Liquid Biopsy in Hepatocellular Carcinoma: Comparison
Please note this is a comparison between Version 2 by Peter Tang and Version 1 by Ismail Labgaa.

Hepatocellular carcinoma (HCC) is one of the deadliest cancer. Clinical guidelines for the management of HCC endorse algorithms deriving from clinical variables whose performances to prognosticate HCC is limited. Liquid biopsy is the molecular analysis of tumor by-products released into the bloodstream. It offers minimally-invasive access to circulating analytes like DNA, RNA, exosomes and cells. This technology demonstrated promising results for various applications in cancers, including prognostication. 

  • liver cancer
  • biomarkers
  • precision medicine
  • circulating
  • prognosis

1. Introduction

Hepatocellular carcinoma (HCC) shows a worrisome epidemiological trajectory [1]. The WHO predicts over 1 million HCC-related deaths in 2030 [2]. A particular feature of HCC is that it typically arises on a chronically damaged organ, mostly cirrhosis, for which viral hepatitis, alcohol use disorder and NAFLD are common causes. This facilitates the identification of patients at risk and has enabled successful surveillance programs for early cancer detection. However, having two potentially life-threatening diseases in the same patient (i.e., HCC and cirrhosis) complicates its clinical management and prognosis prediction. Numerous attempts have been pursued to reliably prognosticate HCC, using various strategies. The most widely used classifications, like the Barcelona Clinic Liver Cancer (BCLC) algorithm [3[3][4],4], relies on clinical variables. Other approaches investigate the contribution of tumor markers like α-fetoprotein (AFP) [5] and molecular markers derived from the tumor or adjacent non-tumor samples [6,7,8,9][6][7][8][9]. Regardless of the strategy, the prognostic performance of these algorithms needs to be improved. Following a ‘precision medicine’ perspective may be a way of improving HCC prognostication. This implies access to genomic data on a patient-basis, which requires biopsy or surgical specimens for tissue samples of the tumor. This is particularly difficult in HCC for which, unlike most solid tumors, diagnosis mostly relies on imaging and tissues samples are rarely available [10,11][10][11]. In addition, tissue biopsies are associated with potential complications and should not be sequentially repeated [12].

This can be circumvented using liquid biopsy, which refers to the molecular analysis of tumor components released from a solid tumor into biological fluids like blood. These analytes include circulating tumor nucleic acids (DNA and RNAs), cells (CTCs) and exosomes (Figure 1). This technology has shown promising results for various applications in the management of different types of cancers including HCC [13,14,15][13][14][15]: early diagnosis [16[16][17],17], detection of minimal residual disease [18], decision-making for systemic therapies [19,20][19][20] or even to decipher complex biological traits of cancers [21,22,23,24][21][22][23][24]. This technology offers a valuable alternative to standard biopsy. Tissue biopsy is indeed invasive and associated with potential risks such as pain, bleeding or even seeding of the cancer (PMID: 18669577). Conversely to standard biopsy, liquid biopsy displays the advantages of being easily repeatable and can thereby help for monitoring, providing a dynamic picture of the disease course. In addition, it may reflect different regions of the tumor and thus recapitulate eventual intra-tumoral heterogeneity (ITH) (Figure 2) [25].

Figure 1.

Concept of liquid biopsy referring to the molecular analysis of tumor-byproducts released into the bloodstream.

Figure 2. Pros and cons of liquid biopsy versus standard biopsy.

2. Circulating Tumor DNA (ctDNA)

DNA fragments are released from solid tumors into the bloodstream via active and passive mechanisms. The latter seems to predominate, being partially driven by cell necrosis and apoptosis [26]. This occurs at any tumor stage and offers minimally-invasive access to key molecular information of the tumor including genomic (copy number variations (CNV) or point mutations) as well as epigenetic (DNA methylations changes) data. Numerous studies show the value of ctDNA as a polyvalent biomarker in cancer. For example, ctDNA allowed detection of minimal residual disease (MRD) in a prospective cohort of 230 patients undergoing surgical resection of stage II colon cancer. Postoperative detection of ctDNA outperformed prognostic factors such as TNM stage, for the prediction of recurrence-free survival [18].

In HCC, a pilot study demonstrated that detection of mutations in the plasma of HCC patients was feasible and recapitulated the ones detected in tumor tissue [27]. Table 1 summarizes reports investigating ctDNA in HCC prognostication.

Table 1. Circulating tumor DNA (ctDNA).

RNAs include a large family of members: micro, long non-coding, messenger or exosomal RNAs. Herein, we will focus on the most commonly investigated circulating RNAs in liquid biopsies (Table 2).

Table 2. Circulating free RNAs (cfRNAs) and exosomes.

Number of Patients

Treatment

Biomarkers

Technique

Main Finding

[Ref.]

miRNA

195 HCC

54 cirrhotic

44 HCC

30 HCV

39 cirrhosis

38 healthy controls

Surgery

NA

Isolation by size of epithelial tumor cells (ISET)

Presence and number of detected CTCs were associated with shorter survival

[77]

[71]

Surgery

Transplant

TACE

RFA

sorafenib

miR-1 and miR-12

qRT-PCR

85 HCC

37 benign liver diseases

20 healthy volunteers 14 miscellaneous advanced cancers other than HCC

Surgery

NA

Low level of miR-1 was associated with lower survival

Antibody-coated magnetic beads

Presence and number of detected CTCs correlated with tumor size, portal vein tumor thrombus, differentiation status, TNM stage and Milan criteria

[78]

[72]

[50]

[45]

122 HCC

Surgery

82 HCC

Surgery

miR-122

Multicolor flow cytometry

qRT-PCR

Circulating cancer stem cells (CSC) are associated with higher rates of intra- and extra-hepatic recurrence, decreased recurrence-free survival (RFS) and overall survival (OS) rates

Low level of miR-122 was associated with lower survival

[79]

[73]

[51]

[46]

120 HCC

96 HCC

31 healthy controls

21 viral hepatitis

8 cirrhosis

Surgery

RFA

Surgery

MiR-21, miR-26a, and miR-29a

Magnetic cell sorting (Lin28B)

qRT-PCR

Detection of CTCs expressing Lin28B was associated with early recurrence

Low levels of miR-26a and miR-29a were associated with lower survival

[80]

[52]

[47]

[

74

]

30 HCC; 30 controls

Surgery

miR-155, miR-96 and miR-99a

qRT-PCR

High levels of miR-155 and miR-96 were associated with lower survival

[53]

[48]

60 HCC

Surgery

NA

Flow cytometry (ICAM-1)

Detection of CTCs expressing ICAM-1 was associated with shorter disease-free survival

[81]

[75]

116 HCC

123 HCC

NA

Surgery

Circulating miR

EpCAM antibody-coated magnetic beads (CellSearch)

Whole miRNome profling

Low levels of miR-424-5p, miR-101-3p or high levels of miR-128, miR-139-5p, miR-382-5p and miR410 were associated with lower survival

Detection of CTCs (EpCAM+) was associated with higher recurrence

[54]

[49]

[

75

]

[69]

41 HCC; 20 controls

Surgery

transplant

miR193a-5p

59 HCC

qRT-PCR

19 controls

High level of miR193a-5p was associated with lower survival

NA

EpCAM antibody-coated magnetic beads (CellSearch)

Detection of CTCs was associated with lower overall survival

[82]

[76]

[55]

[50]

70 HBV-related HCC

70 HBV

50 healthy controls

Surgery

122 HCC

120 controls

Surgery

TACE

Radiotherapy

miRNA-223-3p

qRT-PCR

EpCAM antibody-coated magnetic beads (CellSearch)

Low level of miRNA-223-3p was associated with lower survival

Peri-treatment decrease of detected CTC reflected treatment response

[83]

[77]

[56]

[51]

mRNA

109 HCC

Surgery

TACE

RFA

sorafenib

Flow cytometry (ASGPR and CPS1)

pERK+/pAkt-CTCs correlated with progression-free survival and predicted response to systemic therapy (sorafenib)

[84]

[78]

50 HCC; 50 controls

Surgery

72 HCC

Surgery

VEGF-165

EpCAM antibody-coated magnetic nanoparticals (MagVigen, Nvigen)

qRT-PCR

Detection of CTCs expressing AFP was associated with metastatic disease

Detection of circulating VEGF mRNA (isoform 165) was associated with higher recurrence and recurrence-related mortality

[85]

[79]

[57]

[52]

38 HCC

Surgery

69 HCC

31 controls

Surgery

Transplant

TACE

RFA

Sorafenib

BSC

AFP

Imaging flow cytometry (EpCAM, AFP, glypican-3 and DNA-PK together with analysis of size, morphology and DNA content) (ImageStream)

qRT-PCR

Detection of CTCs was associated with lower survival

Detection of AFP mRNA was associated with extrahepatic recurrence and shorter disease-free survival

[86]

[58]

[53]

[

80

]

343 HCC

Surgery

TACE

RFA

Systemic chemotherapy

Radiotherapy

BSC

AFP and hTERT

qRT-PCR

Detection of AFP mRNA or hTERT mRNA was not associated with survival

[59]

[54]

57 HCC

Surgery

EpCAM antibody-coated magnetic beads (CellSearch)

CTCs detection was associated with higher recurrence and lower recurrence-free survival after liver resection

[87]

[

Exosomes

81

]

14 HCC

16 CCA

4 GBC

Surgery

SE-iFISH

Detection of small CTCs with CNV (chromosome 8) was associated with lower survival

[88]

[82]

59 HCC

Transplant

199 HCC

miR-718

qRT-PCR

Surgery

Recurrence was associated with higher level of exosomal miR-718

Fluorescence-activated cell sorting (FACS)

Anterior approach was associated with a decreased dissemination of CTCs compared to conventional approach, resulting in poorer outcomes.

[89]

[83]

[60]

[55]

30 HCC

Surgery

miR-665

qRT-PCR

High level of exosomal miR-665 was associated with lower survival

73 HCC

Surgery

EpCAM antibody-coated magnetic beads (CellSearch)

[

Analyzes of blood samples collected in different vessels revealed a spatial heterogeneity of CTCs distribution whose biology was associated with recurrence pattern.

61

[90]

[84]

]

[56]

79 HCC

Surgery

Transplant

TACE

RFA

Sorafenib

BSC

miR-21 and lncRNA-ATB

130 HCC

Surgery

TACE

qRT-PCR

qRT-PCR test platform

High levels of exosomal miR-21 and lncRNA-ATB were associated with lower survival

CTCs detection was associated with recurrence after liver resection

[91]

[85]

[62]

[57]

126 HCC; 21 healthy controls

Surgery

miR-638

112 HCC

qRT-PCR

Surgery

Low level of exosomal miR-638 was associated with lower survival

CanPatrolTM system (filtration by size) and Tri-color RNA-ISH assay

The presence of CTCs and the proportion of mesenchymal-CTC (M-CTCs) were associated with recurrence

[92]

[86]

[63]

[58]

31 HCC; 3 CLD; 11 healthy controls

61 HCC

19 non-HCC

NA

RN7SL1 S fragment

qRT-PCR

High expression of RN7SL1 S fragment was associated with lower survival

[64]

[59]

124 HCC; 100 healthy controls

Surgery

AKT3

qRT-PCR

High level of exosomal circulating AKT3 was associated with higher recurrence and lower survival rates

[65]

[60]

104 HCC; 55 CLD; 50 healthy controls

Surgery

miR-320a

qRT-PCR

Low serum exosomal miR-320a was associated with lower survival

[66]

[61]

4. Extracellular Vesicles (EVs): Exosomes

Exosomes are a type of EV, nanoparticles encapsulating a variety of cargo including DNA and RNA fragments in a lipidic double-layer, which protects them from enzymatic degradation. With these unique features, circulating exosomes allow RNAs to circulate without being degraded plasma. Their nature and roles remain largely unknown but exosomes may not only be passively released from apoptotic cells into the bloodstream. Data suggested they may be actively secreted, acting as messengers in the cell-to-cell communication network, conferring them priceless values like accuracy and tissue-specificity [68,69,70,71][62][63][64][65].

In HCC, the data exploring the contribution of exosomes remain limited, particularly for prognosis. However, these analytes have demonstrated promising and polyvalent performance in other cancer types both for diagnosis and prognosis [72,73][66][67].

Several projects analyzed exosomal miRNAs. In a cohort of 59 HCC patients, authors found a correlation between tumor recurrence after liver transplantation and a higher level of miR-718 [60][55]. Similar signals were detected after liver resection and other exosomal miRNAs: high levels of miR-665 or low levels of miR-638 and miR-320a were identified as predictors of poor survival [61,63,66][56][58][61]. In a cohort of 79 HCC patients of different stages receiving various treatments, Lee et al. focused on two candidates: a miRNA (miR-21) and a long non-coding RNA (lncRNA) (lncRNA-ATB). On multivariable analysis, both markers were independently associated with disease progression [62][57]. A recent study profiled 57 plasma cell-free RNA transcriptomes and 20 exosomal RNA transcriptomes to test their diagnostic and prognostic performance. RN7SL1 and its S fragment were promising, showing a high diagnostic accuracy (AUC = 0.87). Furthermore, a higher concentration of RN7SL1 S fragment was an independent factor of worse survival [64][59]. The analyses of blood samples from 124 HCC patients treated with surgical resection and 100 healthy controls identified an exosomal circular RNA (circAKT3) as a prognostic factor; a high level of circAKT3 predicted both higher recurrence and lower survival [65][60].

5. Circulating Tumor Cells (CTCs)

CTCs play a pivotal role during the hematogenous dissemination of cancers. Most technologies to analyze CTCs include two steps: enrichment (isolation) and detection (identification). The development of sensitive and specific technologies is challenging. Estimated to be released by cancers of intermediate and advanced stages, CTCs are probably more useful for prognostication than for early cancer detection. In this context, studies have demonstrated the prognostic value of CTC enumeration in different cancers including HCC [74,75][68][69]. More sophisticated technologies, like single-cell RNA sequencing, have allowed further characterization of CTC subtypes [76][70]. Studies exploring the value of CTCs for HCC prognostication are summarized in Table 3.

Table 3. Circulating tumor cells (CTCs).

Number of Patients

Treatment

Biomarkers

Technique

Main Finding

[Ref.]

CNV

34 HCC

Surgery

ctDNA (harboring SNV or CNV)

Targeted-sequencing and low coverage whole-genome sequencing

ctDNA can detect minimal residual disease (MRD) and predict survival

[28]

151 HCC; 14 healthy controls

Sorafenib

VEGFA amplification

Whole-genome sequencing

High concentration of cell-free DNA (cfDNA) was associated with poor outcomes but VEGFA ratio was not a prognostic factor.

[29]

Mutations

46 HCC

Surgery

Transplant

ctDNA

Targeted-sequencing and exome-sequencing

Detection of ctDNA was associated with increased recurrence

[30]

41 HCC; 10 controls

Surgery

TERT, TP53 and CTNNB1

Targeted-sequencing

Detection of ctDNA predicted shorter recurrence-free survival

[31]

10 HCC

Surgery

TACE

RFA

Methylation of GSTP1 and RASSF1A or TP53 mutation

Methylation-specific PCR and sanger sequencing

Detecting ctDNA in urine was feasible and predicted recurrence

[32]

218 HCC; 81 cirrhotic

NA

TERT promoter mutation (C228T and C250T)

Droplet digital PCR (ddPCR) and sanger sequencing

TERT promoter mutation can be used as an early biomarker of HCC and is associated with survival

[33]

34 HCC

Surgery

ctDNA (harboring SNV or CNV)

Targeted-sequencing and low coverage whole-genome sequencing

ctDNA can detect minimal residual disease (MRD) and predict survival

[28]

95 HCC; 45 cirrhotic

Surgery

TERT promoter mutation (C228T)

Droplet digital PCR (ddPCR)

Detection of mutated TERT promoter was associated with lower survival

[34]

59 HCC

Surgery

TACE

RFA

Systemic chemotherapy

BSC

Single nucleotide variant (SNV) in a panel of 69 genes

Targeted-sequencing

Mutated MLH1 in plasma was associated with lower survival

[35]

130 HCC

TACE

Systemic chemotherapy

TERT promoter mutation

Droplet digital PCR (ddPCR)

Detection of mutated TERT promoter was associated with lower survival

[36]

895 HCC

Surgery/NA

TP53 mutation (R249S)

Droplet digital PCR (ddPCR)

Detection of mutated TP53 was associated with lower survival

[37]

22 HCC

TKI (tyrosine kinase inhibitors)

Genes of the PI3K/MTOR pathway

Targeted-sequencing and ddPCR

Mutations of genes in the PI3K/MTOR pathway are associated with lower survival in patients treated with TKI

[38]

Methylation Changes

72 HCC; 37 benign liver diseases; 41 healthy controls

-

APC, GSTP1, RASSF1A, and SFRP1

Methylation-specific PCR

Methylation of RASSF1A was associated with poor survival

[39]

1098 HCC; 835 controls

NA

8-marker panel

Targeted bisulfite sequencing

Methylation-based classifier predicted survival

[40]

10 HCC

TACE

RFA

Surgery

Methylation of GSTP1 and RASSF1A or TP53 mutation

Methylation-specific PCR and sanger sequencing

Detecting ctDNA in urine was feasible and predicted recurrence

[32]

203 HCC; 104 chronic viral hepatitis B or C; 50 healthy controls

NA

APC, COX2, RASSF1A (+miR-203)

Methylation-specific PCR

Classifier predicted survival

[41]

172 HCC

NA

LINE-1

Methylation-specific PCR

Hypomethylation of LINE-1 was associated with lower survival

[42]

155 HCC; 60 chronic HBV; 20 healthy controls

Surgery

IGFBP7

Methylation-specific PCR

Methylation of IGFBP7 was associated with lower survival

[43]

43 HCC (+347 HCC from TCGA Atlas); 5 cirrhotic; 6 benign liver lesions

-

CTCFL

Methylation-specific PCR

Hypomethylation of CTCFL was associated with higher recurrence and lower survival

[44]

3. Circulating Free RNAs (cfRNAs)

Most studies investigating CTCs included HCC patients undergoing surgical resection. In 2004, Vona G et al. isolated and enumerated CTCs based on their size and morphology, showing that the presence and number of detected CTCs were associated with shorter survival [77][71]. CellSearch® is an isolation system that targets EpCAM positive cells. It was approved by the Food and Drug Administration (FDA) and became the most commonly used technique for CTC enumeration. Its use remains debated in HCC as only around 30% of HCC cells express EpCAM [102][96]. Nonetheless, several studies utilized this approach in HCC, demonstrating that the detection of EpCAM positive CTCs was associated with higher tumor recurrence [75][69] or lower survival [82,87][76][81]. Thereafter, more sophisticated technologies for CTC isolation have been reported, like ImageStream flow cytometry. A study has provided the proof-of-concept of this technology, demonstrating its capacity to detect CTCs using a panel of markers. This technology also generates high-resolution images of isolated CTCs [103][97]. Its value in detecting CTCs was confirmed and the CTC count was further confirmed as an independent prognostic factor [86][80]. Other reports have aimed at exploring the impact of subgroups of CTCs, clustered based on cell surface markers, RNA expression or genomic aberrations. Studies using surface markers to detect CTCs with cancer stem cell-like [79,80,81][73][74][75] or mesenchymal [92][86] features, revealed their clinical value to predict tumor recurrence. CTCs expressing AFP were also associated with an increased risk of metastasis [85][79], whereas CTCs harboring CNV (chr 8) predicted worse survival [88][82]. Ha et al. used a simple isolation technique but introduced the concept of ΔCTC, referring to the perioperative fluctuation of detected CTCs, which appeared as an independent factor of lower survival and higher recurrence rates after partial hepatectomy [95][89]. Besides their intrinsic biological traits, CTC dissemination seemed to be impacted by treatment. Data suggested that surgery-induced manipulation of the liver is associated with a release of CTCs [94][88]. A comparison between anterior and conventional surgical approaches suggested that the latter was associated with a higher release of CTCs as well as poorer outcomes [89][83]. Toso et al. described five steps during orthotopic liver transplant (OLT) in HCC patients to minimize CTC dissemination and thereby the risk of recurrence [104][98].

Recent studies also underscored the relevance of CTC analysis in patients undergoing OLT for HCC, highlighting an association between CTC detection and recurrence [97,101][91][95].

Guiding decision-making would be another application of CTCs. For example, selection of patients who would benefit from adjuvant transarterial chemoembolization (TACE) after surgery or to predict response to systemic therapies like tyrosine kinase inhibitors or immunotherapy [84,99,100][78][93][94]. An interesting study analyzed CTCs using samples collected from different vessels. By doing so, they were able to demonstrate spatial heterogeneity in the distribution of CTCs, with a predominance of epithelial status at release, which gradually switched to EMT-activated phenotype during hematogenous transit [90][84]. Overall, data consistently identified that the number of CTCs was a surrogate of poor prognosis, predicting higher recurrence and/or lower survival. A recent meta-analysis and data from experimental models corroborated these findings [105,106][99][100].

2. Challenges and Future Perspectives

6. Challenges and Future Perspectives

The field of liquid biopsy has numerous challenges. Besides those related to cost and technology, there is a limited understanding of the fundamental mechanisms responsible for the release of tumor molecular components to the bloodstream. A better understanding of these mechanisms would provide new tools and targets to improve the diagnostic and prognostic performance of liquid biopsy analytes. Gasparello et al. performed one of the few studies of liquid biopsies in animal models, identifying potential gateways regulating the detection of ctDNA [107][101]. Experimental models will be instrumental to better understand these mechanisms. ITH has emerged as a major drawback for single-biopsy biomarker development. The clinical impact of ITH is progressively recognized, even at early tumor stages [108][102]. Liquid biopsy can help address the clinical issues posed by ITH as it likely includes a molecular composite of tumor components released by any potential tumor area. Thus, it is not restricted by the specific tumor section sampled by a needle-biopsy. There are few data of integrative analysis of different analytes within the liquid biopsy space (e.g., simultaneous evaluation of ctDNA and CTCs). Finally, it is key to have prospective data to determine the exact role of liquid biopsy as a prognostic biomarker in HCC, and which is the clinical niche that will be better suited for this transformative technology.



3. Conclusions

7. Conclusions

While data on liquid biopsy in HCC remain scanter than for other malignancies, there has been numerous recent publications demonstrating its prognostic value in HCC patients. Potential contributions in HCC prognostication were detected for each of the tumor by-products (e.g., DNA, RNA, exosomes and cells). The next step will be to determine the optimal way of integrating liquid biopsy in the clinical management of HCC patients and to modify current clinical practice guidelines accordingly.



Author Contributions: Study concept and design: I.L., A.V., O.D., N.D., E.M.; Acquisition of data:

I.L.; Analysis and interpretation of data: I.L., A.V., E.M.; Drafting of the manuscript: I.L.; Critical

revision of the manuscript for important intellectual content: I.L., A.V., O.D., N.D., E.M. All authors

have read and agreed to the published version of the manuscript.



Funding: This research received no external funding.



Acknowledgments: The authors would like to thank Jill Gregory for the design of the figures.

Conflicts of Interest: AV has received consulting fees from Guidepoint, Fujifilm, Boehringer Ingelheim, FirstWord, and MHLife Sciences; advisory board fees from Exact Sciences, Nucleix, Gilead and

NGM Pharmaceuticals; and research support from Eisai.



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