Cell free circulating tumor nucleic acids, a revolution in personalized cancer medicine

doi:10.1016/j.critrevonc.2019.102827

Critical Reviews in Oncology/Hematology

Volume 144, December 2019, 102827

https://doi.org/10.1016/j.critrevonc.2019.102827 Get rights and content

Abstract

Innovative diagnostics are becoming an essential component in personalized cancer medicine. These diagnostics are increasingly based on cell-free nucleic acids and membrane vesicles. Isolating and sequencing cell free circulating DNA (cfDNA) in plasma may progressively substitute tumor biopsies. A small albeit now detectable fraction of cfDNA correspond to circulating tumor DNA (ctDNA). In this review, we describe the pre-analytical procedures for collecting ctDNA from plasma, since these procedures should be optimized within laboratories depending on the available infrastructures. We also provide an overview of the technological breakthrough in ctDNA Isolation for instance digital PCR methods and next generation sequencing techniques and discuss their key challenges. The clinical implementations of liquid biopsy and more specifically ctDNA in cancer management are reviewed. We predict in the near future, ctDNA will be used more routinely to guide cancer treatment and provide a new approach to personalize treatment in precision medicine.

Section snippets

The history of liquid biopsy

In 1948, Mandel and Métais detected and quantified the presence of cell-free nucleic acid (cfNA) in human blood of both healthy and diseased patients for the first time (Schwarzenbach et al., 2011). In 1966, researchers discovered high levels of cfDNA in lupus patients (Thierry et al., 2016). These studies attracted some attention in the scientific community and the presence of tumor-specific mutations in cfNA was not reported by scientists until 1994. In the plasma of patients with pancreatic

The source of ctDNA

Circulating tumor DNA or ctDNA can be released from CTCs, primary and secondary tumors into the circulation of cancer patients. They could be presented in many forms; either cfDNA, bound to complex proteins, bound to cell surfaces, or vesicles (Thierry et al., 2016). Most ctDNA is made up of apoptotic and/or necrotic tumor cells that release their divided DNA into the blood (Wang et al., 2017b, 2003) (Fig. 1). Besides, viable tumor cells can release microvesicles (or exosomes), which are

The quantity of ctDNA in bloodstream

The number of cfDNA copies in cancer patients varies extensively (Lange and Laird, 2013), which depends on the tumor type, location and cancer stage (Han et al., 2017). While the concentration of cfDNA in cancer patients' blood is higher than in healthy individuals' blood and non-malignant patients, the concentration of cfDNA varies significantly with an average of 180 ng/mL (Barbany et al., 2019). However, in some studies less than 100 ng/mL has been reported for the most of cancer patients (

Detection methods

Circulating tumor DNA containing the same molecular aberrations as the solid tumor, found in the bloodstream, refers to DNA from cancer cells and tumors (Thierry et al., 2016). Several methods can detect the existence of tumor-derived DNA in cfDNA. Nonetheless, the low amount, high degradation, and high mix of normal cfDNA with ctDNA cause serious challenges to choose the appropriate detection method. Since almost all tumors are marked by various subclonal populations, the problem would be

ctDNA as biomarkers

The detection of ctDNA in plasma could be useful for many diagnostic applications in addition to limiting the need for solid biopsies (Wang et al., 2017a). The discovery of a proportion of circulating DNA in cancer patients has created the potential for a so-called "liquid biopsy" to mark tumor genetic characteristics as an alternative to tissue biopsy (Esposito et al., 2016). CtDNAs are thought to be easily detected even in the early stages of cancer patients’ plasma (Alix-Panabieres and

Challenges for diagnostic and prognostic tests

As we move into the era of personalized cancer medicine, the need for more innovative cancer diagnostic and prognostic assays would seriously raise. Cellular nanoparticulates such as cfNAs (cfDNA, cfRNA) are now considered as important biomarkers with high performance in medicine. There is huge hope that blood-borne cfNA could replace more invasive tumor solid biopsies in order to detect mutation/methylation in cancer and monitor treatment. Usually, conventional techniques for cfDNA biomarker

Future developments in personalized medicine

CTCs and ctDNA analyses have paved new diagnostic and prognostic avenues and are nominated to date the bases of liquid biopsy. To what extent in the future they might replace tumor solid biopsies is not completely known but their contribution in molecular personalized medicine is anticipated. However, they are not expected to entirely replace tumor biopsies since they cannot address many important factors such as changes in and interactions with the tumor microenvironment (Lewis et al., 2015).

Conclusions

In the next few years, liquid biopsy especially cfDNA-based will be implemented in clinical studies and drug development and it will likely become an integral part of diagnostics in oncology but to reach that goal, a more laborious plan of devoted research with appropriate cohort studies and standardized analytical methods is necessary.

Funding

This study was supported financially by Iran National Science Foundation (INSF; proposal number: 93048371).

Authors’ contributions

MAK and AP designed the study. MAK and AP drafted the manuscript. MAK, and JPT coordinated, edited, and finalized the drafting of the manuscript. All authors read and approved the final manuscript.

Declaration of Competing Interest

The authors declare that they have no competing interests.

Acknowledgements

Our sincere thanks go to Mrs. Afsaneh Mojtabanezhad Shariatpanahi, and Ms Marjan Azghandi, who provided good comments and feedback, Ms. Mona Nematy who designed and drew the figures and Mr. Ebrahim Pouladin for his support in cancer research programs.

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Cell free circulating tumor nucleic acids, a revolution in personalized cancer medicine

Abstract

Section snippets

The history of liquid biopsy

The source of ctDNA

The quantity of ctDNA in bloodstream

Detection methods

ctDNA as biomarkers

Challenges for diagnostic and prognostic tests

Future developments in personalized medicine

Conclusions

Funding

Authors’ contributions

Declaration of Competing Interest

Acknowledgements

Gastroenterology

Adv. Clin. Chem.

Cell

Mol. Ther. Nucleic Acids

Clin. Chim. Acta

Pharmacol. Ther.

Clin. Biochem.

EBioMedicine

Crit. Rev. Oncol. Hematol.

J. Invest. Dermatol.

Curr. Probl. Cancer

Genomics Proteomics Bioinformatics

Cancer Cell

Clin. Chim. Acta

Lancet

Am. J. Hum. Genet.

Cancer Treat. Rev.

Methods

Clinical applications of circulating tumor cells and circulating tumor DNA as liquid biopsy

Cancer Discov.

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

Nat. Med.

Detection of pancreas site-specific methylation from circulating DNA of patients with pancreatic Cancer; a potential biomarker for liquid biopsy

Gastroenterology

Androgen receptor gene aberrations in circulating cell-free DNA: biomarkers of therapeutic resistance in castration-resistant prostate Cancer

Clin. Cancer Res.

Cell-free tumour DNA testing for early detection of cancer - a potential future tool

J. Intern. Med.

Detection of circulating tumor DNA in early- and late-stage human malignancies

Sci. Transl. Med.

Direct quantification of cell-free, circulating DNA from unpurified plasma

PLoS One

Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas

Nat. Genet.

Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing

Clin. Chem.

Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer

Gut

Circulating MYCN DNA as a tumor-specific marker in neuroblastoma patients

Cancer Res.

Analysis of circulating tumor DNA to monitor metastatic breast cancer

N. Engl. J. Med.

Circulating mutant DNA to assess tumor dynamics

Nat. Med.

Detection and quantification of mutations in the plasma of patients with colorectal tumors

Proc. Natl. Acad. Sci. U. S. A.

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations

Proc. Natl. Acad. Sci. U. S. A.

Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management

Comput. Struct. Biotechnol. J.

A direct comparison of CellSearch and ISET for circulating tumour-cell detection in patients with metastatic carcinomas

Br. J. Cancer

New evidence that a large proportion of human blood plasma cell-free DNA is localized in exosomes

PLoS One

Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA

Sci. Transl. Med.

Cell-free nucleic acids circulating in the plasma of colorectal cancer patients induce the oncogenic transformation of susceptible cultured cells

Cancer Res.

Blood clearance kinetics and liver uptake of mononucleosomes in mice

J. Immunol.

Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence

N. Engl. J. Med.

Noninvasive detection of HER2 amplification with plasma DNA digital PCR

Clin. Cancer Res.

TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study