An Improved Detection of Circulating Tumor DNA in Extracellular Vesicles-Depleted Plasma

Frontiers in Oncology

Hongbing Shen¹  Li Sun¹  Shukui Wang²  Mu Xu²  Xiaoxiang Chen²  Meijun Du³  Liang Wang⁴  Manish Kohli⁵  Chiang-Ching Huang⁷ 

[1] Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China;Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China;Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States;Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL, United States;Division of Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States;Laboratory Medicine Center, the Second Affiliated Hospital, Nanjing Medical University, Nanjing, China;Zilber School of Public Health, University of Wisconsin, Milwaukee, WI, United States;

关键词: ctDNA;    liquid biopsy;    plasma;    exosome;    copy number variation;   

DOI  :  10.3389/fonc.2021.691798

来源: DOAJ

【 摘 要 】

Circulating tumor DNA (ctDNA) in plasma has been used as a biomarker for cancer detection and outcome prediction. In this study, we collected the five precipitates (fractions 1–5) and leftover supernatant plasma component (fraction 6) by a sequential centrifugation in plasma samples from nine small cell lung cancer (SCLC) patients. The fractions 3, 5 and 6 were large vesicles, exosomes and extracellular vesicles (EVs)-depleted plasma, respectively. Fragment size analysis using DNAs from these fractions showed dramatical differences from a peak of 7–10 kb in fraction 1 to 140–160 bp in fraction 6. To determine ctDNA content, we performed whole genome sequencing and applied copy number-based algorithm to calculate ctDNA percentage. This analysis showed the highest ctDNA content in EV-depleted plasma (average = 27.22%), followed by exosomes (average = 22.09%) and large vesicles (average = 19.70%). Comparatively, whole plasma, which has been used in most ctDNA studies, showed an average of 23.84% ctDNA content in the same group of patients. To further demonstrate higher ctDNA content in fraction 6, we performed mutational analysis in the plasma samples from 22 non-small cell lung cancer (NSCLC) patients with known EGFR mutations. This analysis confirmed higher mutation detection rates in fraction 6 (14/22) than whole plasma (10/22). This study provides a new insight into potential application of using fractionated plasma for an improved ctDNA detection.

【 授权许可】

Unknown