Abstract

Clonal expansion in aged normal tissues has been implicated in the development of cancer. However, the chronology and risk dependence of the expansion are poorly understood. Here we intensively sequence 682 micro-scale oesophageal samples and show, in physiologically normal oesophageal epithelia, the progressive age-related expansion of clones that carry mutations in driver genes (predominantly NOTCH1), which is substantially accelerated by alcohol consumption and by smoking. Driver-mutated clones emerge multifocally from early childhood and increase their number and size with ageing, and ultimately replace almost the entire oesophageal epithelium in the extremely elderly. Compared with mutations in oesophageal cancer, there is a marked overrepresentation of NOTCH1 and PPM1D mutations in physiologically normal oesophageal epithelia; these mutations can be acquired before late adolescence (as early as early infancy) and significantly increase in number with heavy smoking and drinking. The remodelling of the oesophageal epithelium by driver-mutated clones is an inevitable consequence of normal ageing, which—depending on lifestyle risks—may affect cancer development.

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Data availability

All the WES, WGS and SNP array data have been deposited in the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/) under accession numbers EGAS00001003008, EGAS00001003281 and EGAS00001003331, respectively. Data for Figures and Extended Data Figures are available as Source Data. All other data are available from the corresponding author on reasonable request.

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Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Acknowledgements

We thank the Ministry of Education, Culture, Sports, Science and Technology for support (grant references: hp150232 and 15H05909), together with many other funding bodies and individuals (Supplementary Note 1).

Reviewer information

Nature thanks F. Ciccarelli, B. Lehner and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Author notes

  1. These authors contributed equally: Akira Yokoyama, Nobuyuki Kakiuchi, Tetsuichi Yoshizato

  2. These authors jointly supervised this work: Manabu Muto, Seishi Ogawa

Affiliations

  1. Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan

    • Akira Yokoyama
    • , Nobuyuki Kakiuchi
    • , Tetsuichi Yoshizato
    • , Yasuhito Nannya
    • , Hiromichi Suzuki
    • , Yasuhide Takeuchi
    • , Yusuke Shiozawa
    • , Yusuke Sato
    • , Kosuke Aoki
    • , Soo Ki Kim
    • , Yoichi Fujii
    • , Kenichi Yoshida
    • , Keisuke Kataoka
    • , Masahiro M. Nakagawa
    • , Yoshikage Inoue
    • , Tomonori Hirano
    • , Hideki Makishima
    •  & Seishi Ogawa
  2. Department of Clinical Oncology, Kyoto University Hospital, Kyoto, Japan

    • Akira Yokoyama
    • , Yoshitaka Nishikawa
    • , Yusuke Amanuma
    • , Shinya Ohashi
    • , Ikuo Aoyama
    • , Takahiro Horimatsu
    •  & Manabu Muto
  3. Department of Gastroenterology and Hepatology, Kyoto University, Kyoto, Japan

    • Nobuyuki Kakiuchi
    • , Tomonori Hirano
    • , Shin’ichi Miyamoto
    •  & Hiroshi Seno
  4. Department of Diagnostic Pathology, Kyoto University, Kyoto, Japan

    • Yasuhide Takeuchi
    • , Sachiko Minamiguchi
    •  & Hironori Haga
  5. Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan

    • Yoshikage Inoue
    • , Shigeru Tsunoda
    •  & Yoshiharu Sakai
  6. Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

    • Yuichi Shiraishi
    • , Kenichi Chiba
    •  & Satoru Miyano
  7. Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

    • Hiroko Tanaka
    •  & Satoru Miyano
  8. Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan

    • Masashi Sanada
  9. Department of Human Genetics, McGill University, Montreal, Quebec, Canada

    • Maiko Narahara
  10. Laboratory of Molecular Biosciences, Life Science Informatics Research Unit, Kyoto University, Kyoto, Japan

    • J. B. Brown
  11. Sato Clinic, Okayama, Japan

    • Yoshitaka Sato
  12. Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan

    • Genta Sawada
    •  & Koshi Mimori
  13. Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden

    • Seishi Ogawa

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Contributions

A.Y., H. Suzuki, T.Y., N.K., H.M., M.M. and S. Ogawa designed the study. S. Ohashi, Y.A., I.A., T. Horimatsu, S. Miyamoto, S.T., Y. Sakai, Yoshitaka Sato, H. Seno, M.M. and Y. Nishikawa provided specimens. Y.T., S. Minamiguchi and H.H. performed histological analysis. A.Y., H. Suzuki, T.Y., N.K., Y. Shiozawa, Yusuke Sato, K.A., Y.T., S.K.K., Y.F., K.Y., K.K., Y.I., T. Hirano and M.M.N. performed sample preparation. G.S. and K.M. provided sequencing data. M.S., A.Y., H. Suzuki, T.Y., N.K., Y. Shiozawa and Y. Nannya performed mutation calling, validated the results, and analysed copy-number alterations, mutational signature and clonal dynamics. A.Y., H. Suzuki, T.Y., N.K., Y. Shiozawa, K.A., Y.T., Y. Nannya, Y. Shiraishi, K.C., H.T., M.N., J.B.B. and S. Miyano performed bioinformatics analysis. A.Y., H. Suzuki, T.Y., N.K., Y. Nannya, H.M. and S. Ogawa prepared the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Seishi Ogawa.

Extended data figures and tables

  1. Extended Data Fig. 1 Study design.

    ac, Summary of the subjects, samples, methods of sample collection, lifestyle ESCC risks, and histology, as well as sequencing platforms used for analysis of solitary samples (a), single-cell-derived colonies (b) and densely collected samples (c). *In one case (UPN53), only cancer and dysplasia samples were collected. §, UPN36, UPN37 and UPN39; ¶, UPN49; ‡, UPN88; #, UPN56 and UPN61; Φ, UPN58; ††, UPN55, UPN59, UPN60 and UPN65. Samples from these individuals were analysed in indicated multiple experiments (see a, b and c). †Out of 53 PNE samples, 11 were analysed in both solitary and high-density sampling (see a and c). Source data

  2. Extended Data Fig. 2 WES of PNE and cancer samples from a surgical specimen.

    a, Positions of 25 PNE and 2 cancer samples from a surgically resected oesophagus of a 58-year-old, high-risk patient with ESCC (UPN32) are shown by green and red circles, respectively. Calibration is shown on the right. EGJ, oesophagogastric junction. b, MCFs are compared between samples from PNE (green) (n = 25) and cancer (red) (n = 2) samples. c, d, MCF is plotted for all shared (orange) and private (grey) mutations for low-density (c) and high-density (d) sampling. Driver mutations are indicated by arrowheads in indicated colours. The position of each sample is shown on the left. Calibration for the number of mutations depicted in the horizontal axis is separately provided for each sampling. e, For preparation of PNE samples, after submucosal layers were removed from endoscopic biopsy specimens, 0.2-mm2, 0.8-mm2 or 4.0-mm2 samples were collected using a punch biopsy of 0.5 mm or 1.0 mm in diameter, or 2 × 2-mm rectangular excision, respectively, followed by DNA extraction. f, Photographs of punch biopsy devices for 0.5-mm-diameter and 1.0-mm-diameter sampling. Photographs copyright Kai Industries. g, Histogram of DNA recovered from 0.2-mm2, 0.8-mm2 or 4.0-mm2 samples. Box plots represent the median, first quartile and third quartile, with whiskers extending to the furthest value within 1.5× interquartile range. Source data

  3. Extended Data Fig. 3 Somatic mutations in solitary sampling.

    a, Summary of somatic mutations found in 157 PNE, 12 dysplasia and 20 cancer samples from individuals with (pink) or without (green) lifestyle ESCC risks. MCFs are plotted for all mutations (upper panel). Driver mutations are shown by coloured triangles as indicated. Information about histology and sample size is shown on the top lanes. The age of the subject and the total number of mutations are shown in the bottom panels. Status of ESCC, CNAs and mutations are also shown (middle panels). bj, MCFs of somatic mutations detected in WES of multiple samples from PNE, as well as dysplastic and cancer tissues, are depicted separately for shared (orange) and non-shared mutations (grey) in representative cases from 16 independent individuals, for whom multi-regional sampling was performed. Mutations in TP53, NOTCH1, PPM1D and other drivers are indicated by arrowheads in different colours. Positions of tumours and biopsy samples are shown on the left in each panel. Distance from the maxillary dental arch is indicated. Mutations are shared only between cancer samples except in two cases (i and j), in which small numbers of mutations (between 3 and 16) are shared between mutually positioned samples as indicated. Source data

  4. Extended Data Fig. 4 Signatures of mutations in PNE, dysplasia and cancer samples.

    a, Number (middle) and relative frequency (bottom) of mutations allocated to signatures A–D in the individual samples. Information about pathology, lifestyle ESCC risks, cohort and age of the subject is indicated (top). b, Number of mutations allocated to indicated mutational signatures is plotted against the age of the subject for PNE samples from low-risk (blue) and high-risk (red) individuals. Numbers of samples from low-risk and high-risk individuals are 34 and 19 (0.2-mm2 sampling), 19 and 12 (0.8-mm2 sampling), and 40 and 33 (4-mm2 sampling), respectively. Regression lines for samples from low-risk individuals are indicated with R2. P values for significance between samples from high-risk and low-risk individuals are also provided (one-sided Mann–Whitney U-test). c, Mean (± 95% confidence interval) of standardized residuals of the number of mutations allocated to each signature in samples from high-risk individuals against the linear regression model in samples from low-risk individuals is plotted for 0.2-mm2, 0.8-mm2 and 4-mm2 samples and for combined samples in a random-effects model. P value in the random-effects model is indicated, together with the weight from each sample size during the model fitting (two-sided Wald test) (Methods). d, Mean (±s.d.) number of mutations allocated to signature 16 in oesophagus (ESCC) (n = 90) (left), hepatic (LIHC) (n = 361) (middle) and stomach (STAD) (n = 239) (right) cancers from TCGA, are plotted according to the status of the ALDH2 risk allele. P values for significance between samples from risk-positive and risk-negative individuals are also provided (two-sided Mann–Whitney U-test). e, Frequency of mutations allocated to signature C in Japanese ESCC samples is plotted according to the status of alcohol drinking and smoking. According the history of heavy drinking and smoking, the subjects were divided into four groups; drinking- and smoking-negative (n = 18); drinking-negative and smoking-positive (n = 3); drinking-positive and smoking-negative (n = 40); and drinking- and smoking-positive (n = 96), as indicated in the panel. Box plots represent the median, first quartile and third quartile, with whiskers extending to the furthest value within 1.5× interquartile range; points show outliers. Source data

  5. Extended Data Fig. 5 Mutations detected in single-cell-derived colonies in WGS.

    VAF histograms of somatic mutations detected in 13 single-cell-derived colonies analysed with WGS are depicted for each sample. Mutation number and driver genes mutated in each sample are indicated. Source data

  6. Extended Data Fig. 6 Driver mutations in PNE samples.

    a, Distribution of mutations in 157 PNE and 519 ESCC samples is shown for driver genes significantly mutated in PNE or ESCC samples, including NOTCH2, NOTCH3, CREBBP, FAT1, CHEK2, PAX9, EP300 and PIK3CA. Mutations are depicted separately for PNE (top) and ESCC (bottom). b, Frequencies of driver genes in paired cancer and PNE samples from 68 patients with ESCC. Genes in which mutations were observed in 5% or more samples either in PNE or ESCC were evaluated. Significantly differentially mutated genes (q < 0.05) between PNE and ESCC samples are indicated by asterisks. c, d, Number of driver mutations (c) and their maximum MCFs (d) in samples from high-risk and low-risk individuals are plotted against the age of subject, according to sample size. Regression lines are provided with R2. P values for the significance of lifestyle ESCC risks are also indicated (one-sided Mann–Whitney U-test). e, h, Mean (± 95% confidence interval) of standardized difference of mutation number (e) and maximum MCF (h) between samples from high-risk and low-risk individuals are plotted for each sampling size, and combined samples, using a random-effects model. P value in the random-effects model is also indicated, together with the weight from each sample size (in per cent) for the model fitting (two-sided Wald test) (Methods). f, g, Mean (± 95% confidence interval) of standardized residuals of the number of indicated driver mutations (f) and their maximum MCFs (g) in samples from high-risk individuals against the linear regression model in samples from low-risk individuals (Methods); plotted for 0.2-mm2, 0.8-mm2 and 4-mm2 samples. Standardized residuals for combined samples using a random-effects model are also shown. P-value in the random-effects model is also indicated, together with the weight from each sample size (in per cent) for the model fitting (two-sided Wald test) (Methods). In the analyses in ch, the numbers of samples from low-risk and high-risk individuals, respectively, are 34 and 19 (0.2-mm2 sampling), 19 and 12 (0.8-mm2 sampling), and 40 and 33 (4-mm2 sampling) (c, e, f); 26 and 18 (0.2-mm2 sampling), 13 and 12 (0.8-mm2 sampling), and 30 and 31 (4-mm2 sampling) (d, h); 5 and 5 (0.2-mm2 sampling), 4 and 7 (0.8-mm2 sampling), and 8 and 19 (4-mm2 sampling) (TP53 in g); 14 and 18 (0.2-mm2 sampling), 7 and 11 (0.8-mm2 sampling), 21 and 28 (4-mm2 sampling) (NOTCH1 in g); 2 and 4 (0.2-mm2 sampling), 2 and 9 (4-mm2 sampling) (PPM1D in g). Source data

  7. Extended Data Fig. 7 CNAs in PNE, dysplasia and cancer samples.

    a, Colour-gradient maps of CNAs and UPDs as detected by SNP-array karyotyping or sequencing-based assays are shown for PNE samples from high-risk and low-risk individuals, as well as dysplastic tissues (n = 12) and cancer samples (n = 51) (middle panels). Fractions of genomes showing copy-number gains (red), losses (blue) and UPD (green) are also plotted (top panels). Information about histology, age of the subject, sample size and risks of developing ESCC are shown in top panels. b, Box plots of fractions of genomic regions showing CNAs in PNE (n = 188), dysplasia (n = 12) and cancer (n = 45) samples; the median, first and third quartiles, as well as outliers, are indicated with whiskers extending to the furthest value within 1.5 of the interquartile range. P values for significant differences are from two-sided Mann–Whitney U-test. DP, dysplasia. c, Effects of lifestyle ESCC risks and age on CNAs. Mean (± 95% confidence interval) of standardized residuals of the total fraction of genomic regions showing CNAs in samples from high-risk individuals, compared with the linear regression model in samples from low-risk individuals (left panel) and Fisher’s z-transformed correlation of age to the total fraction of genomic regions showing CNAs in samples from low-risk individuals (right panel) are plotted for 0.2-mm2, 0.8-mm2, 4-mm2 and 8-mm2 samples, which are combined using a random-effects model. P value in the random-effects model is also indicated, together with the weight from each sample size (in per cent) for the model fitting (two-sided Wald test) (Methods). Numbers of samples from low-risk and high-risk individuals, respectively, are 34 and 19 (0.2-mm2 sampling), 19 and 12 (0.8-mm2 sampling), 40 and 33 (4-mm2 sampling), and 3 and 28 (8-mm2 sampling). Numbers of samples from low-risk individuals who are <50 years old and ≥50 years old, respectively, are 20 and 14 (0.2-mm2 sampling), 13 and 6 (0.8-mm2 sampling), and 7 and 33 (4-mm2 sampling), respectively. d, f, LOH maps of chromosomes 9 (d) and 17 (f) in PNE (top) and cancer (bottom) samples. Deletions and UPDs are shown by blue and green lines, respectively. Positions and mutation status of CDKN2A, NOTCH1 and TP53 genes are indicated. e, g, Bar plots of frequencies of 9q UPD (e) and 17p LOH (g) in samples from high-risk and low-risk individuals. Individuals of <50 years old (low risk, n = 40; high risk, n = 11) and those of ≥50 years old (low-risk, n = 56; high risk, n = 81) were analysed. Number (n) of samples in each group is also indicated. P values are for significant differences between both risk groups (two-sided Fisher’s exact test). Whiskers indicate the upper bounds of 95% confidence intervals from the binomial distribution. Source data

  8. Extended Data Fig. 8 Spatial architecture of clones in representative PNE biopsies.

    a, Mutation analysis of 341 samples obtained by high-density sampling from 16 biopsy specimens from 14 individuals with different age, lifestyle ESCC risks, and ESCC status (bottom panels), using WES (249 from 10 biopsies) or targeted-capture sequencing of major drivers (92 from 6 biopsies). Total numbers of mutations (top) are depicted for samples analysed by WES. Shared mutations are shown in orange. Mutation status of major drivers and common CNAs are summarized (middle panels). be, MCFs of detected mutations are depicted for each sample obtained by high-density collection from PNE biopsies performed on low-risk healthy individuals in their 20s (bd) and an 81-year-old, low-risk man (e). Four representative examples from 10 biopsies analysed by high-density WES sampling are shown. Mutations shared by a distinct set of samples or isolated samples are integrated to identify unique clones, as shown in different colours. Driver mutations are indicated by downward-pointing arrowheads. Rightward-pointing arrows indicate the clones in the same colour in Fig. 4b, c and Extended Data Fig. 9a, b. Source data

  9. Extended Data Fig. 9 Clones detected in high-density sampling.

    ai, The spatial distribution of clones as revealed by WES or targeted sequencing of driver genes is depicted for biopsies from younger-aged low-risk (a, b), middle-aged low-risk and high-risk (c, d), 70-year-old low-risk (e, f) and elderly high-risk (gi) subjects, as described in Fig. 4. For convenience, samples that share discrete sets of mutations—as indicated by different colours—are summarized for four subjects (a–d); in these subjects, mutations are frequently shared between distant samples, which suggests mosaicism. Sequencing platforms are indicated in each panel. Source data

  10. Extended Data Fig. 10 Phylogenetic analysis of representative clones.

    Phylogenetic trees mapped to the location of samples are depicted for additional representative clones from a total of 29 clones, seen in 5 biopsies from 5 elderly subjects. Imputed clonal structures are depicted in violin plots at the bottom, in which the estimated cellular prevalence of imputed mutational clusters (vertical axis) in each sample are shown as the distribution of posterior probabilities (width of the violin plots) calculated from the PyClone model. Colours correspond to those in the associated phylogenetic trees. Source data

Supplementary information

  1. Supplementary Information

    This file contains Supplementary Methods 1-2 and Supplementary Note 1, which contains the acknowledgements.

  2. Reporting Summary

  3. Supplementary Tables

    This file contains Supplementary Tables 1-10.

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