Page 20 - 2019_04-Haematologica-web

Ferrata Storti Foundation
Liquid biopsy in lymphoma
Haematologica 2019 Volume 104(4):648-652
Background
The term “liquid biopsy” means accessing tumor DNA through a blood sam- pling, without the need of an invasive tissue biopsy. Cell-free fragments of DNA (cfDNA) are shed into the bloodstream by cells undergoing apoptosis and circu- late at a low concentration in plasma as double-stranded DNA fragments that are predominantly short (<200 base pairs).1 In healthy subjects, cfDNA primarily derives from the apoptosis of cells of hematopoietic lineage, with minimal con- tributions from other tissues, and circulates in concentrations of 1-10 ng/mL of plasma.2-8 In lymphoma patients, a proportion of cfDNA derives from apoptotic tumor cells.5 The total amount of cfDNA in lymphoma patients is always increased compared with age- and gender-matched healthy subjects, with a mean concentration of 30 ng/mL of plasma.9-12 Levels of circulating tumor DNA (ctDNA) vary across different lymphoma subtypes, being higher in aggressive lymphomas than in indolent lymphomas. Beside lymphoma type, tumor volume also affects cfDNA levels, which are higher in advanced stage disease than in limited stage disease, and in overt progressive disease than in a disease that is clinically responding to treatment.9,11
This perspective aims at describing the unmet needs in the field of diagnosis, genotyping, and assessment of treatment response in lymphomas that can be addressed by ctDNA technologies, as well as current evidence, and/or further investigations or actions that would be needed before transferring ctDNA tech- nologies into the clinic.
Technologies for ctDNA identification and measurement
By using the tumor mutation profile or the immunoglobulin gene rearrangement as lymphoma fingerprints, normal cfDNA can be discriminated from cfDNA derived from tumor cells, also called circulating tumor DNA (ctDNA).9,12-15 ctDNA fraction in the pool of cfDNA originating from hematopoietic cells is frequently very small. Therefore, the test used for ctDNA detection and quantification must suppress both the technical noise (i.e. reduce the background errors) and the bio- logical noise (i.e. suppress true mutations originating from an underlying clonal hematopoiesis by sequencing paired granulocytes genomic DNA) in order to reach the required analytical sensitivity and specificity.15,16 Finally, sensitivity strongly relies on input material quantity and quality. For example, a single gene test can only achieve a sensitivity of 1 in 10,000 (i.e. 10-4) if the input material matches or exceeds this threshold.
When the mutation profile is used as tumor fingerprint, the type of genetic aberrations being detected guide the choice of the molecular technique to be used for ctDNA identification and quantification. A single, trunk, fully clonal, stereotypic genetic variant, that occurs in most patients, characterizes a few lymphoma types [eg. the MYD88 L265P mutation in lymphoplasmacytic lym- phoma and primary central nervous system lymphoma (PCNSL)].17 Such muta- tions can be detected and quantified by PCR-based methods like mutation-spe- cific droplet digital PCR.17
Molecular aberrations of most lymphomas, however, are heterogeneous. Ultra-deep next-generation sequencing (NGS) methods can overcome the limita- tions of assays covering single somatic variants by detecting a large spectrum of genetic alterations, including single nucleotide variants, insertions/deletions, chromosomal rearrangements, and copy number changes.18-20 The Cancer Personalized Profiling by Deep Sequencing (CAPP-seq) is a targeted capture ultra-deep NGS method for ctDNA detection and quantification in molecular heterogeneous tumors (Figure 1).18,19 CAPP-seq utilizes a disease-specific “selec- tor”, which is a set of exonic and intronic targets chosen to cover regions of
Davide Rossi,1,2 Valeria Spina,1 Alessio Bruscaggin1 and Gianluca Gaidano3
1Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland; 2Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland and 3Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
Correspondence:
DAVIDE ROSSI
davide.rossi@eoc.ch
Received: January 22, 2019. Accepted: February 20, 2019 Pre-published: March 7, 2019.
doi:10.3324/haematol.2018.206177
Check the online version for the most updated information on this article, online supplements, and information on authorship & disclosures: www.haematologica.org/content/104/4/648
©2019 Ferrata Storti Foundation
Material published in Haematologica is covered by copyright. All rights are reserved to the Ferrata Storti Foundation. Use of published material is allowed under the following terms and conditions: https://creativecommons.org/licenses/by-nc/4.0/legalcode. Copies of published material are allowed for personal or inter- nal use. Sharing published material for non-commercial pur- poses is subject to the following conditions: https://creativecommons.org/licenses/by-nc/4.0/legalcode, sect. 3. Reproducing and sharing published material for com- mercial purposes is not allowed without permission in writing from the publisher.
648
haematologica | 2019; 104(4)
PERSPECTIVE ARTICLE