Characterization of the genotype and integration patterns of hepatitis B virus in early‐ and late‐onset hepatocellular carcinoma : Hepatology

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Viral Hepatitis

Characterization of the genotype and integration patterns of hepatitis B virus in early‐ and late‐onset hepatocellular carcinoma

Yan, Hongli1,3,†; Yang, Yuan2,†; Zhang, Ling1; Tang, Guannan1; Wang, YuZhao1; Xue, Geng1; Zhou, Weiping2; Sun, Shuhan*,1

Author Information
Hepatology 61(6):p 1821-1831, May 20, 2015. | DOI: 10.1002/hep.27722



In the June 2015 issue of Hepatology, in the article titled “Characterization of the Genotype and Integration Patterns of Hepatitis B Virus in Early‐ and Late‐Onset Hepatocellular Carcinoma” (volume 61, pages 1821‐1831; doi: 10.1002/hep.27722), by Hongli Yan, Yuan Yang, Ling Zhang, Guannan Tang, YuZhao Wang, Geng Xue, Weiping Zhou, and Shuhan Sun, the institutions that the authors are affiliated with were listed in the wrong order. They should have been written as “1Department of Laboratory Medicine, Changhai Hospital, The Second Military Medical University, Shanghai, China; 2Department of Medical Genetics, Second Military Medical University, Shanghai, China; and 3The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.” Hongli Yan is affiliated with numbers 1 and 2; Ling Zhang, Guannan Tang, YuZhao Wang, Geng Xue, and Shuhan Sun are affiliated with number 2; and Yuan Yang and Weiping Zhou are affiliated with number 3.

Hongli Yan should also have been listed as a corresponding author, with contact information as follows: Department of Laboratory Medicine, Changhai Hospital, The Second Military Medical University, Shanghai, China; E‐mail: [email protected].

We apologize for this error.

Hepatology. 63(3):1064, March 2016.

Potential conflict of interest: Nothing to report.

This work was funded by the National Natural Science Foundation of China (No. 30801328, 81472770), Science Fund for Creative Research Groups (No. 81221061, 81201940), Shanghai Pujiang Project, and New Excellent Youth Plan (XYQ2013074) for financial support.

Hepatocellular carcinoma (HCC) is a common solid tumor and the third leading cause of cancer death worldwide.1 Hepatitis B virus (HBV) is a major etiological agent in China, Southeast Asia, and sub‐Saharan Africa, and individuals with chronic HBV infection are at increased risk of developing HCC, particularly those with chronic liver disease and cirrhosis.2 Average age at onset of HBV‐associated HCC is 50 years3; thus, the recommendations advise HCC screening for Asian male HBV patients older than 40 and Asian female HBV patients older than 50.5 Nonetheless, incidence of HCC in patients younger than 40, especially in high‐risk populations, is relatively high.6 Recent studies have reported a significant prevalence and worse prognosis in early‐onset HCC patients,8 suggesting that there may be different mechanisms of hepatocarcinogenesis between early‐ and late‐onset HCC.10 However, there are limited studies focusing on the etiology of early‐onset HCC.

Given that the hepatocarcinogenic process involves interplay between HBV and host hepatocytes, both genomes may contribute to the final pathogenic outcomes, either individually or synergistically. With regard to the hepatitis B viral factors, the genotype has been increasingly recognized as affecting the clinical outcome of chronic HBV infection, including cirrhosis and HCC.11 Some data have associated genotype B HBV with the development of HCC in young carriers in Taiwan,13 and Livingston et al.14 found that median age of HCC patients with genotype F was much lower than that of patients with other genotypes, indicating that the HBV subgenotype might contribute to early onset of HCC.

In addition, a major proposed pathway by which HCC may arise from chronic HBV infection is integration of HBV DNA into the host genome, resulting in oncogene activation, tumor‐suppressor gene inactivation, or other predisposition to chromosomal instability.15 Many studies have detected evidence of HBV DNA integrated specifically into HCC cells, supporting the hypothesized role of HBV‐DNA integration in hepatocarcinogenesis. However, although conventional polymerase chain reaction (PCR)‐based methods, such as Alu‐HBV PCR, can be used to detect the presence of viral integration, these methods are significantly biased toward Alu regions, and only a small subset of insertions can be detected or only insertions close to viral sequences can be found.16

To investigate the mechanisms underlying early‐onset HCC, we characterized the integration patterns and genotypes of HBV in early‐ and late‐onset HCC patients. We used a high‐throughput viral integration detection (HIVID) method that can effectively detect HBV integration at a single base‐pair (bp) resolution.19 We found that HBV B2 is predominantly present in early‐onset HCC, whereas HBV C2 is mainly found in late‐onset HCC. HBV integration was also found to be a common phenomenon, even in early‐onset HCC, but the hotspots between early‐ and late‐onset disease are rather different. A breakpoint between c‐Myc and PVT1, located in the 8q24 gene desert, was frequently detected in early‐onset HCC, resulting in overexpression of c‐MYC, plasmocytoma variant translocation 1 (PVT1), and microRNA (miR)−1204 in tumors that might contribute to the development of early‐onset HCC.

Materials and Methods

HCC Patient Samples

For HBV genotype analysis, we thoroughly studied 258 Chinese individuals diagnosed with HCC who underwent curative primary hepatectomy at Eastern Hepatobiliary Surgery Hospital (Shanghai, China). Demographic and clinicopathological data for these individuals are summarized in Table 1. These patients were divided into two groups: 113 early‐onset HCC (diagnosis at age <30) and 145 late‐onset HCC (diagnosis at age ≥70). All patients had been diagnosed with HCC with concurrent HBV infection and without for autoimmune hepatitis and metabolic and/or genetic disorders, such as Wilson's disease, hemochromatosis, and primary biliary cirrhosis. No patient had a history of alcoholism, aflatoxin exposure, or hepatitis C virus (HCV) coinfection. Patients with liver cirrhosis (LC) were diagnosed on the basis of histological findings as diffuse fibrosis and formation of pseudolobuli, as well as ultrasonic features of LC plus evidence of hyperplenism. The study protocol conformed to the 1975 Delcaration of Helsinki and was approved by the ethics committees of the Second Military Medical University (Shanghai, China), and an informed written consent was obtained from each patient.

Table 1 - Clinicopathological Features of Patients With HCC for Genotype and Integration Analysis
HBV Genotype Analysis HBV Integration Analysis
Early‐Onset (n = 113) Late‐Onset (n = 145) P Value Early‐Onset (n = 30) Late‐Onset (n = 30) P Value
Age, years 22.8 ± 6.5 72.8 ± 8.0 20.6 ± 4.2 74.2 ± 3.0
Gender (%) NS NS
Male 102 (90.3) 128 (88.3) 24 (80) 26 (86.7)
Female 11 (9.7) 17 (11.7) <0.01 6 (20) 4 (13.3) <0.01
Genotype (%)
A 3 (2.7) 8 (5.5) 0 0
B2 54 (47.8) 38 (26.2) NS 22 (73.3) 6 (20) NS
C1 18 (15.9) 12 (8.3) NS 8 (26.7) 24 (80) NS
C2 38 (33.6) 87 (60.0) 0 0
Tumor size, cm 8.8 ± 2.3 8.7 ± 3.0 NS 8.4 ± 2.8 8.6 ± 1.2 NS
Tumor number (%)
Single 82 (72.6) 108 (74.4) NS 22 (73.3) 21 (70.0) NS
Multiple 31 (27.4) 37 (25.6) NS 8 (26.7) 9 (30) NS
Alpha‐fetoprotein, ng/mL (%) NS NS
≥400 56 (49.5) 78 (53.8) NS 14 (46.7) 15 (50.0) NS
<400 57 (50.5) 67 (46.2) NS 16 (53.3) 15 (50.0) NS
Albumin, g/dL 3.7 ± 4.9 3.9 ± 3.7 <0.001 3.6 ± 4.2 3.4 ± 2.8 <0.01
Platelets, 103/uL 183.7 ± 62.4 192.3 ± 79.6 NS 176.4 ± 48.2 188.0 ± 72.4 NS
Alanine aminotransferase, u/L 58.5 ± 55 62.4 ± 49 60.2 ± 45 64.3 ± 38
Total bilirubin, umol/L 14.8 ± 4.8 15.1 ± 7.8 NS 14.6 ± 3.1 14.8 ± 6.2 NS
Prothrombin time, seconds 13.2 ± 2.3 13.4 ± 1.4 NS 13.3 ± 1.4 13.6 ± 1.8 NS
Cirrhosis (%) 72 (63.7) 121 (83.4) 19 (63.6) 24 (80.0)
Child‐Pugh class (%) NS NS
A 103 (91.2) 139 (96) NS 26 (86.7) 27 (90.0) NS
B 10 (8.8) 6 (4.0) <0.001 4 (12.3) 3 (10.0) <0.001
HBeAg positivity 65 (57.5) 77 (53.1) NS 16 (53.3) 14 (46.7) NS
Preoperative DNA level, IU/mL (%)
≤1,000 69 (61.1) 86 (59.3) 17 (56.7) 16 (53.3)
>1,000 44 (38.9) 59 (40.7) 13 (43.3) 14 (46.7)
Presence of satellite nodules (%) 16 (14.2) 23 (15.9) 3 (10.0) 4 (13.3)
Presence of vascular invasion 12 (10.6) 11 (7.6 %) 5 (16.7) 4 (13.3)
Median survival time (months) 22.0 ± 9.8 44.1 ± 14.2 19.0 ± 10.4 40.3 ± 13.8
BCLC stage (%)
0 12 (10.6) 18 (12.4) 4 (13.3) 3 (10)
A 60 (53.1) 66 (45.5) 16 (53.3) 14 (46.7)
B 31 (27.4) 44 (30.3) 8 (26.6) 10 (33.3)
C 10 (9.7) 17 (11.7) 2 (6.6) 3 (10.0)
Abbreviations: HBeAg, hepatitis B envelope antigen; BCLC, the Barcelona‐Clínic Liver Cancer (BCLC) staging system; NS, not significant. P value <0.05 is shown in bold.

We randomized selected 30 patients in the early‐onset group and 30 patients in the late‐onset group for HBV capture sequencing analysis. Demographic and clinicopathological data for these individuals are also summarized in Table 1.

HBV Capture Sequencing

We used HIVID to detect HBV integration.19 Experimental procedures are described in Fig. 1 and Supporting Materials and Methods.

Figure 1:
Experimental process of HBV virus capture sequencing.
Figure 2:
Distribution of genotypes of HBV in early‐ and late‐onset patients.

PCR and Sanger Sequencing Validation

PCR primers giving products of approximately 200 bp were designed to capture the breakpoints of each HBV integration site. All PCR experiments were performed with tumors on a GeneAmp PCR System 9700 thermal cycler (Life Technologies, Grand Island, NY). For each PCR product, we used Applied Biosystems (Foster City, CA) 3730 DNA analyzers to perform dye terminator Sanger sequencing.

Genotyping of HBV

Determination of HBV genotypes and subgenotypes HBV DNA was extracted from 200 uL of serum of HCC patients using High Pure Viral Nucleic Acid kits (Roche Diagnostics GmbH, Roche Applied Science, Penzberg, Germany) according to the manufacturer's instruction. Tumor samples were also used as the sources of HBV DNA if insufficient serum was obtained. HBV genotypes and subgenotypes were determined by using a multiplex PCR assay.12 HBV genotypes of samples with low levels of HBV DNA were identified by nested multiplex PCR.

RNA Isolation and Quantitative Real‐Time Reverse‐Transcriptase PCR

RNA from tumor (T) and paired adjacent nontumor (NT) samples were isolated as described in a previous work.21 Real‐time PCR was performed using complementary DNA as a template and a standard SYBR‐Green PCR kit on a StepOne Plus system (detailed in Supporting Materials and Methods).

Statistical Analysis

Data are presented as means ± standard deviation for continuous data frequency (n) and percentage for categorical data. To compare the values between the two groups, chi‐square or Fisher's exact tests were performed for categorical variables, as appropriate. Mann‐Whitney's U test was used for continuous variables. All statistical tests were two sided. P < 0.05 was considered statistically significant. All statistical analyses were performed using SPSS 18 for Windows (SPSS, Inc., Chicago, IL).


Subgenotype B2 Is Predominately Found in Early‐Onset Patients

We surveyed HBV genotypes using DNA extracted from serum or tumor tissues of 113 early‐onset (≤30) and 145 late‐onset (≥70) patients with HBV‐associated HCC who underwent curative primary hepatectomy in Eastern Hepatobiliary Surgery Hospital. Demographic and clinicopathological data for these individuals are summarized in Table 1. Compared with late‐onset patients, early‐onset HCC patients display a reduced incidence of cirrhosis (63.7% vs. 83.4%; P < 0.001). In addition, although no significant differences in the male‐to‐female ratios, tumor size and number, and other clinicopathological features were observed in the early‐ and late‐onset groups, median survival time for early‐onset patients was significantly reduced, compared with late‐onset patients (P < 0.001; Table 1).

Of the 258 patients with HBV‐associated HCC, we found 11 (4.3%) patients infected with HBV genotype A, 92 (35.7%) with subgenotype B2, 30 (3.9%) with subgenotype C1, and 125 (48.4%) with subgenotype C2. These results indicate that subgenotypes B2 and C2 are the predominant subgenotypes in East China. Intriguingly, compared with the late‐onset patients, subgenotype B2 was found in 47.8% (54 of 113) of the early‐onset patients, though in only 26.2% (38 of 145) of the late‐onset group. In contrast, subgenotype C2 was found in 33.6% (38 of 113) of the early‐onset patients and was significantly increased to 60% (87 of 145) in the late‐onset patients. These data suggested that HBV subgenotype distribution in early‐ and late‐onset HCC was significantly different (P < 0.01), consistent with data from patients in Taiwan12 and Eastern China.22

HBV Integration Commonly Occurs in Both Early‐ and Late‐Onset HCC

Case‐control studies demonstrate that the HBV genotype C is associated with an increased risk of HCC, compared with the genotype B in Japan23 and Taiwan.12 However, median survival time suggests a poorer early‐onset HCC prognosis, compared with the late‐onset group. These seemingly contradictory results imply that the mechanisms underlying early‐ and late‐onset HCC development might differ.

To investigate whether HBV integration contributes to early‐onset HCC, we randomly selected 30 patients in the early‐onset group and 30 in the late‐onset group and detected HBV integration events in early‐ and late‐onset HCC tumors using an unbiased HIVID. For comparison and analysis purposes, we ensured that the major clinicopathological features, such as ratio of LC, between individuals for HIVID and individuals for HBV genotype analysis are consistent (Table 1).

We first extracted tumor genomic DNA (gDNA) from 30 early‐onset and 30 late‐onset HCCs. Each group was divided into six pooled samples containing an equal amount of gDNA from 5 HCC tumors. Then, we detected HBV integration breakpoints in pooled samples by HIVID. We generated ∼1.8 Gb of sequence data for each pooled sample. Approximately 9 million paired‐end reads were obtained in the analysis. Approximately 85.6% and 0.09% of these reads were aligned to the human genome and HBV genome, respectively. The ratio of the reads mapped to human genome to the HBV genome is 951 (85.6%/0.09%). Given that the human genome is approximately 106‐fold greater than the HBV genome, HBV sequences are significantly increased after HBV capturing. Finally, after paired‐end assembly and remapping, we obtained an average of 1,928 reads supporting HBV integration breakpoints for each pooled sample.

A total of 97 HBV integration breakpoints were detected in six pooled early‐onset samples and 104 integration events in six late‐onset samples by HIVID, with each supported by at least two paired‐end reads. Next, we detected the integration sites obtained from the pooled samples in each separate sample using PCR and sequencing. We successfully validated 74.3% (72 of 97) breakpoints in 23 early‐onset HCC patients and 81.6% (84 of 104) breakpoints in 27 late‐onset patients as real integration sites, indicating that this approach has a high sensitivity and specificity for the detection of HBV integration.

HBV integration events were detected in 76.7% (23 of 30) of early‐onset HCC patients, and the average number of integration breakpoints in early‐onset HCC is 3.13 (range, 1‐6). In late‐onset HCC, the integration detection rate is 90% (27 of 30), and the average number of integration breakpoints is 3.11 (range, 1‐5). Collectively, these results suggest that HBV integration commonly occurs in both early‐ and late‐onset HCC (Supporting Tables 1 and 2).

Table 2 - Recurrent Hotspots of HBV Integration in Late‐ and Early‐Onset Groups
Gene Human_Position Function Virus_Position Affected HBV Gene Affected Patients
Late‐onset group
STAT1 chr2: 191836387 Intronic 3215 Polymerase; pre‐S1/pre‐S2/S G‐17T
chr2: 191836431 Intronic 2936 Polymerase; pre‐S1/pre‐S2/S G‐21T
chr2: 191836431 Intronic 1403 Polymerase; X protein G‐11T
chr2: 191836589 Intronic 1412 Polymerase; X protein G‐23T
ALB chr4: 74271597 Intronic 24 Polymerase; pre‐S1/pre‐S2/S G‐3T
chr4: 74271706 Intronic 2936 Polymerase; pre‐S2/S G‐7T
chr4: 74271597 Intronic 24 Polymerase; pre‐S1/pre‐S2/S G‐9T
chr4: 74271706 Intronic 2936 Polymerase; pre‐S2/S G‐27T
TERT chr5: 1295378 Promoter 1560 Polymerase; X protein G‐2T
chr5: 1295468 Promoter 2318 Polymerase; pre‐core/core G‐5T
chr5: 1295741 Promoter 1831 X protein; pre‐core/core G‐1T
chr5: 1295737 Promoter 1817 X protein; pre‐core/core G‐13T
chr5: 1295549 Promoter 911 Polymerase G‐16T
chr5: 1295500 Promoter 460 Polymerase; S G‐18T
chr5: 1295541 Promoter 1442 Polymerase; X protein G‐14T
chr5: 1295534 Promoter 1288 Polymerase G‐22T
chr5: 1295529 Promoter 1136 Polymerase G‐19T
chr5: 1295516 Promoter 400 Polymerase; S G‐24T
chr5: 1295379 Promoter 1561 Polymerase; X protein G‐23T
ST18 chr8: 53048426 Intronic 1589 Polymerase; X protein G‐25T
chr8: 53048618 Intronic 510 Polymerase; S G‐17T
chr8: 53048633 Intronic 1468 Polymerase; S G‐15T
chr8: 53048633 Intronic 630 Polymerase; S G‐28T
STXBP4 chr17: 53048162 Intronic 1461 Polymerase; X protein G‐25T
chr17: 53048221 Intronic 1342 Polymerase G‐29T
PCMTD2 chr20: 62918375 Intronic 1818 pre‐core/core; X protein G‐6T
chr20: 62918250 Intronic 666 Polymerase; S G‐7T
chr20: 62918250 Intronic 1486 Polymerase; X protein G‐21T
MLL4 chr19: 36212641 Intronic 1467 Polymerase; X protein G‐1T
chr19: 36212743 Intronic 400 Polymerase; S G‐10T
chr19: 36212721 Intronic 504 Polymerase; S G‐21T
chr19: 36212743 Intronic 446 Polymerase; S G‐27T
GPR116 chr6: 46816782 Promoter 489 Polymerase; S G‐21T
chr6: 46816782 Promoter 2225 pre‐core/core G‐1T
chr6: 46816770 Promoter 1244 Polymerase G‐20T
Early‐onset group
FN1 chr2: 216248136 Exonic 2010 pre‐core/core L‐12T
chr2: 216248919 Exonic 1932 pre‐core/core L‐14T
chr2: 216248944 Intronic 967 Polymerase L‐24T
chr2: 216248976 Intronic 2032 pre‐core/core L‐27T
SYT12 chr11: 66807124 Intronic 1314 Polymerase L‐11T
chr11: 66807269 Intronic 1589 Polymerase; X protein L‐7T
MYC/PVT1 chr8: 128764911 Integenic 660 Polymerase; S L‐15T
chr8: 128764911 Integenic 660 Polymerase; S L‐17T
chr8: 128764911 Integenic 660 Polymerase; S L‐5T
chr8: 128764911 Integenic 660 Polymerase; S L‐16T
chr8: 128764911 Integenic 660 Polymerase; S L‐22T
chr8: 128764911 Integenic 660 Polymerase; S L‐29T
chr8: 129229133 Integenic 2387 Polymerase L‐21T
GATM chr15: 45663260 Intronic 1798 X protein L‐19T
chr15: 45663260 Intronic 757 Polymerase L‐23T
chr15: 45661997 Intronic 92 Polymerase; Pre‐S2/S, S L‐26T
ME1 chr6: 83965334 Intronic 835 Polymerase; S L‐3T
chr6: 83965334 Intronic 1825 pre‐core/core; X protein L‐6T
Abbreviations: PCMTD2, protein‐L‐isoaspartate (D‐aspartate) O‐methyltransferase domain containing 2; GPR116, G‐protein‐coupled receptor 116; ME1, malic enzyme 1.

Chronic infection with HBV is associated with increased risk for development of cirrhosis and HCC. However, the relationship between HBV‐DNA integration and cirrhosis remains uncertain and controversial. Of the 23 early‐onset HCC with detected HBV integration, only 56.5% (12 of 23) have cirrhosis, indicating that HBV integration often occurs in patients without cirrhosis.

HBV Preferentially Integrates Into 8p11 and 8q24 in Early‐Onset HCC

Circos plots were employed to visualize and analyze HBV integration patterns at the chromosomal level in early‐ and late‐onset HCC (Fig. 3A,B). Although the detected HBV integration breakpoints in early‐ and late‐onset HCC were both distributed across the entire genome, the hotspots of integration were different (Fig. 3C). Of note, we discovered that 29.2% (21 of 72) of integration sites in early‐onset HCC were localized on chromosome 8. These integration sites are mainly located in 8p11 (5 of 21; 23.8%), a frequent target of genetic alterations in a wide variety of human cancers, including HCC and breast cancer,25 and the 8q24 gene desert (8 of 21; 38.1%), a region involved in susceptibility to various cancers27 (Fig. 4A; Supporting Tables 1 and 2).

Figure 3:
Distribution of HBV integration breakpoints on early‐ (A) and later‐onset (B) HCC genome. In this CIRCOS figure, we show the human chromosomes and the integration frequency of each breakpoint on the level of supporting reads as well as on the level of samples. The outer circle represents 24 chromosomes with different color codes and numbers labeled. Each bar represents the frequency of HBV integration breakpoints at a particular locus in the human genome (hg19). Red and blue bars correspond to the HBV integration events at the RefGene (exons, introns, and promoter) and intergenic regions, respectively.

Genes near these breakpoints in the human genome were annotated using the University of California San Francisco (UCSC) Genome Browser (GRCh37/hg19). The genic region was defined as the combination of promoters (5 kilobases [kb] upstream of the transcription start sites, exons, introns, and 3' untranslated region), which is susceptible to the activation of proto‐oncogene expression or inactivation of tumor‐suppressor genes.28 Enrichment of the integration sites in the genic region was observed in 73.8% (62 of 84) in the late‐onset group and 54.2% (39 of 72) in the early‐onset group, suggesting that HBV integration mediated cis‐activation of proto‐oncogene or inactivation of tumor‐suppressor genes might play an important role in the development of HCC (Fig. 4B).

Figure 4:
(A) Distribution of HBV integration breakpoints on human chromosomes. (B) Pie charts show the proportion of HBV integration sites in genic and intergenic regions in the early‐ and late‐onset groups. (C) Proportion of integration breakpoints at human repeat regions and no human repeat regions. Human repeat sequence was annotated using the RepeatMasker program in the UCSC Genome Browser (GRCh37/hg19).

We found that 59.7% (43 of 72) and 53.5% (45 of 84) of integration sites in early‐ and late‐onset HCC, respectively, are located in human repeat sequences, such as long interspersed nuclear elements (LINE), short interspersed nuclear elements (SINE; which includes the Alu family), or simple repeats (microsatellites; Fig. 4C). Most of the integration sites located in human repeat sequences do not occur in genic regions; therefore, methods based on Alu PCR will not detect numerous HBV integration sites with important functions.

A handful of recurrent hotspots were observed in both early‐ and late‐onset HCC. Of them, fibronectin 1 (FN1), myeloid/lymphoid or mixed‐lineage leukemia 4 (MLL4), and telomerase reverse transcriptase (TERT) have been previously reported on, whereas synaptotagmin XII (SYT12) and glycine amidinotransferase (GATM), an intergenic site between C‐MYC and PVT1 in early‐onset HCC, and signal transducer and activator of transcription 1 (STAT1), albumin (ALB), suppression of tumorigenicity 18 (ST18), and syntaxin binding protein 4 STXBP4 in late‐onset HCC have not been reported on before (Table 2). The most noteworthy observation is that 20% (6 of 30) of tumors in the early‐onset group had HBV integrated sites in human chromosome 8q24, a large gene desert susceptible to chromosomal translocation and viral integration.27 More interestingly, five of the integration sites located between c‐Myc and PVT1 have the exact viral‐human flanking sequence (Fig. 6B). However, this integration site was not found in tumor samples from the late‐onset group. The integrate site was then examined in all the 113 early‐onset and 145 late‐onset HCC samples. In total, we found 12.4% (14 of 113) in early‐onset HCC, but only 1.4% (2 of 145) in late‐onset HCC have this integration site (P < 0.0001).

Integration Sites in the HBV Genome

We also investigated the characteristics of HBV integration breakpoints in the HBV genome (Fig. 5). Among these integration sites, 32.8% (25 of 76, early‐onset group) and 31.0% (26 of 84, late‐onset group) were significantly enriched in a 400‐bp region of the HBV genome from 1,600 to 2,000 bp, close to direct repeat 1 (DR1) and direct repeat 2 (DR2); (DR2), around the 3'‐end of the HBV x gene (HBx) and 5'‐end of the pre‐C/C genes. Consistent with the observation that higher proportion of integration sites occurring at the 3' of HBx gene, these findings were consistent with the results of the WGS study.29 Interestingly, our results also showed that 40.8% (31 of 76) of the breakpoints were located in the pre‐S region (400‐800 bp) in the early‐onset group, significantly higher than the 26.2% (22 of 84) in the late‐onset group (P < 0.001), which has not been reported on previously.

Figure 5:
Distribution of HBV integration breakpoints on the HBV genome. Frequency of integration breakpoints at different loci in the HBV genome (NC_003977) is shown. Locations of the genes encoding HBV polymerase, core, S, and X proteins are shown. Genomic positions are numbered.
Figure 6:
Influence of HBV integration on gene expression in HCC. HBV breakpoint sites on the recurrently affected genes were mapped to the human hg19 reference sequence. Each read ball represents the location of an HBV breakpoint identified. Chr, chromosome. Boxes represent exons, and open arrows show orientation of the genes. Expression of ALB (A), C‐Myc, and PVT1 (n = 16; B) in paired tumors and normal samples was analyzed by real‐time RT‐PCR and normalized to glyceraldehyde 3‐phosphate dehydrogenase expression. Relative levels of miR‐1204 expression were normalized to Hs_RNU6B. Data shown are mean ± standard error of the mean of three separate experiments.

Influence of HBV Integration on Gene Expression in HCC

We next investigated the possible cis‐activating effect of HBV‐DNA integration hotspots on expression of adjacent cellular genes. Compared with samples without these integration sites, HBV integration at the TERT promoter, MLL4 intron, and ALB intron increased gene expression in tumor samples, relative to paired nontumor samples (fold change, T/N>2; Fig. 6A and Supporting Fig. 1A,B).

In the early‐onset group, the recurrent hotspot located in 8q24 is embedded in a SINE repeat sequence (chr8:128764676‐128764961), which is approximately 11 kb downstream of c‐Myc and 30 kb upstream of PVT1. Previous studies have reported that viral integration and human chromosomal translocations can disrupt the expression of genes over hundreds of kilobases away. Therefore, we investigated the expression of c‐MYC, PVT1, and miR‐1204 in tumor samples, relative to paired nontumor samples by real‐time reverse‐transcription (RT)‐PCR analysis. Expression of c‐MYC and PVT1 and miR‐1204 in the 16 samples having the integration site were greatly higher than 7 tumors without this integration site (P < 0.001; Fig. 6B). Therefore, HBV integration into this site potentially contributes to the development of early‐onset HCC, which has not been previously reported on.


Early‐onset HCC accounts for 15%‐20% of total HCCs in Asia, and incidence is increasing. Although HBV infection is the most epidemiologically associated risk factor for early‐onset HCC, its role in hepatocarcinogenesis remains unclear. In the present study, we conducted a comparative analysis of the HBV subgenotype and integration in early‐onset (≤30) and late‐onset (≥70) HCC patients. To the best of our knowledge, this is the first intensive investigation of the role of HBV infection in early‐onset HCC. The present study may help to clarify HCC risk factors in young HBV carriers.

Some data associate genotype B with development of HCC in young HBV carriers. A 15‐year study of 460 carriers of HBV reported that genotype B was the most frequent genotype among 26 children with HBV‐related HCC (found in 74%),31 indicating that the HBV subgenotype might contribute to early‐onset HCC. Of note, the HBV subgenotype B2 distribution is significantly different in early‐ and late‐onset HCC (47.8% vs. 26.2%, respectively; P < 0.001) in our cohort. An epidemiological study with a large cohort including 81,775 patients from various geographical regions in mainland China4 reported that the predominant HBV genotypes found in Eastern China are B2 (25.7%) and C2 (66.2%). Given that the patients in our cohort are also from the same geographical region, the HBV subgenotype B2 is increased in early‐onset HCC, compared with the general distribution of HBV B2 in our geographical area (47.8% vs. 25.7%), indicating that the B2 subgenotype may serve as a risk factor in early‐onset HCC patients. This finding is consistent with the data from Taiwan and Mainland China, regions where genotype B was found to be predominant in younger HCC patients, at 90% in those <35 years of age and most without cirrhosis.16

A significant feature of chronic HBV infection is the integration of subgenomic HBV‐DNA fragments into different locations within the host DNA.32 Furthermore, chronic infection with HBV is associated with increased risk for development of cirrhosis and HCC. However, the role of HBV integration in HCC development remains uncertain. Theoretically, HBV integration is increased in late‐onset HCC given the increased time of HBV infection. Unexpectedly, a high frequency of HBV integration is reported to be more common in early‐onset HCC than in late‐onset HCC.33 We also observed that HBV integration is a common event in both early‐ and late‐onset HCC. Although the reason for the high‐frequency integration in early‐onset patients with HCC is unclear, these findings indicated that HBV integration might also play an important role in HCC development.

Previous studies have suggested that HBV DNA is randomly integrated into the human genome. However, it is important to note that these initial studies were limited by technological constraints to the analysis of only certain portions of the host genome and were also constrained by small sample sizes. Recent studies using the new technology of next‐generation sequencing (NGS) have suggested that HBV integration might accumulate at specific sites in HCC, such as the gene encoding human TERT, MLL4, cyclin E1, SUMO1/sentrin‐specific peptidase 1, and rho‐associated, coiled‐coil containing protein kinase 1.29 Our results also support the notion that HBV integration is not randomly distributed in the human genome. First, we found several recurrent hotspots both in early‐ (SYT12, GATM, and FN1) and late‐onset HCC (STAT1, ALB, MLL4, and TERT). MLL4, TERT, and FN1 have been previously reported as HBV integration hotspots.16 Second, HBV integration often occurs in the human repeat locus, such as LINE, SINE, or microsatellites; these regions are not randomly distributed in the human genome.

The most noteworthy observation is the recurrent hotspot in early‐onset HCC mainly located in 8p11 and 8q24. The short arm of chromosome 8p11‐12 is a frequent target of genetic alterations in a wide variety of human cancers.25 No oncogene from the 8p11‐12 amplification unit has been identified with certainty.26 A recent study by Lau et al.35 reported a recurrent HBV integration hotspot in HBV‐associated HCC, which is located in a LINE1 repeat region in Chr. 8p11 (chr 41,493,923‐41,494,302). This integration site was detected in 21 of 90 HCCs (23.3%). In all cases, the exact viral‐human flanking sequence was found. HBV integration into this site produces an oncogenic HBV‐LINE1 chimeric transcript that activates Wnt signaling and correlates with poorer patient survival.

The 8q24 region has been described as a “gene desert” because of the paucity of functionally annotated genes located within this region.36 However, genome‐wide association studies have identified a large number of single‐nucleotide polymorphisms in chr.8q24 that are linked to susceptibility for different diseases, including cancers of the prostate, breast, esophagus, head and neck, ovarian, colon, and pancreas.37 Interestingly, we also detected a hotspot in 8q24 (between c‐MYC and PVT1) in early‐onset HCC. We found that this integration site has a similar characteristic with the site reported by Lau et al.: They found that HBV integrated into LINE1 and the 5' HBV sequence shared a GTG sequence with the 3' end of the human LINE1. In our cohort, the integration site between c‐MYC and PVT1 is also located in a human SINE sequence (chr8:128764676‐128764961); in addition, 5' HBV sequence also shared a 3‐bp microhomogy sequence (CCA) with the 3' end of the human SINE. These findings provided evidence that HBV integration is not randomly distributed in the human genome, and the mechanism of HBV insertion into the host genome was likely generated by the mediation of microhomology during break‐induced replication repair.39

We found that HBV integration into this site correlates well with c‐MYC, PVT1, and miR‐1204 expression. PVT1 overexpression promotes tumorigenesis by inhibiting cell apoptosis in ovarian and breast cancer.40 In addition, PVT1 is a noncoding host gene that encodes six microRNAs (miR‐1204, −1205, −1206, 1207‐5p, miR‐1207‐3p, and −1208). miR‐1204 has been reported to be a candidate oncogene that enhances oncogenesis in combination with MYC.41 We found that this integration site was detected in 14 of the 113 early‐onset HCCs, whereas it was detected in only 2 of the 145 late‐onset HCC, strongly suggesting that HBV integration into this site potentially contributes to development of early‐onset HCC, which has not been previously reported on.

Several limitations in our study should be addressed. Because next‐generation sequencing remains expensive and cost prohibitive for sequencing a large number of samples, we used pooled samples for HIVID analysis; thus, various integrated breakpoints that occur at a low frequency are potentially missed. In addition, although we identified various distinct features in early‐ and late‐onset HCC groups, these findings need to be further investigated in a large cohort given the limited sample size. It remains unclear at which time in tumor development this integration event occurs and whether it plays an important, causative role in HCC development or progression; therefore, further studies are needed to elucidate the role of this integration site in HCC development or progression.


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