Digital gene expression profiling of primary acute lymphoblastic leukemia cells

Leukemia

Volumn 26, Issue 6, 2012, Pages 1218-1227

  Nordlund, J ^a   Kiialainen, A ^a,h   Karlberg, O ^a   Berglund, E C ^a   Goransson Kultima H ^a   Sonderkaer M ^b   Nielsen, K L ^b   Gustafsson, M G ^a   Behrendtz, M ^c   Forestier, E ^d   Perkkio M ^e   Soderhall S ^f   Lonnerholm G ^g   Syvanen A C ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b AALBORG UNIVERSITY   (Denmark)

^c LINKÖPING UNIVERSITY HOSPITAL   (Sweden)

^d UMEÅ UNIVERSITY   (Sweden)

^e KUOPIO UNIVERSITY HOSPITAL   (Finland)

^f KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^g UNIVERSITY CHILDREN S HOSPITAL   (Sweden)

^h F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

ALL; alternative polyadenylation; antisense transcript; digital gene expression; pediatric acute lymphoblastic leukemia; second generation sequencing

Indexed keywords

INTERFERON; PROTEIN P53; RNA;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; APOPTOSIS; ARTICLE; CELL LINEAGE; CHILD; CHROMOSOME REARRANGEMENT; CHROMOSOME TRANSLOCATION; CLASSIFICATION; CLINICAL ARTICLE; CONTROLLED STUDY; CYTOGENETICS; DIGITAL GENE EXPRESSION PROFILING; DIPLOIDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LOCATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; HUMAN CELL; IMMUNOPHENOTYPING; LEUKEMIA CELL; NUCLEIC ACID PROBE; NUCLEOTIDE SEQUENCE; POLYADENYLATION; POLYMERASE CHAIN REACTION; PRE B LYMPHOCYTE; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SIGNAL TRANSDUCTION; T LYMPHOCYTE;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, LEUKEMIC; HUMANS; INFANT; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRECURSOR B-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PRECURSOR T-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PROGNOSIS; REAL-TIME POLYMERASE CHAIN REACTION; RNA, MESSENGER; TUMOR MARKERS, BIOLOGICAL;

EID: 84862026985     PISSN: 08876924     EISSN: 14765551     Source Type: Journal    
DOI: 10.1038/leu.2011.358     Document Type: Article

References (59)

1. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999; 286: 531-537.
2. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 2002; 1: 133-143. (Pubitemid 41039160)
3. Ross ME, Zhou X, Song G, Shurtleff SA, Girtman K, Williams WK et al. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood 2003; 102: 2951-2959. (Pubitemid 37248870)
4. Holleman A, Cheok MH, den Boer ML, Yang W, Veerman AJ, Kazemier KM et al. Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. N Engl J Med 2004; 351: 533-542.
5. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995; 270: 484-487.
6. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008; 24: 133-141.
7. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010; 11: 31-46.
8. Nielsen KL, Hogh AL, Emmersen J. DeepSAGE-digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res 2006; 34: e133.
9. Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M et al. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res 2010; 20: 1730-1739.
10. t Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008; 36: e141.
11. Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones S et al. Nextgeneration tag sequencing for cancer gene expression profiling. Genome Res 2009; 19: 1825-1835.
12. The Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 50-modified long and short RNAs. Nature 2009; 457: 1028-1032.
13. Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010; 143: 1018-1029.
14. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. The antisense transcriptomes of human cells. Science 2008; 322: 1855-1857.
15. The FANTOM ConsortiumCarninci P, Kasukawa T, Katayama S, Gough J, Frith MC et al. The transcriptional landscape of the mammalian genome. Science 2005; 309: 1559-1563.
16. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M et al. Antisense transcription in the mammalian transcriptome. Science 2005; 309: 1564-1566.
17. Ebralidze AK, Guibal FC, Steidl U, Zhang P, Lee S, Bartholdy B et al. PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. Genes Dev 2008; 22: 2085-2092.
18. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008; 451: 202-206.
19. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites. Science 2008; 320: 1643-1647. (Pubitemid 351931255)
20. Mayr C, Bartel DP. Widespread shortening of 30 UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 2009; 138: 673-684.
21. Galante PA, Vidal DO, de Souza JE, Camargo AA, de Souza SJ. Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol 2007; 8: R40.
22. Morrissy AS, Griffith M, Marra MA. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res 2011; 21: 1203-1212.
23. Milani L, Lundmark A, Kiialainen A, Nordlund J, Flaegstad T, Forestier E et al. DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia. Blood 2010; 115: 1214-1225.
24. Zhang Y, Li J, Kong L, Gao G, Liu QR, Wei L. NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res 2007; 35: D156-D161. (Pubitemid 46056189)
25. Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F et al. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 2009; 93: 213-220.
26. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120: 15-20. (Pubitemid 40094598)
27. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 2001; 25: 402-408. (Pubitemid 34164012)
28. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5: R80.
29. Robinson MD, Smyth GK. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 2008; 9: 321-332. (Pubitemid 351438556)
30. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002; 99: 6567-6572. (Pubitemid 34526173)
31. Witten D, Tibshirani R, Gu SG, Fire A, Lui WO. Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biol 2010; 8: 58.
32. Bishop JO, Morton JG, Rosbash M, Richardson M. Three abundance classes in HeLa cell messenger RNA. Nature 1974; 250: 199-204.
33. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18 000 cancer gene expression profiles. Neoplasia 2007; 9: 166-180.
34. Ohno T, Kimura Y, Sakurada K, Sugimura K, Fujiyoshi T, Saheki T et al. Argininosuccinate synthetase gene expression in leukemias: potential diagnostic marker for blastic crisis of chronic myelocytic leukemia. Leuk Res 1992; 16: 475-483.
35. Mozos A, Royo C, Hartmann E, De Jong D, Baro C, Valera A et al. SOX11 expression is highly specific for mantle cell lymphoma and identifies the cyclin D1-negative subtype. Haematologica 2009; 94: 1555-1562.
36. Gold MR, Ingham RJ, McLeod SJ, Christian SL, Scheid MP, Duronio V et al. Targets of B-cell antigen receptor signaling: the phosphatidylinositol 3-kinase/Akt/glycogen synthase kinase-3 signaling pathway and the Rap1 GTPase. Immunol Rev 2000; 176: 47-68.
37. Juric D, Lacayo NJ, Ramsey MC, Racevskis J, Wiernik PH, Rowe JM et al. Differential gene expression patterns and interaction networks in BCR-ABLpositive and-negative adult acute lymphoblastic leukemias. J Clin Oncol 2007; 25: 1341-1349. (Pubitemid 46706880)
38. Morris KV. The emerging role of RNA in the regulation of gene transcription in human cells. Semin Cell Dev Biol 2011; 22: 351-358.
39. Grinchuk OV, Jenjaroenpun P, Orlov YL, Zhou J, Kuznetsov VA. Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns. Nucleic Acids Res 2010; 38: 534-547.
40. Wang X, Asplund AC, Porwit A, Flygare J, Smith CI, Christensson B et al. The subcellular Sox11 distribution pattern identifies subsets of mantle cell lymphoma: correlation to overall survival. Br J Haematol 2008; 143: 248-252.
41. Gustavsson E, Sernbo S, Andersson E, Brennan DJ, Dictor M, Jerkeman M et al. SOX11 expression correlates to promoter methylation and regulates tumor growth in hematopoietic malignancies. Mol Cancer 2010; 9: 187.
42. Maruyama R, Shipitsin M, Choudhury S, Wu Z, Protopopov A, Yao J et al. Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci USA 2010; e-pub ahead of print 22 November 2010.
43. Zachariadis V, Gauffin F, Kuchinskaya E, Heyman M, Schoumans J, Blennow E et al. The frequency and prognostic impact of dic(9;20)(p13.2;q11.2) in childhood B-cell precursor acute lymphoblastic leukemia: results from the NOPHO ALL-2000 trial. Leukemia 2011; 25: 622-628.
44. Schoumans J, Johansson B, Corcoran M, Kuchinskaya E, Golovleva I, Grander D et al. Characterisation of dic(9;20)(p11-13;q11) in childhood B-cell precursor acute lymphoblastic leukaemia by tiling resolution array-based comparative genomic hybridisation reveals clustered breakpoints at 9p13.2 and 20q11.2. Br J Haematol 2006; 135: 492-499. (Pubitemid 44583413)
45. Sulong S, Moorman AV, Irving JA, Strefford JC, Konn ZJ, Case MC et al. A comprehensive analysis of the CDKN2A gene in childhood acute lymphoblastic leukemia reveals genomic deletion, copy number neutral loss of heterozygosity, and association with specific cytogenetic subgroups. Blood 2009; 113: 100-107.
46. Schiffman JD, Wang Y, McPherson LA, Welch K, Zhang N, Davis R et al. Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia. Cancer Genet Cytogenet 2009; 193: 9-18.
47. Forestier E, Gauffin F, Andersen MK, Autio K, Borgstrom G, Golovleva I et al. Clinical and cytogenetic features of pediatric dic(9;20)(p13.2;q11.2)- positive B-cell precursor acute lymphoblastic leukemias: a Nordic series of 24 cases and review of the literature. Genes Chromosomes Cancer 2008; 47: 149-158.
48. Zhang Y, Xiong Y, Yarbrough WG. ARF promotes MDM2 degradation and stabilizes p53: ARF-INK4a locus deletion impairs both the Rb and p53 tumor suppression pathways. Cell 1998; 92: 725-734. (Pubitemid 28155312)
49. Bungaro S, Dell'Orto MC, Zangrando A, Basso D, Gorletta T, Lo Nigro L et al. Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks. Genes Chromosomes Cancer 2009; 48: 22-38.
50. Shaulian E, Schreiber M, Piu F, Beeche M, Wagner EF, Karin M. The mammalian UV response: c-Jun induction is required for exit from p53-imposed growth arrest. Cell 2000; 103: 897-907.
51. Lecomte S, Desmots F, Le Masson F, Le Goff P, Michel D, Christians ES et al. Roles of heat shock factor 1 and 2 in response to proteasome inhibition: consequence on p53 stability. Oncogene 2010; 29: 4216-4224.
52. Weaver BAA, Cleveland DW. Does aneuploidy cause cancer? [Curr Opin Cell Biol 2006, 18: 658-667]. Curr Opin Cell Biol 2007; 19: 246-246.
53. Passalacqua M, Patrone M, Sparatore B, Melloni E, Pontremoli S. Protein kinase Ctheta is specifically localized on centrosomes and kinetochores in mitotic cells. Biochem J 1999; 337 (Part 1): 113-118. (Pubitemid 29039090)
54. Chattopadhyay A, Chiang CW, Yang E. BAD/BCL-[X(L)] heterodimerization leads to bypass of G0/G1 arrest. Oncogene 2001; 20: 4507-4518. (Pubitemid 32772433)
55. Boise LH, Gonzalez-Garcia M, Postema CE, Ding L, Lindsten T, Turka LA et al. bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death. Cell 1993; 74: 597-608. (Pubitemid 23259741)
56. Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 2006; 34: 3465-3475.
57. Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009; 10: 637-643.
58. Coyaud E, Struski S, Prade N, Familiades J, Eichner R, Quelen C et al. Wide diversity of PAX5 alterations in B-ALL: a Groupe Francophone de Cytogenetique Hematologique study. Blood 2010; 115: 3089-3097.
59. Aifantis I, Raetz E, Buonamici S. Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat Rev Immunol 2008; 8: 380-390. (Pubitemid 351595220)