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Distinct Genetic Pathways Define Pre-Leukemic and Compensatory Clonal Hematopoiesis in Shwachman-Diamond Syndrome

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Distinct Genetic Pathways Define Pre-Leukemic and Compensatory Clonal Hematopoiesis in Shwachman-Diamond Syndrome bioRxiv preprint doi: https://doi.org/10.1101/2020.06.04.134692; this version posted June 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Distinct genetic pathways define pre-leukemic and compensatory clonal hematopoiesis in Shwachman-Diamond syndrome Alyssa L. Kennedy1,2, Kasiani C. Myers3,4, James Bowman1,2,5, Christopher J. Gibson6, Nicholas D. Camarda7 , Elissa Furutani1,2, Gwen M. Muscato8, Robert H. Klein7,8, Kaitlyn Ballotti9, Shanshan Liu10, Chad E. Harris9, Ashley Galvin9, Maggie Malsch9, David Dale11, John M. Gansner12, Taizo A. Nakano13, Alison Bertuch14, Adrianna Vlachos15,16, Jeffrey M. Lipton15,16 , Paul Castillo17, James Connelly18, Jane Churpek19, John R. Edward20, Nobuko Hijiya21 , Richard H. Ho18, Inga Hofmann22, James N. Huang23,24, Siobán Keel25, Adam Lamble26, Bonnie W. Lau27,28, Maxim Norkin29, Elliot Stieglitz23,30, Wendy Stock31, Kelly Walkovich32, Steffen Boettcher33 , Christian Brendel1,2,34, Mark D. Fleming35, Stella M. Davies3,4, Edie A. Weller1,10, Christopher Bahl1,2,5, Scott L. Carter8,36, Akiko Shimamura1,2*, and R. Coleman Lindsley6* 1Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 2Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA, 3Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA, 4Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, 5Institute for Protein Innovation, Boston, MA, USA, 6Department of Medical Oncology, Division of Hematological Malignancies Dana-Farber Cancer Institute, Boston, MA, USA, 7Dana-Farber Cancer Institute, Boston, MA, USA, 8Broad Institute, Boston MA, USA, 9Boston Children’s Hospital, Boston, MA, USA, 10Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA, 11Department of Internal Medicine, University of Washington, Seattle, WA, USA, 12Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA, 13Center for Cancer and Blood Disorders, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, USA, 14Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA, 15Division of Hematology/Oncology and Cellular Therapy, Cohen Children's Medical Center of New York, New Hyde Park, NY, USA, 16Zucker School of Medicine at Hofstra/Northwell School of Medicine, Hempstead, NY, USA, 17Shands Children's Hospital, Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Florida, Gainesville, FL, USA , 18Department of Pediatrics, Division of Pediatric Hematology Oncology, Vanderbilt University Medical Center, Nashville, TN, USA, 19Department of Medicine, Section of Hematology, Oncology, and Palliative Care, The University of Wisconsin- Madison, Madison, Wisconsin, USA, 20Indiana Blood and Marrow Transplantation, Indianapolis, IN, USA, 21Department of Pediatrics, Columbia University Medical Center, New York, NY, USA, 22Department of Pediatrics, Division of Pediatric Hematology/Oncology and BMT, University of Wisconsin, Madison ,WI, USA, 23Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA, 24Division of Pediatric Allergy, Immunology, and Blood & Marrow Transplantation, UCSF Benioff Children's Hospital, San Francisco, California, USA, 25Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, 26Division of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA, 27Dartmouth-Hitchcock Medical Center, Pediatric Hematology Oncology, Geisel School of Medicine, Lebanon, NH, USA, 28Department of Medicine, University of Florida, Gainesville, FL, USA, 29Division of Cancer Medicine, Baptist MD Anderson Cancer Center, Jacksonville, FL, USA, 30UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA, 31Department of Medicine, University of Chicago, Chicago, IL, USA, 32Division of Pediatric Hematology- Oncology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA, 33Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland, 34Harvard Stem Cell Institute, Cambridge, MA, USA, 35Department of Pathology, Boston Children's Hospital, Boston, MA, USA, 36Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, MA, USA *Equal Contribution 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.04.134692; this version posted June 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Shwachman-Diamond syndrome (SDS) is an inherited bone marrow failure syndrome with predisposition to developing leukemia. We found that multiple independent somatic hematopoietic clones arise early in life, most commonly harboring heterozygous mutations in EIF6 or TP53. EIF6 mutations cause functional compensation for the germline deficiency by alleviating the SDS ribosome joining defect, improving translation, and reducing p53 activation. TP53 mutations decrease checkpoint activation without affecting ribosome assembly. We link development of leukemia with acquisition of biallelic TP53 alterations. Our results define distinct pathways of clonal selection driven by germline fitness constraint and provide a mechanistic framework for clinical surveillance. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.04.134692; this version posted June 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genetic predisposition to myeloid malignancy comprises a separate disease entity in the WHO classification1. Diagnosis of leukemia predisposition provides potential opportunities for early intervention, but precision medicine approaches to clinical surveillance are lacking. Shwachman-Diamond syndrome (SDS) is a genetic disorder associated with a high risk of developing myeloid neoplasms early in life2–4. SDS is predominantly caused by biallelic germline mutations in the SBDS gene5. The SBDS protein promotes formation of the mature, translationally active 80S ribosome by cooperating with the GTPase EFL1 to catalyze the removal of EIF6 from the 60S ribosomal subunit. In the absence of SBDS, EIF6 remains bound to the 60S subunit and sterically inhibits its joining to the 40S subunit6. In SDS cells, SBDS deficiency impairs eviction of EIF6 from the nascent 60S subunit, resulting in decreased ribosomal subunit joining and reduced translation efficiency6. Activation of cellular senescence pathways by ribosome stress incurs a global fitness defect in hematopoietic stem and progenitor cells which manifests clinically as bone marrow failure7–9. Survival of patients with SDS who develop myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) is poor10. Therefore, a central goal in clinical care of SDS patients is to identify incipient leukemic transformation and initiate pre-emptive treatment with allogeneic stem cell transplantation. Current surveillance strategies for patients with SDS and other leukemia predisposition syndromes rely on monitoring hematologic status by serial peripheral blood counts to identify worsening cytopenias and bone marrow examinations to identify morphologic changes or development of clonal chromosomal abnormalities11. These tests are insensitive and detect abnormalities that are late signs of impending transformation. 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.04.134692; this version posted June 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The p53 tumor suppressor pathway is activated by defective ribosome biogenesis and aberrant protein translation7,12. Somatic TP53 mutations have been observed in patients with SDS who develop MDS13, raising the possibility that next-generation sequencing could be integrated into surveillance for somatic clones with enhanced leukemia potential. However, TP53 mutations have also been identified in SDS patients without myeloid neoplasms (MN)14, suggesting that additional factors must be uncovered before implementing molecular surveillance as a predictive tool in SDS. To understand the molecular pathogenesis of MN in patients with SDS, we characterized the presence and dynamics of somatic mutations in serial, clinically annotated samples collected prospectively from patients enrolled in the North American SDS Registry and studied the functional consequences of recurrently mutated pathways. Our results show that SDS patients develop frequent somatic hematopoietic clones that either bypass or compensate for the germline defect in ribosome function, and that detection of biallelic TP53 alterations
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