title: Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes.
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.
  
  
  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.
authors.affiliation: Department of Translational Molecular Pathology Department of Pathology.
authors.forename: F A
authors.initials: FA
authors.lastname: San Lucas
authors.affiliation: Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston.
authors.forename: K
authors.initials: K
authors.lastname: Allenson
authors.affiliation: Department of Pathology The University of Texas Graduate School of Biomedical Sciences at Houston, Houston.
authors.forename: V
authors.initials: V
authors.lastname: Bernard
authors.affiliation: Department of Pathology.
authors.forename: J
authors.initials: J
authors.lastname: Castillo
authors.affiliation: Department of Pathology.
authors.forename: D U
authors.initials: DU
authors.lastname: Kim
authors.affiliation: Department of Pathology.
authors.forename: K
authors.initials: K
authors.lastname: Ellis
authors.affiliation: Avera Institute for Human Genetics, Sioux Falls.
authors.forename: E A
authors.initials: EA
authors.lastname: Ehli
authors.affiliation: Avera Institute for Human Genetics, Sioux Falls.
authors.forename: G E
authors.initials: GE
authors.lastname: Davies
authors.affiliation: Avera Institute for Human Genetics, Sioux Falls.
authors.forename: J L
authors.initials: JL
authors.lastname: Petersen
authors.affiliation: Department of Gastrointestinal (GI) Medical Oncology.
authors.forename: D
authors.initials: D
authors.lastname: Li
authors.affiliation: Department of Gastrointestinal (GI) Medical Oncology.
authors.forename: R
authors.initials: R
authors.lastname: Wolff
authors.affiliation: Department of Gastrointestinal (GI) Medical Oncology.
authors.forename: M
authors.initials: M
authors.lastname: Katz
authors.affiliation: Department of Gastrointestinal (GI) Medical Oncology.
authors.forename: G
authors.initials: G
authors.lastname: Varadhachary
authors.affiliation: Department of Translational Molecular Pathology.
authors.forename: I
authors.initials: I
authors.lastname: Wistuba
authors.affiliation: Department of Translational Molecular Pathology Department of Pathology Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas MD Anderson Cancer Center, Houston, USA amaitra@mdanderson.org.
authors.forename: A
authors.initials: A
authors.lastname: Maitra
authors.affiliation: Department of Pathology.
authors.forename: H
authors.initials: H
authors.lastname: Alvarez
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000096:biosynthesis / Q000235:genetics*; D059472:Exome / Q000235:genetics; D055354:Exosomes / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009363:Neoplasm Proteins / Q000096:biosynthesis / Q000235:genetics*; D010190:Pancreatic Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: exosomes; liquid biopsy; next-generation sequencing; pancreatic cancer