Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes

F. A. San Lucas, K. Allenson, V. Bernard, J. Castillo, D. U. Kim, K. Ellis, E. A. Ehli, G. E. Davies, J. L. Petersen, D. Li, R. Wolff, M. Katz, G. Varadhachary, I. Wistuba, A. Maitra, H. Alvarez

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article numbermdv604
Pages (from-to)635-641
Number of pages7
JournalAnnals of Oncology
Volume27
Issue number4
DOIs
StatePublished - Apr 1 2016
Externally publishedYes

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Exosomes
Gene Fusion
Neoplasms
Exome
Biopsy
Point Mutation
Nucleic Acids
Genome
RNA Sequence Analysis
Precision Medicine
Mutation
Tumor Biomarkers
Pancreatic Neoplasms
Transcriptome
DNA

Keywords

  • Exosomes
  • Liquid biopsy
  • Next-generation sequencing
  • Pancreatic cancer

ASJC Scopus subject areas

  • Oncology
  • Hematology

Cite this

San Lucas, F. A., Allenson, K., Bernard, V., Castillo, J., Kim, D. U., Ellis, K., ... Alvarez, H. (2016). Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes. Annals of Oncology, 27(4), 635-641. [mdv604]. https://doi.org/10.1093/annonc/mdv604

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.

In: Annals of Oncology, Vol. 27, No. 4, mdv604, 01.04.2016, p. 635-641.

Research output: Contribution to journalArticle

San Lucas, FA, Allenson, K, Bernard, V, Castillo, J, Kim, DU, Ellis, K, Ehli, EA, Davies, GE, Petersen, JL, Li, D, Wolff, R, Katz, M, Varadhachary, G, Wistuba, I, Maitra, A & Alvarez, H 2016, 'Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes', Annals of Oncology, vol. 27, no. 4, mdv604, pp. 635-641. https://doi.org/10.1093/annonc/mdv604
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. In: Annals of Oncology. 2016 ; Vol. 27, No. 4. pp. 635-641.
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abstract = "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.",
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AU - San Lucas, F. A.

AU - Allenson, K.

AU - Bernard, V.

AU - Castillo, J.

AU - Kim, D. U.

AU - Ellis, K.

AU - Ehli, E. A.

AU - Davies, G. E.

AU - Petersen, J. L.

AU - Li, D.

AU - Wolff, R.

AU - Katz, M.

AU - Varadhachary, G.

AU - Wistuba, I.

AU - Maitra, A.

AU - Alvarez, H.

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N2 - 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.

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