LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 35, 2015, Pages E4894-E4900

  Doucet O'Hare, Tara T ^a   Rodić, Nemanja ^a   Sharma, Reema ^a   Darbari, Isha ^a   Abril, Gabriela ^a   Choi, Jungbin A ^a   Ahn, Ji Young ^a   Cheng, Yulan ^a   Anders, Robert A ^a   Burns, Kathleen H ^a   Meltzer, Stephen J ^a   Kazazian, Haig H ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Barrett's esophagus; Esophageal adenocarcinoma; LINE 1; Retrotransposition; Retrotransposon

Indexed keywords

FORMALDEHYDE; LONG INTERSPERSED ELEMENT 1; ONCOPROTEIN; PARAFFIN; UNCLASSIFIED DRUG; DNA; RETROPOSON;

ARTICLE; BARRETT ESOPHAGUS; CANCER PATIENT; CANCER TISSUE; CARCINOGENESIS; CLINICAL ARTICLE; CLONAL VARIATION; CONTROLLED STUDY; EMBEDDING; ESOPHAGEAL ADENOCARCINOMA; ESOPHAGUS; ESOPHAGUS CARCINOMA; GENE EXPRESSION; GENE INSERTION; GENE SEQUENCE; HISTOPATHOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IMMUNOREACTIVITY; OPEN READING FRAME; PRIORITY JOURNAL; RETROPOSON; TISSUE SECTION; TUMOR CELL; ADENOCARCINOMA; ESOPHAGUS TUMOR; GENETICS; LONG INTERSPERSED REPEAT; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ADENOCARCINOMA; BARRETT ESOPHAGUS; BASE SEQUENCE; DNA; ESOPHAGEAL NEOPLASMS; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MOLECULAR SEQUENCE DATA; RETROELEMENTS;

EID: 84940979605     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1502474112     Document Type: Article

References (62)

1. Badillo R, Francis D (2014) Diagnosis and treatment of gastroesophageal reflux disease. World J Gastrointest Pharmacol Ther 5(3):105-112.
2. Barrett NR (1950) Chronic peptic ulcer of the oesophagus and 'oesophagitis'. Br J Surg 38(150):175-182.
3. Sappati Biyyani RS, Chak A (2013) Barrett's esophagus: Review of diagnosis and treatment. Gastroenterol Rep (Oxf) 1(1):9-18.
4. Modiano N, Gerson LB (2007) Barrett's esophagus: Incidence, etiology, pathophysiology, prevention, and treatment. Ther Clin Risk Manag 3(6):1035-1045.
5. Rasking W, et al. (1992) Persistent clonal areas and clonal expansion in Barrett's esophagus. Cancer Res 52(10):2946-2950.
6. Maley CC, et al. (2013) Selectively advantageous mutations and hitchhikers in neoplasms: p16 lesions are selected in Barrett's esophagus. Cancer Res 64(10):3414-3427.
7. Shukla R, et al. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153(1):101-111.
8. Helman E, et al. (2014) Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res 24(7):1053-1063.
9. Solyom S, et al. (2012) Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res 22(12):2328-2338.
10. Lee E, et al. (2012) Landscape of somatic retrotransposition in human cancers. Science 337(6097):967-971.
11. Tubio JM, et al. (2014) Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345(6196):1251343.
12. Hancks DC, Kazazian HH, Jr (2012) Active human retrotransposons: Variation and disease. Curr Opin Genet Dev 22(3):191-203.
13. Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35(1):41-48.
14. Ostertag EM, Goodier JL, Zhang Y, Kazazian HH, Jr (2003) SVA elements are non-autonomous retrotransposons that cause disease in humans. Am J Hum Genet 73(6):1444-1451.
15. Esnault C, Maestre J, Heidmann T (2000) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24(4):363-367.
16. van der Klift HM, Tops CM, Hes FJ, Devilee P, Wiknen JT (2012) Insertion of an SVA element, a nonautonomous retrotransposon, in PMS2 intron 7 as a novel cause of lynch syndrome. Hum Mutat 33(7):1051-1055.
17. Goodier JL (2014) Retrotransposition in tumors and brains. Mob. DNA 5:11.
18. Goodier JL, Kazazian HH, Jr (2008) Retrotransposons revisited: The restraint and rehabilitation of parasites. Cell 135(1):23-25.
19. Beck CR, Garcia-Perez JL, Badge RM, Moran JV (2011) LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12:187-215.
20. Ewing AD, Kazazian HH, Jr (2010) High-throughput sequencing reveals extensive variation in human specific L1 content in individual human genomes. Genome Res 20(9):1262-1270.
21. Morrish TA, et al. (2002) DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 31(2):159-165.
22. Gilbert N, Lutz-Prigge D, Moran JV (2002) Genomic deletions created upon LINE-1 retrotransposition. Cell 110(3):315-325.
23. Ostertag EM, Kazazian HH, Jr (2001) Twin priming: A proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res 11(12):2059-2065.
24. Rodić N, et al. (2014) Long interspersed element-1 protein expression is a hallmark of many human cancers. Am J Pathol 184(5):1280-1286.
25. Asch HL, et al. (1996) Comparative expression of the LINE-1 p40 protein in human breast carcinomas and normal breast tissues. Oncol Res 8(6):239-247.
26. Bratthauer GL, Fanning TG (1993) LINE-1 retrotransposon expression in pediatric germ cell tumors. Cancer 71(7):2383-2386.
27. Bratthauer GL, Cardiff RD, Fanning TG (1994) Expression of LINE-1 retrotransposons in human breast cancer. Cancer 73(9):2333-2336.
28. Evrony GD, et al. (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151(3):483-496.
29. Baillie JK, et al. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479(7374):534-537.
30. Upton KR, et al. (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161(2):228-239.
31. Grandi FC, Rosser JM, An W (2013) LINE-1-derived poly (A) microsatellites undergo rapid shortening and create somatic and germline mosaicism in mice. Mobile DNA 30(3):503-512.
32. Quesada V, et al. (2011) Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet 44(1):47-52.
33. Wood L, et al. (2007) The genomic landscapes of human breast and colorectal cancers. Science 318(5853):1108-1113.
34. Lee W, et al. (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465(7297):473-477.
35. Futreal PA, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4(3):177-183.
36. Stephens PJ, et al. (2012) The landscape of cancer genes and mutational processes in breast cancer. Nature 486(7403):400-404.
37. Guo G, et al. (2011) Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet 44(1):17-19.
38. Dalgliesh GL, et al. (2010) Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 463(7279):360-363.
39. Onk CK, et al. (2012) Exome sequencing of liver fluke associated cholangiocarcinoma. Nat Genet 44(6):690-693.
40. Berger MF, et al. (2011) The genomic complexity of primary human prostate cancer. Nature 470(7333):214-220.
41. Kan Z, et al. (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature 466(7308):869-873.
42. Ding L, et al. (2010) Genome remodeling in a basal-like breast cancer metastasis and xenograft. Nature 464(7291):999-1005.
43. Puente XS, et al. (2011) Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475(7354):101-105.
44. Shah SP, et al. (2009) Mutational evolution in a lobular breast tumour profiled at a single nucleotide resolution. Nature 461(7265):809-813.
45. Turajlic S, et al. (2012) Whole genome sequencing of matched primary and metastatic acral melanomas. Genome Res 22(2):196-207.
46. Koboldt DC, et al. (2012) Comprehensive molecular portraits of human breast tumours. Nature 490(7418):61-70.
47. Stansky N, et al. (2011) The mutational landscape of head and neck squamous cell carcinoma. Science 333(6046):1157-1160.
48. Wang L, et al. (2012) Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency. Genome Res 22(2):208-219.
49. Clark MJ, et al. (2010) U87MG decoded: The genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet 6(1):e1000832.
50. Wang AG, et al. (2006) Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Biochem Biophys Res Commun 345(3):1022-1032.
51. Akatsuka A, et al. (2010) Tumor cells of non-hematopoietic and hematopoietic origins express activation-induced C-type lectin, the ligand for killer cell lectin-like receptor F1. Int Immunol 22(9):783-790.
52. Ghersi E, Vito P, Lopez P, Abdallah M, D'Adamio L (2004) The intracellular localization of amyloid beta protein precursor (AbetaPP) intracellular domain associated protein-1 (AIDA-1) is regulated by AbetaPP and alternative splicing. J Alzheimers Dis 6(1):67-68.
53. Casagrande G, te Kronnie G, Basso G (2006) The effects of siRNA-mediated inhibition of E2A-PBX1 on EB-1 and Wnt16b expression in the 697 pre-B leukemia cell line. Haematologica 91(6):765-771.
54. San Martin IA, et al. (2009) Impaired cell cycle regulation of the osteoblast-related heterodimeris transcription factor Runx2-Cbfbeta in osteosarcoma cells. J Cell Physiol 221(3):560-571.
55. Van der Deen M, et al. (2012) Genomic promoter occupancy or runt-related transcription factor RUNX2 in Osteosarcoma cells identifies genes involved in cell adhesion and motility. J Biol Chem 287(7):4503-4517.
56. Muller T, et al. (2010) ASAP1 promotes tumor cell motility and invasiveness, stimulates metastasis formation in vivo, and correlates with poor survival in colorectal cancer patients. Oncogene 29(16):2393-2403.
57. Lai F, et al. (2005) WOX1 is essential for UVB irradiation-induced apoptosis and down-regulated via translational blockade in UVB-induced cutaneous squamous cell carcinoma in vivo. Clin Cancer Res 11(16):5769-5777.
58. Ishii H, et al. (2004) Effect of exogenous E2F-1 on the expression of common chromosome fragile site genes, FHIT and WWOX. Biochem Biophys Res Commun 316(4):1088-1093.
59. Potts PR, Yu H (2007) The SMC5/6 complex maintains telomere length in ALT cancer cells through SUMOylation of telomere-binding proteins. Nat Struct Mol Biol 14(7):581-590.
60. Vauhkonen H, Vauhkonen M, Sipponen P, Knuutila S (2007) Oligonucleotide array comparative genomic hybridization refines the structure of 8p23.1, 17q12 and 20q13.2 amplifications in gastric carcinomas. Cytogenet Genome Res 119(1-2):39-45.
61. Korff S, et al. (2008) Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability. BMC Cancer 8:329.
62. Blackburn AC, et al. (2007) Genetic mapping in mice identifies DMBT1 as a candidate modifier of mammary tumors and breast cancer risk. Am J Pathol 170(6):2030-2041.