The patterns and dynamics of genomic instability in metastatic pancreatic cancer

Article metrics

Abstract

Pancreatic cancer is an aggressive malignancy with a five-year mortality of 97–98%, usually due to widespread metastatic disease. Previous studies indicate that this disease has a complex genomic landscape, with frequent copy number changes and point mutations1,2,3,4,5, but genomic rearrangements have not been characterized in detail. Despite the clinical importance of metastasis, there remain fundamental questions about the clonal structures of metastatic tumours6,7, including phylogenetic relationships among metastases, the scale of ongoing parallel evolution in metastatic and primary sites7, and how the tumour disseminates. Here we harness advances in DNA sequencing8,9,10,11,12 to annotate genomic rearrangements in 13 patients with pancreatic cancer and explore clonal relationships among metastases. We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle control, namely dysregulated G1-to-S-phase transition with intact G2–M checkpoint. These initiate amplification of cancer genes and occur predominantly in early cancer development rather than the later stages of the disease. Genomic instability frequently persists after cancer dissemination, resulting in ongoing, parallel and even convergent evolution among different metastases. We find evidence that there is genetic heterogeneity among metastasis-initiating cells, that seeding metastasis may require driver mutations beyond those required for primary tumours, and that phylogenetic trees across metastases show organ-specific branches. These data attest to the richness of genetic variation in cancer, brought about by the tandem forces of genomic instability and evolutionary selection.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Patterns of somatically acquired genomic rearrangements in pancreatic cancer.
Figure 2: Phylogenetic relationships of different metastases within a patient.
Figure 3: Phylogenetic relationships among different metastases and the primary tumour.
Figure 4: Organ-specific signatures of metastasis.

Accession codes

Data deposits

Genome sequence data have been deposited at the European Genome-Phenome Archive (EGA, http://www.ebi.ac.uk/ega/), which is hosted by the European Bioinformatics Institute (EBI), under accession number EGAS00000000064.

References

  1. 1

    Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801–1806 (2008)

  2. 2

    Harada, T. et al. Genome-wide DNA copy number analysis in pancreatic cancer using high-density single nucleotide polymorphism arrays. Oncogene 27, 1951–1960 (2008)

  3. 3

    Fu, B., Luo, M., Lakkur, S., Lucito, R. & Iacobuzio-Donahue, C. A. Frequent genomic copy number gain and overexpression of GATA-6 in pancreatic carcinoma. Cancer Biol. Ther. 7, 1593–1601 (2008)

  4. 4

    Kimmelman, A. C. et al. Genomic alterations link Rho family of GTPases to the highly invasive phenotype of pancreas cancer. Proc. Natl Acad. Sci. USA 105, 19372–19377 (2008)

  5. 5

    Gisselsson, D. et al. Telomere dysfunction triggers extensive DNA fragmentation and evolution of complex chromosome abnormalities in human malignant tumors. Proc. Natl Acad. Sci. USA 98, 12683–12688 (2001)

  6. 6

    Klein, C. A. Parallel progression of primary tumours and metastases. Nature Rev. Cancer 9, 302–312 (2009)

  7. 7

    Kuukasjarvi, T. et al. Genetic heterogeneity and clonal evolution underlying development of asynchronous metastasis in human breast cancer. Cancer Res. 57, 1597–1604 (1997)

  8. 8

    Ding, L. et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464, 999–1005 (2010)

  9. 9

    Mardis, E. R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361, 1058–1066 (2009)

  10. 10

    Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191–196 (2010)

  11. 11

    Pleasance, E. D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184–190 (2010)

  12. 12

    Shah, S. P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809–813 (2009)

  13. 13

    Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genet. 40, 722–729 (2008)

  14. 14

    Stephens, P. J. et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462, 1005–1010 (2009)

  15. 15

    McLintock, B. The stability of broken ends of chromosomes in Zea mays. Genetics 26, 234–282 (1941)

  16. 16

    Bignell, G. R. et al. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 17, 1296–1303 (2007)

  17. 17

    O’Hagan, R. C. et al. Telomere dysfunction provokes regional amplification and deletion in cancer genomes. Cancer Cell 2, 149–155 (2002)

  18. 18

    Bardeesy, N. & DePinho, R. A. Pancreatic cancer biology and genetics. Nature Rev. Cancer 2, 897–909 (2002)

  19. 19

    Maser, R. S. et al. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature 447, 966–971 (2007)

  20. 20

    Sahin, E. & Depinho, R. A. Linking functional decline of telomeres, mitochondria and stem cells during ageing. Nature 464, 520–528 (2010)

  21. 21

    Blow, J. J. & Gillespie, P. J. Replication licensing and cancer—a fatal entanglement? Nature Rev. Cancer 8, 799–806 (2008)

  22. 22

    Hashimoto, Y., Murakami, Y. & Uemura, K. et al. Telomere shortening and telomerase expression during multistage carcinogenesis of intraductal papillary mucinous neoplasms of the pancreas. J. Gastrointest. Surg. 12, 17–29 (2008)

  23. 23

    Campbell, P. J. et al. Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc. Natl Acad. Sci. USA 105, 13081–13086 (2008)

  24. 24

    Liu, W. et al. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nature Med. 15, 559–565 (2009)

  25. 25

    Nguyen, D. X. & Massague, J. Genetic determinants of cancer metastasis. Nature Rev. Genet. 8, 341–352 (2007)

  26. 26

    Klein, C. A. et al. Genetic heterogeneity of single disseminated tumour cells in minimal residual cancer. Lancet 360, 683–689 (2002)

  27. 27

    Embuscado, E. E. et al. Immortalizing the complexity of cancer metastasis: genetic features of lethal metastatic pancreatic cancer obtained from rapid autopsy. Cancer Biol. Ther. 4, 548–554 (2005)

  28. 28

    Quail, M. A. et al. A large genome center’s improvements to the Illumina sequencing system. Nature Methods 5, 1005–1010 (2008)

  29. 29

    Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008)

  30. 30

    Flohr, T. et al. Minimal residual disease-directed risk stratification using real-time quantitative PCR analysis of immunoglobulin and T-cell receptor gene rearrangements in the international multicenter trial AIEOP-BFM ALL 2000 for childhood acute lymphoblastic leukemia. Leukemia 22, 771–782 (2008)

Download references

Acknowledgements

This work was supported by the Wellcome Trust (grant reference 077012/Z/05/Z). P.J.C. is funded through a Wellcome Trust Senior Clinical Research Fellowship (grant reference WT088340MA). S.Y. has support from the Uehara memorial foundation. We would also like to acknowledge the financial support of the Skip Viragh Foundation and the Michael Rolphe Foundation for the autopsy programme, and funding from the National Institutes of Health (grants CA106610 and CA140599). I.V. is supported by a fellowship from The International Human Frontier Science Program Organization. We would like to thank U. McDermott for discussions and a critical reading of the manuscript.

Author information

P.J.C. undertook the analysis of the sequencing data assisted by P.J.S., E.D.P., L.A.S., M.-L.L., D.J.M., I.V., S.A.N.-Z., C.L., M.J., A.M., A.P.B. and J.W.T. Sample collection, processing, establishment of cell lines, DNA extraction and cytogenetic studies were performed by S.Y., L.A.M., C.A.G. and C.I.-D. PCR genotyping, capillary sequencing and downstream validation studies were performed by L.J.M. with assistance from C.L. and S.M. J.B., H.S. and M.A.Q. were responsible for generating libraries and running sequencers. P.J.C., S.Y., M.R.S., C.I.-D. and P.A.F. directed the research and wrote the manuscript, which all authors have approved.

Correspondence to Christine Iacobuzio-Donahue or P. Andrew Futreal.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Results comprising Effects of rearrangements on protein-coding genes, Fold-back inversions, Patterns and dynamics of genomic amplification and Signatures of DNA repair, Supplementary References, Supplementary Figures 1-11 with legends and Supplementary Tables 4 and 5 (see separate files for Supplementary Tables 1-3 and 6-7). (PDF 1706 kb)

Supplementary Table 1

This table shows clinical and pathology characteristics of patients and samples studied by massively parallel, paired-end sequencing. (XLS 19 kb)

Supplementary Table 2

This table shows somatically acquired genomic rearrangements in 13 patients with pancreatic cancer. All structural variants have been confirmed by PCR across the breakpoint, with bidirectional sequencing confirming the segments involved. Most have had the breakpoint annotated to base-pair resolution (‘Seq’ in the Evidence column): for the others, we provide a range of genomic positions encompassing the breakpoints (‘PCR across bkpt’). Length and sequence of either microhomology or non-templated sequence at the junction are shown. (XLS 107 kb)

Supplementary Table 3

This table shows the germline genomic rearrangements in 13 patients with pancreatic cancer. All structural variants have been confirmed by PCR across the breakpoint, with bidirectional sequencing confirming the segments involved. Length and sequence of either microhomology or non templated sequence at the junction are shown. (XLS 53 kb)

Supplementary Table 6

The table shows the genes involved at both breakpoints for each of the somatically acquired genomic rearrangements. (XLS 129 kb)

Supplementary Table 7

This table shows the presence or absence of each somatically acquired genomic rearrangement across the available metastasis and primary tumour samples for 10 patients (1 = present by PCR; 0 = absent by PCR). (XLS 87 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.