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Kutz O, Drukewitz S, Krüger A, Aust D, William D, Oster S, Schröck E, Baretton G, Link T, Wimberger P, Kuhlmann JD. Exploring evolutionary trajectories in ovarian cancer patients by longitudinal analysis of ctDNA. Clin Chem Lab Med 2024; 62:2070-2081. [PMID: 38577791 DOI: 10.1515/cclm-2023-1266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES We analysed whether temporal heterogeneity of ctDNA encodes evolutionary patterns in ovarian cancer. METHODS Targeted sequencing of 275 cancer-associated genes was performed in a primary tumor biopsy and in ctDNA of six longitudinal plasma samples from 15 patients, using the Illumina platform. RESULTS While there was low overall concordance between the mutational spectrum of the primary tumor biopsies vs. ctDNA, TP53 variants were the most commonly shared somatic alterations. Up to three variant clusters were detected in each tumor biopsy, likely representing predominant clones of the primary tumor, most of them harbouring a TP53 variant. By tracing these clusters in ctDNA, we propose that liquid biopsy may allow to assess the contribution of ancestral clones of the tumor to relapsed abdominal masses, revealing two evolutionary patterns. In pattern#1, clusters detected in the primary tumor biopsy were likely relapse seeding clones, as they contributed a major share to ctDNA at relapse. In pattern#2, similar clusters were present in tumors and ctDNA; however, they were entirely cleared from liquid biopsy after chemotherapy and were undetectable at relapse. ctDNA private variants were present among both patterns, with some of them mirroring subclonal expansions after chemotherapy. CONCLUSIONS We demonstrate that tracing the temporal heterogeneity of ctDNA, even below exome scale resolution, deciphers evolutionary trajectories in ovarian cancer. Furthermore, we describe two evolutionary patterns that may help to identify relapse seeding clones for targeted therapy.
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Affiliation(s)
- Oliver Kutz
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute for Clinical Genetics, 9169 University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- ERN GENTURIS, 9169 Hereditary Cancer Syndrome Center , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- 9169 Max Planck Institute of Molecular Cell Biology and Genetics , Dresden, Germany
| | - Stephan Drukewitz
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 Technische Universitat Dresden , Dresden, Sachsen, Germany
| | - Alexander Krüger
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 Technische Universitat Dresden , Dresden, Sachsen, Germany
| | - Daniela Aust
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- Institute for Pathology, 9169 University Hospital Carl Gustav Carus at the TU Dresden , Dresden, Germany
- 9169 Tumor- and Normal Tissue Bank of the NCT/UCC Dresden , Dresden, Germany
| | - Doreen William
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute for Clinical Genetics, 9169 University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- ERN GENTURIS, 9169 Hereditary Cancer Syndrome Center , Dresden, Germany
- 9169 National Center for Tumor Diseases Dresden (NCT/UCC) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- 9169 Max Planck Institute of Molecular Cell Biology and Genetics , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 National Center for Tumor Diseases Dresden (NCT/UCC) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden , Dresden, Germany
| | - Sandra Oster
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 National Center for Tumor Diseases Dresden (NCT/UCC) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden , Dresden, Germany
| | - Evelin Schröck
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute for Clinical Genetics, 9169 University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- ERN GENTURIS, 9169 Hereditary Cancer Syndrome Center , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- 9169 Max Planck Institute of Molecular Cell Biology and Genetics , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 Technische Universitat Dresden , Dresden, Sachsen, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden , Dresden, Germany
| | - Gustavo Baretton
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- Institute for Pathology, 9169 University Hospital Carl Gustav Carus at the TU Dresden , Dresden, Germany
- 9169 Tumor- and Normal Tissue Bank of the NCT/UCC Dresden , Dresden, Germany
| | - Theresa Link
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
| | - Jan Dominik Kuhlmann
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
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2
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Kumar JP, Kosek D, Durell SR, Miller Jenkins LM, Debnath S, Coussens NP, Hall MD, Appella DH, Dyda F, Mazur SJ, Appella E. Crystal structure and mechanistic studies of the PPM1D serine/threonine phosphatase catalytic domain. J Biol Chem 2024; 300:107561. [PMID: 39002674 PMCID: PMC11342775 DOI: 10.1016/j.jbc.2024.107561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
Protein phosphatase 1D (PPM1D, Wip1) is induced by the tumor suppressor p53 during DNA damage response signaling and acts as an oncoprotein in several human cancers. Although PPM1D is a potential therapeutic target, insights into its atomic structure were challenging due to flexible regions unique to this family member. Here, we report the first crystal structure of the PPM1D catalytic domain to 1.8 Å resolution. The structure reveals the active site with two Mg2+ ions bound, similar to other structures. The flap subdomain and B-loop, which are crucial for substrate recognition and catalysis, were also resolved, with the flap forming two short helices and three short β-strands that are followed by an irregular loop. Unexpectedly, a nitrogen-oxygen-sulfur bridge was identified in the catalytic domain. Molecular dynamics simulations and kinetic studies provided further mechanistic insights into the regulation of PPM1D catalytic activity. In particular, the kinetic experiments demonstrated a magnesium concentration-dependent lag in PPM1D attaining steady-state velocity, a feature of hysteretic enzymes that show slow transitions compared with catalytic turnover. All combined, these results advance the understanding of PPM1D function and will support the development of PPM1D-targeted therapeutics.
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Affiliation(s)
- Jay Prakash Kumar
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland, United States
| | - Dalibor Kosek
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States
| | - Stewart R Durell
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland, United States
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland, United States
| | - Subrata Debnath
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland, United States
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States
| | - Daniel H Appella
- Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland, United States
| | - Ettore Appella
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland, United States.
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3
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Zhang L, Hsu JI, Braekeleer ED, Chen CW, Patel TD, Martell AG, Guzman AG, Wohlan K, Waldvogel SM, Uryu H, Tovy A, Callen E, Murdaugh RL, Richard R, Jansen S, Vissers L, de Vries BBA, Nussenzweig A, Huang S, Coarfa C, Anastas J, Takahashi K, Vassiliou G, Goodell MA. SOD1 is a synthetic-lethal target in PPM1D-mutant leukemia cells. eLife 2024; 12:RP91611. [PMID: 38896450 PMCID: PMC11186636 DOI: 10.7554/elife.91611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
The DNA damage response is critical for maintaining genome integrity and is commonly disrupted in the development of cancer. PPM1D (protein phosphatase Mg2+/Mn2+-dependent 1D) is a master negative regulator of the response; gain-of-function mutations and amplifications of PPM1D are found across several human cancers making it a relevant pharmacological target. Here, we used CRISPR/Cas9 screening to identify synthetic-lethal dependencies of PPM1D, uncovering superoxide dismutase-1 (SOD1) as a potential target for PPM1D-mutant cells. We revealed a dysregulated redox landscape characterized by elevated levels of reactive oxygen species and a compromised response to oxidative stress in PPM1D-mutant cells. Altogether, our results demonstrate a role for SOD1 in the survival of PPM1D-mutant leukemia cells and highlight a new potential therapeutic strategy against PPM1D-mutant cancers.
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Affiliation(s)
- Linda Zhang
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of MedicineHoustonUnited States
- Medical Scientist Training Program, Baylor College of MedicineHoustonUnited States
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
| | - Joanne I Hsu
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of MedicineHoustonUnited States
- Medical Scientist Training Program, Baylor College of MedicineHoustonUnited States
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
| | - Etienne D Braekeleer
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeUnited Kingdom
| | - Chun-Wei Chen
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
- Integrated Molecular and Biomedical Sciences Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Tajhal D Patel
- Texas Children’s Hospital Department of Hematology/Oncology, Baylor College of MedicineHoustonUnited States
| | - Alejandra G Martell
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Anna G Guzman
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Sarah M Waldvogel
- Medical Scientist Training Program, Baylor College of MedicineHoustonUnited States
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
- Cancer and Cell Biology Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institute of HealthBethesdaUnited States
| | - Rebecca L Murdaugh
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
| | - Rosemary Richard
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
| | - Sandra Jansen
- Donders Centre for Neuroscience, Radboud University Medical CenterNijmegenNetherlands
| | - Lisenka Vissers
- Donders Centre for Neuroscience, Radboud University Medical CenterNijmegenNetherlands
| | - Bert BA de Vries
- Donders Centre for Neuroscience, Radboud University Medical CenterNijmegenNetherlands
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institute of HealthBethesdaUnited States
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Department of Education, Innovation and Technology, Advanced Technology Cores, University of TexasHoustonUnited States
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Jamie Anastas
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer CenterHoustonUnited States
- Department of Genome Medicine, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - George Vassiliou
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeUnited Kingdom
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Center for Cell and Gene TherapyHoustonUnited States
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Walkley SU, Molholm S, Jordan B, Marion RW, Wasserstein M. Using team-based precision medicine to advance understanding of rare genetic brain disorders. J Neurodev Disord 2024; 16:10. [PMID: 38491427 PMCID: PMC10941544 DOI: 10.1186/s11689-024-09518-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024] Open
Abstract
We describe a multidisciplinary teamwork approach known as "Operation IDD Gene Team" developed by the Rose F. Kennedy Intellectual and Developmental Disabilities Research Center (RFK IDDRC) at the Albert Einstein College of Medicine. This initiative brings families affected by rare genetic diseases that cause intellectual and developmental disability together with physicians, basic scientists, and their trainees. At team meetings, family members share their child's medical and personal history, physicians describe the broader clinical consequences of the condition, and scientists provide accessible tutorials focused on the fundamental biology of relevant genes. When appropriate, possible treatment approaches are also discussed. The outcomes of team meetings have been overwhelmingly positive, with families not only expressing deep gratitude, but also becoming empowered to establish foundations dedicated to their child's specific condition. Physicians, and in particular the scientists and their trainees, have gained a deeper understanding of challenges faced by affected families, broadening their perspective on how their research can extend beyond the laboratory. Remarkably, research by the scientists following the Gene Team meetings have often included focus on the actual gene variants exhibited by the participating children. As these investigations progress and newly created foundations expand their efforts, national as well as international collaborations are forged. These developments emphasize the importance of rare diseases as windows into previously unexplored molecular and cellular processes, which can offer fresh insights into both normal function as well as more common diseases. Elucidating the mechanisms of and treatments for rare and ultra-rare diseases thus has benefits for all involved-families, physicians, and scientists and their trainees, as well as the broader medical community. While the RFK IDDRC's Operation IDD Gene Team program has focused on intellectual disabilities affecting children, we believe it has the potential to be applied to rare genetic diseases impacting individuals of any age and encompassing a wide variety of developmental disorders affecting multiple organ systems.
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Affiliation(s)
- Steven U Walkley
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Sophie Molholm
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bryen Jordan
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Robert W Marion
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Melissa Wasserstein
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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5
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Gibson CJ, Lindsley RC, Gondek LP. Clonal hematopoiesis in the setting of hematopoietic cell transplantation. Semin Hematol 2024; 61:9-15. [PMID: 38429201 PMCID: PMC10978245 DOI: 10.1053/j.seminhematol.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/12/2024] [Accepted: 01/28/2024] [Indexed: 03/03/2024]
Abstract
Clonal hematopoiesis (CH) in autologous transplant recipients and allogeneic transplant donors has genetic features and clinical associations that are distinct from each other and from non-cancer populations. CH in the setting of autologous transplant is enriched for mutations in DNA damage response pathway genes and is associated with adverse outcomes, including an increased risk of therapy-related myeloid neoplasm and inferior overall survival. Studies of CH in allogeneic transplant donors have yielded conflicting results but have generally shown evidence of potentiated alloimmunity in recipients, with some studies showing an association with favorable recipient outcomes.
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Affiliation(s)
| | - R Coleman Lindsley
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA
| | - Lukasz P Gondek
- Division of Hematologic Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD.
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6
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Collie GW, Clark MA, Keefe AD, Madin A, Read JA, Rivers EL, Zhang Y. Screening Ultra-Large Encoded Compound Libraries Leads to Novel Protein-Ligand Interactions and High Selectivity. J Med Chem 2024; 67:864-884. [PMID: 38197367 PMCID: PMC10823476 DOI: 10.1021/acs.jmedchem.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
The DNA-encoded library (DEL) discovery platform has emerged as a powerful technology for hit identification in recent years. It has become one of the major parallel workstreams for small molecule drug discovery along with other strategies such as HTS and data mining. For many researchers working in the DEL field, it has become increasingly evident that many hits and leads discovered via DEL screening bind to target proteins with unique and unprecedented binding modes. This Perspective is our attempt to analyze reports of DEL screening with the purpose of providing a rigorous and useful account of the binding modes observed for DEL-derived ligands with a focus on binding mode novelty.
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Affiliation(s)
| | | | | | | | | | | | - Ying Zhang
- X-Chem,
Inc., Waltham, Massachusetts 02453, United States
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7
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Zhang L, Hsu JI, Braekeleer ED, Chen CW, Patel TD, Martell AG, Guzman AG, Wohlan K, Waldvogel SM, Urya H, Tovy A, Callen E, Murdaugh R, Richard R, Jansen S, Vissers L, de Vries BB, Nussenzweig A, Huang S, Coarfa C, Anastas JN, Takahashi K, Vassiliou G, Goodell MA. SOD1 is a synthetic lethal target in PPM1D-mutant leukemia cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.31.555634. [PMID: 37693622 PMCID: PMC10491179 DOI: 10.1101/2023.08.31.555634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The DNA damage response is critical for maintaining genome integrity and is commonly disrupted in the development of cancer. PPM1D (protein phosphatase, Mg2+/Mn2+ dependent 1D) is a master negative regulator of the response; gain-of-function mutations and amplifications of PPM1D are found across several human cancers making it a relevant pharmacologic target. Here, we used CRISPR/Cas9 screening to identify synthetic-lethal dependencies of PPM1D, uncovering superoxide dismutase-1 (SOD1) as a potential target for PPM1D-mutant cells. We revealed a dysregulated redox landscape characterized by elevated levels of reactive oxygen species and a compromised response to oxidative stress in PPM1D-mutant cells. Altogether, our results demonstrate the protective role of SOD1 against oxidative stress in PPM1D-mutant leukemia cells and highlight a new potential therapeutic strategy against PPM1D-mutant cancers.
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Affiliation(s)
- Linda Zhang
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, TX
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
| | - Joanne I. Hsu
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, TX
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
| | - Etienne D. Braekeleer
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge
| | - Chun-Wei Chen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
- Integrated Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX
| | - Tajhal D. Patel
- Texas Children’s Hospital Department of Hematology/Oncology, Baylor College of Medicine, Houston, TX
| | - Alejandra G. Martell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Anna G. Guzman
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Sarah M. Waldvogel
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX
| | - Hidetaka Urya
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institute of Health, Bethesda, MD
| | - Rebecca Murdaugh
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Rosemary Richard
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Sandra Jansen
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka Vissers
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B.A. de Vries
- Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andre Nussenzweig
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Department of Education, Innovation and Technology, Advanced Technology Cores
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Jamie N. Anastas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Education, Innovation and Technology, Advanced Technology Cores
| | - George Vassiliou
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge
| | - Margaret A. Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Houston, TX
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8
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Martinikova AS, Stoyanov M, Oravetzova A, Kok YP, Yu S, Dobrovolna J, Janscak P, van Vugt M, Macurek L. PPM1D activity promotes the replication stress caused by cyclin E1 overexpression. Mol Oncol 2024; 18:6-20. [PMID: 37067201 PMCID: PMC10766204 DOI: 10.1002/1878-0261.13433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/09/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023] Open
Abstract
Oncogene-induced replication stress has been recognized as a major cause of genome instability in cancer cells. Increased expression of cyclin E1 caused by amplification of the CCNE1 gene is a common cause of replication stress in various cancers. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and has been implicated in termination of the cell cycle checkpoint. Amplification of the PPM1D gene or frameshift mutations in its final exon promote tumorigenesis. Here, we show that PPM1D activity further increases the replication stress caused by overexpression of cyclin E1. In particular, we demonstrate that cells expressing a truncated mutant of PPM1D progress faster from G1 to S phase and fail to complete licensing of the replication origins. In addition, we show that transcription-replication collisions and replication fork slowing caused by CCNE1 overexpression are exaggerated in cells expressing the truncated PPM1D. Finally, replication speed and accumulation of focal DNA copy number alterations caused by induction of CCNE1 expression was rescued by pharmacological inhibition of PPM1D. We propose that increased activity of PPM1D suppresses the checkpoint function of p53 and thus promotes genome instability in cells expressing the CCNE1 oncogene.
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Affiliation(s)
- Andra S. Martinikova
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Miroslav Stoyanov
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Anna Oravetzova
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Yannick P. Kok
- Department of Medical Oncology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Shibo Yu
- Department of Pathology and Medical Biology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Jana Dobrovolna
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Pavel Janscak
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
- Institute of Molecular Cancer ResearchUniversity of ZurichSwitzerland
| | - Marcel van Vugt
- Department of Medical Oncology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
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9
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Burocziova M, Danek P, Oravetzova A, Chalupova Z, Alberich-Jorda M, Macurek L. Ppm1d truncating mutations promote the development of genotoxic stress-induced AML. Leukemia 2023; 37:2209-2220. [PMID: 37709843 PMCID: PMC10624630 DOI: 10.1038/s41375-023-02030-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Hematopoietic stem cells (HSCs) ensure blood cell production during the life-time of an organism, and to do so they need to balance self-renewal, proliferation, differentiation, and migration in a steady state as well as in response to stress or injury. Importantly, aberrant proliferation of HSCs leads to hematological malignancies, and thus, tight regulation by various tumor suppressor pathways, including p53, is essential. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and promotes cell survival upon induction of genotoxic stress. Truncating mutations in the last exon of PPM1D lead to the production of a stable, enzymatically active protein and are commonly associated with clonal hematopoiesis. Using a transgenic mouse model, we demonstrate that truncated PPM1D reduces self-renewal of HSCs in basal conditions but promotes the development of aggressive AML after exposure to ionizing radiation. Inhibition of PPM1D suppressed the colony growth of leukemic stem and progenitor cells carrying the truncated PPM1D, and remarkably, it provided protection against irradiation-induced cell growth. Altogether, we demonstrate that truncated PPM1D affects HSC maintenance, disrupts normal hematopoiesis, and that its inhibition could be beneficial in the context of therapy-induced AML.
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Affiliation(s)
- Monika Burocziova
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
- Department of Hemato-oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Petr Danek
- Department of Hemato-oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Anna Oravetzova
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Zuzana Chalupova
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Meritxell Alberich-Jorda
- Department of Hemato-oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic.
- Childhood Leukaemia Investigation Prague, Department of Pediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague, University Hospital Motol, V Uvalu 84, Praha, 150 06, Czech Republic.
| | - Libor Macurek
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic.
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10
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Belotserkovskaya E, Golotin V, Uyanik B, Demidov ON. Clonal haematopoiesis - a novel entity that modifies pathological processes in elderly. Cell Death Discov 2023; 9:345. [PMID: 37726289 PMCID: PMC10509183 DOI: 10.1038/s41420-023-01590-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 06/02/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
Progress in the development of new sequencing techniques with wider accessibility and higher sensitivity of the protocol of deciphering genome particularities led to the discovery of a new phenomenon - clonal haematopoiesis. It is characterized by the presence in the bloodstream of elderly people a minor clonal population of cells with mutations in certain genes, but without any sign of disease related to the hematopoietic system. Here we will review this recent advancement in the field of clonal haematopoiesis and how it may affect the disease's development in old age.
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Affiliation(s)
| | - Vasily Golotin
- Institute of Cytology RAS, 4 Tikhoretskii prospect, St. Petersburg, 194064, Russia
- Saint Petersburg bra-nch of "VNIRO" ("Gos-NOIRH" named after L.S. Berg), Saint Petersburg, Russia
| | - Burhan Uyanik
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, 7 Boulevard Jeanne d'Arc, Dijon, 21000, France
| | - Oleg N Demidov
- Institute of Cytology RAS, 4 Tikhoretskii prospect, St. Petersburg, 194064, Russia.
- INSERM UMR1231, Laboratory of Excellence LipSTIC and label Ligue Nationale contre le Cancer, 7 Boulevard Jeanne d'Arc, Dijon, 21000, France.
- Sirius University of Science and Technology, 1 Olimpiiskii pr-t, Sochi, 354340, Russian Federation.
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11
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Zanti M, Loizidou MA, O’Mahony DG, Dorling L, Dennis J, Devilee P, Easton DF, Panayiotidis MI, Hadjisavvas A, Michailidou K. Multi-gene panel testing and association analysis in Cypriot breast cancer cases and controls. Front Genet 2023; 14:1248492. [PMID: 37790698 PMCID: PMC10544326 DOI: 10.3389/fgene.2023.1248492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction: It is estimated that around 5% of breast cancer cases carry pathogenic variants in established breast cancer susceptibility genes. However, the underlying prevalence and gene-specific population risk estimates in Cyprus are currently unknown. Methods: We performed sequencing on a population-based case-control study of 990 breast cancer cases and 1094 controls from Cyprus using the BRIDGES sequencing panel. Analyses were conducted separately for protein-truncating and rare missense variants. Results: Protein-truncating variants in established breast cancer susceptibility genes were detected in 3.54% of cases and 0.37% of controls. Protein-truncating variants in BRCA2 and ATM were associated with a high risk of breast cancer, whereas PTVs in BRCA1 and PALB2 were associated with a high risk of estrogen receptor (ER)-negative disease. Among participants with a family history of breast cancer, PTVs in ATM, BRCA2, BRCA1, PALB2 and RAD50 were associated with an increased risk of breast cancer. Furthermore, an additional 19.70% of cases and 17.18% of controls had at least one rare missense variant in established breast cancer susceptibility genes. For BRCA1 and PALB2, rare missense variants were associated with an increased risk of overall and triple-negative breast cancer, respectively. Rare missense variants in BRCA1, ATM, CHEK2 and PALB2 domains, were associated with increased risk of disease subtypes. Conclusion: This study provides population-based prevalence and gene-specific risk estimates for protein-truncating and rare missense variants. These results may have important clinical implications for women who undergo genetic testing and be pivotal for a substantial proportion of breast cancer patients in Cyprus.
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Affiliation(s)
- Maria Zanti
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria A. Loizidou
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Denise G. O’Mahony
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leila Dorling
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Douglas F. Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Mihalis I. Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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12
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Biswas S, Manekar S, Bakshi SR. A Case Study on PPM1D and 9 Other Shared Germline Alterations in a Family. Asian Pac J Cancer Prev 2023; 24:2129-2134. [PMID: 37378944 PMCID: PMC10505862 DOI: 10.31557/apjcp.2023.24.6.2129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The use of high-throughput genotyping techniques has enabled us to identify the rare germline genetic variants with different pathogenicity and penetrance, and understand their role in cancer predisposition. We report here a familial cancer case, a study from Western Indian. METHODS NGS-WES was carried out in a lung cancer patient who has a family history of multiple cancers across generations, including tongue, lung, brain, cervical, urothelial, and esophageal cancer. The results were validated by data mining from available data bases. I-TASSER, RasMol and PyMol were used for protein structure modelling. RESULTS The sequencing by NGS-WES revealed PPM1D c.1654C>T (p.Arg552Ter) mutation in hotspot region exon 6 leading to sudden protein truncation and loss of the C-terminal, due to the substitution of C>T. This mutation was classified as a variant of uncertain significance (VUS), due to limited data on lung cancer, The three unaffected siblings of proband did not show any pathogenic variants and comparative analysis of the four siblings indicate 9 shared genetic variants, classified as benign as per ClinVar. CONCLUSION PPM1D constitutional genetic alterations are rare and uncommon in different ethnic populations. This gene encodes a phosphatase playing role in regulating the P53 tumor suppressor pathway and DNA damage response. Genetic alterations in the PPM1D gene maybe linked to history of gliomas, breast cancer, and ovarian cancer onset in the proband's family. .
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Affiliation(s)
- Shristi Biswas
- Institute of Science, Nirma University, Ahmadabad, Gujarat India.
| | - Swati Manekar
- Institute of Technology, Nirma University, Gujarat India.
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13
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Yun J, Song H, Kim SM, Kim S, Kwon SR, Lee YE, Jeong D, Park JH, Kwon S, Yun H, Lee DS. Analysis of clinical and genomic profiles of therapy-related myeloid neoplasm in Korea. Hum Genomics 2023; 17:13. [PMID: 36814285 PMCID: PMC9948421 DOI: 10.1186/s40246-023-00458-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Therapy-related myeloid neoplasm (T-MN) rarely occurs among cancer survivors, and was characterized by poor prognosis. T-MN has germline predisposition in a considerable proportion. Here, clinical characteristics and germline/somatic variant profiles in T-MN patients were investigated, and the findings were compared with those of previous studies. METHODS A review of medical records, cytogenetic study, targeted sequencing by next-generation sequencing, and survival analysis were performed on 53 patients with T-MN at a single institution in Korea. RESULTS The patients were relatively younger compared to T-MN patients in other studies. Our T-MN patients showed a high frequency of complex karyotypes, -5/del(5q), and -7/del(7q), which was similar to the Japanese study group but higher than the Australian study group. The most common primary disease was non-Hodgkin lymphoma, followed by breast cancer. The detailed distributions of primary diseases were different across study groups. Seven patients (13.2%) harbored deleterious presumed/potential germline variants in cancer predisposition genes (CPG) such as BRIP1, CEBPA, DDX41, FANCM, NBN, NF1, and RUNX1. In the somatic variant profile, TP53 was the most frequently mutated gene, which was consistent with the previous studies about T-MN. However, the somatic variant frequency in our study group was lower than in other studies. Adverse factors for overall survival were male sex, older age, history of previous radiotherapy, previous longer cytotoxic therapy, and -5/del(5q). CONCLUSION The findings of our study corroborate important information about T-MN patients. As well as a considerable predisposition to CPG, the clinical characteristics and somatic variant profile showed distinctive patterns. Germline variant testing should be recommended for T-MN patients. If the T-MN patients harbor pathogenic germline variants, the family members for stem cell donation should be screened for carrier status through germline variant testing to avoid donor-derived myeloid neoplasm. For the prediction of the prognosis in T-MN patients, sex, age, past treatment history, and cytogenetic findings can be considered.
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Affiliation(s)
- Jiwon Yun
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Laboratory Medicine, Chung-Ang University Hospital, Seoul, Republic of Korea
| | - Hyojin Song
- Department of Genomic Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sung-Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soonok Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seok Ryun Kwon
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Young Eun Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Dajeong Jeong
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Genomic Medicine Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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14
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Skitchenko R, Dinikina Y, Smirnov S, Krapivin M, Smirnova A, Morgacheva D, Artomov M. Case report: Somatic mutations in microtubule dynamics-associated genes in patients with WNT-medulloblastoma tumors. Front Oncol 2023; 12:1085947. [PMID: 36713498 PMCID: PMC9877404 DOI: 10.3389/fonc.2022.1085947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/07/2022] [Indexed: 01/14/2023] Open
Abstract
Medulloblastoma (MB) is the most common pediatric brain tumor which accounts for about 20% of all pediatric brain tumors and 63% of intracranial embryonal tumors. MB is considered to arise from precursor cell populations present during an early brain development. Most cases (~70%) of MB occur at the age of 1-4 and 5-9, but are also infrequently found in adults. Total annual frequency of pediatric tumors is about 5 cases per 1 million children. WNT-subtype of MB is characterized by a high probability of remission, with a long-term survival rate of about 90%. However, in some rare cases there may be increased metastatic activity, which dramatically reduces the likelihood of a favorable outcome. Here we report two cases of MB with a histological pattern consistent with desmoplastic/nodular (DP) and classic MB, and genetically classified as WNT-MB. Both cases showed putative causal somatic protein truncating mutations identified in microtubule-associated genes: ARID2, TUBB4A, and ANK3.
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Affiliation(s)
- Rostislav Skitchenko
- Almazov National Medical Research Centre, St. Petersburg, Russia,Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Yulia Dinikina
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Sergey Smirnov
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Mikhail Krapivin
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Anna Smirnova
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Daria Morgacheva
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Mykyta Artomov
- Almazov National Medical Research Centre, St. Petersburg, Russia,Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia,The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, United States,Department of Pediatrics, Ohio State University, Columbus, OH, United States,*Correspondence: Mykyta Artomov,
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15
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Clinical Impact of Next-Generation Sequencing Multi-Gene Panel Highlighting the Landscape of Germline Alterations in Ovarian Cancer Patients. Int J Mol Sci 2022; 23:ijms232415789. [PMID: 36555431 PMCID: PMC9779064 DOI: 10.3390/ijms232415789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
BRCA1 and BRCA2 are the most frequently mutated genes in ovarian cancer (OC) crucial both for the identification of cancer predisposition and therapeutic choices. However, germline variants in other genes could be involved in OC susceptibility. We characterized OC patients to detect mutations in genes other than BRCA1/2 that could be associated with a high risk of developing OC and permit patients to enter the most appropriate treatment and surveillance program. Next-generation sequencing analysis with a 94-gene panel was performed on germline DNA of 219 OC patients. We identified 34 pathogenic/likely pathogenic variants in BRCA1/2 and 38 in other 21 genes. The patients with pathogenic/likely pathogenic variants in the non-BRCA1/2 genes mainly developed OC alone compared to the other groups that also developed breast cancer or other tumors (p = 0.001). Clinical correlation analysis showed that the low-risk patients were significantly associated with platinum sensitivity (p < 0.001). Regarding PARP inhibitors (PARPi) response, the patients with pathogenic mutations in the non-BRCA1/2 genes had worse PFS and OS. Moreover, a statistically significantly worse PFS was found for every increase of one thousand platelets before PARPi treatment. To conclude, knowledge about molecular alterations in genes beyond BRCA1/2 in OC could allow for more personalized diagnostic, predictive, prognostic, and therapeutic strategies for OC patients.
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16
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Loveday C, Garrett A, Law P, Hanks S, Poyastro-Pearson E, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Walker L, Eccles D, Evans DG, Snape K, Hanson H, Houlston RS, Turnbull C. Analysis of rare disruptive germline mutations in 2,135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes. Ann Oncol 2022; 33:1318-1327. [PMID: 36122798 DOI: 10.1016/j.annonc.2022.09.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Breast cancer has a significant heritable basis, of which approximately 60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility. PATIENTS AND METHODS We included 2,135 invasive breast cancer cases recruited via the BOCS study, a retrospective UK study of familial breast cancer. ELIGIBILITY CRITERIA female, BRCA-negative, white European ethnicity, and one of: i) breast cancer family history, ii) bilateral disease, iii) young age of onset (<30 years), iv) concomitant ovarian cancer. We undertook exome sequencing of cases and performed gene-level burden testing of rare damaging variants against those from 51,377 ethnicity-matched population controls from gnomAD. RESULTS 159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2 and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk (odds ratio = 10.6) down to a population minor allele frequency of 4.6 x 10-5 (1 in 10,799, less than one tenth that of BRCA1)and of PALB2-like risk (odds ratio = 5.0) down to a population minor allele frequency of 2.8 x 10-4 (1 in 1,779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (odds ratio = 2-3) like CHEK2 and ATM. CONCLUSIONS This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.
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Affiliation(s)
- C Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - A Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - P Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - S Hanks
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - E Poyastro-Pearson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - J W Adlard
- Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
| | - J Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester National Health Service (NHS) Trust, Leicester, UK
| | - J Berg
- Division of Medical Sciences, Human Genetics, University of Dundee, Dundee, UK
| | - A F Brady
- North West Thames Regional Genetics Service, Kennedy Galton Centre, London, UK
| | - C Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - C Chapman
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - J Cook
- Sheffield Regional Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - R Davidson
- West of Scotland Regional Genetics Service, Ferguson Smith Centre for Clinical Genetics, Glasgow, UK
| | - A Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol, UK
| | - F Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - L Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - A Henderson
- Northern Genetics Service (Cumbria), Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - L Izatt
- South East Thames Regional Genetics Service, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - A Kumar
- North East Thames Regional Genetics Service, Great Ormond St. Hospital, London, UK
| | - F Lalloo
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - Z Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - P J Morrison
- Belfast Health and Social Care (HSC) Trust & Department of Medical Genetics, Northern Ireland Regional Genetics Service, Queen's University Belfast, Belfast, UK
| | - J Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - M Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - M T Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - L Walker
- Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust, Oxford, UK
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- Individual collaborators and their affiliations are listed in the Appendix
| | - D Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton, UK
| | - D G Evans
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - K Snape
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - H Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - R S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - C Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; Royal Marsden NHS Foundation Hospital, London, UK.
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17
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Zhang L, Hsu JI, Goodell MA. PPM1D in Solid and Hematologic Malignancies: Friend and Foe? Mol Cancer Res 2022; 20:1365-1378. [PMID: 35657598 PMCID: PMC9437564 DOI: 10.1158/1541-7786.mcr-21-1018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/26/2022] [Accepted: 06/01/2022] [Indexed: 01/07/2023]
Abstract
In the face of constant genomic insults, the DNA damage response (DDR) is initiated to preserve genome integrity; its disruption is a classic hallmark of cancer. Protein phosphatase Mg2+/Mn2+-dependent 1D (PPM1D) is a central negative regulator of the DDR that is mutated or amplified in many solid cancers. PPM1D overexpression is associated with increased proliferative and metastatic behavior in multiple solid tumor types and patients with PPM1D-mutated malignancies have poorer prognoses. Recent findings have sparked an interest in the role of PPM1D in hematologic malignancies. Acquired somatic mutations may provide hematopoietic stem cells with a competitive advantage, leading to a substantial proportion of mutant progeny in the peripheral blood, an age-associated phenomenon termed "clonal hematopoiesis" (CH). Recent large-scale genomic studies have identified PPM1D to be among the most frequently mutated genes found in individuals with CH. While PPM1D mutations are particularly enriched in patients with therapy-related myeloid neoplasms, their role in driving leukemic transformation remains uncertain. Here, we examine the mechanisms through which PPM1D overexpression or mutation may drive malignancy by suppression of DNA repair, cell-cycle arrest, and apoptosis. We also discuss the divergent roles of PPM1D in the oncogenesis of solid versus hematologic cancers with a view to clinical implications and new therapeutic avenues.
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Affiliation(s)
- Linda Zhang
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Joanne I. Hsu
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Margaret A. Goodell
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Corresponding Author: Margaret A. Goodell, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030. E-mail:
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18
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Development of Antibody-like Proteins Targeting the Oncogenic Ser/Thr Protein Phosphatase PPM1D. Processes (Basel) 2022. [DOI: 10.3390/pr10081501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
PPM1D, a protein Ser/Thr phosphatase, is overexpressed in various cancers and functions as an oncogenic protein by inactivating the p53 pathway. Therefore, molecules that bind PPM1D are expected to be useful anti-cancer agents. In this study, we constructed a phage display library based on the antibody-like small molecule protein adnectin and screened for PPM1D-specific binding molecules. We identified two adnectins, PMDB-1 and PMD-24, that bind PPM1D specific B-loop and PPM1D430 as targets, respectively. Specificity analyses of these recombinant proteins using other Ser/Thr protein phosphatases showed that these molecules bind to only PPM1D. Expression of PMDB-1 in breast cancer-derived MCF-7 cells overexpressing endogenous PPM1D stabilized p53, indicating that PMDB-1 functions as an inhibitor of PPM1D. Furthermore, MTT assay exhibited that MCF-7 cells expressing PMDB-1 showed inhibition of cell proliferation. These data suggest that the adnectin PMDB-1 identified in this study can be used as a lead compound for anti-cancer drugs targeting intracellular PPM1D.
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19
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Yin S, Yang L, Zheng Y, Zang R. MS: Wip1 suppresses angiogenesis through the STAT3-VEGF signalling pathway in serous ovarian cancer. J Ovarian Res 2022; 15:56. [PMID: 35538489 PMCID: PMC9087943 DOI: 10.1186/s13048-022-00990-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/25/2022] [Indexed: 12/20/2022] Open
Abstract
Multifaceted functions of the so-called “oncogene” Wip1 have been reported in a previous study, while its actual role remains to be explored in serous ovarian cancer (SOC). In this study, by performing bioinformatic analysis with a public database and immunohistochemical staining of Wip1 in tumour tissue from SOC, we concluded that decreased expression of Wip1 was associated with a higher rate of tumour metastasis and platinum-based therapy resistance and increased ascites volume, which led to poorer prognosis in SOC patients. We also found that overexpression of Wip1 in SKOV3 cells decreased the levels of several cytokines, including VEGF, by secretome profiling analysis, and Wip1 overexpression suppressed angiogenesis both in vitro and in vivo. Mechanistic studies indicated that overexpression of Wip1 decreased the expression of VEGF at both the protein and mRNA levels and that the inhibitory effect was mediated by dephosphorylation of STAT3 at Ser727. Our study uncovered the role of Wip1 in SOC and provides a novel therapeutic strategy for suppressing angiogenesis.
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Affiliation(s)
- Sheng Yin
- Department of Gynaecologic Oncology, Ovarian Cancer Program, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Obstetrics and Gynecology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lina Yang
- Department of Obstetrics and Gynecology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yiyan Zheng
- Department of Gynaecologic Oncology, Ovarian Cancer Program, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongyu Zang
- Department of Gynaecologic Oncology, Ovarian Cancer Program, Zhongshan Hospital, Fudan University, Shanghai, China.
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20
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Liu JZ, Chen CY, Tsai EA, Whelan CD, Sexton D, John S, Runz H. The burden of rare protein-truncating genetic variants on human lifespan. NATURE AGING 2022; 2:289-294. [PMID: 37117740 PMCID: PMC10154195 DOI: 10.1038/s43587-022-00182-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/20/2022] [Indexed: 04/30/2023]
Abstract
Genetic predisposition has been shown to contribute substantially to the age at which we die. Genome-wide association studies (GWASs) have linked more than 20 loci to phenotypes related to human lifespan1. However, little is known about how lifespan is impacted by gene loss of function. Through whole-exome sequencing of 352,338 UK Biobank participants of European ancestry, we assessed the relevance of protein-truncating variant (PTV) gene burden on individual and parental survival. We identified four exome-wide significant (P < 4.2 × 10-7) human lifespan genes, BRCA1, BRCA2, ATM and TET2. Gene and gene-set, PTV-burden, phenome-wide association studies support known roles of these genes in cancer to impact lifespan at the population level. The TET2 PTV burden was associated with a lifespan through somatic mutation events presumably due to clonal hematopoiesis. The overlap between PTV burden and common variant-based lifespan GWASs was modest, underscoring the value of exome sequencing in well-powered biobank cohorts to complement GWASs for identifying genes underlying complex traits.
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Affiliation(s)
- Jimmy Z Liu
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, USA.
| | - Chia-Yen Chen
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, USA
| | - Ellen A Tsai
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, USA
| | | | - David Sexton
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, USA
| | - Sally John
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, USA
| | - Heiko Runz
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, USA.
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21
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Shah SM, Demidova EV, Lesh RW, Hall MJ, Daly MB, Meyer JE, Edelman MJ, Arora S. Therapeutic implications of germline vulnerabilities in DNA repair for precision oncology. Cancer Treat Rev 2022; 104:102337. [PMID: 35051883 PMCID: PMC9016579 DOI: 10.1016/j.ctrv.2021.102337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022]
Abstract
DNA repair vulnerabilities are present in a significant proportion of cancers. Specifically, germline alterations in DNA repair not only increase cancer risk but are associated with treatment response and clinical outcomes. The therapeutic landscape of cancer has rapidly evolved with the FDA approval of therapies that specifically target DNA repair vulnerabilities. The clinical success of synthetic lethality between BRCA deficiency and poly(ADP-ribose) polymerase (PARP) inhibition has been truly revolutionary. Defective mismatch repair has been validated as a predictor of response to immune checkpoint blockade associated with durable responses and long-term benefit in many cancer patients. Advances in next generation sequencing technologies and their decreasing cost have supported increased genetic profiling of tumors coupled with germline testing of cancer risk genes in patients. The clinical adoption of panel testing for germline assessment in high-risk individuals has generated a plethora of genetic data, particularly on DNA repair genes. Here, we highlight the therapeutic relevance of germline aberrations in DNA repair to identify patients eligible for precision treatments such as PARP inhibitors (PARPis), immune checkpoint blockade, chemotherapy, radiation therapy and combined treatment. We also discuss emerging mechanisms that regulate DNA repair.
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Affiliation(s)
- Shreya M Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Science Scholars Program, Temple University, Philadelphia, PA, United States
| | - Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Kazan Federal University, Kazan, Russian Federation
| | - Randy W Lesh
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Geisinger Commonwealth School of Medicine, Scranton, PA, United States
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Joshua E Meyer
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Martin J Edelman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
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22
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Hong W, Li A, Liu Y, Xiao X, Christiani DC, Hung RJ, McKay J, Field J, Amos CI, Cheng C. Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Cancer Res 2022; 82:199-209. [PMID: 34815255 PMCID: PMC8815061 DOI: 10.1158/0008-5472.can-21-1903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/23/2021] [Accepted: 11/15/2021] [Indexed: 01/12/2023]
Abstract
Clonal hematopoiesis (CH) is a phenomenon caused by expansion of white blood cells descended from a single hematopoietic stem cell. While CH can be associated with leukemia and some solid tumors, the relationship between CH and lung cancer remains largely unknown. To help clarify this relationship, we analyzed whole-exome sequencing (WES) data from 1,958 lung cancer cases and controls. Potential CH mutations were identified by a set of hierarchical filtering criteria in different exonic regions, and the associations between the number of CH mutations and clinical traits were investigated. Family history of lung cancer (FHLC) may exert diverse influences on the accumulation of CH mutations in different age groups. In younger subjects, FHLC was the strongest risk factor for CH mutations. Association analysis of genome-wide genetic variants identified dozens of genetic loci associated with CH mutations, including a candidate SNP rs2298110, which may promote CH by increasing expression of a potential leukemia promoter gene OTUD3. Hundreds of potentially novel CH mutations were identified, and smoking was found to potentially shape the CH mutational signature. Genetic variants and lung cancer risk factors, especially FHLC, correlated with CH. These analyses improve our understanding of the relationship between lung cancer and CH, and future experimental studies will be necessary to corroborate the uncovered correlations. SIGNIFICANCE: Analysis of whole-exome sequencing data uncovers correlations between clonal hematopoiesis and lung cancer risk factors, identifies genetic variants correlated with clonal hematopoiesis, and highlights hundreds of potential novel clonal hematopoiesis mutations.
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Affiliation(s)
- Wei Hong
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ang Li
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Yanhong Liu
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | - Rayjean J Hung
- Mount Sinai Hospital Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - James McKay
- World Health Organization International Agency for Research on Cancer, Lyon CEDEX, France
| | - John Field
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas.
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23
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Takahashi K. Untangling the Relationship Between Clonal Hematopoiesis and Ovarian Cancer Therapies. J Natl Cancer Inst 2021; 114:487-488. [PMID: 34963009 PMCID: PMC9002288 DOI: 10.1093/jnci/djab234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/22/2021] [Indexed: 12/30/2022] Open
Affiliation(s)
- Koichi Takahashi
- Correspondence to: Koichi Takahashi, MD, PhD, Departments of Leukemia and Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 428, Houston, TX 77030, USA (e-mail: )
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24
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Chamberlain V, Drew Y, Lunec J. Tipping Growth Inhibition into Apoptosis by Combining Treatment with MDM2 and WIP1 Inhibitors in p53 WT Uterine Leiomyosarcoma. Cancers (Basel) 2021; 14:cancers14010014. [PMID: 35008180 PMCID: PMC8750798 DOI: 10.3390/cancers14010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
As there is no optimal therapeutic strategy defined for women with advanced or recurrent uLMS, there is an urgent need for the discovery of novel, targeted approaches. One such area of interest is the pharmacological inhibition of the MDM2-p53 interaction with small-molecular-weight MDM2 inhibitors. Growth inhibition and cytotoxic assays were used to evaluate uLMS cell line responses to MDM2 inhibitors as single agents and in combination, qRT-PCR to assess transcriptional changes and Caspase-Glo 3/7 assay to detect apoptosis. RG7388 and HDM201 are potent, selective antagonists of the MDM2-p53 interaction that can effectively stabilise and activate p53 in a dose-dependent manner. GSK2830371, a potent and selective WIP1 phosphatase inhibitor, was shown to significantly potentiate the growth inhibitory effects of RG7388 and HDM201, and significantly increase the mRNA expression of p53 transcriptional target genes in a p53WT cell line at a concentration that has no growth inhibitory effects as a single agent. RG7388, HDM201 and GSK2830371 failed to induce apoptosis as single agents; however, a combination treatment tipped cells into apoptosis from senescence. These data present the possibility of MDM2 and WIP1 inhibitor combinations as a potential treatment option for p53WT uLMS patients that warrants further investigation.
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Affiliation(s)
- Victoria Chamberlain
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (V.C.); (Y.D.)
| | - Yvette Drew
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (V.C.); (Y.D.)
- BC Cancer Centre Vancouver and Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 4EH, Canada
| | - John Lunec
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (V.C.); (Y.D.)
- Correspondence:
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25
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Milosevic J, Treis D, Fransson S, Gallo-Oller G, Sveinbjörnsson B, Eissler N, Tanino K, Sakaguchi K, Martinsson T, Wickström M, Kogner P, Johnsen JI. PPM1D Is a Therapeutic Target in Childhood Neural Tumors. Cancers (Basel) 2021; 13:cancers13236042. [PMID: 34885154 PMCID: PMC8657050 DOI: 10.3390/cancers13236042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Medulloblastoma and neuroblastoma are childhood tumors of the central nervous system or the peripheral nervous system, respectively. These are the most common and deadly tumors of childhood. A common genetic feature of medulloblastoma and neuroblastoma is frequent segmental gain or amplification of chromosome 17q. Located on chromosome 17q23.2 is PPM1D which encodes WIP1, a phosphatase that acts as a regulator of p53 and DNA repair. Overexpression of WIP1 correlates with poor patient prognosis. We investigated the effects of genetic or pharmacologic inhibition of WIP1 activity and found that medulloblastoma and neuroblastoma cells were strongly dependent on WIP1 expression for survival. We also tested a number of small molecule inhibitors of WIP1 and show that SL-176 was the most effective compound suppressing the growth of medulloblastoma and neuroblastoma in vitro and in vivo. Abstract Childhood medulloblastoma and high-risk neuroblastoma frequently present with segmental gain of chromosome 17q corresponding to aggressive tumors and poor patient prognosis. Located within the 17q-gained chromosomal segments is PPM1D at chromosome 17q23.2. PPM1D encodes a serine/threonine phosphatase, WIP1, that is a negative regulator of p53 activity as well as key proteins involved in cell cycle control, DNA repair and apoptosis. Here, we show that the level of PPM1D expression correlates with chromosome 17q gain in medulloblastoma and neuroblastoma cells, and both medulloblastoma and neuroblastoma cells are highly dependent on PPM1D expression for survival. Comparison of different inhibitors of WIP1 showed that SL-176 was the most potent compound inhibiting medulloblastoma and neuroblastoma growth and had similar or more potent effects on cell survival than the MDM2 inhibitor Nutlin-3 or the p53 activator RITA. SL-176 monotherapy significantly suppressed the growth of established medulloblastoma and neuroblastoma xenografts in nude mice. These results suggest that the development of clinically applicable compounds inhibiting the activity of WIP1 is of importance since PPM1D activating mutations, genetic gain or amplifications and/or overexpression of WIP1 are frequently detected in several different cancers.
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Affiliation(s)
- Jelena Milosevic
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Correspondence: (J.M.); (J.I.J.)
| | - Diana Treis
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, 41345 Gothenburg, Sweden; (S.F.); (T.M.)
| | - Gabriel Gallo-Oller
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
| | - Baldur Sveinbjörnsson
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
| | - Nina Eissler
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
| | - Keiji Tanino
- Laboratory of Organic Chemistry II, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan;
| | - Kazuyasu Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan;
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, 41345 Gothenburg, Sweden; (S.F.); (T.M.)
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden; (D.T.); (G.G.-O.); (B.S.); (N.E.) (M.W.); (P.K.)
- Correspondence: (J.M.); (J.I.J.)
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26
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Pharmaco-proteogenomic profiling of pediatric diffuse midline glioma to inform future treatment strategies. Oncogene 2021; 41:461-475. [PMID: 34759345 PMCID: PMC8782719 DOI: 10.1038/s41388-021-02102-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
Diffuse midline glioma (DMG) is a deadly pediatric and adolescent central nervous system (CNS) tumor localized along the midline structures of the brain atop the spinal cord. With a median overall survival (OS) of just 9–11-months, DMG is characterized by global hypomethylation of histone H3 at lysine 27 (H3K27me3), driven by recurring somatic mutations in H3 genes including, HIST1H3B/C (H3.1K27M) or H3F3A (H3.3K27M), or through overexpression of EZHIP in patients harboring wildtype H3. The recent World Health Organization’s 5th Classification of CNS Tumors now designates DMG as, ‘H3 K27-altered’, suggesting that global H3K27me3 hypomethylation is a ubiquitous feature of DMG and drives devastating transcriptional programs for which there are no treatments. H3-alterations co-segregate with various other somatic driver mutations, highlighting the high-level of intertumoral heterogeneity of DMG. Furthermore, DMG is also characterized by very high-level intratumoral diversity with tumors harboring multiple subclones within each primary tumor. Each subclone contains their own combinations of driver and passenger lesions that continually evolve, making precision-based medicine challenging to successful execute. Whilst the intertumoral heterogeneity of DMG has been extensively investigated, this is yet to translate to an increase in patient survival. Conversely, our understanding of the non-genomic factors that drive the rapid growth and fatal nature of DMG, including endogenous and exogenous microenvironmental influences, neurological cues, and the posttranscriptional and posttranslational architecture of DMG remains enigmatic or at best, immature. However, these factors are likely to play a significant role in the complex biological sequelae that drives the disease. Here we summarize the heterogeneity of DMG and emphasize how analysis of the posttranslational architecture may improve treatment paradigms. We describe factors that contribute to treatment response and disease progression, as well as highlight the potential for pharmaco-proteogenomics (i.e., the integration of genomics, proteomics and pharmacology) in the management of this uniformly fatal cancer.
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27
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High Expression of PPM1D Induces Tumors Phenotypically Similar to TP53 Loss-of-Function Mutations in Mice. Cancers (Basel) 2021; 13:cancers13215493. [PMID: 34771656 PMCID: PMC8582939 DOI: 10.3390/cancers13215493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Aberrant expression of the PPM1D gene which encodes a phosphatase called WIP1 is frequently observed in cancers of different origins. WIP1 is a negative regulator of the tumor suppressor p53. Improper inactivation of p53 results in genomic instability and can induce neoplastic transformation. We show that overexpression of PPM1D induces tumors in mice similar to cancers harboring p53 mutations. Our results suggest that PPM1D can act as an oncogenic driver by inducing genomic instability, impaired growth arrest, and apoptotic escape that can result in neoplastic transformation and malignant tumor development. Abstract PPM1D is a negative regulator of p53 and genomic aberrations resulting in increased activity of PPM1D have been observed in cancers of different origins, indicating that PPM1D has oncogenic properties. We established a transgenic mouse model overexpressing PPM1D and showed that these mice developed a wide variety of cancers. PPM1D-expressing mice developed tumors phenotypically and genetically similar to tumors in mice with dysfunctional p53. T-cell lymphoblastic lymphoma was the most frequent cancer observed in these mice (55%) followed by adenocarcinomas (24%), leukemia (12%) and other solid tumors including neuroblastoma. Characterization of T-cell lymphomas in mice overexpressing PPM1D demonstrates Pten-deletion and p53-accumulation similar to mice with p53 loss-of-function. Also, Notch1 mutations which are recurrently observed in T-cell acute lymphoblastic lymphoma (T-ALL) were frequently detected in PPM1D-transgenic mice. Hence, PPM1D acts as an oncogenic driver in connection with cellular stress, suggesting that the PPM1D gene status and expression levels should be investigated in TP53 wild-type tumors.
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Inhibition of the DNA damage response phosphatase PPM1D reprograms neutrophils to enhance anti-tumor immune responses. Nat Commun 2021; 12:3622. [PMID: 34131120 PMCID: PMC8206133 DOI: 10.1038/s41467-021-23330-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
PPM1D/Wip1 is a negative regulator of the tumor suppressor p53 and is overexpressed in several human solid tumors. Recent reports associate gain-of-function mutations of PPM1D in immune cells with worse outcomes for several human cancers. Here we show that mice with genetic knockout of Ppm1d or with conditional knockout of Ppm1d in the hematopoietic system, in myeloid cells, or in neutrophils all display significantly reduced growth of syngeneic melanoma or lung carcinoma tumors. Ppm1d knockout neutrophils infiltrate tumors extensively. Chemical inhibition of Wip1 in human or mouse neutrophils increases anti-tumor phenotypes, p53-dependent expression of co-stimulatory ligands, and proliferation of co-cultured cytotoxic T cells. These results suggest that inhibition of Wip1 in neutrophils enhances immune anti-tumor responses.
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29
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Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study. NPJ Breast Cancer 2021; 7:76. [PMID: 34117267 PMCID: PMC8196173 DOI: 10.1038/s41523-021-00279-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/03/2021] [Indexed: 01/19/2023] Open
Abstract
Breast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. The coding regions and exon–intron boundaries of all candidate genes and 14 previously proposed BC genes were sequenced using custom designed sequencing panels. Pedigree and pathology data were analysed to identify genotype-specific associations. The contribution of ATM, PALB2 and CHEK2 to BC predisposition was confirmed, but not RAD50 and NBN. An overall excess of loss-of-function (LoF) (OR 1.27, p = 9.05 × 10−9) and missense (OR 1.27, p = 3.96 × 10−73) variants was observed in the cases for the 145 candidate genes. Leading candidates harbored LoF variants with observed ORs of 2–4 and individually accounted for no more than 0.79% of the cases. New genes proposed by this study include NTHL1, WRN, PARP2, CTH and CDK9. The new candidate BC predisposition genes identified in BEACCON indicate that much of the remaining genetic causes of high-risk BC families are due to genes in which pathogenic variants are both very rare and convey only low to moderate risk.
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30
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Zheng R, Du M, Ge Y, Gao F, Xin J, Lv Q, Qin C, Zhu Y, Gu C, Wang M, Zhu Q, Guo Z, Ben S, Chu H, Ye D, Zhang Z, Wang M. Identification of low-frequency variants of UGT1A3 associated with bladder cancer risk by next-generation sequencing. Oncogene 2021; 40:2382-2394. [PMID: 33658628 DOI: 10.1038/s41388-021-01672-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 12/31/2022]
Abstract
Although genome-wide association studies (GWASs) have successfully revealed many common risk variants for bladder cancer, the heritability is still largely unexplained. We hypothesized that low-frequency variants involved in bladder cancer risk could reveal the unexplained heritability. Next-generation sequencing of 113 patients and 118 controls was conducted on 81 genes/regions of known bladder cancer GWAS loci. A two-stage validation comprising 3,350 cases and 4,005 controls was performed to evaluate the effects of low-frequency variants on bladder cancer risk. Biological experiments and techniques, including electrophoretic mobility shift assays, CRISPR/Cas9, RNA-Seq, and bioinformatics approaches, were performed to assess the potential functions of low-frequency variants. The low-frequency variant rs28898617 was located in the first exon of UGT1A3 and was significantly associated with increased bladder cancer risk (odds ratio = 1.50, P = 3.10 × 10-6). Intriguingly, rs28898617 was only observed in the Asian population, but monomorphism was observed in the European population. The risk-associated G allele of rs28898617 increased UGT1A3 expression, facilitated UGT1A3 transcriptional activity, and enhanced the binding activity. In addition, UGT1A3 deletion significantly inhibited the proliferation, invasion, and migration of bladder cancer cells and xenograft tumor growth. Mechanistically, UGT1A3 induced LAMC2 expression by binding CBP and promoting histone acetylation, which remarkably promoted the progression of bladder cancer. This is the first targeted sequencing study to reveal that the novel low-frequency variant rs28898617 and its associated gene UGT1A3 are involved in bladder cancer development, providing new insights into the genetic architecture of bladder cancer.
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Affiliation(s)
- Rui Zheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuqiu Ge
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fang Gao
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiang Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chengyuan Gu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengyun Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qiuyuan Zhu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zheng Guo
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China. .,Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.
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31
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Olafsdottir T, Stacey SN, Sveinbjornsson G, Thorleifsson G, Norland K, Sigurgeirsson B, Thorisdottir K, Kristjansson AK, Tryggvadottir L, Sarin KY, Benediktsson R, Jonasson JG, Sigurdsson A, Jonasdottir A, Kristmundsdottir S, Jonsson H, Gylfason A, Oddsson A, Fridriksdottir R, Gudjonsson SA, Zink F, Lund SH, Rognvaldsson S, Melsted P, Steinthorsdottir V, Gudmundsson J, Mikaelsdottir E, Olason PI, Stefansdottir L, Eggertsson HP, Halldorsson BV, Thorsteinsdottir U, Agustsson TT, Olafsson K, Olafsson JH, Sulem P, Rafnar T, Gudbjartsson DF, Stefansson K. Loss-of-Function Variants in the Tumor-Suppressor Gene PTPN14 Confer Increased Cancer Risk. Cancer Res 2021; 81:1954-1964. [PMID: 33602785 DOI: 10.1158/0008-5472.can-20-3065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/16/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
The success of genome-wide association studies (GWAS) in identifying common, low-penetrance variant-cancer associations for the past decade is undisputed. However, discovering additional high-penetrance cancer mutations in unknown cancer predisposing genes requires detection of variant-cancer association of ultra-rare coding variants. Consequently, large-scale next-generation sequence data with associated phenotype information are needed. Here, we used genotype data on 166,281 Icelanders, of which, 49,708 were whole-genome sequenced and 408,595 individuals from the UK Biobank, of which, 41,147 were whole-exome sequenced, to test for association between loss-of-function burden in autosomal genes and basal cell carcinoma (BCC), the most common cancer in Caucasians. A total of 25,205 BCC cases and 683,058 controls were tested. Rare germline loss-of-function variants in PTPN14 conferred substantial risks of BCC (OR, 8.0; P = 1.9 × 10-12), with a quarter of carriers getting BCC before age 70 and over half in their lifetime. Furthermore, common variants at the PTPN14 locus were associated with BCC, suggesting PTPN14 as a new, high-impact BCC predisposition gene. A follow-up investigation of 24 cancers and three benign tumor types showed that PTPN14 loss-of-function variants are associated with high risk of cervical cancer (OR, 12.7, P = 1.6 × 10-4) and low age at diagnosis. Our findings, using power-increasing methods with high-quality rare variant genotypes, highlight future prospects for new discoveries on carcinogenesis. SIGNIFICANCE: This study identifies the tumor-suppressor gene PTPN14 as a high-impact BCC predisposition gene and indicates that inactivation of PTPN14 by germline sequence variants may also lead to increased risk of cervical cancer.
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Affiliation(s)
| | | | | | | | | | - Bardur Sigurgeirsson
- Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kristin Thorisdottir
- Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Arni Kjalar Kristjansson
- Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Redwood City, California
| | - Rafn Benediktsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Endocrinology and Metabolic Medicine, Landspitali University Hospital, Reykjavík, Iceland
| | - Jon G Jonasson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | | | | | - Pall Melsted
- deCODE Genetics/Amgen, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas T Agustsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Endocrinology and Metabolic Medicine, Landspitali University Hospital, Reykjavík, Iceland.,Faculty of Odontology, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | - Karl Olafsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Jon H Olafsson
- Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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32
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Al Hinai ASA, Grob T, Rijken M, Kavelaars FG, Zeilemaker A, Erpelinck-Verschueren CAJ, Sanders MA, Löwenberg B, Jongen-Lavrencic M, Valk PJM. PPM1D mutations appear in complete remission after exposure to chemotherapy without predicting emerging AML relapse. Leukemia 2021; 35:2693-2697. [PMID: 33589749 DOI: 10.1038/s41375-021-01155-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/05/2020] [Accepted: 01/25/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Adil S A Al Hinai
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.,National Genetic Center, Ministry of Health, Muscat, Sultanate of Oman
| | - Tim Grob
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Melissa Rijken
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annelieke Zeilemaker
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Mathijs A Sanders
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mojca Jongen-Lavrencic
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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33
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Phosphatase magnesium-dependent 1 δ (PPM1D), serine/threonine protein phosphatase and novel pharmacological target in cancer. Biochem Pharmacol 2020; 184:114362. [PMID: 33309518 DOI: 10.1016/j.bcp.2020.114362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
Aberrations in DNA damage response genes are recognized mediators of tumorigenesis and resistance to chemo- and radiotherapy. While protein phosphatase magnesium-dependent 1 δ (PPM1D), located on the long arm of chromosome 17 at 17q22-23, is a key regulator of cellular responses to DNA damage, amplification, overexpression, or mutation of this gene is important in a wide range of pathologic processes. In this review, we describe the physiologic function of PPM1D, as well as its role in diverse processes, including fertility, development, stemness, immunity, tumorigenesis, and treatment responsiveness. We highlight both the advances and limitations of current approaches to targeting malignant processes mediated by pathogenic alterations in PPM1D with the goal of providing rationale for continued research and development of clinically viable treatment approaches for PPM1D-associated diseases.
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34
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Husby S, Hjermind Justesen E, Grønbæk K. Protein phosphatase, Mg 2+/Mn 2+-dependent 1D (PPM1D) mutations in haematological cancer. Br J Haematol 2020; 192:697-705. [PMID: 33616916 DOI: 10.1111/bjh.17120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/07/2023]
Abstract
Until recently, the protein phosphatase, Mg2+/Mn2+-dependent 1D (PPM1D) gene had not been examined in haematological cancer, but several studies have now explored the functional role of this gene and its aberrations. It is often mutated in the context of clonal haemopoiesis (including in patients with lymphoma, myeloproliferative neoplasms and myelodysplastic syndrome) and mutations have been associated with exposure to cytotoxic and radiation therapy, development of therapy-related neoplasms and inferior survival. The vast majority of PPM1D mutations found in haematopoietic cells are of the nonsense or frameshift type and located within terminal exon 6. These genetic defects are rarely found in the blood of healthy individuals. PPM1D encodes the PPM1D phosphatase [also named wild-type p53-induced phosphatase 1 (WIP1)], which negatively regulates signalling molecules within the DNA damage response pathway, including tumour suppressor p53. Clonal expansion of PPM1D mutant haematopoietic cells can potentially be prevented with inhibitors; however, human trials are awaited. In the present review, we provide a review of the literature regarding PPM1D and its role in haematological cancer.
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Affiliation(s)
- Simon Husby
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Emma Hjermind Justesen
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Kirsten Grønbæk
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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35
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Development of Specific Inhibitors for Oncogenic Phosphatase PPM1D by Using Ion-Responsive DNA Aptamer Library. Catalysts 2020. [DOI: 10.3390/catal10101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
(1) Background: Ser/Thr protein phosphatase PPM1D is an oncogenic protein. In normal cells, however, PPM1D plays essential roles in spermatogenesis and immune response. Hence, it is necessary to develop novel PPM1D inhibitors without side effects on normal cells. Stimuli-responsive molecules are suitable for the spatiotemporal regulation of inhibitory activity. (2) Methods: In this study, we designed an ion-responsive DNA aptamer library based on G-quadruplex DNA that can change its conformation and function in response to monovalent cations. (3) Results: Using this library, we identified the PPM1D specific inhibitor M1D-Q5F aptamer. The M1D-Q5F aptamer showed anti-cancer activity against breast cancer MCF7 cells. Interestingly, the induction of the structural change resulting in the formation of G-quadruplex upon stimulation by monovalent cations led to the enhancement of the inhibitory activity and binding affinity of M1D-Q5F. (4) Conclusions: These data suggest that the M1D-Q5F aptamer may act as a novel stimuli-responsive anti-cancer agent.
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36
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Lornage X, Quijano-Roy S, Amthor H, Carlier RY, Monnier N, Deleuze JF, Romero NB, Laporte J, Böhm J. Asymmetric muscle weakness due to ACTA1 mosaic mutations. Neurology 2020; 95:e3406-e3411. [DOI: 10.1212/wnl.0000000000010947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/06/2020] [Indexed: 11/15/2022] Open
Abstract
ObjectiveTo characterize 2 unrelated patients with either asymmetric or unilateral muscle weakness at the clinical, genetic, histologic, and ultrastructural level.MethodsThe patients underwent thorough clinical examination, whole-body MRI, and exome sequencing. Muscle morphology was assessed by histology and electron microscopy.ResultsBoth patients presented with early-onset hypotonia, delayed motor milestones, scoliosis, and reduced pulmonary function. Patient P1 manifested unilateral muscle weakness exclusively affecting the left side of the body; the asymmetry was less pronounced in patient P2. Muscle biopsies from both patients showed nemaline rods as the main histopathologic hallmark, and MRI revealed major fatty infiltrations in selective head, proximal, and distal muscles, correlating with the degree of muscle weakness asymmetry. Exome sequencing on blood DNA from both patients identified de novo ACTA1 missense mutations in a small number of reads, suggesting mutation mosaicism. Subsequent Sanger sequencing confirmed the presence of the mutations on muscle DNA, while they were barely detectable on blood DNA.ConclusionsDe novo mutations can occur anytime during embryonic development and may result in a mosaic pattern of affected cells and tissues and lead to the development of an asymmetric clinical picture. The present study points out that mosaic mutations might not be easily detectable on leukocyte DNA and thereby escape routine genetic analysis, and possibly account for a significant number of molecularly undiagnosed patients.
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37
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Martinikova AS, Burocziova M, Stoyanov M, Macurek L. Truncated PPM1D Prevents Apoptosis in the Murine Thymus and Promotes Ionizing Radiation-Induced Lymphoma. Cells 2020; 9:cells9092068. [PMID: 32927737 PMCID: PMC7565556 DOI: 10.3390/cells9092068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 12/20/2022] Open
Abstract
Genome integrity is protected by the cell-cycle checkpoints that prevent cell proliferation in the presence of DNA damage and allow time for DNA repair. The transient checkpoint arrest together with cellular senescence represent an intrinsic barrier to tumorigenesis. Tumor suppressor p53 is an integral part of the checkpoints and its inactivating mutations promote cancer growth. Protein phosphatase magnesium-dependent 1 (PPM1D) is a negative regulator of p53. Although its loss impairs recovery from the G2 checkpoint and promotes induction of senescence, amplification of the PPM1D locus or gain-of-function truncating mutations of PPM1D occur in various cancers. Here we used a transgenic mouse model carrying a truncating mutation in exon 6 of PPM1D (Ppm1dT). As with human cell lines, we found that the truncated PPM1D was present at high levels in the mouse thymus. Truncated PPM1D did not affect differentiation of T-cells in the thymus but it impaired their response to ionizing radiation (IR). Thymocytes in Ppm1dT/+ mice did not arrest in the checkpoint and continued to proliferate despite the presence of DNA damage. In addition, we observed a decreased level of apoptosis in the thymi of Ppm1dT/+ mice. Moreover, the frequency of the IR-induced T-cell lymphomas increased in Ppm1dT/+Trp53+/- mice resulting in decreased survival. We conclude that truncated PPM1D partially suppresses the p53 pathway in the mouse thymus and potentiates tumor formation under the condition of a partial loss of p53 function.
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Affiliation(s)
- Andra S. Martinikova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, CZ14220 Prague, Czech Republic; (A.S.M.); (M.B.); (M.S.)
- Department of Developmental and Cell Biology, Faculty of Science, Charles University, Albertov 6, CZ12800 Prague, Czech Republic
| | - Monika Burocziova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, CZ14220 Prague, Czech Republic; (A.S.M.); (M.B.); (M.S.)
| | - Miroslav Stoyanov
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, CZ14220 Prague, Czech Republic; (A.S.M.); (M.B.); (M.S.)
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, CZ14220 Prague, Czech Republic; (A.S.M.); (M.B.); (M.S.)
- Correspondence: ; Tel.: +42-(0)2-4106-3210
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38
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Skov V. Next Generation Sequencing in MPNs. Lessons from the Past and Prospects for Use as Predictors of Prognosis and Treatment Responses. Cancers (Basel) 2020; 12:E2194. [PMID: 32781570 PMCID: PMC7464861 DOI: 10.3390/cancers12082194] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 12/29/2022] Open
Abstract
The myeloproliferative neoplasms (MPNs) are acquired hematological stem cell neoplasms characterized by driver mutations in JAK2, CALR, or MPL. Additive mutations may appear in predominantly epigenetic regulator, RNA splicing and signaling pathway genes. These molecular mutations are a hallmark of diagnostic, prognostic, and therapeutic assessment in patients with MPNs. Over the past decade, next generation sequencing (NGS) has identified multiple somatic mutations in MPNs and has contributed substantially to our understanding of the disease pathogenesis highlighting the role of clonal evolution in disease progression. In addition, disease prognostication has expanded from encompassing only clinical decision making to include genomics in prognostic scoring systems. Taking into account the decreasing costs and increasing speed and availability of high throughput technologies, the integration of NGS into a diagnostic, prognostic and therapeutic pipeline is within reach. In this review, these aspects will be discussed highlighting their role regarding disease outcome and treatment modalities in patients with MPNs.
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Affiliation(s)
- Vibe Skov
- Department of Hematology, Zealand University Hospital, Vestermarksvej 7-9, 4000 Roskilde, Denmark
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Li B, Hu J, He D, Chen Q, Liu S, Zhu X, Yu M. PPM1D Knockdown Suppresses Cell Proliferation, Promotes Cell Apoptosis, and Activates p38 MAPK/p53 Signaling Pathway in Acute Myeloid Leukemia. Technol Cancer Res Treat 2020; 19:1533033820942312. [PMID: 32691668 PMCID: PMC7375723 DOI: 10.1177/1533033820942312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES This study was to explore the effect of protein phosphatase, Mg2+/Mn2+ dependent 1D knockdown on proliferation and apoptosis as well as p38 MAPK/p53 signaling pathway in acute myeloid leukemia. METHODS The expression of protein phosphatase, Mg2+/Mn2+ dependent 1D was detected in acute myeloid leukemia cell lines including SKM-1, KG-1, AML-193, and THP-1 cells, and normal bone marrow mononuclear cells isolated from healthy donors. The knockdown of protein phosphatase, Mg2+/Mn2+ dependent 1D was conducted by transfecting small interfering RNA into AML-193 cells and KG-1 cells. RESULTS The relative messenger RNA/protein expressions of protein phosphatase, Mg2+/Mn2+ dependent 1D were higher in SKM-1, KG-1, AML-193, and THP-1 cells compared with control cells (normal bone marrow mononuclear cells). After transfecting protein phosphatase, Mg2+/Mn2+ dependent 1D small interfering RNA into AML-193 cells and KG-1 cells, both messenger RNA and protein expressions of protein phosphatase, Mg2+/Mn2+ dependent 1D were significantly reduced, indicating the successful transfection. Most importantly, knockdown of protein phosphatase, Mg2+/Mn2+ dependent 1D suppressed cell proliferation and promoted cell apoptosis in AML-193 cells and KG-1 cells. In addition, knockdown of protein phosphatase, Mg2+/Mn2+ dependent 1D enhanced the expressions of p-p38 and p53 in AML-193 cells and KG-1 cells. The above observation suggested that protein phosphatase, Mg2+/Mn2+ dependent 1D knockdown suppressed cell proliferation, promoted cell apoptosis, and activated p38 MAPK/p53 signaling pathway in acute myeloid leukemia cells. CONCLUSION Protein phosphatase, Mg2+/Mn2+ dependent 1D is implicated in acute myeloid leukemia carcinogenesis, which illuminates its potential role as a treatment target for acute myeloid leukemia.
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Affiliation(s)
- Bin Li
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
| | - Jie Hu
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
| | - Di He
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
| | - Qi Chen
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
| | - Suna Liu
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
| | - Xiaoling Zhu
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
| | - Meijia Yu
- Department of Hematology, The Second People's Hospital of Yunnan Province, Yunnan, China
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40
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Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
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Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
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41
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Coombs CC, Dickherber T, Crompton BD. Chasing ctDNA in Patients With Sarcoma. Am Soc Clin Oncol Educ Book 2020; 40:e351-e360. [PMID: 32598183 DOI: 10.1200/edbk_280749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Liquid biopsies are new technologies that allow cancer profiling of tumor fragments found in body fluids, such as peripheral blood, collected noninvasively from patients with malignancies. These assays are increasingly valuable in clinical oncology practice as prognostic biomarkers, as guides for therapy selection, for treatment monitoring, and for early detection of disease progression and relapse. However, application of these assays to rare cancers, such as pediatric and adult sarcomas, have lagged. In this article, we review the technical challenges of applying liquid biopsy technologies to sarcomas, provide an update on progress in the field, describe common pitfalls in interpreting liquid biopsy data, and discuss the intersection of sarcoma clinical care and commercial assays emerging on the horizon.
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Affiliation(s)
| | | | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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42
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Akamandisa MP, Nie K, Nahta R, Hambardzumyan D, Castellino RC. Inhibition of mutant PPM1D enhances DNA damage response and growth suppressive effects of ionizing radiation in diffuse intrinsic pontine glioma. Neuro Oncol 2020; 21:786-799. [PMID: 30852603 DOI: 10.1093/neuonc/noz053] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Children with diffuse intrinsic pontine glioma (DIPG) succumb to disease within 2 years of diagnosis despite treatment with ionizing radiation (IR) and/or chemotherapy. Our aim was to determine the role of protein phosphatase, magnesium-dependent 1, delta (PPM1D) mutation, present in up to 25% of cases, in DIPG pathogenesis and treatment. METHODS Using genetic and pharmacologic approaches, we assayed effects of PPM1D mutation on DIPG growth and murine survival. We assayed effects of targeting mutated PPM1D alone or with IR on signaling, cell cycle, proliferation, and apoptosis in patient-derived DIPG cells in vitro, in organotypic brain slices, and in vivo. RESULTS PPM1D-mutated DIPG cell lines exhibited increased proliferation in vitro and in vivo, conferring reduced survival in orthotopically xenografted mice, through stabilization of truncated PPM1D protein and inactivation of DNA damage response (DDR) effectors p53 and H2A.X. PPM1D knockdown or treatment with PPM1D inhibitors suppressed growth of PPM1D-mutated DIPGs in vitro. Orthotopic xenografting of PPM1D short hairpin RNA-transduced or PPM1D inhibitor-treated, PPM1D-mutated DIPG cells into immunodeficient mice resulted in reduced tumor proliferation, increased apoptosis, and extended mouse survival. PPM1D inhibition had similar effects to IR alone on DIPG growth inhibition and augmented the anti-proliferative and pro-apoptotic effects of IR in PPM1D-mutated DIPG models. CONCLUSIONS PPM1D mutations inactivate DDR and promote DIPG growth. Treatment with PPM1D inhibitors activated DDR pathways and enhanced the anti-proliferative and pro-apoptotic effects of IR in DIPG models. Our results support continued development of PPM1D inhibitors for phase I/II trials in children with DIPG.
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Affiliation(s)
- Mwangala Precious Akamandisa
- Cancer Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia.,Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Kai Nie
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Rita Nahta
- Department of Pharmacology, Emory University, Atlanta, GA.,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Dolores Hambardzumyan
- Cancer Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia.,Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Robert Craig Castellino
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
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43
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Lee J, Godfrey AL, Nangalia J. Genomic heterogeneity in myeloproliferative neoplasms and applications to clinical practice. Blood Rev 2020; 42:100708. [PMID: 32571583 DOI: 10.1016/j.blre.2020.100708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/22/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022]
Abstract
The myeloproliferative neoplasms (MPN) polycythaemia vera, essential thrombocythaemia and primary myelofibrosis are chronic myeloid disorders associated most often with mutations in JAK2, MPL and CALR, and in some patients with additional acquired genomic lesions. Whilst the molecular mechanisms downstream of these mutations are now clearer, it is apparent that clinical phenotype in MPN is a product of complex interactions, acting between individual mutations, between disease subclones, and between the tumour and background host factors. In this review we first discuss MPN phenotypic driver mutations and the factors that interact with them to influence phenotype. We consider the importance of ongoing studies of clonal haematopoiesis, which may inform a better understanding of why MPN develop in specific individuals. We then consider how best to deploy genomic testing in a clinical environment and the challenges as well as opportunities that may arise from more routine, comprehensive genomic analysis of patients with MPN.
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Affiliation(s)
- Joe Lee
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anna L Godfrey
- Haematopathology and Oncology Diagnostics Service/ Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Hills Rd, Cambridge CB2 0QQ, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; Haematopathology and Oncology Diagnostics Service/ Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Hills Rd, Cambridge CB2 0QQ, UK.
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Muyas F, Zapata L, Guigó R, Ossowski S. The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Genome Med 2020; 12:49. [PMID: 32460841 PMCID: PMC7254727 DOI: 10.1186/s13073-020-00746-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. METHODS Mosaic mutation detection in 49 normal tissues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. RESULTS The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10-8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. CONCLUSIONS In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
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Affiliation(s)
- Francesc Muyas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Luis Zapata
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Lhotova K, Stolarova L, Zemankova P, Vocka M, Janatova M, Borecka M, Cerna M, Jelinkova S, Kral J, Volkova Z, Urbanova M, Kleiblova P, Machackova E, Foretova L, Hazova J, Vasickova P, Lhota F, Koudova M, Cerna L, Tavandzis S, Indrakova J, Hruskova L, Kosarova M, Vrtel R, Stranecky V, Kmoch S, Zikan M, Macurek L, Kleibl Z, Soukupova J. Multigene Panel Germline Testing of 1333 Czech Patients with Ovarian Cancer. Cancers (Basel) 2020; 12:E956. [PMID: 32295079 PMCID: PMC7226062 DOI: 10.3390/cancers12040956] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 12/18/2022] Open
Abstract
Ovarian cancer (OC) is the deadliest gynecologic malignancy with a substantial proportion of hereditary cases and a frequent association with breast cancer (BC). Genetic testing facilitates treatment and preventive strategies reducing OC mortality in mutation carriers. However, the prevalence of germline mutations varies among populations and many rarely mutated OC predisposition genes remain to be identified. We aimed to analyze 219 genes in 1333 Czech OC patients and 2278 population-matched controls using next-generation sequencing. We revealed germline mutations in 18 OC/BC predisposition genes in 32.0% of patients and in 2.5% of controls. Mutations in BRCA1/BRCA2, RAD51C/RAD51D, BARD1, and mismatch repair genes conferred high OC risk (OR > 5). Mutations in BRIP1 and NBN were associated with moderate risk (both OR = 3.5). BRCA1/2 mutations dominated in almost all clinicopathological subgroups including sporadic borderline tumors of ovary (BTO). Analysis of remaining 201 genes revealed somatic mosaics in PPM1D and germline mutations in SHPRH and NAT1 associating with a high/moderate OC risk significantly; however, further studies are warranted to delineate their contribution to OC development in other populations. Our findings demonstrate the high proportion of patients with hereditary OC in Slavic population justifying genetic testing in all patients with OC, including BTO.
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Affiliation(s)
- Klara Lhotova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic;
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Marianna Borecka
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Marta Cerna
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Sandra Jelinkova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Jan Kral
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Zuzana Volkova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Marketa Urbanova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Petra Kleiblova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Jana Hazova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Petra Vasickova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; (E.M.); (L.F.); (J.H.); (P.V.)
| | - Filip Lhota
- Department of Medical Genetics, Centre for Medical Genetics and Reproductive Medicine, Gennet, 170 00 Prague, Czech Republic; (F.L.); (M.K.); (L.C.)
| | - Monika Koudova
- Department of Medical Genetics, Centre for Medical Genetics and Reproductive Medicine, Gennet, 170 00 Prague, Czech Republic; (F.L.); (M.K.); (L.C.)
| | - Leona Cerna
- Department of Medical Genetics, Centre for Medical Genetics and Reproductive Medicine, Gennet, 170 00 Prague, Czech Republic; (F.L.); (M.K.); (L.C.)
| | - Spiros Tavandzis
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, 741 01 Novy Jicin, Czech Republic; (S.T.); (J.I.)
| | - Jana Indrakova
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, 741 01 Novy Jicin, Czech Republic; (S.T.); (J.I.)
| | - Lucie Hruskova
- Department of Medical Genetics, GHC Genetics, 110 00 Prague, Czech Republic;
| | - Marcela Kosarova
- Department of Medical Genetics, Pronatal, 147 00 Prague, Czech Republic;
| | - Radek Vrtel
- Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University Olomouc, 779 00 Olomouc, Czech Republic;
| | - Viktor Stranecky
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12808 Prague, Czech Republic; (V.S.); (S.K.)
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12808 Prague, Czech Republic; (V.S.); (S.K.)
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Hospital Na Bulovce and First Faculty of Medicine, Charles University, 180 81 Prague, Czech Republic;
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic; (K.L.); (L.S.); (P.Z.); (M.J.); (M.B.); (M.C.); (S.J.); (J.K.); (Z.V.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (M.U.); (P.K.)
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Armenian SH, Gibson CJ, Rockne RC, Ness KK. Premature Aging in Young Cancer Survivors. J Natl Cancer Inst 2020; 111:226-232. [PMID: 30715446 DOI: 10.1093/jnci/djy229] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 11/29/2018] [Accepted: 12/10/2018] [Indexed: 12/23/2022] Open
Abstract
Advances in early detection, treatment, and supportive care have resulted in an estimated 16 million cancer survivors who are alive in the United States today. Outcomes have notably improved for children with cancer as well as young adults with hematologic malignancies due, in part, to the intensification of cancer treatment, including the use of hematopoietic cell transplantation. Emerging evidence suggests that these cancer survivors are at risk for premature aging, manifesting as early onset of chronic health conditions and a higher risk of mortality compared with the general population. Although the pathophysiology of premature aging in these survivors has not been fully elucidated, emerging concepts in aging research could help shed light on this phenomenon. Longitudinal studies are needed to better characterize aging in these survivors, setting the stage for much-needed interventions to halt the trajectory of accelerated aging. These efforts will be enhanced through collaborations between translational researchers, clinical oncologists, primary care providers, geriatricians, patient caretakers, and other stakeholders committed to improving the lives of the growing population of survivors.
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Affiliation(s)
| | | | | | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
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Auslander N, Wolf YI, Koonin EV. Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability. Nat Commun 2020; 11:1234. [PMID: 32144251 PMCID: PMC7060240 DOI: 10.1038/s41467-020-15094-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
Driver mutations and chromosomal aneuploidy are major determinants of tumorigenesis that exhibit complex relationships. Here, we identify associations between driver mutations and chromosomal aberrations that define two tumor clusters, with distinct regimes of tumor evolution underpinned by unique sets of mutations in different components of DNA damage response. Gastrointestinal and endometrial tumors comprise a separate cluster for which chromosomal-arm aneuploidy and driver mutations are mutually exclusive. The landscape of driver mutations in these tumors is dominated by mutations in DNA repair genes that are further linked to microsatellite instability. The rest of the cancer types show a positive association between driver mutations and aneuploidy, and a characteristic set of mutations that involves primarily genes for components of the apoptotic machinery. The distinct sets of mutated genes derived here show substantial prognostic power and suggest specific vulnerabilities of different cancers that might have therapeutic potential.
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Affiliation(s)
- Noam Auslander
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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48
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Angeli D, Salvi S, Tedaldi G. Genetic Predisposition to Breast and Ovarian Cancers: How Many and Which Genes to Test? Int J Mol Sci 2020; 21:E1128. [PMID: 32046255 PMCID: PMC7038038 DOI: 10.3390/ijms21031128] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/19/2022] Open
Abstract
Breast and ovarian cancers are some of the most common tumors in females, and the genetic predisposition is emerging as one of the key risk factors in the development of these two malignancies. BRCA1 and BRCA2 are the best-known genes associated with hereditary breast and ovarian cancer. However, recent advances in molecular techniques, Next-Generation Sequencing in particular, have led to the identification of many new genes involved in the predisposition to breast and/or ovarian cancer, with different penetrance estimates. TP53, PTEN, STK11, and CDH1 have been identified as high penetrance genes for the risk of breast/ovarian cancers. Besides them, PALB2, BRIP1, ATM, CHEK2, BARD1, NBN, NF1, RAD51C, RAD51D and mismatch repair genes have been recognized as moderate and low penetrance genes, along with other genes encoding proteins involved in the same pathways, possibly associated with breast/ovarian cancer risk. In this review, we summarize the past and more recent findings in the field of cancer predisposition genes, with insights into the role of the encoded proteins and the associated genetic disorders. Furthermore, we discuss the possible clinical utility of genetic testing in terms of prevention protocols and therapeutic approaches.
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Affiliation(s)
- Davide Angeli
- Biostatistics and Clinical Trials Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
| | - Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
| | - Gianluca Tedaldi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
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Park SJ, Bejar R. Clonal hematopoiesis in cancer. Exp Hematol 2020; 83:105-112. [PMID: 32044376 DOI: 10.1016/j.exphem.2020.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/16/2022]
Abstract
Clonal hematopoiesis is a common premalignant condition defined by the abnormal expansion of clonally derived hematopoietic stem cells carrying somatic mutations in leukemia-associated genes. Apart from increasing age, this phenomenon occurs with higher frequency in individuals with lymphoid or solid tumors and is associated with exposures to genotoxic stress. Clonal hematopoiesis in this context confers a greater risk for developing therapy-related myeloid neoplasms and appears to contribute to adverse cancer-related survival through a variety of potential mechanisms. These include alterations of the bone marrow microenvironment, inflammatory changes in clonal effector cells and modulation of immune responses. Understanding how clonal hematopoiesis drives therapy-related myeloid neoplasm initiation and interactions with non-myeloid malignancies will inform screening and surveillance approaches and suggest targeted therapies in this vulnerable population. Here, we examine the clinical implications of clonal hematopoiesis in the cancer setting and discuss potential strategies to mitigate the adverse consequences of clonal expansion.
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Affiliation(s)
- Soo J Park
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Rafael Bejar
- Moores Cancer Center, University of California San Diego, La Jolla, CA.
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50
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Marneth AE, Mullally A. The Molecular Genetics of Myeloproliferative Neoplasms. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a034876. [PMID: 31548225 DOI: 10.1101/cshperspect.a034876] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Activated JAK-STAT signaling is central to the pathogenesis of BCR-ABL-negative myeloproliferative neoplasms (MPNs) and occurs as a result of MPN phenotypic driver mutations in JAK2, CALR, or MPL The spectrum of concomitant somatic mutations in other genes has now largely been defined in MPNs. With the integration of targeted next-generation sequencing (NGS) panels into clinical practice, the clinical significance of concomitant mutations in MPNs has become clearer. In this review, we describe the consequences of concomitant mutations in the most frequently mutated classes of genes in MPNs: (1) DNA methylation pathways, (2) chromatin modification, (3) RNA splicing, (4) signaling pathways, (5) transcription factors, and (6) DNA damage response/stress signaling. The increased use of molecular genetics for early risk stratification of patients brings the possibility of earlier intervention to prevent disease progression in MPNs. However, additional studies are required to decipher underlying molecular mechanisms and effectively target them.
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Affiliation(s)
- Anna E Marneth
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute, Cambridge, Massachusetts 02142, USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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