Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data

// Alexandra Schrader 1, 2, 10, 11 , Katharina Meyer 3, 6 , Neele Walther 1 , Ailine Stolz 4 , Maren Feist 1, 7 , Elisabeth Hand 1, 6 , Frederike von Bonin 1 , Maurits Evers 3, 6, 13 , Christian Kohler 3, 6 , Katayoon Shirneshan 1 , Martina Vockerodt 5, 8, 10, 12 , Wolfram Klapper 5, 6, 7, 9 , Monika Szczepanowski 5, 6, 7, 9 , Paul G. Murray 8 , Holger Bastians 4 , Lorenz Trumper 1, 2, 5, 7 , Rainer Spang 3, 5, 6, 7 , Dieter Kube 1, 2, 5, 6, 7 1 Department of Haematology and Medical Oncology, University Medical Centre of the Georg-August University Gottingen, Gottingen, Germany 2 GRK1034 of the Deutsche Forschungsgemeinschaft, Georg-August University Gottingen, Gottingen, Germany 3 Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Regensburg, Germany 4 Goettingen Center for Molecular Biosciences (GZMB) and University Medical Center, Institute of Molecular Oncology, Section for Cellular Oncology, Gottingen, Germany 5 Network Molecular Mechanism of Malignant Lymphoma (MMML) of the Deutsche Krebshilfe, Germany 6 BMBF-Network HamatoSys, Germany 7 BMBF-Network Myc-Sys, Germany 8 School of Cancer Sciences, University of Birmingham, Birmingham, UK 9 University-Hospital Schleswig-Holstein, Hematopathology Section and Lymph Node Registry Kiel, Kiel, Germany 10 Department of Anatomy, University Medical Centre of the Georg-August University Gottingen, Gottingen, Germany 11 Present address: Laboratory of Lymphocyte Signaling and Oncoproteome, Department I of Internal Medicine, University Hospital Cologne, Center for Integrated Oncology (CIO) Koln-Bonn, Cologne, Germany 12 Present address: Department of Anatomy, University Medical Centre of the Georg-August University Gottingen, Gottingen, Germany 13 Current address: The John Curtin School of Medical Research the Australian National University Canberra, Australia Correspondence to: Dieter Kube, e-mail: dieter.kube@med.uni-goettingen.de Keywords: lymphoma, B cell receptor signaling, guided clustering, cell cycle delay, chromosomal aberrations Received: September 23, 2015     Accepted: March 31, 2016     Published: May 7, 2016 ABSTRACT To discover new regulatory pathways in B lymphoma cells, we performed a combined analysis of experimental, clinical and global gene expression data. We identified a specific cluster of genes that was coherently expressed in primary lymphoma samples and suppressed by activation of the B cell receptor (BCR) through αIgM treatment of lymphoma cells in vitro . This gene cluster, which we called BCR.1, includes numerous cell cycle regulators. A reduced expression of BCR.1 genes after BCR activation was observed in different cell lines and also in CD10 + germinal center B cells. We found that BCR activation led to a delayed entry to and progression of mitosis and defects in metaphase. Cytogenetic changes were detected upon long-term αIgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc co-regulated genes in distinct groups of lymphoma patients was observed. Finally, we showed that the BCR.1 index discriminates activated B cell-like and germinal centre B cell-like diffuse large B cell lymphoma supporting the functional relevance of this new regulatory circuit and the power of guided clustering for biomarker discovery.