Liu et al. [
1] have presented important research results showing that aberrant fragmentomic features of mitochondrial cell-free DNA (cfDNA) can be used not only for the early diagnosis of hepatocellular carcinoma (HCC), but also for predicting prognosis and monitoring recurrence after HCC treatment (
Fig. 1). In particular, they have demonstrated that the information obtained from circulating cell-free mitochondrial DNA (mtDNA) copy number variation, mutation, and fragmentomics could be comprehensively evaluated to support previous findings in which the diagnostic accuracy was low when only the copy number variation of circulating cell-free mtDNA was used, and that it can be more accurately and clearly used for the diagnosis and prognosis of HCC. In particular, the HCC detection score (HD score) suggested by the authors showed that HCC can be diagnosed with a sensitivity of approximately 90%, even in cases where imaging findings are consistent with HCC [
1]. Meanwhile, alpha-fetoprotein (AFP) as a tumor marker is not increased, as is commonly experienced in clinical practice. In addition, these results proved that they can be equally applied to early HCC, such as stage 0 or A, as early Barcelona Clinic Liver Cancer (BCLC) stages, thereby proving their usefulness as markers for diagnosing early HCC. Diagnosing HCC using conventional screening methods is often difficult, and increases in AFP, AFP-L3, and PIVKA-II may not be observed.
Recently, early diagnosis and prognosis prediction technologies for tumors using liquid biopsy with circulating tumor cells, cfDNA, circulating tumor DNA (ctDNA), and exosomes derived from primary or metastatic tumors have continuously emerged [
2]. Plasma cfDNA is derived from damaged cells and cleaved by nucleases to approximately 160 bp. Most previous studies have focused on and evaluated changes in cell-free nuclear DNA and analyzed tumor-specific mutations, copy number variations, and methylation patterns [
2]. In particular, most studies have evaluated somatic mutations in cfDNA or utilized copy number variation and methylation profiling markers to diagnose and predict tumor prognosis. However, these methods are not suitable for early diagnosis because the concentration of cfDNA is relatively low in early stage cancer, resulting in low sensitivity. Hence, fragmentation features of cell-free nuclear DNA have been derived using whole-genome sequencing data for cell free DNA to utilize them for cancer diagnosis. This is performed to analyze the fragment size, end motifs, and nucleosome relationships of cell free nuclear DNA [
2]. This cfDNA fragmentation reflects changes in the genomics, chromatin, and transcription factor binding sites of patients with HCC, thereby providing a biological basis for patients with HCC and enabling a more accurate early diagnosis of tumors, especially HCC [
3]. However, studies on fragmentomic features using cfDNA are diverse, with short fragments (between 70 and 200 bp in length) and long fragments (up to 21 kb), and have the disadvantages of low representativeness and reproducibility owing to the limitations of low-depth whole-genome sequencing tests [
4].
By contrast, unlike cell-free nuclear DNA, mitochondrial double-stranded circular genomic DNA is 16.6 kb long and has a high copy number [
5]. Mitochondria have their own circular genomic entities and thousands of copies per cell. Moreover, the mutation rate of mtDNA is significantly higher than that of nuclear DNA [
6]. Thus, tumor-specific variants in mtDNA can vary across different tumors, or even within the same tumor type [
7]. Therefore, previous studies have demonstrated that tumor-specific circulating cell-free mtDNA is a good noninvasive blood tumor marker in patients with cancer because of the high mtDNA copy number per cell and the accompanying high mtDNA mutation rate [
7]. Thus, circulating cell-free mtDNA can be used to achieve better tumor specificity than cell-free nuclear DNA. In a previous study, Liu et al. have demonstrated a correlation between somatic mutations and copy number changes in cell-free mtDNA and HCC progression [
8,
9]. In addition, Liu et al. [
1] have suggested that circulating cell-free mtDNA fragmentomics profiling based on tumor-derived circulating cell-free mtDNA mutations, various circulating cell free mtDNA mutation profiling including 5′ end motifs base preference and motif diversity, have cancer type-specific diagnostic capabilities. In addition, they comprehensively evaluated not only the copy number of circulating cell-free mtDNA itself, but also mutation and fragmentomic profiling simultaneously with circulating cell-free mtDNA copy number and demonstrated that it can be utilized for HCC-specific diagnosis and prognosis prediction by utilizing many patient samples including training and validation cohorts. The ability to distinguish HCC specificity by utilizing aberrant fragmentomic features of circulating cell-free mtDNA may be attributable to the diverse types and quantities of nucleases derived from HCC cells within tumors, the decreased expression of mitochondrial transcription factor A, and the systemic or environmental influence on protein binding of the mitochondrial genome [
1].
Thus, circulating cell-free mtDNA in patients with tumors is not only shorter than circulating cell-free nuclear DNA but also more abundant in patients with tumors than in healthy individuals or patients with liver cirrhosis. In addition, as the length of blood circulating cell-free mtDNA derived from patients with HCC is inversely proportional to tumor size and ctDNA, circulating cell-free mtDNA could also be used to monitor tumor size and cancer progression after curative or palliative treatment in patients with HCC [
10]. In addition, because the circulating cell-free mtDNA fragmentomics-based HD score is related to the BCLC stage, it is very useful for evaluating the HCC stage, as it suggests the possibility of distant metastasis that may not be detected at an early stage of HCC diagnosis.
However, this study was based only on circulating cell-free mtDNA before surgical treatment, and no studies have been conducted on the quantitative and qualitative changes in circulating cell-free mtDNA before and after surgical management. Thus, the aberrant fragmentomic pattern may change before and after the surgical management of HCC, and this could also be used to predict the recurrence-free survival of patients. In addition, in most patients with HCC enrolled in this study, the HCC was of chronic viral hepatitis B origin. Moreover, the proportion of HCC caused by chronic viral hepatitis C, alcoholic liver disease, and metabolic dysfunction-associated steatotic liver disease was relatively low, and they were lumped into non-viral hepatitis B and C. Therefore, additional studies are absolutely necessary to determine whether changes in the aberrant fragmentomic pattern of circulating cell-free mtDNA can be sufficiently utilized in the diagnosis and prognosis of HCC resulting from causes other than viral hepatitis. However, the correlation between circulating cell-free mtDNA fragmentomics and the histologic type and tumor differentiation of HCC is unclear. In addition to the clinical characteristics of the tumor, such as size, number, and diameter, the histologic features of the tumor itself may also influence on the patient’s prognosis; therefore, sufficient additional analysis and consideration are necessary. Finally, in the case of degenerative or regenerative nodules, which are relatively common in patients with liver cirrhosis in the clinic, progression to HCC is highly likely. Moreover, as their shape or characteristics are similar to those of HCC, differentiating them radiologically is often difficult; therefore, repeated follow-up imaging tests are often required. As the authors have already mentioned, it would be beneficial if circulating cell-free mtDNA fragmentomics could be used to differentiate whether what may be a degenerative or regenerative nodule on imaging has already advanced histologically into early stage HCC. In addition, even if they have not yet progressed to HCC, circulating cell-free mtDNA fragmentomics would be beneficial for monitoring whether degenerative or regenerative nodules have progressed to HCC, and additional research to support this is also urgently needed.
Finally, circulating cell-free mtDNA is significantly less time-consuming than conventional cfDNA, takes only approximately 5–7 days, and costs only $30 to $40 per sample, making it more economical and noninvasive than blood tests and imaging tests for HCC diagnosis. Therefore, it may be actively utilized for diagnosing HCC and evaluating tumor response after treatment in future clinical practice.
FOOTNOTES
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Conflicts of Interest
The author has no conflicts to disclose.
Figure 1.Diagnostic and therapeutic usefulness of circulating cell-free mitochondrial DNA in hepatocellular carcinoma patients.
Abbreviations
Barcelona Clinic Liver Cancer
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Citations
Citations to this article as recorded by
- Correspondence to editorial on “Aberrant fragmentomic features of circulating cell-free mitochondrial DNA enable early detection and prognosis prediction of hepatocellular carcinoma”
Yang Liu, Fan Peng, Siyuan Wang, Jinliang Xing
Clinical and Molecular Hepatology.2025; 31(2): e166. CrossRef - Reply to correspondence on “Aberrant fragmentomic features of circulating cell-free mitochondrial DNA enable early detection and prognosis prediction of hepatocellular carcinoma”
Hyuk Soo Eun
Clinical and Molecular Hepatology.2025; 31(2): e215. CrossRef
