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Map of Mutations observed in ALK-negative Anaplastic Large Cell Lymphoma (ALCL) aggressive form of non-Hodgkin’s Lymphoma

Reporter: Aviva Lev-Ari, PhD, RN

New study from Columbia University Medical Center (CUMC) and Weill Cornell Medical College

Convergent Mutations and Kinase Fusions Lead to Oncogenic STAT3 Activation in Anaplastic Large Cell Lymphoma

Ramona Crescenzo,1,2,27 Francesco Abate,1,3,4,27 Elena Lasorsa,1,27 Fabrizio Tabbo’,1,2 Marcello Gaudiano,1,2 Nicoletta Chiesa,1 Filomena Di Giacomo,1 Elisa Spaccarotella,1 Luigi Barbarossa,1 Elisabetta Ercole,1 Maria Todaro,1,2 Michela Boi,1,2 Andrea Acquaviva,3 Elisa Ficarra,3 Domenico Novero,5 Andrea Rinaldi,6 Thomas Tousseyn,7 Andreas Rosenwald,8 Lukas Kenner,9 Lorenzo Cerroni,10 Alexander Tzankov,11 Maurilio Ponzoni,12 Marco Paulli,13 Dennis Weisenburger,14 Wing C. Chan,14 Javeed Iqbal,15 Miguel A. Piris,16 Alberto Zamo’,17 Carmela Ciardullo,18 Davide Rossi,18 Gianluca Gaidano,18 Stefano Pileri,19,20 Enrico Tiacci,21 Brunangelo Falini,21 Leonard D. Shultz,22 Laurence Mevellec,23 Jorge E. Vialard,24 Roberto Piva,1,25 Francesco Bertoni,6,26 Raul Rabadan,4, * Giorgio Inghirami,1,2,25, * and The European T-Cell Lymphoma Study Group, T-Cell Project: Prospective Collection of Data in Patients with Peripheral T-Cell Lymphoma and the AIRC 5xMille Consortium ‘‘Genetics-Driven Targeted Management of Lymphoid Malignancies’’ 1Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy 2Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA 3Department of Control and Computer Engineering, Politecnico di Torino, 10129 Torino, Italy 4Department of Biomedical Informatics and Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10027, USA 5Department of Pathology, A.O. Citta` della Salute e della Scienza (Molinette), 10126 Torino, Italy 6Lymphoma and Genomics Research Program, Institute of Oncology Research, 6500 Bellinzona, Switzerland 7Translational Cell and Tissue Research Lab, KU Leuven, 3000 Leuven, Belgium 8Institute of Pathology, University of Wu¨rzburg and Comprehensive Cancer Center Mainfranken, 97080 Wu¨rzburg, Germany 9Ludwing Boltzmann Institute for Cancer Research, 1090 Vienna, Austria 10Research Unit Dermatopathology of the Medical University of Graz, 8036 Graz, Austria 11Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland 12Pathology & Lymphoid Malignancies Units, San Raffaele Scientific Institute, 20132 Milan, Italy 13Department of Human Pathology, University of Pavia and Scientific Institute Fondazione Policlinico San Matteo, 27100 Pavia, Italy 14Department of Pathology, City of Hope Medical Center, Duarte, CA 91010, USA 15Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA 16Cancer Genomics, Instituto de Formacio´ n e Investigacio´ n Marque´ s de Valdecilla and Department of Pathology, Hospital Universitario Marque´ s de Valdecilla, 39008 Santander, Spain 17Department of Pathology and Diagnostics, University of Verona, 37134 Verona, Italy 18Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy 19European Institute of Oncology, 20141 Milano, Italy 20Bologna University School of Medicine, 40126 Bologna, Italy 21Institute of Hematology-Centro di Ricerche Onco-Ematologiche (CREO), Ospedale S. Maria della Misericordia, University of Perugia, 06100 Perugia, Italy 22The Jackson Laboratory, Bar Harbor, ME 04609, USA 23Janssen Research & Development, a Division of Janssen-Cilag, Campus de Maigremont, CS10615, 27106 Val-de-Reuil Cedex, France 24Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium 25Department of Pathology and NYU Cancer Center, New York University School of Medicine, New York, NY 10016, USA 26Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland 27Co-first author *Correspondence: rr2579@cumc.columbia.edu (R.R.), ggi9001@med.cornell.edu (G.I.) http://dx.doi.org/10.1016/j.ccell.2015.03.006

Crescenzo et al., 2015, Cancer Cell 27, 516–532 April 13, 2015 ª2015 Elsevier Inc. http://dx.doi.org/10.1016/j.ccell.2015.03.006

Significance

The JAK/STAT3 signaling pathway is often deregulated in hematopoietic disorders. We describe two mechanisms leading to the constitutive activation of STAT3 in ALK ALCL. Oncogenic JAK1 or STAT3 mutations are associated with hyperactive pSTAT3, which regulates canonical STAT3 and ATF3 genes. Moreover, synergizing JAK1 and STAT3 mutants sustain the neoplastic growth, which can be efficiently controlled in vitro and in an ALCL patient-derived tumorgraft model by JAK1/2 inhibitors. We discovered that chimera, displaying concomitant transcriptional and kinase activities, are power oncogenes capable to sustain via STAT3 the ALCL phenotype. The pharmacological inhibition of JAK/STAT3 represents an alternative strategy for the treatment of molecularly stratified ALCL. 516 Cancer Cell 27, 516–532, April 13, 2015 ª2015 Elsevier Inc.

SUMMARY

A systematic characterization of the genetic alterations driving ALCLs has not been performed. By integrating massive sequencing strategies, we provide a comprehensive characterization of driver genetic alterations (somatic point mutations, copy number alterations, and gene fusions) in ALK ALCLs. We identified activating mutations of JAK1 and/or STAT3 genes in 20% of 155 ALK ALCLs and demonstrated that 38% of systemic ALK ALCLs displayed double lesions. Recurrent chimeras combining a transcription factor (NFkB2 or NCOR2) with a tyrosine kinase (ROS1 or TYK2) were also discovered in WT JAK1/STAT3 ALK ALCL. All these aberrations lead to the constitutive activation of the JAK/STAT3 pathway, which was proved oncogenic. Consistently, JAK/STAT3 pathway inhibition impaired cell growth in vitro and in vivo.

INTRODUCTION

Peripheral T cell lymphomas (PTCLs) are a heterogeneous group of tumors derived from post-thymic lymphocytes (Swerdlow et al., 2008). They are orphan diseases, accounting for 12% to 15% of all non-Hodgkin’s lymphoma in Western populations (Vose et al., 2008), and display great variability in their clinical, morphological, immunophenotypic, cytogenetic, and molecular features. The classification of anaplastic large cell lymphomas (ALCLs) has been revised several times, and ALCLs are nowadays designated as a distinct entity of systemic PTCL (Swerdlow et al., 2008). Meanwhile, cutaneous forms of ALCLs (cALCLs) are recognized as a different variant. Among systemic ALCLs, patients harboring translocations of anaplastic lymphoma kinase (ALK) generally have a more favorable clinical course (Vose et al., 2008), although aggressive outcomes exist (Grewal et al., 2007). In contrast, ALK ALCL patients have high morbidity and mortality, and ALCL remains an incurable disease in 70% of patients (Savage et al., 2008). The genetics of ALK+ ALCL is characterized by translocations of the ALK proto-oncogene leading to ALK fusion proteins. The ALK chimeras activate STAT3, whose deregulated program is required for the maintenance of the neoplastic phenotype in ALK+ ALCL (Chiarle et al., 2005). Conversely, the mechanisms of transformation and maintenance of the ALK ALCLs remain elusive. Recurrent translocations and loss of TP53 and PRDM1/BLIMP1 have been proved to have a pathogenic role associated with less favorable outcomes (Boi et al., 2013; Parilla Castellar et al., 2014). Last, comparative genomic hybridization studies have shown that ALK+ ALCLs display a more stable genome than ALK ALCL or cALCL (Boi et al., 2013). There are several alternative mechanisms leading to hyperactive STAT signaling in human cancers. These include aberrant or chronic stimulation via cytokines and growth factors, constitutive engagement of wild-type (WT) and mutated RTK receptors, and deregulated activation of several G protein-coupled receptors. Likewise, STAT3 hyper-activation occurs within multiple elements of stromal compartment and/or host immune cells, making STAT3 a central actor for inflammation-induced cancers (Bournazou and Bromberg, 2013). Disrupting mutations controlling epigenetically endogenous regulators of STAT3 (Johnston and Grandis, 2011) and somatic mutations of STATs, detectable in rare solid tumors and selected lymphoproliferative disorders, have been described (Kiel et al., 2014; Koskela et al., 2012; Pilati et al., 2011). These data validate STAT3 as a valuable therapeutic target. To characterize the spectrum of mutations in ALK ALCL and to identify potential therapeutic targets, we used massive genomic sequencing of both RNA and DNA. We investigated the landscape of somatic point mutations, copy number alterations, and gene fusions and we infer the associated mutational mechanisms of disease along with a set of in vitro and in vivo models.

RESULTS

Whole-Exome Sequencing Somatic Mutation Analyses Demonstrate the Presence of Recurrent Mutations in ALK– ALCL The number of mutations per case varied markedly (mean of 36 non-synonymous somatic mutations, from 1 to 150) without any preferential chromosomal distribution (Figure 1A). Mutations were largely represented by single-nucleotide substitutions leading to amino acid changes, namely, missense mutations (n = 752 [90%]), but included insertions or deletions (n = 15 [1.8%]), nonsense mutations (n = 63 [7.6%]), and alterations in canonical splice sites (n = 1 [0.1%]) (Figure S1). Mutations were identified in PRDM1/BLIMP1, TP53, STAT3, JAK1, and BANK1 (Figure 1A). Integration of somatic mutations and focal copy number alterations highlighted PRDM1/BLIMP1, TP53, and CSMD2 as commonly mutated or deleted genes. TUBGCP6 and STAT3 genes were shown to be mutated or amplified (Figure 1B). Next we estimated the statistical significance of recurrent mutated genes and identified 13 putative candidate drivers on the basis of known functions and bioinformatics prediction (Figure S1, Tables S1 and S2, and Supplemental Information); those pathogenic roles require further functional studies.

VIEW FIGURES

Sanger Sequencing

Mutations of JAK1 and STAT3 Are Common in ALK– ALCL JAK-STAT pathway genes (i.e., STAT3 and JAK1) were recurrently mutated in the discovery ALK ALCL panel (Figure S1), suggesting that a STAT3-mediated oncogenic mechanism may be shared by all ALCLs, independent of ALK status. To define the mutation recurrence of JAK/STAT3 genes in ALK ALCL, we analyzed by targeted re-sequencing the mutation hot spots of STAT3 (i.e., the SH2 domain) and JAK1-3 (i.e., the kinase domain [KD]) in a validation panel of PTCL. A total of 155 primary ALCL samples (88 ALK and 23 ALK+ ALCLs and 44 cALCLs) and 74 PTCLs (29 angioimmunoblastic T cell lymphomas, 31 PTCLs not otherwise specified

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The first-ever systematic study of the genomes of patients with ALK-negative anaplastic large cell lymphoma (ALCL), a particularly aggressive form of non-Hodgkin’s lymphoma, shows that many cases of the disease are driven by alterations in the JAK/STAT3 cell signaling pathway. The new study from Columbia University Medical Center (CUMC) and Weill Cornell Medical College also demonstrates, in mice implanted with human-derived ALCL tumours, that the disease can be inhibited by compounds that target this pathway, raising hopes that more effective treatments might soon be developed. The open source study is published in the journal Cancer Cell.

The team explain that current therapies for this form of lymphoma fail to work in the majority of cases. However, now that the medical community know the mutations that drive a significant percentage of cases, the reseachers envision a new, precision medicine approach to the treatment of ALK-negative ALCL.

According the the group about 70,000 cases of non-Hodgkin’s lymphoma (NHL) are diagnosed each year; ALCL accounts for about 3 percent of them. Patients with systemic ALCL (disease that has spread to multiple body sites) fall into two groups, depending on whether their cells express an abnormal form of the ALK (anaplastic lymphoma kinase) protein. ALK-positive lymphomas tend to respond well to chemotherapy, with a long-term disease-free survival rate of more than 70 percent. These lymphomas are known to result from the fusion of two genes, which produces an abnormal protein that activates a third gene, STAT3. Patients with ALK-negative lymphomas have a worse prognosis, with a long-term survival rate of less than 50 percent. Very little is known about the cause of this form of the disease.

SOURCE

http://health-innovations.org/2015/04/15/researchers-demystify-rare-deadly-lymphoma/?blogsub=subscribed#blog_subscription-5