Next generation sequencing‑based analysis of mitochondrial DNA characteristics in plasma extracellular vesicles of patients with hepatocellular carcinoma

Abstract

Emerging evidence has revealed that mitochondrial DNA (mtDNA) is encapsulated in plasma extracellular vesicles (EVs). However, the characteristics of mtDNA in EVs from patients with cancer remain largely unexplored, which greatly limits its clinical application. Whole genome and capture-based sequencing found that EV mtDNA covered the whole mitochondrial genome. The medium fragment size in EV mtDNA was significantly larger compared with that in cell-free mtDNA [cfmtDNA; 159 vs. 109 base pairs (bp); P<0.001]. EV DNA appeared to have a higher mtDNA copy number compared with cfDNA. Of note, patients with hepatitis had >300-bp fragments in EV mtDNA compared with patients with hepatocellular carcinoma (HCC) and healthy controls. EV mtDNA fragments >300 bp in length exhibited a significantly higher proportion of EV mtDNA fragment ends than those that were ≤300 bp in length in patients with hepatitis. The EV mtDNA copy number in patients with HCC and hepatitis were significantly lower compared with those in healthy controls. Furthermore, inconsistencies in the mtDNA heteroplasmic variant were observed among HCC tissues, plasma and EVs. In conclusion, EV mtDNA exhibited different characteristics among patients with HCC, hepatitis and healthy controls, indicating the potential value of EV mtDNA as a diagnostic biomarker that complements cfmtDNA.

Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer

“…However, LC-WGS is restricted by the use of samples in which the tumor fraction is relatively high (> 10%), thus the search for alternative sources of circulating DNA is critical 33 . A recent study found that EV-DNA contained a higher mitochondrial DNA copy number than that found in cf-DNA of patients with hepatocellular carcinoma using whole genome and capture-based sequencing, suggesting EV-DNA may be an advantageous source of alternative liquid biopsy 34 . Our study is one of the few published studies that has investigated the utility of LC-WGS as a method of CNA profiling using low-input EV-associated DNA from cancer patients’ plasma with comparison to matched FFPE samples.…”

Glia Maturation Factor Beta as a Novel Biomarker and Therapeutic Target for Hepatocellular Carcinoma

“…The mtDNA copy number gained more and more attention in cancer research. Previous studies showed decreased copy numbers in cancer samples in HCC, bladder cancer, breast cancer, kidney clear cell carcinoma and myeloproliferative neoplasm, and increased copy number detected in chronic lymphocytic leukemia, lung squamous cell carcinoma and pancreatic adenocarcinoma (45)(46)(47)(48)(49)(50). Furthermore, the decrease in mtDNA copy number was more significant in female HCC patients than in males (51).…”

Comparison of Circulating Tumour DNA and Extracellular Vesicle DNA by Low-Pass Whole-Genome Sequencing Reveals Molecular Drivers of Disease in a Breast Cancer Patient

“…Low-pass WGS (LP-WGS) studies of ctDNA in breast cancer have determined that CNVs associated with metastatic progression and treatment response can be observed longitudinally throughout patient treatment [ 5 , 6 ]. Recent data have also indicated that cancer-related CNVs can be detected in the DNA of cancer patient-derived extracellular vesicles (EVs), which are membrane-bound vesicles released from a wide range of cells including tumour cells via exocytosis or membrane budding [ 7 , 8 , 9 , 10 , 11 , 12 ]. Interestingly, EVs are thought to be stable in the blood for up to 30 days, and the DNA within them is protected from nuclease degradation by the vesicle lipid membrane, suggesting that the assessment of EV DNA may be a promising alternative or complement to ctDNA for non-invasive cancer diagnosis and monitoring [ 13 , 14 , 15 ].…”