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SAGE Analysis Highlights the Importance of P53csv, Ddx5, Mapkapk2 and Ranbp2 to Multiple Myeloma Tumorigenesis Q

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SAGE Analysis Highlights the Importance of P53csv, Ddx5, Mapkapk2 and Ranbp2 to Multiple Myeloma Tumorigenesis Q Cancer Letters 278 (2009) 41–48 Contents lists available at ScienceDirect Cancer Letters journal homepage: www.elsevier.com/locate/canlet SAGE analysis highlights the importance of p53csv, ddx5, mapkapk2 and ranbp2 to multiple myeloma tumorigenesis q Roberta S. Felix a,1, Gisele W.B. Colleoni a,1,*, Otavia L. Caballero b,1, Mihoko Yamamoto a, Manuella S.S. Almeida a, Valéria C.C. Andrade a, Maria de Lourdes L.F. Chauffaille a, Wilson A. da Silva Jr. c, Maria Dirlei Begnami d, Fernando Augusto Soares d, Andrew J. Simpson b, Marco Antonio Zago c, André L. Vettore e a Hematology and Hemotherapy Service, Federal University of São Paulo, UNIFESP/EPM, São Paulo, Brazil b Ludwig Institute for Cancer Research, New York Branch, USA c Faculdade de Medicina de Ribeirão Preto/USP, Ribeirão Preto, Brazil d Hospital A. C. Camargo – Fundação Antonio Prudente, São Paulo, Brazil e Ludwig Institute for Cancer Research, São Paulo Branch, Brazil and Biological Science Department, Federal University of São Paulo, UNIFESP/EPM, Diadema, Brazil article info abstract Article history: Serial analysis of gene expression (SAGE) allows a comprehensive profiling of gene expres- Received 12 September 2008 sion within a given tissue and also an assessment of transcript abundance. We generated Received in revised form 11 December 2008 SAGE libraries from normal and neoplastic plasma cells to identify genes differentially Accepted 12 December 2008 expressed in multiple myeloma (MM). Normal plasma cells were obtained from palatine tonsils and MM SAGE library was generated from bone marrow plasma cells of MM patients. We obtained 29,918 SAGE tags from normal and 10,340 tags from tumor libraries. Computer-generated genomic analysis identified 46 upregulated genes in the MM library. Key words: Ten upregulated genes were selected for further investigation. Differential expression was Multiple myeloma SAGE validated by quantitative real-time PCR in purified plasma cells of 31 patients and three Gene expression profiling controls. P53CSV, DDX5, MAPKAPK2 and RANBP2 were found to be upregulated in at least Meta-analysis 50% of the MM cases tested. All of them were also found upregulated in MM when com- pared to normal plasma cells in a meta-analysis using ONCOMINE microarray database. Antibodies specific to DDX5, RANBP2 and MAPKAPK2 were used in a TMA containing 57 MM cases and confirmed the expression of these proteins in 74%, 96%, and 21% of the MM samples, respectively. Analysis of differential expression using SAGE could identify genes important for myeloma tumorigenesis (P53CSV, DDX5, MAPKPK2 and RANBP2) and that could potentially be useful as therapeutic targets. Ó 2008 Elsevier Ireland Ltd. All rights reserved. 1. Introduction of plasma cells in the bone marrow, serum or urinary monoclonal protein, osteolytic lesions, anemia and hyper- Multiple myeloma (MM) remains an incurable malig- calcemia [1]. High-dose chemotherapy followed by autolo- nant neoplasm, characterized by monoclonal proliferation gous stem cell transplantation increases complete response rates and overall survival. However, few patients, if any, will be cured. Allogeneic stem cell transplant can q A study from the clinical genomics project in multiple myeloma, Brazil represent a chance of cure for selected cases but implies * Corresponding author. Address: UNIFESP/EPM – Rua Botucatu, 740, 3° in high mortality and morbidity [2]. Currently, antiangio- andar, Hematologia, CEP 04023-900, Vila Clementino, São Paulo, SP, genic drugs, such as thalidomide and its analogs (lenalido- Brazil. Tel.: +55 11 5579 1550; fax: +55 11 5571 8806. mide), and proteasome inhibitors (bortezomib) have been E-mail address: [email protected] (G.W.B. Colleoni). 1 These authors contributed equally for this paper. used as single or combined agents for relapsed/refractory 0304-3835/$ - see front matter Ó 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.canlet.2008.12.022 42 R.S. Felix et al. / Cancer Letters 278 (2009) 41–48 cases and even as first line therapy [3,4]. Thus, despite of or thalidomide/prednisone). Seven patients were consoli- all these new therapeutic alternatives, MM remains an dated with autologous bone marrow transplantation. incurable disease, with median survival of 3 years [1]. Con- Three pools of normal plasma cells were obtained from sidering the heterogeneity of genetic aspects related with palatine tonsils (from seven children who underwent ton- MM pathogenesis, recent studies have been focused on sillectomy). They were used as source of normal plasma prognostic factors that could define the best therapeutic cells because the number of these reactive cells is higher approach for each case or to contribute for the develop- in tonsils than in normal bone marrow samples (only 1– ment of new therapies [5,6]. In this way, gene expression 5% of plasma cells), mainly after using sorting of CD138- profiling analysis can be very helpful to define such prog- positive cells. Written informed consent was obtained nostic factors. Serial analysis of gene expression (SAGE) al- from all patients and controls, and the study was approved lows the identification of genes expressed in a given tissue by the Ethical Committee of our institution. The main and also the assessment of their expression levels. How- clinical characteristics of all patients are summarized in ever, the most important advantage of using SAGE is the Table 1. The neoplastic plasma cells used in the SAGE li- possibility of undertaking a gene expression profiling with- brary construction were obtained from bone marrow of out prior knowledge of the presence and sequence of genes two IgGj newly diagnosed MM patients who were diag- to be analyzed, as opposed to microarrays [7]. Therefore, nosed at stage IIIA, with International Scoring System the aim of this study was to use SAGE to profile gene (ISS) 2, being one 50 years-old male and one 60 years-old expression of normal and neoplastic plasma cells. fe male. One of them had hypodiploid and the other had hyperdiploid karyotype. Both cases had no chromosome 2. Material and methods 13 deletion. For the SAGE normal library we used purified CD138+ cells (normal plasma cells) obtained from palatine 2.1. Patients and controls tonsils (Fig. 1). Between June 2002 and April 2006, we obtained puri- 2.2. Magnetic sorting of CD-138-positive cells fied CD138-positive MM cells using CD138 (Sydecan-1) Micro Beads selection by Manual Ability Classification Sys- Purified normal and neoplastic plasma cells were ob- tem (MACS) magnetic cell sorter (Miltenyi Biotec Inc., CA, tained after magnetic sorting of CD-138-positive (syndec- USA) from 31 newly diagnosed MM patients, referred to an-1) cells using MACS (Magnetic Cell Sorting of Human the Hematology and Hemotherapy Service of Federal Uni- Cells, Miltenyi Biotec Inc., CA, USA) system, given at least versity of São Paulo, UNIFESP, São Paulo, Brazil. MM diag- 85% of purity, confirmed by flow citometry assays. nosis was based on The International Working Group Criteria [8] and information on tumor stage was obtained for all patients according to Durie Salmon and the Interna- tional Staging System (ISS) [9]. Only patients with no pre- vious chemotherapy, corticosteroids or bisphosphonates treatment were included. Patients were treated with con- ventional chemotherapy (VAD or melphalan/prednisone Table 1 Clinical characteristics of 31 MM patients used in RQ-PCR validation. Clinical characteristics Number Frequency (%) Age median: 62 (27–80) years Sex Female 10 32.3 Male 21 67.7 Isotype IgG 16 51.6 IgA 9 29.0 Light chain 6 19.4 Durie and Salmon stage IA 0 0 IIA 1 3.2 IIIA 19 61.3 IIIB 11 35.5 ISS 1 2 6.5 2 10 32.3 3 17 54.7 NA 2 6.5 ISS = international staging system. NA = not available. Fig. 1. Summary of study design. R.S. Felix et al. / Cancer Letters 278 (2009) 41–48 43 2.3. RNA extraction and SAGE libraries construction 2008 [13–17], comparing (1) normal plasma cells and mul- tiple myeloma samples; (2) monoclonal gammopaties of RNA extraction was performed using TRIzol reagent undetermined significance (MGUS) or smoldering myelo- (Invitrogen, Carslbad, CA, USA) following the manufac- ma with normal plasma cells; (3) monoclonal gammopa- turer’s instructions. RNA quality was checked in 2% agarose ties of undetermined significance (MGUS) or smoldering gel stained with ethidium bromide. SAGE libraries were myeloma and myeloma samples; (4) all studies comparing constructed using the I-SAGE kit (Invitrogen, Carlsbad, different clinical or cytogenetic categories within myeloma CA, USA), according to manufacture’s instructions. cases. ONCOMINETM expression correlations were searched for each gene. Statistical analysis of differences was per- 2.4. Sequencing of SAGE clones formed using ONCOMINE algorithms as previously de- scribed [18]. Sequencing reactions were done on plasmid templates (pZErO-1 – Invitrogen, Carlsbad, CA, USA) using M13 For- 2.8. Immunohistochemistry analyses ward primer (50-CGCCAGGTTTTCCCAGTCACGAC-30) and the ABI Prism BigDye Terminator Sequencing Kit (Applied We analyzed in duplicate the expression of DDX5, RAN- Biosystems, Foster City, CA, USA). The sequencing reaction BP2, MAPKAPK2 in 57 confirmed MM cases using tissue products were analyzed on 3700 ABI sequencer (Applied microarray (TMA) method. Forty-seven samples were ob- Biosystems, Foster City, CA, USA). tained from plasmacytomas of patients with MM diagnosis and 10 samples were obtained from bone marrow of MM 2.5. Genes selected for study patients. This cohort was completely independent (clinical data not shown) from the group of patients in which quan- For further investigation, we selected genes that had titative real-time PCR validation was performed. DDX5 was tags that were unique and upregulated at least 10 times detected with the rabbit polyclonal anti-DDX5 (ab21696 – in the MM library as compared with the normal plasma cell Abcam Inc., Cambridge, MA) at 1:12,000 and presented a library. nuclear localization. Rabbit monoclonal anti-MAPKAPK2 (ab51018 – Abcam Inc., Cambridge, MA) presented nuclear 2.6.
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