Anand, S.

Barbera-Mourelle, A.

Bousquets Muñoz, P.

Delgado, J.

Dunford, A.

Duran-Ferrer, M.

Fernandes, S.

Getz, G.

Hahn, C.

Hess, J.

Knisbacher, B.

Kretzmer, H. 

Lin, Z.

Meissner, A. 

Nadeu, F.

Rassenti, L.

Shaughnessy, C.

Sivina, M.

Stevenson, K.

Tausch, E.

Taylor-Weiner, A.

Wiestner, A.

English

MPG.PuRe

641.CLL: BIOLOGY AND PATHOPHYSIOLOGY, EXCLUDING THERAPY  |  NOVEMBER 5, 2020The CLL-1100 Project: Towards Complete GenomicCharacterization and Improved Prognostics for CLLBinyamin A. Knisbacher, PhD,*,1  Ziao Lin, BS,*,1,2  Cynthia K. Hahn, MD PhD,*,1,3  Ferran Nadeu,*,4,5 Martí Duran-Ferrer,*,4,5  Kristen E. Stevenson, MS,*,6  Eugen Tausch, MD,*,7  Alex Barbera-Mourelle,*,1,8  Andrew Dunford,*,1  Shankara Anand,*,1  Julio Delgado, MD,5,9,4  JulianM. Hess,*,1  Amaro Taylor-Weiner, PhD,*,1  Helene Kretzmer, PhD,*,10  Pablo BousquetsMuñoz,*,11  Conner J. Shaughnessy,*,12  Stacey M. Fernandes, BS,*,3,13  Mariela Sivina,*,14 Laura Z. Rassenti, PhD,15  Alexander Meissner, PhD,*,1,10,16  Adrian Wiestner, MD PhD,17 Jan A. Burger, MD PhD,18  Thomas J. Kipps, MD PhD,15  Jennifer R Brown, MD PhD,2,12 Michael Hallek,19,20,21  François Aguet, PhD,*,1  Donna S. Neuberg, ScD,6  Xose S Puente, PhD,*,11 Chip Stewart, PhD,*,1  José I. Martín-Subero, PhD,*,22,4,5,23  Stephan Stilgenbauer, MD,24,25 Catherine J. Wu, MD,3,1,26,2  Elías Campo, MD PhD,5,23,4,27  Gad Getz, PhD*,2,8,1,281Broad Institute of MIT and Harvard, Cambridge, MA2Harvard Medical School, Boston, MA3Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA4Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain5Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain6Department of Data Science, Dana-Farber Cancer Institute, Boston, MA7Department of Internal Medicine III, Ulm University, Ulm, Germany8Center for Cancer Research, Massachusetts General Hospital, Boston, MA9Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona, Spain10Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany11Departamento de Bioquímica y Biología Molecular, InstitutoUniversitario de Oncología, Universidad de Oviedo, Oviedo, Spain12Dana-Farber Cancer Institute, Boston, MA13Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA14Department of Leukemia, UT M.D. Anderson Cancer Center, Houston, TX15Moores Cancer Center, University of California, San Diego, La Jolla, CA16Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA17Laboratory of Lymphoid Malignancies, National Heart, Lung,and Blood Institute, National Institutes of Health, Bethesda, MD18Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX19Center for Molecular Medicine, Cologne, Germany20Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn CologneDuesseldorf and German CLL Study Group, University of Cologne, Cologne, Germany21Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany22Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain23Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain24Department of Internal Medicine I, Saarland University Medical School, Homburg, Germany25Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany26Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA27Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain28Department of Pathology, Massachusetts General Hospital, Boston, MABlood (2020) 136 (Supplement 1) : 3.http://doi.org/10.1182/blood-2020-140987Although chronic lymphocytic leukemia (CLL) has been consistently at the forefront of genomic discovery,complete characterization of its genomic landscape has been limited by sample size and cohort diversity.To address this challenge, we assembled and generated new genomic data from CLL samples from~1100 patients ('CLL-1100'). In total, we analyzed 984 whole-exome sequences (WES), 177 whole-genome sequences (WGS), RNA-sequencing of 717 cases, and 758 methylome profiles.With our large dataset, we had increased sensitivity to detect candidate drivers even with frequency lessthan 1%. By applying MutSig2CV to the WES data, we identified 89 putative cancer driver genes (q<0.1),46 of which were novel. New candidate driver genes highlighted cellular pathways including metabolism(e.g. GPS2, CHKB, CD36) and protein synthesis/stability (e.g. RPS16, EEF1A1, USP8), thus expandingour knowledge of the processes contributing to CLL leukemogenesis. Analysis of somatic copy numberalterations (CNAs) using GISTIC2 confirmed both high frequency and rarely reported arm-level events, aswell as identified 6 novel focal amplifications and 54 deletions (35 new). Many of these genomic regionsprimarily contained known CLL drivers but also novel drivers found based on somatic single nucleotidevariants (e.g. DDX5), providing further evidence that these likely contribute to pathogenesis. Thus, byapproximately doubling the previously reported number of driver genes in CLL, we are able to assign aputative driving event to >92% of CLL samples within the cohort.The gain in power was most evident in our characterization of the two major molecular subtypes ofCLL, those with mutated (M-CLL) or unmutated (U-CLL) IGHV. Separate WES analyses of 513 M-CLLsand 459 U-CLLs revealed numerous differences between these two subtypes: (i) Mutation analysisrevealed 24 and 59 candidate driver genes in M-CLL and U-CLL, respectively (q<0.1). Only a minorityof genes were significant in both subgroups (n=13; e.g. TP53, SF3B1, NOTCH1), while most weresignificant in either M-CLL (n=11; e.g. MYD88, KLHL6, ITPKB) or U-CLL (n=46; e.g. XPO1, BCOR,KRAS). Moreover, IGHV subtype-specific analyses enabled further sensitivity to identify 13 novel putativedrivers that were not identified in the pan-CLL analysis (e.g. DIS3 in M-CLL; CHKA in U-CLL); (ii) Wefound 37 and 46 putative focal CNA drivers specific to M-CLL and U-CLL; (iii) By evaluating mutationclustering in 3-D protein structures (using CLUMPS), we identified additional drivers enriched in M-CLL(e.g. DICER1) or U-CLL (e.g. RPS23, RAF1, MAP2K2) (q<0.1); and finally (iv) inference of timing andorder of mutation acquisition (by PhylogicNDT) also revealed distinct evolutionary trajectories betweensubtypes. Altogether, these results highlight the divergent genomic landscape of the IGHV subtypes.To further understand disease biology and to develop improved prognostic models for this heterogeneousdisease, we performed transcriptomic analysis of 610 treatment-naive CLLs after correction for knownand inferred covariates (e.g. PEER factors). We identified 8 expression clusters (ECs) that representsubgroups of U-CLL (n=2), M-CLL (n=5) or an intermediate methylation epigenetic subtype (n=1). TheECs were distinguishable based on association (q<0.1) with genomic drivers (e.g. tri(12), SF3B1, XPO1),biological processes (e.g. B-cell differentiation, TNF-# signaling, oxphos, migration, metabolism) and EC-defining marker genes (e.g. LPL, CTLA4, HCK, BCL7A, TOX2). Multivariable analysis including clinicalfeatures and IGHV subtype, revealed distinct outcomes, demonstrating their prognostic potential (OSp=0.013). Of note, ~10% of M-CLLs had U-CLL-like expression profiles and vice-versa. The knowndifference in clinical outcome between the IGHV subtypes was not observed within these non-canonicalcases (OS log-rank p>0.05; p<0.01 for reduced OS difference in comparison to canonical M-CLL vs. U-CLL). Finally, we used machine-learning to robustly classify new samples into these ECs to demonstratethe potential for future clinical utility.Altogether, the CLL-1100 cohort facilitates novel genomic discovery with multiomic insights and cross-validation, showing the distinct molecular spectrum of a diverse patient population. This sets the stage forthe development of comprehensive and more precise genome-based prognostic tools.DisclosuresNadeu: Janssen: Honoraria. Tausch: AbbVie: Consultancy, Honoraria, Research Funding; Roche:Consultancy, Honoraria, Research Funding; Janssen-Cilag: Consultancy, Honoraria, Research Funding.Wiestner: Pharmacyclics LLC, an AbbVie Company, Acerta, Merck, Nurix, Verastem, and Genmab:Research Funding; NIH: Patents & Royalties: NIH. Burger: AstraZeneca: Consultancy; Gilead Sciences:Consultancy, Research Funding; Janssen Pharmaceuticals: Consultancy, Speakers Bureau; Beigene:Research Funding, Speakers Bureau; Pharmacyclics, an AbbVie company: Consultancy, ResearchFunding, Speakers Bureau; TG Therapeutics: Research Funding, Speakers Bureau. Kipps: Ascerta/AstraZeneca, Celgene, Genentech/F. Hoffmann-La Roche, Gilead, Janssen, Loxo Oncology, OcternalTherapeutics, Pharmacyclics/AbbVie, TG Therapeutics, VelosBio, and Verastem: Membership on anentity's Board of Directors or advisory committees; Pharmacyclics/ AbbVie, Breast Cancer ResearchFoundation, MD Anderson Cancer Center, Oncternal Therapeutics, Inc., Specialized Center of Research(SCOR) - The Leukemia and Lymphoma Society (LLS), California Institute for Regenerative Medicine(CIRM): Membership on an entity's Board of Directors or advisory committees, Research Funding,Speakers Bureau; Oncternal Therapeutics, Inc.: Other: Cirmtuzumab was developed by Thomas J. Kippsin the Thomas J. Kipps laboratory and licensed by the University of California to Oncternal Therapeutics,Inc., which provided stock options and research funding to the Thomas J. Kipps laboratory, ResearchFunding; Genentech/Roche: Membership on an entity's Board of Directors or advisory committees,Speakers Bureau; VelosBio: Research Funding; Celgene: Honoraria, Research Funding; Gilead:Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Brown:Gilead, Loxo, Sun, Verastem: Research Funding; Abbvie, Acerta, AstraZeneca, Beigene, Invectys, Juno/Celgene, Kite, Morphosys, Novartis, Octapharma, Pharmacyclics, Sunesis, TG Therapeutics, Verastem:Consultancy; Janssen, Teva: Speakers Bureau. Neuberg: Celgene: Research Funding; Pharmacyclics:Research Funding; Madrigak Pharmaceuticals: Current equity holder in publicly-traded company.Stilgenbauer: Pharmacyclics: Consultancy, Honoraria, Other, Research Funding; Novartis: Consultancy,Honoraria, Other, Research Funding; Mundipharma: Consultancy, Honoraria, Other, Research Funding;Janssen-Cilag: Consultancy, Honoraria, Other: travel support, Research Funding; GlaxoSmithKline:Consultancy, Honoraria, Other: travel support, Research Funding; Gilead: Consultancy, Honoraria,Other: travel support, Research Funding; Genzyme: Consultancy, Honoraria, Other: travel support,Research Funding; Genentech: Consultancy, Honoraria, Other: travel support, Research Funding;F. Hoffmann-LaRoche: Consultancy, Honoraria, Other: travel support, Research Funding; Celgene:Consultancy, Honoraria, Other: travel support, Research Funding; Boehringer-Ingelheim: Consultancy,Honoraria, Other: travel support, Research Funding; Amgen: Consultancy, Honoraria, Other: travelsupport, Research Funding; AbbVie: Consultancy, Honoraria, Other: travel support, Research Funding.Wu: BionTech: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding.Campo: NIH: Consultancy, Other: Co-inventor on a patent related to the MCL35 assay filed at theNational Institutes of Health, United States of America.. Getz: Broad Institute: Patents & Royalties:MuTect, ABSOLUTE, MutSig, MSMuTect, MSMutSig, POLYSOLVER and TensorQTL; Pharmacyclics:Research Funding; IBM: Research Funding; Scorpion Therapeutics: Consultancy, Current equity holder inpublicly-traded company, Other: Founder.Author notes* Asterisk with author names denotes non-ASH members.© 2020 by the American Society of Hematology

The CLL-1100 Project: Towards Complete Genomic Characterization and Improved Prognostics for CLL

http://hdl.handle.net/21.11116/0000-0010-334F-D

The CLL-1100 Project: Towards Complete Genomic Characterization and Improved Prognostics for CLL

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