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Huber S, Baer C, Hutter S, Wossidlo N, Hoermann G, Pohlkamp C, Walter W, Meggendorfer M, Kern W, Haferlach T, Haferlach C. Genomic landscape of CCUS compared to MDS and its implications on risk prediction. Leukemia 2024; 38:1634-1637. [PMID: 38730270 PMCID: PMC11216976 DOI: 10.1038/s41375-024-02273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Affiliation(s)
- Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Natalie Wossidlo
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Christian Pohlkamp
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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Hamilton MP, Sugio T, Noordenbos T, Shi S, Bulterys PL, Liu CL, Kang X, Olsen MN, Good Z, Dahiya S, Frank MJ, Sahaf B, Mackall CL, Gratzinger D, Diehn M, Alizadeh AA, Miklos DB. Risk of Second Tumors and T-Cell Lymphoma after CAR T-Cell Therapy. N Engl J Med 2024; 390:2047-2060. [PMID: 38865660 DOI: 10.1056/nejmoa2401361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
BACKGROUND The risk of second tumors after chimeric antigen receptor (CAR) T-cell therapy, especially the risk of T-cell neoplasms related to viral vector integration, is an emerging concern. METHODS We reviewed our clinical experience with adoptive cellular CAR T-cell therapy at our institution since 2016 and ascertained the occurrence of second tumors. In one case of secondary T-cell lymphoma, a broad array of molecular, genetic, and cellular techniques were used to interrogate the tumor, the CAR T cells, and the normal hematopoietic cells in the patient. RESULTS A total of 724 patients who had received T-cell therapies at our center were included in the study. A lethal T-cell lymphoma was identified in a patient who had received axicabtagene ciloleucel therapy for diffuse large B-cell lymphoma, and both lymphomas were deeply profiled. Each lymphoma had molecularly distinct immunophenotypes and genomic profiles, but both were positive for Epstein-Barr virus and were associated with DNMT3A and TET2 mutant clonal hematopoiesis. No evidence of oncogenic retroviral integration was found with the use of multiple techniques. CONCLUSIONS Our results highlight the rarity of second tumors and provide a framework for defining clonal relationships and viral vector monitoring. (Funded by the National Cancer Institute and others.).
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MESH Headings
- Female
- Humans
- Middle Aged
- Biological Products/adverse effects
- Biological Products/therapeutic use
- Clonal Hematopoiesis
- Herpesvirus 4, Human/immunology
- Herpesvirus 4, Human/genetics
- Immunotherapy, Adoptive/adverse effects
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Lymphoma, T-Cell/etiology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/therapy
- Neoplasms, Second Primary/genetics
- Neoplasms, Second Primary/etiology
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/therapeutic use
- Antineoplastic Agents, Immunological/adverse effects
- Antineoplastic Agents, Immunological/therapeutic use
- Virus Integration
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Affiliation(s)
- Mark P Hamilton
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Takeshi Sugio
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Troy Noordenbos
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Shuyu Shi
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Philip L Bulterys
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Chih Long Liu
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Xiaoman Kang
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Mari N Olsen
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Zinaida Good
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Saurabh Dahiya
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Matthew J Frank
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Bita Sahaf
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Crystal L Mackall
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Dita Gratzinger
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Maximilian Diehn
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - Ash A Alizadeh
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
| | - David B Miklos
- From the Divisions of Oncology (M.P.H., T.S., T.N., C.L.L., X.K., M.N.O., A.A.A.) and Blood and Marrow Transplantation and Cellular Therapy (M.P.H., S.D., M.J.F., D.B.M.), Department of Medicine, the Center for Cancer Cell Therapy (M.P.H., Z.G., S.D., M.J.F., B.S., C.L.M., D.B.M.), Stanford Cancer Institute (T.S., T.N., C.L.L., X.K., M.N.O., C.L.M., M.D., A.A.A., D.B.M.), the Department of Pathology (P.L.B., D.G.), the Department of Biomedical Data Science (Z.G.), the Division of Hematology and Oncology, Department of Pediatrics (C.L.M.), the Department of Radiation Oncology (M.D.), and the Institute for Stem Cell Biology and Regenerative Medicine (M.D., A.A.A.), School of Medicine, and the Department of Bioengineering, Schools of Medicine and Engineering (S.S.), Stanford University, Stanford, CA; and the Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (T.N.)
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Lundgren S, Myllymäki M, Järvinen T, Keränen MAI, Theodoropoulos J, Smolander J, Kim D, Salmenniemi U, Walldin G, Savola P, Kelkka T, Rajala H, Hellström-Lindberg E, Itälä-Remes M, Kankainen M, Mustjoki S. Somatic mutations associate with clonal expansion of CD8 + T cells. SCIENCE ADVANCES 2024; 10:eadj0787. [PMID: 38848368 PMCID: PMC11160466 DOI: 10.1126/sciadv.adj0787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Somatic mutations in T cells can cause cancer but also have implications for immunological diseases and cell therapies. The mutation spectrum in nonmalignant T cells is unclear. Here, we examined somatic mutations in CD4+ and CD8+ T cells from 90 patients with hematological and immunological disorders and used T cell receptor (TCR) and single-cell sequencing to link mutations with T cell expansions and phenotypes. CD8+ cells had a higher mutation burden than CD4+ cells. Notably, the biggest variant allele frequency (VAF) of non-synonymous variants was higher than synonymous variants in CD8+ T cells, indicating non-random occurrence. The non-synonymous VAF in CD8+ T cells strongly correlated with the TCR frequency, but not age. We identified mutations in pathways essential for T cell function and often affected lymphoid neoplasia. Single-cell sequencing revealed cytotoxic TEMRA phenotypes of mutated T cells. Our findings suggest that somatic mutations contribute to CD8+ T cell expansions without malignant transformation.
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Affiliation(s)
- Sofie Lundgren
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Mikko Myllymäki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Timo Järvinen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mikko A. I. Keränen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Johannes Smolander
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Daehong Kim
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Urpu Salmenniemi
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Stem Cell Transplantation Unit, Turku University Hospital, Turku, Finland
| | - Gunilla Walldin
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Paula Savola
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Department of Clinical Chemistry, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tiina Kelkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Hanna Rajala
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Maija Itälä-Remes
- Stem Cell Transplantation Unit, Turku University Hospital, Turku, Finland
| | - Matti Kankainen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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4
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Bernstein N, Spencer Chapman M, Nyamondo K, Chen Z, Williams N, Mitchell E, Campbell PJ, Cohen RL, Nangalia J. Analysis of somatic mutations in whole blood from 200,618 individuals identifies pervasive positive selection and novel drivers of clonal hematopoiesis. Nat Genet 2024; 56:1147-1155. [PMID: 38744975 PMCID: PMC11176083 DOI: 10.1038/s41588-024-01755-1] [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: 07/21/2023] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Human aging is marked by the emergence of a tapestry of clonal expansions in dividing tissues, particularly evident in blood as clonal hematopoiesis (CH). CH, linked to cancer risk and aging-related phenotypes, often stems from somatic mutations in a set of established genes. However, the majority of clones lack known drivers. Here we infer gene-level positive selection in whole blood exomes from 200,618 individuals in UK Biobank. We identify 17 additional genes, ZBTB33, ZNF318, ZNF234, SPRED2, SH2B3, SRCAP, SIK3, SRSF1, CHEK2, CCDC115, CCL22, BAX, YLPM1, MYD88, MTA2, MAGEC3 and IGLL5, under positive selection at a population level, and validate this selection pattern in 10,837 whole genomes from single-cell-derived hematopoietic colonies. Clones with mutations in these genes grow in frequency and size with age, comparable to classical CH drivers. They correlate with heightened risk of infection, death and hematological malignancy, highlighting the significance of these additional genes in the aging process.
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Affiliation(s)
| | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Kudzai Nyamondo
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | | | | | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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5
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Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [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: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
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Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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6
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJF, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun JH, DeMeo D, Levy D, Johnson AD, Mathias RA, Taub MA, Arnett D, North KE, Raffield LM, Carson AP, Doyle MF, Rich SS, Rotter JI, Guo X, Cox NJ, Roden DM, Franceschini N, Desai P, Reiner AP, Auer PL, Scheet PA, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. Nat Commun 2024; 15:3800. [PMID: 38714703 PMCID: PMC11076528 DOI: 10.1038/s41467-024-48190-8] [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: 11/08/2023] [Accepted: 04/23/2024] [Indexed: 05/10/2024] Open
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.
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Affiliation(s)
- Yash Pershad
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Yasminka A Jakubek
- Internal Medicine, Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Adrienne M Stilp
- Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Braxton D Mitchell
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz, Aurora, CO, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ali Shojaie
- Biostatistics, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Donna Arnett
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Margaret F Doyle
- Department of Pathology & Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Weill Cornell Medical College, New York, NY, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Insitute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul A Scheet
- Dept of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | | | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA.
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7
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Winter S, Götze KS, Hecker JS, Metzeler KH, Guezguez B, Woods K, Medyouf H, Schäffer A, Schmitz M, Wehner R, Glauche I, Roeder I, Rauner M, Hofbauer LC, Platzbecker U. Clonal hematopoiesis and its impact on the aging osteo-hematopoietic niche. Leukemia 2024; 38:936-946. [PMID: 38514772 PMCID: PMC11073997 DOI: 10.1038/s41375-024-02226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Clonal hematopoiesis (CH) defines a premalignant state predominantly found in older persons that increases the risk of developing hematologic malignancies and age-related inflammatory diseases. However, the risk for malignant transformation or non-malignant disorders is variable and difficult to predict, and defining the clinical relevance of specific candidate driver mutations in individual carriers has proved to be challenging. In addition to the cell-intrinsic mechanisms, mutant cells rely on and alter cell-extrinsic factors from the bone marrow (BM) niche, which complicates the prediction of a mutant cell's fate in a shifting pre-malignant microenvironment. Therefore, identifying the insidious and potentially broad impact of driver mutations on supportive niches and immune function in CH aims to understand the subtle differences that enable driver mutations to yield different clinical outcomes. Here, we review the changes in the aging BM niche and the emerging evidence supporting the concept that CH can progressively alter components of the local BM microenvironment. These alterations may have profound implications for the functionality of the osteo-hematopoietic niche and overall bone health, consequently fostering a conducive environment for the continued development and progression of CH. We also provide an overview of the latest technology developments to study the spatiotemporal dependencies in the CH BM niche, ideally in the context of longitudinal studies following CH over time. Finally, we discuss aspects of CH carrier management in clinical practice, based on work from our group and others.
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Affiliation(s)
- Susann Winter
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Katharina S Götze
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine and Health, Munich, Germany
- German MDS Study Group (D-MDS), Leipzig, Germany
| | - Judith S Hecker
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine and Health, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich (TUM), Munich, Germany
| | - Klaus H Metzeler
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectious Disease, University of Leipzig Medical Center, Leipzig, Germany
| | - Borhane Guezguez
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, University Medical Center Mainz, Mainz, Germany
| | - Kevin Woods
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, University Medical Center Mainz, Mainz, Germany
| | - Hind Medyouf
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Alexander Schäffer
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Marc Schmitz
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Rebekka Wehner
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ingo Roeder
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martina Rauner
- Division of Endocrinology, Diabetes and Bone Diseases, Department of Medicine III, and Center for Healthy Aging, University Medical Center, TU Dresden, Dresden, Germany
| | - Lorenz C Hofbauer
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Division of Endocrinology, Diabetes and Bone Diseases, Department of Medicine III, and Center for Healthy Aging, University Medical Center, TU Dresden, Dresden, Germany.
| | - Uwe Platzbecker
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German MDS Study Group (D-MDS), Leipzig, Germany.
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectious Disease, University of Leipzig Medical Center, Leipzig, Germany.
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8
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Saygin C, Zhang P, Stauber J, Aldoss I, Sperling AS, Weeks LD, Luskin MR, Knepper TC, Wanjari P, Wang P, Lager AM, Fitzpatrick C, Segal JP, Gharghabi M, Gurbuxani S, Venkataraman G, Cheng JX, Eisfelder BJ, Bohorquez O, Patel AA, Umesh Nagalakshmi S, Jayaram S, Odenike OM, Larson RA, Godley LA, Arber DA, Gibson CJ, Munshi NC, Marcucci G, Ebert BL, Greally JM, Steidl U, Lapalombella R, Shah BD, Stock W. Acute Lymphoblastic Leukemia with Myeloid Mutations Is a High-Risk Disease Associated with Clonal Hematopoiesis. Blood Cancer Discov 2024; 5:164-179. [PMID: 38150184 PMCID: PMC11061587 DOI: 10.1158/2643-3230.bcd-23-0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/05/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023] Open
Abstract
Myeloid neoplasms arise from preexisting clonal hematopoiesis (CH); however, the role of CH in the pathogenesis of acute lymphoblastic leukemia (ALL) is unknown. We found that 18% of adult ALL cases harbored TP53, and 16% had myeloid CH-associated gene mutations. ALL with myeloid mutations (MyM) had distinct genetic and clinical characteristics, associated with inferior survival. By using single-cell proteogenomic analysis, we demonstrated that myeloid mutations were present years before the diagnosis of ALL, and a subset of these clones expanded over time to manifest as dominant clones in ALL. Single-cell RNA sequencing revealed upregulation of genes associated with cell survival and resistance to apoptosis in B-ALL with MyM, which responds better to newer immunotherapeutic approaches. These findings define ALL with MyM as a high-risk disease that can arise from antecedent CH and offer new mechanistic insights to develop better therapeutic and preventative strategies. SIGNIFICANCE CH is a precursor lesion for lymphoblastic leukemogenesis. ALL with MyM has distinct genetic and clinical characteristics, associated with adverse survival outcomes after chemotherapy. CH can precede ALL years before diagnosis, and ALL with MyM is enriched with activated T cells that respond to immunotherapies such as blinatumomab. See related commentary by Iacobucci, p. 142.
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Affiliation(s)
- Caner Saygin
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Pu Zhang
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | - Jacob Stauber
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | - Ibrahim Aldoss
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Adam S. Sperling
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | | | - Pankhuri Wanjari
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Peng Wang
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Angela M. Lager
- Department of Pathology, University of Chicago, Chicago, Illinois
| | | | - Jeremy P. Segal
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Mehdi Gharghabi
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | | | | | - Jason X. Cheng
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Bart J. Eisfelder
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Oliver Bohorquez
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | - Anand A. Patel
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | | | | | | | - Richard A. Larson
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Lucy A. Godley
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Daniel A. Arber
- Department of Pathology, University of Chicago, Chicago, Illinois
| | | | | | - Guido Marcucci
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | | | - John M. Greally
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | - Ulrich Steidl
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | | | | | - Wendy Stock
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
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9
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Vogelsberg A, Harland L, Borgmann V, Otto F, Weller JF, Nann D, Quintanilla-Martinez L, Fend F. Clonal haematopoiesis: A common progenitor for cytotoxic peripheral T-cell lymphoma and angioimmunoblastic T-cell lymphoma. Br J Haematol 2024; 204:2071-2076. [PMID: 38323682 DOI: 10.1111/bjh.19335] [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: 11/26/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/08/2024]
Abstract
Recent studies have shown that follicular helper T-cell lymphoma of angioimmunoblastic type (AITL), the most common nodal peripheral T-cell lymphoma (PTCL), frequently arises in a background of clonal haematopoiesis (CH), a preneoplastic condition affecting up to 40% of elderly individuals. Data on a potential CH association are limited for other PTCL. We report a unique patient who sequentially developed both cytotoxic PTCL, not otherwise specified and AITL with distinct T-cell receptor rearrangements but shared somatic mutations originating from the same CH clone, thus providing convincing evidence that CH can give rise to T-cell neoplasms of different lineage.
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Affiliation(s)
- Antonio Vogelsberg
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
| | - Lennart Harland
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Vanessa Borgmann
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
| | - Franziska Otto
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
| | - Jan F Weller
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Dominik Nann
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
| | - Leticia Quintanilla-Martinez
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
| | - Falko Fend
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tuebingen, Tuebingen, Germany
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10
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Iacobucci I. "Myeloid" Mutations in ALL Are Not Uncommon: Implications for Etiology and Therapies. Blood Cancer Discov 2024; 5:142-145. [PMID: 38689559 PMCID: PMC11061583 DOI: 10.1158/2643-3230.bcd-24-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
SUMMARY In Blood Cancer Discovery, Saygin and colleagues report that somatic variants that are recurrent in myeloid malignancies can also occur with high frequency (16%) in adult acute lymphoblastic leukemia (ALL) where they correlate with older age, diagnosis following genotoxic therapy for a prior malignancy and worse outcome to chemotherapy. Mutations in these "myeloid" genes can precede ALL diagnosis and arise in hematopoietic stem or progenitor cells that clonally expand and differentiate into both lymphoblasts and nonmalignant myeloid cells, supporting a role for clonal hematopoiesis as premalignant state outside the context of myeloid malignancies and providing implications for both ALL etiology and therapeutic intervention. See related article by Saygin et al., p. 164 (4).
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
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11
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [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: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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12
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Lin AE, Bapat AC, Xiao L, Niroula A, Ye J, Wong WJ, Agrawal M, Farady CJ, Boettcher A, Hergott CB, McConkey M, Flores-Bringas P, Shkolnik V, Bick AG, Milan D, Natarajan P, Libby P, Ellinor PT, Ebert BL. Clonal Hematopoiesis of Indeterminate Potential With Loss of Tet2 Enhances Risk for Atrial Fibrillation Through Nlrp3 Inflammasome Activation. Circulation 2024; 149:1419-1434. [PMID: 38357791 PMCID: PMC11058018 DOI: 10.1161/circulationaha.123.065597] [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: 05/16/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Clonal hematopoiesis of indeterminate potential (CHIP), a common age-associated phenomenon, associates with increased risk of both hematological malignancy and cardiovascular disease. Although CHIP is known to increase the risk of myocardial infarction and heart failure, the influence of CHIP in cardiac arrhythmias, such as atrial fibrillation (AF), is less explored. METHODS CHIP prevalence was determined in the UK Biobank, and incident AF analysis was stratified by CHIP status and clone size using Cox proportional hazard models. Lethally irradiated mice were transplanted with hematopoietic-specific loss of Tet2, hematopoietic-specific loss of Tet2 and Nlrp3, or wild-type control and fed a Western diet, compounded with or without NLRP3 (NLR [NACHT, LRR {leucine rich repeat}] family pyrin domain containing protein 3) inhibitor, NP3-361, for 6 to 9 weeks. Mice underwent in vivo invasive electrophysiology studies and ex vivo optical mapping. Cardiomyocytes from Ldlr-/- mice with hematopoietic-specific loss of Tet2 or wild-type control and fed a Western diet were isolated to evaluate calcium signaling dynamics and analysis. Cocultures of pluripotent stem cell-derived atrial cardiomyocytes were incubated with Tet2-deficient bone marrow-derived macrophages, wild-type control, or cytokines IL-1β (interleukin 1β) or IL-6 (interleukin 6). RESULTS Analysis of the UK Biobank showed individuals with CHIP, in particular TET2 CHIP, have increased incident AF. Hematopoietic-specific inactivation of Tet2 increases AF propensity in atherogenic and nonatherogenic mouse models and is associated with increased Nlrp3 expression and CaMKII (Ca2+/calmodulin-dependent protein kinase II) activation, with AF susceptibility prevented by inactivation of Nlrp3. Cardiomyocytes isolated from Ldlr-/- mice with hematopoietic inactivation of Tet2 and fed a Western diet have impaired calcium release from the sarcoplasmic reticulum into the cytosol, contributing to atrial arrhythmogenesis. Abnormal sarcoplasmic reticulum calcium release was recapitulated in cocultures of cardiomyocytes with the addition of Tet2-deficient macrophages or cytokines IL-1β or IL-6. CONCLUSIONS We identified a modest association between CHIP, particularly TET2 CHIP, and incident AF in the UK Biobank population. In a mouse model of AF resulting from hematopoietic-specific inactivation of Tet2, we propose altered calcium handling as an arrhythmogenic mechanism, dependent on Nlrp3 inflammasome activation. Our data are in keeping with previous studies of CHIP in cardiovascular disease, and further studies into the therapeutic potential of NLRP3 inhibition for individuals with TET2 CHIP may be warranted.
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Affiliation(s)
- Amy Erica Lin
- Division of Cardiovascular Medicine, Department of Medicine (A.E.L., P.L.), Brigham and Women’s Hospital, Boston, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Aneesh C. Bapat
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Demoulas Cardiac Arrhythmia Service, Division of Cardiovascular Medicine, Department of Medicine (A.C.B., P.T.E.), Massachusetts General Hospital, Boston
| | - Ling Xiao
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Abhishek Niroula
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
- Department of Laboratory Medicine, Lund University, Sweden (A.N.)
- Institute of Biomedicine, SciLifeLab, University of Gothenburg, Sweden (A.N.)
| | - Jiangchuan Ye
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Waihay J. Wong
- Department of Pathology (W.J.W., C.B.H.), Brigham and Women’s Hospital, Boston, MA
| | - Mridul Agrawal
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Christopher J. Farady
- Novartis Institutes for BioMedical Research Forum 1, Basel, Switzerland (C.J.F., A.B.)
| | - Andreas Boettcher
- Novartis Institutes for BioMedical Research Forum 1, Basel, Switzerland (C.J.F., A.B.)
| | - Christopher B. Hergott
- Department of Pathology (W.J.W., C.B.H.), Brigham and Women’s Hospital, Boston, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Marie McConkey
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Patricio Flores-Bringas
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Veronica Shkolnik
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN (A.G.B.)
| | - David Milan
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Leducq Foundation, Boston, MA (D.M.)
| | - Pradeep Natarajan
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine (A.E.L., P.L.), Brigham and Women’s Hospital, Boston, MA
| | - Patrick T. Ellinor
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Demoulas Cardiac Arrhythmia Service, Division of Cardiovascular Medicine, Department of Medicine (A.C.B., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
- Howard Hughes Medical Institute, Boston, MA (B.L.E.)
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13
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Jakubek YA, Ma X, Stilp AM, Yu F, Bacon J, Wong JW, Aguet F, Ardlie K, Arnett D, Barnes K, Bis JC, Blackwell T, Becker LC, Boerwinkle E, Bowler RP, Budoff MJ, Carson AP, Chen J, Cho MH, Coresh J, Cox N, de Vries PS, DeMeo DL, Fardo DW, Fornage M, Guo X, Hall ME, Heard-Costa N, Hidalgo B, Irvin MR, Johnson AD, Kenny EE, Levy D, Li Y, Lima JA, Liu Y, Loos RJF, Machiela MJ, Mathias RA, Mitchell BD, Murabito J, Mychaleckyj JC, North K, Orchard P, Parker SC, Pershad Y, Peyser PA, Pratte KA, Psaty BM, Raffield LM, Redline S, Rich SS, Rotter JI, Shah SJ, Smith JA, Smith AP, Smith A, Taub M, Tiwari HK, Tracy R, Tuftin B, Bick AG, Sankaran VG, Reiner AP, Scheet P, Auer PL. Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305851. [PMID: 38699360 PMCID: PMC11065036 DOI: 10.1101/2024.04.16.24305851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Mosaic loss of Y (mLOY) is the most common somatic chromosomal alteration detected in human blood. The presence of mLOY is associated with altered blood cell counts and increased risk of Alzheimer's disease, solid tumors, and other age-related diseases. We sought to gain a better understanding of genetic drivers and associated phenotypes of mLOY through analyses of whole genome sequencing of a large set of genetically diverse males from the Trans-Omics for Precision Medicine (TOPMed) program. This approach enabled us to identify differences in mLOY frequencies across populations defined by genetic similarity, revealing a higher frequency of mLOY in the European American (EA) ancestry group compared to those of Hispanic American (HA), African American (AA), and East Asian (EAS) ancestry. Further, we identified two genes ( CFHR1 and LRP6 ) that harbor multiple rare, putatively deleterious variants associated with mLOY susceptibility, show that subsets of human hematopoietic stem cells are enriched for activity of mLOY susceptibility variants, and that certain alleles on chromosome Y are more likely to be lost than others.
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14
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Yu Z, Coorens THH, Uddin MM, Ardlie KG, Lennon N, Natarajan P. Genetic variation across and within individuals. Nat Rev Genet 2024:10.1038/s41576-024-00709-x. [PMID: 38548833 DOI: 10.1038/s41576-024-00709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 04/12/2024]
Abstract
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germline variants are present from conception, but they vary between individuals and accumulate over generations. By contrast, somatic mutations accumulate throughout life in a mosaic manner within an individual due to intrinsic and extrinsic sources of mutations and selection pressures acting on cells. Recent advancements, such as improved detection methods and increased resources for association studies, have drastically expanded our ability to investigate germline and somatic genetic variation and compare underlying mutational processes. A better understanding of the similarities and differences in the types, rates and patterns of germline and somatic variants, as well as their interplay, will help elucidate the mechanisms underlying their distinct yet interlinked roles in human health and biology.
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Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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15
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Saluja S, Bansal I, Bhardwaj R, Beg MS, Palanichamy JK. Inflammation as a driver of hematological malignancies. Front Oncol 2024; 14:1347402. [PMID: 38571491 PMCID: PMC10987768 DOI: 10.3389/fonc.2024.1347402] [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: 12/01/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Hematopoiesis is a tightly regulated process that produces all adult blood cells and immune cells from multipotent hematopoietic stem cells (HSCs). HSCs usually remain quiescent, and in the presence of external stimuli like infection or inflammation, they undergo division and differentiation as a compensatory mechanism. Normal hematopoiesis is impacted by systemic inflammation, which causes HSCs to transition from quiescence to emergency myelopoiesis. At the molecular level, inflammatory cytokine signaling molecules such as tumor necrosis factor (TNF), interferons, interleukins, and toll-like receptors can all cause HSCs to multiply directly. These cytokines actively encourage HSC activation, proliferation, and differentiation during inflammation, which results in the generation and activation of immune cells required to combat acute injury. The bone marrow niche provides numerous soluble and stromal cell signals, which are essential for maintaining normal homeostasis and output of the bone marrow cells. Inflammatory signals also impact this bone marrow microenvironment called the HSC niche to regulate the inflammatory-induced hematopoiesis. Continuous pro-inflammatory cytokine and chemokine activation can have detrimental effects on the hematopoietic system, which can lead to cancer development, HSC depletion, and bone marrow failure. Reactive oxygen species (ROS), which damage DNA and ultimately lead to the transformation of HSCs into cancerous cells, are produced due to chronic inflammation. The biological elements of the HSC niche produce pro-inflammatory cytokines that cause clonal growth and the development of leukemic stem cells (LSCs) in hematological malignancies. The processes underlying how inflammation affects hematological malignancies are still not fully understood. In this review, we emphasize the effects of inflammation on normal hematopoiesis, the part it plays in the development and progression of hematological malignancies, and potential therapeutic applications for targeting these pathways for therapy in hematological malignancies.
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16
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Marchetti A, Pelusi S, Marella A, Malvestiti F, Ricchiuti A, Ronzoni L, Lionetti M, Moretti V, Bugianesi E, Miele L, Vespasiani-Gentilucci U, Dongiovanni P, Federico A, Soardo G, D'Ambrosio R, McCain MV, Reeves HL, La Mura V, Prati D, Bolli N, Valenti L. Impact of clonal hematopoiesis of indeterminate potential on hepatocellular carcinoma in individuals with steatotic liver disease. Hepatology 2024:01515467-990000000-00801. [PMID: 38470216 DOI: 10.1097/hep.0000000000000839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND AND AIMS Metabolic dysfunction-associated steatotic liver disease (MASLD) is a global epidemic and is the most rapidly rising cause of HCC. Clonal hematopoiesis of indeterminate potential (CHIP) contributes to neoplastic and cardiometabolic disorders and is considered a harbinger of tissue inflammation. CHIP was recently associated with increased risk of liver disease. The aim of this study was to examine whether CHIP is associated with HCC development in patients with SLD. APPROACH AND RESULTS We considered individuals with MASLD-HCC (n=208) and controls with (n =414) and without (n =259) advanced fibrosis who underwent whole exome sequencing. CHIP was diagnosed when ≥2 variant callers identified a known myeloid mutation with variant allele frequency ≥2%. CHIP was observed in 116 participants (13.1%), most frequently in DNMT3A, TET2, TP53 , and ASXL1 , and correlated with age ( p <0.0001) and advanced liver fibrosis (p=0.001). Higher aspartate aminotransferase levels predicted non- DNMT3A -CHIP, in particular with variant allele frequency ≥10% (OR: 1.14, 1.03 -1.28 and OR: 1.30, 1.12 -1.49, respectively, p <0.05). After adjustment for sex, diabetes, and a polygenic risk, a score of inherited MASLD predisposition CHIP was associated with cirrhosis (2.00, 1.30 -3.15, p =0.02), and with HCC even after further adjustment for cirrhosis (OR: 1.81, 1.11 -2.00, 1.30 -3.15, p =0.002). Despite the strong collinearity among aging and development of CHIP and HCC, non- DNTM3A -CHIP, and TET2 lesions remained associated with HCC after full correction for clinical/genetics covariates and age (OR: 2.45, 1.35 -4.53; OR: 4.8, 1.60 -17.0, p =0.02). CONCLUSIONS We observed an independent association between CHIP, particularly related to non- DNTM3A and TET2 genetic lesions and MASLD-HCC.
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Affiliation(s)
- Alfredo Marchetti
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Serena Pelusi
- Transfusion Medicine Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessio Marella
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Francesco Malvestiti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Antony Ricchiuti
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luisa Ronzoni
- Transfusion Medicine Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marta Lionetti
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Vittoria Moretti
- Transfusion Medicine Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastroenterology, University of Turin, Turin, Italy
| | - Luca Miele
- Dipartimento Universitario Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
- Area Medicina Interna, Gastroenterologia e Oncologia Medica, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
| | - Umberto Vespasiani-Gentilucci
- Clinical Medicine and Hepatology Unit, Department of Medicine and Surgery, Campus Bio-Medico University of Rome, Rome, Italy
| | - Paola Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandro Federico
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Soardo
- Department of Medicine, Clinica Medica, European Excellence Center for Arterial Hypertension, University of Udine, Udine, Italy
| | - Roberta D'Ambrosio
- Gastroenterology and Hepatology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Misti V McCain
- Newcastle University Translational Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen L Reeves
- Newcastle University Translational Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vincenzo La Mura
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- General Medicine, Haemostasis and Thrombosis, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Prati
- Transfusion Medicine Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Valenti
- Transfusion Medicine Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Biological Resource Center Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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17
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Kapadia CD, Goodell MA. Tissue mosaicism following stem cell aging: blood as an exemplar. NATURE AGING 2024; 4:295-308. [PMID: 38438628 DOI: 10.1038/s43587-024-00589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024]
Abstract
Loss of stem cell regenerative potential underlies aging of all tissues. Somatic mosaicism, the emergence of cellular patchworks within tissues, increases with age and has been observed in every organ yet examined. In the hematopoietic system, as in most tissues, stem cell aging through a variety of mechanisms occurs in lockstep with the emergence of somatic mosaicism. Here, we draw on insights from aging hematopoiesis to illustrate fundamental principles of stem cell aging and somatic mosaicism. We describe the generalizable changes intrinsic to aged stem cells and their milieu that provide the backdrop for somatic mosaicism to emerge. We discuss genetic and nongenetic mechanisms that can result in tissue somatic mosaicism and existing methodologies to detect such clonal outgrowths. Finally, we propose potential avenues to modify mosaicism during aging, with the ultimate aim of increasing tissue resiliency.
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Affiliation(s)
- Chiraag D Kapadia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
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18
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Sequeros CB, Tulstrup M, Bliddal S, Sørensen KM, Nissen I, Rezahosseini O, Brooks PT, Feenstra B, Gang AO, Geller F, Hald A, Harboe ZB, Helleberg M, Jespersen JS, Lebech AM, Lindegaard B, Mogensen TH, Møller MEE, Nielsen CH, Niemann CU, Podlekareva D, Sejdic A, Sørensen E, Teglgaard RS, Tommerup N, Weis N, Brunak S, Pedersen OBV, Banasik K, Feldt-Rasmussen U, Nielsen SD, Ostrowski SR, Grønbæk K. Clonal hematopoiesis and COVID-19 hospitalization in Danish adults. Hemasphere 2024; 8:e58. [PMID: 38463443 PMCID: PMC10924741 DOI: 10.1002/hem3.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Affiliation(s)
- Celia Burgos Sequeros
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Morten Tulstrup
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Biotech Research and Innovation Center (BRIC) University of Copenhagen Copenhagen Denmark
| | - Sofie Bliddal
- Department of Endocrinology and Metabolism Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | | | - Ioanna Nissen
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Omid Rezahosseini
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
| | - Patrick Terrence Brooks
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Bjarke Feenstra
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Epidemiology Research Statens Serum Institut Copenhagen Denmark
| | - Anne Ortved Gang
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Frank Geller
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Epidemiology Research Statens Serum Institut Copenhagen Denmark
| | - Annemette Hald
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Zitta Barrella Harboe
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Marie Helleberg
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Center of Excellence for Health, Immunity and Infections Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Jakob S Jespersen
- Biotech Research and Innovation Center (BRIC) University of Copenhagen Copenhagen Denmark
- The Finsen Laboratory Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Anne-Mette Lebech
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Birgitte Lindegaard
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Trine H Mogensen
- Department of Infectious Diseases Aarhus University Hospital Aarhus Denmark
- Department of Biomedicine Aarhus University Aarhus Denmark
| | | | - Claus Henrik Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Carsten Utoft Niemann
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Daria Podlekareva
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, Bispebjerg Copenhagen Denmark
| | - Adin Sejdic
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Rebecca Svanberg Teglgaard
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine University of Copenhagen Denmark
| | - Nina Weis
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Infectious Diseases Copenhagen University Hospital, Hvidovre Copenhagen Denmark
| | - Søren Brunak
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Ole Birger Vestager Pedersen
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Clinical Immunology Zealand University Hospital Køge Denmark
| | - Karina Banasik
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Gynecology and Obstetrics Copenhagen University Hospital, Hvidovre Copenhagen Denmark
| | - Ulla Feldt-Rasmussen
- Department of Endocrinology and Metabolism Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Susanne Dam Nielsen
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Kirsten Grønbæk
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Biotech Research and Innovation Center (BRIC) University of Copenhagen Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
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19
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Kapadia CD, Rosas G, Thakkar SG, Wu M, Torrano V, Wang T, Grilley BJ, Heslop HE, Ramos CA, Goodell MA, Lulla PD. Incipient clonal hematopoiesis is accelerated following CD30.CAR-T therapy. Cytotherapy 2024; 26:261-265. [PMID: 38149948 PMCID: PMC10922117 DOI: 10.1016/j.jcyt.2023.11.013] [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: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Chimeric antigen receptor (CAR) T-cells are an emerging therapy for refractory lymphomas. Clonal hematopoiesis (CH), the preferential outgrowth of mutated bone marrow progenitors, is enriched in lymphoma patients receiving CAR-T cells. CAR-T therapy requires conditioning chemotherapy and often induces systemic inflammatory reactions, both of which have been shown to promote expansion of CH clones. Thus, we hypothesized that pre-existing CH clones could expand during CAR-T cell treatment. We measured CH at 154 timepoints longitudinally sampled from 26 patients receiving CD30.CAR-T therapy for CD30+ lymphomas on an investigational protocol (NCT02917083). Pre-treatment CH was present in 54% of individuals and did not correlate with survival outcomes or inflammatory toxicities. Longitudinal tracking of single clones in individual patients revealed distinct clone growth dynamics. Initially small clones, defined as VAF <1%, expanded following CAR-T administration, compared with relatively muted expansions of larger clones (3.37-fold vs. 1.20-fold, P = 0.0014). Matched clones were present at low magnitude in the infused CD30.CAR-T product for all CH cases but did not affect the product's immunophenotype or transduction efficiency. As cellular immunotherapies expand to become frontline treatments for hematological malignancies, our data indicates CAR-T recipients could be enriched for CH, and further longitudinal studies centered on CH complications in this population are warranted.
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Affiliation(s)
- Chiraag D Kapadia
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.
| | - Gerardo Rosas
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Sachin G Thakkar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA
| | - Mengfen Wu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Virginia Torrano
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA
| | - Tao Wang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Bambi J Grilley
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Helen E Heslop
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Carlos A Ramos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Margaret A Goodell
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Premal D Lulla
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
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20
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Vlasschaert C, Lanktree MB, Rauh MJ, Kelly TN, Natarajan P. Clonal haematopoiesis, ageing and kidney disease. Nat Rev Nephrol 2024; 20:161-174. [PMID: 37884787 PMCID: PMC10922936 DOI: 10.1038/s41581-023-00778-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
Clonal haematopoiesis of indeterminate potential (CHIP) is a preclinical condition wherein a sizeable proportion of an individual's circulating blood cells are derived from a single mutated haematopoietic stem cell. CHIP occurs frequently with ageing - more than 10% of individuals over 65 years of age are affected - and is associated with an increased risk of disease across several organ systems and premature death. Emerging evidence suggests that CHIP has a role in kidney health, including associations with predisposition to acute kidney injury, impaired recovery from acute kidney injury and kidney function decline, both in the general population and among those with chronic kidney disease. Beyond its direct effect on the kidney, CHIP elevates the susceptibility of individuals to various conditions that can detrimentally affect the kidneys, including cardiovascular disease, obesity and insulin resistance, liver disease, gout, osteoporosis and certain autoimmune diseases. Aberrant pro-inflammatory signalling, telomere attrition and epigenetic ageing are potential causal pathophysiological pathways and mediators that underlie CHIP-related disease risk. Experimental animal models have shown that inhibition of inflammatory cytokine signalling can ameliorate many of the pathological effects of CHIP, and assessment of the efficacy and safety of this class of medications for human CHIP-associated pathology is ongoing.
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Affiliation(s)
| | - Matthew B Lanktree
- Department of Medicine and Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Kingston, Ontario, Canada
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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21
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Stonestrom AJ, Menghrajani KN, Devlin SM, Franch-Expósito S, Ptashkin RN, Patel SY, Spitzer B, Wu X, Jee J, Sánchez Vela P, Milbank JH, Shah RH, Mohanty AS, Brannon AR, Xiao W, Berger MF, Mantha S, Levine RL. High-risk and silent clonal hematopoietic genotypes in patients with nonhematologic cancer. Blood Adv 2024; 8:846-856. [PMID: 38147626 PMCID: PMC10875331 DOI: 10.1182/bloodadvances.2023011262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) identified by somatic gene variants with variant allele fraction (VAF) ≥ 2% is associated with an increased risk of hematologic malignancy. However, CH defined by a broader set of genotypes and lower VAFs is ubiquitous in older individuals. To improve our understanding of the relationship between CH genotype and risk of hematologic malignancy, we analyzed data from 42 714 patients who underwent blood sequencing as a normal comparator for nonhematologic tumor testing using a large cancer-related gene panel. We cataloged hematologic malignancies in this cohort using natural language processing and manual curation of medical records. We found that some CH genotypes including JAK2, RUNX1, and XPO1 variants were associated with high hematologic malignancy risk. Chronic disease was predicted better than acute disease suggesting the influence of length bias. To better understand the implications of hematopoietic clonality independent of mutational function, we evaluated a set of silent synonymous and noncoding mutations. We found that silent CH, particularly when multiple variants were present or VAF was high, was associated with increased risk of hematologic malignancy. We tracked expansion of CH mutations in 26 hematologic malignancies sequenced with the same platform. JAK2 and TP53 VAF consistently expanded at disease onset, whereas DNMT3A and silent CH VAFs mostly decreased. These data inform the clinical and biological interpretation of CH in the context of nonhematologic cancer.
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Affiliation(s)
- Aaron J. Stonestrom
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal N. Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean M. Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sebastià Franch-Expósito
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaodi Wu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin Jee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer H. Milbank
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronak H. Shah
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S. Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Simon Mantha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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22
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Bravo-Perez C, Gurnari C. A tower of babel of acronyms? The shadowlands of MGUS/MBL/CHIP/TCUS. Semin Hematol 2024; 61:43-50. [PMID: 38350765 DOI: 10.1053/j.seminhematol.2024.01.004] [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: 10/25/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
With the advent of outperforming and massive laboratory tools, such as multiparameter flow cytometry and next-generation sequencing, hematopoietic cell clones with putative abnormalities for a variety of blood malignancies have been appreciated in otherwise healthy individuals. These conditions do not fulfill the criteria of their presumed cancer counterparts, and thus have been recognized as their precursor states. This is the case of monoclonal gammopathy of unknown significance (MGUS), the first blood premalignancy state described, preceding multiple myeloma (MM) or Waldenström macroglobulinemia (WM). However, in the last 2 decades, an increasing list of clonopathies has been recognized, including monoclonal B cell lymphocytosis (MBL), which antecedes chronic lymphocytic leukemia (CLL), clonal hematopoiesis of indeterminate potential (CHIP) for myeloid neoplasms (MN), and T-cell clones of uncertain significance (TCUS) for T-cell large chronic lymphocytic leukemia (LGLL). While for some of these entities diagnostic boundaries are precisely set, for others these are yet to be fully defined. Moreover, despite mostly considered of "uncertain significance," they have not only appeared to predispose to malignancy, but also to be capable of provoking set of immunological and cardiovascular complications that may require specialized management. The clinical implications of the aberrant clones, together with the extensive knowledge generated on the pathogenetic events driving their evolution, raises the question whether earlier interventions may alter the natural history of the disease. Herein, we review this Tower of Babel of acronyms pinpointing diagnostic definitions, differential diagnosis, and the role of genomic profiling of these precursor states, as well as potential interventional strategies.
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Affiliation(s)
- Carlos Bravo-Perez
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Department of Hematology and Medical Oncology, Hospital Universitario Morales Meseguer, University of Murcia, IMIB-Pascual Parrilla, CIBERER - Instituto de Salud Carlos III, Murcia, Spain
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy.
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23
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Xie Z, Lasho T, Khurana A, Ferrer A, Finke C, Mangaonkar AA, Ansell S, Fernandez J, Shah MV, Al-Kali A, Gangat N, Abeykoon J, Witzig TE, Patnaik MM. Prognostic relevance of clonal hematopoiesis in myeloid neoplastic transformation in patients with follicular lymphoma treated with radioimmunotherapy. Haematologica 2024; 109:509-520. [PMID: 37646653 PMCID: PMC10828786 DOI: 10.3324/haematol.2023.283727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
While novel radioisotope therapies continue to advance cancer care, reports of therapy-related myeloid neoplasms (t-MN) have generated concern. The prevalence and role of clonal hematopoiesis (CH) in this process remain to be defined. We hypothesized that: (i) CH is prevalent in relapsed follicular lymphoma and is associated with t-MN transformation, and (ii) radiation in the form of radioimmunotherapy (RIT) plays a role in clonal progression. In this retrospective cohort study, we evaluated the prevalence and prognostic impact of CH on clinical outcomes in 58 heavily pre-treated follicular lymphoma patients who received RIT. Patients had been given a median of four lines of therapy before RIT. The prevalence of CH prior to RIT was 46%, while it was 67% (P=0.15) during the course of RIT and subsequent therapies in the paired samples. Fourteen (24%) patients developed t-MN. Patients with t-MN had a higher variant allele fraction (38% vs. 15%; P=0.02) and clonal complexity (P=0.03) than those without. The spectrum of CH differed from that in age-related CH, with a high prevalence of DNA damage repair and response pathway mutations, absence of spliceosome mutations, and a paucity of signaling mutations. While there were no clear clinical associations between RIT and t-MN, or overall survival, patients with t-MN had a higher mutant clonal burden, along with extensive chromosomal abnormalities (median survival, afer t-MN diagnosis, 0.9 months). The baseline prevalence of CH was high, with an increase in prevalence on exposure to RIT and subsequent therapies. The high rates of t-MN with marked clonal complexities and extensive chromosomal damage underscore the importance of better identifying and studying genotoxic stressors accentuated by therapeutic modalities.
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Affiliation(s)
- Zhuoer Xie
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN, United States; Malignant Hematology Department, H. Lee Moffitt Cancer Center and Research Institute, FL
| | - Terra Lasho
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Arushi Khurana
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Alejandro Ferrer
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Christy Finke
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | | | - Stephen Ansell
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Jenna Fernandez
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Mithun Vinod Shah
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Aref Al-Kali
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Naseema Gangat
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Jithma Abeykoon
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Thomas E Witzig
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN
| | - Mrinal M Patnaik
- Mayo Clinic, Department of Internal Medicine, Hematology Division, Rochester, MN.
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24
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Mitchell J, Milite S, Bartram J, Walker S, Volkova N, Yavorska O, Zarowiecki M, Chalker J, Thomas R, Vago L, Sosinsky A, Caravagna G. Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nat Commun 2024; 15:323. [PMID: 38238294 PMCID: PMC10796348 DOI: 10.1038/s41467-023-44158-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
The unexpected contamination of normal samples with tumour cells reduces variant detection sensitivity, compromising downstream analyses in canonical tumour-normal analyses. Leveraging whole-genome sequencing data available at Genomics England, we develop a tool for normal sample contamination assessment, which we validate in silico and against minimal residual disease testing. From a systematic review of [Formula: see text] patients with haematological malignancies and sarcomas, we find contamination across a range of cancer clinical indications and DNA sources, with highest prevalence in saliva samples from acute myeloid leukaemia patients, and sorted CD3+ T-cells from myeloproliferative neoplasms. Further exploration reveals 108 hotspot mutations in genes associated with haematological cancers at risk of being subtracted by standard variant calling pipelines. Our work highlights the importance of contamination assessment for accurate somatic variants detection in research and clinical settings, especially with large-scale sequencing projects being utilised to deliver accurate data from which to make clinical decisions for patient care.
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Affiliation(s)
| | - Salvatore Milite
- Computational Biology Research Centre, Human Technopole, Milan, Italy
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | | | | | | | | | - Jane Chalker
- Specialist Integrated Haematological Malignancy Diagnostic Service - Acquired Genomics, Great Ormond Street Hospital for Children, London, UK
| | - Rebecca Thomas
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Luca Vago
- Research Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS Hospital San Raffaele, Milan, Italy
| | | | - Giulio Caravagna
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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25
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Kishtagari A, Khan MAW, Li Y, Vlasschaert C, Marneni N, Silver AJ, von Beck K, Spaulding T, Stockton S, Snider C, Sochacki A, Dorand D, Mack TM, Ferrell PB, Xu Y, Bejan CA, Savona MR, Bick AG. Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk. Blood Cancer J 2024; 14:6. [PMID: 38225345 PMCID: PMC10789770 DOI: 10.1038/s41408-023-00974-9] [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: 09/05/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Clonal hematopoiesis (CH) can be caused by either single gene mutations (eg point mutations in JAK2 causing CHIP) or mosaic chromosomal alterations (e.g., loss of heterozygosity at chromosome 9p). CH is associated with a significantly increased risk of hematologic malignancies. However, the absolute rate of transformation on an annualized basis is low. Improved prognostication of transformation risk is urgently needed for routine clinical practice. We hypothesized that the co-occurrence of CHIP and mCAs at the same locus (e.g., transforming a heterozygous JAK2 CHIP mutation into a homozygous mutation through concomitant loss of heterozygosity at chromosome 9) might have important prognostic implications for malignancy transformation risk. We tested this hypothesis using our discovery cohort, the UK Biobank (n = 451,180), and subsequently validated it in the BioVU cohort (n = 91,335). We find that individuals with a concurrent somatic mutation and mCA were at significantly increased risk of hematologic malignancy (for example, In BioVU cohort incidence of hematologic malignancies is higher in individuals with co-occurring JAK2 V617F and 9p CN-LOH; HR = 54.76, 95% CI = 33.92-88.41, P < 0.001 vs. JAK2 V617F alone; HR = 44.05, 95% CI = 35.06-55.35, P < 0.001). Currently, the 'zygosity' of the CHIP mutation is not routinely reported in clinical assays or considered in prognosticating CHIP transformation risk. Based on these observations, we propose that clinical reports should include 'zygosity' status of CHIP mutations and that future prognostication systems should take mutation 'zygosity' into account.
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Affiliation(s)
- Ashwin Kishtagari
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - M A Wasay Khan
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yajing Li
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Naimisha Marneni
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly von Beck
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Travis Spaulding
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shannon Stockton
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christina Snider
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew Sochacki
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dixon Dorand
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Taralynn M Mack
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - P Brent Ferrell
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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26
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Moulinet T, Moussu A, Pierson L, Pagliuca S. The many facets of immune-mediated thrombocytopenia: Principles of immunobiology and immunotherapy. Blood Rev 2024; 63:101141. [PMID: 37980261 DOI: 10.1016/j.blre.2023.101141] [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: 08/30/2023] [Revised: 10/08/2023] [Accepted: 11/05/2023] [Indexed: 11/20/2023]
Abstract
Immune thrombocytopenia (ITP) is a rare autoimmune condition, due to peripheral platelet destruction through antibody-dependent cellular phagocytosis, complement-dependent cytotoxicity, cytotoxic T lymphocyte-mediated cytotoxicity, and megakaryopoiesis alteration. This condition may be idiopathic or triggered by drugs, vaccines, infections, cancers, autoimmune disorders and systemic diseases. Recent advances in our understanding of ITP immunobiology support the idea that other forms of thrombocytopenia, for instance, occurring after immunotherapy or cellular therapies, may share a common pathophysiology with possible therapeutic implications. If a decent pipeline of old and new agents is currently deployed for classical ITP, in other more complex immune-mediated thrombocytopenic disorders, clinical management is less harmonized and would deserve further prospective investigations. Here, we seek to provide a fresh overview of pathophysiology and current therapeutical algorithms for adult patients affected by this disorder with specific insights into poorly codified scenarios, including refractory ITP and post-immunotherapy/cellular therapy immune-mediated thrombocytopenia.
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Affiliation(s)
- Thomas Moulinet
- Department of Internal Medicine and Clinical Immunology, Regional Competence Center for Rare and Systemic Auto-Immunes Diseases and Auto-Immune cytopenias, Nancy University Hospital, Lorraine University, Vandoeuvre-lès-Nancy, France; UMR 7365, IMoPA, Lorraine University, CNRS, Nancy, France
| | - Anthony Moussu
- Department of Internal Medicine and Clinical Immunology, Regional Competence Center for Rare and Systemic Auto-Immunes Diseases and Auto-Immune cytopenias, Nancy University Hospital, Lorraine University, Vandoeuvre-lès-Nancy, France
| | - Ludovic Pierson
- Department of Internal Medicine and Clinical Immunology, Regional Competence Center for Rare and Systemic Auto-Immunes Diseases and Auto-Immune cytopenias, Nancy University Hospital, Lorraine University, Vandoeuvre-lès-Nancy, France
| | - Simona Pagliuca
- UMR 7365, IMoPA, Lorraine University, CNRS, Nancy, France; Department of Hematology, Regional Competence Center for Aplastic Anemia and Paroxysmal Nocturnal Hemoglobinuria, Nancy University Hospital, Vandœuvre-lès-Nancy, France.
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27
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Vaidya P, Wang HY, Don MD, Hinds BR, Mangan JK. IDH2-mutated near ETP-ALL with aggressive leukemia cutis and brisk response to venetoclax and decitabine. Leuk Res Rep 2023; 21:100408. [PMID: 38269085 PMCID: PMC10805932 DOI: 10.1016/j.lrr.2023.100408] [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: 05/24/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024] Open
Abstract
Near early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a rare hematologic malignancy, for which second line therapeutic options are limited. T-cell leukemias are also rarely associated with leukemia cutis, which is more often seen in leukemias of myeloid origin. We present the case of an adult male diagnosed with near ETP-ALL, with IDH2 and DNMT3A mutations, suggestive of a myeloid origin, and leukemia cutis. After the patient progressed on hyper-CVAD and nelarabine, we treated him with the BCL-2 inhibitor venetoclax and the hypomethylating agent decitabine. The regimen induced a rapid bone marrow response and resolution of the leukemia cutis.
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Affiliation(s)
- Poorva Vaidya
- Department of Internal Medicine, Division of Hematology-Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | - Huan-You Wang
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Michelle D. Don
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Brian R. Hinds
- Department of Dermatology, University of California, San Diego, La Jolla, CA, United States
| | - James K. Mangan
- Department of Internal Medicine, Division of Blood and Marrow Transplantation, Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
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28
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Weeks LD, Ebert BL. Causes and consequences of clonal hematopoiesis. Blood 2023; 142:2235-2246. [PMID: 37931207 PMCID: PMC10862247 DOI: 10.1182/blood.2023022222] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) is described as the outsized contribution of expanded clones of hematopoietic stem and progenitor cells (HSPCs) to blood cell production. The prevalence of CH increases dramatically with age. CH can be caused by somatic mutations in individual genes or by gains and/or losses of larger chromosomal segments. CH is a premalignant state; the somatic mutations detected in CH are the initiating mutations for hematologic malignancies, and CH is a strong predictor of the development of blood cancers. Moreover, CH is associated with nonmalignant disorders and increased overall mortality. The somatic mutations that drive clonal expansion of HSPCs can alter the function of terminally differentiated blood cells, including the release of elevated levels of inflammatory cytokines. These cytokines may then contribute to a broad range of inflammatory disorders that increase in prevalence with age. Specific somatic mutations in the peripheral blood in coordination with blood count parameters can powerfully predict the development of hematologic malignancies and overall mortality in CH. In this review, we summarize the current understanding of CH nosology and origins. We provide an overview of available tools for risk stratification and discuss management strategies for patients with CH presenting to hematology clinics.
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Affiliation(s)
- Lachelle D. Weeks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Early Detection and Interception of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Early Detection and Interception of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
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29
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Cacic AM, Schulz FI, Germing U, Dietrich S, Gattermann N. Molecular and clinical aspects relevant for counseling individuals with clonal hematopoiesis of indeterminate potential. Front Oncol 2023; 13:1303785. [PMID: 38162500 PMCID: PMC10754976 DOI: 10.3389/fonc.2023.1303785] [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: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has fascinated the medical community for some time. Discovered about a decade ago, this phenomenon links age-related alterations in hematopoiesis not only to the later development of hematological malignancies but also to an increased risk of early-onset cardiovascular disease and some other disorders. CHIP is detected in the blood and is characterized by clonally expanded somatic mutations in cancer-associated genes, predisposing to the development of hematologic neoplasms such as MDS and AML. CHIP-associated mutations often involve DNA damage repair genes and are frequently observed following prior cytotoxic cancer therapy. Genetic predisposition seems to be a contributing factor. It came as a surprise that CHIP significantly elevates the risk of myocardial infarction and stroke, and also contributes to heart failure and pulmonary hypertension. Meanwhile, evidence of mutant clonal macrophages in vessel walls and organ parenchyma helps to explain the pathophysiology. Besides aging, there are some risk factors promoting the appearance of CHIP, such as smoking, chronic inflammation, chronic sleep deprivation, and high birth weight. This article describes fundamental aspects of CHIP and explains its association with hematologic malignancies, cardiovascular disorders, and other medical conditions, while also exploring potential progress in the clinical management of affected individuals. While it is important to diagnose conditions that can lead to adverse, but potentially preventable, effects, it is equally important not to stress patients by confronting them with disconcerting findings that cannot be remedied. Individuals with diagnosed or suspected CHIP should receive counseling in a specialized outpatient clinic, where professionals from relevant medical specialties may help them to avoid the development of CHIP-related health problems. Unfortunately, useful treatments and clinical guidelines for managing CHIP are still largely lacking. However, there are some promising approaches regarding the management of cardiovascular disease risk. In the future, strategies aimed at restoration of gene function or inhibition of inflammatory mediators may become an option.
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Affiliation(s)
- Anna Maria Cacic
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Felicitas Isabel Schulz
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
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30
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Demajo S, Ramis-Zaldivar JE, Muiños F, Grau ML, Andrianova M, López-Bigas N, González-Pérez A. Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.13.23299893. [PMID: 38168256 PMCID: PMC10760256 DOI: 10.1101/2023.12.13.23299893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of a number of hematologic malignancies, cardiovascular diseases and other conditions. Although the most frequently mutated CH driver genes have been identified, a systematic landscape of the mutations capable of initiating this phenomenon is still lacking. Here, we train high-quality machine-learning models for 12 of the most recurrent CH driver genes to identify their driver mutations. These models outperform an experimental base-editing approach and expert-curated rules based on prior knowledge of the function of these genes. Moreover, their application to identify CH driver mutations across almost half a million donors of the UK Biobank reproduces known associations between CH driver mutations and age, and the prevalence of several diseases and conditions. We thus propose that these models support the accurate identification of CH across healthy individuals.
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Affiliation(s)
- Santiago Demajo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Joan Enric Ramis-Zaldivar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel L Grau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Maria Andrianova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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31
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Stacey SN, Zink F, Halldorsson GH, Stefansdottir L, Gudjonsson SA, Einarsson G, Hjörleifsson G, Eiriksdottir T, Helgadottir A, Björnsdottir G, Thorgeirsson TE, Olafsdottir TA, Jonsdottir I, Gretarsdottir S, Tragante V, Magnusson MK, Jonsson H, Gudmundsson J, Olafsson S, Holm H, Gudbjartsson DF, Sulem P, Helgason A, Thorsteinsdottir U, Tryggvadottir L, Rafnar T, Melsted P, Ulfarsson MÖ, Vidarsson B, Thorleifsson G, Stefansson K. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis. Nat Genet 2023; 55:2149-2159. [PMID: 37932435 PMCID: PMC10703693 DOI: 10.1038/s41588-023-01555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
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Affiliation(s)
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Ö Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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32
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Hallermayr A, Keßler T, Steinke-Lange V, Heitzer E, Holinski-Feder E, Speicher M. The utility of liquid biopsy in clinical genetic diagnosis of cancer and monogenic mosaic disorders. MED GENET-BERLIN 2023; 35:275-284. [PMID: 38835734 PMCID: PMC11006364 DOI: 10.1515/medgen-2023-2066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsy for minimally invasive diagnosis and monitoring of cancer patients is progressing toward routine clinical practice. With the implementation of highly sensitive next-generation sequencing (NGS) based assays for the analysis of cfDNA, however, consideration of the utility of liquid biopsy for clinical genetic testing is critical. While the focus of liquid biopsy for cancer diagnosis is the detection of circulating tumor DNA (ctDNA) as a fraction of total cell-free DNA (cfDNA), cfDNA analysis reveals both somatic mosaic tumor and germline variants and clonal hematopoiesis. Here we outline advantages and limitations of mosaic and germline variant detection as well as the impact of clonal hematopoiesis on liquid biopsy in cancer diagnosis. We also evaluate the potential of cfDNA analysis for the molecular diagnosis of monogenic mosaic disorders.
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Affiliation(s)
| | - Thomas Keßler
- MGZ - Medizinisch Genetisches Zentrum München Germany
| | | | - Ellen Heitzer
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria) Graz Austria
| | | | - Michael Speicher
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Neue Stiftingtalstraße 2 Graz Austria
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33
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Köhrer S, Dittrich T, Schorb M, Weinhold N, Haberbosch I, Börmel M, Pajor G, Goldschmidt H, Müller-Tidow C, Raab MS, John L, Seckinger A, Brobeil A, Dreger P, Tornóczky T, Pajor L, Hegenbart U, Schönland SO, Schwab Y, Krämer A. High-throughput electron tomography identifies centriole over-elongation as an early event in plasma cell disorders. Leukemia 2023; 37:2468-2478. [PMID: 37821581 PMCID: PMC10681902 DOI: 10.1038/s41375-023-02056-y] [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: 08/02/2023] [Revised: 09/14/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Abstract
Plasma cell disorders are clonal outgrowths of pre-malignant or malignant plasma cells, characterized by extensive chromosomal aberrations. Centrosome abnormalities are a major driver of chromosomal instability in cancer but their origin, incidence, and composition in primary tumor cells is poorly understood. Using cutting-edge, semi-automated high-throughput electron tomography, we characterized at nanoscale 1386 centrioles in CD138pos plasma cells from eight healthy donors and 21 patients with plasma cell disorders, and 722 centrioles from different control populations. In plasma cells from healthy individuals, over-elongated centrioles accumulated with age. In plasma cell disorders, centriole over-elongation was notably frequent in early, pre-malignant disease stages, became less pronounced in overt multiple myeloma, and almost entirely disappeared in aggressive plasma cell leukemia. Centrioles in other types of patient-derived B cell neoplasms showed no over-elongation. In contrast to current belief, centriole length appears to be highly variable in long-lived, healthy plasma cells, and over-elongation and structural aberrations are common in this cell type. Our data suggest that structural centrosome aberrations accumulate with age in healthy CD138pos plasma cells and may thus play an important role in early aneuploidization as an oncogenic driver in plasma cell disorders.
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Affiliation(s)
- Sebastian Köhrer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Dittrich
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Isabella Haberbosch
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Mandy Börmel
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Gabor Pajor
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Pathology, University of Pécs Medical School and Clinic, Pécs, Hungary
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, GMMG-Studygroup at University of Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Marc S Raab
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Lukas John
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Anja Seckinger
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Alexander Brobeil
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Peter Dreger
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Tamás Tornóczky
- Department of Pathology, University of Pécs Medical School and Clinic, Pécs, Hungary
| | - László Pajor
- Department of Pathology, University of Pécs Medical School and Clinic, Pécs, Hungary
| | - Ute Hegenbart
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Stefan O Schönland
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
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34
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Helal C, Pobel C, Bayle A, Vasseur D, Nicotra C, Blanc-Durand F, Naoun N, Bernard-Tessier A, Patrikidou A, Colomba E, Flippot R, Fuerea A, Auger N, Ngo Camus M, Besse B, Lacroix L, Rouleau E, Ponce S, Italiano A, Loriot Y. Clinical utility of plasma ctDNA sequencing in metastatic urothelial cancer. Eur J Cancer 2023; 195:113368. [PMID: 37897866 DOI: 10.1016/j.ejca.2023.113368] [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: 07/21/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND Genomic stratification may help improve the management of patients with metastatic urothelial cancer (mUC), given the recent identification of targetable alterations. However, the collection of tissue samples remains challenging. Here, we assessed the clinical utility of plasma circulating tumour DNA (ctDNA) sequencing in these patients. METHODS Patients with mUC were prospectively enroled in the STING trial (NCT04932525), in which ctDNA was profiled using the Foundation One Liquid CDx Assay (324 genes, blood tumour mutational burden [bTMB], microsatellite instability status). Each genomic report was reviewed by a multidisciplinary tumor board (MTB). RESULTS Between January 2021 and June 2022, 140 mUC patients underwent molecular profiling. The median time to obtain the assay results was 20 days ((confidence interval) CI95%: [20,21]). The ctDNA analysis reproduced the somatic genomic landscape of previous tissue-based cohorts. Concordance for serial ctDNA samples was strong (r = 0.843 CI95%: [0.631-0.938], p < 0.001). At least one actionable target was detected in 63 patients (45%) with a total of 35 actionable alterations, including bTMB high (≥10 mutations/Mb) (N = 39, 21.1%), FGFR3 (N = 20, 10.8%), and Homologous recombination deficiency (HRD) alterations (N = 14, 7.6%). MTB recommended matched therapy in 63 patients (45.0%). Eight patients (5.7%) were treated, with an overall response rate of 50% (CI95%: 15.70-84.30) and a median progression-free survival (PFS) of 5.2 months (CI95%: 4.1 - NR). FGFR3 alterations were associated with a shorter PFS in patients treated with immunotherapy. CONCLUSION Overall, we demonstrated that genomic profiling with ctDNAs in mUC is a reliable and feasible approach for the timely initiation of genotype-matched therapies.
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Affiliation(s)
- Clara Helal
- Sorbonne University, Paris, France; Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | | | - Arnaud Bayle
- INSERM U981, Gustave Roussy, Villejuif, France; Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Damien Vasseur
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, Gustave Roussy, Université Paris-Saclay, Villejuif, France; AMMICA, INSERM US23/CNRS UMS3655,Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Claudio Nicotra
- Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Félix Blanc-Durand
- Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Natacha Naoun
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Alice Bernard-Tessier
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France; Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Anna Patrikidou
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Emeline Colomba
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Ronan Flippot
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Alina Fuerea
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Nathalie Auger
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Maud Ngo Camus
- Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Benjamin Besse
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Ludovic Lacroix
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Etienne Rouleau
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France
| | - Santiago Ponce
- Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Antoine Italiano
- Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Yohann Loriot
- Département de médecine oncologique, Gustave Roussy, université Paris-Saclay, Villejuif, France; INSERM U981, Gustave Roussy, Villejuif, France; Drug Development Department (DITEP), Gustave Roussy, Université Paris-Saclay, Villejuif, France.
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35
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Nathan DI, Dougherty M, Bhatta M, Mascarenhas J, Marcellino BK. Clonal hematopoiesis and inflammation: A review of mechanisms and clinical implications. Crit Rev Oncol Hematol 2023; 192:104187. [PMID: 37879493 DOI: 10.1016/j.critrevonc.2023.104187] [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: 06/03/2023] [Revised: 09/21/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined by the presence of somatic mutations in hematopoietic stem and progenitor cells (HSPC). CH is associated primarily with advancing age and confers an elevated risk of progression to overt hematologic malignancy and cardiovascular disease. Increasingly, CH is associated with a wide range of diseases driven by, and sequelae of, inflammation. Accordingly, there is great interest in better understanding the pathophysiologic and clinical relationship between CH, aging, and disease. Both observational and experimental findings support the concept that CH is a potential common denominator in the inflammatory outcomes of aging. However, there is also evidence that local and systemic inflammatory states promote the growth and select for CH clones. In this review, we aim to provide an up-to-date summary of the nature of the relationship between inflammation and CH, which is central to unlocking potential therapeutic opportunities to prevent progression to myeloid malignancy.
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Affiliation(s)
- Daniel I Nathan
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Max Dougherty
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manasa Bhatta
- Department of Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Mascarenhas
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bridget K Marcellino
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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36
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Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O'Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2312-2330. [PMID: 37910143 PMCID: PMC10648575 DOI: 10.1158/2767-9764.crc-23-0140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
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Affiliation(s)
- Felicia Gomez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Bryan Fisk
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Joshua F. McMichael
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Matthew Mosior
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Jennifer A. Foltz
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Christopher A. Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Haley Abel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Shan Li
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - David A. Russler-Germain
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Marcus P. Watkins
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Cody A. Ramirez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Alina Schmidt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Lee Trani
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Julia A. Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Michelle D. O'Laughlin
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Amanda F. Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Neha Mehta-Shah
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Brad S. Kahl
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Jason Walker
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Todd A. Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
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Chen CW, Zhang L, Dutta R, Niroula A, Miller PG, Gibson CJ, Bick AG, Reyes JM, Lee YT, Tovy A, Gu T, Waldvogel S, Chen YH, Venters BJ, Estève PO, Pradhan S, Keogh MC, Natarajan P, Takahashi K, Sperling AS, Goodell MA. SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation. Cell Stem Cell 2023; 30:1503-1519.e8. [PMID: 37863054 PMCID: PMC10841682 DOI: 10.1016/j.stem.2023.09.011] [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: 04/27/2023] [Revised: 07/25/2023] [Accepted: 09/27/2023] [Indexed: 10/22/2023]
Abstract
Somatic mutations accumulate in all cells with age and can confer a selective advantage, leading to clonal expansion over time. In hematopoietic cells, mutations in a subset of genes regulating DNA repair or epigenetics frequently lead to clonal hematopoiesis (CH). Here, we describe the context and mechanisms that lead to enrichment of hematopoietic stem cells (HSCs) with mutations in SRCAP, which encodes a chromatin remodeler that also influences DNA repair. We show that SRCAP mutations confer a selective advantage in human cells and in mice upon treatment with the anthracycline-class chemotherapeutic doxorubicin and bone marrow transplantation. Furthermore, Srcap mutations lead to a lymphoid-biased expansion, driven by loss of SRCAP-regulated H2A.Z deposition and increased DNA repair. Altogether, we demonstrate that SRCAP operates at the intersection of multiple pathways in stem and progenitor cells, offering a new perspective on the functional impact of genetic variants that promote stem cell competition in the hematopoietic system.
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Affiliation(s)
- Chun-Wei Chen
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Linda Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Program in Translational Biology and Molecular Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Ravi Dutta
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
| | - Abhishek Niroula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter G Miller
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Alexander G Bick
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jaime M Reyes
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yi-Tang Lee
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayala Tovy
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Tianpeng Gu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Sarah Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Yi-Hung Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | - Pradeep Natarajan
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adam S Sperling
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA.
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38
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Jakubek YA, Zhou Y, Stilp A, Bacon J, Wong JW, Ozcan Z, Arnett D, Barnes K, Bis JC, Boerwinkle E, Brody JA, Carson AP, Chasman DI, Chen J, Cho M, Conomos MP, Cox N, Doyle MF, Fornage M, Guo X, Kardia SLR, Lewis JP, Loos RJF, Ma X, Machiela MJ, Mack TM, Mathias RA, Mitchell BD, Mychaleckyj JC, North K, Pankratz N, Peyser PA, Preuss MH, Psaty B, Raffield LM, Vasan RS, Redline S, Rich SS, Rotter JI, Silverman EK, Smith JA, Smith AP, Taub M, Taylor KD, Yun J, Li Y, Desai P, Bick AG, Reiner AP, Scheet P, Auer PL. Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. Nat Genet 2023; 55:1912-1919. [PMID: 37904051 PMCID: PMC10632132 DOI: 10.1038/s41588-023-01553-1] [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: 11/04/2022] [Accepted: 09/27/2023] [Indexed: 11/01/2023]
Abstract
Megabase-scale mosaic chromosomal alterations (mCAs) in blood are prognostic markers for a host of human diseases. Here, to gain a better understanding of mCA rates in genetically diverse populations, we analyzed whole-genome sequencing data from 67,390 individuals from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program. We observed higher sensitivity with whole-genome sequencing data, compared with array-based data, in uncovering mCAs at low mutant cell fractions and found that individuals of European ancestry have the highest rates of autosomal mCAs and the lowest rates of chromosome X mCAs, compared with individuals of African or Hispanic ancestry. Although further studies in diverse populations will be needed to replicate our findings, we report three loci associated with loss of chromosome X, associations between autosomal mCAs and rare variants in DCPS, ADM17, PPP1R16B and TET2 and ancestry-specific variants in ATM and MPL with mCAs in cis.
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Affiliation(s)
- Yasminka A Jakubek
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Ying Zhou
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jason Bacon
- Department of Computer Science, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Justin W Wong
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Zuhal Ozcan
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington Seattle, Seattle, WA, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nancy Cox
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret F Doyle
- Department of Pathology and Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xiaolong Ma
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Taralynn M Mack
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kari North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Aaron P Smith
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Margaret Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yun Li
- Department of Biostatistics, Department of Genetics, Department of Computer Science, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Paul Scheet
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJ, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun J, DeMeo D, Levy D, Johnson A, Mathias R, Taub M, Arnett D, North K, Raffield LM, Carson A, Doyle MF, Rich SS, Rotter JI, Guo X, Cox N, Roden DM, Franceschini N, Desai P, Reiner A, Auer PL, Scheet P, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.20.23297280. [PMID: 37905118 PMCID: PMC10615010 DOI: 10.1101/2023.10.20.23297280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well-understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our estimates of mCA fitness were correlated (R 2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using a theoretical probability distribution. Individuals with lymphoid-associated mCAs had a significantly higher white blood cell count and faster clonal expansion rate. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified TCL1A , NRIP1 , and TERT locus variants as modulators of mCA clonal expansion rate.
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40
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Ogura Y, Mimura I. Epigenetic roles in clonal hematopoiesis and aging kidney-related chronic kidney disease. Front Cell Dev Biol 2023; 11:1281850. [PMID: 37928907 PMCID: PMC10623128 DOI: 10.3389/fcell.2023.1281850] [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: 08/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Accumulation of somatic hematopoietic stem cell mutations with aging has been revealed by the recent genome-wide analysis. Clonal expansion, known as clonal hematopoiesis of indeterminate potential (CHIP), is a premalignant condition of hematological cancers. It is defined as the absence of definitive morphological evidence of a hematological neoplasm and occurrence of ≥2% of mutant allele fraction in the peripheral blood. In CHIP, the most frequently mutated genes are epigenetic regulators such as DNMT3A, TET2, and ASXL1. CHIP induces inflammation. CHIP is shown to be associated with not only hematological malignancy but also non-malignant disorders such as atherosclerosis, cardiovascular diseases and chronic liver disease. In addition, recent several large clinical trials have shown that CHIP is also the risk factor for developing chronic kidney disease (CKD). In this review article, we proposed novel findings about CHIP and CHIP related kidney disease based on the recent basic and clinical research. The possible mechanism of the kidney injury in CHIP is supposed to be due to the clonal expansion in both myeloid and lymphoid cell lines. In myeloid cell lines, the mutated macrophages increase the inflammatory cytokine level and induce chronic inflammation. It leads to epigenetic downregulation of kidney and macrophage klotho level. In lymphoid cell lines, CHIP might be related to monoclonal gammopathy of renal significance (MGRS). It describes any B cell or plasma cell clonal disorder that does not fulfill the criteria for cancer yet produces a nephrotoxic monoclonal immunoglobulin that leads to kidney injury or disease. MGRS causes M-protein related nephropathy frequently observed among aged CKD patients. It is important to consider the CHIP-related complications such as hematological malignancy, cardiovascular diseases and metabolic disorders in managing the elderly CKD patients. There are no established therapies for CHIP and CHIP-related CKD yet. However, recent studies have supported the development of effective CHIP therapies, such as blocking the expansion of aberrant HSCs and inhibiting chronic inflammation. In addition, drugs targeting the epigenetic regulation of Klotho in the kidney and macrophages might be therapeutic targets of CHIP in the kidney.
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Affiliation(s)
| | - Imari Mimura
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Pascual J, Gil-Gil M, Proszek P, Zielinski C, Reay A, Ruiz-Borrego M, Cutts R, Ciruelos Gil EM, Feber A, Muñoz-Mateu M, Swift C, Bermejo B, Herranz J, Margeli Vila M, Antón A, Kahan Z, Csöszi T, Liu Y, Fernandez-Garcia D, Garcia-Murillas I, Hubank M, Turner NC, Martín M. Baseline Mutations and ctDNA Dynamics as Prognostic and Predictive Factors in ER-Positive/HER2-Negative Metastatic Breast Cancer Patients. Clin Cancer Res 2023; 29:4166-4177. [PMID: 37490393 PMCID: PMC10570672 DOI: 10.1158/1078-0432.ccr-23-0956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 07/27/2023]
Abstract
PURPOSE Prognostic and predictive biomarkers to cyclin-dependent kinases 4 and 6 inhibitors are lacking. Circulating tumor DNA (ctDNA) can be used to profile these patients and dynamic changes in ctDNA could be an early predictor of treatment efficacy. Here, we conducted plasma ctDNA profiling in patients from the PEARL trial comparing palbociclib+fulvestrant versus capecitabine to investigate associations between baseline genomic landscape and on-treatment ctDNA dynamics with treatment efficacy. EXPERIMENTAL DESIGN Correlative blood samples were collected at baseline [cycle 1-day 1 (C1D1)] and prior to treatment [cycle 1-day 15 (C1D15)]. Plasma ctDNA was sequenced with a custom error-corrected capture panel, with both univariate and multivariate Cox models used for treatment efficacy associations. A prespecified methodology measuring ctDNA changes in clonal mutations between C1D1 and C1D15 was used for the on-treatment ctDNA dynamic model. RESULTS 201 patients were profiled at baseline, with ctDNA detection associated with worse progression-free survival (PFS)/overall survival (OS). Detectable TP53 mutation showed worse PFS and OS in both treatment arms, even after restricting population to baseline ctDNA detection. ESR1 mutations were associated with worse OS overall, which was lost when restricting population to baseline ctDNA detection. PIK3CA mutations confer worse OS only to patients on the palbociclib+fulvestrant treatment arm. ctDNA dynamics analysis (n = 120) showed higher ctDNA suppression in the capecitabine arm. Patients without ctDNA suppression showed worse PFS in both treatment arms. CONCLUSIONS We show impaired survival irrespective of endocrine or chemotherapy-based treatments for patients with hormone receptor-positive/HER2-negative metastatic breast cancer harboring plasma TP53 mutations. Early ctDNA suppression may provide treatment efficacy predictions. Further validation to fully demonstrate clinical utility of ctDNA dynamics is warranted.
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Affiliation(s)
- Javier Pascual
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Málaga, Spain
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
| | - Miguel Gil-Gil
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Institut Català d'Oncologia (ICO), Barcelona, Spain
- IDIBELL, L'Hospitalet, Barcelona, Spain
| | - Paula Proszek
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Christoph Zielinski
- Medical Oncology, Central European Cancer Center, Wiener Privatklinik Hospital, Vienna, Austria
- CECOG Central European Cooperative Oncology Group, Vienna, Austria
| | - Alistair Reay
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Manuel Ruiz-Borrego
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Medical Oncology, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Rosalind Cutts
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Eva M. Ciruelos Gil
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Andrew Feber
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Montserrat Muñoz-Mateu
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Department of Medical Oncology and Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Claire Swift
- Ralph Lauren Centre for Breast Cancer Research, London, United Kingdom
| | - Begoña Bermejo
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
- Medical Oncology, Hospital Clínico Universitario de Valencia, Biomedical Research Institute INCLIVA, Valencia, Spain
- Medicine Department, Universidad de Valencia, Valencia, Spain
| | | | - Mireia Margeli Vila
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- B-ARGO Group, Catalan Institute of Oncology-Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Antonio Antón
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
- Medical Oncology, Hospital Universitario Miguel Servet, Medicine Department, Universidad de Zaragoza, Instituto de Investigación Sanitaria Aragón, Zaragoza, Spain
| | - Zsuzsanna Kahan
- CECOG Central European Cooperative Oncology Group, Vienna, Austria
- Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Tibor Csöszi
- CECOG Central European Cooperative Oncology Group, Vienna, Austria
- Jász-Nagykun-Szolnok Megyei Hetényi Géza Kórház-Rendelőintézet, Szolnok, Hungary
| | - Yuan Liu
- Pfizer, La Jolla, San Diego, California
| | | | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Michael Hubank
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Nicholas C. Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
- Ralph Lauren Centre for Breast Cancer Research, London, United Kingdom
| | - Miguel Martín
- GEICAM Spanish Breast Cancer Group, Madrid, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
- Medical Oncology, Instituto de Investigación Sanitaria Gregorio Marañón, Medicine Department, Universidad Complutense, Madrid, Spain
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42
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Watson CJ, Blundell JR. Mutation rates and fitness consequences of mosaic chromosomal alterations in blood. Nat Genet 2023; 55:1677-1685. [PMID: 37697102 PMCID: PMC10562253 DOI: 10.1038/s41588-023-01490-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] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 07/28/2023] [Indexed: 09/13/2023]
Abstract
Mosaic chromosomal alterations (mCAs) are common in cancers and can arise decades before diagnosis. A quantitative understanding of the rate at which these events occur, and their functional consequences, could improve cancer risk prediction and our understanding of somatic evolution. Using mCA clone size estimates from the blood of approximately 500,000 UK Biobank participants, we estimate mutation rates and fitness consequences of acquired gain, loss and copy-neutral loss of heterozygosity events. Most mCAs have moderate to high fitness effects but occur at a low rate, being more than tenfold less common than equivalently fit single-nucleotide variants. Notable exceptions are mosaic loss of X and Y, which we estimate have roughly 1,000-fold higher mutation rates than autosomal mCAs. Although the way in which most mCAs increase in prevalence with age is consistent with constant growth rates, some mCAs exhibit different behavior, suggesting that their fitness may depend on inherited variants, extrinsic factors or distributions of fitness effects.
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Affiliation(s)
- Caroline J Watson
- Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, Cambridgeshire, UK.
| | - Jamie R Blundell
- Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, Cambridgeshire, UK.
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43
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Lehikoinen J, Valori M, Jääskeläinen AJ, Laakso SM, Arstila TP, Tienari PJ. High Epstein-Barr virus capsid antigen IgG level associates with the carriership of CD8+ T cell somatic mutations in the STAT3 SH2 domain. Clin Immunol 2023; 255:109733. [PMID: 37572949 DOI: 10.1016/j.clim.2023.109733] [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: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
High carrier prevalence of STAT3 SH2 domain somatic mutations was recently discovered in CD8+ T cells. We found these low-allele-fraction clones in 26% of donors, without difference between multiple sclerosis (MS) patients and controls. Here we tested whether anti-viral antibodies associate with the carriership of these mutant clones. We compared antibody responses against common viruses in mutation carriers vs. non-carriers. Plasma samples of 152 donors (92 MS patients, 60 controls) were analyzed for antibodies against cytomegalovirus (CMV), Epstein-Barr virus (EBV), human herpesvirus-6A and parvovirus B19. The mutation carrier status associated with EBV VCA IgG level (p = 0.005) and remained significant after logistic regression (p = 0.036). This association was contributed similarly by MS patients and controls. These results suggest that EBV contributes to the generation or growth of these clones. The pathogenic role of the STAT3 mutant clones in MS is presently unclear, but their detailed characterization warrants further study.
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Affiliation(s)
- Joonas Lehikoinen
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland.
| | - Miko Valori
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Anne J Jääskeläinen
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital
| | - Sini M Laakso
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland
| | - T Petteri Arstila
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Bacteriology and Immunology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland
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44
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Salaverria I, Weigert O, Quintanilla-Martinez L. The clinical and molecular taxonomy of t(14;18)-negative follicular lymphomas. Blood Adv 2023; 7:5258-5271. [PMID: 37561599 PMCID: PMC10500559 DOI: 10.1182/bloodadvances.2022009456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/12/2023] Open
Abstract
Follicular lymphoma (FL) is a neoplasm derived from germinal center B cells, composed of centrocytes and centroblasts, with at least a focal follicular growth pattern. The t(14;18) translocation together with epigenetic deregulation through recurrent genetic alterations are now recognized as the hallmark of FL. Nevertheless, FL is a heterogeneous disease, clinically, morphologically, and biologically. The existence of FL lacking the t(14;18) chromosomal alteration highlights the complex pathogenesis of FL, and indicates that there are alternative pathogenetic mechanisms that can induce a neoplasm with follicular center B-cell phenotype. Based on their clinical presentation, t(14;18)-negative FLs can be divided into 3 broad groups: nodal presentation, extranodal presentation, and those affecting predominantly children and young adults. Recent studies have shed some light into the genetic alterations of t(14;18)-negative FL. Within the group of t(14;18)-negative FL with nodal presentation, cases with STAT6 mutations are increasingly recognized as a distinctive molecular subgroup, often cooccurring with CREBBP and/or TNFRSF14 mutations. FL with BCL6 rearrangement shows clinicopathological similarities to its t(14;18)-positive counterpart. In contrast, t(14;18)-negative FL in extranodal sites is characterized mainly by TNFRSF14 mutations in the absence of chromatin modifying gene mutations. FL in children have a unique molecular landscape when compared with those in adults. Pediatric-type FL (PTFL) is characterized by MAP2K1, TNFRSF14, and/or IRF8 mutations, whereas large B-cell lymphoma with IRF4 rearrangement is now recognized as a distinct entity, different from PTFL. Ultimately, a better understanding of FL biology and heterogeneity should help to understand the clinical differences and help guide patient management and treatment decisions.
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Affiliation(s)
- Itziar Salaverria
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Oliver Weigert
- Laboratory for Experimental Leukemia and Lymphoma Research, Ludwig-Maximilians-University Hospital, Munich, Germany
- Department of Medicine III, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology and Comprehensive Cancer Center Tübingen, University Hospital Tübingen, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT “Image-guided and functionally Instructed Tumor therapies,” Eberhard-Karls University of Tübingen, Tübingen, Germany
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45
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [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: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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46
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Brown DW, Cato LD, Zhao Y, Nandakumar SK, Bao EL, Gardner EJ, Hubbard AK, DePaulis A, Rehling T, Song L, Yu K, Chanock SJ, Perry JRB, Sankaran VG, Machiela MJ. Shared and distinct genetic etiologies for different types of clonal hematopoiesis. Nat Commun 2023; 14:5536. [PMID: 37684235 PMCID: PMC10491829 DOI: 10.1038/s41467-023-41315-5] [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: 01/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Clonal hematopoiesis (CH)-age-related expansion of mutated hematopoietic clones-can differ in frequency and cellular fitness by CH type (e.g., mutations in driver genes (CHIP), gains/losses and copy-neutral loss of chromosomal segments (mCAs), and loss of sex chromosomes). Co-occurring CH raises questions as to their origin, selection, and impact. We integrate sequence and genotype array data in up to 482,378 UK Biobank participants to demonstrate shared genetic architecture across CH types. Our analysis suggests a cellular evolutionary trade-off between different types of CH, with LOY occurring at lower rates in individuals carrying mutations in established CHIP genes. We observed co-occurrence of CHIP and mCAs with overlap at TET2, DNMT3A, and JAK2, in which CHIP precedes mCA acquisition. Furthermore, individuals carrying overlapping CH had high risk of future lymphoid and myeloid malignancies. Finally, we leverage shared genetic architecture of CH traits to identify 15 novel loci associated with leukemia risk.
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Affiliation(s)
- Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yajie Zhao
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Bronx, NY, 10461, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alexander DePaulis
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Thomas Rehling
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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47
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Uddin MM, Saadatagah S, Niroula A, Yu B, Hornsby W, Ganesh S, Lannery K, Shuermans A, Honigberg MC, Bick AG, Libby P, Ebert BL, Ballantyne CM, Natarajan P. Long-term longitudinal analysis of 4,187 participants reveals new insights into determinants of incident clonal hematopoiesis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.05.23295093. [PMID: 37732181 PMCID: PMC10508802 DOI: 10.1101/2023.09.05.23295093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Clonal hematopoiesis (CH), characterized by blood cells predominantly originating from a single mutated hematopoietic stem cell, is linked to diverse aging-related diseases, including hematologic malignancy and atherosclerotic cardiovascular disease (ASCVD). While CH is common among older adults, the underlying factors driving its development are largely unknown. To address this, we performed whole-exome sequencing on 8,374 blood DNA samples collected from 4,187 Atherosclerosis Risk in Communities Study (ARIC) participants over a median follow-up of 21 years. During this period, 735 participants developed incident CH. We found that age at baseline, sex, and dyslipidemia significantly influence the incidence of CH, while ASCVD and other traditional risk factors for ASCVD did not exhibit such associations. Our study also revealed associations between germline genetic variants and incident CH, prioritizing genes in CH development. Our comprehensive longitudinal assessment yields novel insights into the factors contributing to incident CH in older adults.
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Affiliation(s)
- Md Mesbah Uddin
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Seyedmohammad Saadatagah
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Center for Translational Research on Inflammatory Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Abhishek Niroula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Biomedicine, SciLifeLab, University of Gothenburg, Gothenburg, Sweden
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Whitney Hornsby
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Shriienidhie Ganesh
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kim Lannery
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Art Shuermans
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Michael C. Honigberg
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Libby
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Benjamin L. Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Pradeep Natarajan
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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48
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Gu M, Kovilakam SC, Dunn WG, Marando L, Barcena C, Mohorianu I, Smith A, Kar SP, Fabre MA, Gerstung M, Cargo CA, Malcovati L, Quiros PM, Vassiliou GS. Multiparameter prediction of myeloid neoplasia risk. Nat Genet 2023; 55:1523-1530. [PMID: 37620601 PMCID: PMC10484784 DOI: 10.1038/s41588-023-01472-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
The myeloid neoplasms encompass acute myeloid leukemia, myelodysplastic syndromes and myeloproliferative neoplasms. Most cases arise from the shared ancestor of clonal hematopoiesis (CH). Here we analyze data from 454,340 UK Biobank participants, of whom 1,808 developed a myeloid neoplasm 0-15 years after recruitment. We describe the differences in CH mutational landscapes and hematology/biochemistry test parameters among individuals that later develop myeloid neoplasms (pre-MN) versus controls, finding that disease-specific changes are detectable years before diagnosis. By analyzing differences between 'pre-MN' and controls, we develop and validate Cox regression models quantifying the risk of progression to each myeloid neoplasm subtype. We construct 'MN-predict', a web application that generates time-dependent predictions with the input of basic blood tests and genetic data. Our study demonstrates that many individuals that develop myeloid neoplasms can be identified years in advance and provides a framework for disease-specific prognostication that will be of substantial use to researchers and physicians.
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Affiliation(s)
- Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sruthi Cheloor Kovilakam
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - William G Dunn
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Clea Barcena
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Biochemistry and Molecular Biology, Universidad de Oviedo, Oviedo, Spain
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alexandra Smith
- Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - Siddhartha P Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Section of Translational Epidemiology, Division of Population Health Sciences, Bristol, Medical School, University of Bristol, Bristol, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Margarete A Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Moritz Gerstung
- Division of Artificial Intelligence in Oncology, DKFZ, Heidelberg, Germany
| | - Catherine A Cargo
- Haematological Malignancy Diagnostic Service, St James's Hospital, Leeds, UK
- Department of Haematology, Leeds Teaching Hospitals, Leeds, UK
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Pedro M Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain.
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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49
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Jung SH, Lee CK, Kwon WS, Yun S, Jung M, Kim HS, Chung HC, Chung YJ, Rha SY. Monitoring the Outcomes of Systemic Chemotherapy Including Immune Checkpoint Inhibitor for HER2-Positive Metastatic Gastric Cancer by Liquid Biopsy. Yonsei Med J 2023; 64:531-540. [PMID: 37634629 PMCID: PMC10462813 DOI: 10.3349/ymj.2023.0096] [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: 04/18/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 08/29/2023] Open
Abstract
PURPOSE For precision medicine, exploration and monitoring of molecular biomarkers are essential. However, in advanced gastric cancer (GC) with visceral lesions, an invasive procedure cannot be performed repeatedly for the follow-up of molecular biomarkers. MATERIALS AND METHODS To verify the clinical implication of serial liquid biopsies targeting circulating tumor DNA (ctDNA) on treatment response, we conducted targeted deep sequencing for serially collected ctDNA of 15 HER2-positive metastatic GC patients treated with anti-PD-1 inhibitor in combination with standard systemic treatment. RESULTS In the baseline ctDNAs, 14 patients (93%) harbored more than one genetic alteration. A number of mutations in well-known cancer-related genes, such as KRAS and PIK3CA, were identified. Copy number alterations were identified in eight GCs (53.3%), and amplification of the ERBB2 gene (6/15, 40.0%) was the most recurrent. When we calculated the mean variant allele frequency (VAF) of mutations in each ctDNA as the molecular tumor burden index (mTBI), the mTBI trend was largely consistent with the VAF profiles in both responder and non-responder groups. Notably, in the longitudinal analysis of ctDNA, mTBI provided 2-42 weeks (mean 13.4 weeks) lead time in the detection of disease progression compared to conventional follow-up with CT imaging. CONCLUSION Our data indicate that the serial genetic alteration profiling of ctDNA is feasible to predict treatment response in HER2-positive GC patients in a minimally invasive manner. Practically, ctDNA profiles are useful not only for the molecular diagnosis of GC but also for the selection of GC patients with poor prognosis for systemic treatment (ClinicalTrials.gov identifier: NCT02901301).
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Affiliation(s)
- Seung-Hyun Jung
- Department of Biochemistry, IRCGP, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Korea
| | - Woo Sun Kwon
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Sujin Yun
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Minkyu Jung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Cheol Chung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Sun Young Rha
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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50
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Belizaire R, Wong WJ, Robinette ML, Ebert BL. Clonal haematopoiesis and dysregulation of the immune system. Nat Rev Immunol 2023; 23:595-610. [PMID: 36941354 PMCID: PMC11140722 DOI: 10.1038/s41577-023-00843-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2023] [Indexed: 03/23/2023]
Abstract
Age-related diseases are frequently linked to pathological immune dysfunction, including excessive inflammation, autoreactivity and immunodeficiency. Recent analyses of human genetic data have revealed that somatic mutations and mosaic chromosomal alterations in blood cells - a condition known as clonal haematopoiesis (CH) - are associated with ageing and pathological immune dysfunction. Indeed, large-scale epidemiological studies and experimental mouse models have demonstrated that CH can promote cardiovascular disease, chronic obstructive pulmonary disease, chronic liver disease, osteoporosis and gout. The genes most frequently mutated in CH, the epigenetic regulators TET2 and DNMT3A, implicate increased chemokine expression and inflammasome hyperactivation in myeloid cells as a possible mechanistic connection between CH and age-related diseases. In addition, TET2 and DNMT3A mutations in lymphoid cells have been shown to drive methylation-dependent alterations in differentiation and function. Here we review the observational and mechanistic studies describing the connection between CH and pathological immune dysfunction, the effects of CH-associated genetic alterations on the function of myeloid and lymphoid cells, and the clinical and therapeutic implications of CH as a target for immunomodulation.
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Affiliation(s)
- Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Waihay J Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Michelle L Robinette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA, USA.
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