Evaluation of the HumanMethylationEPIC v2.0 Bead Chip using low quality and quantity DNA samples DOI

Brando Poggiali,

Mikkel Eriksen Dupont, Marie‐Louise Kampmann

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 28, 2025

Abstract Background: The HumanMethylationEPIC v2.0 BeadChip (EPIC v2.0) microarray is a widely used tool for genome-wide DNA methylation (DNAm) analysis, designed high-quality human with recommended input of 250 ng. However, in clinical and forensic settings, samples may be low quality and/or quantity (highly fragmented available amounts). This study assessed the performance EPIC on various combinations average fragment size (350, 230, 165, 95 bp) amount (100, 50, 20, 10 ng), compared to control sample analyzed under optimal conditions (high-quality ng input). Results: The best was obtained 350 bp 100 (~90% probe detection rate, r = 0.995, median absolute beta value differences |Δβ| 0.012 when sample). Samples lower sizes performed worse, lowest rate (~43%), r 0.946, highest (0.038). those 165 at failed pass (QC). CpG sites intermediate DNAm values (β = 0.1-0.9) showed higher than extreme (β= 0-0.1, β 0.9-1). Finally, we an application by performing epigenetic age observed mean errors (MAEs) below years across four clocks. Conclusions: Both amounts affect analysis v2.0, investigated having greater impact amount. measurements were achieved down 20 input. Highly (95 did not result usable as all QC. Overall, our demonstrates potential limitations samples.

Language: Английский

Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA DOI Creative Commons
Qing Dai, Chang Ye, Iryna Irkliyenko

et al.

Nature Biotechnology, Journal Year: 2024, Volume and Issue: 42(10), P. 1559 - 1570

Published: Jan. 2, 2024

Bisulfite sequencing (BS-seq) to detect 5-methylcytosine (5mC) is limited by lengthy reaction times, severe DNA damage, overestimation of 5mC level and incomplete C-to-U conversion certain sequences. We present ultrafast BS-seq (UBS-seq), which uses highly concentrated bisulfite reagents high temperatures accelerate the ~13-fold, resulting in reduced damage lower background noise. UBS-seq allows library construction from small amounts purified genomic DNA, such as cell-free or directly 1 100 mouse embryonic stem cells, with less higher genome coverage than conventional BS-seq. Additionally, quantitatively maps RNA (m

Language: Английский

Citations

51
RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis DOI Creative Commons
Zhongyu Zou, Xiaoyang Dou, Ying Li

et al.

Nature, Journal Year: 2024, Volume and Issue: 634(8035), P. 986 - 994

Published: Oct. 2, 2024

Mutation of tet methylcytosine dioxygenase 2 (encoded by TET2) drives myeloid malignancy initiation and progression

Language: Английский

Citations

19
Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing DOI Creative Commons
You Wu,

Wenna Shao,

Mengxiao Yan

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 14, 2024

Abstract Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for modification identification. However, concurrently detecting multiple types of modifications in single DRS sample remains challenge. Here, we develop TandemMod, transferable deep learning framework capable data. To train high-performance TandemMod models, generate vitro epitranscriptome datasets from cDNA libraries, containing thousands transcripts labeled with various modifications. We validate the performance on both and vivo human cell lines, confirming its high accuracy profiling m 6 A 5 C sites. Furthermore, perform transfer identifying other such 7 G, Ψ, inosine, significantly reducing training data size running time without compromising performance. Finally, apply to identify 3 rice grown different environments, demonstrating applicability across species conditions. In summary, provide resource ground-truth labels that can serve benchmark nanopore-based identification methods, diverse using sample.

Language: Английский

Citations

18
Profiling the epigenome using long-read sequencing DOI
Tianyuan Liu, Ana Conesa

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

Citations

7
Review Article: Assessing the virological response to direct-acting antiviral therapies in the HBV cure programme. DOI
James Lok, James Michael Harris, Ivana Carey

et al.

Virology, Journal Year: 2025, Volume and Issue: 605, P. 110458 - 110458

Published: Feb. 21, 2025

Language: Английский

Citations

2
Detection, molecular function and mechanisms of m5C in cancer DOI Creative Commons
Linhui Zhang, Yuelong Li, Liqing Li

et al.

Clinical and Translational Medicine, Journal Year: 2025, Volume and Issue: 15(3)

Published: Feb. 26, 2025

Language: Английский

Citations

2
Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach DOI

Liang Lu,

Xiaoting Zhang,

Yuenan Zhou

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(15), P. 2984 - 3000.e8

Published: July 12, 2024

Language: Английский

Citations

11
RNA modifications in cancer DOI Creative Commons

Han Wu,

Shi Chen, Xiang Li

et al.

MedComm, Journal Year: 2025, Volume and Issue: 6(1)

Published: Jan. 1, 2025

Abstract RNA modifications are emerging as critical cancer regulators that influence tumorigenesis and progression. Key modifications, such N6‐methyladenosine (m 6 A) 5‐methylcytosine 5 C), implicated in various cellular processes. These regulated by proteins write, erase, read modulate stability, splicing, translation, degradation. Recent studies have highlighted their roles metabolic reprogramming, signaling pathways, cell cycle control, which essential for tumor proliferation survival. Despite these scientific advances, the precise mechanisms affect remain inadequately understood. This review comprehensively examines role play proliferation, metastasis, programmed death, including apoptosis, autophagy, ferroptosis. It explores effects on epithelial–mesenchymal transition (EMT) immune microenvironment, particularly metastasis. Furthermore, modifications’ potential therapies, conventional treatments, immunotherapy, targeted is discussed. By addressing aspects, this aims to bridge current research gaps underscore therapeutic of targeting improve treatment strategies patient outcomes.

Language: Английский

Citations

1
Integration of CRISPR/dCas9-Based methylation editing with guide positioning sequencing identifies dynamic changes of mrDEGs in breast cancer progression DOI Creative Commons
Baolong Zhang, Jin Li, Wenqiang Yu

et al.

Cellular and Molecular Life Sciences, Journal Year: 2025, Volume and Issue: 82(1)

Published: Jan. 21, 2025

Dynamic changes in DNA methylation are prevalent during the progression of breast cancer. However, critical alterations aberrant and gene expression patterns have not been thoroughly characterized. Here, we utilized guide positioning sequencing (GPS) to conduct whole-genome analysis a unique human cancer model: MCF10 series cell lines (representing benign/normal, atypical hyperplasia, metastatic carcinoma). By integrating with mRNA-seq matched clinical data from The Cancer Genome Atlas (TCGA) Gene Expression Omnibus (GEO), six representative methylation-related differentially expressed genes (mrDEGs) were identified, including CAVIN2, ARL4D, DUSP1, TENT5B, P3H2, MMP28. To validate our findings, independently developed optimized dCas9-DNMT3L-DNMT3A system, achieving high efficiency 98% increase at specific sites. levels significantly increased for genes, CAVIN2 67.75 ± 1.05%, ARL4D 53.29 6.32%, DUSP1 57.63 8.46%, TENT5B 44.00 5.09%, P3H2 58.50 3.90%, MMP28 49.60 5.84%. RT-qPCR confirmed an inverse correlation between expression. Most importantly, mimicked tumor vitro, demonstrating that transcriptional silencing promotes proliferation MCF10A cells owing crosstalk hypermethylation histone deacetylation. This study unveils practical implications dynamics mrDEGs reshaping epigenomic features malignant through integrated methylome transcriptome. application CRISPR/dCas9-based editing technique elucidates regulatory mechanisms functional roles individual within signature, providing valuable insights understanding pathogenesis facilitating potential therapeutic approaches epigenome patients

Language: Английский

Citations

1
5-Methylcytosine RNA modification and its roles in cancer and cancer chemotherapy resistance DOI Creative Commons
Li Fang, Tingting Liu, Yi Dong

et al.

Journal of Translational Medicine, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 3, 2025

Recent advancements in cancer therapies have improved clinical outcomes, yet therapeutic resistance remains a significant challenge because of its complex mechanisms. Among epigenetic factors, m5C RNA modification is emerging as key player drug resistance, similar to the well-known m6A modification. affects metabolism processes, including splicing, export, translation, and stability, thereby influencing efficacy. This review highlights critical roles modulating chemotherapy, targeted therapy, radiotherapy, immunotherapy. also discusses functions regulators, methyltransferases, demethylases, m5C-binding proteins, essential modulators landscape that contribute dynamic regulatory network. Targeting these components offers promising strategy overcome resistance. We highlight need for further research elucidate specific mechanisms by which contributes develop precise m5C-targeted therapies, presenting m5C-focused strategies potential novel anticancer treatments.

Language: Английский

Citations

1