DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches DOI Creative Commons

Melissa Hum,

Ann S. G. Lee

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

Published: April 23, 2025

Breast cancer remains one of the most common cancers in women worldwide. Early detection is critical for improving patient outcomes, yet current screening methods have limitations. Therefore, there a pressing need more sensitive and specific approaches to detect breast its earliest stages. Liquid biopsy has emerged as promising non-invasive method early management. DNA methylation, an epigenetic alteration that often precedes genetic changes, been observed precancerous or stages, making it valuable biomarker. This review explores role methylation potential developing blood-based tests. We discuss advancements methods, recent discoveries biomarkers from both single-omics multi-omics integration studies, machine learning enhancing diagnostic accuracy. Challenges future directions are also addressed. Although challenges remain, advances continue enhance clinical methylation-based biomarkers. Ongoing research crucial further refine these improve outcomes.

Language: Английский

Microfluidic Biochips for Single‐Cell Isolation and Single‐Cell Analysis of Multiomics and Exosomes DOI Creative Commons
Chao Wang, Jiaoyan Qiu, Mengqi Liu

et al.

Advanced Science, Journal Year: 2024, Volume and Issue: 11(28)

Published: May 20, 2024

Abstract Single‐cell multiomic and exosome analyses are potent tools in various fields, such as cancer research, immunology, neuroscience, microbiology, drug development. They facilitate the in‐depth exploration of biological systems, providing insights into disease mechanisms aiding treatment. isolation, which is crucial for single‐cell analysis, ensures reliable cell isolation quality control further downstream analyses. Microfluidic chips small lightweight systems that efficient high‐throughput real‐time analysis on‐ or off‐chip. Therefore, most current technologies based on microfluidic technology. This review offers comprehensive guidance to researchers across different fields selection appropriate chip analysis. describes design principles, separation mechanisms, characteristics, cellular effects available isolation. Moreover, this highlights implications using technology subsequent analyses, including Finally, challenges future prospects outlined multiplex

Language: Английский

Citations

23
Beyond assembly: the increasing flexibility of single-molecule sequencing technology DOI Open Access
Paul W. Hook, Winston Timp

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(9), P. 627 - 641

Published: May 9, 2023

Language: Английский

Citations

38
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing DOI Creative Commons
Billy T. Lau, Alison Almeda,

Marie Schauer

et al.

Genome Medicine, Journal Year: 2023, Volume and Issue: 15(1)

Published: May 3, 2023

Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This generated up 200 million reads single sample from cancer patients, order magnitude improvement over existing nanopore methods. classifier determine whether individual originated tumor or immune cells. Leveraging methylomes matched tumors cells, we characterized patients longitudinal monitoring during treatment.

Language: Английский

Citations

37
Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review DOI Creative Commons
Gianna Di Sario,

Valeria Rossella,

Elvira Smeralda Famulari

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: April 3, 2023

In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative replicable over time. This revolutionary approach can be complementary may, in future, replace tissue biopsy, which is still considered gold standard diagnosis. "Classical" often cannot provide sufficient bioptic material advanced screening, isolated information about disease evolution heterogeneity. Recent literature highlighted how of proteomic, genomic, epigenetic, metabolic alterations. These biomarkers detected investigated using single-omic and, recently, combination through multi-omic approaches. review will an overview most suitable techniques to thoroughly characterize tumor their potential applications, highlighting importance integrated multi-omic, multi-analyte approach. Personalized medical investigations soon allow patients receive predictable prognostic evaluations, early diagnosis, subsequent

Language: Английский

Citations

28
Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling DOI Creative Commons
Li‐Ting Chen, Myrthe Jager,

Dàmi Rebergen

et al.

Genome Research, Journal Year: 2025, Volume and Issue: unknown, P. gr.279144.124 - gr.279144.124

Published: Jan. 13, 2025

Shallow genome-wide cell-free DNA (cfDNA) sequencing holds great promise for non-invasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single nucleotide variations (SNVs) are, however, much harder to identify with low depth due errors. Here we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA consensus calling based on long-read nanopore enable simultaneous multimodal tumor fraction estimation through SNVs, CNAs, fragmentomics. Efficacy of NanoRCS is tested 18 patient samples seven healthy controls, demonstrating its ability reliably detect fractions as 0.24%. In vitro experiments confirm that SNV measurements are essential detecting below 3%. provides the opportunity cost-effective rapid processing, aligns well clinical needs, particularly in settings where quick accurate personalized treatment strategies.

Language: Английский

Citations

1
Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection DOI
Daniel C. Bruhm, Nicholas A. Vulpescu, Zachariah H. Foda

et al.

Nature reviews. Cancer, Journal Year: 2025, Volume and Issue: unknown

Published: March 4, 2025

Language: Английский

Citations

1
“Aging Clocks” Based on Cell-Free DNA DOI
Alexander V. Sergeev, О. V. Kisil,

Andrey A Eremin

et al.

Biochemistry (Moscow), Journal Year: 2025, Volume and Issue: 90(S1), P. S342 - S355

Published: Feb. 1, 2025

Language: Английский

Citations

1
Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing DOI Creative Commons

Xi Hu,

Yuwei Shi,

Suk Hang Cheng

et al.

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: April 14, 2025

Abstract We had previously reported a convolutional neural network (CNN) based approach, called the holistic kinetic model (HK 1), for detecting 5-methylcytosine (5mC) by single molecule real-time sequencing (Pacific Biosciences). In this study, we constructed hybrid with CNN and transformer layers, named HK 2. improve area under receiver operating characteristic curve (AUC) 5mC detection from 0.91 1 to 0.99 further demonstrate that 2 can detect other types of base modifications, such as 5-hydroxymethylcytosine (5hmC) N6-methyladenine (6mA). Using analyze patterns cell-free DNA (cfDNA) molecules, enhanced patients hepatocellular carcinoma, an AUC 0.97. Moreover, 2-based 6mA enables jagged ends cfDNA delineation cellular chromatin structures. is thus versatile tool expanding applications in liquid biopsies.

Language: Английский

Citations

1
A Hitchhiker's Guide to long-read genomic analysis DOI
Medhat Mahmoud, Daniel Paiva Agustinho, Fritz J. Sedlazeck

et al.

Genome Research, Journal Year: 2025, Volume and Issue: 35(4), P. 545 - 558

Published: April 1, 2025

Over the past decade, long-read sequencing has evolved into a pivotal technology for uncovering hidden and complex regions of genome. Significant cost efficiency, scalability, accuracy advancements have driven this evolution. Concurrently, novel analytical methods emerged to harness full potential long reads. These enabled milestones such as first fully completed human genome, enhanced identification understanding genomic variants, deeper insights interplay between epigenetics variation. This mini-review provides comprehensive overview latest developments in DNA analysis, encompassing reference-based de novo assembly approaches. We explore entire workflow, from initial data processing variant calling annotation, focusing on how these improve our ability interpret wide array variants. Additionally, we discuss current challenges, limitations, future directions field, offering detailed examination state-of-the-art bioinformatics sequencing.

Language: Английский

Citations

1
Evolution of genome-wide methylation profiling technologies DOI
Carolina Montaño, Winston Timp

Genome Research, Journal Year: 2025, Volume and Issue: 35(4), P. 572 - 582

Published: April 1, 2025

In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing evolution from traditional methods such as arrays and whole-genome bisulfite sequencing to cutting-edge single-molecule profiling enabled by long-read (LRS) technologies. We highlight how LRS is transforming clinical translational research, particularly its ability simultaneously measure genetic epigenetic information, providing a more comprehensive understanding of complex disease mechanisms. discuss current challenges future directions field, emphasizing need for innovative computational tools robust, reproducible approaches fully harness capabilities molecular diagnostics.

Language: Английский

Citations

1