title: Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid.
abstract: BACKGROUND
  Dietary exposure to cytotoxic and carcinogenic aristolochic acid (AA) causes severe nephropathy typically associated with urologic cancers. Monitoring of AA exposure uses biomarkers such as aristolactam-DNA adducts, detected by mass spectrometry in the kidney cortex, or the somatic A>T transversion pattern characteristic of exposure to AA, as revealed by previous DNA-sequencing studies using fresh-frozen tumors.
  
  
  METHODS
  Here, we report a low-coverage whole-exome sequencing method (LC-WES) optimized for multisample detection of the AA mutational signature, and demonstrate its utility in 17 formalin-fixed paraffin-embedded urothelial tumors obtained from 15 patients with endemic nephropathy, an environmental form of AA nephropathy.
  
  
  RESULTS
  LC-WES identified the AA signature, alongside signatures of age and APOBEC enzyme activity, in 15 samples sequenced at the average per-base coverage of approximately 10×. Analysis at 3 to 9× coverage revealed the signature in 91% of the positive samples. The exome-wide distribution of the predominant A>T transversions exhibited a stochastic pattern, whereas 83 cancer driver genes were enriched for recurrent nonsynonymous A>T mutations. In two patients, pairs of tumors from different parts of the urinary tract, including the bladder, harbored overlapping mutation patterns, suggesting tumor dissemination via cell seeding.
  
  
  CONCLUSIONS
  LC-WES analysis of archived tumor tissues is a reliable method applicable to investigations of both the exposure to AA and its biologic effects in human carcinomas.
  
  
  CONCLUSIONS
  By detecting cancers associated with AA exposure in high-risk populations, LC-WES can support future molecular epidemiology studies and provide evidence-base for relevant preventive measures.
authors.affiliation: Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Castells
authors.affiliation: School of Medicine, University of Zagreb, Department of Nephrology, Hypertension, Dialysis, and Transplantation, University Hospital Center Zagreb, Zagreb, Croatia.
authors.forename: Sandra
authors.initials: S
authors.lastname: Karanović
authors.affiliation: Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Maude
authors.initials: M
authors.lastname: Ardin
authors.affiliation: General Hospital "Dr. Josip Benčević," Slavonski Brod, Croatia.
authors.forename: Karla
authors.initials: K
authors.lastname: Tomić
authors.affiliation: Department of Urology, Weill Cornell Medical College, New York, New York.
authors.forename: Evanguelos
authors.initials: E
authors.lastname: Xylinas
authors.affiliation: Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Geoffroy
authors.initials: G
authors.lastname: Durand
authors.affiliation: Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Villar
authors.affiliation: Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Forey
authors.affiliation: Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Le Calvez-Kelm
authors.affiliation: Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Voegele
authors.affiliation: General Hospital "Dr. Josip Benčević," Slavonski Brod, Croatia.
authors.forename: Krešimir
authors.initials: K
authors.lastname: Karlović
authors.affiliation: General Hospital "Dr. Josip Benčević," Slavonski Brod, Croatia.
authors.forename: Maja
authors.initials: M
authors.lastname: Mišić
authors.affiliation: General Hospital "Dr. Josip Benčević," Slavonski Brod, Croatia.
authors.forename: Damir
authors.initials: D
authors.lastname: Dittrich
authors.affiliation: OCS Genome Technology Center, New York University Langone Medical Center, New York, New York.
authors.forename: Igor
authors.initials: I
authors.lastname: Dolgalev
authors.affiliation: Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: James
authors.initials: J
authors.lastname: McKay
authors.affiliation: Department of Urology, Weill Cornell Medical College, New York, New York.
authors.forename: Shahrokh F
authors.initials: SF
authors.lastname: Shariat
authors.affiliation: Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York.
authors.forename: Viktoria S
authors.initials: VS
authors.lastname: Sidorenko
authors.affiliation: Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York.
authors.forename: Andrea
authors.initials: A
authors.lastname: Fernandes
authors.affiliation: OCS Genome Technology Center, New York University Langone Medical Center, New York, New York.
authors.forename: Adriana
authors.initials: A
authors.lastname: Heguy
authors.affiliation: Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York. Department of Medicine, Stony Brook University, Stony Brook, New York.
authors.forename: Kathleen G
authors.initials: KG
authors.lastname: Dickman
authors.affiliation: Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Olivier
authors.affiliation: Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York. Department of Medicine, Stony Brook University, Stony Brook, New York.
authors.forename: Arthur P
authors.initials: AP
authors.lastname: Grollman
authors.affiliation: School of Medicine, University of Zagreb, Department of Nephrology, Hypertension, Dialysis, and Transplantation, University Hospital Center Zagreb, Zagreb, Croatia.
authors.forename: Bojan
authors.initials: B
authors.lastname: Jelaković
authors.affiliation: Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France. zavadilj@iarc.fr.
authors.forename: Jiri
authors.initials: J
authors.lastname: Zavadil
mesh_terms: D034341:Aristolochic Acids / Q000032:analysis*; D002273:Carcinogens / Q000032:analysis; D059472:Exome / Q000187:drug effects*; D005557:Formaldehyde; D006801:Humans; D009369:Neoplasms / Q000737:chemistry* / Q000235:genetics* / Q000473:pathology; D016612:Paraffin Embedding; D017422:Sequence Analysis, DNA / Q000379:methods; D016707:Tissue Fixation
chemical_list: D034341:Aristolochic Acids; D002273:Carcinogens; D005557:Formaldehyde; C000228:aristolochic acid I