Genomic imbalances in AIDS-related lymphomas: relation with tumoral Epstein–Barr virus status
Vaghefi, Parissaa,b; Martin, Antoinea; Prévot, Sophiec; Charlotte, Frédéricd; Camilleri-Broët, Sophiee; Barli, Elisabetha; Davi, Frédéricd; Gabarre, Jeand; Raphael, Martinef; Poirel, Hélène Ag
From the aHospital Avicenne, University Paris 13, France
bHospital Paul Brousse, Villejuif, University Paris Sud 11, France
cHospital Antoine Béclère Clamart, University Paris Sud 11, France
dHospital Pitié-Salpêtrière, University Paris 6, France
eHospital Hotel Dieu, University Paris 5, France
fHospital Bicêtre, INSERM 4802, University Paris Sud 11, Le Kremlin Bicêtre, France
gCentre de Génétique, Hematological section of the Center of Human Genetics, Cliniques Universitaires St Luc, UCL Bruxelles, Belgium.
Received 17 October, 2005
Revised 23 August, 2006
Accepted 8 September, 2006
Correspondence to M. Raphaël, Service d'Hématologie et Immunologie Biologiques, Cytogénétique - INSERM 4802, CHU Bicêtre, 78 rue du Général Leclerc, 94270 - Le Kremlin Bicêtre, France. Tel: +33 1 45 21 35 94; fax: +33 1 45 21 28 47; e-mail: email@example.com
Background: The pathologic heterogeneity of AIDS related lymphomas (ARL) reflects several pathogenic mechanisms: chronic antigenic stimulation, Epstein–Barr virus (EBV) infection, and genomic abnormalities. Genetic abnormalities, known to play a major role in lymphomas of non-immunocompromised patients, are not well characterized in ARL.
Objective: Characterization of the DNA copy number change (CNC) in ARL and comparison of our findings with tumoral EBV and immune status.
Design and methods: We have studied by comparative genomic hybridization (CGH), 28 ARL well characterized for histopathologic, clonality and EBV findings.
Results: DNA-CNC were detected in 50% of cases. Gains of chromosomal material were much more frequent than losses and involved chromosomes 9p, 11q, 12q, 17q, and 19q recurrently. DNA-CNC tended to be more frequent in EBV-positive lymphomas with latency type II/III than in EBV-positive latency I or EBV-negative lymphomas. Most chromosomal regions affected in HIV-related lymphoma were similar to those already reported in HIV-negative lymphomas.
Conclusion: This CGH study allowed the identification of non-random chromosomal alterations in ARL. The results suggested an inverse relationship between EBV infection (latency II/III), associated with deep acquired immune suppression, and the number of chromosomal alterations which may be explained by a direct role of viral proteins in lymphomagenesis by activation of signalling pathways without needing several genomic alterations.
AIDS-related lymphoma (ARL) is the second most common cancer associated with HIV infection after Kaposi's sarcoma. The introduction of HAART in 1996 has been associated with a dramatic decrease in the incidence of opportunistic infections, but the effect of HAART on ARL has been somewhat inconsistent . However, Besson et al. demonstrated that the decline in the incidence of ARL is correlated to the effectiveness of HAART on CD4 cell counts and the improvement of immune status . ARL consists of a heterogeneous group of malignant disorders. According to the last World Health Organization (WHO) classification, they are divided into: (i) lymphomas usually diagnosed in non-immunocompromised patients-mostly Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL) often involving the central nervous system [primary central nervous system lymphoma (PCNSL)]; (ii) lymphomas much more often seen in the setting of HIV infection-primary effusion lymphoma (PEL) and plasmablastic lymphoma of the oral cavity (PBL); (iii) lymphoma also occurring in other immunodeficiency states-polymorphic B-cell lymphoma (PTLD-like) . While BL tend to occur in patients with preserved immune function, PCNSL, other immunoblastic DLBCL and PEL are associated with profound immune dysfunction . The pathologic heterogeneity of ARL reflects several pathogenic mechanisms: chronic antigenic B-cell stimulation by HIV itself, as well as other coinfecting viruses, such as Epstein–Barr virus (EBV) and human herpes virus 8 (HHV8), cytokine deregulation and genetic aberrations. Chronic polyclonal B-cell hyperactivation associated with HIV infection might result in the proliferation of antigen-selected B-cell cellular clones at the risk of acquiring and accumulating genetic lesions that may lead to malignant transformation [1,5]. EBV is detected in the neoplastic cells of approximately 60% of HIV-related lymphomas, with great heterogeneity between entities, ranging from 30 to 50% in BL, to 70–80% in systemic DLBCL and virtually 100% of PCNSL . The production of B-cell stimulatory cytokines, such as interleukin (IL)-10 and IL-6, has the potential to contribute to tumour development by supporting the growth and viability of neoplastic cells .
Genetic abnormalities are known to play a major role in lymphomas of non-immunocompromised patients, usually leading either to oncogenic activation or tumour suppressor gene alteration. Some genes known to be involved in lymphomagenesis in immunocompetent patients are also involved in ARL . C-myc is activated in nearly all cases of AIDS BL [6,7]. Secondary events such as p53 inactivation , Ras mutations were also reported in ARL . Molecular alterations of the BCL6 proto-oncogene associate with a significant fraction of AIDS DLBCL: rearrangements are detected in 20% [9,10] and mutations of 5′ regulatory sequences in 70% of the cases . Aberrant somatic hypermutations of proto-oncogenes have been reported in various subtypes of ARL . However, chromosomal alterations are not well characterized in ARL owing to limitations associated with culture of infected lymphoid tumour cells in vitro and the frequent complex nature of chromosomal changes. In this context, only few cytogenetic studies have been published on case reports or on very small series. Gain of chromosome 1q [13,14] and 12  were detected in BL and deletions of 6q in DLBCL .
Comparative genomic hybridisation (CGH) is a technique that offers a molecular approach to cytogenetic analysis and allows the detection of DNA copy number changes (CNC), either gains or losses of genomic material across the entire genome, at the resolution of about 10 Mbp [17,18]. Its main advantage is that it bypasses the need for cell culture to harvest metaphase spreads. Since its development, CGH has been applied as a research tool in the field of cancer cytogenetics mostly in solid tumours. A large number of CGH studies has been performed on different types of lymphomas in non-immunocompromised patients: DLBCL [19–21], PCNSL [22–24], PEL  and BL . The number of CGH studies on ARL is limited. These studies have shown frequent and complex genomic imbalances in one case of BL , 14 cases of DLBCL  and eight cases of PEL . Genomic alterations in AIDS-related PCNSL are not yet well defined.
In the present study, we investigated 28 ARL by CGH in order to screen DNA copy number changes that may show the location of relevant oncogenes and tumour suppressor genes, and to compare our findings with the genomic abnormalities known to be involved in lymphomas of the same category occurring in non-immunocompromised patients and with the tumoral EBV status.
Materials and methods
Patients and samples
We have studied tumoral biopsies from 28 HIV-infected patients diagnosed between 1984 and 2002. The sex ratio was 26 men for two women, with a median age of 38 years (range, 27–72 years). The 28 lymphomas were classified according to the WHO classification : 12 BL, 10 systemic DLBCL, four PCNSL (with B-cell immunoblastic features), and two T-cell lymphomas [one PTCL and one anaplastic large cell lymphoma (ALCL)]. Each specimen was evaluated histologically to assure a sufficient proportion of neoplastic cells (more than 70%) in tumour samples. The CD4 cell counts were available for 17 patients (six BL, eight systemic DLBCL and three PCNSL) with a median of 107 cells/μl (range, 2–596 cells/μl). HIV viral loads were available for nine patients (four BL and five systemic DLBCL) with a median of 5.1 log10 copies/ml (range, < 2.3 to > 5.6log10 copies/ml).
Detection of B-cell markers (monoclonal antibody anti-CD20, L26, DAKO, Trappes, France) and T-cell markers (polyclonal anti-CD3 antibody, DAKO) was performed by immunohistochemistry using streptavidine-biotin peroxidase technique with the LSAB commercial kit (DAKO).
The EBV status was analysed in 21 cases (eight BL, eight systemic DLBCL, four PCNSL and the only case of ALCL). On paraffin sections, EBV RNA was detected using in situ hybridization with fluorescein isothiocyanate (FITC)-labelled EBV-encoded small RNA (EBER) 1+2 specific oligonucleotides (DAKO) according to the manufacturer's instructions. The expression of two EBV latency proteins, latent membrane protein (LMP1) and EBV nuclear antigen 2 (EBNA2), were tested with the monoclonal antibodies, CS1-4 and PE2 respectively from DAKO using streptavidine-biotin peroxidase labelling method with the LSAB commercial Kit (DAKO).
The clonality of tumour specimens has been assessed in 19 samples (eight BL, eight systemic DLBCL, one PCNSL and the two T-cell lymphoma cases) either by Southern blotting (cases 1, 7, 9, 10, 15, 16, 22, 26) with a heavy chain joining region (JH) or using PCR systems (cases 2, 4, 11, 12, 14, 17, 18, 19, 20, 23, 24) with consensus primers against three different variable segments (VH), FR3, FR2 and FR1 region. T-cell receptor (TCR) rearrangements were analysed by PCR analysis of VJ rearrangement of the TCR-γ locus followed by denaturing gradient gel electrophoresis.
CGH was performed as described by Kallioniemi et al.  with minor modifications. Briefly, DNA was isolated by conventional phenol–chloroform extraction and ethanol precipitation from frozen tumour specimens after an overnight digestion by proteinase K at 42°C. Preparation of reference metaphase chromosomes and of control DNA were performed from peripheral blood leukocytes of a normal male subject. Tumour DNA was labelled with both fluorescein-12-dUTP and fluorescein–12-dCTP and reference male DNA with both Texas red-5-dUTP and Texas red-5-dCTP (Dupont, Wilmington, Delaware, USA) in a standard nick translation reaction. The optimal size for double-stranded probe fragments was 600–1000 bp. One μg of tumour, 1 μg of reference DNA and 40 μg of human DNA Cot-1 (Gibco-BRL life Technologies, Gaithersburg, Maryland, USA) were co-precipitated before re-suspension in 12 μl of hybridization buffer (50% formamide/10% dextran sulfate/2 × SSC). Target metaphase spreads were denatured separately in 70% formamide/2 × SSC at 72°C for 3 min and dehydrated in a sequence of 70%, 85% and 100% ethanol and air dried. The probe mixture was denatured at 90°C for 10 min, allowed to re-anneal at 37°C for 20 min and hybridized onto normal metaphase chromosomes for 3 days at 37°C in a humid chamber. The slides were washed for 2 min in 0.4 × SSC at 74°C and 1 min in 2 × SSC/1% NP40 at room temperature. The slides were then counterstained with 0.2 mM DAPI (4,5-diamino-2-phenylindole) (Sigma, St. Louis, Missouri, USA) in antifade solution (Vector Laboratories, Burlingame, California, USA).
Image capture and analysis were performed using an Axiophot fluorescence microscope (Zeiss, Oberkochen, Germany) and a CGH digital analysis system (Isis, Metasystems, Altlusshein Germany) on at least 10 metaphases. The software determines the ratio of the green fluorescence versus the red one, all along each chromosome. Chromosomes were classified after DAPI image enhancement. Chromosome regions were interpreted as over-represented if the corresponding colour ratio was higher than 1.25 and as an under-represented if the ratio was lower than 0.75. Chromosomal regions with a strong localized FITC signal and a ratio above 2 were considered as high level amplifications.
The continuous variables were compared using the non-parametric Mann–Whitney U test and the distributions of categorical variables were compared using the Fisher's exact test as appropriate.
CGH analysis revealed DNA copy number changes (DNA-CNC) in 14 out of 28 cases of ARL (50%). A total number of 33 DNA-CNC were detected: over-representation of genomic material was much more frequent than under-representation (27 gains, including one high-level amplification, versus six losses) (Table 1). One to five chromosomal imbalances were found per case (mean, 1.18; range, 0–5). Chromosomal imbalances detected in at least two different cases were considered as non-random. Irrespective of the morphology, five non-random gains were identified in both BL and systemic DLBCL: the commonly affected regions were 11q25, 12q24, 19q13 (three cases each), 9p23-pter and 17q11-q21 (two cases each) (Fig. 1). Whole chromosome gains involved chromosomes 12 (two cases), 17, 19 and 22 (one case each). A high level amplification was localized to the 2p13-p22 chromosome band in one case of systemic DLBCL (case 22) (Fig. 2), associated with three other gains and one deletion.
Correlation with morphologic findings
Chromosomal imbalances were detected in 6 out of 12 cases of BL (50%) and in 7 out of 10 cases of systemic DLBCL (70%). As expected, the mean number of chromosome imbalances per case was higher in systemic DLBCL (mean, 2.3; range, 0–5) than in BL (mean, 0.75; range, 0–3) (Mann–Whitney non-parametric test, P = 0.04). No chromosomal alterations appeared to be specific of a morphological entity. Three out of the four PCNSL had a normal CGH profile, while case 26 showed an over-representation of the short arm of chromosome 9.
Correlation with clonality, CD4 cell count and EBV findings
Clonality evaluation showed that all but one case of ARL were monoclonal (BL, 8/8; systemic DLBCL, 7/8; PCNSL, 1/1; T-cell lymphomas, 2/2). The only polyclonal case of systemic DLBCL (case 14) was detected using PCR amplification of IgH gene rearrangements which might give false-negative results due to somatic mutations that hinder primer annealing. This hypothesis is strengthened by the detection of three chromosomal imbalances.
The CD4 cell count was higher in BL in comparison with the other lymphomas (systemic DLBCL and PCNSL) (Mann–Whitney non-parametric test, P = 0.02). The three EBV-positive cases with a type II/III latency had lower CD4 cell counts than 14 EBV-negative or EBV-positive lymphomas with a type I latency ARL (Mann–Whitney non-parametric test, P = 0.02).
While only one of the eight BL (12.5%) was EBV positive, seven of the eight systemic DLBCL (87.5%) and all of the four PCNSL were EBV positive (Table 1). EBV detection was significantly more frequent in systemic DLBCL than in BL (Fisher's test, P = 0.01). The only EBV-positive BL case had a pattern of type I latency. One of eight EBV-positive systemic DLBCL and all of four PCNSL cases showed type II/III latency. Irrespective of the morphology, the number of chromosomal imbalances tended to be more limited in the five EBV-positive cases with a type II/III latency than in the 16 EBV-negative or EBV-positive cases with a type I latency ARL, but the differences did not reach statistical significance (Mann–Whitney non-parametric test, P = 0.10).
CGH has been shown to be a powerful tool for the study of chromosomal gains and losses in solid tumours. While several studies have been performed to assess the genomic imbalances few data concerning CGH in ARL have been reported. To our knowledge, only two series on different types of ARL, DLBCL and PEL, and one case report of HIV related BL have been reported previously [27–29].
Using CGH we have studied the largest series of 28 ARL, well characterized for histopathologic, clonality and EBV features. Chromosomal imbalances were identified in 50% of ARL. Five non-random gains were detected with the minimal amplified region restricted to 11q25, 12q24, 19q13, 9p23-pter and 17q11-q21. None was specific to ARL in comparison with lymphomas occurring in the general population. Gains of whole or parts of chromosome 12, detected in one BL and two DLBCL, were previously reported in several CGH studies of non-Hodgkin lymphoma (NHL) of HIV-negative DLBCL [20,21,30], BL , PCNSL [23,24], as well as of ARL, DLBCL  and PEL  and one case of BL . The minimal amplified region, 12q24, is a commonly gained region in various lymphomas of immunocompetent patients, such as follicular lymphoma , mediastinal lymphoma  and primary large cell lymphoma of the gastrointestinal tract . High copy number gains on 12q24 have also been detected by micro-array based CGH in aggressive B-cell NHL . However, 12q24 is more telomeric to the frequently amplified region in DLBCL of non-immunocompromised patients (12q13-12q14) which is often associated with advanced stages  and contains candidate proto-oncogenes GLI, CDK4 and MDM2. One candidate gene located in 12q24 is BCL7A which has been shown to be rearranged in BL cell lines . Three cases in our series, one BL and two DLBCL, showed gains of 11q with a minimal amplified region mapping to 11q25. Restricted chromosome breakpoint sites on 11q25 have already been shown in NHL of the general population and suggest the presence of candidate oncogenes or tumour suppressor genes in this region . Gains of chromosome 19 were detected in one BL and two DLBCL with a minimal amplified region restricted to 19q13. One candidate gene mapped to this region is BCL3, a transcriptional co-activator of nuclear factor kappa-β (NF-κβ), which is important in B-cell maturation. Rearrangement and over-expression of BCL3 has been shown to be associated with t(14;19)(q32.3;q13.2), a rare but recurrent translocation occurring in chronic B-cell lymphoproliferations of immunocompetent patients [36,37]. Gains on 9p were present in one BL and one DLBCL, with a minimal amplified region restricted to 9p23-ter. Amplifications of 9p23-24 were previously observed in DLBCL  and primary mediastinal B cell lymphoma (PMBL) of immunocompetent patients [32,39]. The main candidate gene located in this region is JAK2 whose amplification has been detected in PMBL as well as in CD30+ Hodgkin cells [40,41]. Gains of chromosome 17 were detected in two DLBCL, with a minimal affected region restricted to 17q11-q21. It has been shown that in add(1)(p36), a common secondary aberration in NHL carrying t(14;18), extra material comes from 17q11-q21 and is associated with transformation to more aggressive disease .
It is noteworthy that two chromosomal imbalances include two loci of well known proto-oncogenes: REL in the high level amplification of 2p13-p22 and c-myc in the gain of 8q24. Amplification of the REL gene, which encodes a member of the NF-κB family of transcription factors involved in B-cell maturation, was reported in CGH studies of both HIV-negative, often with extra nodal involvement [19,21,43] and HIV-positive DLBCL . Deregulation of the c-myc proto-oncogene (8q24) by chromosomal rearrangements following balanced reciprocal translocations: t(8;14) or one of its variants t(8;22) or t(2;8), well known in lymphomagenesis of BL in non-immunocompromised patients, has also been shown in AIDS associated BL and less frequently DLBCL . However, reciprocal translocations are not detectable by CGH. Therefore, as it has already been suggested [19,21], amplification and rearrangement might be two independent pathways of over-expression of this gene.
Overall incidence of genomic changes was more limited in BL than DLBCL (50% versus 70%). In the same way, the number of changes per case was significantly lower in BL than in systemic DLBCL. These data suggest that, in addition to constant c-myc activation, a few chromosomal alterations could result in the development of BL which often occurs in the initial stages of the HIV infection in the presence of a relatively preserved immune function. The higher CD4 cell count found in BL favours this hypothesis. The incidence of chromosomal changes in different histological types seemed to be lower than the frequency reported in lymphoma of the same category in non-immunocompromised patients [19,20,22–24,26,30]. This is in agreement with a previous CGH study on DLBCL of HIV-positive and HIV-negative patients . The most striking difference concerned PCNSL: while PCNSL occurring in immunocompetents patients show multiple chromosomal imbalances but are EBV negative [22–24], in our study, three of four EBV-positive PCNSL had a normal CGH profile. AIDS-PCNSL are associated with advanced stages of HIV infection with profoundly disrupted immune function and virtually all of them harbour EBV infection . As the occurrence of genomic alterations may be modified by the association of the expression of EBV latency proteins in lymphoma cells, we evaluated the relationship between the detection of EBV and especially the EBV latency type and the occurrence of chromosomal imbalances. While Tiirikainen et al.  found no correlation between genomic changes and EBV infection regardless of latency type, in our study the number of chromosomal abnormalities seemed to be lower in latency type II/III, irrespective of the morphological WHO classification. However, this result did not reach statistical significance and it should be confirmed on a larger series. This might be explained by the different patterns of EBV latent protein expression according to the EBV latency type. In latency II/III, different EBV latent proteins having key functions in immortalization and transformation, such as LMP1 and EBNA2, are expressed in lymphoid B-cells and may induce the oncogenic process. While the absence of viral immortalizing proteins in EBV-negative or EBV-positive latency type I (EBNA 1 expression) may be overcome by genomic changes that could modify the expression and/or the structure of genes regulating cell proliferation. The lower number of CD4 cells in EBV-positive latency type II/III in comparison with EBV-positive type I/ EBV-negative supports this hypothesis. Indeed profoundly disrupted immune function is associated with viral reactivation and the expression of proteins with well known oncogenic properties.
In conclusion, our CGH study performed on the largest series to date showed that chromosomal imbalances are similar to those observed in immunocompetent NHL of the same category but (i) the number of chromosomal imbalances in ARL is lower than the number reported in lymphoma of the same category occurring in immunocompetent patients; (ii) it seems that there is an inverse correlation between the expression of EBV oncogenic proteins (LMP1 and EBNA2) and the number of chromosomal imbalances. This study emphasizes the necessity to evaluate the functional consequences of such genomic alterations in association with EBV protein expression by a combined approach using CGH-array and gene expression profiling.
This study was supported by the Agence Nationale de Recherches sur le SIDA (ANRS).
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non-Hodgkin's lymphoma; AIDS; CGH; EBV; chromosomal imbalances
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