title: A candidate gene study of capecitabine-related toxicity in colorectal cancer identifies new toxicity variants at DPYD and a putative role for ENOSF1 rather than TYMS.
abstract: OBJECTIVE
  Capecitabine is an oral 5-fluorouracil (5-FU) pro-drug commonly used to treat colorectal carcinoma and other tumours. About 35% of patients experience dose-limiting toxicity. The few proven genetic biomarkers of 5-FU toxicity are rare variants and polymorphisms, respectively, at candidate loci dihydropyrimidine dehydrogenase (DPYD) and thymidylate synthase (TYMS).
  
  
  METHODS
  We investigated 1456 polymorphisms and rare coding variants near 25 candidate 5-FU pathway genes in 968 UK patients from the QUASAR2 clinical trial.
  
  
  RESULTS
  We identified the first common DPYD polymorphisms to be consistently associated with capecitabine toxicity, rs12132152 (toxicity allele frequency (TAF)=0.031, OR=3.83, p=4.31×10(-6)) and rs12022243 (TAF=0.196, OR=1.69, p=2.55×10(-5)). rs12132152 was particularly strongly associated with hand-foot syndrome (OR=6.1, p=3.6×10(-8)). The rs12132152 and rs12022243 associations were independent of each other and of previously reported DPYD toxicity variants. Next-generation sequencing additionally identified rare DPYD variant p.Ala551Thr in one patient with severe toxicity. Using functional predictions and published data, we assigned p.Ala551Thr as causal for toxicity. We found that polymorphism rs2612091, which lies within an intron of ENOSF1, was also associated with capecitabine toxicity (TAF=0.532, OR=1.59, p=5.28×10(-6)). ENSOF1 is adjacent to TYMS and there is a poorly characterised regulatory interaction between the two genes/proteins. Unexpectedly, rs2612091 fully explained the previously reported associations between capecitabine toxicity and the supposedly functional TYMS variants, 5'VNTR 2R/3R and 3'UTR 6 bp ins-del. rs2612091 genotypes were, moreover, consistently associated with ENOSF1 mRNA levels, but not with TYMS expression.
  
  
  CONCLUSIONS
  DPYD harbours rare and common capecitabine toxicity variants. The toxicity polymorphism in the TYMS region may actually act through ENOSF1.
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, UK.
authors.forename: Dan
authors.initials: D
authors.lastname: Rosmarin
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK.
authors.forename: Claire
authors.initials: C
authors.lastname: Palles
authors.affiliation: Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK.
authors.forename: Alistair
authors.initials: A
authors.lastname: Pagnamenta
authors.affiliation: Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK.
authors.forename: Kulvinder
authors.initials: K
authors.lastname: Kaur
authors.affiliation: Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Melchor Fernández Almagro 3, Madrid, Spain.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Pita
authors.affiliation: Department of Medical Oncology, Instituto de Investigacion Sanitaria Hospital General Universitario Gregorio Marañón, Universidad Complutense, Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Martin
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK.
authors.forename: Enric
authors.initials: E
authors.lastname: Domingo
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK.
authors.forename: Angela
authors.initials: A
authors.lastname: Jones
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK.
authors.forename: Kimberley
authors.initials: K
authors.lastname: Howarth
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK.
authors.forename: Luke
authors.identifier: http://orcid.org/0000-0001-7868-8528
authors.initials: L
authors.lastname: Freeman-Mills
authors.affiliation: Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, UK.
authors.forename: Elaine
authors.initials: E
authors.lastname: Johnstone
authors.affiliation: Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, UK.
authors.forename: Haitao
authors.initials: H
authors.lastname: Wang
authors.affiliation: Centre for Statistics in Medicine, University of Oxford, Botnar Research Centre, Oxford, UK.
authors.forename: Sharon
authors.initials: S
authors.lastname: Love
authors.affiliation: OCTO, University of Oxford, Old Road Campus Research Building, Oxford, UK.
authors.forename: Claire
authors.initials: C
authors.lastname: Scudder
authors.affiliation: OCTO, University of Oxford, Old Road Campus Research Building, Oxford, UK.
authors.forename: Patrick
authors.initials: P
authors.lastname: Julier
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK.
authors.forename: Ceres
authors.initials: C
authors.lastname: Fernández-Rozadilla
authors.affiliation: Galician Public Foundation of Genomic Medicine (FPGMX), CIBERER, Genomics Medicine Group, Hospital Clinico, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain.
authors.forename: Clara
authors.initials: C
authors.lastname: Ruiz-Ponte
authors.affiliation: Galician Public Foundation of Genomic Medicine (FPGMX), CIBERER, Genomics Medicine Group, Hospital Clinico, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain.
authors.forename: Angel
authors.initials: A
authors.lastname: Carracedo
authors.affiliation: Genetic Susceptibility to Colorectal Cancer Group, Gastrointestinal & Pancreatic Oncology Team, IDIBAPS/CIBERehd/Hospital Clínic, Centre Esther Koplowitz (CEK), Barcelona, Spain.
authors.forename: Sergi
authors.initials: S
authors.lastname: Castellvi-Bel
authors.affiliation: Institute of Digestive and Metabolic Diseases, Hospital Clínic, Barcelona, Spain.
authors.forename: Antoni
authors.initials: A
authors.lastname: Castells
authors.affiliation: Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Melchor Fernández Almagro 3, Madrid, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Gonzalez-Neira
authors.affiliation: Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK.
authors.forename: Jenny
authors.initials: J
authors.lastname: Taylor
authors.affiliation: Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Kerr
authors.affiliation: Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK.
authors.forename: David
authors.initials: D
authors.lastname: Kerr
authors.affiliation: Molecular and Population Genetics Laboratory, Oxford, UK Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Oxford, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Tomlinson
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000964:Antimetabolites, Antineoplastic / Q000009:adverse effects*; D000069287:Capecitabine; D015179:Colorectal Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D003841:Deoxycytidine / Q000009:adverse effects / Q000031:analogs & derivatives*; D042943:Dihydrouracil Dehydrogenase (NADP) / Q000235:genetics*; D005260:Female; D005472:Fluorouracil / Q000009:adverse effects / Q000031:analogs & derivatives*; D056726:Genetic Association Studies; D006801:Humans; D006836:Hydro-Lyases; D008297:Male; D008875:Middle Aged; D011110:Polymorphism, Genetic; D011506:Proteins / Q000235:genetics*; D013940:Thymidylate Synthase / Q000235:genetics*; D055815:Young Adult
chemical_list: D000964:Antimetabolites, Antineoplastic; D011506:Proteins; D003841:Deoxycytidine; D000069287:Capecitabine; D042943:Dihydrouracil Dehydrogenase (NADP); D013940:Thymidylate Synthase; C108693:ENOSF1 protein, human; D006836:Hydro-Lyases; D005472:Fluorouracil
keywords: Cancer; Cancer Genetics; Chemotherapy; Pharmacogenetics