Background/Objectives: Immunotherapy has become a cornerstone in the treatment of recurrent and metastatic head and neck squamous cell carcinoma (R/M HNSCC), but reliable noninvasive biomarkers of prognosis remain limited. We investigated the associations between markers of biological aging and survival outcomes among patients with R/M HNSCC treated with immune checkpoint inhibitors (ICIs). Methods: Peripheral blood samples collected prior to ICI initiation from 100 patients with R/M HNSCC underwent DNA methylation profiling using the Illumina Infinium MethylationEPIC array. Four epigenetic age acceleration measures were estimated from DNA methylation levels and evaluated for associations with progression-free survival (PFS) and overall survival (OS). Results: Greater intrinsic and extrinsic epigenetic age acceleration were each associated with longer PFS (p = 0.025 and p = 0.048, respectively) and OS (p = 0.024 and p = 0.029, respectively). Significant interactions between GrimAge acceleration and chronological age were observed for both PFS (p = 0.010) and OS (p < 0.001). Greater GrimAge acceleration was associated with improved PFS among patients less than 65 years of age but shorter OS among patients 65 years of age or older. Conclusions: In this exploratory study, pretreatment epigenetic aging measures were associated with survival outcomes among patients with R/M HNSCC receiving ICIs. These findings suggest biological aging metrics may have clinical relevance and warrant further investigation as potential noninvasive prognostic biomarkers.
Mikania micrantha, a highly invasive weed, faces constraints on its northward range expansion in South China due to low winter temperatures. Although DNA methylation is increasingly recognized as a mediator of plant stress adaptation, it remains unknown whether epigenetic regulation couples cold-stress tolerance with the production of allelopathic secondary metabolites in invasive plants. Here, we comprehensively characterized genome-wide DNA methylation dynamics and their transcriptional consequences in germinating embryos under three temperature regimes (14 °C, 25 °C, and 30 °C) by integrating whole-genome bisulfite sequencing and RNA-Seq. Exposure to 14 °C significantly delayed germination without arresting the process. Global methylation levels were highest at CG sites (80.21–84.63%), followed by CHG (63.67–66.77%) and CHH (6.63–7.51%) contexts. Integrative analysis identified 1103 differentially methylated region-associated genes, of which 434 were also differentially expressed. Notably, KEGG enrichment of the 434 overlapping genes revealed significant overrepresentation of the sesquiterpenoid and triterpenoid biosynthesis pathways, with key mevalonate (MVA) pathway genes showing altered expression in association with DMRs at 14 °C. Because this is an integrative methylome–transcriptome association study without metabolite quantification or functional validation, these results are consistent with the hypothesis that cold-induced epigenetic reprogramming is associated with transcriptional changes in terpenoid biosynthesis, which may contribute to antioxidant and membrane-protective functions under chilling stress; the possible accumulation of allelopathic sesquiterpene lactones and any role in maintaining competitive advantage during cold seasons remain working hypotheses that require experimental validation. The results of this study offer new epigenetic perspectives and supporting data for the management and prevention of M. micrantha invasion.
Plants are important sources for obtaining diverse secondary metabolites which have pharmaceutical importance. Out of multiple factors that modulate their accumulation in vitro and in vivo, epigenetic factors play critical roles, adding an extra layer of regulation. This review focuses on (a) dynamic changes that occur in DNA methylation, histone acetylation, and the role of small RNAs in transcriptional and post-transcriptional modulation that alter secondary metabolism in plants under abiotic stress and (b) the role of epigenetics in secondary metabolite accumulation in the plant cell cultures. Such epigenetic factors are manipulated by applying inhibitors of DNA methylation like 5-azacytidine or histone deacetylation such as trichostatin A in intact plants as well as in cultured plant cells and hairy roots for enhanced production. This article synthesizes current findings on epigenetic engineering for improved synthesis of anticancer compounds and nutraceuticals and lists out limitations and challenges that the pharmaceutical industry is facing for their large scale production and commercialization. Main conclusion: Through epigenetic changes such as DNA methylation, histone acetylation, and non-coding RNAs, plants dynamically fine-tune specific gene expressions to adjust to environmental stresses and mediate secondary metabolite accumulation as a chemical combat mechanism.
Background/Objectives: The aim of this scoping review was to investigate the current role and possible clinical applications of long non-coding RNAs (lncRNAs) in breast cancer diagnosis and treatment. Methods: A thorough search of the PubMed/MEDLINE and Scopus/EMBASE databases was carried out in accordance with the PRISMA-ScR guidelines. The inclusion criteria were as follows: Studies with lncRNA analyses of specimens from breast cancer patients and clinically relevant studies. The exclusion criteria were as follows: in silico and in vitro studies involving animal models; reviews; case series; case reports; comments; editorials; and papers not written in English. The study protocol was registered in the Open Science Framework. Results: After the identification of 1139 records, 312 publications were retrieved and 228 articles were selected for data extraction. Data analysis and the synthesis of evidence showed that lncRNA studies were conducted in breast tumor specimens in 212 studies and in blood samples from breast cancer patients in 20 studies. The most commonly used method was quantitative RT-PCR (in 216 studies), while many studies were complemented by in vitro (n = 177) and animal experiments (n = 75). There were 39 studies that included at least 100 specimens from breast cancer patients. Conclusions: At present, lncRNA analysis is not used in routine clinical practice. Clinically relevant findings coupled by results from in vitro and animal experiments suggest that various lncRNAs after appropriate validation may be used as biomarkers for breast cancer diagnosis and treatment, most notably HSAT164, CCAT2, HOTAIR, and MALAT1. To this end, larger studies involving clinical specimens from clinically relevant subgroups of breast cancer patients will be needed.
Background/Objectives: Bacterial DNA methylation is a reversible genetic modification affecting gene regulation without significant DNA sequence alteration, thereby enabling rapid adaptation to various environments. However, traditional motif-based approaches detect DNA methylation at low resolution, limiting the identification of DNA methylation variation and often restricting analysis of multiple methylation forms. Methods: Here, we used Oxford Nanopore Technologies sequencing to examine genome-wide variation in three DNA methylation forms (N6-methyladenine, N4-methylcytosine, and 5-methylcytosine) and DNA fragment density between the exponential and stationary phases of Escherichia coli and Lactobacillus acidophilus. Results: During the exponential phase, regions surrounding the replication terminus displayed lower DNA fragment density in both species and lower 5-methylcytosine levels in Escherichia coli. Methylation calling on each genomic locus revealed almost 21% more differentially methylated sites than motif-based detection. Through the locus-based detection, the majority (72%) of differentially methylated genes in Escherichia coli were differentially expressed. The functions of these genes were associated with the physiological response to growth phase transition, such as cell membrane synthesis and translation. Incorporating multiple DNA methylation forms and including all methylated loci, not just those within common motifs, resulted in higher concordance between differentially expressed genes and differentially methylated genes compared to single-form or motif-based approaches. Conclusions: Our findings suggest that the bacterial DNA methylation pattern is affected by growth phase transition, and that a locus-based differential methylation analysis using Nanopore sequencing can estimate microbial activity in some cases, especially in microbiome studies where the transcriptome-genome link is difficult to establish. Impact Statement: Bacterial DNA methylation is a reversible genetic modification affecting gene regulation, enabling rapid adaptation. There are three major DNA methylation forms in bacteria, namely N6-methyladenine, N4-methylcytosine, and 5-methylcytosine. Using Oxford Nanopore sequencing, we found that DNA methylation levels (N6-methyladenine and 5-methylcytosine) are globally and regionally lower during the exponential phase compared to the stationary phase. Our results showed that differentially methylated genes can robustly estimate the overall transcriptomic profile in Escherichia coli. The inclusion of multiple DNA methylation forms and all methylated loci can improve concordance with differentially expressed genes. Our findings reveal that the bacterial DNA methylation pattern shifts during growth phase transition, and indicate that methylation could be an accessible method for estimating microbial activity.
