Deterministic evolution and stringent selection during preneoplasia

The earliest events during human tumor initiation, while poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult pre-neoplasia by bi-allelically inactivating TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over two years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single cell sequencing of TP53 deficient gastric organoids similarly indicates progression towards malignant transcriptional programs. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programs repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference, and a striking degree of phenotypic convergence in pre-malignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and reveal evolutionary constraints and barriers to malignant transformation with implications for earlier detection and interception of aggressive, genome instable tumors.

[1]  A. Krasnitz,et al.  Ordered and deterministic cancer genome evolution after p53 loss , 2022, Nature.

[2]  A. Teschendorff,et al.  Novel epigenetic network biomarkers for early detection of esophageal cancer , 2022, Clinical epigenetics.

[3]  Lucian P. Smith,et al.  Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression , 2021, Nature Communications.

[4]  L. M. Marques,et al.  Evaluating the presence of Mycoplasma hyorhinis, Fusobacterium nucleatum, and Helicobacter pylori in biopsies of patients with gastric cancer , 2021, Infectious agents and cancer.

[5]  S. Teichmann,et al.  Molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition , 2021, Science.

[6]  Jihan Wang,et al.  Global Analysis of Microbiota Signatures in Four Major Types of Gastrointestinal Cancer , 2021, Frontiers in Oncology.

[7]  Kieran R. Campbell,et al.  Clonal fitness inferred from time-series modelling of single-cell cancer genomes , 2021, Nature.

[8]  Santiago J. Carmona,et al.  Interpretation of T cell states from single-cell transcriptomics data using reference atlases , 2021, Nature Communications.

[9]  P. Iglesias,et al.  On the role of p53 in the cellular response to aneuploidy , 2021, Cell reports.

[10]  G. Crabtree,et al.  A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation. , 2021, Cancer discovery.

[11]  D. Stange,et al.  Gastric organoids—an in vitro model system for the study of gastric development and road to personalized medicine , 2020, Cell death and differentiation.

[12]  Dehu Chen,et al.  Galectin-1 promotes vasculogenic mimicry in gastric adenocarcinoma via the Hedgehog/GLI signaling pathway , 2020, Aging.

[13]  David A. Knowles,et al.  Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs , 2020, Cell.

[14]  S. Killcoyne,et al.  Genomic copy number predicts esophageal cancer years before transformation , 2020, Nature Medicine.

[15]  H. Clevers,et al.  Establishment and Culture of Human Intestinal Organoids Derived from Adult Stem Cells , 2020, Current protocols in immunology.

[16]  E. Kuipers,et al.  Recent advances in the detection and management of early gastric cancer and its precursors , 2020, Frontline Gastroenterology.

[17]  Shuofeng Hu,et al.  Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing , 2020, Gut.

[18]  Nuno A. Fonseca,et al.  Patterns of somatic structural variation in human cancer genomes , 2020, Nature.

[19]  James M. McFarland,et al.  Early TP53 Alterations Engage Environmental Exposures to Promote Gastric Premalignancy in an Integrative Mouse Model , 2019, Nature Genetics.

[20]  Benjamin J. Raphael,et al.  Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data , 2018, Nature Communications.

[21]  Howard Y. Chang,et al.  Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia , 2019, Nature Biotechnology.

[22]  Sasha F. Levy,et al.  High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast , 2019, Nature.

[23]  S. Mandal,et al.  Fluoroquinolone antibiotics show genotoxic effect through DNA-binding and oxidative damage. , 2019, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[24]  Hanlee P. Ji,et al.  Single-Cell Genomic Characterization Reveals the Cellular Reprogramming of the Gastric Tumor Microenvironment , 2019, Clinical Cancer Research.

[25]  James M. McFarland,et al.  Mutant p53 induces a hypoxia transcriptional program in gastric and esophageal adenocarcinoma. , 2019, JCI insight.

[26]  Peng Zhang,et al.  Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer. , 2019, Cell reports.

[27]  R. Satija,et al.  Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression , 2019, Genome Biology.

[28]  J. Pearson,et al.  Complex structural rearrangements are present in high-grade dysplastic Barrett’s oesophagus samples , 2019, BMC Medical Genomics.

[29]  Ville Mustonen,et al.  The repertoire of mutational signatures in human cancer , 2018, Nature.

[30]  H. Tettelin,et al.  Mycoplasma promotes malignant transformation in vivo, and its DnaK, a bacterial chaperone protein, has broad oncogenic properties , 2018, Proceedings of the National Academy of Sciences.

[31]  Bertrand Z. Yeung,et al.  Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics , 2018, Genome Biology.

[32]  Chiara Sabatti,et al.  Organoid Modeling of the Tumor Immune Microenvironment , 2018, Cell.

[33]  Hans Clevers,et al.  A Comprehensive Human Gastric Cancer Organoid Biobank Captures Tumor Subtype Heterogeneity and Enables Therapeutic Screening. , 2018, Cell stem cell.

[34]  Christoph Hafemeister,et al.  Comprehensive integration of single cell data , 2018, bioRxiv.

[35]  S. Sleijfer,et al.  Pan-cancer whole genome analyses of metastatic solid tumors , 2018, bioRxiv.

[36]  Ville Mustonen,et al.  The evolutionary landscape of colorectal tumorigenesis , 2018, Nature Ecology & Evolution.

[37]  Adrian Baez-Ortega,et al.  sigfit: flexible Bayesian inference of mutational signatures , 2018, bioRxiv.

[38]  A. Halpern,et al.  Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.

[39]  Christopher T. Saunders,et al.  Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.

[40]  Peter J Park,et al.  Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data , 2018, Genome research.

[41]  Jesper Eisfeldt,et al.  Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants , 2018, bioRxiv.

[42]  Matthew D. Young,et al.  Intra-tumour diversification in colorectal cancer at the single-cell level , 2018, Nature.

[43]  Christopher D. McFarland,et al.  Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice , 2018, Nature Genetics.

[44]  Benjamin J. Raphael,et al.  The evolutionary history of 2,658 cancers , 2017, Nature.

[45]  Benjamin H. Good,et al.  The Dynamics of Molecular Evolution Over 60,000 Generations , 2017, Nature.

[46]  Ville Mustonen,et al.  Clonal Heterogeneity Influences the Fate of New Adaptive Mutations , 2016, bioRxiv.

[47]  Andrea Sottoriva,et al.  Between-Region Genetic Divergence Reflects the Mode and Tempo of Tumor Evolution , 2017, Nature Genetics.

[48]  Cheng Li,et al.  GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses , 2017, Nucleic Acids Res..

[49]  Joachim Weischenfeldt,et al.  SvABA: genome-wide detection of structural variants and indels by local assembly , 2018, Genome research.

[50]  K. Takeda,et al.  Regulation of intestinal homeostasis by the ulcerative colitis-associated gene RNF186 , 2016, Mucosal Immunology.

[51]  Marc J. Williams,et al.  Quantification of subclonal selection in cancer from bulk sequencing data , 2018, Nature Genetics.

[52]  Alan M. Kwong,et al.  Next-generation genotype imputation service and methods , 2016, Nature Genetics.

[53]  Joshua F. McMichael,et al.  Visualizing tumor evolution with the fishplot package for R , 2016, bioRxiv.

[54]  A. Urooj,et al.  A Review on Dietary and Non-Dietary Risk Factors Associated with Gastrointestinal Cancer , 2016, Journal of Gastrointestinal Cancer.

[55]  V. Seshan,et al.  FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing , 2016, Nucleic acids research.

[56]  Xiaoyu Chen,et al.  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..

[57]  Hans Clevers,et al.  Sequential cancer mutations in cultured human intestinal stem cells , 2015, Nature.

[58]  M. Johansson,et al.  New developments in goblet cell mucus secretion and function , 2015, Mucosal Immunology.

[59]  Joshua M. Korn,et al.  Studying clonal dynamics in response to cancer therapy using high-complexity barcoding , 2015, Nature Medicine.

[60]  Gavin Sherlock,et al.  Quantitative evolutionary dynamics using high-resolution lineage tracking , 2015, Nature.

[61]  C. Curtis,et al.  A Big Bang model of human colorectal tumor growth , 2015, Nature Genetics.

[62]  Hans Clevers,et al.  In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. , 2015, Gastroenterology.

[63]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[64]  Sohrab P. Shah,et al.  TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data , 2014, Genome research.

[65]  B. van Steensel,et al.  Easy quantitative assessment of genome editing by sequence trace decomposition , 2014, Nucleic acids research.

[66]  N. McGranahan,et al.  Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer. , 2014, Cancer research.

[67]  Paul Shannon,et al.  VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants , 2014, Bioinform..

[68]  John B. Hogenesch,et al.  Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive , 2014, bioRxiv.

[69]  Shibing Deng,et al.  Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer , 2014, Nature Genetics.

[70]  Hans Clevers,et al.  Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. , 2013, Cell stem cell.

[71]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[72]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[73]  A. Lynch,et al.  Evaluating the genotoxicity of topoisomerase-targeted antibiotics. , 2012, Mutagenesis.

[74]  Hans Clevers,et al.  Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. , 2011, Gastroenterology.

[75]  C. Cole,et al.  COSMIC: the catalogue of somatic mutations in cancer , 2011, Genome Biology.

[76]  Shicai Wang,et al.  COSMIC: the Catalogue Of Somatic Mutations In Cancer , 2018, Nucleic Acids Res..

[77]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[78]  David J Weber,et al.  Deletion of p53 in human mammary epithelial cells causes chromosomal instability and altered therapeutic response , 2010, Oncogene.

[79]  S. Nee.  More than meets the eye , 2004, Nature.

[80]  R. P. Blankfield,et al.  Helicobacter pylori infection and the development of gastric cancer. , 2001, The New England journal of medicine.

[81]  S. Tavaré,et al.  Genetic reconstruction of individual colorectal tumor histories. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[82]  Carissa A. Sanchez,et al.  Evolution of neoplastic cell lineages in Barrett oesophagus , 1999, Nature Genetics.

[83]  R. Lenski,et al.  Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations , 1991, The American Naturalist.

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

[85]  H. Brenner,et al.  [The early detection of cancer]. , 1972, Harefuah.