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Zhang J, Yuan Y, Gao S, Zhao X, Li H. Diagnostic performance of circulating cell-free DNA for hepatocellular carcinoma: a systematic review and meta-analysis. Biomark Med 2021; 15:219-239. [PMID: 33470842 DOI: 10.2217/bmm-2020-0334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022] Open
Abstract
Background: We aimed to assess the diagnostic performance of circulating cell-free DNA (cfDNA) in hepatocellular carcinoma (HCC). Materials & methods: After a systematic literature search bivariate linear mixed models were used to integrate sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio. The area under receiver operating characteristics curves of the included studies was used to estimate the diagnostic value. Results: Thirty-eight articles enrolled in quantitative synthesis. In overall analysis the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio and area under receiver operating characteristics curves for cfDNA in distinguishing HCC patients from healthy controls were 0.54, 0.90, 5.23, 0.51, 10.27 and 0.82, respectively. Conclusion: This study suggests that cfDNA has a promising diagnostic accuracy in detection of HCC.
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Affiliation(s)
- Jinmei Zhang
- Department of Infectious Diseases, Weifang Yidu Central Hospital, Qingzhou 262500, China
| | - Yuan Yuan
- Department of Infectious Diseases, Weifang Yidu Central Hospital, Qingzhou 262500, China
| | - Shuxia Gao
- GI Medicine Department, Weifang Yidu Central Hospital, Qingzhou 262500, China
| | - Xue Zhao
- Respiratory Department, Weifang Yidu Central Hospital, Qingzhou 262500, China
| | - Hong Li
- Department of Infectious Diseases, Weifang Yidu Central Hospital, Qingzhou 262500, China
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Elsewify WAE, Hassan EA, Mekky MA, Abd El-Rehim ASED, Sayed ZEAA, Abdel Malek MO, ElMelegy TTH, Sabry A. Usefulness of Circulating Methylated p16 as a Noninvasive Molecular Biomarker for Hepatitis C-Related Hepatocellular Carcinoma with Normal Serum Alpha-Fetoprotein Levels. Int J Gen Med 2020; 13:147-155. [PMID: 32431531 PMCID: PMC7200244 DOI: 10.2147/ijgm.s249272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Background Screening of hepatocellular carcinoma (HCC) is challenged especially in patients with normal alpha-fetoprotein (AFP) levels. Aberrant p16 methylation has been implicated in HCC. Objectives and Aims This study aimed to assess serum methylated p16 (MP16) expression levels and to evaluate MP16 diagnostic performance in HCC detection among HCV-infected Egyptian patients with normal AFP levels. Methods MP16 levels were quantified using real-time PCR in 230 serum samples (30 healthy controls, 95 with HCV-HCC, 40 with chronic hepatitis C "CHC" and 65 with HCV cirrhosis). Diagnostic performance of MP16 for diagnosis of HCC was done using receiver operator characteristic curve analysis. Results Serum MP16 levels were significantly higher in HCC than CHC, cirrhosis, and healthy subjects and significantly higher in HCC with normal AFP levels than those with higher AFP. ROC curves revealed promising diagnostic performance for MP16 in discriminating HCC with normal AFP levels from non-HCC cases. This predictive ability improved by combining MP16 and AFP (AUC of 0.872 with 100% sensitivity, 76.5% specificity, 79.1% positive predictive value, 100% negative predictive value, and 87.5% accuracy). Conclusion MP16 can be a potential noninvasive molecular biomarker for HCC detection in patients with hepatic mass(es) and normal AFP levels especially in those where liver biopsy and radiological imaging cannot be done.
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Affiliation(s)
| | - Elham Ahmed Hassan
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohamed A Mekky
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | | | - Mohamed Omar Abdel Malek
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Tarek T H ElMelegy
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Abeer Sabry
- Department of Internal Medicine, Faculty of Medicine, Helwan University, Cairo, Egypt
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Zhou Y, Wang XB, Qiu XP, Shuai Zhang, Wang C, Zheng F. CDKN2A promoter methylation and hepatocellular carcinoma risk: A meta-analysis. Clin Res Hepatol Gastroenterol 2018; 42:529-541. [PMID: 30143452 DOI: 10.1016/j.clinre.2017.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/17/2017] [Accepted: 07/28/2017] [Indexed: 02/04/2023]
Abstract
AIM Lots of studies have explored cyclin-dependent kinase inhibitor 2A (CDKN2A) promoter methylation in hepatocellular carcinoma (HCC), but the established results were controversial. Hence, we conducted the meta-analysis to comprehensively investigate the association between CDKN2A promoter methylation and HCC risk. METHODS A comprehensive search was implemented through searching PubMed, Web of Science and Embase. Associations of CDKN2A promoter methylation with HCC risk, clinicopathological features, and CDKN2A expression were assessed by the pooled odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Subgroup analyses and meta-regression were served for exploring the potential sources of heterogeneity. RESULTS A total of 59 articles including 3067 cases and 2951 controls were incorporated in this meta-analysis. Overall, we observed a high CDKN2A promoter methylation rate (58.18%) in HCC and a significant association between the methylation and HCC risk (OR, 7.07; 95% CI, 5.67-8.80). Furthermore, CDKN2A promoter methylation was robustly associated with decreased mRNA (OR, 13.89; 95% CI, 5.44-35.45) and protein (OR, 48.19; 95% CI, 5.56-417.29). In addition, we found the methylation was related with HBV infection (OR, 3.31; 95% CI, 1.47-7.47), HCV infection (OR, 2.76; 95% CI, 1.80-4.23), cirrhosis status (OR, 1.57; 95% CI, 1.01-2.44) and older age (OR, 1.83; 95% CI, 1.14-2.94). CONCLUSIONS Our results indicated that CDKN2A promoter methylation was associated with an enhancive HCC risk and played a crucial role in the process of HCC with a potential value to being a triage marker for HCC.
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Affiliation(s)
- Ye Zhou
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Xue-Bin Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Xue-Ping Qiu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Shuai Zhang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Chen Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei, China.
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Liao W, Mao Y, Ge P, Yang H, Xu H, Lu X, Sang X, Zhong S. Value of quantitative and qualitative analyses of circulating cell-free DNA as diagnostic tools for hepatocellular carcinoma: a meta-analysis. Medicine (Baltimore) 2015; 94:e722. [PMID: 25860220 PMCID: PMC4554041 DOI: 10.1097/md.0000000000000722] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/08/2015] [Accepted: 03/09/2015] [Indexed: 12/24/2022] Open
Abstract
Qualitative and quantitative analyses of circulating cell-free DNA (cfDNA) are potential methods for the detection of hepatocellular carcinoma (HCC). Many studies have evaluated these approaches, but the results have been variable. This meta-analysis is the first to synthesize these published results and evaluate the use of circulating cfDNA values for HCC diagnosis. All articles that met our inclusion criteria were assessed using QUADAS guidelines after the literature research. We also investigated 3 subgroups in this meta-analysis: qualitative analysis of abnormal concentrations of circulating cfDNA; qualitative analysis of single-gene methylation alterations; and multiple analyses combined with alpha-fetoprotein (AFP). Statistical analyses were performed using the software Stata 12.0. We synthesized these published results and calculated accuracy measures (pooled sensitivity and specificity, positive/negative likelihood ratios [PLRs/NLRs], diagnostic odds ratios [DORs], and corresponding 95% confidence intervals [95% CIs]). Data were pooled using bivariate generalized linear mixed model. Furthermore, summary receiver operating characteristic curves and area under the curve (AUC) were used to summarize overall test performance. Heterogeneity and publication bias were also examined. A total of 2424 subjects included 1280 HCC patients in 22 studies were recruited in this meta-analysis. Pooled sensitivity and specificity, PLR, NLR, DOR, AUC, and CIs of quantitative analysis were 0.741 (95% CI: 0.610-0.840), 0.851 (95% CI: 0.718-0.927), 4.970 (95% CI: 2.694-9.169), 0.304 (95% CI: 0.205-0.451), 16.347 (95% CI: 8.250-32.388), and 0.86 (95% CI: 0.83-0.89), respectively. For qualitative analysis, the values were 0.538 (95% CI: 0.401-0.669), 0.944 (95% CI: 0.889-0.972), 9.545 (95% CI: 5.298-17.196), 0.490 (95% CI: 0.372-0.646), 19.491 (95% CI: 10.458-36.329), and 0.87 (95% CI: 0.84-0.90), respectively. After combining with AFP assay, the values were 0.818 (95% CI: 0.676-0.906), 0.960 (95% CI: 0.873-0.988), 20.195 (95% CI: 5.973-68.282), 0.190 (95% CI: 0.100-0.359), 106.270 (95% CI: 22.317-506.055), and 0.96 (95% CI: 0.94-0.97), respectively. The results in this meta-analysis suggest that circulating cfDNA have potential value for HCC diagnosis. However, it would not be recommended for using independently, which is based on the nonrobust results. After combining with AFP, the diagnostic performance will be improved. Further investigation with more data is needed.
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Affiliation(s)
- Wenjun Liao
- From the Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Beijing, 100730, China
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Huang G, Krocker JD, Kirk JL, Merwat SN, Ju H, Soloway RD, Wieck LR, Li A, Okorodudu AO, Petersen JR, Abdulla NE, Duchini A, Cicalese L, Rastellini C, Hu PC, Dong J. Evaluation of INK4A promoter methylation using pyrosequencing and circulating cell-free DNA from patients with hepatocellular carcinoma. Clin Chem Lab Med 2014; 52:899-909. [PMID: 24406287 DOI: 10.1515/cclm-2013-0885] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/02/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hyper-methylation of CpG dinucleotides in the promoter region of inhibitor of cyclin-dependent kinase 4A (INK4A) has been reported in 60%-80% of hepatocellular carcinoma (HCC). As INK4A promoter hypermethylation event occurs early in HCC progression, the quantification of INK4A promoter methylation in blood sample may represent a useful biomarker for non-invasive diagnosis and prediction of response to therapy. METHODS We examined INK4A promoter methylation using circulating cell-free DNA (ccfDNA) in a total of 109 serum specimens, including 66 HCC and 43 benign chronic liver diseases. Methylation of the individual seven CpG sites was examined using pyrosequencing. RESULTS Our results showed that there were significantly higher levels of methylated INK4A in HCC specimens than controls and that the seven CpG sites had different levels of methylation and might exist in different PCR amplicons. The area under receiver operating characteristic (ROC) curve was 0.82, with 65.3% sensitivity and 87.2% specificity at 5% (LOD), 39.0% sensitivity and 96.5% specificity at 7% LOD, and 20.3% sensitivity and 98.8% specificity at 10% LOD, respectively. CONCLUSIONS Our results support additional studies incorporating INK4A methylation testing of ccfDNA to further validate the diagnostic, predictive, and prognostic characteristics of this biomarker in HCC patients. The knowledge of the existence of epi-alleles should help improve assay design to maximize detection.
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Affiliation(s)
- Gengming Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Joseph D Krocker
- Molecular Genetic Technology Program, School of Health Sciences, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jason L Kirk
- Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Shehzad N Merwat
- Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Hyunsu Ju
- Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, USA
| | - Roger D Soloway
- Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Lucas R Wieck
- Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Albert Li
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Anthony O Okorodudu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - John R Petersen
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nihal E Abdulla
- Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrea Duchini
- Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Luca Cicalese
- Surgery, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Peter C Hu
- Molecular Genetic Technology Program, School of Health Sciences, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jianli Dong
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0743, USA
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Kadam SK, Farmen M, Brandt JT. Quantitative measurement of cell-free plasma DNA and applications for detecting tumor genetic variation and promoter methylation in a clinical setting. J Mol Diagn 2012; 14:346-56. [PMID: 22579630 DOI: 10.1016/j.jmoldx.2012.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/26/2012] [Accepted: 03/15/2012] [Indexed: 12/31/2022] Open
Abstract
An elevated cell-free DNA (cfDNA) level is often reported in patients with advanced cancer and is thought to represent nuclear material from a distant inaccessible tumor. cfDNA can become a valuable source to monitor tumor dynamics and evaluate genetic markers for predictive, prognostic, and diagnostic testing. DNA extraction and quantification were optimized with plasma collected from 20 patients with advanced cancer and 16 healthy controls. Plasma cfDNA from patients with advanced cancer was evaluated for TP53 genetic variation and methylation status of CpG islands in several promoters of known disease-related genes. Tumor biopsy and corresponding plasma specimens were collected from study participants to determine whether the same genetic variations were present in both samples. The cfDNA isolation method provided a lower DNA detection limit of 144 pg, equivalent to DNA from approximately 24 cells. Normal pooled human plasma cfDNA averaged 110 copies/mL of the ACTB gene. Extracted cfDNA was suitable for gene-specific variant detection, sequencing, and promoter methylation analysis. DNA extracted from tumor biopsy and corresponding plasma specimens from two patients with advanced cancer revealed an identical, nonsynonymous variant present in both samples. Immunohistochemical analysis confirmed the TP53 mutant phenotype in the tumor specimens. Quantitative measurement of cfDNA represents a useful biomarker to follow treatment outcome and is a valuable tool with which to characterize specific genetic alterations for both patient selection and personalized treatment.
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Affiliation(s)
- Sunil K Kadam
- Division of Translational Medicine, Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, IN 46285, USA.
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High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Mol Genet Genomics 2010; 283:341-9. [PMID: 20165882 DOI: 10.1007/s00438-010-0522-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 01/27/2010] [Indexed: 02/07/2023]
Abstract
Methylation of promoter CpG islands has been associated with gene silencing and demonstrated to lead to chromosomal instability. Therefore, some postulate that aberrantly methylated CpG regions may be important biomarkers indicative of cancer development. In this study we used the Illumina GoldenGate Methylation BeadArray Cancer Panel I for simultaneously profiling methylation of 1,505 CpG sites in order to identify methylation differences in 76 liver tissues ranging from normal to pre-neoplastic and neoplastic states. CpG sites for ESR1, GSTM2, and MME were significantly differentially methylated when comparing the pre-neoplastic tissues from patients with concomitant hepatocellular carcinoma (HCC) to the pre-neoplastic tissues from patients without HCC. When comparing paired HCC tissues to their corresponding pre-neoplastic non-tumorous tissues, eight CpG sites, including one CpG site that was hypermethylated (APC) and seven (NOTCH4, EMR3, HDAC9, DCL1, HLA-DOA, HLA-DPA1, and ERN1) that were hypomethylated in HCC, were identified. Our study demonstrates that high-throughput methylation technologies may be used to identify differentially methylated CpG sites that may prove to be important molecular events involved in carcinogenesis.
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Nano-bio-technology and sensing chips: new systems for detection in personalized therapies and cell biology. SENSORS 2010; 10:526-43. [PMID: 22315554 PMCID: PMC3270855 DOI: 10.3390/s100100526] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/30/2009] [Accepted: 01/05/2010] [Indexed: 11/17/2022]
Abstract
Further advances in molecular medicine and cell biology also require new electrochemical systems to detect disease biomarkers and therapeutic compounds. Microelectronic technology offers powerful circuits and systems to develop innovative and miniaturized biochips for sensing at the molecular level. However, microelectronic biochips proposed in the literature often do not show the right specificity, sensitivity, and reliability required by biomedical applications. Nanotechnology offers new materials and solutions to improve the surface properties of sensing probes. The aim of the present paper is to review the most recent progress in Nano-Bio-Technology in the area of the development of new electrochemical systems for molecular detection in personalized therapy and cell culture monitoring.
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Is the role of circulating DNA as a biomarker of cancer being prematurely overrated? Clin Biochem 2009; 43:26-36. [PMID: 19747472 DOI: 10.1016/j.clinbiochem.2009.08.027] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 08/21/2009] [Accepted: 08/26/2009] [Indexed: 12/19/2022]
Abstract
BACKGROUND Circulating DNA is utilized widely as a genetic biomarker in a variety of pathological conditions, mainly in cancerous conditions. Quantification of circulating DNA and identifying the frequencies of a variety of mutations, microsatellite alterations and gene promoter methylation are the main foci of research on circulating DNA. CONTENT A compilation of research reports available to us were reviewed to highlight the rather great variety of methods presently used to isolate circulating DNA, the lack of uniformity in presenting and interpreting quantitative research data as well as the virtual absence of information regarding the structure and function of circulating DNA. CONCLUSIONS The information compelled us to conclude that the application of circulating DNA as an unambiguous biomarker is currently overrated. We therefore emphasize the need for elucidating the prevailing questions regarding the origin, function and significance of these nucleic acid molecules before utilizing circulating DNA as a biomarker.
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Chen JG, Kuang SY, Egner PA, Lu JH, Zhu YR, Wang JB, Zhang BC, Chen TY, Muñoz A, Kensler TW, Groopman JD. Acceleration to Death from Liver Cancer in People with Hepatitis B Viral Mutations Detected in Plasma by Mass Spectrometry. Cancer Epidemiol Biomarkers Prev 2007; 16:1213-8. [PMID: 17548687 DOI: 10.1158/1055-9965.epi-06-0905] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver cancer is the leading cause of cancer death in many regions of the world. With the goal to discover biomarkers that reflect subsets of high-risk individuals and their prognosis, we nested our study in a male cohort of 5,581 hepatitis B surface antigen carriers in Qidong, People's Republic of China, who were recruited starting in 1989. By December 2003, 667 liver cancer cases were diagnosed in this group and plasma samples collected at the initial screening at enrollment were available in 515 cases who had succumbed to liver cancer. Hepatitis B virus (HBV) DNA could be isolated in 355 (69%) of these samples. In 14%, 15%, 19%, 31%, and 22%, screening took place at < or = 1.5, 1.51 to 3, 3.01 to 5, 5.01 to 9, and > 9 years before death, respectively; and 39% died at age below 45 years. The relation between mutations in HBV and time to death were determined by logistic regression for the odds of mutation and by survival analyses methods with age as the time scale. In 279 (79%) of these individuals, the samples contained a two-nucleotide 1762T/1764A HBV mutation. Sixteen samples lacking the 1762T/1764A mutation had novel mutations elsewhere in the 1761 to 1767 region of the HBV genome. There was a statistically significant difference (P = 0.012) for the high prevalence of the HBV mutations in the men who died from hepatocellular carcinoma under the age of 45 years relative to those who died after 55 years of age and HBV mutations accelerated death (relative hazard, 1.40; 95% confidence interval, 1.06-1.85) and that the effect was attenuated by age from 2.04 for age 35 years to 1.0 for age 65 years with the 90% confidence band being above 1 for ages < 50 years. These findings provide a conceptual framework to explain the acceleration of mortality in individuals infected with HBV.
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Affiliation(s)
- Jian Guo Chen
- Qidong Liver Cancer Institute, Qidong, Jiangsu Province, People's Republic of China
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Zhang C, Li Z, Cheng Y, Jia F, Li R, Wu M, Li K, Wei L. CpG island methylator phenotype association with elevated serum alpha-fetoprotein level in hepatocellular carcinoma. Clin Cancer Res 2007; 13:944-52. [PMID: 17289889 DOI: 10.1158/1078-0432.ccr-06-2268] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE CpG island methylator phenotype (CIMP) involves hypermethylation targeted toward the promoters of multiple genes. To gain insight into the role of epigenetic aberration of tumor-related genes in hepatocarcinogenesis, we determined a hypermethylation profile in hepatocellular carcinoma (HCC). EXPERIMENTAL DESIGN We examined the promoter methylation status of nine genes in 50 HCCs, 50 paired nontumor tissues, and 6 normal liver tissues by methylation-specific PCR. CIMP+ was defined as having five genes that are concordantly methylated. RESULTS The frequency of promoter methylation of nine genes in 50 HCCs varied from 10% in P53 to 94% in c-Myc. The methylation status of P14, P15, P16, ER, RASSF1A, WT1, and c-Myc was significantly correlated with HCC and nontumor tissues (P<0.05). Hypermethylation of one or more genes was found in 96% of HCC. CIMP was more frequent in HCC than in nontumor tissues (70% and 12%, P<0.001). There is a significant association between CIMP and methylation of P14, P15, P16, ER, RSAAF1A, and WT1 (P<0.05) and serum alpha-fetoprotein (AFP) level (P=0.017). CIMP+ was more frequent in HCC with AFP>or=30 microg/L than those with AFP<30 microg/L (P=0.005). In addition, the promoter hypermethylation of P15 and P16 was associated with elevated serum AFP levels in 35 HCC samples with CIMP+ (P<0.05). CONCLUSIONS Positive correlation of CIMP and AFP levels in HCC suggests that CIMP can serve as a molecular marker of late-stage HCC development.
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Affiliation(s)
- Changsong Zhang
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
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Gormally E, Caboux E, Vineis P, Hainaut P. Circulating free DNA in plasma or serum as biomarker of carcinogenesis: practical aspects and biological significance. Mutat Res 2007; 635:105-117. [PMID: 17257890 DOI: 10.1016/j.mrrev.2006.11.002] [Citation(s) in RCA: 325] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 11/29/2006] [Accepted: 11/29/2006] [Indexed: 12/26/2022]
Abstract
The presence of small amounts of tumor DNA in cell free DNA (CFDNA) circulating in the plasma or serum of cancer patients was first demonstrated 30 years ago. Since then, overall plasma DNA concentration in cancer patients and genetic or epigenetic alterations specific to tumor DNA have been investigated in patients diagnosed with different types of cancer. The proportion of patients with altered CFDNA varies with the pathology and the nature of the marker. However, several studies have reported the presence of altered CFDNA in over 50% of cancer patients, suggesting that this marker may be common and amenable for a variety of clinical and epidemiological studies. Because the mechanisms and timing of CFDNA release in the blood stream are poorly understood, only few studies have addressed the use of CFDNA for early cancer detection or as a biomarker for mutagenesis and tumourigenesis in molecular epidemiology. In this review, we discuss the technical issues involved in obtaining, using and analyzing CFDNA in cancer or healthy subjects. We also summarize the literature available on the mechanisms of CDNA release as well as on cross-sectional or prospective studies aimed at assessing the clinical and biological significance of CFDNA. These studies show that, in some circumstances, CFDNA alterations are detectable ahead of cancer diagnosis, raising the possibility of exploiting them as biomarkers for monitoring cancer occurrence. Testing these hypotheses will require well-designed studies, assessing multiple markers with quantitative and sensitive methods, with adequate follow-up of subjects, and we provide recommendations for the development of such studies.
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Affiliation(s)
- Emmanuelle Gormally
- Université Catholique de Lyon, 25 rue du Plat, 69288 Lyon Cedex 02, France; International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Elodie Caboux
- International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Paolo Vineis
- Department of Epidemiology and Public Health, Imperial College of Science, Technology and Medicine, Norfolk Place, W2 1PG London, UK
| | - Pierre Hainaut
- International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 08, France.
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Tangkijvanich P, Hourpai N, Rattanatanyong P, Wisedopas N, Mahachai V, Mutirangura A. Serum LINE-1 hypomethylation as a potential prognostic marker for hepatocellular carcinoma. Clin Chim Acta 2007; 379:127-33. [PMID: 17303099 DOI: 10.1016/j.cca.2006.12.029] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 12/26/2006] [Accepted: 12/28/2006] [Indexed: 12/24/2022]
Abstract
BACKGROUND We investigated the clinical implications of global hypomethylation, one of the most consistent epigenetic changes in cancer, in the sera of patients with hepatocellular carcinoma (HCC). METHODS Combined bisulfite restriction analysis PCR was used to assess the methylation status of LINE-1 repetitive sequences in genomic DNA derived from sera of 85 patients with HCC, 73 patients with cirrhosis, 20 healthy carriers of hepatitis B virus (HBV) and 30 healthy controls. RESULTS Serum genome hypomethylation, the percentage of unmethylated LINE-1, was significantly increased in patients with HCC (P<0.001). The levels of serum LINE-1 hypomethylation at initial presentation correlated significantly with the presence of HBsAg, large tumor sizes, and advanced tumor stages classified by the CLIP score. Multivariate analyses showed that serum LINE-1 hypomethylation was a significant and independent prognostic factor of overall survival. CONCLUSION Serum LINE-1 hypomethylation may serve as a prognostic marker for patients with HCC.
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Affiliation(s)
- Pisit Tangkijvanich
- Department of Bichemistry, Faculty of Medicine, Chulalongkorn University, Thailand
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Chuang CK, Chu DC, Tzou RD, Liou SI, Chia JH, Sun CF. Hypermethylation of the CpG islands in the promoter region flanking GSTP1 gene is a potential plasma DNA biomarker for detecting prostate carcinoma. ACTA ACUST UNITED AC 2007; 31:59-63. [PMID: 17291695 DOI: 10.1016/j.cdp.2006.11.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2006] [Indexed: 11/23/2022]
Abstract
OBJECTIVES To investigate the possibility of identifying DNA hypermethylation in the circulation of prostate cancer patients. METHODS Plasma DNA samples were extracted from 36 prostate cancer patients and 27 benign prostate hyperplasia (BPH) cases. After extensive methylation-sensitive restriction enzyme digestion, the DNA samples were subjected to the real-time quantitative PCR amplification. Dissociation curve analysis was applied to determine if hypermethylation occurred in the promoter region flanking the GSTP1 gene, a well-documented epigenetic event among prostate cancer cells, in these plasma DNA samples. RESULTS 11 of 36 prostate cancer patients showed positive peak pattern, indicating methylation changes occurred. Concordant data were obtained from the corresponding paraffin-embedded tissue samples available from the Tumor Bank. Twenty-five of the 27 BPH cases showed negative results, suggesting no methylation changes happened in the CpG islands in these cases. CONCLUSIONS We have successfully identified prostate cancer genome hypermethylation in the peripheral circulation in prostate cancer patients with this protocol. This method can effectively distinguish BPH from prostate neoplasm. Although a larger number of samples are necessary to validate the capability of the protocol in practice, using plasma DNA sample is an ideal non-invasive approach for prostate neoplasm detection.
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Affiliation(s)
- Cheng-Keng Chuang
- Division of Urology, Department of Surgery, Chang Gung Memorial Hospital, Lin-kou, Taiwan
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17
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Fleischhacker M, Schmidt B. Circulating nucleic acids (CNAs) and cancer--a survey. Biochim Biophys Acta Rev Cancer 2006; 1775:181-232. [PMID: 17137717 DOI: 10.1016/j.bbcan.2006.10.001] [Citation(s) in RCA: 418] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 10/04/2006] [Accepted: 10/04/2006] [Indexed: 12/23/2022]
Abstract
It has been known for decades that it is possible to detect small amounts of extracellular nucleic acids in plasma and serum of healthy and diseased human beings. The unequivocal proof that part of these circulating nucleic acids (CNAs) is of tumor origin, initiated a surge of studies which confirmed and extended the original observations. In the past few years many experiments showed that tumor-associated alterations can be detected at the DNA and RNA level. At the DNA level the detection of point mutations, microsatellite alterations, chromosomal alterations, i.e. inversion and deletion, and hypermethylation of promoter sequences were demonstrated. At the RNA level the overexpression of tumor-associated genes was shown. These observations laid the foundation for the development of assays for an early detection of cancer as well as for other clinical means.
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Affiliation(s)
- M Fleischhacker
- Charité, Universitätsmedizin Berlin, Medizinische Klinik mS Onkologie u Hämatologie, CCM, Charitéplatz 1, 10117 Berlin, Germany.
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19
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Promoter hypermethylation of p16 gene and DAPK gene in sera from hepatocellular carcinoma (HCC) patients. Chin J Cancer Res 2005. [DOI: 10.1007/s11670-005-0020-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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20
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Kuang SY, Jackson PE, Wang JB, Lu PX, Muñoz A, Qian GS, Kensler TW, Groopman JD. Specific mutations of hepatitis B virus in plasma predict liver cancer development. Proc Natl Acad Sci U S A 2004; 101:3575-80. [PMID: 14990795 PMCID: PMC373504 DOI: 10.1073/pnas.0308232100] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Indexed: 12/18/2022] Open
Abstract
A major risk factor for hepatocellular carcinoma (HCC) is hepatitis B virus (HBV), whose pathogenesis is exacerbated by the acquisition of mutations that accelerate carcinogenesis. We examined, with mass spectrometry, the temporality of an HBV 1762(T)/1764(A) double mutation in plasma and tumors. Initial studies found that 52 of 70 (74.3%) tumors from patients residing in Qidong, People's Republic of China, contained this HBV mutation. Paired plasma samples were available for six of the tumor specimens; four tumors had the HBV 1762(T)/1764(A) mutation, whereas three of the paired plasma samples were also positive. The potential predictive value of this biomarker was explored by using stored plasma samples from a study of 120 residents of Qidong who had been monitored for aflatoxin exposure and HBV infection. After 10 years of passive follow-up, there were six cases of major liver disease including HCC (four cases), hepatitis (one case), and cirrhosis (one case). All six cases had detectable levels of the HBV 1762(T)/1764(A) mutation up to 8 years before diagnosis. Finally, 15 liver cancers were selected from a prospective cohort of 1,638 high-risk individuals in Qidong on the basis of available plasma samples spanning the years before and after diagnosis. The HBV 1762(T)/1764(A) mutation was detected in 8 of the 15 cases (53.3%) before cancer. The persistence of detection of this mutation was statistically significant (P = 0.022, two-tailed). We therefore found that a prediagnosis biomarker of specific HBV mutations can be measured in plasma and suggest this marker for use as an intermediate endpoint in prevention and intervention trials.
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Affiliation(s)
- Shuang-Yuan Kuang
- Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
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21
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Chu HJ, Heo J, Seo SB, Kim GH, Kang DH, Song GA, Cho M, Yang US. Detection of aberrant p16INK4A methylation in sera of patients with liver cirrhosis and hepatocellular carcinoma. J Korean Med Sci 2004; 19:83-6. [PMID: 14966347 PMCID: PMC2822270 DOI: 10.3346/jkms.2004.19.1.83] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinomas (HCCs) show genomic alterations, including DNA rearrangements associated with HBV DNA integration, loss of heterozygosity, and chromosomal amplification. The genes most frequently involved are those encoding tumor suppressors. The p16INK4A tumor suppressor gene frequently displays genetic alteration in HCC tissues. The present study was performed to examine the incidence of methylated p16INK4A in the sera of liver cirrhosis (LC) and HCC patients, and to evaluate its role as a tumor marker of HCC. The sera of 23 LC patients and 46 HCC patients were examined in this study. The methylation status of p16INK4A was evaluated by methylation-specific PCR of serum samples. Methylated p16INK4A was detected in 17.4% (4/23) of LC patients and in 47.8% (22/46) of HCC patients. No association was demonstrated between p16INK4A methylation and serum AFP level. As the status of p16INK4A methylation was not associated with serum AFP level, it may have a role as a tumor marker of HCC.
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Affiliation(s)
- Hyung Jun Chu
- Department of Internal Medicine, Pusan National University College of Medicine, 1-10 Ami-dong, Seo-gu, Busan 602-739, Korea.
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22
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Abstract
Circulating tumor nucleic acids in blood have been demonstrated to reflect the biologic characteristics of tumors. During tumor progression, aberrant DNA methylation can lead to transcriptional silencing of tumor suppressor genes, DNA repair genes, and metastasis-inhibitor genes. Hypermethylation of multiple genes, detectable in the blood of cancer patients, has demonstrated increasing promise as a specific and sensitive molecular marker for detecting and monitoring cancer. In addition to these epigenetic markers, a number of mRNA markers may also enable cancer detection in the blood of patients with different cancer types. Quantification of circulating tumor cell mRNAs in cancer patients appears to be useful for monitoring cancer progression and response to treatment. DNA methylation markers and mRNA markers in the blood may open up diagnostic and prognostic possibilities.
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Affiliation(s)
- Ivy H N Wong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, N.T., Hong Kong Special Administrative Region
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23
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Lui YYN, Dennis YML. Circulating DNA in plasma and serum: biology, preanalytical issues and diagnostic applications. Clin Chem Lab Med 2002; 40:962-8. [PMID: 12476933 DOI: 10.1515/cclm.2002.169] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The recent studies in circulating nucleic acids have brought about a new dimension to medical diagnostics. In oncology, various tumor-associated molecular alterations have been detected in the plasma/serum of cancer patients. These findings have important implications for the diagnosis, prognostication and monitoring of many types of malignancies. In pregnancy, the discovery of fetal DNA in maternal circulation has opened up a new source of fetal genetic material for noninvasive analysis for numerous fetal conditions and detection of certain pregnancy-associated disorders. The measurement of circulating DNA has also found potential application in the post-treatment monitoring of transplant patients and the assessment and prognostication of trauma patients. Although much attention has focused on circulating DNA, the knowledge of its biology is still at an early stage. For example, the origin and mechanisms of release of circulating DNA remain to be elucidated. The eventual clinical application of circulating DNA technology would also require the thorough elucidation of preanalytical factors that may affect its measurement in clinical laboratories.
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Affiliation(s)
- Yanni Y N Lui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR
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Lo YM. Quantitative analysis of Epstein-Barr virus DNA in plasma and serum: applications to tumor detection and monitoring. Ann N Y Acad Sci 2001; 945:68-72. [PMID: 11708496 DOI: 10.1111/j.1749-6632.2001.tb03865.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The recent interest in cell-free tumor-derived DNA in the plasma and serum of cancer patients has opened up numerous diagnostic possibilities. One type of tumor-derived DNA that has been detected in plasma/serum is viral DNA. One example of circulating viral nucleic acid is Epstein-Barr virus (EBV) DNA, which has been found in the plasma and serum of patients with nasopharyngeal carcinoma (NPC), certain lymphomas, and gastric carcinoma. Quantitative analysis of circulating EBV DNA in NPC has demonstrated a positive correlation with disease stage and a strong relationship with clinical events, as well as being of prognostic importance. For EBV-associated lymphomas, quantitative EBV DNA analysis has also been found to correlate closely with clinical progress. It is expected that plasma/serum EBV DNA analysis will soon be incorporated into the routine investigative protocol of EBV-associated malignancies.
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Affiliation(s)
- Y M Lo
- Department of Chemical Pathology and Institute of Molecular Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region.
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25
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Abstract
The recent interest in nucleic acids in plasma and serum has opened up numerous new areas of investigation and new possibilities for molecular diagnosis. In oncology, tumor-derived genetic changes, epigenetic alterations, and viral nucleic acids have been found in the plasma/serum of cancer patients. These findings have important implications for the detection, monitoring, and prognostication of many types of malignancies. In prenatal diagnosis, the discovery of fetal DNA in maternal plasma and serum has provided a noninvasive source of fetal genetic material for analysis. This development has important implications for the realization of noninvasive prenatal diagnosis and has provided new methods for the monitoring of pregnancy-associated disorders. Plasma DNA technology has also found recent applications in the fields of organ transplantation, posttrauma monitoring, and infectious agent detection. Future areas of study include circulating RNA in plasma and the elucidation of the biology of release, clearance, and possible functionality of plasma nucleic acids.
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Affiliation(s)
- Y M Lo
- Department of Chemical Pathology and Institute of Molecular Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region.
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26
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Wong IH, Yeo W, Leung T, Lau WY, Johnson PJ. Circulating tumor cell mRNAs in peripheral blood from hepatocellular carcinoma patients under radiotherapy, surgical resection or chemotherapy: a quantitative evaluation. Cancer Lett 2001; 167:183-91. [PMID: 11369140 DOI: 10.1016/s0304-3835(01)00455-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We assessed whether current therapies could lead to hematogenous dissemination of malignant hepatocytes in hepatocellular carcinoma (HCC) patients using semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) for alpha-fetoprotein (afp) and albumin (alb) mRNAs. We analyzed 137 peripheral blood samples before, during and after treatment from 84 patients under radiotherapy, surgical resection or chemotherapy. As compared to the upper limit for 53 healthy/non-HCC controls, alb- mRNA levels increased 2-10-fold in 6% of patients pre-treatment and 2-2.6x10(4)-fold in 32% post-treatment. Levels of afp- mRNA increased 3-210-fold in 17% pre-treatment and 4-5x10(5)-fold in 30% post-treatment. During a longitudinal follow-up of eight patients under radiotherapy or radiotherapy/resection, alb-mRNA levels were normal before treatment, whereas afp-mRNA levels increased 10-fold in two patients. During treatment, alb-mRNA and afp-mRNA levels increased 2-61-fold in three patients and 2.5-5-fold in two patients, respectively. After treatment, alb-mRNA levels declined to normal in all three patients within 3.5 months, but afp-mRNA levels increased 127-5x10(5)-fold in three patients within 5 months. We show evidence that HCC cells disseminating mostly post-treatment may be the 'seed' of recurrence/metastasis. In conjunction with the serum alpha-fetoprotein test, sequential afp-mRNA quantification could predict clinical metastasis/recurrence in 56% of patients during a 4-year follow-up.
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MESH Headings
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carcinoma, Hepatocellular/blood
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/secondary
- Carcinoma, Hepatocellular/therapy
- Combined Modality Therapy
- Follow-Up Studies
- Humans
- Liver Neoplasms/blood
- Liver Neoplasms/diagnosis
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Liver Neoplasms/therapy
- Neoplastic Cells, Circulating/metabolism
- Prognosis
- RNA, Messenger/blood
- Serum Albumin/genetics
- Serum Albumin/metabolism
- Survival Analysis
- Treatment Outcome
- Tumor Cells, Cultured
- alpha-Fetoproteins/genetics
- alpha-Fetoproteins/metabolism
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Affiliation(s)
- I H Wong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
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