Abstract
Non-Hodgkin lymphomas represent a frequent complication of human immunodeficiency virus (HIV) infection, occurring at higher frequency than in immunocompetent individuals, and causing morbidity and mortality. Here, we present the method we have followed to analyze the genomic lesions in HIV-related and in other immunodeficiency-related lymphomas, as well in diffuse large B-cell lymphoma (DLBCL) samples derived from immunocompetent hosts. The technology we have used is represented by the GeneChip Human Mapping 250K NspI arrays (Affymetrix, Santa Clara, CA, USA), arrays based on 25mer oligonucleotides initially designed for large-scale genotyping, that is, the detection of thousands of single-nucleotide polymorphisms (SNPs), then shown to be applicable for the detection of cancer alterations. The protocol is shown in all its steps with suggestions and tips. Applications of the technology and obtained results are also briefly summarized.
Key words
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dunleavy K, Wilson WH (2010) HIV-associated lymphoid neoplasms. In: Magrath IT (ed) The lymphoid neoplasms, 3rd edn. Hodder Arnold, London, pp 1421–1439
Levine AM, Said JW (2010) Management of acquired immunodeficiency syndrome-related lymphoma. In: Armitage JO, Coiffier B, Dalla Favera R, Harris NL, Mauch PM (eds) Non-Hodgkin lymphomas, 2nd edn. Lippincott Williams & Wilkins, Philadelphia, PA, pp 507–526
Carbone A, Gloghini A (2005) AIDS-related lymphomas: from pathogenesis to pathology. Br J Haematol 130(5):662–670
Spano JP, Costagliola D, Katlama C, Mounier N, Oksenhendler E, Khayat D (2008) AIDS-related malignancies: state of the art and therapeutic challenges. J Clin Oncol 26(29):4834–4842
Grogg KL, Miller RF, Dogan A (2007) HIV infection and lymphoma. J Clin Pathol 60(12): 1365–1372
Cheung MC, Pantanowitz L, Dezube BJ (2005) AIDS-related malignancies: emerging challenges in the era of highly active antiretroviral therapy. Oncologist 10(6):412–426
Carbone A, Gloghini A, Capello D, Gaidano G (2001) Genetic pathways and histogenetic models of AIDS-related lymphomas. Eur J Cancer 37(10):1270–1275
Carbone A, Cesarman E, Spina M, Gloghini A, Schulz TF (2009) HIV-associated lymphomas and gamma-herpesviruses. Blood 113(6): 1213–1224
Nair P, Pan H, Stallings RL, Gao SJ (2006) Recurrent genomic imbalances in primary effusion lymphomas. Cancer Genet Cytogenet 171(2):119–121
Klein U, Gloghini A, Gaidano G, Chadburn A, Cesarman E, Dalla-Favera R, Carbone A (2003) Gene expression profile analysis of AIDS-related primary effusion lymphoma (PEL) suggests a plasmablastic derivation and identifies PEL-specific transcripts. Blood 101(10):4115–4121
Jenner RG, Maillard K, Cattini N, Weiss RA, Boshoff C, Wooster R, Kellam P (2003) Kaposi’s sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile. Proc Natl Acad Sci USA 100(18):10399–10404
Capello D, Gloghini A, Martini M, Spina M, Tirelli U, Bertoni F, Rinaldi A, Morra E, Rambaldi A, Sinigaglia F, Larocca LM, Carbone A (2011) Mutations of CD79A, CD79B and EZH2 genes in immunodeficiency-related non-Hodgkin lymphomas. Br J Haematol 152(6):777–780
Capello D, Scandurra M, Poretti G, Rancoita PM, Mian M, Gloghini A, Deambrogi C, Martini M, Rossi D, Greiner TC, Chan WC, Ponzoni M, Moreno SM, Piris MA, Canzonieri V, Spina M, Tirelli U, Inghirami G, Rinaldi A, Zucca E, Favera RD, Cavalli F, Larocca LM, Kwee I, Carbone A, Gaidano G, Bertoni F (2010) Genome wide DNA-profiling of HIV-related B-cell lymphomas. Br J Haematol 148(2):245–255
Rinaldi A, Capello D, Scandurra M, Greiner TC, Chan WC, Bhagat G, Rossi D, Morra E, Paulli M, Rambaldi A, Rancoita PMV, Inghirami G, Ponzoni M, Moreno SM, Piris MA, Mian M, Chigrinova E, Zucca E, Dalla Favera R, Gaidano G, Kwee I, Bertoni F (2010) SNP-arrays provide new insights in the pathogenesis of post-transplant diffuse large B-cell lymphoma. Br J Haematol 149(7):569–577
Scandurra M, Mian M, Greiner TC, Rancoita PMV, de Campos CP, Chan WC, Vose JM, Chigrinova E, Inghirami G, Chiappella A, Baldini L, Ponzoni M, Ferreri AJM, Franceschetti S, Gaidano G, Moreno SM, Piris MA, Facchetti F, Tucci A, Nomdedeu JF, Lazure T, Lambotte O, Uccella S, Pinotti G, Pruneri G, Martinelli G, Young KH, Tibiletti MG, Rinaldi A, Zucca E, Kwee I, Bertoni F (2010) Genomic lesions associated with a different clinical outcome in diffuse large B-cell lymphoma treated with R-CHOP. Br J Haematol 151(3):221–231
Kwee I, Capello D, Rinaldi A, Rancoita PM, Bhagat G, Greiner TC, Spina M, Gloghini A, Chan WC, Paulli M, Zucca E, Tirelli U, Carbone A, Gaidano G, Bertoni F (2012) Genomic aberrations affecting the outcome of immunodeficiency-related diffuse large B-cell lymphoma. Leuk Lymphoma 53(1):71–76
Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R (2004) Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 14(3):414–425
Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SP, Jones KW (2003) Large-scale genotyping of complex DNA. Nat Biotechnol 21(10): 1233–1237
Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, Futreal PA, Wooster R, Jones KW, Shapero MH (2004) Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1(4):287–299
Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 64(9):3060–3071
Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R (2004) High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14(2):287–295
Treff NR, Su J, Tao X, Northrop LE, Scott RT Jr (2011) Single-cell whole-genome amplification technique impacts the accuracy of SNP microarray-based genotyping and copy number analyses. Mol Hum Reprod 17(6): 335–343
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99(8):5261–5266
Glasel JA (1995) Validity of nucleic acid purities monitored by 260nm/280nm absorbance ratios. Biotechniques 18(1):62–63
Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5(4):557–572
Rancoita PMV, Hutter M, Bertoni F, Kwee I (2009) Bayesian DNA copy number analysis. BMC Bioinformatics 10(1):10
Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C (2004) dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 20(8): 1233–1240
Rancoita PM, Hutter M, Bertoni F, Kwee I (2010) An integrated Bayesian analysis of LOH and copy number data. BMC Bioinformatics 11:321
Lenz G, Wright GW, Emre NC, Kohlhammer H, Dave SS, Davis RE, Carty S, Lam LT, Shaffer AL, Xiao W, Powell J, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Campo E, Jaffe ES, Delabie J, Smeland EB, Rimsza LM, Fisher RI, Weisenburger DD, Chan WC, Staudt LM (2008) Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc Natl Acad Sci USA 105(36): 13520–13525
Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, Sellers WR (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA 104(50):20007–20012
Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, Weber BL, Maris JM, Grant GR (2006) STAC: a method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res 16(9):1149–1158
Mullighan CG, Zhang J, Kasper LH, Lerach S, Payne-Turner D, Phillips LA, Heatley SL, Holmfeldt L, Collins-Underwood JR, Ma J, Buetow KH, Pui CH, Baker SD, Brindle PK, Downing JR (2011) CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471(7337):235–239
Novak U, Rinaldi A, Kwee I, Nandula SV, Rancoita PMV, Compagno M, Cerri M, Rossi D, Murty VV, Zucca E, Gaidano G, Dalla Favera R, Pasqualucci L, Bhagat G, Bertoni F (2009) The NF-ΚB negative regulator TNFAIP3 (A20) is commonly inactivated by somatic mutations and genomic deletions in marginal zone B-cell lymphomas. Blood 113(20):4918–4921
Compagno M, Lim WK, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L (2009) Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature 459(7247): 717–721
Kato M, Sanada M, Kato I, Sato Y, Takita J, Takeuchi K, Niwa A, Chen Y, Nakazaki K, Nomoto J, Asakura Y, Muto S, Tamura A, Iio M, Akatsuka Y, Hayashi Y, Mori H, Igarashi T, Kurokawa M, Chiba S, Mori S, Ishikawa Y, Okamoto K, Tobinai K, Nakagama H, Nakahata T, Yoshino T, Kobayashi Y, Ogawa S (2009) Frequent inactivation of A20 in B-cell lymphomas. Nature 459(7247):712–716
Rinaldi A, Mian M, Chigrinova E, Arcaini L, Bhagat G, Novak U, Rancoita PM, De Campos CP, Forconi F, Gascoyne RD, Facchetti F, Ponzoni M, Govi S, Ferreri AJ, Mollejo M, Piris MA, Baldini L, Soulier J, Thieblemont C, Canzonieri V, Gattei V, Marasca R, Franceschetti S, Gaidano G, Tucci A, Uccella S, Tibiletti MG, Dirnhofer S, Tripodo C, Doglioni C, Dalla Favera R, Cavalli F, Zucca E, Kwee I, Bertoni F (2011) Genome-wide DNA profiling of marginal zone lymphomas identifies subtype-specific lesions with an impact on the clinical outcome. Blood 117(5):1595–1604
Deffenbacher KE, Iqbal J, Liu Z, Fu K, Chan WC (2010) Recurrent chromosomal alterations in molecularly classified AIDS-related lymphomas: an integrated analysis of DNA copy number and gene expression. J Acquir Immune Defic Syndr 54(1):18–26
Roy D, Sin SH, Damania B, Dittmer DP (2011) Tumor suppressor genes FHIT and WWOX are deleted in primary effusion lymphoma (PEL) cell lines. Blood 118(7): e32–e39
Acknowledgments
Work supported by: Oncosuisse grant OCS-1939-8-2006 (Bern, Switzerland); Cantone Ticino “Computational life science/Ticino in rete” program (Bellinzona, Switzerland); Fondazione per la Ricerca e la Cura sui Linfomi (Bellinzona, Switzerland); Nelia et Amadeo Barletta Foundation (Lausanne, Switzerland); Ricerca Sanitaria Finalizzata, Regione Piemonte (Torino, Italy); VI Programma Nazionale di Ricerca sull’AIDS, ISS (Rome, Italy); PRIN-MIUR 2006; Novara-AIL Onlus (Novara, Italy); Fondazione CRT (Torino, Italy).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Rinaldi, A., Capello, D., Zucca, E., Gaidano, G., Bertoni, F. (2013). Genome-Wide DNA Profiling of HIV-Related B-Cell Lymphomas. In: Banerjee, D., Shah, S. (eds) Array Comparative Genomic Hybridization. Methods in Molecular Biology, vol 973. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-281-0_14
Download citation
DOI: https://doi.org/10.1007/978-1-62703-281-0_14
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-280-3
Online ISBN: 978-1-62703-281-0
eBook Packages: Springer Protocols