Document Detail

Variants Identified by Hepatocellular Carcinoma and Chronic Hepatitis B Virus Infection Susceptibility GWAS Associated with Survival in HBV-Related Hepatocellular Carcinoma.
Jump to Full Text
MedLine Citation:
PMID:  24987808     Owner:  NLM     Status:  In-Data-Review    
Recent genome-wide association studies (GWAS) have identified several common susceptibility loci associated with the risk of hepatocellular carcinoma (HCC) or chronic hepatitis B infection (CHB). However, the relationship between these genetic variants and survival of patients with hepatitis B virus (HBV)-related HCC is still unknown. In this study, 22 single nucleotide polymorphisms (SNPs) were genotyped among 330 HBV-related HCC patients using the MassARRAY system from Sequenom. Cox proportional hazards regression was used to examine the effects of genotype on survival time under an additive model with age, sex, smoking status and clinical stage as covariates. We identified four SNPs on 6p21 (rs1419881 T>C, rs7453920 G>A,rs3997872 G>A and rs7768538 T>C), and two SNPs on 8p12 (rs2275959 C>T and rs7821974 C>T) significantly associated with survival time of HBV-related HCC patients. Our results suggest that HCC or CHB susceptibility loci might also affect the prognosis of patients with HBV-related HCC.
Cong Li; Xinyu Bi; Ying Huang; Jianjun Zhao; Zhiyu Li; Jianguo Zhou; Meng Zhang; Zhen Huang; Hong Zhao; Jianqiang Cai
Related Documents :
24889558 - Associations between human trim22 gene expression and the response to combination thera...
22006408 - The protease inhibitor, gs-9256, and non-nucleoside polymerase inhibitor tegobuvir alon...
24714408 - Pretreatment serum interleukin-12 levels in predicting sustained virological response a...
25000718 - Cloacolithiasis and intestinal lymphosarcoma in an african black-footed penguin (spheni...
9502468 - Characteristics of patients with chronic infection due to hepatitis c virus of mixed su...
19807338 - Cost-effectiveness of managing hiv infection.
Publication Detail:
Type:  Journal Article     Date:  2014-07-02
Journal Detail:
Title:  PloS one     Volume:  9     ISSN:  1932-6203     ISO Abbreviation:  PLoS ONE     Publication Date:  2014  
Date Detail:
Created Date:  2014-07-03     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101285081     Medline TA:  PLoS One     Country:  United States    
Other Details:
Languages:  eng     Pagination:  e101586     Citation Subset:  IM    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Full Text
Journal Information
Journal ID (nlm-ta): PLoS One
Journal ID (iso-abbrev): PLoS ONE
Journal ID (publisher-id): plos
Journal ID (pmc): plosone
ISSN: 1932-6203
Publisher: Public Library of Science, San Francisco, USA
Article Information
Download PDF
Copyright: 2014 Li et al
Received Day: 4 Month: 5 Year: 2014
Accepted Day: 8 Month: 6 Year: 2014
collection publication date: Year: 2014
Electronic publication date: Day: 2 Month: 7 Year: 2014
Volume: 9 Issue: 7
E-location ID: e101586
PubMed Id: 24987808
ID: 4079718
Publisher Id: PONE-D-14-19915
DOI: 10.1371/journal.pone.0101586

Variants Identified by Hepatocellular Carcinoma and Chronic Hepatitis B Virus Infection Susceptibility GWAS Associated with Survival in HBV-Related Hepatocellular Carcinoma Alternate Title:GWAS-Identified SNPs Associated with Survival of HBV-Related HCC
Cong Li1
Xinyu Bi1
Ying Huang2
Jianjun Zhao1
Zhiyu Li1
Jianguo Zhou1
Meng Zhang2
Zhen Huang1
Hong Zhao1*
Jianqiang Cai1*
Xiaoping Miaoedit1 Role: Editor
1Department of Abdominal Surgical Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
2Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, China
Correspondence: * E-mail: (HZ); (JC)
[conflict] Competing Interests: The authors have declared that no competing interests exist.
Contributed by footnote: Conceived and designed the experiments: JC HZ. Performed the experiments: CL XB YH MZ. Analyzed the data: CL XB YH HZ. Contributed reagents/materials/analysis tools: XB HZ ZL MZ ZH J. ZHAO J. ZHOU. Contributed to the writing of the manuscript: CL YH. Helped to answer reviewers' comments: CL XB.


Hepatocellular carcinoma (HCC) is the sixth common cancer and the second leading cause of cancer deaths worldwide. The prevalence of HCC varies considerably, with the highest in East, Southeast Asia and Sub-Saharan Africa, and China alone accounts for approximately 50% of all cases [1]. The known etiologies of HCC include chronic infections with hepatitis B or C virus (HBV or HCV), aflatoxin B1 exposure, alcohol consumption, and drug abuse [2]. Among them, chronic infection with HBV is the main etiological factor for developing HCC to majority of HCC cases in China. More than 90% of perinatal infection by vertical transmission results in persistent chronic HBV infection (CHB). In contrast, more than 90% of individuals infected with HBV in adulthood eliminate the viruses spontaneously [3]. Among persistently infected individuals, only 10–30% of individuals with CHB eventually develop liver cirrhosis and HCC. These epidemiology studies indicated that an individual's genetic makeup might play an important role in the HCC carcinogenesis [4].

In the recent years, several genome-wide association studies (GWAS) identified 31 loci in 10 chromosomal regions associated with susceptibility of CHB [5][11] or HBV-related HCC [12][16]. Evidence has been accumulated to show that some susceptible variants might also be associated with survival time of patients with colorectal cancer, gastric cancer or prostate cancer [17][20]. However, relationship between these GWAS-identified susceptibility loci and survival of HCC patients are still unknown. To evaluate the association between CHB or HBV-related HCC susceptibility SNPs and survival in patients with HBV-related HCC, we included a cohort of patients with HBV-related HCC to perform a comprehensive study.

Materials and Methods
Study subjects

In this study, 360 patients with HBV-related HCC were recruited from January 1999 to December 2012 at Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China. Due to lack of some clinicalpathological information, 30 out of the 360 patients (8.3%) were excluded from the study and finally 330 patients were enrolled in the further study. All patients were unrelated ethnic Han Chinese. The diagnosis of HCC was all histopathologically confirmed by at least two local pathologists. We selected the samples for HBV positive but HCV negative according to serology tests and infection history. Serum hepatitis B surface Antigen (HBsAg), hepatitis B surface antibody (anti-HBs), hepatitis B e Antigen (HBeAg), hepatitis B e Antibody (anti-HBe), hepatitis B core antibody (anti-HBc), and antibody to the hepatitis C virus (anti-HCV) were measured by ELISA (Roche, Shanghai, China) according to the manufacturer's instruction. In addition, patients had to meet criteria as follows: a Karnofsky performance score (KPS) of at least 70, a life expectancy of at least three months, and having adequate organ functions. We collected demographic data of each patient such as sex, age, smoking status, and alcohol consumption. Tumor-node-metastasis (TNM) stages were evaluated and classified according to American Joint Commission for Cancer Staging (AJCCS) in 2009, the seventh edition. Individuals who smoked daily for at least one year were defined as smokers, and those who consumed alcohol drinks more than one time per week for over six months were considered drinkers. Written informed consent was obtained from each patient and this study was approved by the Institutional Review Board of Chinese Academy of Medical Sciences Cancer Institute.

Follow-up study

Overall survival (OS) time of patients was measured from the date of treatment to the date of last follow-up or death. Whether and when a patient had died was obtained from inpatient and outpatient records, patients' relatives, or local Public Security Census Register Office through follow-up telephone calls. The last date of follow-up was 30th December 2013 and no patients were lost. Patients alive on the last follow-up date were considered censored. The median follow-up time was 68 months for this cohort.

SNP selection and genotype analysis

Genomic DNA were extracted from patients' peripheral blood samples. Blood DNA kit (catalog number: DP31902) was provided by Tiangen Biochemical Technology Co., Ltd. (Beijing, China). The procedure was performed strictly following the manufacturer's instructions. 31 SNPs were reported by six CHB and five HCC susceptibility GWAS in Asian population [5][16]. Among them, 22 SNPs with minor allele frequency>0.05 in Chinese Han population were selected based on the genotypes of samples from 1000 Genome project November 2010 ASN (Asian) and genotyped using the MassARRAY system from Sequenom. Genotyping of the other nine SNPs failed because of no appropriate primers for them. Several quality-control measures implemented in genotyping analysis are as follows: duplicated samples were mixed in the plates; persons performing the genotyping assays were not aware of the status of the duplicated samples; both positive and negative (no DNA) control samples were included on every 384­well assay plate; and 20% random samples were genotyped twice by different investigators and all results were completely concordant, with the concordance being 100%.

Statistical analysis

Kaplan-Meier method was used to estimate survival curves. Log-rank test was adopted to assess the association between SNPs and OS, demographic characteristics, and clinical features. The Cox regression under a log additive genetic model was used to assess the effect of individual SNPs on OS. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated with adjustment for age, sex (male or female), KPS (70, 80 or ≥90), smoking status (nonsmoker or smoker), drinking status (nondrinker or drinker), surgery and TNM stage. All data were analyzed using SAS software (version 9.2; SAS Institute Inc., Cary, NC, USA) with two-sided P-values (P<0.05 were considered significant).

Characteristics of the Study Population

The demographic and clinical characteristics of the 330 patients enrolled in this study are shown in Table 1. During the follow-up period, 256 (77.6%) patients died of HCC, with a median survival time (MST) of 18 months. The median age at diagnosis was 54 years (range, 25–88 years). 282 males (85.5%) and 48 females (14.5%) were included. There were 184 smokers (55.8%) and drinkers (68.8%). 65 (19.7%), 126 (38.2%), and 139 (42.2%) patients were with KPS 70, 80, and 90–100, respectively. 90 (27.3%) patients received liver resection, and the other 240 (72.7%) patients received non-surgery treatment including transcatheter arterial chemoembolization (TACE), TACE combined with radiofrequency ablation, or TACE combined with targeted therapy. 100 (30.3%) patients were at stage I, 106 (32.1%) patients were at stage II and 124 (37.6%) patients were at Stage III; corresponding MST were 51, 25, and 10 months, respectively. TNM stage, drinking status, KPS, and surgical treatment showed a significant association with OS in patients with HBV-related HCC (Log-rank P<0.05).

Genetic variants associated with OS in patients with HBV-related HCC

Among 22 SNPs genotyped, three SNPs (rs1419881 T>C, rs7453920 G>A and rs7768538 T>C) identified by CHB susceptibility GWAS and three SNPs (rs2275959 C>T, rs7821974 C>T and rs3997872 G>A) identified by HCC susceptibility GWAS, were significantly associated with OS in patients with HBV-related HCC in this study using the Cox regression after adjusting for covariates including age, gender, KPS, smoke, alcohol, surgery, and TNM stage (Table 2). (Kaplan-Meier survival curves for patients with HBV-related HCC stratified by genotypes of these six SNPs are shown in Figure 1)

The rs7768538 A>C locus was the most significant one, with the adjusted HR for death of patients being 0.48 (95% CI, 0.32–0.72; P = 0.0004) under the additive model (Table 2). The MST for the rs7768538 AA and AC genotypes was 16 and 54 months, respectively. The adjusted HR for death of patients with the rs7768538 AC genotype was 0.49 (95% CI, 0.31–0.77; P = 0.0022), compared with the AA genotype (Table 3). In a dominant model, patients with the rs7768538 AC or CC genotype had significantly longer MST (55 months) than those with the AA genotype, with the adjusted HR being 0.45 (95%CI, 0.29–0.71; P = 0.0005) (Table 3).

The rs7453920 G>A, rs3997872 G>A, rs7821974 C>T, and rs1419881 T>C were also significantly associated with survival time in HBV-related HCC patients, with the adjusted HR being 0.52 (95% CI, 0.36–0.75; P = 0.0004), 0.48 (95% CI, 0.25–0.92; P = 0.0266), 0.81 (95% CI, 0.67–0.98; P = 0.0351), and 0.81 (95% CI, 0.66–0.99; P = 0.0364), respectively (Table 2). In the dominant model, patients carrying one or two minor alleles would survive significantly longer, compared to those carrying homozygous common genotypes. Patients carrying the rs7453920 G>A, rs3997872 G>A, rs7821974 C>T, and rs1419881 T>C were with the adjusted HR being 0.51 (95%CI,0.34–0.75; P = 0.0007), 0.48 (95%CI, 0.25–0.92; P = 0.0266), 0.66 (95%CI, 0.49–0.88; P = 0.0046), and 0.73 (95%CI, 0.56–0.95; P = 0.0204), respectively (Table 3).

In contrast with the above five loci showing decreased risk of minor alleles on patient's survival, rs2275959 C>T locus was significantly associated with an increased risk of death, with the adjusted HR for death of patients being 1.22 (95% CI, 1.01–1.46; P = 0.0351) under the additive model. In addition, rs2275959 was significantly associated with an increased HBV-related HCC risk in a recessive manner. Patients with TT genotype had significant shorter survival time (MST, 15 months; adjusted HR = 1.50, 95% CI, 1.12–2.01; P = 0.0067) compared to those with the CT or CC genotype.

Cumulative effects of risk genotypes associated with OS in HBV-related HCC patients

We further estimated the cumulative effects of risk genotypes associated with OS in HBV-related HCC patients by counting the number of associated genotypes in each subject on the basis of the best-fitting genetic model from single-locus analysis. For rs7453920 and rs7768538 at chromosome 6p21 were in strong linkage disequilibrium (r2 = 0.82), we only selected rs7768538, which was more significantly associated with survival in HBV-related HCC patients, for the cumulative analysis. Compared with individuals carrying less than one unfavorable genotype, individuals carrying two or three and four or five unfavorable genotypes had an adjusted HR of 2.14 (95%CI, 1.29–3.581; P = 0.0034) and 3.17 (95%CI, 1.77–5.68; P = 0.0001), respectively. There was a significant trend of increasing risk of death (Ptrend = 6.23×10−6) with increasing number of putative high-risk alleles (Table 4). Kaplan-Meier analysis showed a trend for significantly shorter MST with increasing number of risk alleles for the OS in patients with HBV-related HCC (Log-rank P = 7.72×10−6; Figure 2).


In this study, we found that GWAS-identified CHB and HCC susceptibility SNPs (rs2275959 and rs37821974 on 8p12; rs1419881, rs3997872, rs7453920, and rs7768538 on 6p21) may individually or jointly affect clinical outcomes for HBV-related HCC patients. To the best of our knowledge, this is the first study to report the association of CHB and HCC susceptibility loci with survival in patients with HBV-related HCC.

rs2275959 C>T and rs7821974 C>T are two susceptibility loci on 8p12 for HBV-related HCC identified by a GWAS in Southern Chinese population. Region 8p was one of the most frequently deleted regions in HCCs, and the loss of heterozygosity in 8p was associated with metastasis of HCC [21]. Moreover, a liver cancer suppressor gene named DLC-1, which induces apoptosis and exerts inhibitory effects on the cell proliferation of HCC cells [22],[23], is located in a site of ∼24 Mb upstream of the two SNPs (rs2275959 and rs37821974) on 8p12. Therefore, we suppose that risk-associated 8p12 SNPs might have an interacting effect on the DLC1 locus. Our data show that the variant genotypes of rs2275959 and rs37821974 respectively increase and decrease the risk of death in HBV-related HCC patients, indicating that the two SNPs might play different roles on the interaction with DLC-1. Additionally, Chan et al found a 2.3-kb expressed sequence tag (EST) in the region 8p12 using in-silico data mining, sequencing analysis and in-vitro protein translation study, which suggested that the transcript might function as a long non-coding RNA (lncRNA) [14]. Accumulating studies have demonstrated that lncRNAs might be dysregulated in HCC and closely related with carcinogenesis, metastasis, or prognosis [24][26]. However, the biological and molecular mechanisms of lncRNAs are not yet fully understood. The relationship between 8p12 SNPs and lncRNA on the prognosis in HBV-related HCC patients is unknown and further studies are required.

rs3997872, which was located in a site of ∼23 kb downstream of HLA-DRB1 in the major histocompatibility complex (MHC) class II locus, was associated with the decreased risk of death in patients with HBV-related HCC. MHC class II molecules present antigen to CD4+ T cells. Clifford et al discovered that rs3997872 and other two SNPs might be associated with altered MHC class II proteins that result in an ineffective T-cell response and be involved in antigen processing and presentation pathway [12]. Immune response has been proven to play an important role on development and clinical outcomes of HCC [27][29]. Furthermore, HLA-DR expression was one of the independent risk factors for early intrahepatic recurrence of HCC, which was strongly in correlation with poor prognosis of HCC [30]. These previous findings enhance the biological plausibility that genetic polymorphism in MHC class II region may play an important role on survival in HCC patients.

Due to only a subset of CHB patients develop HCC, it is of great interest to identify whether genetic factors of CHB susceptibility have an effect on the prognosis of HBV-related HCC patients. We identified three SNPs on 6p21, including rs7453920 (HLA-DQB2), rs7768538 (HLA-DQB2), and rs1419881 (TCF19), whose variant allele frequencies significantly associated with decreased death risk in such patients. rs7453920 and rs7768538 are situated in HLA-DQ genes, which are highly polymorphic, especially in exon 2 which encodes antigen-binding sites. Recent studies have showed that HLA-DQ molecules might be critical for the HBV clearance and play an important role in the development of CHB [9],[15]. HBV-DNA has been confirmed as the most important predictor of disease progression and HCC development in CHB whereas the benefit of HBV clearance for HCC patients' survival time is still far from completely understood [31]. Our findings provided a novel insight that genetic variants in HLA-DQ locus might influence the long-term outcomes in patients with HBV-related HCC through impact of HBV clearance.

rs1419881 on 6p21.3 is located in the 3' untranslated region of transcription factor 19 (TCF19). TCF19 was suggested as a late growth-regulated gene related to the risk of type 1 diabetes and psoriasis vulgaris, playing an important role in the transcription of genes required for the later stages of cell cycle progression [32][35]. However, whether TCF19 correlated to survival of HBV-related HCC remains uncertain, and further functional analysis is warranted to fully clarify the molecular mechanism whereby these variations confer survival of HBV-related HCC.

Since the process in clearance of HBV, development of CHB, and progression of HCC are complex, it is unlikely that any single variation would have a dramatic effect on clinical outcomes of HBV-related HCC. However, a combined influence of several SNPs may exert synergistic protection against the development or progression of HCC. Our results support the cumulative effects of risk-associated genotypes of SNPs in modulating survival time of HBV-related HCC, suggesting that screening of these SNPs may provide valuable information in clinical practice to predict different death risk for such patients.

In summary, this is the first study exploring the association of GWAS-identified HCC and CHB susceptibility SNPs with clinical outcomes of patients with HBV-related HCC. GWAS-identified SNPs, including rs2275959, rs37821974, rs1419881, rs3997872, rs7453920, and rs7768538, are significantly associated with survival time of HBV-related HCC. The GWASs from which these SNPs derived are all based on Asian population, making this study more reasonable. Results from cumulative analysis show a gene-dosage effect in these SNPs. Future independent validations in larger population are necessary before these findings translated into clinical practice and beneficial to prognosis in such patients.

Supporting Information Table S1

Primers for genotyping of candidate SNPs.


Click here for additional data file (pone.0101586.s001.xls)

We thank Professor Chen Wu for the valuable suggestion on this work.


Conceived and designed the experiments: JC HZ. Performed the experiments: CL XB YH MZ. Analyzed the data: CL XB YH HZ. Contributed reagents/materials/analysis tools: XB HZ ZL MZ ZH J. ZHAO J. ZHOU. Contributed to the writing of the manuscript: CL YH. Helped to answer reviewers' comments: CL XB.

1. Ferlay J, Soerjomataram I, Ervik M, Dikshit R, Eser S, et al. (2013) Cancer Incidence and Mortality Worldwide: IARC CancerBase No. 11 [Internet]. GLOBOCAN 2012 v1.0. Available:, accessed on day/month/year.
2. Fares N,, Peron JM, (Year: 2013) [Epidemiology, natural history, and risk factors of hepatocellular carcinoma]. Rev Prat63: 216–217, 220–21223513788
3. El-Serag HB, (Year: 2012) Epidemiology of viral hepatitis and hepatocellular carcinoma. Gastroenterology142: 1264–1273.e126122537432
4. Chen CJ,, Chen DS, (Year: 2002) Interaction of hepatitis B virus, chemical carcinogen, and genetic susceptibility: multistage hepatocarcinogenesis with multifactorial etiology. Hepatology36: 1046–104912395312
5. Kamatani Y,, Wattanapokayakit S,, Ochi H,, Kawaguchi T,, Takahashi A,, et al. (Year: 2009) A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet41: 591–59519349983
6. Liu L,, Li J,, Yao J,, Yu J,, Zhang J,, et al. (Year: 2011) A genome-wide association study with DNA pooling identifies the variant rs11866328 in the GRIN2A gene that affects disease progression of chronic HBV infection. Viral Immunol24: 397–40222004137
7. Mbarek H,, Ochi H,, Urabe Y,, Kumar V,, Kubo M,, et al. (Year: 2011) A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population. Hum Mol Genet20: 3884–389221750111
8. Nishida N,, Sawai H,, Matsuura K,, Sugiyama M,, Ahn SH,, et al. (Year: 2012) Genome-wide association study confirming association of HLA-DP with protection against chronic hepatitis B and viral clearance in Japanese and Korean. PLoS One7: e3917522737229
9. Hu Z,, Liu Y,, Zhai X,, Dai J,, Jin G,, et al. (Year: 2013) New loci associated with chronic hepatitis B virus infection in Han Chinese. Nat Genet45: 1499–150324162738
10. Kim YJ,, Kim HY,, Lee JH,, Yu SJ,, Yoon JH,, et al. (Year: 2013) A genome-wide association study identified new variants associated with the risk of chronic hepatitis B. Hum Mol Genet. 22: 4233–423823760081
11. Al-Qahtani A,, Khalak HG,, Alkuraya FS,, Al-hamoudi W,, Alswat K,, et al. (Year: 2013) Genome-wide association study of chronic hepatitis B virus infection reveals a novel candidate risk allele on 11q22.3. J Med Genet50: 725–73224065354
12. Clifford RJ,, Zhang J,, Meerzaman DM,, Lyu MS,, Hu Y,, et al. (Year: 2010) Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma. Hepatology52: 2034–204321105107
13. Zhang H,, Zhai Y,, Hu Z,, Wu C,, Qian J,, et al. (Year: 2010) Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. Nat Genet42: 755–75820676096
14. Chan KY,, Wong CM,, Kwan JS,, Lee JM,, Cheung KW,, et al. (Year: 2011) Genome-wide association study of hepatocellular carcinoma in Southern Chinese patients with chronic hepatitis B virus infection. PLoS One6: e2879822174901
15. Jiang DK,, Sun J,, Cao G,, Liu Y,, Lin D,, et al. (Year: 2013) Genetic variants in STAT4 and HLA-DQ genes confer risk of hepatitis B virus-related hepatocellular carcinoma. Nat Genet45: 72–7523242368
16. Li S,, Qian J,, Yang Y,, Zhao W,, Dai J,, et al. (Year: 2012) GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers. PLoS Genet8: e100279122807686
17. Phipps AI,, Newcomb PA,, Garcia-Albeniz X,, Hutter CM,, White E,, et al. (Year: 2012) Association between colorectal cancer susceptibility loci and survival time after diagnosis with colorectal cancer. Gastroenterology143: 51–54.e5422580541
18. Bao BY,, Pao JB,, Huang CN,, Pu YS,, Chang TY,, et al. (Year: 2012) Significant associations of prostate cancer susceptibility variants with survival in patients treated with androgen-deprivation therapy. Int J Cancer130: 876–88421445969
19. Dai J,, Gu J,, Huang M,, Eng C,, Kopetz ES,, et al. (Year: 2012) GWAS-identified colorectal cancer susceptibility loci associated with clinical outcomes. Carcinogenesis33: 1327–133122505654
20. Kang M,, Ding X,, Xu M,, Zhu H,, Liu S,, et al. (Year: 2014) Genetic variation rs10484761 on 6p21.1 derived from a genome-wide association study is associated with gastric cancer survival in a Chinese population. Gene536: 59–6424325909
21. Wu X,, Jia HL,, Wang YF,, Ren N,, Ye QH,, et al. (Year: 2006) HTPAP gene on chromosome 8p is a candidate metastasis suppressor for human hepatocellular carcinoma. Oncogene25: 1832–184016261160
22. Zhou X,, Thorgeirsson SS,, Popescu NC, (Year: 2004) Restoration of DLC-1 gene expression induces apoptosis and inhibits both cell growth and tumorigenicity in human hepatocellular carcinoma cells. Oncogene23: 1308–131314647417
23. Wong CM,, Lee JM,, Ching YP,, Jin DY,, Ng IO, (Year: 2003) Genetic and epigenetic alterations of DLC-1 gene in hepatocellular carcinoma. Cancer Res63: 7646–765114633684
24. Wang X,, Arai S,, Song X,, Reichart D,, Du K,, et al. (Year: 2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature454: 126–13018509338
25. Bond AM,, Vangompel MJ,, Sametsky EA,, Clark MF,, Savage JC,, et al. (Year: 2009) Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci12: 1020–102719620975
26. He Y,, Meng XM,, Huang C,, Wu BM,, Zhang L,, et al. (Year: 2014) Long noncoding RNAs: Novel insights into hepatocelluar carcinoma. Cancer Lett344: 20–2724183851
27. Flecken T,, Schmidt N,, Hild S,, Gostick E,, Drognitz O,, et al. (Year: 2014) Immunodominance and functional alterations of tumor-associated antigen-specific CD8(+) T-cell responses in hepatocellular carcinoma. Hepatology59: 1415–142624002931
28. Pan QZ,, Pan K,, Zhao JJ,, Chen JG,, Li JJ,, et al. (Year: 2013) Decreased expression of interleukin-36alpha correlates with poor prognosis in hepatocellular carcinoma. Cancer Immunol Immunother62: 1675–168524061617
29. Liao R,, Sun J,, Wu H,, Yi Y,, Wang JX,, et al. (Year: 2013) High expression of IL-17 and IL-17RE associate with poor prognosis of hepatocellular carcinoma. J Exp Clin Cancer Res32: 323305119
30. Matoba K,, Iizuka N,, Gondo T,, Ishihara T,, Yamada-Okabe H,, et al. (Year: 2005) Tumor HLA-DR expression linked to early intrahepatic recurrence of hepatocellular carcinoma. Int J Cancer115: 231–24015688398
31. Diepolder HM (2014) Clearance of HBV markers and HCC risk: who is safe? Gut.
32. Ku DH,, Chang CD,, Koniecki J,, Cannizzaro LA,, Boghosian-Sell L,, et al. (Year: 1991) A new growth-regulated complementary DNA with the sequence of a putative trans-activating factor. Cell Growth Differ2: 179–1861868030
33. Krishnan BR,, Jamry I,, Chaplin DD, (Year: 1995) Feature mapping of the HLA class I region: localization of the POU5F1 and TCF19 genes. Genomics30: 53–588595903
34. Oka A,, Tamiya G,, Tomizawa M,, Ota M,, Katsuyama Y,, et al. (Year: 1999) Association analysis using refined microsatellite markers localizes a susceptibility locus for psoriasis vulgaris within a 111 kb segment telomeric to the HLA-C gene. Hum Mol Genet8: 2165–217010545595
35. Cheung YH,, Watkinson J,, Anastassiou D, (Year: 2011) Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC. Hum Genet129: 161–17621076979


[Figure ID: pone-0101586-g001]
doi: 10.1371/journal.pone.0101586.g001.
Figure 1  Kaplan-Meier survival curves for patients with HBV-related HCC stratified by genotypes of the six SNPs: A. rs1419881 (did not reach statistical significance for overall survival by log-rank test with P = 0.0538 while was significant using the Cox progression model with P = 0.00364); B. rs2275959; C. rs3997872; D. rs7453920; E. rs7768538; F. rs7821974.

[Figure ID: pone-0101586-g002]
doi: 10.1371/journal.pone.0101586.g002.
Figure 2  Kaplan–Meier curve of HBV-related HCC patients stratified by the number of unfavorable genotypes.

[TableWrap ID: pone-0101586-t001] doi: 10.1371/journal.pone.0101586.t001.
Table 1  Demographic and Clinical characteristics of 330 patients with HBV-related HCC.
Characteristics N = 330
No. (%) MST (month) P
Dead 521 (59.6) 18
Alive 353 (40.4)
Sex 0.9064
Male 282 (85.5) 18
Female 48 (14.5) 23
Age 0.8157
<54 years 164 (49.7) 18
≥54 years 166 (50.3) 21
Smoking status 0.0904
Nonsmoker 184 (55.8) 23
Smoker 146 (44.2) 15
Drinking status
Nondrinker 227 (68.8) 24 0.0346
Drinker 103 (31.2) 14
TNM stage <0.0001
I 100 (30.3) 51
II 106 (32.1) 25
III 124 (37.6) 10
Surgery <0.0001
No 240 (72.7) 13
Yes 90 (27.3) 67
KPS 0.0049
70 65 (19.7) 11
80 126 (38.2) 15
90 139 (42.1) 28

Abbreviation: No., number of patients; MST, median survival time.

P values for log-rank test.

[TableWrap ID: pone-0101586-t002] doi: 10.1371/journal.pone.0101586.t002.
Table 2  Associations of 22 candidate SNPs and overall survival in patients with HBV-related HCC.
SNP ID Chr. Gene Minor Allele MAF HR (95% CI) P
rs7768538* 6 HLA-DQB2 C 0.19 0.48 (0.32–0.72) 0.0004
rs7453920* 6 HLA-DQB2 A 0.12 0.52 (0.36–0.75) 0.0004
rs3997872* 6 HLA-DQA1 A 0.06 0.48 (0.25–0.92) 0.0266
rs7821974* 8 LOC101929604 T 0.49 0.81 (0.67–0.98) 0.0335
rs2275959* 8 LOC101929604 A 0.43 1.22 (1.01–1.46) 0.0351
rs1419881* 6 TCF19 A 0.49 0.81 (0.66-0.99) 0.0364
rs3077 6 HLA-DPA1 A 0.38 0.86 (0.70–1.06) 0.1512
rs2647073 6 LOC100507709 C 0.08 1.17 (0.96–1.44) 0.1277
rs6468418 8 LOC101929604 A 0.42 0.87 (0.71–1.06) 0.1737
rs4821116 22 UBE2L3 T 0.36 0.88 (0.71–1.09) 0.2330
rs4678680 3 GLB1 G 0.06 0.79 (0.53–1.18) 0.2505
rs17401966 1 KIF1B A 0.29 1.12 (0.90–1.40) 0.3003
rs2844619 6 HLA-C A 0.19 1.07 (0.78–1.48) 0.6798
rs9272218 6 HLA-DQA1 A 0.48 0.94 (0.79–1.11) 0.4435
rs9444730 6 BACH2 G 0.12 0.93 (0.72–1.20) 0.5773
rs9267673 6 C2 T 0.13 1.15 (0.88–1.49) 0.3035
rs7749730 6 BACH2 G 0.12 0.95 (0.73–1.22) 0.6618
rs2724432 11 FDX1 T 0.06 0.90 (0.53–1.52) 0.6876
rs12100561 14 EFCAB11 A 0.38 1.04 (0.86–1.25) 0.7098
rs455804 21 GRIK1 A 0.34 1.04 (0.84–1.28) 0.7346
rs11866328 16 GRIN2A T 0.18 1.04 (0.82–1.31) 0.7577
rs7574865 2 STAT4 T 0.35 1.00 (0.82–1.23) 0.9916

Abbreviation: MAF, minor allele frequency; HR, hazard ratio; CI, confidence interval.

*The SNPs with P<0.05.

Calculated with multivariate Cox regression under an additive genetic model adjusted for age, sex, smoking status, drinking status, KPS, surgery, and clinical stage.

[TableWrap ID: pone-0101586-t003] doi: 10.1371/journal.pone.0101586.t003.
Table 3  HR and MST of patients with HBV-related HCC for the six significant SNPs.
Genotype No. Dead/Alive MST HR (95% CI) P
AA 273 220/53 16 1.00 (Reference)
AC 36 22/14 54 0.49 (0.31–0.77) 0.0022
CC 3 1/2 na 0.17 (0.02–1.25) 0.0823
AC+CC 39 23/16 55 0.45 (0.29–0.71) 0.0005
GG 279 225/54 17 1.00 (Reference)
GA 47 29/18 54 0.55 (0.37–0.82) 0.0030
AA 3 1/2 na 0.16 (0.02–1.19) 0.0740
GA+AA 50 30/20 54 0.51(0.34–0.75) 0.0007
TT 306 243/63 18 1.00 (Reference)
TA 22 11/11 66 0.48 (0.25–0.92) 0.0266
AA 0 0/0 na na na
TA+AA 22 11/11 66 0.48 (0.25–0.92) 0.0266
CC 92 81/11 15 1.00 (Reference)
CT 140 100/40 21 0.64 (0.46–0.88) 0.0059
TT 70 53/17 21 0.69 (0.47–1.00) 0.0525
CT+TT 210 153/57 21 0.66 (0.49–0.88) 0.0046
GG 91 69/22 21 1.00 (Reference)
GA 159 114/45 20 1.00 (0.73–1.36) 0.9980
AA 80 73/7 15 1.45 (1.02–2.07) 0.0395
GA+AA 239 187/52 18 1.13 (0.85–1.51) 0.3942
GG 132 109/23 18 1.00 (Reference)
GA 151 112/39 19 0.72 (0.55–0.96) 0.0258
AA 45 33/12 24 0.78 (0.51–1.18) 0.2330
GA+AA 196 145/51 21 0.73 (0.56–0.95) 0.0204

Abbreviation: No., number of patients; MST, median survival time; HR, hazard ratio; CI, confidence interval. Because of genotyping failure of some DNA samples, the number of subjects may not add up to the total number.

Calculated with multivariate Cox regression models adjusted for age, sex, smoking status, drinking status, KPS, surgery and clinical stage.

[TableWrap ID: pone-0101586-t004] doi: 10.1371/journal.pone.0101586.t004.
Table 4  Cumulative effect of risk genotypes on survival in HBV-related HCC patients.
Nuamber of risk genotypes No. Dead/Alive MST HR (95% CI) P Plog-rank
0–1 (low risk) 35 17/18 56 1.00 (Reference)
2–3 (medium risk) 223 173/50 19 2.14 (1.29–3.58) 0.0034 7.72×10−6
4–5 (high risk) 72 66/6 13 3.17 (1.77–5.68) 0.0001
Ptrend 6.23×10−6

Abbreviation: No., number of patients; MST, median survival time; HR, hazard ratio; CI, confidence interval.

Calculated with multivariate Cox regression models adjusted for age, sex, smoking status, drinking status, KPS, surgery and clinical stage.

Article Categories:
  • Research Article
Article Categories:
  • Biology and Life Sciences
    • Genetics
      • Human Genetics
        • Genetic Association Studies
        • Genome-Wide Association Studies
      • Population Genetics
        • Genetic Polymorphism
Article Categories:
  • Medicine and Health Sciences
    • Gastroenterology and Hepatology
      • Liver Diseases
        • Hepatocellular Carcinoma
    • Oncology
      • Cancers and Neoplasms
        • Carcinomas
          • Hepatocellular Carcinoma
        • Gastrointestinal Tumors
          • Hepatocellular Carcinoma

Previous Document:  Syntheses of Cyclotriveratrylene Analogues and Their Long Elusive Triketone Congeners.
Next Document:  Effect of Ambient Light and Macular Degeneration on Precision Walking.