Circulating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer
Authors: Qi Zhao
Guoliang Xu
Wenqiu Wang
Huiyan Luo
Shaohua Yi
Rui-Hua Xu
Weimin Li
Gen Li
Chaofeng Li
Hengying Pu
Zhixiang Zuo
Zexian Liu
Lianghong Zheng
Sumei Cao
Sarah Gibson
Xiaoke Hao
Hui Sheng
Yuying Liu
Kang Zhang
Haiyu Mo
Wanli Liu
Chuanbo Xie
Zhaolei Zeng
Wei Wei
Journal: Science Translational Medicine (2020)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Circulating tumor DNA; ctDNA; methylation markers; colorectal cancer; CRC
Affiliations: Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China., Guangzhou Youze Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, P.R. China., Huazhong University of Science and Technology Tongji Medical College, Wuhan 430030, P. R. China., Guangzhou Women and Children's Medical Center, Guangzhou 510623, P. R. China., Shanghai General Hospital, Shanghai 200080, P. R. China., Molecular Medicine Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China., Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, P. R. China., Faculty of Medicine, Macau University of Science and Technology, Macau 999078, P. R. China., Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P. R. China. .

Abstract:  Circulating tumor DNA (ctDNA) has emerged as a useful diagnostic and prognostic biomarker in many cancers. Here, we conducted a study to investigate the potential use of ctDNA methylation markers for the diagnosis and prognostication of colorectal cancer (CRC) and used a prospective cohort to validate their effectiveness in screening patients at high risk of CRC. We first identified CRC-specific methylation signatures by comparing CRC tissues to normal blood leukocytes. Then, we applied a machine learning algorithm to develop a predictive diagnostic and a prognostic model using cell-free DNA (cfDNA) samples from a cohort of 801 patients with CRC and 1021 normal controls. The obtained diagnostic prediction model discriminated patients with CRC from normal controls with high accuracy (area under curve = 0.96). The prognostic prediction model also effectively predicted the prognosis and survival of patients with CRC (P &lt; 0.001). In addition, we generated a ctDNA-based molecular classification of CRC using an unsupervised clustering method and obtained two subgroups of patients with CRC with significantly different overall survival (P = 0.011 in validation cohort). Last, we found that a single ctDNA methylation marker, cg10673833, could yield high sensitivity (89.7%) and specificity (86.8%) for detection of CRC and precancerous lesions in a high-risk population of 1493 participants in a prospective cohort study. Together, our findings showed the value of ctDNA methylation markers in the diagnosis, surveillance, and prognosis of CRC. 

Retracted: No

PubPeer comments:
 EoC: On 1 January 2020, Science Translational Medicine published the Research Article u201cCirculating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal canceru201d by H. Luo, Q. Zhao, W. Wei, L. Zheng, S. Yi, G. Li, W. Wang, H. Sheng, H. Pu, H. Mo, Z. Zuo, Z. Liu, C. Li, C. Xie, Z. Zeng, W. Li, X. Hao, Y. Liu, S. Cao, W. Liu, S. Gibson, K. Zhang, G. Xu, R.-h. Xu (1). Subsequently, it was brought to our attention that the methylation status at cg10673833 could not have been measured using the Behavioral Diagnostics assay indicated in the Materials and Methods, because this assay exclusively detects methylation at cg05575921. When Science Translational Medicine queried the authors, they provided a different description of their methods, stating that the primers and probes for their PCR-based assay were custom-designed and ordered from Thermo Fisher Scientific. However, it remains unclear why the erroneous information about the Behavioral Diagnostics assay was presented in the Materials and Methods. Given our continuing concerns about how exactly methylation at cg10673833 was measuredu2014the foundation upon which the results in this Research Article are basedu2014Science Translational Medicine is publishing an Editorial Expression of Concern in addition to an erratum to alert the scientific community to these concerns. Erratum for the Research Article: In the Research Article u201cCirculating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer,u201d the procedure for performing droplet digital PCR was incorrect in the Supplementary Materials and Methods. The original text stated that u201can aliquot of each sample was pre-amplified, diluted 1: 3000, and then PCR-amplified using fluorescent, dual-labeled primer-probe sets specific for cg10673833 from Behavioral Diagnostics (available for sale via IBI Scientific, www.ibisci.com) and Universal Digital PCR reagents and protocols from Bio-Rad.u201d The authors have corrected this text to indicate that u201cthe PCR primers and dual labeled fluorescent probes in the ddPCR assay were as following: forward primer, 5 - GTTTTATAAGGAGGTTGTGTT; reverse primer, 5 -AACIAAAAACCCTCCAAA; probe for methylated allele detection, 5 - FAM GAGGGGTCGGATGTTGG BHQ1-3 ; and probe for unmethylated allele detection, 5 -HEX GAGGGGTTGGATGTTGGG BHQ1-3 . The following cycling conditions were used: 98u00b0C for 10 min, followed by 40 cycles at 98u00b0C for 30 s and 53u00b0C for 60 s, and finally 98u00b0C for 10 min. The primers and probes were custom designed and synthesized by Thermo Fisher Scientific (www.thermofisher.com cn en home life-science oligonucleotides-primers-probes-genes applied-biosystems-custom-primers-probes.html). The ddPCR Supermix for Probes (Cat.18630125) and other universal Digital PCR reagents and protocols were purchased from Bio-Rad (www.bio-rad.com en-cn category digital-pcr?ID=M9HE2R15).u201d The Supplementary Materials PDF has been corrected. Via: https: retractionwatch.com 2020 04 22 former-ucsd-prof-who-resigned-amid-investigation-into-china-ties-has-paper-flagged-for-using-the-wrong-test ,