Decreased DNA Methylation Research Articles

Sex and tissue-specificity of piRNA regulation in adult mice following perinatal lead (Pb) exposure

ABSTRACT Lead (Pb) is a neurotoxicant with early life exposure linked to long-term health effects. Piwi-interacting RNAs (piRNAs) are small non-coding RNAs that associate with PIWIL proteins to induce DNA methylation. It remains unknown whether Pb exposure influences piRNA expression. This study evaluated how perinatal Pb exposure (32 ppm in drinking water) impacts piRNA expression in adult mice and assessed piRNA dysregulation as a potential mechanism for Pb-induced toxicity. Pb exposure effects on piRNA expression and associated gene repression in the germline (testis/ovary) and soma (liver and brain) were evaluated. Small RNA sequencing was used to determine differentially expressed piRNAs, RT-qPCR to examine piRNA target expression, and whole genome bisulfite sequencing to evaluate target DNA methylation status. Three piRNAs (mmpiR-1500602, mmpiR-0201406, and mmpiR-0200026) were significant after multiple testing correction (all downregulated in the male Pb-exposed brain in comparison to control; FDR < 0.05). Within piOxiDB, TAO Kinase 3 was identified as a downstream mRNA target for one of the three Pb-sensitive piRNA. The Pb-exposed male brain exhibited increased Taok3 expression (p < 0.05) and decreased DNA methylation (FDR < 0.01). The results demonstrate that perinatal Pb exposure stably influences longitudinal piRNA expression in a tissue- and sex-specific manner, potentially via DNA methylation-directed mechanisms.

CGAS deficient mice display premature aging associated with de-repression of LINE1 elements and inflammation.

Aging-associated inflammation, or 'inflammaging" is a driver of multiple age-associated diseases. Cyclic GMP-AMP Synthase (cGAS) is a cytosolic DNA sensor that functions to activate interferon response upon detecting viral DNA in the cytoplasm. cGAS contributes to inflammaging by responding to endogenous signals such as damaged DNA or LINE1 (L1) cDNA which forms in aged cells. While cGAS knockout mice are viable their aging has not been examined. Unexpectedly, we found that cGAS knockout mice exhibit accelerated aging phenotype associated with induction of inflammation. Transcription of L1 elements was increased in both cGAS knockout mice and in cGAS siRNA knockdown cells associated with high levels of cytoplasmic L1 DNA and expression of ORF1 protein. Cells from cGAS knockout mice showed increased chromatin accessibility and decreased DNA methylation on L1 transposons. Stimulated emission depletion microscopy (STED) showed that cGAS forms nuclear condensates that co-localize with H3K9me3 heterochromatin marks, and H3K9me3 pattern is disrupted in cGAS knockout cells. Taken together these results suggest a previously undescribed role for cGAS in maintaining heterochromatin on transposable elements. We propose that loss of cGAS leads to loss of chromatin organization, de-repression of transposable elements and induction of inflammation resulting in accelerated aging.

Whole genome methylation sequencing in blood from persons with mild cognitive impairment and dementia due to Alzheimer's disease identifies cognitive status.

Whole genome methylation sequencing (WGMS) in blood identifies differential DNA methylation in persons with late-onset dementia due to Alzheimer's disease (AD) but has not been tested in persons with mild cognitive impairment (MCI). We used WGMS to compare DNA methylation levels at 25,244,219 CpG loci in 382 blood samples from 99 persons with MCI, 109 with AD, and 174 who are cognitively unimpaired (CU). WGMS identified 9,756 differentially methylated positions (DMPs) in persons with MCI, including 1,743 differentially methylated genes encoding proteins in biological pathways related to synapse organization, dendrite development, and ion transport. 447 DMPs exhibit progressively increasing or decreasing DNA methylation levels between CU, MCI, and AD that correspond to cognitive status. WGMS identifies DMPs in known and newly detected genes in blood from persons with MCI and AD that support blood DNA methylation levels as candidate biomarkers of cognitive status.

Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs

Retrotransposons have invaded eukaryotic centromeres in cycles of repeat expansion and purging, but the function of centromeric retrotransposons has remained unclear. In Arabidopsis, centromeric ATHILA retrotransposons give rise to epigenetically activated short interfering RNAs in mutants in DECREASE IN DNA METHYLATION1 (DDM1). Here we show that mutants that lose both DDM1 and RNA-dependent RNA polymerase have pleiotropic developmental defects and mis-segregate chromosome 5 during mitosis. Fertility and segregation defects are epigenetically inherited with centromere 5, and can be rescued by directing artificial small RNAs to ATHILA5 retrotransposons that interrupt tandem satellite repeats. Epigenetically activated short interfering RNAs promote pericentromeric condensation, chromosome cohesion and chromosome segregation in mitosis. We propose that insertion of ATHILA silences centromeric transcription, while simultaneously making centromere function dependent on retrotransposon small RNAs in the absence of DDM1. Parallels are made with the fission yeast Schizosaccharomyces pombe, where chromosome cohesion depends on RNA interference, and with humans, where chromosome segregation depends on both RNA interference and HELLSDDM1.

TNC upregulation promotes glioma tumourigenesis through TDG-mediated active DNA demethylation

Gliomas represent the most predominant primary malignant tumor in central nervous system. Thymine DNA glycosylase (TDG) is a central component in active DNA demethylation. However, the specific mechanisms of TDG-mediated active DNA demethylation in gliomas remain unclear. This research indicates TDG expression is overexpressed in gliomas and correlated with poor prognosis. TDG knockdown suppressed the malignant phenotype of gliomas both in vitro and vivo. Notably, RNA-seq analysis revealed a strong association between TDG and tenascin-C (TNC). ChIP-qPCR and MeDIP-qPCR assays were undertaken to confirm that TDG participates in TNC active DNA demethylation process, revealing decreased DNA methylation levels and elevated TNC expression as a result. Silencing TNC expression also suppressed the tumor malignant phenotype in both in vitro and in vivo experiments. Additionally, simultaneous silencing of TNC reduced or even reversed the glioma promotion caused by TDG overexpression. Based on our findings, we conclude that TDG exerts an indispensable role in TNC active DNA demethylation in gliomas. The DNA demethylation process leads to alternations in TNC methylation levels and promotes its expression, thereby contributing to the development of gliomas. These results suggest a novel epigenetic therapeutic strategy targeting active DNA demethylation in gliomas.

Prenatal Arsenic Exposure on DNA Methylation of C18ORF8 and ADAMTS9 Genes of Newborns from the POSGRAD Birth Cohort Study.

Exposure to arsenic (As) is a public health problem associated with cancer (skin and colon) and it has been reported that epigenetic changes may be a potential mechanism of As carcinogenesis. It is pertinent to evaluate this process in genes that have been associated with cancer, such as ADAMTS9 and C18ORF8. Gestation and delivery data were obtained from the POSGRAD study. Exposure to As was measured in urine during pregnancy. Gene methylation was performed by sodium bisulfite sequencing; 26 CpG sites for the C18ORF8 gene and 21 for ADAMTS9 were analyzed. These sites are located on the CpG islands near the start of transcription. Sociodemographic characteristics were obtained by a questionnaire. The statistical analysis was performed using multiple linear regression models adjusted for potential confounders. Newborns with an As exposure above 49.4 μg g-1 showed a decrease of 0.21% on the methylation rate in the sites CpG15, CpG19, and CpG21 of the C18ORF8 gene (adjusted ß = -0.21, p-value = 0.02). No statistically significant association was found between prenatal exposure to As and methylation of the ADAMTS9 gene. Prenatal exposure to As was associated with decreased DNA methylation at the CpG15, CpG19, and CpG21 sites of the C18ORF8 gene. These sites can provide information to elucidate epigenetic mechanisms associated with prenatal exposure to As and cancer.

Azacitidine as epigenetic priming for chemotherapy is safe and well-tolerated in infants with newly diagnosed KMT2A-rearranged acute lymphoblastic leukemia: Children's Oncology Group trial AALL15P1.

Infants less than 1 year old diagnosed with KMT2A-rearranged (KMT2A-r) acute lymphoblastic leukemia (ALL) are at high risk of remission failure, relapse, and death due to leukemia, despite intensive therapies. Infant KMT2A-r ALL blasts are characterized by DNA hypermethylation. Epigenetic priming with DNA methyltransferase inhibitors increases the cytotoxicity of chemotherapy in preclinical studies. The Children's Oncology Group trial AALL15P1 tested the safety and tolerability of five days of azacitidine immediately prior to the start of chemotherapy on day six, in four post-induction chemotherapy courses for infants with newly diagnosed KMT2A-r ALL. The treatment was welltolerated, with only two of 31 evaluable patients (6.5%) experiencing dose-limiting toxicity. Whole genome bisulfite sequencing of peripheral blood mononuclear cells (PBMCs) demonstrated decreased DNA methylation in 87% of samples tested following five days of azacitidine. Event-free survival was similar to prior studies of newly diagnosed infant ALL. Azacitidine is safe and results in decreased DNA methylation of PBMCs in infants with KMT2A-r ALL, but the incorporation of azacitidine to enhance cytotoxicity did not impact survival. Clinicaltrials.gov identifier: NCT02828358.

Altered DNA methylation and Dnmt expression in obese uterus may cause implantation failure.

Obesity is defined by increased adipose tissue volume and has become a major risk factor for reproduction. Recent studies have revealed a substantial link between obesity and epigenetics. The epigenome is dynamically regulated mainly by DNA methylation. DNA methylation, which is controlled by DNA methyltransferases (Dnmts), has been widely studied because it is essential for imprinting and regulation of gene expression. In our previous study, we showed that the levels of Dnmt1, Dnmt3a and global DNA methylation was dramatically altered in the testis and ovary of high-fat diet (HFD)-induced obese mice. However, the effect of HFD on Dnmts and global DNA methylation in mouse uterus has not yet been demonstrated. Therefore, in the present study, we aimed to evaluate the effect of HFD on the level of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l and global DNA methylation in uterus. Our results showed that HFD significantly altered the levels of Dnmts and global DNA methylation in the uterus. The total expression of Dnmt1, Dnmt3a and Dnmt3b was significantly upregulated, while level of Dnmt3l and global DNA methylation were dramatically decreased (p < 0.05). Furthermore, we observed that the expression of Dnmt3b and Dnmt3l was significantly increased in endometrium including gland and epithelium (p < 0.05). Although Dnmt3b was the only protein whose expression significantly increased, the level of global DNA methylation and Dnmt3l significantly decreased in stroma and myometrium (p < 0.05). In conclusion, our results show for the first time that obesity dramatically alters global DNA methylation and expression of Dnmts, and decreased DNA methylation and Dnmt expression may cause abnormal gene expression, especially in the endometrium.

Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures

The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we determined the cryo-EM structures of DDM1-nucleosomeH2A and DDM1-nucleosomeH2A.W complexes at near-atomic resolution in the presence of the ATP analog ADP-BeFx. The structures show that nucleosomal DNA is unwrapped more on the surface of the histone octamer containing histone H2A than that containing histone H2A.W. DDM1 embraces one DNA gyre of the nucleosome and interacts with the N-terminal tails of histone H4. Although we did not observe DDM1-H2A.W interactions in our structures, the results of the pull-down experiments suggest a direct interaction between DDM1 and the core region of histone H2A.W. Our work provides mechanistic insights into the heterochromatin remodeling process driven by DDM1 in plants.

TNFα Induces DNA and Histone Hypomethylation and Pulmonary Artery Smooth Muscle Cell Proliferation Partly via Excessive Superoxide Formation.

Objective: The level of tumor necrosis factor-α (TNF-α) is upregulated during the development of pulmonary vascular remodeling and pulmonary hypertension. A hallmark of pulmonary arterial (PA) remodeling is the excessive proliferation of PA smooth muscle cells (PASMCs). The purpose of this study is to investigate whether TNF-α induces PASMC proliferation and explore the potential mechanisms. Methods: PASMCs were isolated from 8-week-old male Sprague-Dawley rats and treated with 0, 20, or 200 ng/mL TNF-α for 24 or 48 h. After treatment, cell number, superoxide production, histone acetylation, DNA methylation, and histone methylation were assessed. Results: TNF-α treatment increased NADPH oxidase activity, superoxide production, and cell numbers compared to untreated controls. TNF-α-induced PASMC proliferation was rescued by a superoxide dismutase mimetic tempol. TNF-α treatment did not affect histone acetylation at either dose but did significantly decrease DNA methylation. DNA methyltransferase 1 activity was unchanged by TNF-α treatment. Further investigation using QRT-RT-PCR revealed that GADD45-α, a potential mediator of DNA demethylation, was increased after TNF-α treatment. RNAi inhibition of GADD45-α alone increased DNA methylation. TNF-α impaired the epigenetic mechanism leading to DNA hypomethylation, which can be abolished by a superoxide scavenger tempol. TNF-α treatment also decreased H3-K4 methylation. TNF-α-induced PASMC proliferation may involve the H3-K4 demethylase enzyme, lysine-specific demethylase 1 (LSD1). Conclusions: TNF-α-induced PASMC proliferation may be partly associated with excessive superoxide formation and histone and DNA methylation.

Decitabine-based nanoparticles for enhanced immunotherapy of hepatocellular carcinoma via DNA hypermethylation reversal

DNA methyltransferase (DNMT) inhibitor represents the first clinical breakthrough via targeting aberrant cancer epigenomes. Demethylation drugs such as decitabine can restore tumor suppressor gene (TSG) expression and function to achieve anti-tumor effect. Despite DNMT inhibitors have shown significant efficacy for treating leukemia, their application in solid tumor such as HCC is limited due to short in vivo half-lives. In this study, the DNMT1 inhibitor decitabine was first loaded into the Polylactic-co-glycolic acid (PLGA) spherical nanoparticles (Dec@PLGA). The vesicle of PD-L1 antibody and macrophage membrane (aMM) was further coated onto the surface of Dec@PLGA to finally synthesize Dec@PLGA@aMM. Dec@PLGA@aMM was in uniformed spherical structure with hydrodynamic particle size of 95.7 ± 9.1 nm and surface zeta potential of −15.1 ± 3.3 mV. Dec@PLGA@aMM significantly increased the expression of both p14 and p16 in a concentration-dependent manner. Dec@PLGA@aMM could enhance the tumor suppression through restoration of TSGs, which were epigenetically silenced by DNA hypermethylation. The Dec@PLGA@aMM group showed significantly (P < 0.05) less tumor volume than PBS group, PLGA@MM group, aPD-L1 group, PLGA@aMM group, decitabine group, Dec + aPD-L1 group, and Dec@PLGA@MM group. The decitabine could enhance aPD-L1-mediated immunotherapy of HCC via epigenetic alteration. This novel targeted PLGA NPs are aimed to treat HCC by decreasing DNA methylation and blocking PD-L1, thus providing new ideas for effective treatments via epigenetic alteration for HCC patients clinically.

The Role of FKBPs in Complex Disorders: Neuropsychiatric Diseases, Cancer, and Type 2 Diabetes Mellitus.

Stress is a common denominator of complex disorders and the FK-506 binding protein (FKBP)51 plays a central role in stress. Hence, it is not surprising that multiple studies imply the involvement of the FKBP51 protein and/or its coding gene, FKBP5, in complex disorders. This review summarizes such reports concentrating on three disorder clusters-neuropsychiatric, cancer, and type 2 diabetes mellitus (T2DM). We also attempt to point to potential mechanisms suggested to mediate the effect of FKBP5/FKBP51 on these disorders. Neuropsychiatric diseases considered in this paper include (i) Huntington's disease for which increased autophagic cellular clearance mechanisms related to decreased FKBP51 protein levels or activity is discussed, Alzheimer's disease for which increased FKBP51 activity has been shown to induce Tau phosphorylation and aggregation, and Parkinson's disease in the context of which FKBP12 is mentioned; and (ii) mental disorders, for which significant association with the single nucleotide polymorphism (SNP) rs1360780 of FKBP5 intron 7 along with decreased DNA methylation were revealed. Since cancer is a large group of diseases that can start in almost any organ or tissue of the body, FKBP51's role depends on the tissue type and differences among pathways expressed in those tumors. The FKBP51-heat-shock protein-(Hsp)90-p23 super-chaperone complex might function as an oncogene or as a tumor suppressor by downregulating the serine/threonine protein kinase (AKt) pathway. In T2DM, two potential pathways for the involvement of FKBP51 are highlighted as affecting the pathogenesis of the disease-the peroxisome proliferator-activated receptor-γ (PPARγ) and AKt.

DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner

The dynamic balance of DNA methylation and demethylation is required for erythropoiesis. Our previous transcriptomic analyses revealed that DNA methyltransferase 1 (DNMT1) is abundantly expressed in erythroid cells at all developmental stages. However, the role and molecular mechanisms of DNMT1 in human erythropoiesis remain unknown. Here we found that DNMT1 deficiency led to cell cycle arrest of erythroid progenitors which was partially rescued by treatment with a p21 inhibitor UC2288. Mechanically, this is due to decreased DNA methylation of p21 promoter, leading to upregulation of p21 expression. In contrast, DNMT1 deficiency led to increased apoptosis during terminal stage by inducing endoplasmic reticulum (ER) stress in a p21 independent manner. ER stress was attributed to the upregulation of RPL15 expression due to the decreased DNA methylation at RPL15 promoter. The upregulated RPL15 expression subsequently caused a significant upregulation of core ribosomal proteins (RPs) and thus ultimately activated all branches of unfolded protein response (UPR) leading to the excessive ER stress, suggesting a role of DNMT1 in maintaining protein homeostasis during terminal erythroid differentiation. Furthermore, the increased apoptosis was significantly rescued by the treatment of ER stress inhibitor TUDCA. Our findings demonstrate the stage-specific role of DNMT1 in regulating human erythropoiesis and provide new insights into regulation of human erythropoiesis.

A new high-throughput screening methodology for the discovery of cancer-testis antigen using multi-omics data

BackgroundCancer/testis antigens (CTAs), also known as tumor-specific antigens (TSAs) are specifically expressed in cancer cells and exhibit high immunogenicity, making them promising targets for immunotherapy and cancer vaccines. MethodsA new integrated high-throughput screening methodology for CTAs was proposed in this study through combining DNA methylation and RNA sequencing data. Briefly, the genes with increased transcript level and decreased DNA methylation were identified by multi-omics analysis. RNA sequencing studies in cell lines exposed to DNA methyltransferase (DNMT) inhibitors were performed to validate the inherent causal relationship between DNA hypomethylation and gene expression upregulation. ResultsWe proposed a new integrated high-throughput screening methodology for identification of CTAs using multi-omics analysis. In addition, we tested the feasibility of this method using gastric cancer (GC) as an example. In GC, we identified over 2000 primary candidate CTAs and ultimately identified 20 CTAs with significant tissue-specificity, including a testis-specific serine protease TESSP1/PRSS41. Integrated analysis confirmed that PRSS41 expression was reactivated in gastrointestinal cancers by promoter DNA hypomethylation at the CpG site (cg08104780). Additionally, DNA hypomethylation of PRSS41 predicted a poor prognosis in GC. ConclusionWe propose a new high-throughput screening method for the identification of CTAs in cancer and validate its effectiveness. Our work emphasizes that serine protease PRSS41 is a novel TSA that is reactivated in GC due to promoter DNA hypomethylation.

DNA methylation regulates the secondary metabolism of saponins to improve the adaptability of Eleutherococcus senticosus during drought stress

Plant growth and development can be significantly impacted by drought stress. Plants will adjust the synthesis and accumulation of secondary metabolites to improve survival in times of water constraint. Simultaneously, drought stress can lead to modifications in the DNA methylation status of plants, and these modifications can directly impact gene expression and product synthesis by changing the DNA methylation status of functional genes involved in secondary metabolite synthesis. However, further research is needed to fully understand the extent to which DNA methylation modifies the content of secondary metabolites to mediate plants’ responses to drought stress, as well as the underlying mechanisms involved. Our study found that in Eleutherococcus senticosus (E. senticosus), moderate water deprivation significantly decreased DNA methylation levels throughout the genome and at the promoters of EsFPS, EsSS, and EsSE. Transcription factors like EsMYB-r1, previously inhibited by DNA methylation, can re-bind to the EsFPS promotor region following DNA demethylation. This process promotes gene expression and, ultimately, saponin synthesis and accumulation. The increased saponin levels in E. senticosus acted as antioxidants, enhancing the plant’s adaptability to drought stress.

Abstract 3: Multiomics analyses reveal functional DNA, methylation pattern changes in clinical transgenic T-cell receptor cell therapy products

Abstract Background: Transgenic T-cell receptor T-cells (TCR-T) directed against tumor-specific antigens are associated with robust initial clinical responses. However, these responses are often not durable, and patients relapse frequently. Therefore, there is a significant need to understand how these cells change at the epigenomic level over time following infusion into the patient. Methods: We analyzed MART-1 TCR-T products from 8 patients treated under a clinical trial at UCLA (NCT00910650). Samples from the baseline infusion product and samples from day +30 recovered from peripheral circulation were sorted for TCR+ cells via flow cytometry, and were then subjected to whole genome bisulfite sequencing (WGBS), ATACseq, and RNAseq in parallel. Differential chromatin accessibility and gene expression by the ATACseq and RNAseq datasets, respectively, were analyzed via DESeq2, with P adjusted less than 0.1. WGBS datasets were analyzed via Metilene, and differentially methylated regions (DMRs) were defined as those regions with CpG loci containing a methylation difference &amp;gt;= 10% and a P adjusted &amp;lt; 0.05. Functional DMRs were defined as those repressed over time (increased DNA methylation with decreased chromatin accessibility/gene expression relative to infusion product), or activated over time (decreased DNA methylation with increased chromatin accessibility/gene expression relative to infusion product). Functional DMRs were then analyzed via EnrichR to evaluate gene ontology and pathways significantly enriched in gene lists. Results: We collectively identified three genes with repressed DMR activity and 49 genes with activated DMR activity compared to baseline infusion products. Our findings revealed that genes associated with repressed DMRs included IL2RA, FBLN7, and ZNRF1. These genes were collectively associated with a decrease in T-cell activation, cytokine signaling, and migration activity, potentially impacting the functional capabilities of T-cells in the post-infusion environment. Conversely, genes associated with activated DMRs included PDCD1 (PD1), FGR, KIR3DL1, KIR2DL4, and KLF3, with pathway enrichment analysis indicating a significant shift in the T-cell landscape towards reduced anti-tumor activity, decreased T-cell proliferation, T-cell aging, and the promotion of immune escape tumor phenotypes. Conclusions: This comprehensive multi-omics approach showcases an atlas of genes in clinical TCR-T cell therapeutics which are subject to functional changes in DNA methylation over time in vivo. These findings shed light on the complex interplay between DNA methylation, chromatin accessibility, and gene expression in the context of TCR-T cell therapy, with implications for the development of more effective immunotherapeutic strategies. Citation Format: Giulia Protti, Cole Peters, Moe Kawakami, Conner Kidd, Varsha Subramanyam, Analynn Lechien, Andrew Dinh, Antoni Ribas, Matteo Pellegrini, Theodore S. Nowicki. Multiomics analyses reveal functional DNA, methylation pattern changes in clinical transgenic T-cell receptor cell therapy products [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3.

Abstract 3485: Global DNA methylation level is associated with the sensitivity of cytotoxic and senotherapeutic drugs in gastrointestinal tumors

Abstract Background: Gastrointestinal cancer has become a severe burden around the world. Marker-guided treatment and clinical trials with sensitive anti-tumor drugs are critical for improving cancer survival. The decreasing DNA methylation levels of repetitive elements, such as LINE-1 and ALU, have been identified as the common biomarkers in cancer and aging. However, it remains unclear whether the methylation levels of repetitive elements can imply the drug sensitivity in gastrointestinal cancer. We investigated the association of LINE-1 and ALU methylations with the sensitivity of cytotoxic and senotherapeutic drugs in gastric cancer (GC) and colorectal cancer (CRC). Methods: The profiles of DNA methylation and gene expression were obtained from GC and CRC patients from the TCGA cohorts. Then, we calculated the averaging methylation level of two repetitive elements (LINE-1 and ALU) to quantify the global methylation levels by using the probes targeting the repetitive elements in 450K methylation array. The sensitivity of anti-tumor drugs, including the cytotoxic (oxaliplatin and fluorouracil) and five senotherapeutic agents (Dasatinib, Nutlin-3a, Navitoclax, Rapamycin, ABT737), were inferred with Oncopredict R package based on the gene expression profile. The Pearson analysis was conducted to test the correlation between DNA methylation and drug sensitivity. Results: The ALU methylation was associated with the sensitivities of cytotoxic (oxaliplatin: r = 0.171, P = 0.001; fluorouracil: r = 0.158, P = 0.002) and senotherapeutic agents (Dasatinib: r = 0.162, P = 0.002, Nutlin-3a: r = 0.109, P = 0.037, Navitoclax: r = 0.007, P = 0.931, Rapamycin: r = 0.144, P = 0.006, ABT737: r = 0.054, P = 0.523) in GC, while the association of LINE-1 methylation with drug sensitivities was observed in less drugs with weak correlation, including the cytotoxic (oxaliplatin: r = 0.132, P = 0.013; fluorouracil: r = 0.122, P = 0.019) and senotherapeutic agents (Dasatinib: r = 0.129, P = 0.014, Nutlin-3a: r = 0.109, P = 0.037, Rapamycin: r = 0.110, P = 0.034). In CRC, there was no correlation between DNA methylation levels of repetitive elements and drug sensitivity except Dasatinib (ALU: r = -0.107, P = 0.043). Conclusion: DNA methylation of repetitive elements could serve as a biomarker for cytotoxic and senotherapeutic drugs in GC. In addition, our findings suggested the promising value of ALU and LINE-1 methylation-guided chemotherapy with senotherapeutics in GC. Keywords: global DNA methylation, repetitive elements, gastrointestinal cancer, drug sensitivity, senotherapeutics Citation Format: Kaixin Lin, Xiaolin Wang, Yanxin Luo, Huichuan Yu. Global DNA methylation level is associated with the sensitivity of cytotoxic and senotherapeutic drugs in gastrointestinal tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3485.

Abstract P382: Epigenetic Regulation of the NF-kB Pathway by the Neural-Hematopoietic-Inflammatory Axis as a Potential Link Between Psychosocial Stress and Cardiovascular Risk: Data From the Washington DC Cardiovascular Health and Needs Assessment

Introduction: Chronic psychosocial stress (cPSS) is associated with cardiovascular disease (CVD) risk, caused in part by dysregulation of the neural-hematopoietic-inflammatory axis and epigenetic changes. cPSS may also affect NF-kB dependent pathways, suggesting a potential link to accelerated CVD risk and health inequities for populations most impacted by adverse social determinants. Hypothesis: We propose cPSS associates with greater amygdala activity (AmygA), a stress marker, and splenic activity (SpleenA), a hematopoietic activation measure. This relates to higher pro-inflammatory cytokine levels, partially due to less DNA methylation of NF-kB pathway-related genes. Methods: 60 African American adults (93.3% female, mean age 61) with CVD risk, living in the Washington, D.C. area underwent 18 FDG PET/CT to evaluate AmygA and SpleenA. DNA methylation analysis assessed epigenetic associations of the NF- κ B1/2 gene in PBMCs and ELISA- measured serum IL-1β and TNFα. Multivariable regression analysis adjusted for atherosclerotic CVD 10-year risk score and BMI was used to examine associations. Results: Greater AmygA and SpleenA were significantly associated with one another (β=0.26; p=0.003) and both were associated with greater pro-inflammatory cytokines IL1-β (AmygA:β =0.36, SpleenA:β=0.72, p&lt;0.05) and TNF-α (AmygA:β=0.31, SpleenA:β=0.58, p&lt;0.05). Further, we identified 2 significant methylation sites out of 81 on the NF- κ B1/2 gene. Notably, AmygA and SpleenA were inversely associated with the NF-κB1 cg01983105 and cg07955720 methylation sites (Table). Conclusions: We highlight a possible link between AmygA and SpleenA with decreased DNA methylation of the NF- κB gene. Our findings demonstrate a potential relationship between chronic stress-related neural activity and CVD risk through immune function and epigenetic alterations. These results should be examined in larger, diverse population-based cohorts with longitudinal data to identify intervention targets for reducing health inequities.

Cellular senescence gene TACC3 associated with colorectal cancer risk via genetic and DNA methylated alteration.

Cell senescence genes play a vital role in the pathogenesis of colorectal cancer, a process that may involve the triggering of genetic variations and reversible phenotypes caused by epigenetic modifications. However, the specific regulatory mechanisms remain unclear. Using CellAge and The Cancer Genome Atlas databases and in-house RNA-seq data, DNA methylation-modified cellular senescence genes (DMCSGs) were validated by Support Vector Machine and correlation analyses. In 1150 cases and 1342 controls, we identified colorectal cancer risk variants in DMCSGs. The regulatory effects of gene, variant, and DNA methylation were explored through dual-luciferase and 5-azacytidine treatment experiments, complemented by multiple database analyses. Biological functions of key gene were evaluated via cell proliferation assays, SA-β-gal staining, senescence marker detection, and immune infiltration analyses. The genetic variant rs4558926 in the downstream of TACC3 was significantly associated with colorectal cancer risk (OR=1.35, P=3.22×10-4). TACC3 mRNA expression increased due to rs4558926 C>G and decreased DNA methylation levels. The CpG sites in the TACC3 promoter region were regulated by rs4558926. TACC3 knockdown decreased proliferation and senescence in colorectal cancer cells. In addition, subjects with high-TACC3 expression presented an immunosuppressive microenvironment. These findings provide insights into the involvement of genetic variants of cellular senescence genes in the development and progression of colorectal cancer.

Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.

Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.