Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
Drug resistance is an almost inevitable consequence of cancer therapy and ultimately proves fatal for the majority of patients. In many cases, this is the consequence of specific gene mutations that have the potential to be targeted to resensitize the tumor. The ability to uniformly saturate the genome with point mutations without chromosome or nucleotide sequence context bias would open the door to identify all putative drug resistance mutations in cancer models. Here, we describe such a method for elucidating drug resistance mechanisms using genome-wide chemical mutagenesis allied to next-generation sequencing. We show that chemically mutagenizing the genome of cancer cells dramatically increases the number of drug-resistant clones and allows the detection of both known and novel drug resistance mutations. We used an efficient computational process that allows for the rapid identification of involved pathways and druggable targets. Such a priori knowledge would greatly empower serial monitoring strategies for drug resistance in the clinic as well as the development of trials for drug-resistant patients.
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Jonathan S
JS
Brammeld
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Mia
M
Petljak
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Inigo
I
Martincorena
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Steven P
SP
Williams
European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge CB10 1SA, United Kingdom.
Luz Garcia
LG
Alonso
Pathology Department, Hospital del Mar, 08003 Barcelona, Spain.
Alba
A
Dalmases
Pathology Department, Hospital del Mar, 08003 Barcelona, Spain.
Beatriz
B
Bellosillo
Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro 76230, Mexico.
Carla Daniela
CD
Robles-Espinoza
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Stacey
S
Price
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Syd
S
Barthorpe
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Patrick
P
Tarpey
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Constantine
C
Alifrangis
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Graham
G
Bignell
Cancer Research Program, FIMIM and Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain.
Joana
J
Vidal
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Jamie
J
Young
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Lucy
L
Stebbings
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Kathryn
K
Beal
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Michael R
MR
Stratton
European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge CB10 1SA, United Kingdom.|RWTH Aachen University Hospital, 52062 Aachen, Germany.
Julio
J
Saez-Rodriguez
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Mathew
M
Garnett
Cancer Research Program, FIMIM and Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain.
Clara
C
Montagut
European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge CB10 1SA, United Kingdom.
Francesco
F
Iorio
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom.
Ultan
U
McDermott
D045744:Cell Line, Tumor; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D000067552:Mutation Accumulation; D059645:Mutation Rate; D017354:Point Mutation