In the discovery set, we found 4625 differentially methylated positions (DMPs) between cancer group and healthy controls. ZFHX3 (0.16 ± 0.04 vs. 0.18 ± 0.04, P = 0.001), cg01904886 (0.84 ± 0.05 vs. 0.81 ± 0.04, P = 0.02) and NUMBL (0.96 ± 0.005 vs. 0.957 ± 0.005, P = 0.04) were found to be significantly different in training set. The locus with more significant differences, namely ZFHX3, was used for further validation and to establish a combined diagnostic panel with CA19-9. In the validation set, the ROC curve indicated that the AUC value of ZFHX3 was 0.75. The AUC value of the combined model (AUC = 0.92) was higher than that of CA19-9 alone (AUC = 0.88). In patients with normal CA19-9 levels, the ZFHX3 methylation biomarker still maintained good diagnostic efficacy (AUC = 0.71). Our study preliminarily suggests that ZFHX3 methylation combined with CA19-9 can improve the detection rate of PDAC. Especially in patients with normal CA19-9, ZFHX3 methylation can maintain stable diagnostic efficacy. The diagnostic value of ZFHX3 methylation still needs to be prospectively validated. [ABSTRACT FROM AUTHOR]

Schizophrenia is associated with chronic subclinical inflammation and decreased integrity of the corpus callosum (CC). Our previous study showed associations between peripheral IL-6 levels and the integrity of the CC. Epigenetic studies show associations between methylation of the genes related to immunological processes and integrity of the CC. To investigate correlations between methylation status of IL-6 promotor and peripheral IL-6 levels and the integrity of the CC in schizophrenia. The participants were 29 chronic schizophrenia patients (SCH) and 29 controls. Decreased integrity of the CC was understood as increased mean diffusivity (MD) and/or decreased fractional anisotropy (FA) in diffusion tensor imaging. Peripheral IL-6 concentrations were measured in serum samples and IL-6 promoter methylation status of 6 CpG sites was analyzed in peripheral leukocytes by pyrosequencing. Moderate positive correlations were found between CpG1 methylation and the MD of proximal regions of the CC (CCR1–CCR3) and between CpG mean and MD of CCR1 in SCH. Weaker positive correlations were found for CpG mean with CCR2 and CCR3 and negative correlations were found for CpG1 and FA of CCR3 in SCH. Multivariate regression showed that methylation of CpG1, type of antipsychotic treatment, and their interaction were significant independent predictors of MD of CCR1 in SCH. Methylation of CpG2 was negatively correlated with serum IL-6 in SCH. The methylation level of the IL-6 promotor region in peripheral leukocytes is associated with the integrity of the CC in schizophrenia and this association may depend on the type of antipsychotic treatment. Further studies are necessary to explain the mechanisms of the observed associations. [ABSTRACT FROM AUTHOR]

[Display omitted] • Fn was positively correlated with METTL3 expression in the ESCC tissues. • Fn-infection induced the upregulated-expression of METTL3 in ESCC. • Fn mediated METTL3/Myc axis to promote ESCC cells proliferation and migration in vitro. • Fn accelerates ESCC tumorigenesis and metastasis via METTL3-mediated c-Myc mRNA m6A modification in vivo. The tumor-associated microbiota plays a vital role in cancer development. Accumulating evidence shows that Fusobacterium nucleatum (Fn) participates in the progression of multiple tumor types. However, the underlying mechanisms remain unclear. This study examined the expression of methyltransferase-like protein 3 (METTL3) during Fn infection and elucidated the function and pathway of Fn-induced m6A methylation in esophageal squamous cell carcinoma (ESCC). The abundance of Fn in patient tissues was determined by qPCR. Western blot, qRT-PCR, and immunohistochemistry were performed to measure METTL3 expression in cells and tissues. METTL3 function was evaluated in vitro by colony formation and cell migration assays. MeRIP-qPCR was performed to determine the relationship between METTL3 and c-Myc. In addition, the half-lives of genes that are downstream of METTL3 were determined with RNA stability assays. Fn was enriched in hepatocellular carcinoma (HCC), breast cancer (BRCA), ESCC, and colorectal cancer (CRC) tumor tissues. METTL3 expression was positively associated with Fn abundance in ESCC tissues. Fn could survive and proliferation as well as increase METTL3 expression in ESCC, HCC, CRC, and BRCA cells. Moreover, METTL3 overexpression promoted ESCC cells proliferation, migration in vivo and in vitro. Mechanistically, Intracellular Fn infection increases METTL3 transcription. METTL3 promoted c-Myc mRNA methylation in the 3′-untranslated Region (3′-UTR) and enhanced its mRNA stability in a YTH N6-Methyladenosine RNA binding protein 1(YTHDF1)-dependent manner, which contributes to Fn induced ESCC proliferation and metastasis. This study indicates that intracellular Fn infection promotes ESCC development and metastasis, and eradicating Fn infection may be a promising strategy for treating ESCC. [ABSTRACT FROM AUTHOR]

Ultraviolet (UV) damage is closely related to skin photoaging and many skin diseases, including dermatic tumors. N6-methyladenosine (m6A) modification is an important epigenetic regulatory mechanism. However, the role of m6A methylation in apoptosis induced by repeated UV irradiation has not been characterized. To explore m6A methylation changes and regulatory mechanisms in the repeated UV-induced skin damage process, especially apoptosis. HaCaT cells and BALB/c-Nu nude mice were exposed to repeated UVB/UVA+UVB irradiation. Colorimetry and flow cytometry were used to measure cellular viability and apoptosis. m6A-modified genes were detected via colorimetry and methylated RNA immunoprecipitation (MeRIP) sequencing. Methyltransferases and demethylases were detected via RT-PCR, western blotting and immunohistochemistry. Transfection of siRNA and plasmid was performed to knock down or overexpress the selected genes. After UVB irradiation, 861 m6A peaks were increased and 425 m6A peaks were decreased in HaCaT cells. The differentially modified genes were enriched in apoptosis-related pathways. The m6A demethylase FTO was decreased in both HaCaT cells and mouse skin after UV damage. Overexpressing FTO could improve cell viability, inhibit apoptosis and decrease RNA-m6A methylation, including LPCAT3-m6A, which increase LPCAT3 expression, cell viability promotion and apoptosis inhibition. Our study identified the cell m6A methylation change lists after repeated UVB irradiation, and revealed that FTO and LPCAT3 play key roles in the m6A methylation pathogenesis of UV-induced skin cell apoptosis. FTO-m6A-LPCAT3 might serve as a novel upstream target for preventing and treating photoaging and UV-induced skin diseases. • FTO-mediated RNA methylation was involved in skin UV damage. • FTO is involved in skin UV damage by regulating cell viability and apoptosis. • m6A modification of LPCAT3 was involved in this process. [ABSTRACT FROM AUTHOR]

Although cognitive remediation therapy (CRT) produces cognitive benefits in schizophrenia, we do not yet understand whether molecular changes are associated with this cognitive improvement. A gene central to synaptic plasticity, the BDNF , has been proposed as one potential route. This study assesses whether BDNF methylation changes following CRT-produced cognitive improvement are detected. A randomized and controlled trial was performed with two groups (CRT, n = 40; TAU: Treatment as Usual, n = 20) on a sample of participants with schizophrenia. CRT was delivered by trained therapists using a web-based computerized program. Mixed Models, where the interaction of treatment (CRT, TAU) by time (T0: 0 weeks, T1: 16 weeks) was the main effect were used. Then, we tested the association between the treatment and methylation changes in three CpG islands of the BDNF gene. CRT group showed significant improvements in some cognitive domains. Between-groups differential changes in 5 CpG units over time were found, 4 in island 1 (CpG1.2, CpG1.7, CpG1.10, CpG1.17) and 1 in island 3 (CpG3.2). CRT group showed increases in methylation in CpG1.2, CpG1.7 and decreases in pG1.10, CpG1.17, and CpG3.2. Differences in the degree of methylation were associated with changes in Speed of Processing, Working Memory, and Verbal Learning within the CRT group. Those findings provide new data on the relationship between cognitive improvement and changes in peripheral methylation levels of BDNF gene, a key factor involved in neuroplasticity regulation. Trial Registration: NCT04278027. [ABSTRACT FROM AUTHOR]

Methionine is a sulfur-containing essential amino acid that is important for a broad array of fundamental cellular processes, and is crucial for the proliferation, stress resistance, and overall functions of both cancer cells and immune cells. Dietary methionine regulates antitumor immunity by directly influencing immune cell function and indirectly modulating the immune system through interactions with the gut microbiota and cancer cells. The ultimate effect of dietary MR on tumor growth and therapeutic response depends on the relative reliance of T cells versus cancer cells on methionine in the tumor microenvironment. Any possible anticancer benefits of dietary MR require careful consideration of the immune system, microbiota, and tumor stage. Methionine restriction (MR) has been shown to suppress tumor growth and improve the responses to various anticancer therapies. However, methionine itself is required for the proliferation, activation, and differentiation of T cells that are crucial for antitumor immunity. The dual impact of methionine, that influences both tumor and immune cells, has generated concerns regarding the potential consequences of MR on T cell immunity and its possible role in promoting cancer. In this review we systemically examine current literature on the interactions between dietary methionine, cancer cells, and immune cells. Based on recent findings on MR in immunocompetent animals, we further discuss how tumor stage-specific methionine dependence of immune cells and cancer cells in the tumor microenvironment could ultimately dictate the response of tumors to MR. [ABSTRACT FROM AUTHOR]

The integration of multiple data sources is becoming increasingly important in the field of medical imaging for the purpose of improving predictions. In this study, we investigated the use of a unique combination of imaging and genomic data to predict the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT). Utilizing a stacking generalization approach, our model achieved promising results. The classification report from the stacking ensemble shows a precision of 0.82, recall of 0.81, and an F1-score of 0.80. These findings demonstrate the potential of integrating diverse data sources in medical imaging to enhance predictive capabilities, specifically in the context of MGMT methylation status. Our study highlights the importance of ongoing research to refine and optimize the integration of multiple data sources, ultimately leading to more accurate predictions and tailored treatment strategies. This research has the potential to significantly impact patient outcomes by facilitating personalized interventions based on precise predictions of MGMT methylation status. [ABSTRACT FROM AUTHOR]

• Our systematic review of publications related to methylation biomarkers in breast cancer identifies potential genes that can be evaluated for non-invasive early detection of breast cancer. • Evaluation of the literature demonstrates that comprehensive prospective studies are yet needed to bring these findings to the patients. Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer. Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review. Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations. Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer. [ABSTRACT FROM AUTHOR]

The N 6-methyladenosine (m6A) modification is the most prevalent modification of eukaryotic mRNAs and plays a crucial role in various physiological processes by regulating the stability or function of target mRNAs. Accumulating evidence has suggested that m6A methylation may be involved in the pathological process of major depressive disorder (MDD), a common neuropsychiatric disorder with an unclear aetiology. Here, we found that the levels of the circular RNA HECW2 (circHECW2) were significantly increased in the plasma of both MDD patients and the chronic unpredictable stress (CUS) mouse model. Notably, the downregulation of circHECW2 attenuated astrocyte dysfunction and depression-like behaviors induced by CUS. Furthermore, we demonstrated that the downregulation of circHECW2 increased the expression of the methylase WTAP, leading to an increase in Gng4 expression via m6A modifications. Our findings provide functional insight into the correlation between circHECW2 and m6A methylation, suggesting that circHECW2 may represent a potential target for MDD treatment. Increased expression of circHECW2 stimulated ubiquitin-mediated degradation of WTAP, resulting in the decreased methylation of Gng4 with a concomitant decrease in Gng4 mRNA stability and expression, and subsequent astrocyte dysfunction. [Display omitted] [ABSTRACT FROM AUTHOR]

• The combination of GE P. putida and RS promoted As methylation and volatilization. • Bioaugmentation and BC+RS promoted As methylation but reduced its volatilization. • The highest As volatilization is the GE P. putida and RS without flooding. • The As methylation ability of GE P. putida was stronger under non-flooded conditions. • Methylated As, DOC and pH in porewater can preferably model the As volatilization. Arsenic (As) fate in paddy fields has been one of the most significant current issues due to the strong As accumulation potential of rice plants under flooded conditions. However, no attempt was done to explore As methylation and volatilization under non-flooded conditions. Herein, we investigated the effects of water management on As methylation and volatilization in three arsenic-contaminated soils enhanced by biostimulation with straw-derived organic matter and bioaugmentation with genetic engineered Pseudomonas putida KT2440 (GE P. putida). Under flooded conditions, the application of biochar (BC), rice straw (RS) and their combination (BC+RS) increased total As in porewater. However, these effects were greatly attenuated under non-flooded conditions. Compared with RS amendment alone, the combination of GE P. putida and RS further promoted the As methylation and volatilization, and the promotion percentage under non-flooded conditions were significantly higher than that under flooded conditions. The combined GE P. putida and RS showed the highest efficiency in As methylation (88 µg/L) and volatilization (415.4 µg/(kg·year)) in the non-flooded soil with moderate As contamination. Finally, stepwise multiple linear regression analysis presented that methylated As, DOC and pH in porewater were the most important factors contributing to As volatilization. Overall, our findings suggest that combination of bioaugmentation with GE P. putida and biostimulation with RS/BC+RS is a potential strategy for bioremediation of arsenic-contaminated soils by enhancing As methylation and volatilization under non-flooded conditions. [Display omitted] [ABSTRACT FROM AUTHOR]

Translation elongation factor 1A (eEFIA) is an essential and highly conserved protein required for protein synthesis in eukaryotes. In both Saccharomyces cerevisiae and human, five different methyltransferases methylate specific residues on eEF1A, making eEF1A the eukaryotic protein targeted by the highest number of dedicated methyltransferases after histone H3. eEF1A methyltransferases are highly selective enzymes, only targeting eEF1A and each targeting just one or two specific residues in eEF1A. However, the mechanism of this selectivity remains poorly understood. To reveal how S. cerevisiae elongation factor methyltransferase 4 (Efm4) specifically methylates eEF1A at K316, we have used AlphaFold-Multimer modeling in combination with cross-linking mass spectrometry (XL-MS) and enzyme mutagenesis. We find that a unique beta-hairpin motif, which extends out from the core methyltransferase fold, is important for the methylation of eEF1A K316 in vitro. An alanine mutation of a single residue on this beta-hairpin, F212, significantly reduces Efm4 activity in vitro and in yeast cells. We show that the equivalent residue in human eEF1A-KMT2 (METTL10), F220, is also important for its activity towards eEF1A in vitro. We further show that the eEF1A guanine nucleotide exchange factor, eEF1Ba, inhibits Efm4 methylation of eEF1A in vitro, likely due to competitive binding. Lastly, we find that phosphorylation of eEF1A at S314 negatively crosstalks with Efm4-mediated methylation of K316. Our findings demon-strate how protein methyltransferases can be highly selective towards a single residue on a single protein in the cell. [ABSTRACT FROM AUTHOR]

Exercise-induced adaptation is achieved by altering the epigenetic landscape of the entire genome leading to the expression of genes involved in various processes including regulatory, metabolic, adaptive, immune, and myogenic functions. Clinical and experimental data suggest that the methylation pattern/levels of promoter/enhancer is not linearly correlated with gene expression and proteome levels during physical activity implying a level of complexity and interplay with other regulatory modulators. It has been shown that a higher level of physical fitness is associated with a slower DNA methylation-based aging clock. There is strong evidence supporting exercise-induced ROS being a key regulatory mediator through overlapping events, both as signaling entities and through oxidative modifications to various protein mediators and DNA molecules. ROS generated by physical activity shapes epigenome both directly and indirectly, a complexity we are beginning to unravel within the epigenetic arrangement. Oxidative modification of guanine to 8-oxoguanine is a non-genotoxic alteration, does not distort DNA helix and serves as an epigenetic-like mark. The reader and eraser of oxidized guanine is the 8-oxoguanine DNA glycosylase 1, contributing to changes in gene expression. In fact, it can modulate methylation patterns of promoters/enhancers consequently leading to multiple phenotypic changes. Here, we provide evidence and discuss the potential roles of exercise-induced ROS in altering cytosine methylation patterns during muscle adaptation processes. [Display omitted] • Physical activity significantly contributes to specific DNA base methylation and oxidation signatures. • ROS modification serves not only for the re-establishment of redox homeostasis but also plays an epigenetic role. • 8-oxoGua functions as a ROS-generated epigenetic-like mark and can potentially interfere with DNA methylation. • OGG1.•8-oxoGua signaling regulates satellite cell functions, providing a new mechanism for muscle regeneration. [ABSTRACT FROM AUTHOR]

Because analytic technologies improve, increasing amounts of data on methylation differences between assisted reproductive technology (ART) and unassisted conceptions are available. However, various studies use different tissue types and different populations in their analyses, making data comparison and integration difficult. To compare and integrate data on genome-wide analyses of methylation differences due to ART, allowing exposure of overarching themes. All studies undertaking genome-wide analysis of human methylation differences due to ART or infertility in any tissue type across the lifespan were assessed for inclusion. Seventeen studies were identified that met the inclusion criteria. One study assessed trophectoderm biopsies, 2 first-trimester placenta, 1 first-trimester fetal tissue, 2 term placenta, 7 cord blood, 3 newborn dried blood spots, 1 childhood buccal smears, 1 childhood peripheral blood, and 2 adult peripheral blood. Eleven studies compared tissues from in vitro fertilization (IVF) conceptions with those of unassisted conceptions, 4 compared intracytoplasmic sperm injection with unassisted conceptions, 4 compared non-IVF fertility treatment (NIFT) with unassisted conceptions, 4 compared NIFT with IVF, and 5 compared an infertile population (conceiving via various methods) with an unassisted presumably fertile population. In studies assessing placental tissue, 1 gene with potential methylation changes due to IVF when compared with unassisted conceptions was identified by 2 studies. In blood, 11 potential genes with methylation changes due to IVF compared with unassisted conceptions were identified by 2 studies, 1 of which was identified by 3 studies. Three potentially affected genes were identified by 2 studies involving blood between intracytoplasmic sperm injection and unassisted populations. There were no overlapping genes identified in any tissue type between NIFT and unassisted populations, between NIFT and IVF, or the infertility combined population when compared with the unassisted fertile population. Comparing studies is challenging due to differing variables between analyses. However, even in similar tissue types and populations, overlapping methylation changes are limited, suggesting that differences due to ART are minimal. Information from this systematic review is significant for providers and patients who provide and use ART to understand methylation risks that may be associated with the technology. [ABSTRACT FROM AUTHOR]

Les papillomavirus humains à haut risque oncogène (HPV-HR) sont des virus à tropisme muqueux dont la persistance est responsable du développement de cancers. Un HPV-HR est retrouvé dans près de 100 % des cas de cancer du col, 90 % des cancers anaux, 50 % des cancers génitaux et 30 % des cancers ORL. Les oncoprotéines E6 et E7 des HPV-HR, l'intégration du génome viral et des mécanisme épigénétiques participent à la mise en place du processus carcinogène. Parmi les marqueurs biologiques associés à la présence de lésions précancéreuses ou cancéreuses, on retrouve la détection et le typage des HPV-HR, le double immunomarquage pl6/Ki67, l'analyse de méthylation des gènes viraux ou cellulaires, l'intégration du génome viral ou encore la sérologie dirigée contre les oncoprotéines virales. Néanmoins, tous ces marqueurs n'ont pas la même performance et celle-ci varie en fonction du type de cancer. Pour celui du col, la détection des HPV-HR a un rôle central dans le dépistage et les autres biomarqueurs, notamment de méthylation, doivent encore être évalués et bénéficier de processus d'automatisation avant de trouver leur place dans l'algorithme de dépistage. Pour le cancer de l'anus, le typage de l'HPV16 a récemment intégré l'algorithme de dépistage tandis que la méthylation et la sérologie doivent encore bénéficier de validations cliniques pour confirmer leur intérêt. Les cancers ORL liés aux HPV ne bénéficient pas, à ce jour, de biomarqueurs pertinents de dépistage. Les nouveaux développés présentent souvent une très bonne sensibilité, mais une spécificité insuffisante pour envisager leur utilisation dans le cadre d'une stratégie de dépistage. High-risk human papillomaviruses (HPV-HR) are viruses with a mucosal tropism whose persistence is responsible for the development of cancers. HPV-HR is found in almost 100 % of cervical cancers, 80 % of anal cancers, 50 % of genital cancers and 30 % of ENT cancers. HPV-HR oncoproteins E6 and E7, viral genome integration and epigenetic mechanisms all play a part in setting up the carcinogenic process. Biological markers associated with the presence of pre-cancerous or cancerous lesions include HPV-HR typing, pl6/Ki67 double immunostaining, viral or cellular gene methylation analysis, viral genome integration and serology directed against viral oncoproteins. However, not all these markers have the same performance, and this varies according to the type of cancer. For cervical cancer, HPV-HR typing plays a central role in screening, while other biomarkers, notably methylation, still need to be evaluated and automated before they can find their place in the screening algorithm. In the case of anal cancer, HPV16 typing has recently been incorporated into the screening algorithm, while methylation and serology have yet to benefit from clinical validation to confirm their value. HPV-related ENT cancers do not currently benefit from relevant screening biomarkers. The new biomarkers that have been developed often have very good sensitivity, but insufficient specificity to be used as part of a screening strategy. [ABSTRACT FROM AUTHOR]

DNA methylation provides an important epigenetic mechanism that critically regulates gene expression, genome imprinting, and retrotransposon silencing. In plants, DNA methylation is prevalent not only in a CG dinucleotide context but also in non-CG contexts, namely CHG and CHH (H = C, T, or A) methylation. It has been established that plant non-CG DNA methylation is highly context dependent, with the +1- and +2-flanking sequences enriched with A/T nucleotides. How DNA sequence, conformation, and dynamics influence non-CG methylation remains elusive. Here, we report structural and biochemical characterizations of the intrinsic substrate preference of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), a plant DNA methyltransferase responsible for establishing all cytosine methylation and maintaining CHH methylation. Among nine CHH motifs, the DRM2 methyltransferase (MTase) domain shows marked substrate preference toward CWW (W = A or T) motifs, correlating well with their relative abundance in planta. Furthermore, we report the crystal structure of DRM2 MTase in complex with a DNA duplex containing a flexible TpA base step at the +1/+2-flanking sites of the target nucleotide. Comparative structural analysis of the DRM2-DNA complexes provides a mechanism by which flanking nucleotide composition impacts DRM2-mediated DNA methylation. Furthermore, the flexibility of the TpA step gives rise to two alternative DNA conformations, resulting in different interactions with DRM2 and consequently temperature-dependent shift of the substrate preference of DRM2. Together, this study provides insights into how the interplay between the conformational dynamics of DNA and temperature as an environmental factor contributes to the context-dependent CHH methylation by DRM2. [ABSTRACT FROM AUTHOR]

Matrix Gla protein (MGP) was first identified as a calcification physiological inhibitor and the causal agent of the Keutel syndrome. MGP has been suggested to play a role in development, cell differentiation, and tumorigenesis. This study aimed to compare MGP expression and methylation status in different tumors and adjacent tissues, using The Cancer Genome Atlas (TCGA) data repository. We investigated if changes in MGP mRNA expression were correlated to cancer progression and whether the correlation coefficients could be used for prognosis. Strong correlations were observed between altered MGP levels and disease progression in breast, kidney, liver, and thyroid cancers, suggesting that it could be used to complement current clinical biomarker assays, for early cancer diagnosis. We have also analyzed MGP methylation and identified CpG sites in its promoter and first intron with clear differences in methylation status between healthy and tumoral tissue providing evidence for epigenetic regulation of MGP transcription. Furthermore, we demonstrate that these alterations correlate with the overall survival of the patients suggesting that its assessment can serve as an independent prognostic indicator of patients' survival. • Differential DNA methylation patterns in MGP promoter were found in different types of TCGA tumors. • MGP gene expression is negatively correlated with DNA methylation. • High Matrix Gla Protein mRNA expression is associated with a short Overall Survival. • MGP mRNA expression as a prognostic factor for patients Overall Survival. [ABSTRACT FROM AUTHOR]

• The DRD2 expression is regulated by its promoter region upstream factors or methylation status. • Cancer cell proliferation improved the upregulation of DRD2 and decreased DRD2's downregulation. • DRD2 plays a critical role in the FLNA-ERK signaling pathway. • DRD2 gene is hypomethylated in hormone-receptor-negative breast cancer or it's high-risk factor. We investigated the effect of stem cell marker dopamine receptor D2 (DRD2) on the proliferation of hormone-receptor-negative breast cancer cells. High-throughput DNA methylation sequencing on an 850 K chip was used to pre-screen breast cancer tissues with significant methylation differences. The expression of DRD2 in breast cancer and normal breast tissues, and clinical risk factors, were detected by pyrophosphoric acid validation and immunohistochemistry. In vitro and in vivo experiments verified the possible molecular signaling pathways. DRD2 promoter region was hypomethylated in hormone-receptor-negative breast cancer or with high-risk factors compared to the normal tissues. The proliferation of breast cancer cells was enhanced after DRD2 was upregulated and decreased after DRD2 was downregulated. In vivo experiments found that tumor growth and the expression of antigen KI-67 (Ki67) and the cluster of differentiation 31 (CD31) were improved by the overexpression of DRD2 and inhibited by the down expression of DRD2. In vivo and in vitro experiments demonstrated the phosphorylation of filamin A and extracellular signal-regulated kinase (FLNA-ERK) was influenced by the expression of DRD2, suggesting DRD2 plays a role in the FLNA-ERK signaling pathway. Methylation inhibitors (5-aza-2-deoxycytidine, 5-azadc) partially reversed the inhibitory effect of DRD2 down expression on cell proliferation, migration, and tumor growth in animal models, indicating that inhibition of DRD2 methylation promotes cancer development. This study demonstrated the DRD2 promoter region is hypomethylated in hormone-receptor-negative breast cancer or with high-risk factors. The methylation status of the DRD2 promoter and FLNA-ERK signaling pathway and the DRD2 expression in breast cancer treatment need to be considered. [ABSTRACT FROM AUTHOR]

The aim of our study was to identify differentially expressed genes associated with abnormal DNA methylation as biomarkers for predicting the outcome of Kidney renal papillary cell carcinoma (KIRP). We identified 8 differentially expressed genes (DEGs) (CSRP1, HLA-DMB, LIFR, LTB4R2, MAP3K14, NR2F1, SECTM1, and VIM) that were independently associated with the OS of KIRP. Time dependent AUC for each ROC of the risk assessment model at 1, 3, 5, and 10-years reached 0.8415, 0.8131, 0.7873, and 0.7667. The risk assessment model was correlated with several immune cells and factors. The AUC value of the diagnosis model using those 8 DEGs reached 0.99. The risk assessment model constructed by those 8 DEGs was well able to predict the prognosis and diagnose of KIRP. However, whether the prognosis and diagnosis model could be applied in clinical practice requires further study. Background: Kidney renal papillary cell carcinoma (KIRP) is a common type of renal cell carcinoma. DNA methylation plays an important role in the development of several cancers. The aim of our study was to identify differentially expressed genes associated with abnormal DNA methylation as biomarkers for predicting the outcome of KIRP. Method: We downloaded KIRP methylation data, RNA sequencing (RNAseq) data, and their corresponding clinical information from the Cancer Genome Atlas (TCGA) database. ChAMP and DEGseq2 packages in R software were used to screen differentially methylated probes (DMPs) and differentially expressed genes (DEGs). Univariate and multivariate Cox regression analyses were used to identify suitable immune related genes correlated with aberrant methylations as prognosis biomarkers. Results: We identified 8 DEGs (Cysteine And Glycine Rich Protein 1 [CSRP1], major histocompatibility complex, Class II, DM Beta [HLA-DMB], LIF Receptor Subunit Alpha [LIFR], Leukotriene B4 receptor 2 [LTB4R2], Mitogen-Activated Protein Kinase Kinase Kinase 14 [MAP3K14], Nuclear Receptor Subfamily 2 Group F Member 1 [NR2F1], Secreted And Transmembrane 1 [SECTM1], and Vimentin [VIM]) that were independently associated with the overall survival (months) (OS) of KIRP. The time dependent area under the curve (AUC) for each receiver operating characteristic (ROC) of the risk assessment model at 1, 3, 5, and 10-years reached 0.8415, 0.8131, 0.7873, and 0.7667. The risk assessment model was correlated with several immune cells and factors. The AUC value of the diagnosis model using those 8 DEGs reached 0.99. Conclusions: The risk assessment model constructed by those 8 DEGs was well able to predict the prognosis and diagnose of KIRP. However, whether the prognosis and diagnosis model could be applied in clinical practice requires further study. [ABSTRACT FROM AUTHOR]

Prenatal maternal psychological distress (PMPD) is a known risk factor for adverse birth outcomes. N6-methyladenosine RNA (m6A) methylation is crucial in moderating RNA biology. This study aimed to evaluate the relationships between PMPD, birth outcomes, and placental m6A methylation. This was a prospective cohort study. PMPD exposure was assessed by questionnaires about prenatal stress, depression, and anxiety. Placental m6A methylation was measured using a colorimetric assay. The relationships between PMPD, m6A methylation, gestational age (GA), and birth weight (BW) were analyzed using structural equation models (SEMs). Maternal weight gain during pregnancy and infant sex were included as covariables. The study included 209 mother-infant dyads. In an adjusted SEM, PMPD was associated with BW (B = −26.034; 95 % CI: −47.123, −4.868) and GA (B = −0.603; 95 % CI: −1.102, −0.154). M6A methylation was associated with PMPD (B = 0.055; 95 % CI: 0.040,0.073) and BW (B = −305.799; 95 % CI: −520.164, −86.460) but not GA. The effect of PMPD on BW was partially mediated by m6A methylation (B = −16.817; 95 % CI: −31.348, −4.638) and GA (B = −12.280; 95 % CI: −23.612, −3.079). Maternal weight gain was associated with BW (B = 5.113; 95 % CI: 0.229,10.438). The study sample size was small, and the specific mechanism of m6A methylation on birth outcomes needs to be further explored. In this study, PMPD exposure negatively affected BW and GA. Placental m6A methylation was associated with PMPD and BW and partially mediated the effect of PMPD on BW. Our findings highlight the importance of perinatal psychological evaluation and intervention. • Maternal depression, anxiety, and stress were integrated to describe Prenatal maternal psychological distress. • SEMs were used to evaluate relationships between prenatal maternal psychological distress and birth outcomes. • Placental m6A methylation was associated with maternal psychological distress and mediated the effects on birth weight. [ABSTRACT FROM AUTHOR]

Enzymes that regulate the degree of histone H3 lysine 4 (H3K4) methylation are crucial for proper cellular differentiation and are frequently mutated in cancer. The Mixed lineage leukemia (MLL) family of enzymes deposit H3K4 mono-, di-, or trimethylation at distinct genomic locations, requiring precise spatial and temporal control. Despite evidence that the degree of H3K4 methylation is controlled in part by a hierarchical assembly pathway with key subcomplex components, we previously found that the assembled state of the MLL1 core complex is not favored at physiological temperature. To better understand this paradox, we tested the hypothesis that increasing the concentration of subunits in a biomolecular condensate overcomes this thermodynamic barrier via mass action. Here, we demonstrate that MLL1 core complex phase separation stimulates enzymatic activity up to 60-fold but not primarily by concentrating subunits into droplets. Instead, we found that stimulated activity is largely due to the formation of an altered oligomeric scaffold that greatly reduces substrate Km. We posit that phase separation-induced scaffolding of the MLL1 core complex is a potential "switch-like" mechanism for spatiotemporal control of H3K4 methylation through the rapid formation or dissolution of biomolecular condensates within RNA Pol II transcription factories. [ABSTRACT FROM AUTHOR]

The protein lysine methyltransferase SET domain-containing protein 6 (SETD6) has been shown to influence different cellular activities and to be critically involved in the regulation of diverse developmental and pathological processes. However, the upstream signals that regulate the mRNA expression of SETD6 are not known. Bioinformatic analysis revealed that the SETD6 promoter has a binding site for the transcription factor E2F1. Using various experimental approaches, we show that E2F1 binds to the SETD6 promoter and regulates SETD6 mRNA expression. Our further observation that this phenomenon is SETD6 dependent suggested that SETD6 and E2F1 are linked. We next demonstrate that SETD6 monomethylates E2F1 specifically at K117 in vitro and in cells. Finally, we show that E2F1 methylation at K117 positively regulates the expression level of SETD6 mRNA. Depletion of SETD6 or overexpression of E2F1 K117R mutant, which cannot be methylated by SETD6, reverses the effect. Taken together, our data provide evidence for a positive feedback mechanism, which regulates the expression of SETD6 by E2F1 in a SETD6 methylation-dependent manner, and highlight the importance of protein lysine methyltransferases and lysine methylation signaling in the regulation of gene transcription. [ABSTRACT FROM AUTHOR]

Neointimal hyperplasia is a major clinical complication of coronary artery bypass graft and percutaneous coronary intervention. Smooth muscle cells (SMCs) play a vital roles in neointimal hyperplasia development and undergo complex phenotype switching. Previous studies have linked glucose transporter member 10(Glut10) to the phenotypic transformation of SMCs. In this research, we reported that Glut10 helps maintain the contractile phenotype of SMCs. The Glut10-TET2/3 signaling axis can arrest neointimal hyperplasia progression by improving mitochondrial function via promotion of mtDNA demethylation in SMCs. Glut10 is significantly downregulated in both human and mouse restenotic arteries. Global Glut10 deletion or SMC-specific Glut10 ablation in the carotid artery of mice accelerated neointimal hyperplasia, while Glut10 overexpression in the carotid artery triggered the opposite effects. All of these changes were accompanied by a significant increase in vascular SMCs migration and proliferation. Mechanistically, Glut10 is expressed primarily in the mitochondria after platelet-derived growth factor-BB (PDGF-BB) treatment. Glut10 ablation induced a reduction in ascorbic acid (VitC) concentrations in mitochondria and mitochondrial DNA (mtDNA) hypermethylation by decreasing the activity and expression of the Ten-eleven translocation (TET) protein family. We also observed that Glut10 deficiency aggravated mitochondrial dysfunction and decreased the adenosinetriphosphate (ATP) content and the oxygen consumption rate, which also caused SMCs to switch their phenotype from contractile to synthetic phenotype. Furthermore, mitochondria-specific TET family inhibition partially reversed these effects. These results suggested that Glut10 helps maintain the contractile phenotype of SMCs. The Glut10-TET2/3 signaling axis can arrest neointimal hyperplasia progression by improving mitochondrial function via the promotion of mtDNA demethylation in SMCs. [ABSTRACT FROM AUTHOR]

The future health of the offspring can be influenced by longstanding maternal anxiety and depression disorders during pregnancy. The present study aimed to explore the effect of psychiatric disorders during pregnancy on placental epigenetics. We measured DNA methylation patterns in term-placentas of women either suffering longstanding anxiety and depression symptoms (Index group, with overt symptoms), or a healthy population (Control, none/only mild symptoms). Whole genome DNA methylation profiling was performed using the TruSeq® Methyl Capture EPIC Library Prep Kit (Illumina, San Diego, CA, USA) for library preparation and NGS technology for genomic DNA sequencing. The results of high-throughput DNA methylation analysis revealed that the Index group had differential DNA methylation at epigenome-wide significance (p < 0.05) in 226 genes in the placenta. Targeted enrichment analyses identified hypermethylation of genes associated with psychiatric disorders (BRINP1 , PUM1), and ion homeostasis (COMMD1), among others. The ECM (extracellular matrix)-receptor interaction pathway was significantly dysregulated in the Index group compared to the Control. In addition, DNA methylation/mRNA integration analyses revealed that four genes with key roles in neurodevelopment and other important processes (EPB41L4B, BMPR2, KLHL18, and UBAP2) were dysregulated at both, DNA methylation and transcriptome levels in the Index group compared to Control. The presented results increase our understanding of how maternal psychiatric disorders may affect the newborn through placental differential epigenome, suggesting DNA methylation status as a biomarker when aiming to design new preventive techniques and interventions. • Pregnancy anxiety and depression may compromise the health of the newborn. • Maternal psychiatric disorders affect placental DNA methylation status. • Dysregulated placental DNA methylation may alter gene function. [ABSTRACT FROM AUTHOR]

Feeding pregnant cows rumen-protected choline (RPC) may have the potential to affect the growth and health of offspring, but little is known about the optimal dose, or the potential mechanisms of action. The objectives of this experiment were to 1) determine if increasing RPC supplementation during late gestation in multiparous Holstein cows would improve calf growth and 2) determine if maternal choline supplementation alters global DNA methylation patterns. Pregnant multiparous Holstein cows (n = 116) were randomly assigned to diets targeting 0g choline ion (0.0 ± 0.000 choline ion, %DM, control; CTL), 15g of choline ion (recommended dose; RD) from an established RPC product (0.10 ± 0.004 choline ion, %DM, RPC1 RD ; ReaShure, Balchem Corp.; positive control), or 15g (0.09 ± 0.004 choline ion, %DM, RPC2 RD) or 22g (0.13 ± 0.005 choline ion, %DM, high dose; RPC2 HD) of choline ion from a concentrated RPC prototype (RPC2; Balchem Corp.). Treatments were mixed into a total mixed ration and cows had ad libitum access via a roughage intake control system (Hokofarm Group, Marknesse, Netherlands). All female Holstein (n = 49) and Holstein × Angus calves (male, n = 18; female, n = 30) were enrolled and fed colostrum from a cow within the same treatment. Holstein calves and Holstein × Angus calves were fed an accelerated and traditional milk replacer program, respectively, and offered ad libitum access to calf starter. Jugular vein blood samples were collected, and body weight was measured at 7, 14, 28, 42, and 56 d of age. Categorical treatment and continuous effects of actual prepartum maternal choline ion intake were analyzed using mixed effect models. An interaction of treatment with sex, nested within breed, resulted in any choline treatment increasing the proportion of methylated whole blood DNA in male, but not female calves. Although 37% of Holstein calves across all treatments experienced abomasal bloat, no evidence for differences in health measurements (signs of respiratory disease and fecal consistency) were observed across treatments. During the first 2 wk of life in Holstein calves, RPC2 HD tended to increase average daily gain (ADG) and feed efficiency (FE) compared with CTL and increasing maternal choline ion intake linearly increased ADG and FE. Maternal choline supplementation increased plasma glucose compared with CTL, while increasing serum insulin-like growth factor-1 and decreasing serum lipopolysaccharide binding protein at 7 d of age in Holstein calves. In Holstein × Angus calves, the effect of treatment on ADG tended to interact with sex: in males, RPC2 HD increased ADG after 2 wk of life compared with CTL, without evidence of a treatment effect in female calves. Increasing maternal choline ion intake linearly increased ADG after 2 wk of age in male Holstein × Angus calves, while quadratically increasing FE in both sexes. Altered global DNA methylation patterns in male Holstein × Angus calves, and changes in blood metabolites in Holstein calves, provide 2 potential mechanisms for observed improvements in calf growth. Continuous treatment models demonstrated that the effects of maternal choline supplementation are sensitive to the amount of maternal choline ion intake, with greater benefit to calves observed at higher maternal intakes. [ABSTRACT FROM AUTHOR]

• EE induces exon specific upregulation in Bdnf expression in the PFC. • EE reduces methylation levels at two CpG sites of exon IV of the Bdnf gene. • EE exposure for 32-day does not affect anxiety behaviour as measured by EPM. Environmental enrichment (EE) is a condition characterized by its complexity regarding social contact, exposure to novelty, tactile stimuli and voluntary exercise, also is considered as a eustress model. The impact of EE on brain physiology and behavioral outcomes may be at least partly underpinned by mechanisms involving the modulation of the brain-derived neurotrophic factor (BDNF), but the connection between specific Bdnf exon expression and their epigenetic regulation remain poorly understood. This study aimed to dissect the transcriptional and epigenetic regulatory effect of 54-day exposure to EE on BDNF by analysing individual BDNF exons mRNA expression and the DNA methylation profile of a key transcriptional regulator of the Bdnf gene, exon IV, in the prefrontal cortex (PFC) of C57BL/6 male mice (sample size = 33). Bdnf exons II, IV, VI and IX mRNA expression were upregulated and methylation levels at two CpG sites of exon IV were reduced in the PFC of EE mice. As deficit in exon IV expression has also been causally implicated in stress-related psychopathologies, we also assessed anxiety-like behavior and plasma corticosterone levels in these mice to determine any potential correlation. However, no changes were observed in EE mice. The findings may suggest an EE-induced epigenetic control of BDNF exon expression via a mechanism involving exon IV methylation. The findings of this study contribute to the current literature by dissecting the Bdnf gene topology in the PFC where transcriptional and epigenetic regulatory effect of EE takes place. [ABSTRACT FROM AUTHOR]

The study aimed to investigate the role of LINC00346 in colon adenocarcinoma (COAD) metastasis. qRT-PCR, methylation-specific PCR, immunohistochemistry and western blotting were used to measure the expression levels of LINC00346, miR-589–5p, and CCL5 in COAD cells and tissues. Dual-luciferase assays, RNA immunoprecipitation, and RNA pull-down were used to validate the targeting relationship between LINC00346/CCL5 and miR-589–5p. In vivo experiments were conducted to study the impact of LINC00346 on COAD progression. MTT, colony formation assay, transwell assay and wound healing assay were used to detect the COAD cell proliferation, colony formation, invasion and migration. The results showed that COAD cells and tissues had high expression of LINC00346 and CCL5, and low expression of miR-589–5p. LINC00346 expression was upregulated due to DNA hypomethylation in its promoter region. miR-589–5p targets both LINC00346 and CCL5. LINC00346 facilitated the malignant progression of COAD by preventing the degradation of CCL5 via competitively binding to miR-589–5p. Rescue experiments indicated a ceRNA pattern consisting of LINC00346, miR-589–5p, and CCL5. Overall, LINC00346 promotes COAD progression via the miR-589–5p/CCL5 axis and may be a potential therapeutic target for COAD. [Display omitted] • LINC00346 was hypomethylated and highly expressed in COAD. • LINC00346 fostered cell proliferation, migration and invasion of COAD. • LINC00346, as a ceRNA, competitively sponged miR-589–5p to modulate CCL5 level, thereby enhancing malignant progression of COAD. [ABSTRACT FROM AUTHOR]

Protein posttranslation modifications (PTMs) are a critical regulatory mechanism of protein function. Protein a-N-terminal (Na) methylation is a conserved PTM across prokaryotes and eukaryotes. Studies of the Na methyltransferases responsible for Na methylation and their substrate proteins have shown that the PTM involves diverse biological processes, including protein synthesis and degradation, cell division, DNA damage response, and transcription regulation. This review provides an overview of the progress toward the regulatory function of Na methyltransferases and their substrate landscape. More than 200 proteins in humans and 45 in yeast are potential substrates for protein Na methylation based on the canonical recognition motif, XP [KR]. Based on recent evidence for a less stringent motif requirement, the number of substrates might be increased, but further validation is needed to solidify this concept. A comparison of the motif in substrate orthologs in selected eukaryotic species indicates intriguing gain and loss of the motif across the evolutionary landscape. We discuss the state of knowledge in the field that has provided insights into the regulation of protein Na methyltransferases and their role in cellular physiology and disease. We also outline the current research tools that are key to understanding Na methylation. Finally, challenges are identified and discussed that would aid in unlocking a system-level view of the roles of Na methylation in diverse cellular pathways. [ABSTRACT FROM AUTHOR]

FAM86A is a class I lysine methyltransferase (KMT) that generates trimethylation on the eukaryotic translation elongation factor 2 (EEF2) at Lys525. Publicly available data from The Cancer Dependency Map project indicate high dependence of hundreds of human cancer cell lines on FAM86A expression. This classifies FAM86A among numerous other KMTs as potential targets for future anticancer therapies. However, selective inhibition of KMTs by small molecules can be challenging due to high conservation within the S-adenosyl methionine (SAM) cofactor binding domain among KMT subfamilies. Therefore, understanding the unique interactions within each KMT-substrate pair can facilitate developing highly specific inhibitors. The FAM86A gene encodes an N-terminal FAM86 domain of unknown function in addition to its C-terminal methyltransferase domain. Here, we used a combination of Xray crystallography, the AlphaFold algorithms, and experimental biochemistry to identify an essential role of the FAM86 domain in mediating EEF2 methylation by FAM86A. To facilitate our studies, we also generated a selective EEF2K525 methyl antibody. Overall, this is the first report of a biological function for the FAM86 structural domain in any species and an example of a noncatalytic domain participating in protein lysine methylation. The interaction between the FAM86 domain and EEF2 provides a new strategy for developing a specific FAM86A small molecule inhibitor, and our results provide an example in which modeling a protein-protein interaction with AlphaFold expedites experimental biology. [ABSTRACT FROM AUTHOR]

Proliferation, migration and invasion of extravillous trophoblasts (EVTs) play an important role in the progression of preeclampsia (PE). The purpose of this study was to investigate the molecular mechanism by which DNA methylase regulates the transcription level of APLNR and affects the phenotypic function of EVTs. PE mice model and H/R model in HTR8/Svneo cells were constructed. Clinical samples of normal pregnant women and PE patients were collected. Expression and methylation level of APLNR in vivo and in vitro were detected. ChIP-qPCR was used to detect the binding of DNA methyltransferase at the APLNR promoter. The expression of DNA methyltransferase 1 (DNMT1), NO and eNOS in vitro were detected. EVTs proliferation, migration and invasion in vitro were detected. In placental tissues or HTR8/Svneo cells of the PE model group, the expression of APLNR was reduced and APLNR methylation level was up-regulated. There was no significant difference in the APLNR expression in placental tissues between normal pregnant women and PE patients. H/R conditions only promote the binding of DNMT1 at the APLNR promoter. DNMT1 interference decreased the enrichment degree of DNMT1 in APLNR promoter region and up-regulated the mRNA and protein levels of APLNR in vivo and in vitro. The activation of APLNR by Elabela (ELA) can promote eNOS transcription, thereby promoting cell proliferation and NO level, while eNOS inhibitor can reverse this effect. DNMT1 down-regulation inhibted APLNR methylation level, promoted eNOS transcription, and promoted EVTs proliferation, migration and invasion, which could be revised by the interference of APLNR. DNMT1 promotes eNOS transcription by inhibting APLNR methylation level, and promotes EVTs proliferation, migration and invasion, thus providing a new and broad application prospect for PE treatment. [ABSTRACT FROM AUTHOR]

Protein synthesis is a fundamental step in gene expression, with modulation of mRNA translation at the elongation step emerging as an important regulatory node in shaping cellular proteomes. In this context, five distinct lysine methylation events on eukaryotic elongation factor 1A (eEF1A), a fundamental nonribosomal elongation factor, are proposed to influence mRNA translation elongation dynamics. However, a lack of affinity tools has hindered progress in fully understanding how eEF1A lysine methylation impacts protein synthesis. Here we develop and characterize a suite of selective antibodies to investigate eEF1A methylation and provide evidence that methylation levels decline in aged tissue. Determination of the methyl state and stoichiometry on eEF1A in various cell lines by mass spectrometry shows modest cell-tocell variability. We also find by Western blot analysis that knockdown of individual eEF1A-specific lysine methyltransferases leads to depletion of the cognate lysine methylation event and indicates active crosstalk between different sites. Further, we find that the antibodies are specific in immunohistochemistry applications. Finally, application of the antibody toolkit suggests that several eEF1A methylation events decrease in aged muscle tissue. Together, our study provides a roadmap for leveraging methyl state and sequenceselective antibody reagents to accelerate discovery of eEF1A methylation-related functions and suggests a role for eEF1A methylation, via protein synthesis regulation, in aging biology. [ABSTRACT FROM AUTHOR]

Mercury and ferrous iron commonly co-exist in anaerobic environments, the hotspots of microbial mercury methylation that leads to formation of neurotoxic methylmercury. However, the influence of ferrous iron on mercury bioavailability and methylation remains unclear. Here, we discover that microbial methylmercury production is inhibited by iron addition in a non-monotonical manner, reaching the minimal level at the initial molar ratio of dissolved Fe/Hg as 1/3, when highly aggregated Hg–S–Fe nanoparticles occur and prevent the nanoparticle–bacteria interactions. The dominant mercury species formed upon Hg–S–Fe co-precipitation is iron-incorporated nano-metacinnabar with short-range structural disorder. The methylation potential of this mercury species is inversely correlated with the aggregation state of nanoparticles. The non-monotonical trends of the aggregation state and subsequent methylation of nano-metacinnabar are due to the opposite effects of ferrous iron on the nucleation and particle attachment that determine the formation of nanoparticle aggregates. Increased Fe/Hg ratio hinders particle nucleation and thus decreases the density of particle monomers for aggregation. However, Fe substitution of sub-surface Hg weakens the inner-sphere coordination of surface Hg with natural thiol ligands and consequently enhances nano-metacinnabar aggregation. This new mechanistic insight is important for assessing and minimizing the risks of mercury methylation, and informs how intertwined iron and sulfur cycling may influence metal bioavailability in the changing environment. [ABSTRACT FROM AUTHOR]

Early detection of cancer offers the opportunity to identify candidates when curative treatments are achievable. The THUNDER study (THe UNintrusive Detection of EaRly-stage cancers, NCT04820868) aimed to evaluate the performance of enhanced linear-splinter amplification sequencing, a previously described cell-free DNA (cfDNA) methylation-based technology, in the early detection and localization of six types of cancers in the colorectum, esophagus, liver, lung, ovary, and pancreas. A customized panel of 161 984 CpG sites was constructed and validated by public and in-house (cancer: n = 249; non-cancer: n = 288) methylome data, respectively. The cfDNA samples from 1693 participants (cancer: n = 735; non-cancer: n = 958) were retrospectively collected to train and validate two multi-cancer detection blood test (MCDBT-1/2) models for different clinical scenarios. The models were validated on a prospective and independent cohort of age-matched 1010 participants (cancer: n = 505; non-cancer: n = 505). Simulation using the cancer incidence in China was applied to infer stage shift and survival benefits to demonstrate the potential utility of the models in the real world. MCDBT-1 yielded a sensitivity of 69.1% (64.8%-73.3%), a specificity of 98.9% (97.6%-99.7%), and tissue origin accuracy of 83.2% (78.7%-87.1%) in the independent validation set. For early-stage (I-III) patients, the sensitivity of MCDBT-1 was 59.8% (54.4%-65.0%). In the real-world simulation, MCDBT-1 achieved a sensitivity of 70.6% in detecting the six cancers, thus decreasing late-stage incidence by 38.7%-46.4%, and increasing 5-year survival rate by 33.1%-40.4%, respectively. In parallel, MCDBT-2 was generated at a slightly low specificity of 95.1% (92.8%-96.9%) but a higher sensitivity of 75.1% (71.9%-79.8%) than MCDBT-1 for populations at relatively high risk of cancers, and also had ideal performance. In this large-scale clinical validation study, MCDBT-1/2 models showed high sensitivity, specificity, and accuracy of predicted origin in detecting six types of cancers. • MCDBT-1 had a sensitivity of 69.1% and a specificity of 98.9% in detecting six cancers. • In the real world, MCDBT-1 decreased late-stage incidence by 38.7%-46.4% and increased 5-year survival rate by 33.1%-40.4%. • In parallel, MCDBT-2 was set at a lower specificity but a higher sensitivity than MCDBT-1 and had an ideal performance. [ABSTRACT FROM AUTHOR]

DNA methylation is a key epigenetic marker, and its alternations may be involved in Alzheimer's disease (AD). CpGs sharing similar biological functions or pathways tend to be co-methylated. We performed an integrative network-based DNA methylation analysis on 2 independent cohorts (N = 941) using brain DNA methylation profiles and RNA-sequencing as well as AD pathology data. Weighted co-methylation network analysis identified 6 modules as significantly associated with neuritic plaque burden. In total, 15 hub CpGs including 3 novel CpGs were identified and replicated as being significantly associated with AD pathology. Furthermore, we identified and replicated 4 target genes (ATP6V1G2 , VCP , RAD52 , and LST1) as significantly regulated by DNA methylation at hub CpGs. In particular, VCP gene expression was also associated with AD pathology in both cohorts. This integrative network-based multiomics study provides compelling evidence for a potential role of DNA methylation alternations and their target genes in AD. [ABSTRACT FROM AUTHOR]

• The impact of environmental factors on epigenetics signatures testing among preanalytical procession. • Simulate the temperature, time, and multiple freeze–thaw cycles that blood samples may face during collection, transportation, storage, and handling. • The changing trend of DNA methylation along with short-term storage time in different temperatures. • The temperature sensitivity differs between different genes. • Call for blood samples processing quality control and sample collection detailed Standard Operating Procedure among national biobank and population-based research. Stability is crucial for the clinical applicable biomarker such as DNA methylation profiles. However, the influence of various blood processing on the DNA methylation signatures have been barely studied. Here, we systematically evaluated the impact of temporary storage and frozen and thaw on the levels of DNA methylation. The methylation intensities of 13 CpG loci from 53 individuals (42 healthy participants and 11 lung cancer patients) whose blood samples were processed by up to 14 various protocols were quantitatively determined by the mass spectrometry, obtaining more than 8,000 quantitative data. We disclosed a trend of accumulatively increased DNA methylation along with time when the blood from healthy people were stored for up to 96 h at room temperature (RT), whereas the storage at 4°C had much weaker effects or no impact. On the contrary, the methylation patterns in the blood of lung cancer patients were more stable at both RT and 4°C even for 96 h. Multiple cycles of frozen and thaw could result in demethylation, but was more significant to the blood than to the extracted DNA. Our study indicated that the blood processing in vitro could influence the DNA methylation signatures and introduce unexpected biases. [ABSTRACT FROM AUTHOR]

Glioblastoma (GBM) is the most common primary malignant brain tumour in adults and frequently relapses. The aim of this study was to assess the efficacy and safety of metronomic temozolomide (TMZ) in the recurrent GBM population. All patients treated at our centre between September 2013 and March 2021 were retrospectively reviewed. The main inclusion criteria were first-line therapy with the Stupp protocol, relapse after the first or subsequent line of therapy, treatment with a metronomic TMZ schedule (50 mg/m2 continuously) and histological diagnosis of isocitrate dehydrogenase wild-type GBM according to World Health Organization 2016 classification. In total, 120 patients were enrolled. The median follow-up was 15.6 months, the median age was 59 years, Eastern Cooperative Oncology Group performance status (ECOG-PS) was 0–2 in 107 patients (89%). O6-methylguanine-DNA-methyltransferase (MGMT) was methylated in 66 of 105 (62%) evaluable patients. The median number of prior lines of treatment was 2 (range 1–7). Three (2%) patients showed a partial response; 48 (40%) had stable disease; 69 (57%) had progressive disease. The median overall survival from the start of metronomic TMZ was 5.4 months (95% confidence interval 4.3–6.4), whereas the median progression-free survival (PFS) was 2.6 months (95% confidence interval 2.3–2.8). At univariate analysis, MGMT methylated and unmethylated patients had a median PFS of 2.9 and 2.1 months (P = 0.001) and a median overall survival of 5.6 and 4.4 months (P = 0.03), respectively. At multivariate analysis, the absence of MGMT methylation (hazard ratio = 2.3, 95% confidence interval 1.3–3.9, P = 0.004) and ECOG-PS ≤ 2 (hazard ratio = 0.5, 95% confidence interval 0.3–0.9, P = 0.017) remained significantly associated with PFS, whereas ECOG-PS ≤ 2 (hazard ratio = 0.4, 95% confidence interval 0.3–07, P = 0.001) was the only factor associated with overall survival. The most common grade 3–4 toxicities were haematological (lymphopenia 10%, thrombocytopenia 3%). Rechallenge with metronomic TMZ is a well-tolerated option for recurrent GBM, even in pretreated patients. Patients with methylated MGMT disease and good ECOG-PS seem to benefit the most from this treatment. • Glioblastoma is the most common primary brain tumour in adults. • There is no general consensus about the best therapy at relapse. • Temozolomide at 50 mg/m2 continuously can be a viable therapeutic option for recurrent glioblastoma patients. • Heavily pretreated patients could benefit from metronomic temozolomide with a satisfying safety profile. [ABSTRACT FROM AUTHOR]

As confusion mounts over RNA isoforms involved in phenotypic plasticity, aberrant CpG methylation-mediated disruption of alternative splicing is increasingly recognized as a driver of intratumor heterogeneity (ITH). Protease serine 3 (PRSS3), possessing four splice variants (PRSS3-SVs ; PRSS3-V1 – V4), is an indispensable trypsin that shows paradoxical effects on cancer development. Here, we found that PRSS3 transcripts and their isoforms were divergently expressed in lung cancer, exhibiting opposing functions and clinical outcomes, namely, oncogenic PRSS3-V1 and PRSS3-V2 versus tumor-suppressive PRSS3-V3, by targeting different downstream genes. We identified an intragenic CpG island (iCpGI) in PRSS3. Hypermethylation of iCpGI was mediated by UHRF1/DNMT1 complex interference with the binding of myeloid zinc finger 1 (MZF1) to regulate PRSS3 transcription. The garlic-derived compound diallyl trisulfide cooperated with 5-aza-2′-deoxycytidine to exert antitumor effects in lung adenocarcinoma cells through site-specific iCpGI demethylation specifically allowing MZF1 to upregulate PRSS3-V3 expression. Epigenetic silencing of PRSS3-V3 via iCpGI methylation (iCpGIm) in BALF and tumor tissues was associated with early clinical progression in patients with lung cancer but not in those with squamous cell carcinoma or inflammatory disease. Thus, UHRF1/DNMT1–MZF1 axis-modulated site-specific iCpGIm regulates divergent expression of PRSS3-SVs , conferring nongenetic functional ITH, with implications for early detection of lung cancer and targeted therapies. UHRF1/DNMT1–MZF1 axis modulates PRSS3 iCpGIm increasing transcript heterogeneity. DATS cooperates with 5-aza-2′-deoxycytidine to exert antitumor effects on lung adenocarcinoma through site-specific demethylation of iCpGI for MZF1 to upregulate tumor-suppressive PRSS3-V3 expression. [Display omitted] [ABSTRACT FROM AUTHOR]

Follicular atresia is a normal physiological event in mammals, yet its mechanism remains to be studied. Granulosa cell (GC) autophagy is closely associated with follicular atresia. The N6-methyladenosine (m6A) modification is the most common post-transcriptional modification in eukaryotes, but its role in follicular atresia is still unknown. In this study, the possible relationship amongst follicular atresia, GC autophagy and m6A modification was studied. Our results showed that the level of autophagy in GCs increased with the degree of follicle atresia, whereas the overall m6A level decreased. Rapamycin treatment induced atresia in vitro cultured follicles, whereas 3-Methyladenine inhibited follicular atresia. Progressed atretic follicle (PAF) GCs had significantly lower METTL3 levels and significantly higher FTO levels than healthy follicle (HF) GCs. Differential gene expression analysis of GCs in PAF and HF by RNA sequencing was showed that the autophagy-related genes ULK1 , ULK2 , ATG2A , and ATG2B were significantly elevated in the PAF. In cultured GCs, overexpression of METTL3 significantly decreased the mRNA level of ULK1 , as well as the autophagy level, whereas knockdown of METTL3 by RNAi significantly increased the mRNA level of ULK1 , as well as the autophagy level. Our results indicate that m6A modification can regulate autophagy in GCs and play a role in the process of porcine follicular atresia. • The level of autophagy in GCs increased with the degree of follicle atresia, while the overall m6A level decreased. • Rapamycin treatment induced atresia in vitro cultured follicles, while 3-Methyladenine inhibited follicular atresia. • m6A modification can regulate autophagy in GCs and play a role in the process of porcine follicular atresia. [ABSTRACT FROM AUTHOR]

Purpose/objective(s): Established prognostic factors for head and neck squamous cell carcinoma (HNSCC) mostly consist of clinical and tumor features assessed prior to treatment. We report a novel application of DNA methylation in peripheral blood before and after radiotherapy to further improve outcomes stratification.Materials/methods: Peripheral blood samples from patients with non-metastatic HNSCC were obtained for methylation analysis 1 week before and 1 month after radiotherapy. Patients were randomized 1:1 to a Discovery Cohort or a Validation Cohort. In the Discovery Cohort, associations between genome-wide methylation change (post-treatment minus pre-treatment) and recurrence-free survival (RFS) as well as overall survival (OS) were evaluated using Cox regression. A methylation risk score (MRS) was then constructed from methylation levels at the top associated sites, filtered for residing within the regulatory regions of genes expressed in cells of hematopoietic lineage. The prognostic value of MRS was separately assessed in the Discovery and Validation Cohorts.Results: Between December 2013 and September 2018, 115 patients participated in this study. HPV negative status, oral cavity cancer, gastrostomy tube insertion, and higher neutrophil count before radiotherapy were associated with shorter RFS and OS (P<0.05). Genes downstream of the methylation sites comprising MRS are HIF1A, SF1, LGALS9, and FUT5, involved in hypoxia response, blood cell maturation, and immune modulation. High MRS (in the top third) was significantly associated with worse RFS (HR 7.1, 95% CI 1.4-35.5, P=0.016) and OS (HR 15.9, 95% CI 1.6-153.6, P=0.017) in the Discovery Cohort, independent of the aforementioned risk factors. These findings were replicated in the Validation Cohort, for which high MRS also independently predicted worse RFS (HR 10.2, 95% CI 2.4-43.4, P=0.002) and OS (HR 3.7, 95% CI 1.3-10.4, P=0.015).Conclusion: We successfully trained and validated a signature of DNA methylation in peripheral blood before and after radiotherapy that stratified outcomes among patients with HNSCC, implicating the potential for genomics-tailored surveillance and consolidation treatment. [ABSTRACT FROM AUTHOR]

In machine learning, multimodal classifiers can provide more generalised performance than unimodal classifiers. In clinical practice, physicians usually also rely on a range of information from different examinations for diagnosis. In this study, we used BRAF mutation status prediction in melanoma as a model system to analyse the contribution of different data types in a combined classifier because BRAF status can be determined accurately by sequencing as the current gold standard, thus nearly eliminating label noise. We trained a deep learning-based classifier by combining individually trained random forests of image, clinical and methylation data to predict BRAF-V600 mutation status in primary and metastatic melanomas of The Cancer Genome Atlas cohort. With our multimodal approach, we achieved an area under the receiver operating characteristic curve of 0.80, whereas the individual classifiers yielded areas under the receiver operating characteristic curve of 0.63 (histopathologic image data), 0.66 (clinical data) and 0.66 (methylation data) on an independent data set. Our combined approach can predict BRAF status to some extent by identifying BRAF-V600 specific patterns at the histologic, clinical and epigenetic levels. The multimodal classifiers have improved generalisability in predicting BRAF mutation status. • A combined DL classifier predicts BRAF-V600 mutations in malignant melanoma. • Combining data modalities improves performance and generalisation capability. • Multimodal classifiers have the potential to be used as predictive biomarkers. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease characterized by synovitis, cartilage damage and bone resorption. Methylation of deoxyribonucleic acid plays a crucial role in repressing gene expression. Receptor activator of nuclear factor-kappa ligand (RANKL) controls bone homeostasis. To assess the serum level of RANKL and its gene promoter methylation in RA patients and to determine its association with clinical characteristics and disease activity. The study included 40 RA patients and 40 control. The disease activity score (DAS28) was assessed. Frequency of RANKL gene promoter methylation was determined by quantitative methylation specific PCR (QMSP) and serum RANKL level by enzyme linked immunosorbant assay (ELISA). Patients mean age was 46.8 ± 10.6 years, 36 females and 4 males (F:M 9:1) with median disease duration 4.5 years. Positive rheumatoid factor, anti-cyclic citrullinated peptide and C-reactive protein were present in 65 %, 75 % and 55 % of cases. Methylation percentage of RANKL gene promoter was significantly lower in patients (3.4 %) than in controls (3.7 %)(p = 0.035) while serum level was significantly increased in patients (9.1 ng/ml,5.3–11.8 ng/ml) than in controls (5.7 ng/ml, 4.5–8 ng/ml)(p = 0.003). RANKL methylation frequency was inversely associated with serum level (rs = -0.21,p = 0.06). There was no significant correlation of RANKL serum level and methylation with DAS28 (r = 0.03,p = 0.87 and r = 0.06,p = 0.73 respectively). RANKL serum level (>9.5 ng/ml) and methylation percentage (≤9%) significantly discriminate RA cases from control (sensitivity 47.5 %, specificity 91.9 %; p = 0.001 and sensitivity 100 %, specificity 40 %; p = 0.03 respectively). RA patients expressed elevated serum RANKL with low methylation. [ABSTRACT FROM AUTHOR]