ArticleGenome medicine2024
Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma.
Article in Genome medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Mitochondrial DNA methylation: State-of-the-art in molecular mechanisms and disease implications.Journal of advanced research · 2026Review
- Mitochondrial DNA mutations and intercellular mitochondrial transfer in cancer: mechanisms, biological effects, and clinical potential.Biomarker research · 2026Review
- Impacts of Mitochondrial Status After Neoadjuvant Chemotherapy in Esophageal Squamous Cell Carcinoma Patients.Cancer science · 2026Article
- Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP.Genomics, proteomics & bioinformatics · 2025Article
- Comparative evaluation of DNA and RNA probes for capture-based mitochondrial DNA next-generation sequencing.BMC biology · 2025Article
- Survival Impacts of Mitochondrial Status in Esophageal Squamous Cell Carcinoma Patients.Annals of surgical oncology · 2025Article
- Next-generation sequencing of mitochondrial DNA reveals pathogenic variants and protective haplogroup D4 in esophageal cancer.Frontiers in genetics · 2025Article
- Mitochondrial DNA Mutations as a Factor in the Heritability of Atherosclerosis and Other Diseases.Current medicinal chemistry · 2025Review
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Authors and funding
10 authors at 6 institutions in 3 countries.
Funding
Abstract
backgroundMitochondria play essential roles in tumorigenesis; however, little is known about the contribution of mitochondrial DNA (mtDNA) to esophageal squamous cell carcinoma (ESCC). Whole-genome sequencing (WGS) is by far the most efficient technology to fully characterize the molecular features of mtDNA; however, due to the high redundancy and heterogeneity of mtDNA in regular WGS data, methods for mtDNA analysis are far from satisfactory.
methodsHere, we developed a likelihood-based method dMTLV to identify low-heteroplasmic mtDNA variants. In addition, we described fNUMT, which can simultaneously detect non-reference nuclear sequences of mitochondrial origin (non-ref NUMTs) and their derived artifacts. Using these new methods, we explored the contribution of mtDNA to ESCC utilizing the multi-omics data of 663 paired tumor-normal samples.
resultsdMTLV outperformed the existing methods in sensitivity without sacrificing specificity. The verification using Nanopore long-read sequencing data showed that fNUMT has superior specificity and more accurate breakpoint identification than the current methods. Leveraging the new method, we identified a significant association between the ESCC overall survival and the ratio of mtDNA copy number of paired tumor-normal samples, which could be potentially explained by the differential expression of genes enriched in pathways related to metabolism, DNA damage repair, and cell cycle checkpoint. Additionally, we observed that the expression of CBWD1 was downregulated by the non-ref NUMTs inserted into its intron region, which might provide precursor conditions for the tumor cells to adapt to a hypoxic environment. Moreover, we identified a strong positive relationship between the number of mtDNA truncating mutations and the contribution of signatures linked to tumorigenesis and treatment response.
conclusionsOur new frameworks promote the characterization of mtDNA features, which enables the elucidation of the landscapes and roles of mtDNA in ESCC essential for extending the current understanding of ESCC etiology. dMTLV and fNUMT are freely available from https://github.com/sunnyzxh/dMTLV and https://github.com/sunnyzxh/fNUMT , respectively.
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