Somatic mutation of CDKN1B in small intestine neuroendocrine tumors

Nature Genetics

Volumn 45, Issue 12, 2013, Pages 1483-1486

  Francis, Joshua M ^a,b   Kiezun, Adam ^a   Ramos, Alex H ^a,b,o   Serra, Stefano ^c   Pedamallu, Chandra Sekhar ^a,b   Qian, Zhi Rong ^b   Banck, Michaela S ^d,e   Kanwar, Rahul ^d   Kulkarni, Amit A ^d   Karpathakis, Anna ^f,g   Manzo, Veronica ^b   Contractor, Tanupriya ^h   Philips, Juliet ^b   Nickerson, Elizabeth ^a   Pho, Nam ^a   Hooshmand, Susanne M ^b   Brais, Lauren K ^b   Lawrence, Michael S ^a   Pugh, Trevor ^a   McKenna, Aaron ^a   Sivachenko, Andrey ^a   Cibulskis, Kristian ^a   Carter, Scott L ^a   Ojesina, Akinyemi I ^a,b   Freeman, Samuel ^b   Jones, Robert T ^b   Voet, Douglas ^a   Saksena, Gordon ^a   Auclair, Daniel ^a   Onofrio, Robert ^a   Shefler, Erica ^a   Sougnez, Carrie ^a   Grimsby, Jonna ^a   Green, Lisa ^a   Lennon, Niall ^a   Meyer, Tim ^f,g   Caplin, Martyn ^g   Chung, Daniel C ⁱ   Beutler, Andreas S ^d,e   Ogino, Shuji ^b,j,k   Thirlwell, Christina ^f,g   Shivdasani, Ramesh ^b   Asa, Sylvia L ^c,l   Harris, Chris R ^h,m,n   Getz, Gad ^a   Kulke, Matthew ^b   Meyerson, Matthew ^a,b   more..

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

^b DANA FARBER CANCER INSTITUTE   (United States)

^c UNIVERSITY HEALTH NETWORK   (Canada)

^d MAYO CLINIC   (United States)

^e MAYO CLINIC CANCER CENTER   (United States)

^f UNIVERSITY COLLEGE LONDON   (United Kingdom)

^g ROYAL FREE HOSPITAL   (United Kingdom)

^h Raymond and Beverly Sackler Foundation   (United States)

ⁱ MASSACHUSETTS GENERAL HOSPITAL   (United States)

^j BRIGHAM AND WOMEN S HOSPITAL   (United States)

^k HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^l UNIVERSITY OF TORONTO   (Canada)

^m RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

ⁿ UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY   (United States)

^o EISAI INC   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 1B;

ARTICLE; CELL CYCLE; CHROMOSOME 18; CHROMOSOME LOSS; FRAMESHIFT MUTATION; GENE DELETION; HUMAN; HUMAN TISSUE; INDEL MUTATION; MUTATION RATE; NEUROENDOCRINE TUMOR; PRIORITY JOURNAL; SMALL INTESTINE; SMALL INTESTINE NEUROENDOCRINE TUMOR; SOMATIC MUTATION;

CELL CYCLE; COHORT STUDIES; CYCLIN-DEPENDENT KINASE INHIBITOR P27; GENES, TUMOR SUPPRESSOR; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INTESTINAL NEOPLASMS; INTESTINE, SMALL; MUTATION; NEUROENDOCRINE TUMORS; SEQUENCE ANALYSIS, DNA;

EID: 84888369188     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2821     Document Type: Article

References (51)

1. Vinik, A. I. et al. NANETS consensus guidelines for the diagnosis of neuroendocrine tumor. Pancreas 39, 713-734 (2010).
2. Jiao, Y. et al. DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331, 1199-1203 (2011).
3. Kulke, M. H. et al. High-resolution analysis of genetic alterations in small bowel carcinoid tumors reveals areas of recurrent amplification and loss. Genes Chromosom. Cancer 47, 591-603 (2008). (Pubitemid 351748345)
4. Cunningham, J. L. et al. Common pathogenetic mechanism involving human chromosome 18 in familial and sporadic ileal carcinoid tumors. Genes Chromosom. Cancer 50, 82-94 (2011).
5. Banck, M. S. et al. The genomic landscape of small intestine neuroendocrine tumors. J. Clin. Invest. 123, 2502-2508 (2013).
6. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213-219 (2013).
7. Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
8. Futreal, P. A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177-183 (2004). (Pubitemid 38337497)
9. Getz, G. et al. Comment on "The consensus coding sequences of human breast and colorectal cancers". Science 317, 1500 (2007).
10. Hatta, Y., Takeuchi, S., Yokota, J. & Koeffler, H. P. Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12. 3-13. 1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes. Br. J. Cancer 75, 1256-1262 (1997). (Pubitemid 27179813)
11. Kibel, A. S., Freije, D., Isaacs, W. B. & Bova, G. S. Deletion mapping at 12p12-13 in metastatic prostate cancer. Genes Chromosom. Cancer 25, 270-276 (1999). (Pubitemid 29266696)
12. Takeuchi, S. et al. Frequent loss of heterozygosity in region of the KIP1 locus in non-small cell lung cancer: evidence for a new tumor suppressor gene on the short arm of chromosome 12. Cancer Res. 56, 738-740 (1996). (Pubitemid 26055460)
13. Pietenpol, J. A. et al. Assignment of the human p27Kip1 gene to 12p13 and its analysis in leukemias. Cancer Res. 55, 1206-1210 (1995).
14. Hetet, G. et al. Recurrent molecular deletion of the 12p13 region, centromeric to ETV6/TEL, in T-cell prolymphocytic leukemia. Hematol. J. 1, 42-47 (2000).
15. Le Toriellec, E. et al. Haploinsufficiency of CDKN1B contributes to leukemogenesis in T-cell prolymphocytic leukemia. Blood 111, 2321-2328 (2008). (Pubitemid 351451440)
16. Barbieri, C. E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685-689 (2012).
17. Muraoka, R. S. et al. ErbB2/Neu-induced, cyclin D1-dependent transformation is accelerated in p27-haploinsufficient mammary epithelial cells but impaired in p27-null cells. Mol. Cell Biol. 22, 2204-2219 (2002). (Pubitemid 34224627)
18. Gao, H. et al. A critical role for p27kip1 gene dosage in a mouse model of prostate carcinogenesis. Proc. Natl. Acad. Sci. USA 101, 17204-17209 (2004). (Pubitemid 39627798)
19. Sancho, R. et al. F-box and WD repeat domain-containing 7 regulates intestinal cell lineage commitment and is a haploinsufficient tumor suppressor. Gastroenterology 139, 929-941 (2010).
20. Ying, H. et al. PTEN is a major tumor suppressor in pancreatic ductal adenocarcinoma and regulates an NF-?B-cytokine network. Cancer Discov. 1, 158-169 (2011).
21. Kumar, M. S. et al. Dicer1 functions as a haploinsufficient tumor suppressor. Genes Dev. 23, 2700-2704 (2009).
22. Zimmer, S. N. et al. Crebbp haploinsufficiency in mice alters the bone marrow microenvironment, leading to loss of stem cells and excessive myelopoiesis. Blood 118, 69-79 (2011).
23. Kiyokawa, H. et al. Enhanced growth of mice lacking the cyclin-dependent kinase inhibitor function of p27(Kip1). Cell 85, 721-732 (1996).
24. Nakayama, K. et al. Mice lacking p27(Kip1) display increased body size, multiple organ hyperplasia, retinal dysplasia, and pituitary tumors. Cell 85, 707-720 (1996).
25. Fero, M. L. et al. A syndrome of multiorgan hyperplasia with features of gigantism, tumorigenesis, and female sterility in p27(Kip1)-deficient mice. Cell 85, 733-744 (1996).
26. Fero, M. L., Randel, E., Gurley, K. E., Roberts, J. M. & Kemp, C. J. The murine gene p27Kip1 is haplo-insufficient for tumour suppression. Nature 396, 177-180 (1998). (Pubitemid 28523620)
27. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
28. Solimini, N. L. et al. Recurrent hemizygous deletions in cancers may optimize proliferative potential. Science 337, 104-109 (2012).
29. Rudin, C. M. et al. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat. Genet. 44, 1111-1116 (2012).
30. Peifer, M. et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat. Genet. 44, 1104-1110 (2012).
31. Banerji, S. et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 486, 405-409 (2012).
32. Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150, 1107-1120 (2012).
33. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883-892 (2012).
34. Habbe, N., Fendrich, V., Heverhagen, A., Ramaswamy, A. & Bartsch, D. K. Outcome of surgery for ileojejunal neuroendocrine tumors. Surg. Today 43, 1168-1174 (2013).
35. Polish, A., Vergo, M. T. & Agulnik, M. Management of neuroendocrine tumors of unknown origin. J. Natl. Compr. Canc. Netw. 9, 1397-1402 (2011).
36. Curtit, E. et al. Discordances in estrogen receptor status, progesterone receptor status, and HER2 status between primary breast cancer and metastasis. Oncologist 18, 667-674 (2013).
37. Park, S. et al. Discordance of molecular biomarkers associated with epidermal growth factor receptor pathway between primary tumors and lymph node metastasis in non-small cell lung cancer. J. Thorac. Oncol. 4, 809-815 (2009).
38. Polyak, K. et al. Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals. Cell 78, 59-66 (1994).
39. Toyoshima, H. & Hunter, T. p27, a novel inhibitor of G1 cyclin-Cdk protein kinase activity, is related to p21. Cell 78, 67-74 (1994). (Pubitemid 24228301)
40. The Cancer Genome Atlas. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
41. Stephens, P. J. et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 486, 400-404 (2012).
42. Pellegata, N. S. et al. Germ-line mutations in p27Kip1 cause a multiple endocrine neoplasia syndrome in rats and humans. Proc. Natl. Acad. Sci. USA 103, 15558-15563 (2006). (Pubitemid 44625631)
43. Milne, T. A. et al. Menin and MLL cooperatively regulate expression of cyclin-dependent kinase inhibitors. Proc. Natl. Acad. Sci. USA 102, 749-754 (2005). (Pubitemid 40282737)
44. Karnik, S. K. et al. Menin regulates pancreatic islet growth by promoting histone methylation and expression of genes encoding p27Kip1 and p18INK4c. Proc. Natl. Acad. Sci. USA 102, 14659-14664 (2005). (Pubitemid 41457112)
45. Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).
46. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
47. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
48. Pugh, T. J. et al. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature 488, 106-110 (2012).
49. Saunders, C. T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28, 1811-1817 (2012).
50. Chiang, D. Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103 (2009).
51. Mermel, C. H. et al. GISTIC2. 0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).