Gene Methylation Research Articles

Differences in DNA Methylation in Genes Involved in Vitamin D Metabolism Are Related to Insulin Requirement in Pregnant Women with Gestational Diabetes Mellitus.

In a previous study performed by our group, pregnant women with Gestational Diabetes (GDM) showed higher vitamin D (VitD) levels in the last trimester, particularly in those requiring insulin. This phenomenon was not linked to factors like season or supplementation. This study aimed to investigate if insulin treatment in GDM affects DNA methylation in VitD metabolism genes. Thirty-two pregnant women were selected, half of whom had GDM, and were divided into insulin-treated and lifestyle groups. The DNA methylation levels in CpGs from 47 VitD metabolism-related genes were analyzed at the diagnostic visit (24-28 weeks) and before delivery. At week 36-38 of pregnancy, twenty-six CpG sites were differentially methylated (DMPs) in the insulin-treated group compared with the control group and the lifestyle group. Twenty-two of these DMPs were not different at the diagnostic visit. Six CpGs (cg18276810 (CTNNB1), cg03919554 (FGFR3), cg03984919 (NCOA1), cg19218509 (ASIP), cg09922639 (SMAD3), and cg25356935 (PDZD3)) showed significant correlations with VitD levels, not only before childbirth, but also in the postpartum period and at one year later. This suggests that insulin treatment in GDM could influence DNA methylation in genes involved in vitamin D metabolism, affecting VitD levels during and after pregnancy. Further research is warranted to elucidate these findings' clinical implications.

Integrative Analysis of Acupuncture Targets and Immune Genes in Diabetes, Diabetic Peripheral Neuropathy, and Adjunct Therapy of Cancer.

Acupuncture may help treat diabetes mellitus (DM), diabetic peripheral neuropathy (DPN), and adjunct therapy for cancer, but the biological mechanisms and immune-related genes involved are unclear; this study aims to clarify these aspects. Comprehensive gene expression analysis revealed differentially expressed genes (DEGs) among DM, DPN, and control samples. Key genes from WGCNA were intersected with DEGs and acupuncture targets. Inflammatory responses, immune processes, signaling pathways, immune cell infiltration, and microRNA-gene interactions were studied. Hub immune-related genes' dysregulation was analyzed for copy number variation and gene methylation. A pan-cancer nomogram model was created to predict survival based on various factors, linking hub genes to cancer properties. Our analysis found 3,217 and 2,191 DEGs in DM/control and DPN/DM comparisons, respectively, and identified 1,830 potential acupuncture targets. We pinpointed 21 key genes in DM and 43 in DPN, involved in inflammatory responses, immune processes, CAMKK2, and cAMP signaling pathways. Distinct immune cell infiltration patterns, including M0 and M2 macrophages, neutrophils, and follicular helper T cells, were noted. Further analysis revealed microRNAs and TF genes interacting with immune hub genes in both conditions. Dysregulation of eight hub immune-related genes was linked to copy number variation and gene methylation, correlating with cancer prognosis. Co-occurrence of single nucleotide variations and oncogenic mutations was observed in these genes. The pan-cancer nomogram model showed strong prognostic capabilities, and a significant association was found between the eight genes and cancer properties like angiogenesis, EMT, and cell cycle progression. Our findings underscore the pivotal roles of MAPK3, IL1RN, SOD2, CTSD, ESR1, SLC1A1, NPY, and CCR2 in the immune response mediated by acupuncture in the context of DM, DPN, and adjunct therapy for cancer.

Integrative multiomic analysis unveils the molecular nexus of mitochondrial dysfunction in the pathogenesis of age-related macular degeneration

Mitochondrial dysfunction is linked to age-related macular degeneration (AMD), but its mechanisms and related molecular networks remain unclear. We explored the association between mitochondrial-related genes and AMD by integrating multiomic data. We acquired summary-level data on mitochondrial-related protein abundance, gene expression, and gene methylation from quantitative trait locus studies. Genetic associations with AMD were sourced from the International Age-related Macular Degeneration Genomics Consortium (discovery), FinnGen (replication), and UK Biobank (replication) studies. We used summary-data-based Mendelian randomization to assess the correlations between mitochondrial-related gene molecular characteristics and AMD. Furthermore, colocalization analysis was performed to ascertain if the detected signal pairings had a common causative genetic variation. Mitochondrial-relatedl gene NFKB1 demonstrated a protective role in AMD (tier 1 evidence), whereas HSPA1A and HSPA1B genes were also associated with decreased AMD risk (tier 2 evidence). The methylation of cg09390974 and cg15409712 in NFKB1 was associated with increased NFKB1 expression, consistent with the protective effect on AMD risk, whereas inverse associations were observed between gene methylation and gene expression for HSPA1B (cg04835051 and cg16372051), supporting the risk roles of methylation in AMD. At circulating protein level, genetically predicted higher levels of HSPA1A (odds ratio [OR] 0.28, 95% confidence interval [CI] 0.19−0.41, P<0.001), HSPA1B (OR 0.13, 95% CI 0.06−0.27, P<0.001), and NFKB1 (OR 0.43, 95% CI 0.27−0.68, P<0.001) were inversely associated with AMD risk. These associations were corroborated in the colocalization analysis. We identified AMD-linked mitochondrial-related genes, potentially improving the understanding of its pathophysiological mechanisms and aiding the identification of novel pharmaceutical targets.

Histone MARylation regulates lipid metabolism in colorectal cancer by promoting IGFBP1 methylation

In the global health community, colorectal cancer (CRC) is a major concern, with a high rate of incidence. Mono-ADP-ribosylation (MARylation) is a type of epigenetics and recognized as one of the causes of CRC development and progression. Although the modification level and target proteins in CRC remain unclear, it has been found that MARylation of arginine-117 of histone 3 (H3R117) promotes the proliferation, upregulates methylation of tumor suppressor gene, and is tightly associated with the metabolic processes in LoVo cells. Lipid metabolism disorder is involved in the development of CRC at the early stage. Our study revealed that MARylation of H3R117 of the LoVo cells modulated lipid metabolism, increased cholesterol synthesis, promoted lipid raft (LR) protein IGF-1R distribution, and inhibited cell apoptosis through IGFBP1. In addition, bioinformatics analyses revealed that IGFBP1 promoter was hypermethylated in CRC when compared to that in normal tissues. Moreover, H3R117 MARylation upregulated the methylation of IGFBP1 promoter through histone H3 citrullination (H3cit) by increasing the H3K9me2, heterochromatin protein1 (HP1), and DNA methyltransferase 1 (DNMT1) enrichment of IGFBP1 promoter. Accordingly, IGFBP1 may function as a tumor suppressor gene, while H3R117 MARylation may promote CRC development. Our study findings enrich the available data on epigenetics of CRC and provide a new idea and experimental basis for H3R117 MARylation as a target in CRC treatment.

Effect of body mass index on semen quality, sperm chromatin integrity and sperm DNA methylation

Obesity represents a growing problem due to its impacts on human health and reproduction. In this study, we analysed semen quality, sperm DNA integrity and gene-specific CpG methylation in 116 healthy men from normal population. The men were divided into three groups according to their body mass index (BMI), and their ejaculates were analysed using standard methods, sperm chromatin structure assay (SCSA), methylation next generation sequencing (NGS) and amplicon sequencing. The sperm methylation NGS revealed six significantly differentially methylated regions (DMRs). Using subsequent targeted amplicon sequencing in 116 men, two of the DMRs were proved as differentially methylated in sperm of men with normal BMI vs. BMI ≥ 25. The DMRs were located in the EPHA8 and ANKRD11 gene. Also, we detected a significant decline in the EPHA8, ANKRD11 and CFAP46 gene methylation in association with increasing BMI values. The genes EPHA8 and ANKRD11 are involved in the nervous system and brain development; the CFAP46 gene plays a role in a flagellar assembly and is associated with sperm motility. Significantly lower rates of motile and progressive motile sperm were observed in men with BMI ≥ 30. Our results show that excess body weight can modify CpG methylation of specific genes, affect sperm motility, and compromise sperm chromatin integrity. These factors can stand behind the observed reduced fertility in men with obesity. The methylation changes might be transmitted to their offspring through sperm, and become a basis for possible developmental and reproductive issues in the next generation.

Multi-omics analysis of sea urchin (Strongylocentrotus intermedius) adaptation to salt stress reveals epigenetic regulatory mechanisms

Increased precipitation and surface runoff due to global warming has reduced surface seawater and nearshore water salinity, affecting marine organism survival. Nevertheless, the epigenetic mechanisms underlying the adaptation of sea urchins (Strongylocentrotus intermedius) to low-salinity stress remains unknown. This study utilized response surface methodology to formulate growth models for S. intermedius at different salinity levels and shell diameters. Whole genome bisulphite sequencing, RNA-sequencing, and metabolome analysis were performed on low-salinity stressed sea urchins, and a total of 3006 differential methylated regions, 945 differential methylated genes, 886 differentially expressed genes, and 271 differential metabolites were identified. Multi-omics analysis revealed significant alterations in the gene expression and DNA methylation of key genes (e.g., SPHK2, Arpc1a, and SLC23A1) in S. intermedius under low-salinity stress conditions. These changes subsequently influenced the metabolism of substances, including sphingosine-1-phosphate, ethanolamine phosphate, vitamin C, taurine, and choline. These alterations impacted functions related to immunity, osmoregulation, and energy metabolism in the organism. This study was to comprehensively elucidate the epigenetic mechanisms of S. intermedius under low-salinity stress from the perspective of DNA-RNA-metabolites, providing new insights into salinity adaptation of marine invertebrates.

Peripheral Blood ABCG1 Gene DNA Methylation: Mediating the Relationship between Dietary Intake of Methyl Donor Nutrients and Stroke Risk

Dysregulation of methyl donor nutrients interferes with DNA methylation and is associated with neurological diseases. ABCG1 gene regulates cholesterol to HDL-C, maintains lipid homeostasis, and has been linked to both methyl nutrition and neurological risks. The aim was to investigate whether there is an effect of ABCG1 DNA methylation on the relationship between intake of methyl donor nutrients and the risk of stroke occurrence. We hypothesize that the intake of methyl donor nutrients may influence stroke occurrence by modulating the methylation status of ABCG1. This study utilized a case-control design and selected 52 stroke patients along with 52 healthy controls from Northwest China. Dietary information was collected using a FFQ, and methylation levels were measured at 29 CpG sites of the ABCG1 gene. A significant linear trend was found between dietary intake of the methyl donor nutrient choline and CpG_19.20 methylation of the ABCG1 gene (β = -0.037, P = 0.033). Additionally, a significant association was observed between CpG_19.20 methylation and the risk of stroke (OR 2.325, 95% CI 1.210 - 4.466). Mediation analysis revealed that choline intake indirectly influenced stroke occurrence through its effect on CpG_19.20 methylation levels in the ABCG1 gene (β = -0.015, SE = 0.013, 95% CI = [-0.053, -0.001]). We found that DNA methylation at specific CpG sites of the peripheral blood ABCG1 gene mediates the association between dietary methyl donor nutrient intake and stroke risk in an adult population from Northwest China. New insights are provided on the prevention and treatment of stroke.

Midseason draining of paddy water suppresses microbial arsenic methylation in soil and alleviates rice straighthead disease

Arsenic (As) methylation is an important component of As biogeochemical cycle. Microbial As methylation is enhanced under anoxic conditions in paddy soil, producing dimethylarsenate (DMA) which can cause physiological straighthead disease in rice. We conducted field experiments at two sites to test the effect of midseason draining of paddy water on microbial As methylation and the incidence of straighthead disease. Compared to continuous flooding, midseason draining increased soil Eh, decreased the abundances of microbial genes for arsenate reduction (arsC and arrA) and arsenite methylation (arsM), and lowered the concentrations of both inorganic As and DMA in soil porewater. Draining shifted microbial composition, resulting in decreases in the relative abundance of 17–132 amplicon sequence variants. Draining decreased the accumulation of DMA in rice husk and of inorganic As and DMA in rice grain, decreased the incidence of straighthead disease, and increased grain yield by 20–45 %. Further experiments were conducted at eight field sites to assess the effect of midseason draining in a split field design. Draining decreased husk DMA concentration by 40–65 % and increased grain yield by 25–209 %. This study demonstrates that midseason draining can effectively suppress microbial As methylation and alleviate rice straighthead disease, benefiting both grain yield and safety.

The Long COVID: Further Advances in Our Understanding about the Role of Specific Chemokines (CCR5, CCR6, CCR9 and CCL3) in Pediatrics

Introduction: Long COVID, also known as post-COVID-19 syndrome (PCS), is a condition where individuals continue to experience symptoms for weeks or months after recovering from COVID-19. The aim of this study was to evaluate the long-term effects of severe COVID-19 on promotor methylation and expression genes including CCR5, CCR6, CCR9 and CCL3 in children. Material and Methods: Clinical data and blood samples from 94 long COVID patients and 25 healthy subjects were collected. The control group was age-matched. Promotor methylation and mRNA expression of CCR5, CCR6, CCR9 and CCL3 genes in these patients and control group were assessed through methylation-specific PCR and Real-time PCR assay. Results: Our result indicated that promotor of CCR5 (p = 0.01) and CCL3 (p = 0.006) in long COVID children were hyper-methylated compared to healthy control group. Subsequently CCR5 and CCL3 transcript was decreased compared to control group (p = 0.01). In addition, CCL3 transcript in children with long COVID was decreased compared to control group (p = 0.008). On the other hand, we did not observe any significant modification in the transcript levels of CCR6 (p = 0.7) and CCR9 (p = 0.46) in children with long COVID in comparison to all control groups. Conclusion: The CCR5 and CCL3 promoter region DNA methylation and the subsequent decrease in the expression of these genes were possibly correlated with long COVID occurrence in children. Our study revealed additional data on the SARS-CoV-2 mediated inflammatory response. conclusion: The CCR5 and CCL3 promoter region DNA methylation and the subsequent decrease in the expression of these genes were possibly correlated with long COVID occurrence in children. Our study revealed additional data on the SARS-CoV-2 mediated inflammatory response.

Exploring the effects of Merkel cell polyomavirus T antigens expression in REH and MCC13 cells by methylome and transcriptome profiling.

Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer with a tripled incidence in the US and Europe over the past decade. Around 80% of MCC is linked to Merkel cell polyomavirus, but the cell of origin remains unknown. We stably introduced Merkel cell polyomavirus (MCPyV)-sT) and LT antigens to MCC13 and REH cell lines, analyzing DNA methylation and gene transcriptional regulation. Gene ontology analysis assessed MCPyV effects, and integrative analysis correlated gene expression and methylation. Expression patterns were compared with 15 previously sequenced primary MCCs. We found that MCPyV-LT induces DNA methylation changes in both cell lines, while MCPyV-sT only affected REH cells. Greater gene expression changes are observed in MCC13 cells, with upregulated genes associated with cellular components and downregulated genes related to biological processes. Integrative analysis of differentially expressed genes (DEG) and differentially methylated regions (DMR) of REH cell lines revealed that no genes were commonly methylated and differentially expressed. The study compared DEGs and DMG in MCC13 and REH cells to overlapping genes in MCPyV-positive cell lines (MKL1, MKL2, and WaGa), identifying hypomethylated genes in the gene body and hypermethylated genes at TSS1500. GO analysis of the two cell lines showed that MCPyV-TAs can downregulate genes in MHC-I pathways; this downregulation offers a target that can be used to create novel and efficient MCC immunotherapy approaches. Finally, it was confirmed that MCPyV-LT controls gene expression in MCC tissues using an integrative investigation of DNA methylation and gene expression.

Association of PPARGC1A gene polymorphism and mtDNA methylation with coal-burning fluorosis: a case–control study

BackgroundCoal-burning fluorosis is a chronic poisoning resulting from the prolonged use of locally available high-fluoride coal for heating and cooking. Prolonged fluoride exposure has been demonstrated to decrease PPARGC1A levels. Therefore, this case-control aims to evaluate the genetic association of PPARGC1A gene polymorphisms and methylation of the mitochondrial D-loop region with coal-burning fluorosis.ResultThe results showed that the TT genotype at rs13131226 and the AA genotype at rs1873532 increased the risk of coal-burning fluorosis (OR = 1.84, P = 0.004; OR = 1.97, P = 0.007), the CT and CC genotypes at rs7665116 decreased the risk of coal-burning fluorosis (OR = 0.54, P = 0.003). The TT genotype at the rs2970847 site and the AA genotype at the rs2970870 site increase the risk of developing skeletal fluorosis (OR = 4.12, P = 0.003; OR = 2.22, P = 0.011). Haplotype AG constructed by rs3736265-rs1873532 increased the risk of the prevalence of coal-burning fluorosis (OR = 1.465, P = 0.005); CG decreased the risk of the prevalence of coal-burning fluorosis (OR = 0.726, P = 0.020). Haplotype CGGT constructed by rs6821591-rs768695-rs3736265-rs2970847 increased the risk of the prevalence of skeletal fluorosis (OR = 1.558, P = 0.027). A 1% increase in CpG_4 methylation levels in the mtDNA D-loop region is associated with a 2.3% increase in the risk of coal-burning fluorosis. Additionally. There was a significant interaction between rs13131226 and rs1873532; CpG_4 and CpG_8.9; rs13131224,rs6821591 and rs7665116 were observed in the occurrence of fluorosis in the Guizhou population (χ2 = 16.917, P < 0.001; χ2 = 21.198, P < 0.001; χ2 = 36.078, P < 0.001).ConclusionPPARGC1A polymorphisms rs13131226 and rs1873532 and the mitochondrial DNA D-loop methylation site CpG_4 have been associated with an increased risk of fluorosis, conversely polymorphism rs7665116 was associated with a decreased risk of fluorosis. Polymorphisms rs2970870 were associated with increased risk of skeletal fluorosis, and polymorphism rs2970847 was associated with decreased risk of skeletal fluorosis. These SNPs and CpG can be used as potential targets to assess fluorosis risk.

DNA Methylation Participates in Drought Stress Memory and Response to Drought in Medicago ruthenica.

Background: Drought is currently a global environmental problem, which inhibits plant growth and development and seriously restricts crop yields. Many plants exposed to drought stress can generate stress memory, which provides some advantages for resisting recurrent drought. DNA methylation is a mechanism involved in stress memory formation, and many plants can alter methylation levels to form stress memories; however, it remains unclear whether Medicago ruthenica exhibits drought stress memory, as the epigenetic molecular mechanisms underlying this process have not been described in this species. Methods: We conducted methylome and transcriptome sequencing to identify gene methylation and expression changes in plants with a history of two drought stress exposures. Results: Methylation analysis showed that drought stress resulted in an approximately 4.41% decrease in M. ruthenica genome methylation levels. The highest methylation levels were in CG dinucleotide contexts, followed by CHG contexts, with CHH contexts having the lowest levels. Analysis of associations between methylation and transcript levels showed that most DNA methylation was negatively correlated with gene expression except methylation within CHH motifs in gene promoter regions. Genes were divided into four categories according to the relationship between methylation and gene expression; the up-regulation of hypo-methylated gene expression accounted for the vast majority (692 genes) and included genes encoding factors key for abscisic acid (ABA) and proline synthesis. The hypo-methylation of the promoter and body regions of these two gene groups induced increased gene transcription levels. Conclusions: In conclusion, DNA methylation may contribute to drought stress memory formation and maintenance in M. ruthenica by increasing the transcription levels of genes key for ABA and proline biosynthesis.

DNA methylation analysis of the SDC2, SEPT9 and VIM genes in fecal DNA for colorectal cancer diagnosis.

Colorectal cancer is one of the most common cancers worldwide. DNA methylation sites may serve as a new gene signature for colorectal cancer diagnosis. The search for representative DNA methylation sites is urgently needed. This study aimed to systematically identify a methylation gene panel for colorectal cancer diagnosis via tissue and fecal samples. A total of 181 fecal and 50 tumor tissue samples were collected. They were obtained from 83 colorectal cancer patients and 98 healthy subjects. These samples were evaluated for DNA methylation of 9 target genes via quantitative bisulfite next-generation sequencing. We employed the rank-sum test to screen the colorectal cancer-specific methylation sites in the tissue and fecal cohorts. A data model was subsequently constructed and validated via the dedicated validation dataset. Compared with the fecal and negative control samples, the colorectal cancer tissue samples presented significantly higher methylation rates for all the selected gene sites. The methylation rates of the tissue and preoperative fecal samples showed the same high and low rates at the same sites. After screening, a panel of 29 loci in the SDC2, SEPT9, and VIM genes proved to be reliable biomarkers for colorectal cancer diagnosis in fecal samples. Logistic regression models were then constructed and validated using this panel. The sensitivity of the model was 91.43% (95% CI = [89.69, 93.17]), the specificity was 100% (95% CI = [100,100]), and the AUC value is 99.31% (95% CI = [99,99.62]). The diagnostic accuracy of the model for stage I and stage II colorectal cancer was 100% (11/11) and 91.3% (21/23), respectively. Overall, this study confirms that the gene locus panel and the model can be used to diagnose colorectal cancer effectively through feces. Our study identified a set of key methylation sites for colorectal cancer diagnosis from fecal samples, highlighting the importance of using tissue and fecal samples to accurately assess DNA methylation levels to screen for methylation sites, and developing an effective diagnostic model for colorectal cancer.

Predictive nomogram of the clinical outcomes of colorectal cancer based on methylated SEPT9 and intratumoral IL-10+ Tregs infiltration

BackgroundGene methylation and the immune-related tumor microenvironment (TME) are highly correlated in tumor progression and therapeutic efficacy. Although both of them can be used to predict the clinical outcomes of colorectal cancer (CRC) patients, their predictive value is still unsatisfactory. Whether a combination risk model comprising these two prediction parameters performs better predictive effectiveness than independent factor is still unclear. Methylated Septin9 (mSEPT9) is an early diagnosis biomarker of CRC, in this study, we aimed to investigate mSEPT9-related biomarkers of immunosuppressive TME and identify the value of the combination risk model in predicting the clinical outcomes of CRC.MethodsImmunofluorescence staining was performed to clarify the correlation between intratumoral IL-10+ Treg infiltration and mSEPT9 in peripheral blood. Survival time, response to 5-fluorouracil (5-FU)-based chemotherapy and PD-1 blockade, and the probability of recurrence or metastasis were analyzed in study (197 CRC samples) and validation (195 CRC samples) sets to evaluate the efficacy of combination risk model. Potential mechanisms were explored by mRNA sequencing.ResultsHypermethylated SEPT9 in the peripheral blood of patients with CRC (stage I-III, and stage IV with resectable M1) before radical resection was positively correlated with high intratumoral IL-10+ Treg infiltration. The high-risk model revealed poor overall survival and progression-free survival, inferior therapeutic response to 5-FU-based chemotherapy and PD-1 blockade, and high probability of recurrence or metastasis. The underlying mechanisms may be associated with the increase in mSEPT9 and mediation of IL-10 via methionine metabolic reprogramming-induced infiltration of IL-10+ Tregs in the TME, which promotes tumor progression and resistance to 5-FU-based chemotherapy and PD-1 blockade.ConclusionsThe combination risk model of peripheral mSETP9 and intratumoral IL-10+ Treg infiltration in CRC can effectively predict prognosis, responsiveness to 5-FU-based chemotherapy and PD-1 blockade, and the probability of recurrence or metastasis. Therefore, this model can be used for precision treatment of CRC.

The Genome Architecture of the Copepod Eurytemora carolleeae, the Highly Invasive Atlantic Clade of the E. affinis Species Complex.

Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and are food sources for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations. Here, we presented the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage long-read and high-throughput chromosome conformation capture sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 megabase (Mb) (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transporter gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transporter genes and the significant clustering of these genes on each chromosome. This genome represents one of the most contiguous copepod genomes to date and among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.

Pan-cancer analysis of the prognostic and immunological role of hippo-YAP signaling pathway

The Hippo-Yes-associated protein (Hippo-YAP) signaling pathway, a conserved pathway that regulates organ size, participates in tumor progression. However, there are few comprehensive analyses of tumor prognosis and immunity. In the present study, TCGA, GTEx, GEO, TIMER2, STRING, GSCA, ImmuCellAI, and other bioinformatics tools were used to reveal the involvement of the Hippo-YAP signaling pathway in the prognosis and immunity of pan-cancers. The obtained results showed that mRNA expression differences of Hippo-YAP pathway genes between normal samples and tumor samples in pan-cancers and some genes (such as TEAD4, MAP4K4, and STK3) might affect the prognosis of patients with skin cutaneous melanoma (SKCM) and pancreatic adenocarcinoma (PAAD). Furthermore, mutation and methylation of the Hippo-YAP signaling pathway genes in normal and primary tumor tissues differ in various cancers (KIRP, BRCA). Additionally, the relationship between the tumor microenvironment, molecular pathways, and the Hippo-YAP pathway indicated that it might lead to a suppressive immune microenvironment that affects the efficacy of immunotherapy. This is a pan-cancer overview of the Hippo-YAP signaling pathway genes, which explores the aberrant expression or mutation of this pathway that regulates the tumor microenvironment and immunotherapy.

WIMOAD: Weighted Integration of Multi-Omics data for Alzheimer's Disease (AD) Diagnosis.

As the most common subtype of dementia, Alzheimer's disease (AD) is characterized by a progressive decline in cognitive functions, especially in memory, thinking, and reasoning ability. Early diagnosis and interventions enable the implementation of measures to reduce or slow further regression of the disease, preventing individuals from severe brain function decline. The current framework of AD diagnosis depends on A/T/(N) biomarkers detection from cerebrospinal fluid or brain imaging data, which is invasive and expensive during the data acquisition process. Moreover, the pathophysiological changes of AD accumulate in amino acids, metabolism, neuroinflammation, etc., resulting in heterogeneity in newly registered patients. Recently, next generation sequencing (NGS) technologies have found to be a non-invasive, efficient and less-costly alternative on AD screening. However, most of existing studies rely on single omics only. To address these concerns, we introduce WIMOAD, a weighted integration of multi-omics data for AD diagnosis. WIMOAD synergistically leverages specialized classifiers for patients' paired gene expression and methylation data for multi-stage classification. The resulting scores were then stacked with MLP-based meta-models for performance improvement. The prediction results of two distinct meta-models were integrated with optimized weights for the final decision-making of the model, providing higher performance than using single omics only. Remarkably, WIMOAD achieves significantly higher performance than using single omics alone in the classification tasks. The model's overall performance also outperformed most existing approaches, highlighting its ability to effectively discern intricate patterns in multi-omics data and their correlations with clinical diagnosis results. In addition, WIMOAD also stands out as a biologically interpretable model by leveraging the SHapley Additive exPlanations (SHAP) to elucidate the contributions of each gene from each omics to the model output. We believe WIMOAD is a very promising tool for accurate AD diagnosis and effective biomarker discovery across different progression stages, which eventually will have consequential impacts on early treatment intervention and personalized therapy design on AD.

Clinicopathological Characteristics and Outcomes of Colorectal Cancer With Heterogenous Staining of Mismatch Repair Protein.

Scant data are available on heterogenous staining of mismatch repair protein in colorectal cancer. This study aimed to improve insights into clinicopathologic features and prognosis of colorectal cancer harboring heterogenous mismatch repair protein staining. A single-center retrospective observational study. This study was conducted in a tertiary referral center in China between 2014 and 2018. Colorectal cancers with heterogenous staining of mismatch repair protein were included. Clinicopathologic and molecular features, and survival outcomes were analyzed. A total of 151 out of 6721 colorectal cancers (2.2%) exhibited heterogenous staining for at least one mismatch repair protein, with intraglandular heterogeneity being the most common pattern (89.4%). Heterogenous MLH1 staining was significantly associated with distant metastasis (p = 0.03), while heterogenous MSH2 staining was associated with left-sided (p = 0.03) and earlier pT stage tumors (p = 0.02). The rates of microsatellite instability-high, KRAS and BRAF mutation were 12.6%, 47.3% and 3.4%, respectively. Microsatellite instability-high was significantly associated with higher intraglandular MSH6 heterogeneity frequency (p < 0.001) and decreased MSH6 expression level (< 27.5%, p = 0.01). BRAF mutation was associated with the coexistence of intraglandular and clonal heterogeneity (p = 0.003) and decreased PMS2 expression level (p = 0.01). Multivariable analysis revealed that progression-free survival was significantly associated with tumor stage (p = 0.003), stroma fraction (p = 0.004), and heterogenous PMS2 staining (p = 0.02). Overall survival was linked to tumor stage (p = 0.006) and BRAF mutation (p = 0.01). The limitations of this study include the absence of testing for MLH1 promoter methylation and mismatch repair gene mutations, its retrospective design, and insufficient data related to direct comparison with deficient mismatch repair and proficient mismatch repair colorectal cancer. Heterogenous mismatch repair protein staining in colorectal cancer exhibits distinct associations with tumor location, stage, microsatellite instability, BRAF mutation and prognosis. It is recommended to report MSH6 heterogeneity as it may indicate microsatellite instability-high. See Video Abstract.

Effects of fumonisin B1 on gene-specific DNA methylation related to cancer pathways of p53 signalling and PI3K/Akt signalling in human kidney cells

Abstract Fumonisin B1 (FB1), which is emerged by contamination of corn and similar products with Fusarium species, causes a high risk for human and animal health. FB1 shows hepatotoxic, nephrotoxic, neurotoxic, immunotoxic and teratogenic effects. FB1 has also been linked to carcinogenesis processes that are unrelated to genotoxic pathways. Our goal was to investigate the role of gene-specific DNA methylation and expression of tumour suppressor genes in the toxicity of FB1 in human kidney (HK-2) cells. Using array panels, effects of FB1 exposure (10-100 μM) for 24 h on methylation levels of tumour suppressor genes were investigated. ToppGene Suite (Toppfun) portal was used to perform gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and Reactome enrichment studies. The most of the genes were hypermethylated significantly at 100 μM concentrations of FB1. These results are consistent with the expression results which downregulate the selected genes of CD44, CDKN1A, CDKN2B, CTNNB1, MYC and p16. Functional enrichment analysis further elucidated the molecular mechanisms of FB1 in cancer-related pathways especially p53 signalling and PI3K/Akt signaling. It has been expected that the present study could contribute to the studies on the mechanisms that play a role in FB1 induced carcinogenesis.

The mediating role of abnormal ZEB1 methylation in the association between nickel exposure and non-syndromic orofacial cleft

Our previous study found a positive relationship between fetal nickel exposure and the risk of OFCs. The teratogenic mechanism of nickel is not clear. In this study, we aim to examine the mediating effect of DNA methylation on the association of nickel(Ni) exposure with NSOFC in fetuses. 10 cases and 10 controls was used for screening target gene by Illumina Infinium Methylation EPIC(850k) BeadChip. 36 cases and 78 controls was conducted to determine DNA methylation level of selected gene in umbilical cord blood by Mass spectrometry assay. Mediation analysis was used to evaluate the potential mediating effect of selected gene methylation on the relation between concentrations of Ni and the risk for NSOFC. In the discovery stage, ZEB1 gene was identified to be hypermethylated in both nickel exposure and NSOFC group for validation. In the verification stage, the overall average methylation level of ZEB1 was significant higher in NSOFC cases(median = 8.70, interquartile range(IQR): 5.75–11.53) as compared to controls (median = 5.35, IQR: 4.30–7.78). The risk for NSOFC was increased by 1.43-fold with hypermethylation of ZEB1. Significant correlation was observed between concentrations of Ni in umbilical cord and methylation level of ZEB1. The hypermethylation of ZEB1 had a mediating effect by 20.47 % of total effect of Ni on NSOFC risk. Hypermethylation of ZEB1 is associated with the risk for NSOFC and may partially explain the association between Ni exposure and NSOFC risk. Our findings provide new insights into the epigenetic mechanisms underlying NSOFC and suggesting potential targets for future therapeutic interventions.