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Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes
BACKGROUND: The ability to perform comprehensive profiling of cancers at high resolution is essential for precision medicine. Liquid biopsies using shed exosomes provide high-quality nucleic acids to obtain molecular characterization, which may be especially useful for visceral cancers that are not...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803451/ https://www.ncbi.nlm.nih.gov/pubmed/26681674 http://dx.doi.org/10.1093/annonc/mdv604 |
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author | San Lucas, F. A. Allenson, K. Bernard, V. Castillo, J. Kim, D. U. Ellis, K. Ehli, E. A. Davies, G. E. Petersen, J. L. Li, D. Wolff, R. Katz, M. Varadhachary, G. Wistuba, I. Maitra, A. Alvarez, H. |
author_facet | San Lucas, F. A. Allenson, K. Bernard, V. Castillo, J. Kim, D. U. Ellis, K. Ehli, E. A. Davies, G. E. Petersen, J. L. Li, D. Wolff, R. Katz, M. Varadhachary, G. Wistuba, I. Maitra, A. Alvarez, H. |
author_sort | San Lucas, F. A. |
collection | PubMed |
description | BACKGROUND: The ability to perform comprehensive profiling of cancers at high resolution is essential for precision medicine. Liquid biopsies using shed exosomes provide high-quality nucleic acids to obtain molecular characterization, which may be especially useful for visceral cancers that are not amenable to routine biopsies. PATIENTS AND METHODS: We isolated shed exosomes in biofluids from three patients with pancreaticobiliary cancers (two pancreatic, one ampullary). We performed comprehensive profiling of exoDNA and exoRNA by whole genome, exome and transcriptome sequencing using the Illumina HiSeq 2500 sequencer. We assessed the feasibility of calling copy number events, detecting mutational signatures and identifying potentially actionable mutations in exoDNA sequencing data, as well as expressed point mutations and gene fusions in exoRNA sequencing data. RESULTS: Whole-exome sequencing resulted in 95%–99% of the target regions covered at a mean depth of 133–490×. Genome-wide copy number profiles, and high estimates of tumor fractions (ranging from 56% to 82%), suggest robust representation of the tumor DNA within the shed exosomal compartment. Multiple actionable mutations, including alterations in NOTCH1 and BRCA2, were found in patient exoDNA samples. Further, RNA sequencing of shed exosomes identified the presence of expressed fusion genes, representing an avenue for elucidation of tumor neoantigens. CONCLUSIONS: We have demonstrated high-resolution profiling of the genomic and transcriptomic landscapes of visceral cancers. A wide range of cancer-derived biomarkers could be detected within the nucleic acid cargo of shed exosomes, including copy number profiles, point mutations, insertions, deletions, gene fusions and mutational signatures. Liquid biopsies using shed exosomes has the potential to be used as a clinical tool for cancer diagnosis, therapeutic stratification and treatment monitoring, precluding the need for direct tumor sampling. |
format | Online Article Text |
id | pubmed-4803451 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48034512016-03-23 Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes San Lucas, F. A. Allenson, K. Bernard, V. Castillo, J. Kim, D. U. Ellis, K. Ehli, E. A. Davies, G. E. Petersen, J. L. Li, D. Wolff, R. Katz, M. Varadhachary, G. Wistuba, I. Maitra, A. Alvarez, H. Ann Oncol Original Articles BACKGROUND: The ability to perform comprehensive profiling of cancers at high resolution is essential for precision medicine. Liquid biopsies using shed exosomes provide high-quality nucleic acids to obtain molecular characterization, which may be especially useful for visceral cancers that are not amenable to routine biopsies. PATIENTS AND METHODS: We isolated shed exosomes in biofluids from three patients with pancreaticobiliary cancers (two pancreatic, one ampullary). We performed comprehensive profiling of exoDNA and exoRNA by whole genome, exome and transcriptome sequencing using the Illumina HiSeq 2500 sequencer. We assessed the feasibility of calling copy number events, detecting mutational signatures and identifying potentially actionable mutations in exoDNA sequencing data, as well as expressed point mutations and gene fusions in exoRNA sequencing data. RESULTS: Whole-exome sequencing resulted in 95%–99% of the target regions covered at a mean depth of 133–490×. Genome-wide copy number profiles, and high estimates of tumor fractions (ranging from 56% to 82%), suggest robust representation of the tumor DNA within the shed exosomal compartment. Multiple actionable mutations, including alterations in NOTCH1 and BRCA2, were found in patient exoDNA samples. Further, RNA sequencing of shed exosomes identified the presence of expressed fusion genes, representing an avenue for elucidation of tumor neoantigens. CONCLUSIONS: We have demonstrated high-resolution profiling of the genomic and transcriptomic landscapes of visceral cancers. A wide range of cancer-derived biomarkers could be detected within the nucleic acid cargo of shed exosomes, including copy number profiles, point mutations, insertions, deletions, gene fusions and mutational signatures. Liquid biopsies using shed exosomes has the potential to be used as a clinical tool for cancer diagnosis, therapeutic stratification and treatment monitoring, precluding the need for direct tumor sampling. Oxford University Press 2016-04 2015-12-17 /pmc/articles/PMC4803451/ /pubmed/26681674 http://dx.doi.org/10.1093/annonc/mdv604 Text en © The Author 2015. Published by Oxford University Press on behalf of the European Society for Medical Oncology. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Original Articles San Lucas, F. A. Allenson, K. Bernard, V. Castillo, J. Kim, D. U. Ellis, K. Ehli, E. A. Davies, G. E. Petersen, J. L. Li, D. Wolff, R. Katz, M. Varadhachary, G. Wistuba, I. Maitra, A. Alvarez, H. Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
title | Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
title_full | Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
title_fullStr | Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
title_full_unstemmed | Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
title_short | Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
title_sort | minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803451/ https://www.ncbi.nlm.nih.gov/pubmed/26681674 http://dx.doi.org/10.1093/annonc/mdv604 |
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