- Short report
- Open Access
Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH): revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma
Journal of Hematology & Oncologyvolume 2, Article number: 47 (2009)
Plasmablastic lymphoma (PL) is a subtype of diffuse large B-cell lymphoma (DLBCL). Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM). The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related) and PCM using array-based comparative genomic hybridization.
Examination of genomic data in PL revealed that the most frequent segmental gain (> 40%) include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related) cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation.
To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related) than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.
Plasmablastic lymphoma (PL), one of the most frequent oral malignancies in human immunodeficiency virus (HIV) infected patients, was first characterized by Delecluse et al . They proposed that this constituted a new subtype of diffuse large B cell lymphoma (DLBCL); it was suggested as a distinct entity based on its blastic morphology, its clinical behavior involving predominantly extramedullary sites (particularly oral cavity), and its limited antigenic phenotype data suggesting differentiation toward plasmacytic differentiation (CD20-, CD79a+ and VS38c+). The incidence of PL has increased following the introduction of highly active antiretroviral therapy (HAART) [2, 3]. By WHO Classification, PL is categorized as a subtype of DLBCL associated with HIV and Epstein-Barr virus [1, 4, 5].
Recent morphologic and immunohistochemical studies, however, have suggested that tumors with PL morphology may represent a heterogeneous group of neoplasms with different clinicopathologic characteristics, corresponding to different entities including PL, DLBCL with plasmacytic differentiation, and extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM) [6, 7]. To further delineate the relationship between PL, DLBCL and PCM, we evaluated the genetic lesions among PL, DLBCL (AIDS-related and non AIDS-related) and PCM using array-based comparative genomic hybridization (array CGH) technology [8, 9].
Materials and methods
Archived formalin-fixed paraffin-embedded blocks of PL (n = 16, demographic data in Table 1), DLBCL (AIDS-related, n = 13; non-AIDS-related, n = 13) and PCM (n = 8) were retrieved from Department of Pathology at The Methodist Hospital or Baylor College of Medicine (BCM), AIDS and Cancer Specimen Resource and Hematopathology Section, Laboratory of Pathology, National Cancer Institute. The use of these materials was approved by the Institutional Review Boards of participating institutions.
One H&E section of each case was reviewed to confirm that more than 80% of cells were neoplastic cells. DNA was then extracted from the consecutive section of each case or sections of paraffin embedded reactive tonsils (as control) using DNAeasy kit (Quiagen, Valencia, CA). For each sample, tumor DNA and control DNA was the labeled with Cy5 or Cy3 reversely in the replicate experiment (i.e. dye swap) to address the confounding effect of the dye and experiment and hybridized to array slides containing 2621 BAC clones at an average of 1-Mbp resolution (SpectralChip 2600 array, PerkinElmer, Waltham, MA) according to the manufacturer's protocol. The slides were imaged using an Axon 4000B scanner and GenePix Pro 6.0 scanning software.
After scanning of the slide, the fluorescent intensities of the Cy3 and Cy5 channels were background subtracted. The resulting values were normalized by intensity based local weighted regression method (Lowess) to correct for systematic bias in dye labeling and fluorescent intensity . Then the ratio of the Cy3/Cy5 channel of each clone was calculated and log base 2 transformed (log ratios).
After normalization, values for duplicated spots representing one clone were averaged. For each case, clones were excluded from further analysis if their values for forward hybridization failed to show reciprocal changes with the dye-reversed hybridization or if they were with 10% or more polymorphism within a normal population http://projects.tcag.ca/variation/. The top 75 clones showing highest degrees of gain or loss based on log2 ratio were then selected for each case. The neighboring clones (based on cytoband positioning) of the selected clones were further examined and three consecutive BAC clones with the same change (gain or loss) were selected as a segment of gain or loss. The frequencies of segmental gains and losses among different types of tumors were recorded. Two PL cases were also validated by 10K SNP array by Affymetrix as described previously . The gains of 16p13.3 in PL cases were further validated with FISH using RP11-417B20 BAC clone with the methods published previously .
Results and Discussions
To the best of our knowledge, the current study represents the first genomic exploration of plasmablastic lymphoma, a rare type of lymphoma occurring commonly in oral cavity of AIDS patients. In the PL cases, segmental gains and losses ranging in size from 0.2 Mb to 37.7 Mb and 0.2 Mb to 27.7 Mb, respectively, were detected in all specimens. On average, 12.63 +/- 5.92 (range, 6 - 29) segmental gains per specimen were detected, with slightly fewer segmental losses per specimen (mean +/- SD = 6.94 +/- 4.22; range, 1 - 16 segmental losses). Recurring (common) segmental gain or loss (occurring in at least 2 cases) were detected on all autosomes except chromosome 12, ranging in size from 0.7 Mb to 15.9 Mb for gain and from 0.5 Mb to 16.4 Mb for loss (Table 2). The most frequent segmental gains (> 40%) in PL include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. However, the segmental losses were more heterogeneous with frequencies up to only 23% (Table 2).
Overall, the genomic aberration pattern of PL is more similar to that of DLBCL (AIDS-related or non-AIDS-related) than to that of PCM (measured by Pearson correlation coefficient, Figure 1A). One of the altered chromosomal regions identified by CGH [gain of 16p13.3, frequently occurring in PL (6/16), DLBCL (AIDS-related, 7/13 or non-AIDS-related, 10/13) but not in PCM, 0/8] was validated by FISH analysis (Figure 1B). FISH performed in subsets of cases including 6 cases of PL and 6 cases of myeloma showed gain of this region in 3 of 6 PL cases but in none of myeloma cases. Of note, our previous immunohistochemical studies using a limited panel of antibodies showed that PL and PCM had almost identical immunophenotypic patterns which are quite different from those of DLBCL . However, the results of the current study suggest that PL is best classified as a subtype of DLBCL at least at the genomic level. However, it should be noted that most of PL cases studied do not arise from oral cavities. It would be of great interest to study more cases of oral cavity PL in the future to further confirm our observation.
Additionally, it would be of great interest to further correlate the array CGH findings with gene expression profiling of these types of lymphoma's to further clarify the relationship among these types of lymphoma. Also, it would have been important to study the similarity and difference between HIV+ or HIV- PL cases versus HIV+ group of DLBCL, as well as HIV- group of DLBCL. However, in the current study, the HIV negative PL cases were too few in our cohort and make this comparison impossible. Future studies to include more HIV negative PL cases are indicated to illustrate this important issue.
Potential biomarkers for diagnosing PL are suggested by our approach. Several segmental gains in 1p35.1-1p36.12 (10 of 16 cases or 10/16), 1q21.1-1q23.1 (8/16), 1p36.11-1p36.33 (7/16), were only present in PL but not in other cases (PL vs. others, p < 0.05 for lesions shown, Fisher's exact test with correction for false discovery rate using the Benjamini and Hochberg method ). BAC clones in these regions, including RP5-886K2, RP3-462O23, RP11-452O22, RP11-77I10, RP3-491M17, RP11-33M12, RP3-438L4, RP11-219C24, RP4-726F20, may be further developed for the diagnosis of PL using FISH technology. As mentioned, by morphologic and immunohistochemical evaluation, features of PL overlap significantly with DLBCL and PCM . Additionally, these regions contain important oncogenes such as: PRAME, PDPN, COPA, and NHLH1 [14–17]. Of interest, segmental gains of 16p12-16p13.2 and 11q14-11q14, occurred more frequently in HIV positive cases suggesting that these lesions may be related to HIV associated malignancies (PL-HIV+ = 4/10 and AIDS-related DLBCL = 9/13 vs. 1/27 HIV-negative cases for 16p12-16p13.2 and PL-HIV+ = 3/10 and AIDS-related DLBCL = 12/13 vs. 1/27 HIV-negative cases for 11q14-11q14, p < 0.05, Fisher's exact test with correction for false discovery rate using the Benjamini and Hochberg method ). The potential candidate genes include PLA2 . This gene has been shown to be activated by HIV envelope glycoproteins and may participate in the fusion of HIV and lymphocytes. Studies to investigate the roles of this gene and other genes in these regions in HIV-related PL and/or AIDS-related DLBCL are indicated.
Using the same platform of BAC array CGH on DNA extracted from frozen tissue samples, Chen et al have recently reported many genomic gains and losses in DLBCL . Most (55.17%) of the regions identified by Chen el al were also identified in our cases of DLBCL (AIDS- or non-AIDS-related). Similarly, our CGH studies of PCM produce similar findings to the study of Carrasco et al, who used the oligonucleotide format by Agilent Technologies (data not shown) . These findings further support the validity of the CGH data obtained using paraffin-embedded tissues.
Delecluse HJ, Anagnostopoulos I, Dallenbach F, Hummel M, Marafioti T, Schneider U, Huhn D, Schmidt-Westhausen A, Reichart PA, Gross U, Stein H: Plasmablastic lymphomas of the oral cavity: a new entity associated with the human immunodeficiency virus infection. Blood. 1997, 89: 1413-1420.
Gates AE, Kaplan LD: AIDS malignancies in the era of highly active antiretroviral therapy. Oncology (Huntingt). 2002, 16: 657-665.
Thirlwell C, Sarker D, Stebbing J, Bower M: Acquired immunodeficiency syndrome-related lymphoma in the era of highly active antiretroviral therapy. Clin Lymphoma. 2003, 4: 86-92. 10.3816/CLM.2003.n.016.
Gatter K, Warnke R: From Diffuse large B-cell lymphoma. Pathology and Genetics of Tumours of Haematopoietic and Lymphoid Tissues. Edited by: Jaffe ES, Harris NL, Stein H, Vardiman JW. 2001, Lyon: IARC Press, 171-174. 3
Gaidano G, Cerri M, Capello D, Berra E, Deambrogi C, Rossi D, Larocca LM, Campo E, Gloghini A, Tirelli U, Carbone A: Molecular histogenesis of plasmablastic lymphoma of the oral cavity. Br J Haematol. 2002, 119: 622-628. 10.1046/j.1365-2141.2002.03872.x.
Colomo L, Loong F, Rives S, Pitaluga S, Martinez A, Lopez-Guillermo A, Ojanguren J, Romagosa V, Jaff ES, Campo E: Diffuse Large B-cell Lymphomas With Plasmablastic Differentiation Represent a Heterogeneous Group of Disease Entities. Am J Surg Pathol. 2004, 28: 736-747. 10.1097/01.pas.0000126781.87158.e3.
Vega F, Chang CC, Medeiros LJ, Udden MM, Cho-Vega JH, Lau CC, Finch CJ, Vilchez RA, McGregor D, Jorgensen JL: Plasmablastic lymphomas and plasmablastic plasma cell myelomas have nearly identical immunophenotypic profiles. Mod Pathol. 2005, 18: 806-815. 10.1038/modpathol.3800355.
Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Linb V, MacAulay C, Lam WL: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet. 2004, 36: 299-303. 10.1038/ng1307.
Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998, 20: 207-211. 10.1038/2524.
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30: e15-10.1093/nar/30.4.e15.
Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R: Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Mod Pathol. 2008, 21: 599-608. 10.1038/modpathol.2008.20.
Man TK, Lu XY, Jaeweon K, Perlaky L, Harris C, Shah S, Ladanyi M, Gorlick R, Lau C, Rao P: Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma. BMC Cancer. 2004, 4: 45-10.1186/1471-2407-4-45.
Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological. 1995, 57: 289-300.
Scrideli CA, Carlotti CG, Okamoto OK, Andrade VS, Cortez MA, Motta FJ, Lucio-Eterovic AK, Neder L, Rosemberg S, Oba-Shinjo SM, Marie Sk, Tone LG: Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR. J Neurooncol. 2008, 88: 281-291. 10.1007/s11060-008-9579-4.
Wong N, Chan A, Lee SW, Lam E, To KF, Lai PB, Li XN, Liew CT, Johnson PJ: Positional mapping for amplified DNA sequences on 1q21-q22 in hepatocellular carcinoma indicates candidate genes over-expression. J Hepatol. 2003, 38: 298-306. 10.1016/S0168-8278(02)00412-9.
De Smaele E, Fragomeli C, Ferretti E, Pelloni M, Po A, Canettieri G, Coni S, Di Marcotullio L, Greco A, Moretti M, Di Rocco C, Pazzaglia S, Maroder M, Screpanti I, Giannini G, Gulino A: An integrated approach identifies Nhlh1 and Insm1 as Sonic Hedgehog-regulated genes in developing cerebellum and medulloblastoma. Neoplasia. 2008, 10: 89-98. 10.1593/neo.07891.
Watari K, Tojo A, Nagamura-Inoue T, Nagamura F, Takeshita A, Fukushima T, Motoji T, Tani K, Asano S: Identification of a melanoma antigen, PRAME, as a BCR/ABL-inducible gene. FEBS Lett. 2000, 466: 367-371. 10.1016/S0014-5793(00)01112-1.
Mavoungou E, Georges-Courbot MC, Poaty-Mavoungou V, Nguyen HT, Yaba P, Delicat A, Georges AJ, Russo-Marie F: HIV and SIV envelope glycoproteins induce phospholipase A2 activation in human and macaque lymphocytes. Acquir Immune Defic Syndr Hum Retrovirol. 1997, 16: 1-9.
Chen W, Houldsworth J, Olshen AB, Nanjangud G, Chaganti S, Venkatraman ES, Halaas J, Teruya-Feldstein J, Zelenetz AD, Changanti RSK: Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas. Blood. 2006, 107: 2477-2485. 10.1182/blood-2005-07-2950.
Carrasco DR, Tonon G, Huang Y, Zhang Y, Sinha R, Feng B, Stewart JP, Zhan F, Khatry D, Protopopova M, Protopopov A, Sukhdeo K, Hanamura I, Stephens O, Barlogie B, Anderson KC, Chin L, Shaughnessy JD, Brennan C, Depinho RA: High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cell. 2006, 9: 313-325. 10.1016/j.ccr.2006.03.019.
The authors would like to express appreciation to AIDS and Cancer Specimen Resource, National Cancer Institute for providing some specimens for this study. This study was supported by a grant from National Institute of Dental and Craniofacial Research, National Institute of Health (DE017086) (C-C.C.).
The authors declare that they have no competing interests.
Contribution: CCC and CCL organized research plan, analyzed data, and wrote the paper; XZ, WH, XR, JJT, YF, SH, and CJC analyzed the data and helped write the paper; PHR and FM preformed validation experiment; XL preformed array CGH and analyzed data; FF and ESJ provided samples and clinical data and wrote the paper. All authors read and approved the final manuscript.
Authors’ original submitted files for images
Below are the links to the authors’ original submitted files for images.