Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

Jarno Drost; Ruben van Boxtel; Francis Blokzijl; Tomohiro Mizutani; Nobuo Sasaki; Valentina Sasselli; Joep de Ligt; Sam Behjati; Judith E Grolleman; Tom van Wezel; Serena Nik-Zainal; Roland P Kuiper; Edwin Cuppen; Hans Clevers

doi:10.1126/science.aao3130

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

Jarno Drost, Ruben van Boxtel, Francis Blokzijl, Tomohiro Mizutani, Nobuo Sasaki, Valentina Sasselli, Joep de Ligt, Sam Behjati, Judith E Grolleman, Tom van Wezel, Serena Nik-Zainal, Roland P Kuiper, Edwin Cuppen, Hans Clevers

Group Clevers

Research output: Contribution to journal › Article › peer-review

324 Citations (Scopus)

Abstract

Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology and could hold diagnostic and prognostic value. We developed a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR-Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed subcloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers. Application of this strategy to the cancer predisposition gene NTHL1, which encodes a base excision repair protein, revealed a mutational footprint (signature 30) previously observed in a breast cancer cohort. We show that signature 30 can arise from germline NTHL1 mutations.

Original language	English
Pages (from-to)	234-238
Number of pages	5
Journal	Science
Volume	358
Issue number	6360
DOIs	https://doi.org/10.1126/science.aao3130
Publication status	Published - 13 Oct 2017

Keywords

Breast Neoplasms/genetics
CRISPR-Cas Systems
Colon
Colorectal Neoplasms/genetics
DNA Mismatch Repair/genetics
DNA Repair/genetics
DNA Replication
Deoxyribonuclease (Pyrimidine Dimer)/genetics
Female
Germ-Line Mutation
Humans
INDEL Mutation
MutL Protein Homolog 1/genetics
Mutagenesis
Neoplasms/genetics
Organoids
Stem Cells

Access to Document

10.1126/science.aao3130

Cite this

Drost, J., van Boxtel, R., Blokzijl, F., Mizutani, T., Sasaki, N., Sasselli, V., de Ligt, J., Behjati, S., Grolleman, J. E., van Wezel, T., Nik-Zainal, S., Kuiper, R. P., Cuppen, E., & Clevers, H. (2017). Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Science, 358(6360), 234-238. https://doi.org/10.1126/science.aao3130

@article{4009984ec2104eada08fd19ab50ec18a,

title = "Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer",

abstract = "Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology and could hold diagnostic and prognostic value. We developed a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR-Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed subcloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers. Application of this strategy to the cancer predisposition gene NTHL1, which encodes a base excision repair protein, revealed a mutational footprint (signature 30) previously observed in a breast cancer cohort. We show that signature 30 can arise from germline NTHL1 mutations.",

keywords = "Breast Neoplasms/genetics, CRISPR-Cas Systems, Colon, Colorectal Neoplasms/genetics, DNA Mismatch Repair/genetics, DNA Repair/genetics, DNA Replication, Deoxyribonuclease (Pyrimidine Dimer)/genetics, Female, Germ-Line Mutation, Humans, INDEL Mutation, MutL Protein Homolog 1/genetics, Mutagenesis, Neoplasms/genetics, Organoids, Stem Cells",

author = "Jarno Drost and {van Boxtel}, Ruben and Francis Blokzijl and Tomohiro Mizutani and Nobuo Sasaki and Valentina Sasselli and {de Ligt}, Joep and Sam Behjati and Grolleman, {Judith E} and {van Wezel}, Tom and Serena Nik-Zainal and Kuiper, {Roland P} and Edwin Cuppen and Hans Clevers",

note = "Copyright {\textcopyright} 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.",

year = "2017",

month = oct,

day = "13",

doi = "10.1126/science.aao3130",

language = "English",

volume = "358",

pages = "234--238",

journal = "Science",

issn = "1095-9203",

publisher = "American Association for the Advancement of Science",

number = "6360",

}

Drost, J , van Boxtel, R, Blokzijl, F, Mizutani, T, Sasaki, N, Sasselli, V, de Ligt, J, Behjati, S, Grolleman, JE, van Wezel, T, Nik-Zainal, S, Kuiper, RP, Cuppen, E & Clevers, H 2017, 'Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer', Science, vol. 358, no. 6360, pp. 234-238. https://doi.org/10.1126/science.aao3130

TY - JOUR

T1 - Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

AU - Drost, Jarno

AU - van Boxtel, Ruben

AU - Blokzijl, Francis

AU - Mizutani, Tomohiro

AU - Sasaki, Nobuo

AU - Sasselli, Valentina

AU - de Ligt, Joep

AU - Behjati, Sam

AU - Grolleman, Judith E

AU - van Wezel, Tom

AU - Nik-Zainal, Serena

AU - Kuiper, Roland P

AU - Cuppen, Edwin

AU - Clevers, Hans

PY - 2017/10/13

Y1 - 2017/10/13

N2 - Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology and could hold diagnostic and prognostic value. We developed a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR-Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed subcloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers. Application of this strategy to the cancer predisposition gene NTHL1, which encodes a base excision repair protein, revealed a mutational footprint (signature 30) previously observed in a breast cancer cohort. We show that signature 30 can arise from germline NTHL1 mutations.

AB - Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology and could hold diagnostic and prognostic value. We developed a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR-Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed subcloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers. Application of this strategy to the cancer predisposition gene NTHL1, which encodes a base excision repair protein, revealed a mutational footprint (signature 30) previously observed in a breast cancer cohort. We show that signature 30 can arise from germline NTHL1 mutations.

KW - Breast Neoplasms/genetics

KW - CRISPR-Cas Systems

KW - Colon

KW - Colorectal Neoplasms/genetics

KW - DNA Mismatch Repair/genetics

KW - DNA Repair/genetics

KW - DNA Replication

KW - Deoxyribonuclease (Pyrimidine Dimer)/genetics

KW - Female

KW - Germ-Line Mutation

KW - Humans

KW - INDEL Mutation

KW - MutL Protein Homolog 1/genetics

KW - Mutagenesis

KW - Neoplasms/genetics

KW - Organoids

KW - Stem Cells

UR - http://www.scopus.com/inward/record.url?scp=85029574202&partnerID=8YFLogxK

U2 - 10.1126/science.aao3130

DO - 10.1126/science.aao3130

M3 - Article

C2 - 28912133

SN - 1095-9203

VL - 358

SP - 234

EP - 238

JO - Science

JF - Science

IS - 6360

ER -

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

Abstract

Keywords

Access to Document

Fingerprint

Cite this