Methylation Profiles Research Articles

COL25A1 and METAP1D DNA methylation are promising liquid biopsy epigenetic biomarkers of colorectal cancer using digital PCR

BackgroundColorectal cancer is a public health issue and was the third leading cause of cancer-related death worldwide in 2022. Early diagnosis can improve prognosis, making screening a central part of colorectal cancer management. Blood-based screening, diagnosis and follow-up of colorectal cancer patients are possible with the study of cell-free circulating tumor DNA. This study aimed to identify novel DNA methylation biomarkers of colorectal cancer that can be used for the follow-up of patients with colorectal cancer.MethodsA DNA methylation profile was established in the Gene Expression Omnibus (GEO) database (n = 507) using bioinformatics analysis and subsequently confirmed using The Cancer Genome Atlas (TCGA) database (n = 348). The in silico profile was then validated on local tissue and cell-free DNA samples using methylation-specific digital PCR in colorectal cancer patients (n = 35) and healthy donors (n = 35).ResultsThe DNA methylation of COL25A1 and METAP1D was predicted to be a colorectal cancer biomarker by bioinformatics analysis (ROC AUC = 1, 95% CI [0.999–1]). The two biomarkers were confirmed with tissue samples, and the combination of COL25A1 and METAP1D yielded 49% sensitivity and 100% specificity for cell-free DNA.ConclusionBioinformatics analysis of public databases revealed COL25A1 and METAP1D DNA methylation as clinically applicable liquid biopsies DNA methylation biomarkers. The specificity implies an excellent positive predictive value for follow-up, and the high sensitivity and relative noninvasiveness of a blood-based test make these biomarkers compatible with colorectal cancer screening. However, the clinical impact of these biomarkers in colorectal cancer screening and follow-up needs to be established in further prospective studies.

MYB/MYBL1-altered gliomas frequently harbor truncations and non-productive fusions in the MYB and MYBL1 genes

Astrocytomas that harbor recurrent genomic alterations in MYB or MYBL1 are a group of Pediatric-type diffuse low-grade gliomas that were newly recognized in the 2021 WHO Classification of Tumors of the Central Nervous System. These tumors are described in the WHO classification as harboring fusions in MYB or MYBL1. In this report, we examine 14 consecutive cases in which a MYB or MYBL1 alteration was identified, each with diagnostic confirmation by genome-wide DNA methylation profiling (6 Angiocentric gliomas and 8 Diffuse astrocytomas, MYB- or MYBL1-altered), for their specific genomic alterations in these genes. Using RNA sequencing, we find productive in-frame fusions of the MYB or MYBL1 genes in only 5/14 cases. The remaining 9 cases show genomic alterations that result in truncation of the gene, without evidence of an in-frame fusion partner. Gene expression analysis showed overexpression of the MYB(L1) genes, regardless of the presence of a productive fusion. In addition, QKI, a recognized fusion partner common in angiocentric glioma, was generally up-regulated in these 14 cases, compared to a cohort comprising >1000 CNS tumors of various types, regardless of whether a genomic alteration in QKI was present. Overall, the results show that truncations, in the absence of a productive fusion, of the MYB(L1) genes can likely drive the tumors and have implications for the analysis and diagnosis of Angiocentric glioma and Diffuse astrocytoma, MYB- or MYBL1-altered, especially for cases that are tested on panels designed to focus on fusion detection.

Associations Between Loneliness, Epigenetic Aging, and Multimorbidity Through Older Adulthood.

Loneliness is a pressing public health concern, but the mechanisms by which it leads to declining physical health are uncertain. Prior work has begun to explore epigenetic pathways, with some evidence suggesting a link between loneliness and DNA methylation, though it is unclear whether epigenetic variation can help explain loneliness-health associations. Associations between loneliness and epigenetic age acceleration (EAA) were estimated, as well as the degree to which EAA mediated and moderated the association between loneliness and the development of chronic physical health conditions (multimorbidity) in older adulthood. The sample consisted of Health and Retirement Study participants who provided blood draws and consented to methylation profiling (n = 4,018). Baseline loneliness was associated with greater EAA in the GrimAge measure net of demographic and behavioral covariates (β = 0.07, p = .003). Loneliness and GrimAge each predicted increasing condition counts, but there was no evidence of an interactive effect. The association between loneliness and increasing condition counts was, however, significantly mediated by GrimAge (indirect path β = 0.020, p = .003). These results suggest that the impact of loneliness on multimorbidity may, in part, operate through DNA methylation. The specific intermediary, physiological mechanisms that are involved will require further research, but EAA measures like GrimAge are promising in helping to understand the health impacts of loneliness.

P16.10.A UNRAVELING THE CLINICAL IMPLICATIONS OF TRIM24::NTRK2 FUSION GENE IN PEDIATRIC HIGH-GRADE GLIOMA: A CASE STUDY

Abstract BACKGROUND High-grade gliomas are among the deadliest of all childhood cancers and the leading cause of cancer-related mortality in children. The standard treatment is resection followed by chemotherapy, most often temozolomide and radiation therapy. Unfortunately, there is no evidence that temozolomide influences survival in pediatric patients and only a limited number of new drugs have been identified for specific subgroups of tumors. The identification of fusion genes as possible drivers of the disease offers an opportunity for targeted therapies. We present a case of a six-year-old patient with a novel TRIM24::NTRK2 fusion positive epithelioid glioblastoma with subsequent relapses. METHODS We investigated the ramification of this fusion and evolution of the tumor through whole genome sequencing, RNA-sequencing and DNA methylation profiling, and studied the effect of the patient’s treatment using patient-derived cell cultures. RESULTS Our studies show that the TRIM24::NTRK2 fusion has oncogenic abilities but loses its importance as the tumor evolves. In addition, we demonstrate an increased drug resistance over time, further indicating the diminished driver function of the fusion. CONCLUSION The use of resequencing revealed parallel development of tumor subclones with different genomic alterations, highlighting the importance of genomic profiling from various parts of the tumor. FUNDING This work was supported by the Swedish Research Council, the Swedish Childhood Cancer Foundation, and the Swedish Cancer Society

Back pain exercise therapy remodels human epigenetic profiles in buccal and human peripheral blood mononuclear cells: an exploratory study in young male participants.

With its high and increasing lifetime prevalence, back pain represents a contemporary challenge for patients and healthcare providers. Monitored exercise therapy is a commonly prescribed treatment to relieve pain and functional limitations. However, the benefits of exercise are often gradual, subtle, and evaluated by subjective self-reported scores. Back pain pathogenesis is interlinked with epigenetically mediated processes that modify gene expression without altering the DNA sequence. Therefore, we hypothesize that therapy effects can be objectively evaluated by measurable epigenetic histone posttranslational modifications and proteome expression. Because epigenetic modifications are dynamic and responsive to environmental exposure, lifestyle choices-such as physical activity-can alter epigenetic profiles, subsequent gene expression, and health traits. Instead of invasive sampling (e.g., muscle biopsy), we collect easily accessible buccal swabs and plasma. The plasma proteome provides a systemic understanding of a person's current health state and is an ideal snapshot of downstream, epigenetically regulated, changes upon therapy. This study investigates how molecular profiles evolve in response to standardized sport therapy and non-controlled lifestyle choices. We report that the therapy improves agility, attenuates back pain, and triggers healthier habits. We find that a subset of participants' histone methylation and acetylation profiles cluster samples according to their therapy status, before or after therapy. Integrating epigenetic reprogramming of both buccal cells and peripheral blood mononuclear cells (PBMCs) reveals that these concomitant changes are concordant with higher levels of self-rated back pain improvement and agility gain. Additionally, epigenetic changes correlate with changes in immune response plasma factors, reflecting their comparable ability to rate therapy effects at the molecular level. We also performed an exploratory analysis to confirm the usability of molecular profiles in (1) mapping lifestyle choices and (2) evaluating the distance of a given participant to an optimal health state. This pre-post cohort study highlights the potential of integrated molecular profiles to score therapy efficiency. Our findings reflect the complex interplay of an individual's background and lifestyle upon therapeutic exposure. Future studies are needed to provide mechanistic insights into back pain pathogenesis and lifestyle-based epigenetic reprogramming upon sport therapy intervention to maintain therapeutic effects in the long run.

DNA methylation profiles of transgenerational rat hyperactivity primed by silver nanoparticles: Comparison with valproate model rats of autism

There is an increasing body of evidence suggesting that a single exposure to certain chemicals can have transgenerational effects, with the underlying mechanism believed to be epigenetic. However, it remains largely unknown whether psychiatric conditions like ADHD or autism, induced by environmental chemicals, can be inherited across generations. Pregnant rats were purchased from a commercial breeder. On the 7th day of gestation (E7), they were divided into two groups: one group was orally exposed to silver nanoparticles (AgNP; 4 mg/kg), while the control group received vehicle alone. The subsequent generation (F1) underwent spontaneous motor activity (SMA) measurements at 8–11 weeks of age. For breeding at 26 weeks of age, rats with higher SMA were selected from hyperactive litters, while untreated rats were randomly selected. This process was continued for four generations in both groups. The AgNP-primed rats at 4th generation displayed significantly higher SMA, 1.8 times greater than that of untreated rats. Intraperitoneal injection of valproic acid (150 mg/kg), an epigenetic modifier to 5-day-old rats causes adult hyperactivity (1.4-fold), suggesting that epigenetic modification contributes to rat hyperactivity. Global DNA methylation profiles in the mesencephalon were positively correlated in both groups of hyperactive rats. Furthermore, there were 7–8 common genes showing both hypermethylation and hypomethylation, which are involved in neuronal development, neuronal function, transcriptional activity, DNA binding activity, cell differentiation, ubiquitination processes, or histone modification, including Pax 6 and Mecp 2. Thus, it is most likely that rats retain hyperactivity through mesencephalic DNA methylation status across transgeneration.

Developing a DNA Methylation Signature to Differentiate High-Grade Serous Ovarian Carcinomas from Benign Ovarian Tumors.

Epithelial ovarian cancer (EOC) represents a significant health challenge, with high-grade serous ovarian cancer (HGSOC) being the most common subtype. Early detection is hindered by nonspecific symptoms, leading to late-stage diagnoses and poor survival rates. Biomarkers are crucial for early diagnosis and personalized treatment OBJECTIVE: Our goal was to develop a robust statistical procedure to identify a set of differentially methylated probes (DMPs) that would allow differentiation between HGSOC and benign ovarian tumors. Using the Infinium EPIC Methylation array, we analyzed the methylation profiles of 48 ovarian samples diagnosed with HGSOC, borderline ovarian tumors, or benign ovarian disease. Through a multi-step statistical procedure combining univariate and multivariate logistic regression models, we aimed to identify CpG sites of interest. We discovered 21 DMPs and developed a predictive model validated in two independent cohorts. Our model, using a distance-to-centroid approach, accurately distinguished between benign and malignant disease. This model can potentially be used in other types of sample material. Moreover, the strategy of the model development and validation can also be used in other disease contexts for diagnostic purposes.

Methylomic signature of current cannabis use in two first-episode psychosis cohorts.

The rising prevalence and legalisation of cannabis worldwide have underscored the need for a comprehensive understanding of its biological impact, particularly on mental health. Epigenetic mechanisms, specifically DNA methylation, have gained increasing recognition as vital factors in the interplay between risk factors and mental health. This study aimed to explore the effects of current cannabis use and high-potency cannabis on DNA methylation in two independent cohorts of individuals experiencing first-episode psychosis (FEP) compared to control subjects. The combined sample consisted of 682 participants (188 current cannabis users and 494 never users). DNA methylation profiles were generated on blood-derived DNA samples using the Illumina DNA methylation array platform. A meta-analysis across cohorts identified one CpG site (cg11669285) in the CAVIN1 gene that showed differential methylation with current cannabis use, surpassing the array-wide significance threshold, and independent of the tobacco-related epigenetic signature. Furthermore, a CpG site localised in the MCU gene (cg11669285) achieved array-wide significance in an analysis of the effect of high-potency (THC = > 10%) current cannabis use. Pathway and regional analyses identified cannabis-related epigenetic variation proximal to genes linked to immune and mitochondrial function, both of which are known to be influenced by cannabinoids. Interestingly, a model including an interaction term between cannabis use and FEP status identified two sites that were significantly associated with current cannabis use with a nominally significant interaction suggesting that FEP status might moderate how cannabis use affects DNA methylation. Overall, these findings contribute to our understanding of the epigenetic impact of current cannabis use and highlight potential molecular pathways affected by cannabis exposure.

Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation

BackgroundRecent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy.MethodsWe enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples.ResultsWe identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%.ConclusionsOur study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy.

Diagnosis of acute lymphoblastic leukaemia: an overview of the current genomic classification, diagnostic approaches, and future directions.

B-acute lymphoblastic leukaemia (B-ALL) is a haematological disease resulting from haematopoietic system dysfunction, leading to the unchecked growth of immature B lymphoblasts. The disease's complexity is underscored by the spectrum of genetic aberrations that underlie B-ALL entities, necessitating advanced genetic analyses for precise classification and risk determination. Prior to the adoption of next-generation sequencing into standard diagnostic practices, up to 30% of B-ALL cases were not assigned to specific entities due to the limitations of traditional diagnostic methods. The advent of comprehensive genomic analysis, especially whole-genome transcriptome sequencing, has significantly enhanced our understanding of B-ALL's molecular heterogeneity, paving the way for the exploration of novel, tailored treatment strategies. Furthermore, recent technological innovations, such as optical genome mapping, methylation profiling, and single-cell sequencing, have propelled forward the fields of cancer research and B-ALL management. These innovations introduce novel diagnostic approaches and prognostic markers, facilitating a deeper, more nuanced understanding of individual patient disease profiles. This review focuses on the latest diagnostic standards and assays for B-ALL, the importance of new technologies and biomarkers in enhancing diagnostic accuracy, and the expected role of innovative advancements in the future diagnosis and treatment of B-ALL.

DNA Methylation Profiling Confirms a Challenging Glioblastoma, Atypical Mesenchymal Type Which Mimics Intracranial Mesenchymal Tumor

Abstract Introduction/Objective Brain tumors exhibit distinct DNA methylation patterns that reflect their cellular origin, molecular subtype, and clinical behavior. DNA methylation signatures provide valuable insights into tumor heterogeneity, evolution, and treatment response, guiding personalized therapeutic strategies. Our case, glioblastoma, atypical mesenchymal type confirmed by DNA methylation profile and it reflects the clonal evolution of the glioblastoma metaplasia with minimal glial component which was histologically challenging. Methods/Case Report A 56-year-old gentleman presented with headaches. MRI brain demonstrated a heterogeneous enhancing mass with areas of central necrosis in the left temporal lobe, measuring approximately 49 x 34 mm, with surrounding T2 FLAIR hyperintensity extending into the left basal ganglia, causing compression of the left lateral ventricle and uncal herniation. He underwent left-sided craniotomy for tumor resection. Microscopic examination revealed hypercellular spindle cell neoplasm, forming fascicles. Brisk mitotic activity and geographic necrosis were evident. GFAP highlighted narrow margins of the tumor which could represent the entrapped glial tissue. CD99 stained the tumor cells, Other immunohistochemical stains for spindle cell work up, like S100, EMA, PR STAT6 and desmin were all negative. A diagnosis of intracranial mesenchymal tumor /sarcoma was considered. Methylation profiling results showed class calibrated scores of 0.9741, compatible with Glioblastoma, IDH-wildtype, atypical mesenchymal type with a cytogenetic profile including gain of chromosome 7 (including EGFR) and loss of chromosome 10 (including PTEN), and loss of CDKN2A/B. Results (if a Case Study enter NA) NA Conclusion Although histopathological examination and immunohistochemical study are fundamental in diagnosing brain tumors, the rapid development of cytogenetic and molecular diagnostic modalities has significantly contributed to diagnostic accuracy and the potential for targeted treatment. Particularly, DNA methylation profiling has proven valuable in diagnosing morphologically challenging cases with prognostic value. Eventually, DNA methylation profiling will be adopted as a major cancer diagnostic criterion and will become a standard procedure performed at major academic centers.

THE MOLECULAR HISTORY OF IDH-MUTANT ASTROCYTOMAS WITHOUT ADJUVANT TREATMENT

Abstract AIMS Hypermutation and malignant transformation are potential complications arising from temozolomide treatment of IDH-mutant gliomas. However, the natural history of IDH-mutant low-grade gliomas without temozolomide treatment is relatively un-studied. We set out to study the molecular history of paired IDH-mutant astrocytomas without adjuvant treatment in the interim. METHOD We retrieved retrospectively from our hospitals paired tumors from 19 patients with IDH-mutant, 1p19q noncodeleted Grade 2 astrocytomas where no interim adjuvant treatment with either temozolomide or radiotherapy was given between primary and first recurrences. Two patients had multiple resected recurrences and radiotherapy but not temozolomide was given before the last specimens were resected. We studied the natural molecular history of these low-grade IDH-mutant astrocytomas without pressure of temozolomide with methylation profiling and copy number variation (CNV) analyses, target DNA sequencing, TERTp sequencing, FISH for ALT and selected biomarkers. RESULTS Recurrences were mostly higher grades (15/19 patients) and characterized by new CNVs not present in the primary tumors (17/19 cases). Few novel mutations were identified in recurrences. Tumors from 17/19 (89.5%) patients showed either CDKN2A homozygous deletion, MYC or PDGFRA amplification at recurrences. There was no case of hypermutation. Phylogenetic trees constructed for tumors for the two patients with multiple recurrences showed a conserved evolution pattern. CONCLUSION In summary, our studies demonstrated in contrast to the phenomenon of temozolomide-induced hypermutation, IDH-mutant, 1p19q non-codeleted Grade 2 astrocytomas which were not treated by temozolomide instead acquired new CNVs at tumor recurrences. These findings improve our understanding of the molecular life history of IDH-mutant astrocytomas.

Genome-wide methylation profiling reveals extracellular vesicle DNA as an ex vivo surrogate of cancer cell-derived DNA

Extracellular vesicle-derived DNA (evDNA) encapsulates the complete genome and mutational status of cells; however, whether cancer cell-derived evDNA mirrors the epigenetic features of parental genomic DNA remains uncertain. This study aimed to assess and compare the DNA methylation patterns of evDNA from cancer cell lines and primary cancer tissues with those of the nuclear genomic DNA. We isolated evDNA secreted by two cancer cell lines (HCT116 and MDA-MB-231) from various subcellular compartments, including the nucleus and cytoplasm. Additionally, we obtained evDNA and nuclear DNA (nDNA) from the primary cancer tissues of colon cancer patients. We conducted a comprehensive genome-wide DNA methylation analysis using the Infinium Methylation EPIC BeadChip, examining > 850,000 CpG sites. Remarkable similarities were observed between evDNA and nDNA methylation patterns in cancer cell lines and patients. This concordance extended to clinical cancer tissue samples, showcasing the potential utility of evDNA methylation patterns in deducing cellular origin within heterogeneous populations through methylation-based deconvolution. The observed concordance underscores the potential of evDNA as a noninvasive surrogate marker for discerning tissue origin, particularly in cancer tissues, offering a promising future for cancer diagnostics. This finding enhances our understanding of cellular origins and would help develop innovative diagnostic and therapeutic strategies for cancer.

IMPACT OF DNA METHYLATION PROfiLING IN REfiNING MENINGIOMA RECURRENCE RISK STRATIfiCATION AND CLINICAL FOLLOW UP

Abstract AIMS To assess clinical impact of the additive information gained from Integrated Meningioma Risk Score on the risk of meningioma recurrence. METHOD DNA methylation (Illumina EPIC Array) analysis was performed on all recurrent meningioma tumours, primary tumours CNS5 WHO grade 2, 3 and grade 1 with unusual morphological features from Dec 2021 to Jan 2024. DNA methylation analysis was performed, and data files were processed on the DKFZ Heidelberg Classifier v12.5/6 (molecularneuropathology.org). The output from the classifier including methylation class combined with WHO Grade and chromosomal loss (1p, 6q,14q) was used to produce an integrated meningioma risk score for recurrence. RESULTS 70 meningioma cases were profiled. This included 68 cranial meningiomas, ((WHO grade 1, n=19; recurrences=7), (grade 2, n=47; recurrences =9), (grade 3 n=2; recurrences=1)) and 2 spinal meningiomas (grade 1 n=1, grade2 n=1). 3 tumours were excluded due to poor calibration scores. Of the 67 cases the diagnosis was revised in 1 case following DNA methylation analysis due to presence of CDKN2A/B loss. Molecular-morphologic integrated risk score was calculated for all 67 cases. In 10% of overall patients the predicted risk of meningioma recurrence was increased to either intermediate or high, whilst 32% had the risk lowered mainly from intermediate to low. Interestingly, 1 patient who underwent a gross total resection of a WHO Grade 2 meningioma, experienced recurrence with the integrated meningioma risk score indicating low risk of recurrence, which is contrary to the clinical aggressiveness of the tumour. CONCLUSION Meningioma integrated risk stratification by DNA methylation profiling has shown concordance of integrated risk score with WHO Grade in 58% of cases. In 42% of cases the predicted risk was altered when compared to the WHO Grade alone. These results need to be further validated with long term data on patient outcomes.

Decoding Cancer through Silencing the Mitochondrial Gatekeeper VDAC1.

Mitochondria serve as central hubs for regulating numerous cellular processes that include metabolism, apoptosis, cell cycle progression, proliferation, differentiation, epigenetics, immune signaling, and aging. The voltage-dependent anion channel 1 (VDAC1) functions as a crucial mitochondrial gatekeeper, controlling the flow of ions, such as Ca2+, nucleotides, and metabolites across the outer mitochondrial membrane, and is also integral to mitochondria-mediated apoptosis. VDAC1 functions in regulating ATP production, Ca2+ homeostasis, and apoptosis, which are essential for maintaining mitochondrial function and overall cellular health. Most cancer cells undergo metabolic reprogramming, often referred to as the "Warburg effect", supplying tumors with energy and precursors for the biosynthesis of nucleic acids, phospholipids, fatty acids, cholesterol, and porphyrins. Given its multifunctional nature and overexpression in many cancers, VDAC1 presents an attractive target for therapeutic intervention. Our research has demonstrated that silencing VDAC1 expression using specific siRNA in various tumor types leads to a metabolic rewiring of the malignant cancer phenotype. This results in a reversal of oncogenic properties that include reduced tumor growth, invasiveness, stemness, epithelial-mesenchymal transition. Additionally, VDAC1 depletion alters the tumor microenvironment by reducing angiogenesis and modifying the expression of extracellular matrix- and structure-related genes, such as collagens and glycoproteins. Furthermore, VDAC1 depletion affects several epigenetic-related enzymes and substrates, including the acetylation-related enzymes SIRT1, SIRT6, and HDAC2, which in turn modify the acetylation and methylation profiles of histone 3 and histone 4. These epigenetic changes can explain the altered expression levels of approximately 4000 genes that are associated with reversing cancer cells oncogenic properties. Given VDAC1's critical role in regulating metabolic and energy processes, targeting it offers a promising strategy for anti-cancer therapy. We also highlight the role of VDAC1 expression in various disease pathologies, including cardiovascular, neurodegenerative, and viral and bacterial infections, as explored through siRNA targeting VDAC1. Thus, this review underscores the potential of targeting VDAC1 as a strategy for addressing high-energy-demand cancers. By thoroughly understanding VDAC1's diverse roles in metabolism, energy regulation, mitochondrial functions, and other cellular processes, silencing VDAC1 emerges as a novel and strategic approach to combat cancer.

Accelerated Epigenetic Aging is Associated with Faster Glaucoma Progression: A DNA Methylation Study.

To investigate the association between epigenetic age acceleration and glaucoma progression. Retrospective cohort study. 100 primary open-angle glaucoma (POAG) patients with fast progression and 100 POAG patients with slow progression. Subjects were classified as fast or slow progressors based on rates of change in standard automated perimetry (SAP) mean deviation (MD) and retinal nerve fiber layer (RNFL) thickness. Epigenetic age was calculated using the Horvath, Hannum, PhenoAge, and GrimAge clocks from DNA methylation profiles obtained from blood samples. Age acceleration (AgeAccel) was defined as the residual from a linear regression of epigenetic age on chronologic age, with positive values suggesting faster biological aging. Multivariable logistic regression models estimated the association between AgeAccel and likelihood of fast progression, adjusting for confounders. Difference in epigenetic age acceleration between fast and slow glaucoma progressors. The mean rate of SAP MD change in the fastest progressing eye was -1.06 dB/year (95% CI: -1.28 to -0.85) for fast progressors compared to -0.10 dB/year (95% CI: -0.16 to -0.04) for slow progressors (P<0.001). For RNFL thickness, corresponding values were -1.60 μm/year (95% CI: -1.97 to -1.23) and -0.76 μm/year (95% CI: -1.04 to -0.48), respectively (P<0.001). Fast progressors demonstrated significantly greater age acceleration compared to slow progressors for the Horvath clock (mean difference = 2.93 years, 95% CI: 1.48 to 4.39, P<0.001) and Hannum clock (mean difference = 1.24 years, 95% CI: 0.03 to 2.46, P=0.045). In multivariable models, each year of Horvath AgeAccel was associated with 15% higher odds of fast progression (OR 1.15, 95% CI 1.07-1.23, P<0.001), after adjusting for sex, race, intraocular pressure, central corneal thickness, baseline disease severity, smoking status and follow-up time. Hannum and GrimAge clocks also showed significant associations with fast progression. The association between AgeAccel and fast progression was stronger in subjects with relatively low IOP during follow-up. Accelerated epigenetic aging was associated with faster glaucoma progression. These findings suggest that faster biological age, as reflected in DNA methylation, may increase optic nerve susceptibility to damage, highlighting epigenetic age as a potential prognostic biomarker.

Cannabinoids shift the basal ganglia miRNA m6A methylation profile towards an anti-inflammatory phenotype in SIV-infected Rhesus macaques.

Epitranscriptomic modifications modulate diverse biological processes, such as regulation of gene expression, abundance, location and function. In particular, N6-methyladenosine (m6A) methylation has been shown to regulate various disease processes, including cancer and inflammation. While there is evidence that m6A modification is functionally relevant in neural development and differentiation, the role of m6A modification in HIV neuropathogenesis is unknown. Here, we identified direct m6A modifications in miRNAs from BG tissues of Rhesus Monkeys (RMs) that were either vehicle-treated uninfected (VEH), SIV-infected combination anti-retroviral therapy (cART) treated (VEH/SIV/cART), or THC:CBD treated VEH/SIV/cART (THC:CBD/SIV/cART) RMs. We detected m6A modifications across all BG tissues. SIV infection promoted an overall hypomethylated m6A profile. While the overall hypomethylated m6A profile was not significantly impacted by THC:CBD treatment, specific miRNAs, particularly those predicted to target proinflammatory genes showed markedly reduced m6A methylation levels compared to the VEH treated RMs. Additionally, we found that specific BG tissue miRNAs bearing m6A epi-transcriptomic marks were also transferred to BG-derived extracellular vesicles (EVs). Mechanistically, we identified the DRACH motif of the seed region of miR-194-5p to be significantly m6A hypomethylated, which was predicted to directly target STAT1, an important interferon-activated transcription factor known to drive neuroinflammation, in diseases ranging from Alzheimer to Parkinson and Huntington disease. Notably, THC:CBD treatments significantly reduced m6A methylation of 43 miRNA species directly involved in regulating CNS network genes, thus providing a possible mechanist explanation on the beneficial effects of THC:CBD treatments noted in several disease involving neuroinflammation. Our findings also underscore the need for investigating the qualitative, posttranscriptional modification changes in the RNA profiles along with the more traditional, qualitative alterations in pathological conditions or after various treatment regimens.

Exploring nanopore direct sequencing performance of forensic STRs, SNPs, InDels, and DNA methylation markers in a single assay

IntroductionThe field of forensic DNA analysis has undergone rapid advancements in recent decades. The integration of massively parallel sequencing (MPS) has notably expanded the forensic toolkit, moving beyond identity matching to predicting phenotypic traits and biogeographical ancestry. This shift is of particular significance in cases where conventional DNA profiling fails to identify a single suspect. Supplementing forensic analyses with estimated biological age may be valuable but involves a complex and time-consuming DNA methylation analysis. This study explores and validates the performance of a comprehensive forensic third-generation sequencing assay utilizing Oxford Nanopore Technologies (ONT) in an adaptive and direct sequencing approach. We incorporated the most widely used forensic markers, i.e., STRs, SNPs, InDels, mitochondrial DNA (mtDNA), and two methylation-based clock classifiers, thereby combining forensic genetic and epigenetic analysis in one single workflow. Methods and resultsIn our investigation, DNA from six anonymous individuals was sequenced using the ONT standard adaptive direct sequencing approach, reaching a mean percentage of on-target reads ranging from 6.6 % to 7.7 % per sample. ONT data was compared to standard MPS data and Illumina EPIC DNA methylation profiles. Basecalling employed recommended ONT software packages. TREAT was used for ONT-based analysis of autosomal and Y-chromosome STRs, achieving 90–92 % correct calls depending on allelic read depth thresholds. InDel analyses for two lower-quality samples proved challenging due to inadequate read depth, while the remaining four samples significantly contributed to the observed percentage markers (60.9 %) and correct calls (97.8 %). SNP analysis achieved a 98 % call rate, with only two mismatches and two missed alleles. ONT-generated DNA methylation data demonstrated Pearson’s correlation coefficients with EPIC data ranging from 0.67 to 0.97 for Horvath’s clock. Additional age-associated markers exhibited Pearson’s correlation coefficients with chronological age between 0.14 (ELOVL2) and 0.96 (FHL2) at read depths of <30 and <20, respectively. Despite excluding mtDNA from our targeted sequencing approach, adaptive proof-reading fragments covered the complete mtDNA with an average read depth of 21–72, showing 100 % concordance with reference data. DiscussionOur exploratory study using ONT adaptive sequencing for conventional forensic and age associated DNA methylation markers showed high sequencing accuracy for a significant number of markers, showcasing ONT as a promising (epi)genetic forensic method. Future studies must address three critical aspects: determining clear quantity and quality measures and detection thresholds for accuracy, optimizing input DNA quantity for forensic casework expectations, and addressing ethical considerations associated with phenotype and ancestry analysis to prevent ethnic biases.

Spinal diffuse midline glioma: An unusual case presentation

Primary spinal cord neoplasms are rare, accounting for 1% of paediatric central nervous system tumours. The majority of which are low-grade gliomas (LGG). A teenage male presented with rapidly progressive lower limb paralysis. He subsequently underwent a near-total resection of an intramedullary thoracic tumour. Although the initial histopathology report suggested a LGG, closer review of the morphology and immunohistochemical staining revealed a diffusely infiltrating high-grade astrocytoma. Methylation profiling later confirmed a H3K27M-mutated spinal DMG. He underwent spinal radiation to the tumour bed soon after surgery but succumbed to his disease 8 days after completing radiation, and 3 months after presentation.Conclusion: Spinal DMGs are rare, can lead to diagnostic challenges and have a poor prognosis.

Uterine mesenchymal tumours harboring the KAT6B/A::KANSL1 gene fusion represent a distinct type of uterine sarcoma based on DNA methylation profiles.

Uterine mesenchymal tumours harboring KAT6B/A::KANSL1 gene fusions typically exhibit histological and immunophenotypic overlap with endometrial stromal and smooth muscle tumours. To date it remains uncertain whether such neoplasms should be regarded as variants of smooth muscle or endometrial stromal neoplasm, or if they constitute a distinct tumour type. In this study we investigated DNA methylation patterns and copy number variations (CNVs) in a series of uterine tumours harboring KAT6B/A::KANSL1 gene fusions in comparison to other mesenchymal neoplasms of the gynecological tract. Unsupervised hierarchical clustering and t-SNE analysis of DNA methylation data (Illumina EPIC array) identified a distinct cluster for 8/13 KAT6B/A::KANSL1 tumours (herein referred to as core cluster). The other 5 tumours (herein referred to as outliers) did not assign to the core cluster but clustered near various other tumour types. CNV analysis did not identify significant alterations in the core cluster. In contrast, various alterations, including deletions at the CDKN2A/B and NF1 loci were identified in the outlier group. Analysis of the DNA methylation clusters in relation to histological features revealed that while tumours in the core KAT6B/A::KANSL1 cluster were histologically bland, outlier tumours frequently exhibited "high-grade" histologic features in the form of significant nuclear atypia, increased mitotic activity and necrosis. Three of the five patients with outlier tumours died from their disease while clinical follow-up in the remaining two patients was limited (less than 12months). In comparison, none of the 7 out of 8 patients with tumors in the core KAT6B/A::KANSL1 sarcoma cluster, where follow-up was available, died from disease. Furthermore, only 1 out of 7 patients recurred (mean follow-up of 30months). In conclusion, KAT6B/A::KANSL1 uterine sarcoma is a molecularly unique type of uterine tumour that should be recognized as a distinct entity. These tumors typically exhibit low-grade histologic features but are occasionally morphologically high-grade; the latter have a DNA methylation profile different from the typical low-grade neoplasms and may be associated with aggressive behaviour.