-
Systems Biology in Reproductive Medicine Dec 2024The assessment of epigenetic profiles in sperm is sensitive to somatic cell contamination, which can influence methylation signals at gene promoters. This contamination...
The assessment of epigenetic profiles in sperm is sensitive to somatic cell contamination, which can influence methylation signals at gene promoters. This contamination is particularly problematic in the assessment of DNA methylation in samples with low sperm counts, where fractional amounts of somatic cell DNA can lead to significant shifts in measured methylation state. In this study, a new method of detecting possible somatic cell contamination is proposed through two multi-region bioinformatic models: a traditional differential methylation analysis and a machine learning logistic regression model. These models were trained on publicly available sperm ( = 489) and blood ( = 1029) DNA methylation array data and tested on a contamination set, wherein the sperm of four donors with normal sperm counts were run on a 450k methylation array with four permutations each, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm ( = 16). The DMR and logistic regression model classified the contamination testing set with 100% and 94% accuracy, respectively. These new methods of detecting the effects of somatic cell contamination allow for more accurate differentiation between epigenetic profiles that contain a biological somatic-like shift and those that have somatic-like signatures because of contamination.
Topics: Male; Humans; Spermatozoa; DNA Methylation; Computational Biology; Machine Learning; Epigenesis, Genetic; Logistic Models; Sperm Count
PubMed: 38908909
DOI: 10.1080/19396368.2024.2368716 -
BMJ Open Jun 2024Generation Scotland (GS) is a large family-based cohort study established as a longitudinal resource for research into the genetic, lifestyle and environmental...
PURPOSE
Generation Scotland (GS) is a large family-based cohort study established as a longitudinal resource for research into the genetic, lifestyle and environmental determinants of physical and mental health. It comprises extensive genetic, sociodemographic and clinical data from volunteers in Scotland.
PARTICIPANTS
A total of 24 084 adult participants, including 5501 families, were recruited between 2006 and 2011. Within the cohort, 59% (approximately 14 209) are women, with an average age at recruitment of 49 years. Participants completed a health questionnaire and attended an in-person clinic visit, where detailed baseline data were collected on lifestyle information, cognitive function, personality traits and mental and physical health. Genotype array data are available for 20 026 (83%) participants, and blood-based DNA methylation (DNAm) data for 18 869 (78%) participants. Linkage to routine National Health Service datasets has been possible for 93% (n=22 402) of the cohort, creating a longitudinal resource that includes primary care, hospital attendance, prescription and mortality records. Multimodal brain imaging is available in 1069 individuals.
FINDINGS TO DATE
GS has been widely used by researchers across the world to study the genetic and environmental basis of common complex diseases. Over 350 peer-reviewed papers have been published using GS data, contributing to research areas such as ageing, cancer, cardiovascular disease and mental health. Recontact studies have built on the GS cohort to collect additional prospective data to study chronic pain, major depressive disorder and COVID-19.
FUTURE PLANS
To create a larger, richer, longitudinal resource, 'Next Generation Scotland' launched in May 2022 to expand the existing cohort by a target of 20 000 additional volunteers, now including anyone aged 12+ years. New participants complete online consent and questionnaires and provide postal saliva samples, from which genotype and salivary DNAm array data will be generated. The latest cohort information and how to access data can be found on the GS website (www.generationscotland.org).
Topics: Humans; Scotland; Female; Male; Longitudinal Studies; Middle Aged; Adult; Family Health; Life Style; Aged; Young Adult; COVID-19; DNA Methylation; Mental Health; Health Status; Adolescent; SARS-CoV-2
PubMed: 38908846
DOI: 10.1136/bmjopen-2024-084719 -
Bioorganic & Medicinal Chemistry Letters Sep 2024The role of G-quadruplex (G4) in cellular processes can be investigated by the covalent modification of G4-DNA using alkylating reagents. Controllable alkylating...
The role of G-quadruplex (G4) in cellular processes can be investigated by the covalent modification of G4-DNA using alkylating reagents. Controllable alkylating reagents activated by external stimuli can react elegantly and selectively. Herein, we report a chemical activation system that can significantly boost the reaction rate of methylamine-protected vinyl-quinazolinone (VQ) derivative for the alkylation of G4-DNA. The two screened activators can transform low-reactive VQ-NHR' to highly reactive intermediates following the Michael addition mechanism. This approach expands the toolbox of activable G4 alkylating reagents.
Topics: Alkylation; G-Quadruplexes; Methylamines; Quinazolinones; Humans; Molecular Structure; DNA; Vinyl Compounds
PubMed: 38908766
DOI: 10.1016/j.bmcl.2024.129855 -
Neurosurgical Review Jun 2024To evaluate the utility of magnetic resonance imaging (MRI) histogram parameters in predicting O(6)-methylguanine-DNA methyltransferase promoter (pMGMT) methylation...
To evaluate the utility of magnetic resonance imaging (MRI) histogram parameters in predicting O(6)-methylguanine-DNA methyltransferase promoter (pMGMT) methylation status in IDH-wildtype glioblastoma (GBM). From November 2021 to July 2023, forty-six IDH-wildtype GBM patients with known pMGMT methylation status (25 unmethylated and 21 methylated) were enrolled in this retrospective study. Conventional MRI signs (including location, across the midline, margin, necrosis/cystic changes, hemorrhage, and enhancement pattern) were assessed and recorded. Histogram parameters were extracted and calculated by Firevoxel software based on contrast-enhanced T1-weighted images (CET1). Differences and diagnostic performance of conventional MRI signs and histogram parameters between the pMGMT-unmethylated and pMGMT-methylated groups were analyzed and compared. No differences were observed in the conventional MRI signs between pMGMT-unmethylated and pMGMT-methylated groups (all p > 0.05). Compared with the pMGMT-methylated group, pMGMT-unmethylated showed a higher minimum, mean, Perc.01, Perc.05, Perc.10, Perc.25, Perc.50, and coefficient of variation (CV) (all p < 0.05). Among all significant CET1 histogram parameters, minimum achieved the best distinguishing performance, with an area under the curve of 0.836. CET1 histogram parameters could provide additional value in predicting pMGMT methylation status in patients with IDH-wildtype GBM, with minimum being the most promising parameter.
Topics: Humans; Glioblastoma; Magnetic Resonance Imaging; Male; Female; Brain Neoplasms; Middle Aged; Promoter Regions, Genetic; Adult; DNA Methylation; Aged; Isocitrate Dehydrogenase; Retrospective Studies; O(6)-Methylguanine-DNA Methyltransferase
PubMed: 38907038
DOI: 10.1007/s10143-024-02522-w -
Nature Communications Jun 2024Determining the balance between DNA double strand break repair (DSBR) pathways is essential for understanding treatment response in cancer. We report a method for...
Determining the balance between DNA double strand break repair (DSBR) pathways is essential for understanding treatment response in cancer. We report a method for simultaneously measuring non-homologous end joining (NHEJ), homologous recombination (HR), and microhomology-mediated end joining (MMEJ). Using this method, we show that patient-derived glioblastoma (GBM) samples with acquired temozolomide (TMZ) resistance display elevated HR and MMEJ activity, suggesting that these pathways contribute to treatment resistance. We screen clinically relevant small molecules for DSBR inhibition with the aim of identifying improved GBM combination therapy regimens. We identify the ATM kinase inhibitor, AZD1390, as a potent dual HR/MMEJ inhibitor that suppresses radiation-induced phosphorylation of DSBR proteins, blocks DSB end resection, and enhances the cytotoxic effects of TMZ in treatment-naïve and treatment-resistant GBMs with TP53 mutation. We further show that a combination of G2/M checkpoint deficiency and reliance upon ATM-dependent DSBR renders TP53 mutant GBMs hypersensitive to TMZ/AZD1390 and radiation/AZD1390 combinations. This report identifies ATM-dependent HR and MMEJ as targetable resistance mechanisms in TP53-mutant GBM and establishes an approach for simultaneously measuring multiple DSBR pathways in treatment selection and oncology research.
Topics: Humans; Ataxia Telangiectasia Mutated Proteins; Glioblastoma; Tumor Suppressor Protein p53; DNA Breaks, Double-Stranded; Temozolomide; Cell Line, Tumor; Mutation; Drug Resistance, Neoplasm; DNA Repair; Brain Neoplasms; Animals; DNA End-Joining Repair; Mice; Phosphorylation
PubMed: 38906885
DOI: 10.1038/s41467-024-49316-8 -
Life Science Alliance Sep 2024Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage....
Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage. Although they are already applied against myeloid cancers, important aspects of their mode of action remain unknown, highly limiting their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA damage. Under low DNMT activity, only decitabine has a substantial impact. Conversely, when DNMT activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA hypomethylation or RNA-associated processes. By investigating proteome dynamics on chromatin, we show that decitabine induces a strictly DNMT-dependent multifaceted DNA damage response based on chromatin recruitment, but not expression-level changes of repair-associated proteins. The choice of DNA repair pathway hereby depends on the severity of decitabine-induced DNA lesions. Although under moderate DNMT activity, mismatch (MMR), base excision (BER), and Fanconi anaemia-dependent DNA repair combined with homologous recombination are activated in response to decitabine, high DNMT activity and therefore immense replication stress induce activation of MMR and BER followed by non-homologous end joining.
Topics: Decitabine; DNA Damage; Humans; DNA Repair; DNA Methylation; Azacitidine; Antimetabolites, Antineoplastic; Cell Line, Tumor; DNA (Cytosine-5-)-Methyltransferases; Chromatin; DNA Modification Methylases
PubMed: 38906675
DOI: 10.26508/lsa.202302437 -
Chinese Journal of Natural Medicines Jun 2024Diffuse large B-cell lymphoma (DLBCL) is characterized by significant treatment resistance. Palmitic acid (PA) has shown promising antitumor properties. This study aims...
Diffuse large B-cell lymphoma (DLBCL) is characterized by significant treatment resistance. Palmitic acid (PA) has shown promising antitumor properties. This study aims to elucidate the molecular mechanisms by which PA influences DLBCL progression. We quantified the expression levels of microRNAs (miRNAs), Forkhead box protein O1 (FOXO1), and DNA methyltransferase 3A (DNMT3A) in both untreated and PA-treated DLBCL tumors and cell lines. Assessments were made of cell viability, apoptosis, and autophagy-related protein expression following PA administration. Interaction analyses among miR-429, DNMT3A, and FOXO1 were conducted using luciferase reporter assays and methylation-specific (MSP) Polymerase chain reaction (PCR). After transfecting the miR-429 inhibitor, negative control (NC) inhibitor, shRNA against DNMT3A (sh-DNMT3A), shRNA negative control (sh-NC), overexpression vector for DNMT3A (oe-DNMT3A), or overexpression negative control (oe-NC), we evaluated the effects of miR-429 and DNMT3A on cell viability, mortality, and autophagy-related protein expression in PA-treated DLBCL cell lines. The efficacy of PA was also tested in vivo using DLBCL tumor-bearing mouse models. MiR-429 and FOXO1 expression levels were downregulated, whereas DNMT3A was upregulated in DLBCL compared to the control group. PA treatment was associated with enhanced autophagy, mediated by the upregulation of miR-429 and downregulation of DNMT3A. The luciferase reporter assay and MSP confirmed that miR-429 directly inhibits DNMT3A, thereby reducing FOXO1 methylation. Subsequent experiments demonstrated that PA promotes autophagy and inhibits DLBCL progression by upregulating miR-429 and modulating the DNMT3A/FOXO1 axis. In vivo PA significantly reduced the growth of xenografted tumors through its regulatory impact on the miR-429/DNMT3A/FOXO1 axis. Palmitic acid may modulate autophagy and inhibit DLBCL progression by targeting the miR-429/DNMT3A/FOXO1 signaling pathway, suggesting a novel therapeutic target for DLBCL management.
Topics: MicroRNAs; Lymphoma, Large B-Cell, Diffuse; Humans; Forkhead Box Protein O1; Animals; DNA Methyltransferase 3A; Mice; Palmitic Acid; Cell Line, Tumor; DNA Methylation; DNA (Cytosine-5-)-Methyltransferases; Promoter Regions, Genetic; Mice, Nude; Male; Gene Expression Regulation, Neoplastic; Female; Apoptosis; Autophagy; Mice, Inbred BALB C
PubMed: 38906602
DOI: 10.1016/S1875-5364(24)60655-2 -
Bioinformatics (Oxford, England) Jul 2024With single-cell DNA methylation studies yielding vast datasets, existing data formats struggle with the unique challenges of storage and efficient operations,...
MOTIVATION
With single-cell DNA methylation studies yielding vast datasets, existing data formats struggle with the unique challenges of storage and efficient operations, highlighting a need for improved solutions.
RESULTS
BAllC (Binary All Cytosines) emerges as a tailored format for methylation data, addressing these challenges. BAllCools, its complementary software toolkit, enhances parsing, indexing, and querying capabilities, promising superior operational speeds and reduced storage needs.
AVAILABILITY AND IMPLEMENTATION
https://github.com/jksr/ballcools.
Topics: DNA Methylation; Single-Cell Analysis; Software; Humans; Computational Biology
PubMed: 38905499
DOI: 10.1093/bioinformatics/btae404 -
Molecular Biology Reports Jun 2024SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes....
BACKGROUND
SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes. Despite the assumed functional link between DNA methylation and SETDB1-mediated H3K9 trimethylations, several studies have shown that SETDB1 operates autonomously of DNA methylation in a region- and cell-specific manner. This study analyzes SETDB1-null HAP1 cells through a linked methylome and transcriptome analysis, intending to explore genes controlled by SETDB1-involved DNA methylation.
METHODS AND RESULTS
We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1's function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells.
CONCLUSIONS
SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
Topics: Histone-Lysine N-Methyltransferase; Humans; Zinc Fingers; DNA Methylation; Promoter Regions, Genetic; Up-Regulation; DNA Demethylation; Cell Line; CpG Islands; Gene Deletion; Histones
PubMed: 38904842
DOI: 10.1007/s11033-024-09703-2 -
BMJ Open Jun 2024WHO recommends human papillomavirus (HPV) testing for cervical screening, with triage of high-risk HPV (hrHPV) positive women. However, there are limitations to... (Observational Study)
Observational Study
Performance of and methylation as triage markers for early detection of cervical cancer in self-collected and clinician-collected samples: an exploratory observational study in Papua New Guinea.
OBJECTIVE
WHO recommends human papillomavirus (HPV) testing for cervical screening, with triage of high-risk HPV (hrHPV) positive women. However, there are limitations to effective triage for low-resource, high-burden settings, such as Papua New Guinea. In this exploratory study, we assessed the performance of host methylation as triage tools for predicting high-grade squamous intraepithelial lesions (HSIL) in self-collected and clinician-collected samples.
DESIGN
Exploratory observational study.
SETTING
Provincial hospital, same-day cervical screen-and-treat trial, Papua New Guinea.
PARTICIPANTS
44 hrHPV+women, with paired self/clinician-collected samples (4 squamous cell carcinomas (SCC), 19 HSIL, 4 low-grade squamous intraepithelial lesions, 17 normal).
PRIMARY AND SECONDARY OUTCOME MEASURES
Methylation levels of and analysed by methylation-specific PCRs against the clinical endpoint of HSIL or SCC (HSIL+) measured using liquid-based-cytology/p16-Ki67 stain.
RESULTS
In clinician-collected samples, and methylation levels were significantly higher with increasing grade of disease (p=0.0046 and p<0.0015, respectively). was the best predictor of HSIL (area under the curve, AUC 0.819) while of SCC (AUC 0.856). In self-collected samples, best predicted HSIL (AUC 0.595) while SCC (AUC 0.812). Combined methylation yielded sensitivity and specificity for HSIL+ of 90.5% (95% CI 69.6% to 98.8%) and 70% (95% CI 45.7% to 88.1%), respectively, in clinician-collected samples, and 81.8% (95% CI 59.7% to 94.8%) and 47.6% (95% CI 25.7% to 70.2%), respectively, in self-collected samples. plus HPV16/HPV18 improved sensitivity for HSIL+ (95.2%, 95% CI 76.2% to 99.9%) but decreased specificity (55.0%, 95% CI 31.5% to 76.9%).
CONCLUSION
methylation is a potential triage strategy for the detection of HSIL/SCC in low-income and middle-income country.
Topics: Humans; Female; MicroRNAs; Uterine Cervical Neoplasms; Papua New Guinea; Early Detection of Cancer; Cell Adhesion Molecule-1; Adult; Triage; DNA Methylation; Middle Aged; Myelin and Lymphocyte-Associated Proteolipid Proteins; Papillomavirus Infections; Biomarkers, Tumor; Carcinoma, Squamous Cell; Specimen Handling; Young Adult; Sensitivity and Specificity; Vaginal Smears
PubMed: 38904134
DOI: 10.1136/bmjopen-2023-081282