B-cell lymphoma (BCL) is the most common hematologic malignancy. While sequencing studies gave insights into BCL genetics, identification of non-mutated cancer genes remains challenging. Here, we describe PiggyBac transposon tools and mouse models for recessive screening and show their application to study clonal B-cell lymphomagenesis. In a genome-wide screen, we discover BCL genes related to diverse molecular processes, including signaling, transcriptional regulation, chromatin regulation, or RNA metabolism. Cross-species analyses show the efficiency of the screen to pinpoint human cancer drivers altered by non-genetic mechanisms, including clinically relevant genes dysregulated epigenetically, transcriptionally, or post-transcriptionally in human BCL. We also describe a CRISPR/Cas9-based in vivo platform for BCL functional genomics, and validate discovered genes, such as Rfx7, a transcription factor, and Phip, a chromatin regulator, which suppress lymphomagenesis in mice. Our study gives comprehensive insights into the molecular landscapes of BCL and underlines the power of genome-scale screening to inform biology.

Center for Translational Cancer Research TUM School of Medicine Technische Universität München Munich 81675 Germany

Center of Life Sciences Skolkovo Institute of Science and Technology Moscow 121205 Russia

Center of Molecular Medicine CEITEC Masaryk University Brno 601 77 Czech Republic

Cluster of Excellence EXC 1003 Cells in Motion Münster 48149 Germany

Comparative Experimental Pathology Technische Universität München Munich 81675 Germany

Departamento de Bioquímica y Biología Molecular Facultad de Medicina Instituto Universitario de Oncología Universidad de Oviedo Oviedo 33006 Spain

Department of Cardiac Development and Remodeling Max Planck Institute for Heart and Lung Research Bad Nauheim 61231 Germany

Department of Haematology Cambridge University Hospitals NHS Trust Cambridge CB2 0PT UK

Department of Haematology PathWest and Sir Charles Gairdner Hospital Queen Elizabeth 2 Medical Centre Nedlands 6009 Australia

Department of Medicine 2 Klinikum rechts der Isar Technische Universität München Munich 81675 Germany

Department of Medicine 3 Klinikum rechts der Isar Technische Universität München Munich 81675 Germany

Department of Medicine A University Hospital Münster Münster 48149 Germany

Divison of Chronic Inflammation and Cancer German Cancer Research Center Heidelberg 69120 Germany

Genomics of Adaptive Immunity Department Shemyakin Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Science Moscow 117997 Russia

German Cancer Consortium Heidelberg 69120 Germany

German Center for Cardiovascular Research Rhine Main Germany

Helmholtz Zentrum München Research Unit Gene Vectors Munich 81377 Germany

Helmholtz Zentrum München Research Unit Radiation Cytogenetics Neuherberg 85764 Germany

Hematology and Oncology Campus Benjamin Franklin Charité Universitätsmedizin Berlin Berlin 12203 Germany

Institute of Molecular Oncology and Functional Genomics TUM School of Medicine Technische Universität München Munich 81675 Germany

Institute of Pathology and Comprehensive Cancer Center Eberhard Karls Universität Tübingen Tübingen 72076 Germany

Instituto de Medicina Oncológica y Molecular de Asturias Oviedo 33193 Spain

Laboratory of Genomics of Antitumor Adaptive Immunity Privolzhsky Research Medical University Nizhny Novgorod 603005 Russia

Li Ka Shing Faculty of Medicine Stem Cell and Regenerative Medicine Consortium School of Biomedical Sciences University of Hong Kong Hong Kong China

Pirogov Russian National Research Medical University Moscow 117997 Russia

School of Medicine University of Western Australia Crawley 6009 Australia

The Wellcome Trust Sanger Institute Genome Campus Hinxton Cambridge CB10 1SA UK

Wellcome Trust MRC Stem Cell Institute Cambridge Biomedical Campus University of Cambridge CB2 0XY Cambridge UK

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Distinct organization of adaptive immunity in the long-lived rodent Spalax galili