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Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway

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RESEARCH ARTICLE Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway Zhaoqi Liu1,2, Ioan Filip1,2, Karen Gomez1,2, Dewaldt Engelbrecht3, Shabnum Meer4, Pooja N. Lalloo3, Pareen Patel3, Yvonne Perner5, Junfei Zhao1,2, Jiguang Wang6, Laura Pasqualucci7–9, Raul Rabadan1,2, and Pascale Willem3 Downloaded from https://bloodcancerdiscov.aacrjournals.org by guest on September 29, 2021. Copyright 2020 American Copyright 2020 by AssociationAmerican for Association Cancer Research. for Cancer Research. ABSTRACT Plasmablastic lymphoma (PBL) is an aggressive B-cell non-Hodgkin lymphoma associated with immunodeficiency in the context of human immunodeficiency virus (HIV) infection or iatrogenic immunosuppression. While a rare disease in general, the incidence is dramatically increased in regions of the world with high HIV prevalence. The molecular pathogenesis of this disease is poorly characterized. Here, we defined the genomic features of PBL in a cohort of 110 patients from South Africa (15 by whole-exome sequencing and 95 by deep targeted sequenc- ing). We identified recurrent mutations in genes of the JAK–STAT signaling pathway, includingSTAT3 (42%), JAK1 (14%), and SOCS1 (10%), leading to its constitutive activation. Moreover, 24% of cases harbored gain-of-function mutations in RAS family members (NRAS and KRAS). Comparative analysis with other B-cell malignancies uncovered PBL-specific somatic mutations and transcriptional pro- grams. We also found recurrent copy number gains encompassing the CD44 gene (37%), which encodes for a cell surface receptor involved in lymphocyte activation and homing, and was found expressed at high levels in all tested cases, independent of genetic alterations. These findings have implications for the understanding of the pathogenesis of this disease and the development of personalized medicine approaches. SIGNIFICANCE: Plasmablastic lymphoma is a poorly studied and extremely aggressive tumor. Here we define the genomic landscape of this lymphoma in HIV-positive individuals from South Africa and iden- tify pervasive mutations in JAK–STAT3 and RAS–MAPK signaling pathways. These data offer a genomic framework for the design of improved treatment strategies targeting these circuits. INTRODUCTION (HIV)-related or iatrogenic immunodeficiency (1). As an AIDS- defining illness with a dismal prognosis, PBL is a particularly Plasmablastic lymphoma (PBL) is a highly aggressive lym- compelling problem in the Sub-Saharan African region, which phoma of preterminally differentiated B cells, which predomi- accounts for approximately 54% of the estimated 37.9 million nantly occurs in patients with human immunodeficiency virus people living with HIV. Despite the national rollout offering combination anti- 1Program for Mathematical Genomics, Columbia University, New York, retroviral therapy (cART) in South Africa since 2004, the prev- 2 New York. Departments of Systems Biology and Biomedical Informatics, alence of HIV-associated mature B-cell lymphomas increases Columbia University, New York, New York. 3Department of Haematology and Molecular Medicine, National Health Laboratory Service, Faculty of yearly (2). The burden of HIV-associated lymphomas on Health Sciences, University of the Witwatersrand, Johannesburg, South the country’s encumbered health are further compounded Africa. 4Department of Oral Pathology, Faculty of Health Sciences, Uni- by the younger presentation age of HIV-infected patients, versity of the Witwatersrand, Johannesburg, South Africa. 5Department the challenging classification of these lymphomas, and an of Anatomical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South exceptionally aggressive clinical disease course that, although Africa. 6Division of Life Science, Department of Chemical and Biological curable in a significant fraction of patients (3), often results Engineering, Center for Systems Biology and Human Health and State Key in fatalities (4). Laboratory of Molecular Neuroscience, The Hong Kong University of Sci- Previously being classified as diffuse large B-cell lymphoma 7 ence and Technology, Hong Kong SAR, China. Institute for Cancer Genetics. (DLBCL), PBL was later recognized as a distinct entity (5) 8Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York. 9Department of Pathology and Cell Biology, Herbert Irving with well-defined histopathologic features including large Comprehensive Cancer Center, Columbia University, New York, New York. plasmablastic or immunoblastic cell morphology, loss of Note: Supplementary data for this article are available at Blood Cancer B-cell lineage markers (CD20, PAX5), expression of plasma- Discovery Online (http://bloodcancerdiscov.aacrjournals.org/). cytic differentiation markers (CD38, CD138, IRF4/MUM1, L. Pasqualucci, R. Rabadan, and P. Willem contributed equally to this article. BLIMP1), a high proliferation index, and frequent infection Corresponding Authors: Laura Pasqualucci, Institute for Cancer Genetics, by the Epstein-Barr virus (EBV; ref. 6). While EBV infection Columbia University, 1130 St Nicholas Ave, Room 507B, New York, NY 10032. and activating MYC translocations have been reported as Phone: 212-851-5248; Fax: 212-851-5256; E-mail: [email protected]; the major features of these tumors in a number of studies Raul Rabadan, Columbia University Irving Medical Center, 622 West 168th (7), the molecular pathology of PBL remains elusive in both Street, PH18-200, New York, NY 10032. Phone: 212-305-3896; Fax: 212- 851-5149; Email: [email protected]; and Pascale Willem, University HIV-positive and -negative individuals. Numerous case stud- of the Witwatersrand and the National Health Laboratory Service, Wits Medi- ies and some cohorts have been well described and reviewed cal School, 7 York Road Parktown, Johannesburg 2193, South Africa. Phone: (6–9). Only two studies have partially explored genetic aber- 271-1489-8406; Fax: 271-1489-8480; E-mail: [email protected] rations in this disease: a comparative genomic hybridiza- Blood Cancer Discov 2020;1–14 tion study showed a pattern of segmental gains in PBL doi: 10.1158/2643-3230.BCD-20-0051 that more closely resembled DLBCL than plasma cell mye- ©2020 American Association for Cancer Research. loma (10). The second study compared the transcriptional 2020 BLOOD CANCER DISCOVERY | OF2 Downloaded from https://bloodcancerdiscov.aacrjournals.org by guest on September 29, 2021. Copyright 2020 American Association for Cancer Research. RESEARCH ARTICLE Liu et al. profiles of 15 PBL cases to DLBCL and extraosseous plasma- PBL cohort (Fig. 1A–E). The most frequent genetic lesions cytoma (11), and showed that B-cell receptor signaling genes affected the JAK–STAT signaling pathway with, in total, including CD79A/B, BLK, LYN, and SWAP70 among others, 62% of cases (68/110) harboring a mutation in at least one were significantly downregulated in PBL compared with of five genes STAT3,( JAK1, SOCS1, JAK2, and PIM1, a direct DLBCL; in contrast, targets of MYB and the oncogene MYC, transcriptional target of STAT3/5 that functions as part of as well as genes reflecting the known plasmacytic immu- a negative feedback loop; Fig. 1A). Among these, STAT3 was nophenotype of PBL, were overexpressed. More recently, the predominant target of mutations, with 46 of 110 cases MYC and PRDM1 were investigated for mutations, struc- (42%) harboring clonal events (Supplementary Fig. S2A and tural rearrangements, and copy number gains in 36 PBL S2B). With three exceptions, the identified variants were het- cases (12). PRDM1 mutations were found in 8 of 16 cases, erozygous missense mutations clustering in exons 19 to 22, frequently in association with MYC overexpression, sug- encoding part of the SH2 domain that is required for STAT3 gesting a coordinate role in the pathogenesis of the disease. molecular activation via receptor association and tyrosine While these studies have shed light on this rare disorder, a phosphodimer formation (14). In particular, the majority systematic characterization of protein-changing alterations of the mutations resulted in the amino acid changes Y640F in PBL has not been performed. (n = 11), D661V (n = 9), S614R (n = 5), and E616G/K (n = 4; The elucidation of genes and pathways that drive the Fig. 1B), which have been categorized as gain-of-function initiation and maintenance of PBL is essential to better or likely gain-of-function mutations based on experimental understand the biology of this cancer and, critically, to imple- validation (https://oncokb.org/gene/STAT3), and overlap ment improved biomarkers and more effective treatment with the STAT3 mutation pattern described in other aggres- options. Here, we combined whole-exome and transcriptome sive B-cell lymphomas and T-cell and natural killer (NK) sequencing followed by targeted resequencing of 110 HIV- cell malignancies (15, 16). Three additional cases showed a associated PBL cases to elucidate the mutational, transcrip- >75% variant allele frequency in the absence of copy number tional, and copy number landscape of this disease. We show changes, consistent with a copy neutral loss of heterozygo- that mutations in various components of the JAK–STAT and sis. Sanger-based resequencing of the involved STAT3 exons, MAPK–ERK pathway pervade this lymphoma, revealing this performed in 23 cases, validated all computationally identi- signaling cascade as
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