Genome wide copy number analysis of paediatric Burkitt lymphoma using formalin-fixed tissues reveals a subset with gain of chromosome 13q and corresponding miRNA over expression

British Journal of Haematology

Volumn 155, Issue 4, 2011, Pages 477-486

  Schiffman, Joshua D ^a,b   Lorimer, Patrick D ^c   Rodic, Vladimir ^c   Jahromi, Mona S ^b   Downie, Jonathan M ^b   Bayerl, Michael G ^d   Sanmann, Jennifer N ^e   Althof, Pamela A ^e   Sanger, Warren G ^e   Barnette, Phillip ^a   Perkins, Sherrie L ^c   Miles, Rodney R ^c  

^a UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^d PENN STATE COLLEGE OF MEDICINE   (United States)

^e UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

Chromosome 13q; Copy number analysis; Formalin fixed paraffin embedded; MIR17HG; Molecular inversion probes; Paediatric Burkitt lymphoma

Indexed keywords

FORMALDEHYDE; MICRORNA;

ADOLESCENT; ADULT; ARTICLE; BURKITT LYMPHOMA; CANCER RELAPSE; CHILD; CHROMOSOME 13Q; CHROMOSOME INVERSION; CHROMOSOME TRANSLOCATION; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; FEMALE; FLOW CYTOMETRY; GENE LOCUS; GENETIC ASSOCIATION; HUMAN; IMMUNOHISTOCHEMISTRY; MALE; MOLECULAR CLONING; PRESCHOOL CHILD; PRIORITY JOURNAL; PROGNOSIS; PROTEIN EXPRESSION; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY;

ADOLESCENT; BURKITT LYMPHOMA; CHILD; CHILD, PRESCHOOL; CHROMOSOMES, HUMAN, PAIR 13; DNA COPY NUMBER VARIATIONS; FEMALE; FORMALDEHYDE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MICRORNAS; PARAFFIN EMBEDDING; TISSUE FIXATION;

EID: 80054975666     PISSN: 00071048     EISSN: 13652141     Source Type: Journal    
DOI: 10.1111/j.1365-2141.2011.08883.x     Document Type: Article

References (34)

1. Bea, S., Salaverria, I., Armengol, L., Pinyol, M., Fernandez, V., Hartmann, E.M., Jares, P., Amador, V., Hernandez, L., Navarro, A., Ott, G., Rosenwald, A., Estivill, X. & Campo, E. (2009) Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling. Blood, 113, 3059-3069.
2. Cairo, M.S., Krailo, M.D., Morse, M., Hutchinson, R.J., Harris, R.E., Kjeldsberg, C.R., Kadin, M.E., Radel, E., Steinherz, L.J., Morris, E., Finlay, J.L. & Meadows, A.T. (2002) Long-term follow-up of short intensive multiagent chemotherapy without high-dose methotrexate ('Orange') in children with advanced non-lymphoblastic non-Hodgkin's lymphoma: a children's cancer group report. Leukemia, 16, 594-600.
3. Cairo, M.S., Gerrard, M., Sposto, R., Auperin, A., Pinkerton, C.R., Michon, J., Weston, C., Perkins, S.L., Raphael, M., McCarthy, K. & Patte, C. (2007) Results of a randomized international study of high-risk central nervous system B non-Hodgkin lymphoma and B acute lymphoblastic leukemia in children and adolescents. Blood, 109, 2736-2743.
4. Capello, D., Scandurra, M., Poretti, G., Rancoita, P.M., Mian, M., Gloghini, A., Deambrogi, C., Martini, M., Rossi, D., Greiner, T.C., Chan, W.C., Ponzoni, M., Moreno, S.M., Piris, M.A., Canzonieri, V., Spina, M., Tirelli, U., Inghirami, G., Rinaldi, A., Zucca, E., Favera, R.D., Cavalli, F., Larocca, L.M., Kwee, I., Carbone, A., Gaidano, G. & Bertoni, F. (2009) Genome wide DNA-profiling of HIV-related B-cell lymphomas. British Journal of Haematology, 148, 245-255.
5. Dave, S.S., Fu, K., Wright, G.W., Lam, L.T., Kluin, P., Boerma, E.J., Greiner, T.C., Weisenburger, D.D., Rosenwald, A., Ott, G., Muller-Hermelink, H.K., Gascoyne, R.D., Delabie, J., Rimsza, L.M., Braziel, R.M., Grogan, T.M., Campo, E., Jaffe, E.S., Dave, B.J., Sanger, W., Bast, M., Vose, J.M., Armitage, J.O., Connors, J.M., Smeland, E.B., Kvaloy, S., Holte, H., Fisher, R.I., Miller, T.P., Montserrat, E., Wilson, W.H., Bahl, M., Zhao, H., Yang, L., Powell, J., Simon, R., Chan, W.C. & Staudt, L.M. (2006) Molecular diagnosis of Burkitt's lymphoma. New England Journal of Medicine, 354, 2431-2442.
6. Diosdado, B., van de Wiel, M.A., Terhaar Sive Droste, J.S., Mongera, S., Postma, C., Meijerink, W.J., Carvalho, B. & Meijer, G.A. (2009) MiR-17-92 cluster is associated with 13q gain and c-myc expression during colorectal adenoma to adenocarcinoma progression. British Journal of Cancer, 101, 707-714.
7. Gaidano, G., Ballerini, P., Gong, J.Z., Inghirami, G., Neri, A., Newcomb, E.W., Magrath, I.T., Knowles, D.M. & Dalla-Favera, R. (1991) p53 mutations in human lymphoid malignancies: association with Burkitt lymphoma and chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences USA, 88, 5413-5417.
8. Hammond, S.M. (2006) MicroRNAs as oncogenes. Current Opinion in Genetics and Development, 16, 4-9.
9. Hayashita, Y., Osada, H., Tatematsu, Y., Yamada, H., Yanagisawa, K., Tomida, S., Yatabe, Y., Kawahara, K., Sekido, Y. & Takahashi, T. (2005) A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Research, 65, 9628-9632.
10. He, L., Thomson, J.M., Hemann, M.T., Hernando-Monge, E., Mu, D., Goodson, S., Powers, S., Cordon-Cardo, C., Lowe, S.W., Hannon, G.J. & Hammond, S.M. (2005) A microRNA polycistron as a potential human oncogene. Nature, 435, 828-833.
11. Hummel, M., Bentink, S., Berger, H., Klapper, W., Wessendorf, S., Barth, T.F., Bernd, H.W., Cogliatti, S.B., Dierlamm, J., Feller, A.C., Hansmann, M.L., Haralambieva, E., Harder, L., Hasenclever, D., Kuhn, M., Lenze, D., Lichter, P., Martin-Subero, J.I., Moller, P., Muller-Hermelink, H.K., Ott, G., Parwaresch, R.M., Pott, C., Rosenwald, A., Rosolowski, M., Schwaenen, C., Sturzenhofecker, B., Szczepanowski, M., Trautmann, H., Wacker, H.H., Spang, R., Loeffler, M., Trumper, L., Stein, H. & Siebert, R. (2006) A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling. New England Journal of Medicine, 354, 2419-2430.
12. Karpova, M.B., Schoumans, J., Blennow, E., Ernberg, I., Henter, J.I., Smirnov, A.F., Nordenskjold, M. & Fadeel, B. (2006) Combined spectral karyotyping, comparative genomic hybridization, and in vitro apoptyping of a panel of Burkitt's lymphoma-derived B cell lines reveals an unexpected complexity of chromosomal aberrations and a recurrence of specific abnormalities in chemoresistant cell lines. International Journal of Oncology, 28, 605-617.
13. Klapper, W., Szczepanowski, M., Burkhardt, B., Berger, H., Rosolowski, M., Bentink, S., Schwaenen, C., Wessendorf, S., Spang, R., Moller, P., Hansmann, M.L., Bernd, H.W., Ott, G., Hummel, M., Stein, H., Loeffler, M., Trumper, L., Zimmermann, M., Reiter, A. & Siebert, R. (2008) Molecular profiling of pediatric mature B-cell lymphoma treated in population-based prospective clinical trials. Blood, 112, 1374-1381.
14. Leventaki, V., Rodic, V., Jahromi, M.S., Downie, J.M., Tripp, S.R., Bayerl, M.G., Perkins, S.L., Barnette, P., Schiffman, J.D. & Miles, R.R. (2011) The p53 pathway is frequently deregulated in pediatric Burkitt lymphoma, but over expression of MDM2 or HDM4 is not a common mechanism. Modern Pathology, 24, 306A.
15. Lones, M.A., Sanger, W.G., Le Beau, M.M., Heerema, N.A., Sposto, R., Perkins, S.L., Buckley, J., Kadin, M.E., Kjeldsberg, C.R., Meadows, A., Siegel, S., Finlay, J., Bergeron, S. & Cairo, M.S. (2004) Chromosome abnormalities may correlate with prognosis in Burkitt/Burkitt-like lymphomas of children and adolescents: a report from Children's Cancer Group Study CCG-E08. Journal of Pediatric Hematology/Oncology, 26, 169-178.
16. Nagy, N. & Klein, E. (2010) Deficiency of the proapoptotic SAP function in X-linked lymphoproliferative disease aggravates Epstein-Barr virus (EBV) induced mononucleosis and promotes lymphoma development. Immunology Letters, 130, 13-18.
17. Navarro, A., Bea, S., Fernandez, V., Prieto, M., Salaverria, I., Jares, P., Hartmann, E., Mozos, A., Lopez-Guillermo, A., Villamor, N., Colomer, D., Puig, X., Ott, G., Sole, F., Serrano, S., Rosenwald, A., Campo, E. & Hernandez, L. (2009) MicroRNA expression, chromosomal alterations, and immunoglobulin variable heavy chain hypermutations in Mantle cell lymphomas. Cancer Research, 69, 7071-7078.
18. Nelson, M., Perkins, S.L., Dave, B.J., Coccia, P.F., Bridge, J.A., Lyden, E.R., Heerema, N.A., Lones, M.A., Harrison, L., Cairo, M.S. & Sanger, W.G. (2009) An increased frequency of 13q deletions detected by fluorescence in situ hybridization and its impact on survival in children and adolescents with Burkitt lymphoma: results from the Children's Oncology Group study CCG-5961. British Journal of Haematology, 148, 600-610.
19. O'Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V. & Mendell, J.T. (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature, 435, 839-843.
20. Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
21. O'Shea, D., O'Riain, C., Gupta, M., Waters, R., Yang, Y., Wrench, D., Gribben, J., Rosenwald, A., Ott, G., Rimsza, L.M., Holte, H., Cazier, J.B., Johnson, N.A., Campo, E., Chan, W.C., Gascoyne, R.D., Young, B.D., Staudt, L.M., Lister, T.A. & Fitzgibbon, J. (2009) Regions of acquired uniparental disomy at diagnosis of follicular lymphoma are associated with both overall survival and risk of transformation. Blood, 113, 2298-2301.
22. Patte, C., Auperin, A., Gerrard, M., Michon, J., Pinkerton, R., Sposto, R., Weston, C., Raphael, M., Perkins, S.L., McCarthy, K. & Cairo, M.S. (2007) Results of the randomized international FAB/LMB96 trial for intermediate risk B-cell non-Hodgkin lymphoma in children and adolescents: it is possible to reduce treatment for the early responding patients. Blood, 109, 2773-2780.
23. Poirel, H.A., Cairo, M.S., Heerema, N.A., Swansbury, J., Auperin, A., Launay, E., Sanger, W.G., Talley, P., Perkins, S.L., Raphael, M., McCarthy, K., Sposto, R., Gerrard, M., Bernheim, A. & Patte, C. (2009) Specific cytogenetic abnormalities are associated with a significantly inferior outcome in children and adolescents with mature B-cell non-Hodgkin's lymphoma: results of the FAB/LMB 96 international study. Leukemia, 23, 323-331.
24. Robertus, J.L., Kluiver, J., Weggemans, C., Harms, G., Reijmers, R.M., Swart, Y., Kok, K., Rosati, S., Schuuring, E., van Imhoff, G., Pals, S.T., Kluin, P. & van den Berg, A. (2010) MiRNA profiling in B non-Hodgkin lymphoma: a MYC-related miRNA profile characterizes Burkitt lymphoma. British Journal of Haematology, 149, 896-899.
25. Salaverria, I., Zettl, A., Bea, S., Hartmann, E.M., Dave, S.S., Wright, G.W., Boerma, E.J., Kluin, P.M., Ott, G., Chan, W.C., Weisenburger, D.D., Lopez-Guillermo, A., Gascoyne, R.D., Delabie, J., Rimsza, L.M., Braziel, R.M., Jaffe, E.S., Staudt, L.M., Muller-Hermelink, H.K., Campo, E. & Rosenwald, A. (2008) Chromosomal alterations detected by comparative genomic hybridization in subgroups of gene expression-defined Burkitt's lymphoma. Haematologica, 93, 1327-1334.
26. Sandlund, J.T., Downing, J.R. & Crist, W.M. (1996) Non-Hodgkin's lymphoma in childhood. New England Journal of Medicine, 334, 1238-1248.
27. Schiffman, J.D., Wang, Y., McPherson, L.A., Welch, K., Zhang, N., Davis, R., Lacayo, N.J., Dahl, G.V., Faham, M., Ford, J.M. & Ji, H.P. (2009) Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia. Cancer Genetics and Cytogenetics, 193, 9-18.
28. Schiffman, J.D., Hodgson, J.G., VandenBerg, S.R., Flaherty, P., Polley, M.Y., Yu, M., Fisher, P.G., Rowitch, D.H., Ford, J.M., Berger, M.S., Ji, H., Gutmann, D.H. & James, C.D. (2010) Oncogenic BRAF mutation with CDKN2A inactivation is characteristic of a subset of pediatric malignant astrocytomas. Cancer Research, 70, 512-519.
29. Scholtysik, R., Kreuz, M., Klapper, W., Burkhardt, B., Feller, A.C., Hummel, M., Loeffler, M., Rosolowski, M., Schwaenen, C., Spang, R., Stein, H., Thorns, C., Trumper, L., Vater, I., Wessendorf, S., Zenz, T., Siebert, R. & Kuppers, R. (2010) Detection of genomic aberrations in molecularly defined Burkitt's lymphoma by array-based, high resolution, single nucleotide polymorphism analysis. Haematologica, 95, 2047-2055.
30. Swerdlow, S.H., Campo, E., Harris, N.L., Jaffe, E.S., Pileri, S.A., Stein, H., Thiele, J. & Vardiman, J.W. (ed.) (2008) WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. IARC Press, Lyon, France.
31. Tagawa, H., Karube, K., Tsuzuki, S., Ohshima, K. & Seto, M. (2007) Synergistic action of the micro RNA-17 polycistron and Myc in aggressive cancer development. Cancer Science, 98, 1482-1490.
32. Toujani, S., Dessen, P., Ithzar, N., Danglot, G., Richon, C., Vassetzky, Y., Robert, T., Lazar, V., Bosq, J., Da Costa, L., Perot, C., Ribrag, V., Patte, C., Wiels, J. & Bernheim, A. (2009) High resolution genome-wide analysis of chromosomal alterations in Burkitt's lymphoma. PLoS One, 4, e7089.
33. Wang, Y., Moorhead, M., Karlin-Neumann, G., Falkowski, M., Chen, C., Siddiqui, F., Davis, R.W., Willis, T.D. & Faham, M. (2005) Allele quantification using molecular inversion probes (MIP). Nucleic Acids Research, 33, e183.
34. Wang, Y., Moorhead, M., Karlin-Neumann, G., Wang, N.J., Ireland, J., Lin, S., Chen, C., Heiser, L.M., Chin, K., Esserman, L., Gray, J.W., Spellman, P.T. & Faham, M. (2007) Analysis of molecular inversion probe performance for allele copy number determination. Genome Biology, 8, R246.