Cell-of-origin chromatin organization shapes the mutational landscape of cancer

Nature

Volumn 518, Issue 7539, 2015, Pages 360-364

  Polak, Paz ^a,b   Karlic, Rosa ^c   Koren, Amnon ^a,b   Thurman, Robert ^d   Sandstrom, Richard ^d   Lawrence, Michael S ^b   Reynolds, Alex ^d   Rynes, Eric ^d   Vlahovicek, Kristian ^c,e   Stamatoyannopoulos, John A ^d,f   Sunyaev, Shamil R ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c UNIVERSITY OF ZAGREB   (Croatia)

^d UNIVERSITY OF WASHINGTON   (United States)

^e UNIVERSITY OF OSLO   (Norway)

^f UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER; CELL ORGANELLE; CHROMOSOME; GENOME; MUTATION;

ARTICLE; CANCER GENETICS; CELL SHAPE; CHROMATIN STRUCTURE; DNA SEQUENCE; EPIGENETICS; GENE EXPRESSION; GENE MUTATION; HUMAN; NEOPLASM; PRIORITY JOURNAL; SOMATIC MUTATION; ANTIBODY SPECIFICITY; CHEMISTRY; CHROMATIN; DNA REPLICATION TIMING; GENETIC EPIGENESIS; GENETICS; HUMAN GENOME; MELANOCYTE; MELANOMA; METABOLISM; MUTATION; PATHOLOGY; TUMOR CELL LINE;

CHROMATIN;

CELL LINE, TUMOR; CHROMATIN; DNA REPLICATION TIMING; EPIGENESIS, GENETIC; EPIGENOMICS; GENOME, HUMAN; HUMANS; MELANOCYTES; MELANOMA; MUTATION; NEOPLASMS; ORGAN SPECIFICITY;

EID: 84923358817     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14221     Document Type: Article

References (29)

1. Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
2. Hodgkinson, A., Chen, Y. & Eyre-Walker, A. The large-scale distribution of somatic mutations in cancer genomes. Hum. Mutat. 33, 136-143 (2012).
3. Liu, L., De, S. & Michor, F. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nature Commun. 4, 1502 (2013).
4. Schuster-Böckler, B. & Lehner, B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488, 504-507 (2012).
5. Woo, Y. H. & Li, W. H. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nature Commun. 3, 1004 (2012).
6. Zhu, J. et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642-654 (2013).
7. Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
8. The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
9. Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature http://dx.doi.org/10.1038/nature14248 (this issue).
10. Ryba, T. et al. Evolutionarily conserved replication timing profiles predict longrange chromatin interactions and distinguish closely related cell types. Genome Res. 20, 761-770 (2010).
11. Berger, M. F. et al. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature 485, 502-506 (2012).
12. Chapman, M.A. et al. Initial genomesequencingandanalysis ofmultiplemyeloma. Nature 471, 467-472 (2011).
13. Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinomawith massively parallel sequencing. Cell 150, 1107-1120 (2012).
14. Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nature Genet. 43, 464-469 (2011).
15. Bass, A. J. et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2fusion.NatureGenet.43,964-96810.1038/ng.936(2011).
16. Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462-477 (2013).
17. Dulak, A. M. et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nature Genet. 45, 478-486 (2013).
18. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519-525 (2012).
19. Hansen, R. S. et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc. Natl Acad. Sci. USA 107, 139-144 (2010).
20. Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
21. Alexandrov, L. B. et al. Signatures ofmutational processes in humancancer. Nature 500, 415-421 (2013).
22. Pleasance, E. D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184-190 (2010).
23. Reid, B. J., Li, X., Galipeau, P. C. & Vaughan, T. L. Barrett's oesophagus and oesophageal adenocarcinoma: time for a new synthesis. Nature Rev. Cancer 10, 87-101 (2010).
24. Hudson, T. J. et al. International network of cancer genome projects. Nature 464, 993-998 (2010).
25. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213-219 (2013).
26. Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919-1920 (2012).
27. Koren,A. et al. DifferentialRelationship ofDNAreplicationtimingto different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033-1040 (2012).
28. Breiman, L. Random Forests. Mach. Learn. 45, 5-32 (2001).
29. Altmann, A., Tolosi, L., Sander, O. & Lengauer, T. Permutation importance: a corrected feature importance measure. Bioinformatics 26, 1340-1347 (2010).