Tumor evolution: Linear, branching, neutral or punctuated?☆
TLDR
Data is discussed that supports the theory that most human tumors evolve from a single cell in the normal tissue, and suggests that models may change during tumor progression or operate concurrently for different classes of mutations.About:
This article is published in Biochimica et Biophysica Acta.The article was published on 2017-04-01 and is currently open access. It has received 255 citations till now. The article focuses on the topics: Tumor progression.read more
Citations
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SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer
TL;DR: A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell.
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Epigenetic plasticity and the hallmarks of cancer
TL;DR: It is proposed that chromatin and epigenetic aberrations have the potential to confer on cells the full range of oncogenic properties represented in the classic “hallmarks” depiction of cancer, and it is suggested that genetic, environmental, and metabolic factors can make chromatin aberrantly permissive or restrictive.
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Eleven grand challenges in single-cell data science
David Lähnemann,David Lähnemann,Johannes Köster,Johannes Köster,Ewa Szczurek,Davis J. McCarthy,Davis J. McCarthy,Stephanie C. Hicks,Mark D. Robinson,Catalina A. Vallejos,Catalina A. Vallejos,Kieran R Campbell,Kieran R Campbell,Niko Beerenwinkel,Niko Beerenwinkel,Ahmed Mahfouz,Ahmed Mahfouz,Luca Pinello,Luca Pinello,Pavel Skums,Alexandros Stamatakis,Alexandros Stamatakis,Camille Stephan Otto Attolini,Samuel Aparicio,Samuel Aparicio,Jasmijn A. Baaijens,Marleen Balvert,Marleen Balvert,Buys de Barbanson,Antonio Cappuccio,Giacomo Corleone,Bas E. Dutilh,Bas E. Dutilh,Maria Florescu,Victor Guryev,Rens Holmer,Katharina Jahn,Katharina Jahn,Thamar Jessurun Lobo,Emma M. Keizer,Indu Khatri,Szymon M. Kielbasa,Jan O. Korbel,Alexey M. Kozlov,Tzu Hao Kuo,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,Ion I. Mandoiu,John C. Marioni,John C. Marioni,John C. Marioni,Tobias Marschall,Tobias Marschall,Felix Mölder,Amir Niknejad,Lukasz Raczkowski,Marcel J. T. Reinders,Marcel J. T. Reinders,Jeroen de Ridder,Antoine-Emmanuel Saliba,Antonios Somarakis,Oliver Stegle,Oliver Stegle,Fabian J. Theis,Huan Yang,Alexander Zelikovsky,Alexander Zelikovsky,Alice C. McHardy,Benjamin J. Raphael,Sohrab P. Shah,Alexander Schönhuth,Alexander Schönhuth +71 more
TL;DR: This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years in single-cell data science.
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Tumour heterogeneity and metastasis at single-cell resolution.
TL;DR: Recent advances in single-cell technologies are reviewed and discussed in detail how they can be leveraged to understand tumour heterogeneity and metastasis.
Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity
Vanessa Almendro,Yu-Kang Cheng,Amanda Randles,Shalev Itzkovitz,Andriy Marusyk,Elisabet Ametller,Xavier Gonzalez-Farre,Hege G. Russnes,Inga H. Rye,Anne Lise Børresen-Dale,Reo Maruyama,Alexander van Oudenaarden,Mitchell Dowsett,Robin L. Jones,Jorge S. Reis-Filho,Pere Gascón,Franziska Michor,Kornelia Polyak,Montse Muñoz,Åslaug Helland,Mithat Gonen +20 more
TL;DR: The analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response.
References
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Journal ArticleDOI
Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer
Muhammed Murtaza,Sarah-Jane Dawson,Sarah-Jane Dawson,Sarah-Jane Dawson,Katherine Pogrebniak,Oscar M. Rueda,Elena Provenzano,Elena Provenzano,John Grant,Suet-Feung Chin,Dana W.Y. Tsui,Francesco Marass,Davina Gale,H. Raza Ali,Pankti Shah,Tania Contente-Cuomo,Hossein Farahani,Karey Shumansky,Zoya Kingsbury,Sean Humphray,David Bentley,Sohrab P. Shah,Matthew G. Wallis,Matthew G. Wallis,Nitzan Rosenfeld,Carlos Caldas,Carlos Caldas +26 more
TL;DR: A comparison of biopsy and plasma samples in a single patient with metastatic breast cancer shows that circulating tumour DNA can allow real-time sampling of multifocal clonal evolution.
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Evolving responsively: adaptive mutation
TL;DR: The emerging mechanisms of adaptive genetic change cast evolution, development and heredity into a new perspective, indicating new models for the genetic changes that fuel these processes.
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Combination of p53 cancer vaccine with chemotherapy in patients with extensive stage small cell lung cancer
Scott J. Antonia,Noweeda Mirza,Ingo Fricke,Alberto Chiappori,Patricia A. Thompson,Nicholas Williams,Gerold Bepler,George R. Simon,William J. Janssen,Ji-Hyun Lee,Kerstin B. Menander,Sunil Chada,Dmitry I. Gabrilovich +12 more
TL;DR: Clinical support for an emerging paradigm in cancer immunotherapy, wherein optimal use of vaccination might be more effective, not as a separate modality, but in direct combination with chemotherapy, is provided.
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Punctuated copy number evolution and clonal stasis in triple-negative breast cancer
Ruli Gao,Alexander Davis,Thomas O. McDonald,Emi Sei,Xiuqing Shi,Yong Wang,Pei Ching Tsai,Anna Casasent,Jill Waters,Hong Zhang,Funda Meric-Bernstam,Franziska Michor,Nicholas Navin +12 more
TL;DR: A highly multiplexed single-nucleus sequencing method is developed to investigate copy number evolution in patients with triple-negative breast cancer, showing that the majority of copy number aberrations are acquired at the earliest stages of tumor evolution, in short punctuated bursts that form the tumor mass.
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PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
Amit G. Deshwar,Shankar Vembu,Christina K. Yung,Gun Ho Jang,Lincoln Stein,Lincoln Stein,Quaid Morris +6 more
TL;DR: A principled phylogenic correction for VAFs in loci affected by copy number alterations is introduced and it is shown that this correction greatly improves subclonal reconstruction compared to existing methods.
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Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future.
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Marco Gerlinger,Andrew Rowan,Stuart Horswell,James Larkin,David Endesfelder,Eva Grönroos,Pierre Martinez,Nicholas Matthews,Aengus Stewart,Patrick S. Tarpey,Ignacio Varela,Benjamin Phillimore,Sharmin Begum,Neil Q. McDonald,Adam Butler,David T. 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 Szallasi,Zoltan Szallasi,Julian Downward,P. Andrew Futreal,Charles Swanton +30 more