Table 2.
Summary of selected research output on detection of HCC using methylation patterns
| Marker | Blood-based | Description | Ref. | |
|---|---|---|---|---|
| 1 | RASSF1A | + | Mean rate of 30% and 65% methylation in HCV-related cirrhosis and HCC tissues respectively | [165] |
| 2 | RASSF1A | Mean rate of 26.1% and 59.1% methylation in cirrhosis and HCC tissues respectively | [166] | |
| DOK1 | Mean rate of 19.6% and 56.0% methylation in cirrhosis and HCC tissues respectively | |||
| 3 | RASSF1A | + | Mean rate of 70% methylation on top of HCV-associated cirrhosis, with serum AFP combined to improve sensitivity | [167] |
| 4 | RASSF1A | + |
Hypermethylated sequences in 93% of HCC, 58% of HBV carriers, and 8% of the healthy individuals High RASSF1A at diagnosis or 1-year after resection relates to poor prognosis (p < 0.01) RASSF1A increase after cancer diagnosis (p < 0.014) |
[168] |
| 5 | CHFR, VASH2, GRID2IP, CCNJ, F12 CpG sites | + | HCC detection sensitivity was 84.5% at 95% specificity and 0.94 AUC using the count of methylated reads on combined specific genes. | [169] |
| 6 | WISP1 | + | Hypomethylation, increased plasma soluble WISP1 improved diagnostic power combining with AFP | [170] |
| 7 | Six hypermethylated CpGs sites | A combination of six hypermethylated HCC-specific CpGs sites has a 92% sensitivity predicting HCC, and 98% specificity differentiating from normal liver or other cancers | [171] | |
| 8 | Long interspersed element-1 (LINE-1) | + | Global hypomethylation measured in LINE-1 repeats in blood leukocytes DNA correlates with elevated risk of HCC (p = 0.004) | [172] |
| 9 | RASSF1A sequence | + |
Higher methylation in HCC (64.2%) than patients with LC (17.5%), CHB (5.0%) and healthy individuals (0). Associated with a worse OS (p < 0.05) |
[173] |
| 10 | CDH1, DNMT3b, ESR1 promoter | + |
Higher methylation in HBV-related HCC compared with LC, CHB and NC. Combined methylation is a better diagnostic marker than AFP. |
[174] |
| 11 | RASSF1A, E-Cadherin, RUNX3 | + |
Hypermethylation in HCC higher than cirrhosis and healthy group (p < 0.001). RASSF1A and E-Cadherin were predictors of HCC within cirrhosis cases. |
[175] |
| 12 | Methylated p16 | + |
Methylated p16 is higher in HCC than CHC, cirrhosis and healthy subjects Higher in patients with normal AFP than higher AFP |
[176] |
| 13 | TLX1, GALR1, ZNF154 | + | Multi-cancer methylation biomarkers combining three methylation markers have a sensitivity and specificity of 37.3% and 83.3% on HCC respectively. | [177] |
| 14 | 38 DNA methylation regions | + | Machine learning method for systematic analysis with a 96% of sensitivity and 98% of specificity in an independent training cohort. | [178] |
| 15 | Enzymatic methyl sequencing | + | Sequencing utilizing enzymatic conversion of unmethylated bases as a screening model to distinguish HCC patients from non-HCC individuals | [179] |
| 16 | TGR5 | + |
Hypermethylation of the TGR5 promoter is significantly higher in HCC than CHB and HCs (p < 0.01) Increased sensitivity when combined with AFP |
[111] |
| 17 | RASSF1A promoter | Hypermethylation of RASSF1A in HCC, but not NC. Reduced RASSF1A is related to TNM stage, metastasis, AFP, portal vein embolus, capsular infiltration, and multiple tumor nodes. | [180] | |
| 18 | UBE2Q1 | + | Hypomethylation of UBE2Q1 in HCC than LC (p = 0.026), CHB (p = 0.006), and HCs (p = 0.011). Negatively associated with TNM stage. Increase sensitivity with AFP combined. | [113] |
| 19 | SEPT9 | + | Increase methylation of SEPT9 in HCC than at-risk and healthy individuals (p < 0.0001) | [181] |
| 20 | INK4A | + | Hypermethylated INK4A in HCC than controls | [116] |
| 21 | ELF, RASSF1A, p16, GSTP1 | Hypermethylation in tumor than non-tumor tissues (p < 0.05), and also combined markers (p < 0.001). Increase sensitivity with AFP combined | [182] | |
| 22 | APC, GSTP1, FASSF1A, SFRP1 | + |
Hypermethylation in all four genes in HCC than normal or benign controls. Methylated RASSF1A is a prognostic marker of overall survival. |
[183] |
| 23 | APC | Methylation status of APC complement with AFP to predict HCC | [184] | |
| 24 | MT1M and MT1G | + |
Hypermethylated MT1M and MT1G in HCC than CHB and NC group (p < 0.001), with a specificity of 94.6%. MT1M promoter methylation positively correlates with tumor size (p < 0.001), and metastasis when combined with MT1G. |
[185] |
| 25 | P16 | + | P16 methylation increases from benign liver disease to HCC progression. | [186] |
| 26 | HOXA1, TSPYL5, B3GALT6 | + | The multi-target HCC blood test utilized three methylation markers and demonstrated high concordance (> = 97%) to predict HCC without significant interference observed. | [187] |
| 27 | Methylation Fingerprint Panel | + | The study identified three panels: cancer-specific biomarker panels, a pan-GI panel, and a multi-cancer prediction panel, with high AUC values ranging from 0.85 to 0.98 for detecting various gastrointestinal cancers. | [118] |
| 28 | RNF135, LDHB | + | Combined RNF135 and LDHB methylation level analysis has a sensitivity of 57% on HCC, compared with AFP at 45%. When combined with HCC, the sensitivity is 70%. | [119] |
| 29 | SEPT9 | + | A significantly higher copy number of methylated SEPT9 was observed in the HCC group than in the control group (p < 0.001) | [188] |
| 30 | SEPT9 | + | SEPT9 methylation pattern is a better predictor than serum AFP for diagnostic performance. | [189] |
| 31 | IGFBP7 | + | Frequency of serum IGFBP7 promoter methylation is higher in HCC than in CHB and HC controls (p < 0.001). | [190] |
| 32 | GNB4, Riplet | + | Circulating tumor cells combined with methylation patterns have a sensitivity of 88.2% and an AUC value of 0.98. | [124] |
| 33 | CCND1 | + | The methylation status of the CCND1 promoter outperforms serum AFP in both AUC and specificity to predict HBV-HCC versus CHB. | [191] |
| 34 | SOX1, VIM | + | Higher frequency of SOX and VIM promoter methylation than LC, CHB, and HC subjects (p < 0.001). | [192] |
| 35 | LINE-1, RASSF1A | + |
LINE-1 was hypomethylated in 66.7% and RASSFIA promoter was hypermethylated in 73.3% of HCC serum. Associated with HBsAg positivity, tumor size, AFP, and lymph node metastasis. |
[193] |
| 36 | BARD1, MAGEB3, BRUNOL5, FXYD6, TET1, TSPAN5, DPPA5, KIAA1210, and LSP1 | + |
Neighboring CpG sites on 9 genes are predictable for prospective HCC development from HBV-negative cirrhotic patients. DPPA5, KIAA1210, LSP1 are hypermethylated, while BARD1, MAGEB3, BRUNOL5, FXYD6, TET1, TSPAN5 are hypomethylated, compared with controls. |
[194] |
| 37 | EXO1 | DNA methylation status in five CpG islands of the EXO1 gene was associated with the prognosis of HCC | [195] | |
| 38 | Wnt/beta-catenin signaling pathway | + | Hypermethylation of Wnt/Beta-catenin signaling pathway is correlated with tumor size, TNM stage, distant metastasis, and HBV infection (p < 0.05). | [126] |
| 39 | SEPT9 | + | Serum methylated SEPT9 test has a high diagnostic accuracy for HCC on cirrhotic patients (AUROC 0.944, p < 0.0001), and is the only variable associated with HCC diagnosis in this cohort. | [196] |
| 40 | RASSF1A, SOCS1 | + | RASSF1A and SOCS-1 methylation were detected in 40% and 38% of HCC patients. RASSF1A/SOCS-1/AFP panel detects HCC at sensitivity of 86% and specificity of 75%. | [197] |
| 41 | CCND2 | + | CCND2 methylation is significantly higher in HCC patients (p < 0.001). Advanced HCC is associated with higher CCND2 methylation and lower CCND2 mRNA levels than early-stage disease. | [198] |
| 42 | GSTP1 | + | Higher GSTP1 promoter region methylation frequency in pre-ACHBLF patients compared to CHB and HCs. Lower GSTP1 mRNA levels in pre-ACHBLF patients. Increased ACHBLF incidence in pre-ACHBLF patients with methylated GSTP1. | [199] |
| 43 | MAGE-A1, MAGE-A3 | Different methylation patterns in several CpG sites among the MAGE-A1 and MAGE-A3 promoters in HCC cells. Clinical sensitivity and specificity were 91.2% and 100%. | [200] | |
| 44 | KLHL35, PAX5, PENK, and SPDYA | These genes are significantly more highly methylated in HCC than in non-cancerous liver tissue, irrespective of the hepatitis virus status. LINE-1 hypomethylation was prevalent in HCC. | [201] | |
| 45 | A1AT, SERPINA1 | + | More fully-methylated SERPINA1 promoters in control than HCC samples, and higher hemimethylation in stage I compared to stage II and III HCC. Higher AFP and A1AT levels in hemimethylated patients (p < 0.001). | [202] |
| 46 | TFPI2 | Methylation of TFPI2 gene was detected in 44.9% of primary HCC samples, 10.7% of the corresponding non-tumorous liver samples, and 5.0% of the normal liver samples. Lower expression of TFPI2 is correlated with TNM stage, and methylation is associated with poorer prognosis (p < 0.001). | [203] | |
| 47 | RUNX3, p16, RASSF1A, CDH1 | + | 88%, 100%, 50%, and 13% of HCC patients were detected with hypermethylation of RUNX3, p16, RASSF1A and CDH1. The inclusion of RUNX3 in the gene panel can potentiate the detection of advanced cancer. | [204] |
| 48 | MAPK10 | Methylation of MAPK10 detected in 58% of HCC cell lines, and 666% of primary HCC tissues, results in downregulated expression of MAPK10 proteins. | [205] | |
| 49 | SOX11 | + | Higher methylation of SOX11 promoter in HCC patients (69.4%) compared to CHB patients (13.6%) and healthy controls (10.7%). Significant difference in SOX11 promoter methylation between HCC patients with vascular invasion and those without. SOX11 methylation demonstrates a 69% sensitivity in distinguishing HCC from CHB, higher than the 57% sensitivity of serum AFP. | [206] |
| 50 | HCCS1 | + | HCCS1 promoter methylation frequency higher in HCC patients compared to CHB patients and healthy controls (P < 0.001). HCCS1 promoter methylation associated with TNM stage (P = 0.01). 62.5% sensitivity for serum HCCS1 promoter methylation in discriminating HCC from CHB, compared to 55% for AFP alone, and sensitivity combined with AFP level is 81.7%. | [207] |
| 51 | Sat2 | Correlation between hypomethylation Sat2 with a breakpoint in chromosome 1(p < 0.001). Sat2 demethylation play a role in early stage of liver carcinogenesis. | [208] | |
| 52 | Sat2, LINE-1 | Sat2 hypomethylation associated with HCC risk. LINE-1 is not associated with HCC risk by age. Decrease in Sat2 methylation and LINE-1 hypomethylation associated with increased risk of HCC for HBsAg carriers. | [209] | |
| 53 | Sat2, LINE-1 | + | Negative relationship between urinary aflatoxin B albumin levels and LINE-1 and Sat2 methylation. It is associated with the risk of HCC development. | [210] |
| 54 | SFRP2 | + | SFRP2 methylation levels significantly higher in patients with HBV-HCC than in those with CHB and healthy controls (p < 0.001). SFRP2 mRNA level significantly lower in HCC group compared to the others (p < 0.05). SFRP2 methylation level showed better diagnostic value than AFP. | [211] |
| 55 | SGIP1 | + | Elevated levels of SGIP1 methylation in HCC patients associated with poorer OS, PFS, and MFS compared to those with low levels (p < 0.05). | [212] |
| 56 | SCAND3, Myo1g | + | SCAND3 and Myo1g methylation were high in HCC cell lines and tissues, and serum SCAND3, Myo1g, and SCAND3 + Myo1g methylation values showed better detection and early detection of HCC than AFP alone. In the AFP-negative HCC group, SCAND3 and Myo1g methylation also can predict diagnosis. | [213] |
| 57 | LZP | Methylation of LZP promoter decreases mRNA expression, and is negatively related to the HCC status. | [214] | |
| 58 | ATM | Higher ATM promoter methylation in HCC tissues, and associated with ATM expression (p < 0.001). Methylation of ATM promoter associated with better outcomes in locally advanced HCC patients who received radiotherapy | [215] | |
| 59 | IL-6 | + | IL-6 promoter methylation levels lower in HCC patients than in CHB patients (p < 0.001). IL-6 promoter methylation level is an independent factor in HCC development, and its diagnostic value is superior to AFP. Combined use of AFP and IL-6 methylation level improves AUC (0.773). | [216] |
| 60 | CDO1 | + | CDO1 promoter methylation frequency higher in HBV-related HCC than in LC, CHB, and healthy controls (p < 0.001). Higher frequency of CDO1 promoter methylation in advanced stages HCC compared to early stages. Improved diagnostic value combined with serum AFP. | [217] |
| 61 | CDH13 | + | Higher methylation frequency of CDH13 promoter in HCC patients compared to NCs and CHB groups (p < 0.05). Methylation level of CDH13 promoter influenced by TBil, ALB, and AFP. Combined methylated CDH13 level and AFP level show better diagnostic score (AUC = 0.796). CDH13 methylation is an independent predictor for HCC prognosis (p < 0.05). | [218] |
| 62 | FES | FES hypermethylation correlated with tumor size, serum AFP, and tumor differentiation (p < 0.005). Both FES hypermethylation and protein downregulation associated with PFS and OS of HCC patients. | [219] | |
| 63 | NLRP7, NLRP2, NLRP3 | + | Hypomethylation of programmed-cell death genes (PRGs) including NLRP7, NLRP2, and NLRP3 in HCC tissues; NLRP3 methylation levels correlated with expression level (r = 0.51). Hypomethylated PRGs can discriminate between early HCC patients and healthy controls in cfDNA analysis (AUC = 0.94), and associated with poor HCC prognosis. | [142] |
| 64 | DBX2, THY1 | + | DBX2 and THY1 are hypomethylated in HCC. Diagnostic sensitivity and specificity of DBX2 for differentiating healthy controls and early stage HCC were 88.89% and 87.10% respectively. Diagnostic sensitivity and specificity of THY1 were 85.19% and 80.65% respectively. | [220] |
| 65 | F-box protein 43 promoter | + | F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than in chronic hepatitis B and healthy control PBMCs (P < 0.001). This was superior to those of AFP levels in the diagnosis of HCC. Combination of F-box protein 43 promoter methylation and AFP levels improved the AUC to 0.888 with sensitivity of 76.42% and specificity of 86.08%. | [221] |
| 66 | RASSF1A, p16, p15 | + | Abnormal methylation was found in blood samples 1 to 9 years before HCC was diagnosed. RASSF1A had the highest rate of increased methylation (70%), followed by p16 (44%) and p15 (22%). Combined risk factors and methylation markers, the accuracy of predicting HCC was 89%, with 84% sensitivity and 94% specificity | [222] |
| GNB4, Riplet | + | In tissue validation, GNB4 and Riplet had an AUC of 100%, with 100% sensitivity and specificity for detecting any-stage HCC. In blood tests, this combination showed a high sensitivity of 84.39% and specificity of 91.92%, with an AUC of 92.51% for detecting any-stage HCC. The dual-marker panel was more sensitive for detecting stage I HCC than AFP. It had a high sensitivity (70.27%) for detecting a single tumour of size 3 cm or less. | [144] |