Modern Pathology (2012) 25, 651–660 & 2012 USCAP, Inc. All rights reserved 0893-3952/12 $32.00 651 Genomic analysis of marginal zone and lymphoplasmacytic lymphomas identified common and disease-specific abnormalities Esteban Braggio1, Ahmet Dogan2, Jonathan J Keats3, Wee J Chng4, Gaofeng Huang4, Julie M Matthews5, Matthew J Maurer2, Mark E Law2, David S Bosler6, Michael Barrett3, Izidore S Lossos7, Thomas E Witzig2 and Rafael Fonseca8 1Department of Biochemistry and Molecular Biology, Mayo Clinic, Scottsdale, AZ, USA; 2Division of Anatomic Pathology, Mayo Clinic, College of Medicine, Rochester, MN, USA; 3Translational Genomics, Phoenix, AZ, USA; 4Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore; 5Department of Molecular and Cellular Pharmacology, University of Miami, FL, USA; 6Cleveland Clinic, Cleveland, OH, USA; 7Division of Hematology-Oncology, Department of Medicine, Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, University of Miami, FL, USA and 8Department of Hematology – Oncology, Mayo Clinic, Scottsdale, AZ, USA Lymphoplasmacytic lymphomas and marginal zone lymphomas of nodal, extra-nodal and splenic types account for 10% of non-Hodgkin lymphomas. They are similar at the cell differentiation level, sometimes making difficult to distinguish them from other indolent non-Hodgkin lymphomas. To better characterize their genetic basis, we performed array-based comparative genomic hybridization in 101 marginal zone lymphomas (46 MALT, 35 splenic and 20 nodal marginal zone lymphomas) and 13 lymphoplasmacytic lymphomas. Overall, 90% exhibited copy-number abnormalities. Lymphoplasmacytic lymphomas demonstrated the most complex karyotype (median ¼ 7 copy-number abnormalities), followed by MALT (4), nodal (3.5) and splenic marginal zone lymphomas (3). A comparative analysis exposed a group of copy-number abnormalities shared by several or all the entities with few disease-specific abnormalities. Gain of chromosomes 3, 12 and 18 and loss of 6q23-q24 (TNFAIP3) were identified in all entities. Losses of 13q14.3 (MIRN15A-MIRN16-1) and 17p13.3-p12 (TP53) were found in lymphoplasmacytic and splenic marginal zone lymphomas; loss of 11q21-q22 (ATM) was found in nodal, splenic marginal zone and lymphoplasmacytic lymphomas and loss of 7q32.1-q33 was found in MALT, splenic and lymphoplasmacytic lymphomas. Abnormalities affecting the nuclear factor kappa B pathway were observed in 70% of MALT and lymphoplasmacytic lymphomas and 30% of splenic and nodal marginal zone lymphomas, suggesting distinct roles of this pathway in the pathogenesis/progression of these subtypes. Elucidation of the genetic alterations contributing to the pathogenesis of these lymphomas may guide to design-specific therapeutic approaches. Modern Pathology (2012) 25, 651–660; doi:10.1038/modpathol.2011.213; published online 3 February 2012 Keywords: aCGH; copy-number abnormalities; LPL; MZL; NF-kB pathway Nodal marginal zone lymphoma, extra-nodal mar- are indolent lymphomas accounting for B10% ginal zone lymphoma of MALT, splenic marginal of all non-Hodgkin lymphomas.1,2 MALT lymphoma zone lymphoma and lymphoplasmacytic lymphoma is the most frequent subtype, representing 50–70% of marginal zone lymphomas, followed by splenic and nodal marginal zone lymphomas, which repre- Correspondence: Dr A Dogan, MD, PhD, Division of Anatomic sent 20% and 10% of cases, respectively. Lympho- Pathology, Mayo Clinic, College of Medicine, 200 First Street SW, plasmacytic lymphoma, accounting for 1% of Rochester, MN 55905, USA. E-mail: [email protected] non-Hodgkin lymphomas, is a heterogeneous entity Received 7 September 2011; revised 15 December 2011; accepted with cytological spectrum ranging from small B-cell 21 December 2011; published online 3 February 2012 lymphocytes, plasmacytoid lymphocytes to mature www.modernpathology.org Genomic analysis in low-grade B-cell lymphomas 652 E Braggio et al plasma cells and is characterized by frequent each frozen tissue used for the study were also involvement of lymph nodes and bone marrow.3 reviewed by histological examination and immuno- MALT lymphomas harbor several characteristic histochemistry. All cases were diagnosed accord- chromosomal abnormalities, including trisomies 3 ing to the criteria established by the 2008 World and 18, deletion of 6q and a number of transloca- Health Organization Classification of Lymphoid tions, including t(11;18)(q21;q21) API2-MALT1, t(14;18) Neoplasms.24 (q32;q21) IGH-MALT1, t(1;14)(p22;q32) IGH-BCL10, The Waldenstro¨m’s macroglobulinemia cases t(3;14)(q27;q32) and t(3;14)(p14.1;q32) IGH-FOXP1.4–12 were excluded from this study. The cases fulfilling The translocations are mutually exclusive, but often the criteria for Waldenstro¨m’s macroglobulinemia they are present in conjunction with other genomic according to the 2008 World Health Organization abnormalities, with the exception of the t(11;18) API2- Classification and International Workshop On Wal- MALT1, which usually is the sole chromosomal denstro¨m’s Macroglobulinemia25,26 were published abnormality.13 Interestingly, at least four of these in a previous study.21 The diagnostic criteria for translocations cause overexpression of MALT1 Waldenstro¨m’s macroglobulinemia are the presence or BCL10, leading to constitutive activation of the of (i) a lymphoplasmacytic lymphoma morphology nuclear factor kappa B (NF-kB) signaling path- as described in the 2008 World Health Organization ways—a common pathogenesis pathway in MALT classification, (ii) bone marrow involvement and (iii) lymphomas.14–16 However, depending on the ana- any level of IgM paraprotein. The cases included in tomic location, 25–75% of MALT lymphomas do not this study either lacked evidence of bone marrow harbor any of these chromosomal translocations. involvement or IgM paraprotein. Of the 13 cases Knowledge surrounding the genetic events char- of lymphoplasmacytic lymphomas analyzed in this acterizing splenic, nodal and lymphoplasmacytic study, 6 cases lacked a monoclonal gammopathy at lymphoma is more limited. The splenic marginal presentation. Remaining cases either had IgG or IgA zone lymphoma is mainly characterized by the pre- gammopathy or IgM gammopathy without evidence sence of recurrent deletions on 7q32-q35.11,17–19 of the bone marrow involvement. The lympho- Whole or partial gains of chromosomes 3 and 12 plasmacytic lymphomas cases were composed of a and losses of 17p have also been identified in this mixture of small lymphocytes, small lymphoplasma- entity.18,20 In the nodal marginal zone lymphoma cytoid cells and occasional plasma cells. Archi- some initial studies have highlighted the presence of tecturally the infiltrate was diffused with a pre- whole or partial gains on chromosomes 3, 6p, 12 and dominantly paracortical and medullary pattern 18,10 but no unique abnormalities have been identi- often sparing the medullary sinuses. In contrast, fied. Finally, few recurrent abnormalities (6q deletion, the nodal marginal zone lymphoma cases contained 6p gain and whole or partial gains on chromosomes intermediate sized cells with abundant pale cyto- 3, 4 and 18) have been identified in lymphoplasma- plasm (so-called monocytoid cytology). They lacked cytic lymphoma, mainly in cases associated with lymphoplasmacytoid cells and plasma cell differ- Waldenstro¨m’s macroglobulinemia.21–23 entiation was minimal or absent. The cases that Consequently, there is a limited knowledge cannot be clearly classified into these two categories regarding the pathogenesis of these diseases and were not included in the study. Finally, the so-called what are the genetic events contributing to malig- variants such as splenic lymphoma villous lympho- nant transformation. The aim of this study was to cytes or splenic B-cell lymphoma unclassified were perform a comprehensive high-resolution genomic not studied. analysis in a large series of marginal zone/lympho- In all, 8 of the 46 MALT lymphomas were pre- plasmacytic lymphoma to better characterize the viously shown to have t(11;18)(q21;q21) API2-MALT1 genetic basis of the different entities and identify by FISH analysis.27 Tumor purity was estimated molecular mechanisms involved in the patho- by percent of CD20-positive cells in the tumors genesis of these indolent B-cell non-Hodgkin lym- with a median of 70% (range 20–100%). Tissues phomas. analyzed of each case are shown in Supplemen- tary Table S1. Biospecimens were collected after informed consent was obtained in accordance with the Declaration of Helsinki in each of the participat- Materials and methods ing centers and the study was conducted following Patient Samples the Institutional Review Board approval in all the centers. In all, 114 patients were included in this study: 46 MALT lymphomas (22 pulmonary, 11 salivary glands, 7 lacrimal glands and 6 gastrointestinal), 35 splenic Array-Based Comparative Genomic Hybridization marginal zone lymphomas, 20 nodal marginal zone lymphomas and 13 non-Waldenstro¨m’s macro- Genomic DNA was obtained from snap-frozen tissue globulinemia lymphoplasmacytic lymphomas. All using standard phenol-chloroform extraction methods. cases were reviewed before the study on paraffin High-resolution array-based comparative genomic sections with immunohistochemistry. Sections of hybridization was performed with the Human Genome Modern Pathology (2012) 25, 651–660 Genomic analysis in low-grade B-cell lymphomas E Braggio et al 653 244A microarray