Promoter Methylation Levels Research Articles

Placental expression and methylation of angiogenic factors in assisted reproductive technology pregnancies from India.

This study aims to examine the gene expression and DNA methylation patterns of angiogenic factors in the placentae of Indian women who underwent assisted reproductive technology (ART) procedures and their association with maternal one-carbon metabolites and birth outcome. Placental gene expression and DNA methylation of angiogenic factors (VEGF, PlGF, FLT-1, KDR) in Indian women who underwent ART procedures (n = 64) and women who conceived naturally (Non-ART) (n = 93) was investigated using RT-qPCR and Epitect Methyl-II PCR assay kits. Maternal plasma one-carbon metabolites were assessed by CMIA technology. Gene expression of FLT-1 and KDR was higher (p < 0.05) in the ART placentae. Placental global DNA methylation levels were higher (p < 0.01) and DNA methylation levels of VEGF promoter were lower (p < 0.05) in ART compared to non-ART women. Maternal plasma folate and vitamin B12 levels were higher (p < 0.01) in the ART group. Gene expression of PlGF was negatively associated with maternal plasma folate (p < 0.05) whereas KDR was positively associated with maternal plasma homocysteine (p < 0.05). Gene expression of KDR was positively associated with chest circumference of the baby (p < 0.05). Hypomethylation of VEGF and increased expression of FLT-1 and KDR was observed in the placentae of women who underwent ART procedure.

Discovery and validation of Hsa-microRNA-3665 promoter methylation as a potential biomarker for the prognosis of esophageal squaous cell carcinoma.

Methylation of microRNA (miRNA) promoters associated with diseases is a common epigenetic mechanism in the development of various human cancers. However, its relationship with prognosis in esophageal squamous cell carcinoma (ESCC) remains unclear. This study aims to explore the association between the methylation level of has-miR-3665 promoter and prognosis in ESCC. Human miRNA data were downloaded from miRbase, and we identified CpG islands of these human miRNAs by genomics browser analysis. MiRNA methylation levels were detected by methylation-specific high-resolution melting. Gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to explore the molecular mechanism of hsa-miR-3665. Cox regression analysis was used to investigate prognostic factors. The overall survival rate was predicted by a nomogram. We found that 88 human miRNAs had promoter methylatio, of which 15 miRNAs were found to be epigenetically regulated in ESCC cells compared with their normal counterparts, including hsa-miR-3665. Meanwhile, hsa-miR-3665 expression was significantly lower in ESCC tumour tissue than in adjacent tissue (P = 0.03). GO and KEGG analyses demonstrated that the target genes are involved in protein transport, transcription regulator activity, MAPK and RAS signaling pathway. High hsa-miR-3665 promoter methylation levels were associated with a poor prognosis (HR = 3.89, 95% CI 1.11 ~ 13.55). Moreover, a nomogram incorporating the hsa-miR-3665 methylation level and clinical factors presented a good performance for predicting survival in the training and validation tests, with C-indices of 0.748 and 0.751, respectively. High hsa-miR-3665 promoter methylation levels may be a potential biomarker for the progression of ESCC.

Mex3a promoter hypomethylation can be utilized to diagnose HBV-associated hepatocellular carcinoma: a randomized controlled trial.

Hepatocellular carcinoma remains a health challenge for humanity. Therefore, there is an urgent need to develop novel biomarkers with high efficiency yet fast ability to meet the requirements of hepatocellular carcinoma treatment. A total of 229 patients with HBV-associated hepatocellular carcinoma (HCC), 298 patients with chronic hepatitis B (CHB), and 96 healthy controls were retrospectively analyzed. Methylation levels of the Mex3a promoter in peripheral blood mononuclear cells (PBMCs) were measured using MethyLight to obtain clinical and laboratory parameters. The Mex3a promoter methylation level in HCC patients (median: 0.289% and interquartile range: 0.126%-0.590%) was significantly lower than that in CHB patients (median: 0.999%, interquartile range: 0.417%-1.268%, and p < 0.001) and healthy people (median: 2.172%, interquartile range: 1.225%-3.098%, and p < 0.001). The Mex3a mRNA levels in HCC patients (median: 12.198 and interquartile range: 3.112-18.996) were significantly higher than those in CHB patients (median: 1.623 and interquartile range: 0.066-6.000, and p < 0.001) and healthy controls (median: 0.329, interquartile range: 0.031-1.547, and p < 0.001). MethyLight data were expressed as a percentage of the methylated reference (PMR) value. The Mex3a PMR value was negatively correlated with the mRNA expression level (Spearman's R = -0.829 and p < 0.001). The Mex3a PMR value of HCC patients was significantly correlated with age (Spearman's R = 0.113 and p = 0.044), and the mRNA level was significantly correlated with ALT (Spearman's R = 0.132 and p = 0.046). The Mex3a promoter methylation levels and mRNA levels were also independent factors in the development of liver cancer. The Mex3a promoter methylation and mRNA levels were better at distinguishing HCC from CHB than AFP [area under the receiver operating characteristic curve (AUC) for predicting HCC vs. CHB: 0.915 vs. 0.715: p < 0.001]. The combined use of AFP and Mex3a methylation levels and mRNA levels further improved the area under the receiver operating characteristic curve. The presence of Mex3a promoter hypomethylation in hepatocellular carcinoma can be used as a non-invasive biomarker for the early detection of liver cancer.

The impact of site-specific DNA methylation in KCNJ11 promoter on type 2 diabetes

AimsThis study explores the correlation between site-specific methylation levels of the KCNJ11 promoter and type 2 diabetes mellitus (T2DM), analyzing potential molecular mechanisms. MethodsThirty patients newly diagnosed with T2DM and 30 healthy controls were selected to determine the CpG methylation levels in the promoter region of the KCNJ11 gene using the bisulfite assay. The online software JASPAR was used to predict transcription factors binding to differentially methylated sites. Key transcription factors were further validated through quantitative PCR (q-PCR) and chromatin immunoprecipitation followed by PCR (ChIP-PCR). ResultsMethylation at multiple CpG sites within the KCNJ11 gene promoter was generally reduced in newly diagnosed T2DM patients compared with healthy individuals. The methylation status of CpG-471, a site crucial for the binding of the transcription factor TCF12, emerged as potentially influential in T2DM pathogenesis. This reduction in methylation at CpG-471 may enhance TCF12 binding, thereby altering KCNJ11 expression. ConclusionHypomethylation of specific CpG sites in the promoter region of the KCNJ11 gene in patients with incipient T2DM potentially contributes to the disease's pathogenesis. This hypomethylation may influence TCF12 binding, with potential regulatory effects on KCNJ11 expression and pancreatic beta-cell function, though further studies are needed to confirm the exact mechanisms involved.

ALDH2 mediates the effects of sodium-glucose cotransporter 2 inhibitors (SGLT2i) on improving cardiac remodeling

BackgroundSodium-glucose cotransporter-2 inhibitors (SGLT2i) are now recommended for patients with heart failure, but the mechanisms that underlie the protective role of SGLT2i in cardiac remodeling remain unclear. Aldehyde dehydrogenase 2 (ALDH2) effectively prevents cardiac remodeling. Here, the key role of ALDH2 in the efficacy of SGLT2i on cardiac remodeling was studied.MethodsAnalysis of multiple transcriptomic datasets and two-sample Mendelian randomization were performed to find out the differentially expressed genes between pathological cardiac hypertrophy models (patients) and controls. A pathological cardiac hypertrophy mouse model was established via transverse aortic constriction (TAC) or isoproterenol (ISO). Cardiomyocyte-specific ALDH2 knockout mice (ALDH2CMKO) and littermate control mice (ALDH2flox/flox) were generated to determine the critical role of ALDH2 in the preventive effects of dapagliflozin (DAPA) on cardiac remodeling. RNA sequencing, gene knockdown or overexpression, bisulfite sequencing PCR, and luciferase reporter assays were performed to explore the underlying molecular mechanisms involved.ResultsOnly ALDH2 was differentially expressed when the differentially expressed genes obtained via Mendelian analysis and the differentially expressed genes obtained from the multiple transcriptome datasets were combined. Mendelian analysis revealed that ALDH2 was negatively related to the severity of myocardial hypertrophy in patients. DAPA alleviated cardiac remodeling in mouse hearts subjected to TAC or ISO. ALDH2 expression was reduced, whereas ALDH2 expression was restored by DAPA in hypertrophic hearts. Cardiomyocyte specific ALDH2 knockout abolished the protective role of DAPA in preventing cardiac remodeling. ALDH2 expression and activity were increased in DAPA-treated neonatal rat primary cardiomyocytes (NRCMs), H9C2 cells and AC16 cells. Moreover, DAPA upregulated ALDH2 in peripheral blood mononuclear cells (PBMCs) from patients with type 2 diabetes. Sodium/proton exchanger 1 (NHE1) inhibition contributed to the regulation of ALDH2 by DAPA. DAPA suppressed the production of reactive oxygen species (ROS), downregulated DNA methyltransferase 1 (DNMT1) and subsequently reduced the ALDH2 promoter methylation level. Further studies revealed that DAPA enhanced the binding of nuclear transcription factor Y, subunit A (NFYA) to the promoter region of ALDH2, which was due to the decreased promoter methylation level of ALDH2.ConclusionsThe upregulation of ALDH2 plays a critical role in the protection of DAPA against cardiac remodeling. DAPA enhances the binding of NFYA to the ALDH2 promoter by reducing the ALDH2 promoter methylation level through NHE1/ROS/DNMT1 pathway.Graphical abstract

Adenomatous Polyposis Coli (APC) Promoter Gene Methylation in Urine-Derived DNA: A Non-invasive Biomarker for Early Bladder Cancer Detection and Tumor Aggressiveness.

Background Bladder urothelial carcinoma (BLCA) is a major cause of morbidity and mortality worldwide, largely due to the high frequency of disease relapse and the lack of efficient endoscopic diagnostic methods. This study aimed to address this clinical gap by evaluating the potential of using adenomatous polyposis coli (APC) gene promoter methylation as a biomarker detectable in urine DNA of individuals with BLCA. Methods Methylation-specific PCR was used to determine the methylation status of the APC promoter gene in 50 bladder carcinoma patients and 50 apparently healthy individuals. Electrophoresis on agarose gel was performed for the detection of PCR products. Statistical analysis was conducted using Excel, SPSS, and Python to assess correlations and significance. Results APC promoter methylation was detected in 34 (68%) of bladder cancer cases but in only eight (16%) of healthy controls, indicating a strong association between APC promoter methylation and bladder cancer (p < 0.001). High-grade tumors were found to have significantly higher levels of APC promoter methylation, suggesting a link between APC methylation and tumor aggressiveness (p = 0.048). Smoking was identified as a significant risk factor for BLCA (p < 0.001), but no correlation was observed with the tumor stage. Conclusion APC promoter gene methylation shows a diagnostic value for BLCA and may be useful as a non-invasive marker for early detection. This study highlights the clinical utility of using a simple urine test to detect bladder cancer, particularly in early stages, and suggests that combining APC methylation with other specific biomarkers could enhance diagnostic accuracy.

Bioinformatic analysis of neuropeptide related genes in patients diagnosed with invasive breast carcinoma

PurposeNeuropeptide receptors are expressed in many malignancies. Effectors involved in the action mechanisms of HCRTR1, HCRTR2, NPY4R (PPYR1) may be related to breast cancer (BC). Genes encoding these receptors and PPY and PTPN11 genes were aimed to examine via bioinformatics tools in the BRCA cohort. To our knowledge, this is the first study in which these receptor genes and PP, which have not found much research in BC, are examined together with PTPN11 and analyzed comprehensively in large patient cohorts from public databases. MethodscBioPortal was used for gene alteration analyses, GeneMania for association analyses with other genes, Kaplan-Meier Plotter for Overall Survival (OS) and Relapse Free Survival (RFS) analyses, UALCAN for methylation analyses, TIMER2.0 for expression analyses, The Human Protein Atlas database for expression validations, TIMER for immune infiltration analyses, WEKA 3.8.6 for diagnostic classification performances of the genes based on Random Forest Classifier and Enrichr-KG for Gene Ontology (GO) Biological Process (BP) and KEGG analysis. Results19 (1.9 %) nucleotide changes were found in 996 cases. Missense mutation is most common. Decreased expression levels of the HCRTR1 gene were associated with shorter OS and RFS, but decreased expression levels of the PTPN11 gene were associated with longer OS and RFS. Decreased expression levels NPY4R (PPYR1) gene were associated with shorter RFS. Increased expression levels of HCRTR2 and PPY genes were associated with longer RFS. HCRTR1 and NPY4R (PPYR1) genes were statistically hypermethylated; conversely HCRTR2 and PPY genes were hypomethylated. There was no significant change in PTPN11 gene promoter methylation level. HCRTR1, NPY4R (PPYR1) and PTPN11 gene expressions were downregulated; conversely, HCRTR2 and PPY gene expressions upregulated. Weak correlations were observed between NPY4R (PPYR1) gene expression and CD4+ T Cell, Neutrophil, Dendritic Cell and between PTPN11 gene expression and CD8+ T Cell, Macrophage, Neutrophil, Dendritic Cell infiltrations. Area under the receiver operating characteristics curve values of the 10-fold cross-validation and by splitting the dataset in a ratio of 80:20 models were 0.930 and 0.963 respectively. HCRTR2 and HCRTR1 belong to regulation of cytosolic calcium ion concentration, cellular calcium ion homeostasis GO BPs. ConclusionIn BC patients, increases in HCRTR2 and PPY gene expressions could be considered as positive prognostic factors. Decreases in HCRTR1 and NPY4R (PPYR1) gene expressions could be considered as negative prognostic factors. Decreased expression of PTPN11 gene may have a positive prognostic factor. Changes in existing genes are likely to be both a biomarker and therapeutic target for BC. However, experimental and clinical studies are needed to elucidate the mechanisms underlying these neuropeptide receptors in terms of breast carcinogenesis.

Hypermethylation of the sodium channel beta subunit gene promoter is associated with colorectal cancer

AimsTo better understand the role of sodium channel beta subunit (SCNN1B) in the initiation and progression of colorectal cancer (CRC) and to identify potential biomarkers for the early detection and prognosis of CRC.MethodsA total of 74 pairs of CRC tissues and their adjacent normal tissues were collected between October 2016 and November 2017. The methylation levels of the SCNN1B promoter region in CRC tissues and their adjacent normal tissues were investigated by pyrosequencing. The expression of both SCNN1B mRNA and protein were detected by RT‒qPCR and immunohistochemistry, respectively.ResultsThe results showed that the methylation levels of the SCNN1B promoter region were significantly higher in CRC tissues than in adjacent normal tissues. The expression levels of SCNN1B mRNA and protein were significantly lower in the CRC tissues than in their adjacent normal tissues. Moreover, Pearson’s correlation analysis showed that the methylation levels of the SCNN1B promoter were negatively correlated with the SCNN1B mRNA levels in CRC tissues. In addition, the high methylation levels and low mRNA expression of SCNN1B showed a significant association with advanced tumour stage, increased risk of lymph node metastasis and poor prognosis of CRC patients.ConclusionThis study suggested that the decreased expression of SCNN1B due to its promoter hypermethylation may play an important role in the progression and prognosis of CRC, and the methylation levels of the SCNN1B promoter may serve as an effective molecular marker for predicting the progression and prognosis of CRC.

A Pan-Cancer Analysis of GAPDH as a Common Biomarker for Various Cancers

Background: The present study aimed to investigate the expression level of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and explore its prognostic value across 24 different human cancers. This investigation was conducted using comprehensive bioinformatics and in vitro approaches that involved multiple layers of analysis. Methods: GAPDH expression and methylation levels were assessed via bioinformatics tools and validated using cell lines through RNA sequencing and targeted bisulfite sequencing analyses. The potential prognostic significance of GAPDH was evaluated through the use of a Kaplan–Meier plotter. Additionally, cBioPortal was employed to investigate genetic alterations associated with this gene. Pathway analysis was conducted using DAVID. Furthermore, a correlation analysis between GAPDH expression and CD8+ T immune cells was performed using TIMER and CDT. Lastly, a gene-drug interaction network analysis was conducted using Cytoscape to examine the relationship between GAPDH and drugs. Results: The GAPDH was found commonly up-regulated in 24 types of human cancers and its up-regulation was significantly correlated with the poor relapse-free survival (RFS) and overall survival (OS) of BLCA, CESC, HNSC, KIRP, LIHC, and LUAD. This implies that GAPDH plays a significant role in the development of these cancers. The GAPDH up-regulation was also noticed to be associated with the different clinicopathological features of BLCA, CESC, HNSC, KIRP, LIHC, and LUAD patients. Pathway analysis has shown GAPDH involvement in different diverse pathways. Furthermore, notable correlations were observed between the expression of GAPDH and its promoter methylation level, genetic alterations, as well as the level of CD8+ T immune cells. Moreover, we identified significant regulatory drugs targeting GAPDH that have the potential to modulate its expression and potentially prevent conditions such as BLCA, CESC, HNSC, KIRP, LIHC, and LUAD. Conclusion: Based on our findings, GAPDH emerged as a promising diagnostic and prognostic biomarker for BLCA, CESC, HNSC, KIRP, LIHC, and LUAD.

CHH hypermethylation contributes to the early ripening of grapes revealed by DNA methylome landscape of “Kyoho” and its bud mutant

Abstract DNA methylation is a stable epigenetic mark that plays a crucial role in plant life processes. However, the specific functions of DNA methylation in grape berry development remain largely unknown. In this study, we performed whole-genome bisulfite sequencing on “Kyoho” grape and its early-ripening bud mutant “Fengzao” at different developmental stages. Our results revealed that transposons (TEs) and gene flanking regions exhibited high levels of methylation, particularly in “Fengzao”, attributed to CHH site methylation. Interestingly, the methylation patterns in these two cultivars showed distinct dynamics during berry development. While methylation levels of genes and TEs increased gradually in “Kyoho” throughout berry development, “Fengzao” did not display consistent changes. Notably, “Fengzao” exhibited higher methylation levels in promoters compared to “Kyoho”, suggesting that hypermethylation of promoters may contribute to its early ripening phenotype. Integration of methylome and transcriptome data highlighted differentially methylated genes (DMGs) and expressed genes (DEGs) associated with secondary metabolite biosynthesis, with 38 genes identified as potential candidates involved in grape berry development. Furthermore, the study identified a jasmonate-induced oxygenase gene (JOX1) as a negative regulator of ripening in Arabidopsis and grapes, indicating that hypermethylation of JOX1 may play a role in the early ripening of “Fengzao”. Overall, our findings provide insights into the distinct DNA methylation patterns during grape berry development, shedding light on the epigenetic regulatory mechanisms underlying the early-ripening bud mutant.

PER3 promoter hypermethylation correlates to the progression of pan-cancer

BackgroundMalignant cells exhibit reduced period circadian regulator 3 (PER3) expression. However, the underlying mechanisms of variations in PER3 expression in cancers and the specific function of PER3 in tumor progression remain poorly understood.ResultsWe explored multiple public databases, conducted bioinformatics analyses, and performed in vitro and in vivo experiments for validation. We found PER3 expression was decreased in most types of cancers, and PER3 downregulation was associated with a poor prognosis in 8 types of cancer. PER3 promoter methylation levels were increased in 11 types of cancer. Promoter hypermethylation (CpG islands [CGIs] cg12258811 and cg14204433) correlated with decreased PER3 expression in six cancers (breast invasive carcinoma, colon adenocarcinoma, head and neck squamous cell carcinoma, kidney renal papillary cell carcinoma [KIRP], lung adenocarcinoma [LUAD], and uterine corpus endometrial carcinoma). CGI cg12258811 hypermethylation was associated with reduced survival time and advanced cancer stages. Moreover, the bisulfite pyrosequencing assay confirmed CGI cg12258811 hypermethylation and its negative correlation with PER3 expression. In vitro and in vivo experiments demonstrated that PER3 inhibited KIRP and LUAD progression. Decitabine enhanced PER3 expression and inhibited KIRP cell functions by reducing promoter (cg12258811) methylation level.ConclusionsOur findings advanced the mechanistic understanding of variations in PER3 expression in cancers and confirmed the tumor-associated function of PER3 hypermethylation and downregulation.

EBNA1BP2 identified as potential prognostic biomarker for multiple tumor types in pan-cancer analysis

BackgroundEpstein-Barr virus (EBV) infection has been closely linked to the development of various types of cancer. EB nuclear antigen 1 binding protein 2 (EBNA1BP2) is a crucial molecule for stable isolation of EBV in latent infection. However, the role of EBNA1BP2 in multiple tumor types is remains unclear. In this study, we comprehensively analyzed the functional characteristics of EBNA1BP2 and investigate its potential as a prognostic biomarker in pan-cancer.MethodsWe utilized data from TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus) databases and employed various bioinformatics analysis tools, including TIMER2.0, HPA, GEPIA2.0, PrognoScan, cBioPortal, CancerSEA, and BioGRID to explore the expression pattern, prognostic value, immune infiltration, and methylation level of EBNA1BP2 in pan-cancer. Additionally, we conducted enrichment analysis of genes associated with EBNA1BP2 to identify potential biological functions and pathways.ResultsOur analysis revealed that EBNA1BP2 expression was significantly higher in tumor tissues compared to tumor-adjacent tissues. We observed that lower expression of EBNA1BP2 in adrenocortical carcinoma (ACC), brain lower grade glioma (LGG), sarcoma (SARC), and uterine carcinosarcoma (UCS) was significantly associated with improved overall survival (OS) and disease-free survival (DFS). Furthermore, the promoter methylation level of EBNA1BP2 was downregulated in the majority of cancer types. At the single-cell level, EBNA1BP2 was found to be positively correlated with cell cycle and DNA repair processes, while negatively correlated with hypoxia. Additionally, EBNA1BP2 was associated with the infiltration of immune cells such as B cells, cancer-associated fibroblast cells, and CD8+ T cells. Gene enrichment analysis indicated that EBNA1BP2 was mainly involved in nucleoplasm and RNA binding pathways.ConclusionOur findings suggest that EBNA1BP2 may serve as a potential prognostic biomarker for survival in pan-cancer. Further experimental studies are needed to validate these findings and explore the underlying mechanisms by which EBNA1BP2 contributes to tumorigenesis.

FAS gene expression, prognostic significance and molecular interactions in lung cancer.

FAS has been implicated in the development of various cancers, but its involvement in lung cancer has not been systematically characterized. In this study, we performed data mining in online tumor databases to investigate the expression, methylation, alterations, protein interactions, co-expression and prognostic significance of FAS in lung cancer. The expression, prognostic significance and molecular interactions of FAS in lung cancer was mined and analyzed using GENT2, GEPIA2, UALCAN, cBioPortal, STRING, GeneMANIA, UCSC Xena, Enrichr, and OSluca databases. FAS expression was subsequently investigated at the protein level in samples from 578 lung cancer patients to understand its protein-level expression. In vitro validation of FAS gene expression was performed on H1299, H1993, A549 and HBE cell lines. We found that the expression of FAS was significantly downregulated in both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) compared to normal lung tissue. In addition, we observed a higher level of FAS promoter methylation in LUSC tissue than in normal tissue. FAS alterations were rare (1.9%) in lung cancer samples, with deep deletions being more common than missense mutations, which occurred mainly in the TNFR-like cysteine-rich domain and the death domain. We also identified a list of proteins interacting with FAS and genes co-expressed with FAS, with LUAD having 11 co-expressed genes and LUSC having 90 co-expressed genes. Our results also showed that FAS expression has limited prognostic significance (HR=1.302, 95% CI=0.935-1.139, P=0.530). Protein level investigation revealed that FAS expression varied among individuals, with nTPM values ranging from 5.2 to 67.2. This study provides valuable insights into the involvements and characteristics of FAS in lung cancer. Further studies are needed to investigate the clinical significance of FAS alterations in lung cancer and to explore the potential of targeting FAS for therapeutic intervention.

A Pan-Cancer Analysis of GAPDH as a Common Biomarker for Various Cancers

Objective: To investigate the expression levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and explore its prognostic value across 24 different human cancers. This investigation was conducted using comprehensive bioinformatics and in vitro approaches, incorporating multiple layers of analysis. Methods: GAPDH expression and methylation levels were assessed using bioinformatics tools and validated in cell lines through RNA-seq and targeted bisulfite-seq analyses. The potential prognostic significance of GAPDH was evaluated using the KM plotter. Additionally, cBioPortal was employed to investigate genetic alterations associated with this gene. Pathway analysis was conducted using DAVID. Furthermore, a correlation analysis between GAPDH expression and CD8+ T immune cells was performed using TIMER and CDT. Finally, a gene-drug interaction network analysis was conducted using Cytoscape to examine the relationship between GAPDH and various drugs. Results: GAPDH was found to be commonly upregulated in 24 types of human cancers, with its upregulation significantly correlated with poor relapse-free survival (RFS) and overall survival (OS) in BLCA, CESC, HNSC, KIRP, LIHC, and LUAD. This suggests that GAPDH plays a significant role in the development of these cancers. GAPDH upregulation was also associated with various clinicopathological features in patients with BLCA, CESC, HNSC, KIRP, LIHC, and LUAD. Pathway analysis revealed GAPDH’s involvement in diverse pathways. Additionally, notable correlations were observed between GAPDH expression and its promoter methylation level, genetic alterations, and CD8+ T immune cell levels. Moreover, several regulatory drugs targeting GAPDH were identified, with the potential to modulate its expression and potentially prevent conditions such as BLCA, CESC, HNSC, KIRP, LIHC, and LUAD. Conclusion: Based on our findings, GAPDH emerges as a promising diagnostic and prognostic biomarker for BLCA, CESC, HNSC, KIRP, LIHC, and LUAD.

Expression and Prognostic Potential of ESR1 in Breast Cancer

This study aims to explore the potential of ESR1 as a biomarker in breast cancer (BRCA) using bioinformatics analysis tools. The up-regulation of ESR1 expression in BRCA was investigated using UALCAN and GEPIA2, illustrating its role in BRCA progression. Furthermore, analyses based on various variables such as gender, age, race, and pathological stages of BRCA patients revealed a consistent up-regulation of ESR1, emphasizing its role in the development and progression of BRCA. Additionally, an analysis of ESR1 promoter methylation levels across various parameters revealed hypomethylation, affirming the inverse correlation between methylation and ESR1 expression. Prognostic analysis further indicated that overexpression of ESR1 is associated with poor overall survival, highlighting its potential as a prognostic biomarker in BRCA. Moreover, genetic mutation analysis using cBioPortal disclosed a minor role of ESR1 genetic mutations in BRCA, with only 2.5% of genetic alterations observed. The STRING and DAVID tools were utilized to conduct pathway enrichment analysis, revealing diverse biological functions of ESR1 and its 10 interconnected genes. Altogether, these results underscore the significance of understanding ESR1 up-regulation in BRCA and demonstrate its potential as a therapeutic, diagnostic, and prognostic biomarker.

ART altered DNA methylation of the imprinted gene H19 in fetal tissue after multifetal pregnancy reduction

PurposeThis study aimed to assess whether assisted reproductive technology alters DNA methylation levels at the H19 promoter and H19 imprinting control element (ICE) in fetal tissues obtained after multifetal pregnancy reduction.MethodsFetal tissues from multiple pregnancies were obtained, including fresh and frozen-thawed embryos: nine from conventional in vitro fertilization (c-IVF), four from intracytoplasmic sperm injection (ICSI), ten from cryopreserved IVF embryos (cryo-IVF), and six from cryopreserved ICSI (cryo-ICSI) embryos. Next-generation sequencing-based bisulfite PCR was used to determine the DNA methylation status of three CpG islands (H19-1, H19-2, and H19-3) in the H19 promoter and H19 ICE. The primary outcome was H19-1 DNA methylation status, whereas secondary outcomes assessed H19-2, H19-3, and ICE methylation.ResultsThe ICSI (β = -3.189, 95% CI = -5.034 to -1.345, p = 0.0026), cryo-IVF (β = -2.150, 95% CI = -3.706 to -0.593, p = 0.0129), and cryo-ICSI (β = -2.238, 95% CI = -3.817 to -0.659, p = 0.0110) groups exhibited significantly lower methylation levels in the primary outcome H19-1 region than the c-IVF group after adjustment. For the secondary outcome H19-2 region, significant decreases were observed in the cryo-IVF (β = -2.132, 95% CI = -4.071 to -0.192, p = 0.0425) and cryo-ICSI groups (β = -2.598, 95% CI = -4.566 to -0.630, p = 0.0168).ConclusionsThese findings further indicate that embryo cryopreservation and potentially ICSI can lower the methylation level of the H19 promoter, advocating for careful use of these techniques when necessary.

Hypomethylation in promoters of PGC-1α involved in exercise-driven skeletal muscular alterations in old age.

Exercise training can significantly improve skeletal muscle mitochondrial function and has been proven to be highly relevant to alterations in skeletal muscle DNA methylation. However, it remains unclear whether late-in-life exercise has an effect on promoter methylation of PGC-1α, a key regulator of mitochondrial biogenesis. Here we employed two distinct exercise modalities, constant medium intensity exercise training (CMIT) and high-intensity interval exercise training (HIIT), to investigate their impacts on PGC-1α expression and methylation regulation in skeletal muscle of aged mice. The results revealed a notable decrease in PGC-1α expression in skeletal muscle of aged mice, accompanied by elevated methylation levels of the PGC-1α promoter, and increased DNA methyltransferase (DNMT) protein expressions. However, both forms of exercise training significantly corrected PGC-1α epigenetic changes, increased PGC-1α expression, and ameliorated skeletal muscle reduction. Furthermore, exercise training led to elevated expression of proteins related to mitochondrial biogenesis and energy metabolism in skeletal muscle, improving mitochondrial structure and function. In conclusion, late-in-life exercise improved skeletal muscle function, morphology, and mitochondria biogenesis, which may be associated with hypomethylation in promoters of PGC-1α and increased content of skeletal muscle PGC-1α. Notably, there was no clear difference between HIIT and CMIT in PGC-1α expression and skeletal muscle function.

Pan-cancer exploration of PNO1: A prospective prognostic biomarker with ties to immune infiltration

The partner of NOB1 homolog (PNO1) is an RNA-binding protein that participates in ribosome biogenesis and protein modification. The functions of this molecule are largely unknown in cancers, particularly breast cancer. We employed bioinformatics methods to probe the putative oncogenic functions of PNO1 based on expression profiles and clinical data from the cancer genome atlas (TCGA), genotype-tissue expression project (GTEx), human protein atlas (HPA), cancer cell line encyclopedia (CCLE), UALCAN, drug sensitivity in cancer (GDSC) and UCSC XENA databases. Our analyses revealed that PNO1 was overexpressed in 31 malignancies, which excluded kidney chromophobe (KICH) and acute myeloid leukemia (LAML). Prognostic assessments have demonstrated that high PNO1 expression was significantly correlated with poor overall and disease-specific survival in various cancers. The promoter methylation level of PNO1 is significantly decreased in breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), kidney renal papillary cell carcinoma (KIRP), prostate adenocarcinoma (PRAD), thyroid carcinoma (THCA) and uterine corpus endometrial carcinoma (UCEC). Furthermore, inhibition of PNO1 decreased the viability, migration and invasion of breast cancer cells, and these results were confirmed by mouse xenograft models of breast cancer. In addition, we discovered that tumor microenvironment (TME), immune infiltration, and chemotherapy sensitivity were influenced by PNO1 expression. Concordantly, our analyses revealed a significant positive correlation between PNO1 and programmed cell death ligand 1 (PD-L1) expression across breast carcinoma samples. In conclusion, these findings indicate that PNO1 could act as a promising prognostic biomarker and adjunct diagnostic indicator, because it affects tumor growth and invasion. Our study offers valuable new perspectives on the oncogenic role of PNO1 in various types of cancers.

LncRNA FAM83H-AS1 inhibits ferroptosis of endometrial cancer by promoting DNMT1-mediated CDO1 promoter hypermethylation

Endometrial cancer (EC) is the most prevalent gynecological epithelial malignancy. DNA methylation is a promising cancer biomarker, but limited use for detecting EC. We previously found that the level of cysteine dioxygenase 1 (CDO1) promoter methylation was elevated in EC patients through methylomics, but the role and mechanism of CDO1 in EC remained unclear. Here, the methylation level of CDO1 promoter was detected by Bisulfite-sequencing PCR (BSP) and methylation-specific PCR (MSP) (bisulfite-conversion-based PCR methods, which remain the most commonly used techniques for methylation detection). Cells were incubated with erastin (the ferroptosis activator). Cell vitality was measured using the cell counting kit-8 (CCK-8) assay. FAM83H-AS1 cellular distribution was analyzed by the fluorescence in situ hybridization (FISH) assay. Lipid ROS level was examined by BODIPY-C11 staining. The interactions between FAM83H-AS1, CDO1, and DNA methyltransferase1 (DNMT1) were analyzed by RNA binding protein immunoprecipitation (RIP) or chromatin immunoprecipitation (ChIP) assay. The xenograft mouse model was utilized to test CDO1 and FAM83H-AS1's influence on tumor development in vivo. Results showed that CDO1 was hypermethylated and downregulated in EC. CDO1 knockdown reduced erastin-induced ferroptosis in EC cells. Mechanistically, DNMT1 is a DNA methyltransferase, which can transfer methyl groups to cytosine nucleotides in genomic DNA. Long non-coding RNA (lncRNA) FAM83H-AS1 increased CDO1 promoter methylation level and inhibited its expression in EC cells by recruiting DNMT1. CDO1 knockdown or FAM83H-AS1 overexpression promoted EC tumor growth in vivo. LncRNA FAM83H-AS1 inhibited ferroptosis in EC by recruiting DNMT1 to increase CDO1 promoter methylation level and inhibit its expression.

DNA Methylation of Postnatal Liver Development in Pigs.

DNA methylation plays an important role in the development and tissue differentiation of eukaryotes. In this study, bisulfite sequencing (BS-seq) technology was used to analyze the DNA methylation profiles of liver tissues taken from Rongchang pigs at three postnatal feeding stages, including newborn, suckling, and adult. The DNA methylation pattern across the genomes or genic region showed little difference between the three stages. We observed 419 differentially methylated regions (DMRs) in promoters, corresponding to 323 genes between newborn and suckling stages, in addition to 288 DMRs, corresponding to 134 genes, between suckling and adult stages and 351 DMRs, corresponding to 293 genes, between newborn and adult stages. These genes with DMRs were mainly enriched in metabolic, immune-related functional processes. Correlation analysis showed that the methylation level of gene promoters was significantly negatively correlated with gene expression. Further, we found that genes related to nutritional metabolism, e.g., carbohydrate metabolism (FAHD1 and GUSB) or fatty acid metabolism (LPIN1 and ACOX2), lost DNA methylation in their promoter, with mRNA expression increased in newborn pigs compared with those in the suckling stage. A few fatty acid metabolism-related genes (SLC27A5, ACOX2) were hypomethylated and highly expressed in the newborn stage, which might satisfy the nutritional requirements of Rongchang pigs with high neonatal birth rates. In the adult stage, HMGCS2-which is related to fatty acid β-oxidation-was hypomethylated and highly expressed, which explains that the characteristics of high energy utilization in adult Rongchang pigs and their immune-related genes (CD68, STAT2) may be related to the establishment of liver immunity. This study provides a comprehensive analysis of genome-wide DNA methylation patterns in pig liver postnatal development and growth. Our findings will serve as a valuable resource in hepatic metabolic studies and the agricultural food industry.