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 & 10 others Aron C. Eklund, Bradley Spencer-Dene, Graham Clark, Lisa Pickering, Gordon Stamp, Martin Gore, Zoltan Szallasi, Julian Downward, Andrew Futreal, Charles Swanton

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Abstract

Background: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods: To 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 languageEnglish (US)
Pages (from-to)883-892
Number of pages10
JournalNew England Journal of Medicine
Volume366
Issue number10
DOIs
StatePublished - Mar 8 2012

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Neoplasms
Ploidies
Precision Medicine
Mutation
Sirolimus
Phosphotransferases
Allelic Imbalance
Exome
Biopsy
S 6
Genomics
Tumor Suppressor Genes
Transcriptome
Chromosome Aberrations
Biomedical Research
Biomarkers
Phosphorylation
Carcinoma
Kidney
Messenger RNA

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., ... Swanton, C. (2012). Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New England Journal of Medicine, 366(10), 883-892. https://doi.org/10.1056/NEJMoa1113205

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

In: New England Journal of Medicine, Vol. 366, No. 10, 08.03.2012, p. 883-892.

Research output: Contribution to journalArticle

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, Z, Downward, J, Futreal, A & Swanton, C 2012, 'Intratumor heterogeneity and branched evolution revealed by multiregion sequencing' New England Journal of Medicine, vol. 366, no. 10, pp. 883-892. https://doi.org/10.1056/NEJMoa1113205
Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New England Journal of Medicine. 2012 Mar 8;366(10):883-892. https://doi.org/10.1056/NEJMoa1113205
Gerlinger, Marco ; Rowan, Andrew J. ; Horswell, Stuart ; Larkin, James ; Endesfelder, David ; Gronroos, Eva ; Martinez, Pierre ; Matthews, Nicholas ; Stewart, Aengus ; Tarpey, Patrick ; Varela, Ignacio ; Phillimore, Benjamin ; Begum, Sharmin ; McDonald, Neil Q. ; Butler, Adam ; Jones, David ; Raine, Keiran ; Latimer, Calli ; Santos, Claudio R. ; Nohadani, Mahrokh ; Eklund, Aron C. ; Spencer-Dene, Bradley ; Clark, Graham ; Pickering, Lisa ; Stamp, Gordon ; Gore, Martin ; Szallasi, Zoltan ; Downward, Julian ; Futreal, Andrew ; Swanton, Charles. / Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. In: New England Journal of Medicine. 2012 ; Vol. 366, No. 10. pp. 883-892.
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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 C.

AU - Spencer-Dene, Bradley

AU - Clark, Graham

AU - Pickering, Lisa

AU - Stamp, Gordon

AU - Gore, Martin

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AU - Downward, Julian

AU - Futreal, Andrew

AU - Swanton, Charles

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N2 - Background: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods: To 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.)

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