Skip to main content
SpringerLink
Log in

Genome-Wide DNA Profiling of HIV-Related B-Cell Lymphomas

  • Protocol
  • First Online:
Array Comparative Genomic Hybridization

Part of the book series: Methods in Molecular Biology ((MIMB,volume 973))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Dunleavy K, Wilson WH (2010) HIV-associated lymphoid neoplasms. In: Magrath IT (ed) The lymphoid neoplasms, 3rd edn. Hodder Arnold, London, pp 1421–1439

    Chapter  Google Scholar 

  2. 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

    Google Scholar 

  3. Carbone A, Gloghini A (2005) AIDS-related lymphomas: from pathogenesis to pathology. Br J Haematol 130(5):662–670

    Article  PubMed  CAS  Google Scholar 

  4. 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

    Article  PubMed  Google Scholar 

  5. Grogg KL, Miller RF, Dogan A (2007) HIV infection and lymphoma. J Clin Pathol 60(12): 1365–1372

    Article  PubMed  CAS  Google Scholar 

  6. 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

    Article  PubMed  CAS  Google Scholar 

  7. 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

    Article  PubMed  CAS  Google Scholar 

  8. Carbone A, Cesarman E, Spina M, Gloghini A, Schulz TF (2009) HIV-associated lymphomas and gamma-herpesviruses. Blood 113(6): 1213–1224

    Article  PubMed  CAS  Google Scholar 

  9. Nair P, Pan H, Stallings RL, Gao SJ (2006) Recurrent genomic imbalances in primary effusion lymphomas. Cancer Genet Cytogenet 171(2):119–121

    Article  PubMed  CAS  Google Scholar 

  10. 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

    Article  PubMed  CAS  Google Scholar 

  11. 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

    Article  PubMed  CAS  Google Scholar 

  12. 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

    Article  PubMed  CAS  Google Scholar 

  13. 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

    Article  PubMed  CAS  Google Scholar 

  14. 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

    Article  PubMed  CAS  Google Scholar 

  15. 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

    Article  PubMed  Google Scholar 

  16. 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

    Article  PubMed  CAS  Google Scholar 

  17. 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

    Article  PubMed  CAS  Google Scholar 

  18. 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

    Article  PubMed  CAS  Google Scholar 

  19. 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

    Article  PubMed  CAS  Google Scholar 

  20. 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

    Article  PubMed  CAS  Google Scholar 

  21. 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

    Article  PubMed  CAS  Google Scholar 

  22. 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

    Article  PubMed  CAS  Google Scholar 

  23. 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

    Article  PubMed  CAS  Google Scholar 

  24. Glasel JA (1995) Validity of nucleic acid purities monitored by 260nm/280nm absorbance ratios. Biotechniques 18(1):62–63

    PubMed  CAS  Google Scholar 

  25. 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

    Article  PubMed  Google Scholar 

  26. Rancoita PMV, Hutter M, Bertoni F, Kwee I (2009) Bayesian DNA copy number analysis. BMC Bioinformatics 10(1):10

    Article  PubMed  Google Scholar 

  27. 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

    Article  PubMed  CAS  Google Scholar 

  28. Rancoita PM, Hutter M, Bertoni F, Kwee I (2010) An integrated Bayesian analysis of LOH and copy number data. BMC Bioinformatics 11:321

    Article  PubMed  Google Scholar 

  29. 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

    Article  PubMed  CAS  Google Scholar 

  30. 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

    Article  PubMed  CAS  Google Scholar 

  31. 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

    Article  PubMed  CAS  Google Scholar 

  32. 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

    Article  PubMed  CAS  Google Scholar 

  33. 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

    Article  PubMed  CAS  Google Scholar 

  34. 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

    Article  PubMed  CAS  Google Scholar 

  35. 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

    Article  PubMed  CAS  Google Scholar 

  36. 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

    Article  PubMed  CAS  Google Scholar 

  37. 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

    PubMed  Google Scholar 

  38. 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

    Article  PubMed  Google Scholar 

Download references

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

  1. Fondazione per la Ricerca e la Cura sui Linfomi, IOR Institute of Oncology Research, Lymphoma & Genomics Research Program, Bellinzona, Switzerland

    Andrea Rinaldi, Daniela Capello, Emanuele Zucca, Gianluca Gaidano & Francesco Bertoni

Authors
  1. Andrea Rinaldi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniela Capello
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Emanuele Zucca
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gianluca Gaidano
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Francesco Bertoni
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Francesco Bertoni .

Editor information

Editors and Affiliations

  1. , Dept. of Pathology & Lab. Medicine, The Ottawa Hospital, Smyth Road 501, Ottawa, K1H 8L6, Ontario, Canada

    Diponkar Banerjee

  2. , Dept. of Molecular Oncology, BC Cancer Agency, West 10th Avenue 675, Vancouver, V5T 4E6, British Columbia, Canada

    Sohrab P. Shah

Rights and permissions

Reprints 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

Publish with us

Policies and ethics

Search

Navigation