Correction: Corrigendum: The reverse evolution from multicellularity to unicellularity during carcinogenesis

Theoretical reasoning suggests that human cancer may result from knocking down the genetic constraints evolved for maintenance of the metazoan multicellularity, which, however, requires a critical test. Using xenograft-based experimental evolution we characterized for the first time the full life history from initiation to metastasis of a tumor at the genomic and transcriptomic levels, and observed metastasis-driving positive selection for generally loss-of-function mutations on a set of multicellularity-related genes, which is further supported by large-scale exome data of clinical tumor samples. Subsequent expression analysis revealed mainly expression down-regulation of multicellularity-related genes, which form an evolving expression profile approaching that of embryonic stem cells, the cell type with the most characteristics of unicellular life. The theoretical conjecture predicts that genes born at the emergence of metazoan multicellularity tend to be cancer drivers, which we validated using a rigorous phylostratigraphy analysis on the birth rate of genes annotated by Cancer Gene Census. Also, the number of loss-of-function tumor suppressors often predominates over activated oncogenes in a typical tumor of human patients. These data collectively suggest that, different from typical organismal evolution in which gain of new genes is the mainstream, cancer represents a loss-of-function-driven degenerative evolution back to the unicellular ground state. This cancer evolution model may explain the enormous tumoral genetic heterogeneity in the clinic, underlie how distant-organ metastases originate in primary tumors despite distinct environmental requirements, and hold implications for designing effective cancer therapy.

[1]  H. Land,et al.  Advanced mammalian gene transfer: high titre retroviral vectors with multiple drug selection markers and a complementary helper-free packaging cell line. , 1990, Nucleic acids research.

[2]  A. S. Alvarado Cellular Hyperproliferation and Cancer as Evolutionary Variables , 2012, Current Biology.

[3]  Peter J. Campbell,et al.  Evolution of the cancer genome , 2012, Nature Reviews Genetics.

[4]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[5]  L. Loeb,et al.  Human cancers express mutator phenotypes: origin, consequences and targeting , 2011, Nature Reviews Cancer.

[6]  J. Rosen,et al.  Modelling breast cancer: one size does not fit all , 2007, Nature Reviews Cancer.

[7]  F. Miller,et al.  Xenograft model of progressive human proliferative breast disease. , 1993, Journal of the National Cancer Institute.

[8]  Christopher D. Brown,et al.  Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data , 2011, Proceedings of the National Academy of Sciences.

[9]  S. Lowe,et al.  Intrinsic tumour suppression , 2004, Nature.

[10]  B. Vogelstein,et al.  A genetic model for colorectal tumorigenesis , 1990, Cell.

[11]  Jianzhi Zhang,et al.  Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation , 2012, Proceedings of the National Academy of Sciences.

[12]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[13]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[14]  C. Lineweaver,et al.  Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors , 2011, Physical biology.

[15]  Paula D. Bos,et al.  Metastasis: from dissemination to organ-specific colonization , 2009, Nature Reviews Cancer.

[16]  J. W. Valentine,et al.  Developmental evolution of metazoan bodyplans: the fossil evidence. , 1996, Developmental biology.

[17]  S. Donovan,et al.  The adequacy of the fossil record , 1998 .

[18]  Kevin R. Thornton,et al.  The origin of new genes: glimpses from the young and old , 2003, Nature Reviews Genetics.

[19]  S. Morris The fossil record and the early evolution of the Metazoa , 1993, Nature.

[20]  Wenfeng Qian,et al.  The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast. , 2012, Cell reports.

[21]  Carlo C. Maley,et al.  Cancer in Light of Experimental Evolution , 2012, Current Biology.

[22]  R. Grosberg,et al.  The Evolution of Multicellularity: A Minor Major Transition? , 2007 .

[23]  M V Olson,et al.  When less is more: gene loss as an engine of evolutionary change. , 1999, American journal of human genetics.

[24]  Esti Yeger-Lotem,et al.  Cancer Evolution Is Associated with Pervasive Positive Selection on Globally Expressed Genes , 2014, PLoS genetics.

[25]  J. Salk Clonal evolution in cancer , 2010 .

[26]  Nicholas H. Putnam,et al.  The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution , 2013, Science.

[27]  Diethard Tautz,et al.  Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa , 2010, BMC Biology.

[28]  Robert A. Weinberg,et al.  Tumor Metastasis: Molecular Insights and Evolving Paradigms , 2011, Cell.

[29]  Todd H. Oakley,et al.  The Amphimedon queenslandica genome and the evolution of animal complexity , 2010, Nature.

[30]  C. Markert,et al.  Evolution of the Gene , 1948, Nature.

[31]  C. Maley,et al.  Cancer is a disease of clonal evolution within the body1–3. This has profound clinical implications for neoplastic progression, cancer prevention and cancer therapy. Although the idea of cancer as an evolutionary problem , 2006 .

[32]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[33]  R. Lenski,et al.  The population genetics of ecological specialization in evolving Escherichia coli populations , 2000, Nature.

[34]  S A Forbes,et al.  The Catalogue of Somatic Mutations in Cancer (COSMIC) , 2008, Current protocols in human genetics.

[35]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[36]  J. DeGregori Evolved tumor suppression: why are we so good at not getting cancer? , 2011, Cancer research.

[37]  Xionglei He,et al.  The reverse evolution from multicellularity to unicellularity during carcinogenesis , 2015, Nature Communications.

[38]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[39]  R. Lenski,et al.  Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.

[40]  D. Roze,et al.  Cooperation and conflict in the evolution of multicellularity , 2001, Heredity.

[41]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[42]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[43]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[44]  Jianzhi Zhang,et al.  Gene Losses during Human Origins , 2006, PLoS biology.

[45]  M. Huss,et al.  Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model , 2013, Proceedings of the National Academy of Sciences.

[46]  Keith Bradnam,et al.  Assessing the gene space in draft genomes , 2008, Nucleic acids research.

[47]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[48]  Michael M. Desai,et al.  Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations , 2013, Nature.

[49]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[50]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[52]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[53]  S. Carroll,et al.  Animal Evolution and the Molecular Signature of Radiations Compressed in Time , 2005, Science.

[54]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[55]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[56]  Joshua F. McMichael,et al.  Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.

[57]  P. Nowell The clonal evolution of tumor cell populations. , 1976, Science.

[58]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[59]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[60]  Jianzhi Zhang,et al.  RNA sequencing shows no dosage compensation of the active X-chromosome , 2010, Nature Genetics.

[61]  Cori Bargmann,et al.  Mechanism of activation of a human oncogene , 1982, Nature.

[62]  John D. Storey A direct approach to false discovery rates , 2002 .