Single-Molecule Sequencing Reveals DNA Mismatch and Damage Patterns Underlying Mutations and Disease

Core Concepts

Single-molecule sequencing method (HiDEF-seq) can detect single-strand DNA mismatches and damage, providing insights into the initiating events of mutations that lead to cancer and other diseases.

Abstract

The article presents a new single-molecule sequencing method called Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq) that can accurately resolve single-strand DNA mismatches and damage events. This is an important advancement over current DNA sequencing technologies, which can only detect double-strand mutations as the end-point of the mutation process. The key highlights and insights from the article are: Mutations accumulate in the genome over a person's lifetime, leading to cancer and other diseases. Most mutations start as single-strand mismatches or damage before becoming double-strand mutations. HiDEF-seq can detect single-strand mismatches and cytosine deamination (a common DNA damage event) with single-molecule fidelity. The authors profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derived single-strand mismatch and damage signatures. They found correspondences between these single-strand signatures and known double-strand mutational signatures, which helps identify the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading showed distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. A single-strand damage signature for APOBEC3A was defined. In the mitochondrial genome, the findings support a mutagenic mechanism occurring primarily during replication. Detecting single-strand events will enable studies of how mutations arise in various contexts, especially in cancer and aging.

Stats

Profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes.

Quotes

"Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2." "However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events." "As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing."

Key Insights Distilled From

DNA mismatch and damage patterns revealed by single-molecule sequencing - Nature

by Mei Hong Liu... at www.nature.com 06-12-2024

https://www.nature.com/articles/s41586-024-07532-8

Deeper Inquiries

How can the single-strand mismatch and damage signatures identified by HiDEF-seq be used to develop new diagnostic or therapeutic approaches for cancer and other diseases?

The single-strand mismatch and damage signatures identified by HiDEF-seq can provide valuable insights into the early stages of mutagenesis, allowing for the identification of specific DNA lesions that can lead to cancer and other diseases. By understanding the initiating events at the single-molecule level, researchers and clinicians can develop targeted diagnostic tools to detect these signatures early on, potentially enabling the early detection of cancer predisposition syndromes or other genetic diseases. Furthermore, by linking these single-strand signatures to known double-strand mutational patterns, it becomes possible to tailor personalized therapeutic approaches based on the specific mutational processes at play in an individual's genome. This precision medicine approach could lead to more effective treatments with fewer side effects, ultimately improving patient outcomes.

What are the potential limitations or challenges in applying HiDEF-seq to clinical samples or large-scale studies?

While HiDEF-seq offers the unique advantage of single-molecule fidelity for base substitutions and the detection of DNA damage, there are several limitations and challenges in applying this technology to clinical samples or large-scale studies. One major limitation is the cost associated with single-molecule sequencing, which can be prohibitive for large-scale studies or routine clinical use. Additionally, the complexity of data analysis and interpretation from HiDEF-seq experiments may require specialized bioinformatics expertise, posing a challenge for widespread adoption in clinical settings. Another potential limitation is the need for high DNA input amounts, which may be difficult to obtain from precious clinical samples or low-input samples. Furthermore, the sensitivity and specificity of HiDEF-seq in detecting rare mutations or low-frequency DNA damage events need to be carefully validated to ensure its reliability in clinical applications.

How might the insights from single-strand mutation patterns inform our understanding of the fundamental mechanisms of DNA replication, repair, and mutagenesis in different cell types and contexts?

The insights gained from single-strand mutation patterns identified by HiDEF-seq can significantly advance our understanding of the fundamental mechanisms of DNA replication, repair, and mutagenesis in various cell types and contexts. By characterizing the specific types of DNA lesions that initiate mutagenesis at the single-molecule level, researchers can unravel the intricate interplay between DNA replication fidelity, repair mechanisms, and mutational processes. This knowledge can shed light on how different cell types respond to DNA damage, how mutations arise in specific genomic regions, and how environmental factors or genetic predispositions influence mutagenesis. Understanding these mechanisms at a granular level can lead to the development of targeted interventions to modulate DNA repair pathways, prevent mutagenic events, or enhance genome stability in different cellular contexts, ultimately paving the way for novel therapeutic strategies in cancer treatment and beyond.