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. 2021 Apr 1;22(7):3667.
doi: 10.3390/ijms22073667.

Exosomes from Plasma of Neuroblastoma Patients Contain Doublestranded DNA Reflecting the Mutational Status of Parental Tumor Cells

Chiara Degli Esposti  1 , Barbara Iadarola  1 , Simone Maestri  1 , Cristina Beltrami  1 , Denise Lavezzari  1 , Martina Morini  2 , Patrizia De Marco  3 , Giovanni Erminio  4 , Alberto Garaventa  5 , Federico Zara  3 , Massimo Delledonne  1 , Marzia Ognibene  3 , Annalisa Pezzolo  6
Affiliations

Exosomes from Plasma of Neuroblastoma Patients Contain Doublestranded DNA Reflecting the Mutational Status of Parental Tumor Cells

Chiara Degli Esposti et al. Int J Mol Sci. .

Abstract

Neuroblastoma (NB) is an aggressive infancy tumor, leading cause of death among preschool age diseases. Here we focused on characterization of exosomal DNA (exo-DNA) isolated from plasma cell-derived exosomes of neuroblastoma patients, and its potential use for detection of somatic mutations present in the parental tumor cells. Exosomes are small extracellular membrane vesicles secreted by most cells, playing an important role in intercellular communications. Using an enzymatic method, we provided evidence for the presence of double-stranded DNA in the NB exosomes. Moreover, by whole exome sequencing, we demonstrated that NB exo-DNA represents the entire exome and that it carries tumor-specific genetic mutations, including those occurring on known oncogenes and tumor suppressor genes in neuroblastoma (ALK, CHD5, SHANK2, PHOX2B, TERT, FGFR1, and BRAF). NB exo-DNA can be useful to identify variants responsible for acquired resistance, such as mutations of ALK, TP53, and RAS/MAPK genes that appear in relapsed patients. The possibility to isolate and to enrich NB derived exosomes from plasma using surface markers, and the quick and easy extraction of exo-DNA, gives this methodology a translational potential in the clinic. Exo-DNA can be an attractive non-invasive biomarker for NB molecular diagnostic, especially when tissue biopsy cannot be easily available.

Keywords: ALK; exo-DNA; exosomes; genotypability; neuroblastoma; tumor mutation load.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Exo-DNA size profiling (Tape Station 4150). (A) Representative electropherogram of exo-DNA. (B) Exo-DNA library. (C) Target enrichment capture of exo-DNA (FU = fluorescence unit; bp = base pair).
Figure 2
Figure 2
Circular view of chromosomes coverage for two representative cases. Each color represents a different DNA specimen: Tumor DNA (red), exo-DNA at onset (blue), exo-DNA at relapse (green).
Figure 3
Figure 3
Venn diagrams of somatic single nucleotide variants (SNVs) shared by exo-DNA and tumor DNA. (A) SNVs in common between exo-DNA at onset and the corresponding tumor DNA. (B) SNVs in common among exo-DNA at onset, exo-DNA at relapse, and the corresponding tumor DNA. (C) SNVs in common between exo-DNA at onset and exo-DNA at relapse.
Figure 4
Figure 4
Somatic SNVs frequency in neuroblastoma (NB) cases with exo-DNA at onset and tumor DNA.
Figure 5
Figure 5
Somatic SNVs frequency in NB cases with exo-DNA at relapse.
Figure 6
Figure 6
Frequency of the somatic SNVs in common between tumor DNA and exo-DNA at onset (VAF = variant allele frequency).
Figure 7
Figure 7
Frequency of the somatic SNVs in common between exo-DNA at relapse and tumor DNA/exo-DNA at onset. (VAF = variant allele frequency).
Figure 8
Figure 8
Mutation types in exo-DNA and in tumor DNA.
See this image and copyright information in PMC

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