Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Marco Gerlinger; Andrew J. Rowan; Stuart Horswell; James Larkin; David Endesfelder; Eva Gronroos; Pierre Martinez; Nicholas Matthews; Aengus Stewart; Patrick Tarpey; Ignacio Varela; Benjamin Phillimore; Sharmin Begum; Neil Q. McDonald; Adam Butler; David Jones; Keiran Raine; Calli Latimer; Claudio R. Santos; Mahrokh Nohadani; Aron Charles Eklund; Bradley Spencer-Dene; Graham Clark; Lisa Pickering; Gordon Stamp; Martin Gore; Zoltan Imre Szallasi; Julian Downward; P. Andrew Futreal; Charles Swanton

doi:10.1056/NEJMoa1113205

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Marco Gerlinger, Andrew J. Rowan, Stuart Horswell, James Larkin, David Endesfelder, Eva Gronroos, Pierre Martinez, Nicholas Matthews, Aengus Stewart, Patrick Tarpey, Ignacio Varela, Benjamin Phillimore, Sharmin Begum, Neil Q. McDonald, Adam Butler, David Jones, Keiran Raine, Calli Latimer, Claudio R. Santos, Mahrokh NohadaniAron Charles Eklund, Bradley Spencer-Dene, Graham Clark, Lisa Pickering, Gordon Stamp, Martin Gore, Zoltan Imre Szallasi, Julian Downward, P. Andrew Futreal, Charles Swanton

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

BACKGROUND: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.METHODSTo examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression.RESULTS: Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors.CONCLUSIONS: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

Original language	English
Journal	The New England Journal of Medicine
Volume	366
Issue number	10
Pages (from-to)	883-892
ISSN	0028-4793
DOIs	https://doi.org/10.1056/NEJMoa1113205
Publication status	Published - 2012

Keywords

Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common
human KDM5C gene [Hominidae]
human PTEN gene [Hominidae]
human SETD2 gene [Hominidae]
mammalian target of rapamycin kinase
messenger RNA mRNA
03502, Genetics - General
03508, Genetics - Human
10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
15506, Urinary system - Pathology
24004, Neoplasms - Pathology, clinical aspects and systemic effects
Molecular Genetics
Nephrology
Oncology
renal carcinoma Kidney Neoplasms (MeSH) Carcinoma (MeSH) urologic disease, neoplastic disease
branched evolution
intratumor heterogeneity
Biochemistry and Molecular Biophysics
Human Medicine, Medical Sciences
chromosome aberration analysis laboratory techniques, genetic techniques
exome sequencing laboratory techniques, genetic techniques
immunohistochemical analysis laboratory techniques, immunologic techniques
multiregion sequencing laboratory techniques, genetic techniques
mutation functional analysis laboratory techniques, genetic techniques
ploidy profiling laboratory techniques, genetic techniques

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1056/NEJMoa1113205

OpenUrl availability

Full text

Cite this

Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., Varela, I., Phillimore, B., Begum, S., McDonald, N. Q., Butler, A., Jones, D., Raine, K., Latimer, C., Santos, C. R., ... Swanton, C. (2012). Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. The New England Journal of Medicine, 366(10), 883-892. https://doi.org/10.1056/NEJMoa1113205

@article{73ca94b7e51045779971fe057a2283ec,

title = "Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing",

abstract = "BACKGROUND: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.METHODSTo examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression.RESULTS: Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors.CONCLUSIONS: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)",

keywords = "Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common, human KDM5C gene [Hominidae], human PTEN gene [Hominidae], human SETD2 gene [Hominidae], mammalian target of rapamycin kinase, messenger RNA mRNA, 03502, Genetics - General, 03508, Genetics - Human, 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines, 15506, Urinary system - Pathology, 24004, Neoplasms - Pathology, clinical aspects and systemic effects, Molecular Genetics, Nephrology, Oncology, renal carcinoma Kidney Neoplasms (MeSH) Carcinoma (MeSH) urologic disease, neoplastic disease, branched evolution, intratumor heterogeneity, Biochemistry and Molecular Biophysics, Human Medicine, Medical Sciences, chromosome aberration analysis laboratory techniques, genetic techniques, exome sequencing laboratory techniques, genetic techniques, immunohistochemical analysis laboratory techniques, immunologic techniques, multiregion sequencing laboratory techniques, genetic techniques, mutation functional analysis laboratory techniques, genetic techniques, ploidy profiling laboratory techniques, genetic techniques",

author = "Marco Gerlinger and Rowan, {Andrew J.} and Stuart Horswell and James Larkin and David Endesfelder and Eva Gronroos and Pierre Martinez and Nicholas Matthews and Aengus Stewart and Patrick Tarpey and Ignacio Varela and Benjamin Phillimore and Sharmin Begum and McDonald, {Neil Q.} and Adam Butler and David Jones and Keiran Raine and Calli Latimer and Santos, {Claudio R.} and Mahrokh Nohadani and Eklund, {Aron Charles} and Bradley Spencer-Dene and Graham Clark and Lisa Pickering and Gordon Stamp and Martin Gore and Szallasi, {Zoltan Imre} and Julian Downward and Futreal, {P. Andrew} and Charles Swanton",

year = "2012",

doi = "10.1056/NEJMoa1113205",

language = "English",

volume = "366",

pages = "883--892",

journal = "The New England Journal of Medicine",

issn = "0028-4793",

publisher = "Massachusetts Medical Society",

number = "10",

}

Gerlinger, M, Rowan, AJ, Horswell, S, Larkin, J, Endesfelder, D, Gronroos, E, Martinez, P, Matthews, N, Stewart, A, Tarpey, P, Varela, I, Phillimore, B, Begum, S, McDonald, NQ, Butler, A, Jones, D, Raine, K, Latimer, C, Santos, CR, Nohadani, M, Eklund, AC, Spencer-Dene, B, Clark, G, Pickering, L, Stamp, G, Gore, M, Szallasi, ZI, Downward, J, Futreal, PA & Swanton, C 2012, 'Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing', The New England Journal of Medicine, vol. 366, no. 10, pp. 883-892. https://doi.org/10.1056/NEJMoa1113205

TY - JOUR

T1 - Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

AU - Gerlinger, Marco

AU - Rowan, Andrew J.

AU - Horswell, Stuart

AU - Larkin, James

AU - Endesfelder, David

AU - Gronroos, Eva

AU - Martinez, Pierre

AU - Matthews, Nicholas

AU - Stewart, Aengus

AU - Tarpey, Patrick

AU - Varela, Ignacio

AU - Phillimore, Benjamin

AU - Begum, Sharmin

AU - McDonald, Neil Q.

AU - Butler, Adam

AU - Jones, David

AU - Raine, Keiran

AU - Latimer, Calli

AU - Santos, Claudio R.

AU - Nohadani, Mahrokh

AU - Eklund, Aron Charles

AU - Spencer-Dene, Bradley

AU - Clark, Graham

AU - Pickering, Lisa

AU - Stamp, Gordon

AU - Gore, Martin

AU - Szallasi, Zoltan Imre

AU - Downward, Julian

AU - Futreal, P. Andrew

AU - Swanton, Charles

PY - 2012

Y1 - 2012

N2 - BACKGROUND: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.METHODSTo examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression.RESULTS: Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors.CONCLUSIONS: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

AB - BACKGROUND: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.METHODSTo examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression.RESULTS: Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors.CONCLUSIONS: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

KW - Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common

KW - human KDM5C gene [Hominidae]

KW - human PTEN gene [Hominidae]

KW - human SETD2 gene [Hominidae]

KW - mammalian target of rapamycin kinase

KW - messenger RNA mRNA

KW - 03502, Genetics - General

KW - 03508, Genetics - Human

KW - 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines

KW - 15506, Urinary system - Pathology

KW - 24004, Neoplasms - Pathology, clinical aspects and systemic effects

KW - Molecular Genetics

KW - Nephrology

KW - Oncology

KW - renal carcinoma Kidney Neoplasms (MeSH) Carcinoma (MeSH) urologic disease, neoplastic disease

KW - branched evolution

KW - intratumor heterogeneity

KW - Biochemistry and Molecular Biophysics

KW - Human Medicine, Medical Sciences

KW - chromosome aberration analysis laboratory techniques, genetic techniques

KW - exome sequencing laboratory techniques, genetic techniques

KW - immunohistochemical analysis laboratory techniques, immunologic techniques

KW - multiregion sequencing laboratory techniques, genetic techniques

KW - mutation functional analysis laboratory techniques, genetic techniques

KW - ploidy profiling laboratory techniques, genetic techniques

U2 - 10.1056/NEJMoa1113205

DO - 10.1056/NEJMoa1113205

M3 - Journal article

SN - 0028-4793

VL - 366

SP - 883

EP - 892

JO - The New England Journal of Medicine

JF - The New England Journal of Medicine

IS - 10

ER -

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

Abstract

Keywords

UN SDGs

Access to Document

OpenUrl availability

Fingerprint

Cite this