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Genetic landscape of esophageal squamous cell carcinoma

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Abstract

Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers1. We performed exome sequencing on 113 tumor-normal pairs, yielding a mean of 82 non-silent mutations per tumor, and 8 cell lines. The mutational profile of ESCC closely resembles those of squamous cell carcinomas of other tissues but differs from that of esophageal adenocarcinoma. Genes involved in cell cycle and apoptosis regulation were mutated in 99% of cases by somatic alterations of TP53 (93%), CCND1 (33%), CDKN2A (20%), NFE2L2 (10%) and RB1 (9%). Histone modifier genes were frequently mutated, including KMT2D (also called MLL2; 19%), KMT2C (MLL3; 6%), KDM6A (7%), EP300 (10%) and CREBBP (6%). EP300 mutations were associated with poor survival. The Hippo and Notch pathways were dysregulated by mutations in FAT1, FAT2, FAT3 or FAT4 (27%) or AJUBA (JUB; 7%) and NOTCH1, NOTCH2 or NOTCH3 (22%) or FBXW7 (5%), respectively. These results define the mutational landscape of ESCC and highlight mutations in epigenetic modulators with prognostic and potentially therapeutic implications.

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Figure 1: Genome-wide mutational landscape of ESCC identified by whole-exome sequencing.
Figure 2: Recurrent histone modifier gene mutations in ESCC.
Figure 3: Alterations of Hippo pathway regulators in AJUBA.
Figure 4: Somatically altered pathways in ESCC.

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  • 11 September 2014

    In the version of this article initially published online, the word "alternations" in the abstract should have been "alterations," in Figure 1c "30" should have been "33," in the legend to Figure 1 "MIR458K" should have been "MIR548K," labels in Figure 2h were in the wrong position, and in the 'DNA constructs and mutagenesis' section in the Online Methods "BamHI" should have been "EcoRV" and the penultimate sentence should have been deleted. These errors have been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank M.-H. Xiong and all the staff and assistants in the Lab and Tumor Bank of the Department of Thoracic Surgery for their support in collecting and processing samples. This work was supported by the National High-Tech Research and Development Program of China (2012AA02A503), the National Natural Science Foundation of China (81172336, 81372219, 81301851 and U1302223), the Program for Changjiang Scholars and Innovative Research Team in University of China (IRT13006) and the Beijing Municipal Natural Science Foundation (7141011).

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Authors

Contributions

J.H. devised and supervised this project. J.H. and Y.-B.G. designed the study and wrote the manuscript. J.H., F.-W.T., B.Q., N.L., K.S., Li-Jian Zhang, Lan-Jun Zhang, Q.X. and S.-G.G. contributed clinical samples and information. X.-L.F. and S.-S.S. performed pathological review. Y.-B.G., Z.-L.C., J.-G.L., Y.-D.Z., J.S., C.-C.Z., R.Y., S.-Y.W., P.W., N.S., B.-H.Z., J.-S.D., Y.Y., M.L. and F. Zhou processed the samples and performed the experiments. Y.-B.G. and Y.-D.Z. performed EP300 HAT domain sequencing. Y.-B.G. and X.-D.H. performed bioinformatic and statistical analyses. F. Zhang, Z.-R.Z., Z.-T.L., Y.-D.Z. and S.-Y.W. validated genetic variations. X.-J.S., Z.-M.S. and Z.-Y.L. performed cellular biology experiments. Y.-B.G., Z.-L.C., J.-G.L., X.-D.H., X.-J.S. and J.H. analyzed and discussed the data.

Corresponding author

Correspondence to Jie He.

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Integrated supplementary information

Supplementary Figure 1 Distribution of somatic mutations detected by exome sequencing in the ESCC patient cohort.

The average, median and range of mutation numbers in each category are shown.

Supplementary Figure 2 Landscape of somatic copy number alterations detected by exome sequencing in the ESCC patient cohort.

Chromosomes are arranged circularly end to end, with the cytobands frequently affected marked in the outer rim. The inner space displays copy number data inferred from whole-exome sequencing, with red dots indicating copy number gains and blue dots indicating copy number losses. Amplifications are arranged as inward radiations in proportion to the fold change.

Supplementary Figure 3 Substitution composition of smokers and non-smokers in the ESCC exome.

(a) Comparison of the average substitution rates at non-CpG dinucleotides and at CpG dinucleotides between smokers and non-smokers. Most of the excessive substitution of C>T over C>A/G occurred at CpG dinucleotides. (b) Comparison of the average rates of all possible single-base substitutions between ESCC smokers (n = 77) and non-smokers (n = 36). Error bars indicate s.e.m. No significant difference was found between smokers and non-smokers.

Supplementary Figure 4 Distribution of non-silent mutations or SCNAs of known cancer genes.

(a) Mapping of cancer signaling pathways in ESCC, indicated by the number of mutations per capita and by the fraction of tumors carrying at least one mutation in the corresponding pathway. (b) Fraction of tumors carrying mutations in known oncogenes and tumor suppressor genes (TSGs). Pathway definition and gene classification are as shown in Supplementary Table 14.

Supplementary Figure 5 Recurrently mutated COSMIC Cancer Census genes in ESCC cell lines.

Supplementary Figure 6 Somatic alterations of RB1, NOTCH1, CCND1 and MIR548K correlate with clinical features.

(a) Mutation spectrum of RB1 (n = 10). (b) RB1 mutation was associated with younger age of onset of ESCC (P = 0.010, Student’s t test, two-tailed). (c) Mutation spectrum of NOTCH1 (n = 16). (d) NOTCH1 mutation was associated with older age of onset of ESCC (P = 0.001, Student’s t test, two-tailed). Amplifications of (e) CCND1 and (f) MIR548K were associated with poor overall survival (P = 0.006 and P = 0.022, log-rank test).

Supplementary Figure 7 Western blot confirmation of p300 knockdown efficiency in KYSE-150 and KYSE-450 cells.

Supplementary Figure 8 Representative fields of immunohistochemistry results.

The proteins of interest are designated in rows. Immunoreactivity scores are listed above. p-YAP1, phosphorylated YAP1.

Supplementary Figure 9 Somatic alterations in the PI3K-Ras and Notch pathways in ESCC.

Genes are shown along with the percentage of samples with alterations, including somatic mutations (blue), homozygous deletions (green) and amplifications (red).

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Gao, YB., Chen, ZL., Li, JG. et al. Genetic landscape of esophageal squamous cell carcinoma. Nat Genet 46, 1097–1102 (2014). https://doi.org/10.1038/ng.3076

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