Comparison of Genetic and Epigenetic Alterations of Primary Tumors and Matched Plasma Samples in Patients with Colorectal Cancer

被引:38
作者
Danese, Elisa [1 ]
Minicozzi, Anna Maria [2 ]
Benati, Marco [1 ]
Montagnana, Martina [1 ]
Paviati, Elisa [1 ]
Salvagno, Gian Luca [1 ]
Lima-Oliveira, Gabriel [1 ]
Gusella, Milena [3 ]
Pasini, Felice [4 ]
Lippi, Giuseppe [5 ]
Guidi, Gian Cesare [1 ]
机构
[1] Univ Hosp Verona, Dept Life & Reprod Sci, Lab Clin Biochem, Verona, Italy
[2] Queen Mary Univ London, Barts & London NHS Trust, Acad Surg Unit, NCBRSI, London, England
[3] Rovigo Gen Hosp, Lab Pharmacol & Mol Biol, Dept Oncol, Rovigo, Italy
[4] Rovigo Hosp, Dept Med Oncol, Rovigo, Italy
[5] Acad Hosp Parma, Lab Clin Chem & Hematol, Parma, Italy
关键词
CELL-FREE DNA; KRAS MUTATIONS; PERIPHERAL-BLOOD; BRAF MUTATIONS; METHYLATION; CETUXIMAB; EVOLUTION; THERAPY; BIOPSY; SERUM;
D O I
10.1371/journal.pone.0126417
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background Although recent advances in circulating DNA analysis allow the prediction of tumor genomes by noninvasive means, some challenges remain, which limit the widespread introduction of cfDNA in cancer diagnostics. We analyzed the status of the two best characterized colorectal cancer (CRC) genetic and epigenetic alterations in a cohort of CRC patients, and then compared the degree to which the two patterns move from tissue to plasma in order to improve our understanding of biology modulating the concordance between tissues and plasma methylation and mutation profiles. Methods Plasma and tumor tissues were collected from 85 patients (69 +/- 14 years, 56 males). KRAS and SEPT9 status was assessed by allele refractory mutation system quantitative PCR and quantitative methylation-specific PCR, respectively. Six of the most common point mutations at codon 12 and 13 were investigated for KRAS analysis. Results KRAS mutations and SEPT9 promoter methylation were present in 34% (29/85) and in 82% (70/85) of primary tumor tissue samples. Both genetic and epigenetic analyses of cfDNA revealed a high overall concordance and specificity compared with tumor-tissue analyses. Patients presenting with both genetic and epigenetic alterations in tissue specimens (31.8%, 27/85) were considered for further analyses. The median methylation rates in tumour tissues and plasma samples were 64.5%(12.2-99.8%) and 14.5%(0-45.5%), respectively. The median KRAS mutation load (for matched mutations) was 33.6% (1.886.3%) in tissues and 2.9% (0-17.3) in plasma samples. The plasma/tissue (p/t) ratio of SEPT9 methylation rate was significantly higher than the p/t ratio of KRAS mutation load, especially in early stage cancers (p=0.0108). Conclusion The results of this study show a discrepant rate of epigenetic vs. genetic alterations moving from tissue to plasma. Many factors could affect mutation cfDNA analysis, including both presence of tumor clonal heterogeneity and strict compartmentalization of KRAS mutation profile. The present study highlights the importance of considering the nature of the alteration when analyzing tumor-derived cfDNA.
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页数:11
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