A biocomposite-based rapid sampling assay for circulating cell-free DNA in liquid biopsy samples from human cancers

Eo Jin Kim,Yong Shin,Huifang Liu,Yun-Yong Park,Bonhan Koo,Song Cheol Kim,Seok-Byung Lim,Eunsung Jun

doi:10.1038/s41598-020-72163-8

Eo Jin Kim, Yong Shin + Show 6 more

Open Access

https://doi.org/10.1038/s41598-020-72163-8

Copy DOI

Abstract

Cell-free nucleic acids (cfNAs) in liquid biopsy samples are emerging as important biomarkers for cancer diagnosis and monitoring, and for predicting treatment outcomes. Many cfNA isolation methods have been developed recently. However, most of these techniques are time-consuming, complex, require large equipment, and yield low-purity cfNAs because the genetic background of normal cells is amplified during cell lysis, which limits their clinical application. Here, we report a rapid and simple cfNA sampling platform that can overcome the limitations of conventional methods. We synthesised a biocomposite by combining amine-modified diatomaceous earth (DE) and cucurbituril (CB). The biocomposite platform showed high capture efficiency (86.78–90.26%) with genomic DNA and amplified DNA products (777, 525 and 150 bp). The biocomposite platform allowed the isolation of high purity and quantity cfDNAs from the plasma of 13 cancer patients (three colorectal cancer and ten pancreatic cancer samples) without requiring a lysis step or special equipment. The biocomposite platform may be useful to isolate cfNAs for the diagnosis and treatment of cancers in clinical applications.

Highlights

Cell-free nucleic acids in liquid biopsy samples are emerging as important biomarkers for cancer diagnosis and monitoring, and for predicting treatment outcomes
We performed Fourier transform infrared spectroscopy (FTIR) analysis to identify the properties of the biocomposite after the Cell-free DNA (cfDNA) binding
The application of the biocomposite platform includes the following steps (Fig. 1): (1) Mixing of blood plasma with biocomposite the biocomposite is mixed with blood plasma samples and shaken by hand to capture cfDNA. (2) Binding to cfDNA the amine groups of the fragmented cfDNA covalently bind to the C=O of the carbonyl portal of CB on the diatomaceous earth (DE)

Summary

Introduction

Cell-free nucleic acids (cfNAs) in liquid biopsy samples are emerging as important biomarkers for cancer diagnosis and monitoring, and for predicting treatment outcomes. Many cfNA isolation methods have been developed recently Most of these techniques are time-consuming, complex, require large equipment, and yield low-purity cfNAs because the genetic background of normal cells is amplified during cell lysis, which limits their clinical application. The biocomposite platform allowed the isolation of high purity and quantity cfDNAs from the plasma of 13 cancer patients (three colorectal cancer and ten pancreatic cancer samples) without requiring a lysis step or special equipment. To reduce the genetic background while increasing the detection sensitivity of ctDNA obtained from liquid biopsy, Jin et al developed a simple microfluidic platform to isolate cfDNA from colorectal cancer (CRC) samples without cell lysis[22]. There is no standard method of cfNA isolation and analysis for clinical application

Methods

Results

Conclusion