title: Tracking a CAD-ALK gene rearrangement in urine and blood of a colorectal cancer patient treated with an ALK inhibitor.
abstract: BACKGROUND
  Monitoring response and resistance to kinase inhibitors is essential to precision cancer medicine, and is usually investigated by molecular profiling of a tissue biopsy obtained at progression. However, tumor heterogeneity and tissue sampling bias limit the effectiveness of this strategy. In addition, tissue biopsies are not always feasible and are associated with risks due to the invasiveness of the procedure. To overcome these limitations, blood-based liquid biopsy analysis has proven effective to non-invasively follow tumor clonal evolution.
  
  
  METHODS
  We exploited urine cell-free, trans-renal DNA (tr-DNA) and matched plasma circulating tumor DNA (ctDNA) to monitor a metastatic colorectal cancer patient carrying a CAD-ALK translocation during treatment with an ALK inhibitor.
  
  
  RESULTS
  Using a custom next generation sequencing panel we identified the genomic CAD-ALK rearrangement and a TP53 mutation in plasma ctDNA. Sensitive assays were developed to detect both alterations in urine tr-DNA. The dynamics of the CAD-ALK rearrangement in plasma and urine were concordant and paralleled the patient's clinical course. Detection of the CAD-ALK gene fusion in urine tr-DNA anticipated radiological confirmation of disease progression. Analysis of plasma ctDNA identified ALK kinase mutations that emerged during treatment with the ALK inhibitor entrectinib.
  
  
  CONCLUSIONS
  We find that urine-based genetic testing allows tracing of tumor-specific oncogenic rearrangements. This strategy could be effectively applied to non-invasively monitor tumor evolution during therapy. The same approach could be exploited to monitor minimal residual disease after surgery with curative intent in patients whose tumors carry gene fusions. The latter could be implemented without the need of patient hospitalization since urine tr-DNA can be self-collected, is stable over time and can be shipped at specified time-points to central labs for testing.
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.|Department of Oncology, University of Torino, Candiolo.|FIRC Institute of Molecular Oncology (IFOM), Milan.
authors.forename: G
authors.initials: G
authors.lastname: Siravegna
authors.affiliation: Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Sartore-Bianchi
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.
authors.forename: B
authors.initials: B
authors.lastname: Mussolin
authors.affiliation: Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Cassingena
authors.affiliation: Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Amatu
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.
authors.forename: L
authors.initials: L
authors.lastname: Novara
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.
authors.forename: M
authors.initials: M
authors.lastname: Buscarino
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.
authors.forename: G
authors.initials: G
authors.lastname: Corti
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.|Department of Oncology, University of Torino, Candiolo.
authors.forename: G
authors.initials: G
authors.lastname: Crisafulli
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.
authors.forename: A
authors.initials: A
authors.lastname: Bartolini
authors.affiliation: Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Tosi
authors.affiliation: Trovagene, San Diego, USA.
authors.forename: M
authors.initials: M
authors.lastname: Erlander
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.|Department of Oncology, University of Torino, Candiolo.
authors.forename: F
authors.initials: F
authors.lastname: Di Nicolantonio
authors.affiliation: Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.|Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Siena
authors.affiliation: Candiolo Cancer Institute-FPO, IRCCS.|Department of Oncology, University of Torino, Candiolo.
authors.forename: A
authors.initials: A
authors.lastname: Bardelli
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D001221:Aspartate Carbamoyltransferase / Q000235:genetics*; D001549:Benzamides / Q000627:therapeutic use*; D014408:Biomarkers, Tumor; D002223:Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) / Q000235:genetics*; D015179:Colorectal Neoplasms / Q000097:blood / Q000188:drug therapy* / Q000235:genetics* / Q000652:urine; D004080:Dihydroorotase / Q000235:genetics*; D019008:Drug Resistance, Neoplasm; D005260:Female; D050939:Gene Fusion; D015321:Gene Rearrangement; D006801:Humans; D007191:Indazoles / Q000627:therapeutic use*; D008875:Middle Aged; D016133:Polymerase Chain Reaction / Q000379:methods; D020794:Receptor Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors* / Q000235:genetics
chemical_list: D001549:Benzamides; D014408:Biomarkers, Tumor; C033626:CAD trifunctional enzyme; D007191:Indazoles; D001221:Aspartate Carbamoyltransferase; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases; D004080:Dihydroorotase; D002223:Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing); C000607349:entrectinib
keywords: ALK inhibitor; ALK translocation; circulating DNA; colorectal cancer; liquid biopsy; trans-renal DNA