1
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David C, Arango-Franco CA, Badonyi M, Fouchet J, Rice GI, Didry-Barca B, Maisonneuve L, Seabra L, Kechiche R, Masson C, Cobat A, Abel L, Talouarn E, Béziat V, Deswarte C, Livingstone K, Paul C, Malik G, Ross A, Adam J, Walsh J, Kumar S, Bonnet D, Bodemer C, Bader-Meunier B, Marsh JA, Casanova JL, Crow YJ, Manoury B, Frémond ML, Bohlen J, Lepelley A. Gain-of-function human UNC93B1 variants cause systemic lupus erythematosus and chilblain lupus. J Exp Med 2024; 221:e20232066. [PMID: 38869500 PMCID: PMC11176256 DOI: 10.1084/jem.20232066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/29/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
UNC93B1 is a transmembrane domain protein mediating the signaling of endosomal Toll-like receptors (TLRs). We report five families harboring rare missense substitutions (I317M, G325C, L330R, R466S, and R525P) in UNC93B1 causing systemic lupus erythematosus (SLE) or chilblain lupus (CBL) as either autosomal dominant or autosomal recessive traits. As for a D34A mutation causing murine lupus, we recorded a gain of TLR7 and, to a lesser extent, TLR8 activity with the I317M (in vitro) and G325C (in vitro and ex vivo) variants in the context of SLE. Contrastingly, in three families segregating CBL, the L330R, R466S, and R525P variants were isomorphic with respect to TLR7 activity in vitro and, for R525P, ex vivo. Rather, these variants demonstrated a gain of TLR8 activity. We observed enhanced interaction of the G325C, L330R, and R466S variants with TLR8, but not the R525P substitution, indicating different disease mechanisms. Overall, these observations suggest that UNC93B1 mutations cause monogenic SLE or CBL due to differentially enhanced TLR7 and TLR8 signaling.
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Affiliation(s)
- Clémence David
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
| | - Carlos A. Arango-Franco
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Department of Microbiology and Parasitology, Group of Primary Immunodeficiencies, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Julien Fouchet
- Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Gillian I. Rice
- Faculty of Biology, Medicine and Health, Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Blaise Didry-Barca
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
| | - Lucie Maisonneuve
- Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Luis Seabra
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
| | - Robin Kechiche
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
- Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, Assistance publique–hôpitaux de Paris (AP-HP), Paris, France
| | - Cécile Masson
- Bioinformatics Core Facility, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité, Paris, France
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
| | - Katie Livingstone
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Carle Paul
- Université Toulouse Paul Sabatier, Toulouse, France
| | - Gulshan Malik
- Paediatric Rheumatology, Royal Aberdeen Children’s Hospital, Aberdeen, UK
| | - Alison Ross
- Paediatric Rheumatology, Royal Aberdeen Children’s Hospital, Aberdeen, UK
| | - Jane Adam
- Paediatric Rheumatology, Royal Aberdeen Children’s Hospital, Aberdeen, UK
| | - Jo Walsh
- Department of Paediatric Rheumatology, Royal Hospital for Children, Glasgow, UK
| | - Sathish Kumar
- Department of Pediatrics, Pediatric Rheumatology, Christian Medical College, Vellore, India
| | - Damien Bonnet
- Medical and Surgical Unit of Congenital and Paediatric Cardiology, Reference Centre for Complex Congenital Heart Defects—M3C, University Hospital Necker-Enfants Malades, Paris, France
- Université Paris Cité, Paris, France
| | - Christine Bodemer
- Department of Dermatology, Hospital Necker-Enfants Malades, AP-HP. Université Paris Cité, Paris, France
| | - Brigitte Bader-Meunier
- Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, Assistance publique–hôpitaux de Paris (AP-HP), Paris, France
- Centre for Inflammatory Rheumatism, AutoImmune Diseases and Systemic Interferonopathies in Children (RAISE), Paris, France
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Yanick J. Crow
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Université Paris Cité, Paris, France
| | - Bénédicte Manoury
- Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Marie-Louise Frémond
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
- Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, Assistance publique–hôpitaux de Paris (AP-HP), Paris, France
- Centre for Inflammatory Rheumatism, AutoImmune Diseases and Systemic Interferonopathies in Children (RAISE), Paris, France
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
| | - Alice Lepelley
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
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2
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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; 25:548-562. [PMID: 38548833 DOI: 10.1038/s41576-024-00709-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: 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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3
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Mack T, Vlasschaert C, von Beck K, Silver AJ, Heimlich JB, Poisner H, Condon HR, Ulloa J, Sochacki AL, Spaulding TP, Kishtagari A, Bejan CA, Xu Y, Savona MR, Jones A, Bick AG. Cost-Effective and Scalable Clonal Hematopoiesis Assay Provides Insight into Clonal Dynamics. J Mol Diagn 2024; 26:563-573. [PMID: 38588769 DOI: 10.1016/j.jmoldx.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon in which hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP mutations are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or to serial sequencing. In this study, an affordable (approximately US $8 per sample), accurate, and scalable sequencing assay for CHIP is introduced and validated. The efficacy of the assay was demonstrated by identifying CHIP mutations in a cohort of 456 individuals with DNA collected at multiple time points in Vanderbilt University's biobank and quantifying clonal expansion rates over time. A total of 101 individuals with CHIP/clonal cytopenia of undetermined significance were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction at both time points. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. Additionally, mutation co-occurrence and clonal competition between multiple driver mutations were explored.
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Affiliation(s)
- Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Kelly von Beck
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander J Silver
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - J Brett Heimlich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Henry R Condon
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jessica Ulloa
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Andrew L Sochacki
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Travis P Spaulding
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ashwin Kishtagari
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Angela Jones
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alexander G Bick
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee; Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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4
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Simitsis P, Nohria A, Kelleher J, Boulet J, Wanderley MRB, Natarajan P, Libby P, Mehra MR. Clonal Hematopoiesis of Indeterminate Potential and Long-term Outcomes in Heart Transplantation. J Card Fail 2024:S1071-9164(24)00204-5. [PMID: 38885783 DOI: 10.1016/j.cardfail.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Clonal hematopoiesis of indeterminate potential (CHIP) mutations, a trait of aging, has been associated with the progression of cardiovascular disease and the development of malignancy. Uncertainty prevails regarding a robust association between CHIP and heart-transplantation (HT) outcomes. OBJECTIVES To determine the prevalence of CHIP mutations in HT and their association with long-term outcomes, including cardiac allograft vasculopathy (CAV), graft failure, malignancy, and all-cause mortality. METHODS We conducted a mixed retrospective-prospective observational study of HT recipients with targeted sequencing for CHIP mutations (variant allele frequency [VAF] of ≥ 2%). The primary composite outcome was the first occurrence of CAV grade ≥ 2, graft failure, malignancy, cardiac retransplantation, or all-cause death. Secondary outcomes were the individual components of the composite primary outcome. Sensitivity analyses with base-case and extreme scenarios were performed. RESULTS Among 95 HT recipients, 30 had CHIP mutations (31.6%). DNMT3A mutations were most common (44.7%), followed by PPM1D (13.2%), SF3B1 (10.5%), TET2 (7.9%), and TP53 (7.9%). The only significant independent predictor of CHIP was age at enrollment or age at transplantation. After multivariable adjustment, CHIP mutations were not associated with the primary outcome, which occurred in 44 (46.3%) patients (HR = 0.487; 95% CI:0.197-1.204; P = 0.119), nor were they associated with mlalignancy alone, or death. CONCLUSION We demonstrated no association between CHIP mutations and post-transplant outcomes, including CAV, graft failure, malignancy, and all-cause mortality. In line with previously published data, our analysis provides additional evidence about the lack of clinical value of using CHIP mutations as a biomarker for surveillance in outcomes after HT.
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Affiliation(s)
- Panagiotis Simitsis
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Anju Nohria
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jane Kelleher
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jacinthe Boulet
- Department of Medicine, Division of Cardiology, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Mauro R B Wanderley
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mandeep R Mehra
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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5
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Werneth CM, Patel ZS, Thompson MS, Blattnig SR, Huff JL. Considering clonal hematopoiesis of indeterminate potential in space radiation risk analysis for hematologic cancers and cardiovascular disease. COMMUNICATIONS MEDICINE 2024; 4:105. [PMID: 38862635 PMCID: PMC11166645 DOI: 10.1038/s43856-023-00408-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/16/2023] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Expanding human presence in space through long-duration exploration missions and commercial space operations warrants improvements in approaches for quantifying crew space radiation health risks. Currently, risk assessment models for radiogenic cancer and cardiovascular disease consider age, sex, and tobacco use, but do not incorporate other modifiable (e.g., body weight, physical activity, diet, environment) and non-modifiable individual risk factors (e.g., genetics, medical history, race/ethnicity, family history) that may greatly influence crew health both in-mission and long-term. For example, clonal hematopoiesis of indeterminate potential (CHIP) is a relatively common age-related condition that is an emerging risk factor for a variety of diseases including cardiovascular disease and cancer. CHIP carrier status may therefore exacerbate health risks associated with space radiation exposure. METHODS In the present study, published CHIP hazard ratios were used to modify background hazard rates for coronary heart disease, stroke, and hematologic cancers in the National Aeronautics and Space Administration space radiation risk assessment model. The risk of radiation exposure-induced death for these endpoints was projected for a future Mars exploration mission scenario. RESULTS Here we show appreciable increases in the lifetime risk of exposure-induced death for hematologic malignancies, coronary heart disease, and stroke, which are observed as a function of age after radiation exposure for male and female crew members that are directly attributable to the elevated health risks for CHIP carriers. CONCLUSIONS We discuss the importance of evaluating individual risk factors such as CHIP as part of a comprehensive space radiation risk assessment strategy aimed at effective risk communication and disease surveillance for astronauts embarking on future exploration missions.
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Affiliation(s)
| | - Zarana S Patel
- Center for Scientific Review, National Institutes of Health, Bethesda, MD, USA
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Silver AJ, Vlasschaert C, Mack T, Sharber B, Xu Y, Bick AG, Pinson CW, Savona MR. Solid Organ Transplant Recipients Exhibit More TET2-Mutant Clonal Hematopoiesis of Indeterminate Potential Not Driven by Increased Transplantation Risk. Clin Cancer Res 2024; 30:2475-2485. [PMID: 38551504 DOI: 10.1158/1078-0432.ccr-23-3840] [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: 12/10/2023] [Revised: 02/14/2024] [Accepted: 03/26/2024] [Indexed: 06/04/2024]
Abstract
PURPOSE Solid organ transplant recipients comprise a unique population of immunosuppressed patients with increased risk of malignancy, including hematologic neoplasms. Clonal hematopoiesis of indeterminate potential (CHIP) represents a known risk factor for hematologic malignancy and this study describes the prevalence and patterns of CHIP mutations across several types of solid organ transplants. EXPERIMENTAL DESIGN We use two national biobank cohorts comprised of >650,000 participants with linked genomic and longitudinal phenotypic data to describe the features of CHIP across 2,610 individuals who received kidney, liver, heart, or lung allografts. RESULTS We find individuals with an allograft before their biobank enrollment had an increased prevalence of TET2 mutations (OR, 1.90; P = 4.0e-4), but individuals who received transplants post-enrollment had a CHIP mutation spectrum similar to that of the general population, without enrichment of TET2. In addition, we do not observe an association between CHIP and risk of incident transplantation among the overall population (HR, 1.02; P = 0.91). And in an exploratory analysis, we do not find evidence for a strong association between CHIP and rates of transplant complications such as rejection or graft failure. CONCLUSIONS These results demonstrate that recipients of solid organ transplants display a unique pattern of clonal hematopoiesis with enrichment of TET2 driver mutations, the causes of which remain unclear and are deserving of further study.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Taralynn Mack
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Brian Sharber
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - C Wright Pinson
- Transplant Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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7
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Arends CM, Kopp K, Hablesreiter R, Estrada N, Christen F, Moll UM, Zeillinger R, Schmitt WD, Sehouli J, Kulbe H, Fleischmann M, Ray-Coquard I, Zeimet A, Raspagliesi F, Zamagni C, Vergote I, Lorusso D, Concin N, Bullinger L, Braicu EI, Damm F. Dynamics of clonal hematopoiesis under DNA-damaging treatment in patients with ovarian cancer. Leukemia 2024; 38:1378-1389. [PMID: 38637689 PMCID: PMC11147769 DOI: 10.1038/s41375-024-02253-3] [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: 02/10/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Clonal hematopoiesis (CH) driven by mutations in the DNA damage response (DDR) pathway is frequent in patients with cancer and is associated with a higher risk of therapy-related myeloid neoplasms (t-MNs). Here, we analyzed 423 serial whole blood and plasma samples from 103 patients with relapsed high-grade ovarian cancer receiving carboplatin, poly(ADP-ribose) polymerase inhibitor (PARPi) and heat shock protein 90 inhibitor (HSP90i) treatment within the phase II EUDARIO trial using error-corrected sequencing of 72 genes. DDR-driven CH was detected in 35% of patients and was associated with longer duration of prior PARPi treatment. TP53- and PPM1D-mutated clones exhibited substantially higher clonal expansion rates than DNMT3A- or TET2-mutated clones during treatment. Expansion of DDR clones correlated with HSP90i exposure across the three study arms and was partially abrogated by the presence of germline mutations related to homologous recombination deficiency. Single-cell DNA sequencing of selected samples revealed clonal exclusivity of DDR mutations, and identified DDR-mutated clones as the origin of t-MN in two investigated cases. Together, these results provide unique insights into the architecture and the preferential selection of DDR-mutated hematopoietic clones under intense DNA-damaging treatment. Specifically, PARPi and HSP90i therapies pose an independent risk for the expansion of DDR-CH in a dose-dependent manner.
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Affiliation(s)
- Christopher Maximilian Arends
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Klara Kopp
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raphael Hablesreiter
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Natalia Estrada
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Friederike Christen
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ute Martha Moll
- Department of Pathology, Stony Brook University Cancer Center, Stony Brook, NY, 11794, USA
| | - Robert Zeillinger
- Department of Obstetrics and Gynaecology, Molecular Oncology Group, Comprehensive Cancer Center-Gynaecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Daniel Schmitt
- Department of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Virchow Klinikum, Berlin, Germany
- North Eastern German Society for Gynecological Cancer. Tumor Bank Ovarian Cancer Network, Berlin, Germany
| | - Hagen Kulbe
- Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Virchow Klinikum, Berlin, Germany
- North Eastern German Society for Gynecological Cancer. Tumor Bank Ovarian Cancer Network, Berlin, Germany
| | - Maximilian Fleischmann
- Klinik für Innere Medizin II, Abteilung Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Isabelle Ray-Coquard
- Centre Anticancereux Léon Bérard, University Claude Bernard Lyon, GINECO Group, Lyon, France
| | - Alain Zeimet
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Austrian AGO, Innsbruck, Austria
| | | | - Claudio Zamagni
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Leuven Cancer Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Belgium and Luxembourg Gynaecological Oncology Group (BGOG), Leuven, Belgium
| | | | - Nicole Concin
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Austrian AGO, Innsbruck, Austria
| | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elena Ioana Braicu
- Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Virchow Klinikum, Berlin, Germany
- North Eastern German Society for Gynecological Cancer. Tumor Bank Ovarian Cancer Network, Berlin, Germany
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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8
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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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9
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Borsi E, Vigliotta I, Poletti A, Mazzocchetti G, Solli V, Zazzeroni L, Martello M, Armuzzi S, Taurisano B, Kanapari A, Pistis I, Zamagni E, Pantani L, Rocchi S, Mancuso K, Tacchetti P, Rizzello I, Rizzi S, Dan E, Sinigaglia B, Cavo M, Terragna C. Single-Cell DNA Sequencing Reveals an Evolutionary Pattern of CHIP in Transplant Eligible Multiple Myeloma Patients. Cells 2024; 13:657. [PMID: 38667272 PMCID: PMC11049155 DOI: 10.3390/cells13080657] [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: 02/21/2024] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) refers to the phenomenon where a hematopoietic stem cell acquires fitness-increasing mutation(s), resulting in its clonal expansion. CHIP is frequently observed in multiple myeloma (MM) patients, and it is associated with a worse outcome. High-throughput amplicon-based single-cell DNA sequencing was performed on circulating CD34+ cells collected from twelve MM patients before autologous stem cell transplantation (ASCT). Moreover, in four MM patients, longitudinal samples either before or post-ASCT were collected. Single-cell sequencing and data analysis were assessed using the MissionBio Tapestri® platform, with a targeted panel of 20 leukemia-associated genes. We detected CHIP pathogenic mutations in 6/12 patients (50%) at the time of transplant. The most frequently mutated genes were TET2, EZH2, KIT, DNMT3A, and ASXL1. In two patients, we observed co-occurring mutations involving an epigenetic modifier (i.e., DNMT3A) and/or a gene involved in splicing machinery (i.e., SF3B1) and/or a tyrosine kinase receptor (i.e., KIT) in the same clone. Longitudinal analysis of paired samples revealed a positive selection of mutant high-fitness clones over time, regardless of their affinity with a major or minor sub-clone. Copy number analysis of the panel of all genes did not show any numerical alterations present in stem cell compartment. Moreover, we observed a tendency of CHIP-positive patients to achieve a suboptimal response to therapy compared to those without. A sub-clone dynamic of high-fitness mutations over time was confirmed.
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Affiliation(s)
- Enrica Borsi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Ilaria Vigliotta
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Andrea Poletti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Gaia Mazzocchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Vincenza Solli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Luca Zazzeroni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Marina Martello
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Silvia Armuzzi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Barbara Taurisano
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ajsi Kanapari
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ignazia Pistis
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Elena Zamagni
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Lucia Pantani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Serena Rocchi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Katia Mancuso
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Paola Tacchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Rizzello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Simonetta Rizzi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Elisa Dan
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Barbara Sinigaglia
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Michele Cavo
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Carolina Terragna
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
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10
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Fabre MA, Vassiliou GS. The lifelong natural history of clonal hematopoiesis and its links to myeloid neoplasia. Blood 2024; 143:573-581. [PMID: 37992214 DOI: 10.1182/blood.2023019964] [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: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
ABSTRACT The study of somatic mutations and the associated clonal mosaicism across the human body has transformed our understanding of aging and its links to cancer. In proliferative human tissues, stem cells compete for dominance, and those with an advantage expand clonally to outgrow their peers. In the hematopoietic system, such expansion is termed clonal hematopoiesis (CH). The forces driving competition, namely heterogeneity of the hematopoietic stem cell (HSC) pool and attrition of their environment, become increasingly prominent with age. As a result, CH becomes progressively more common through life to the point of becoming essentially ubiquitous. We are beginning to unravel the specific intracellular and extracellular factors underpinning clonal behavior, with somatic mutations in specific driver genes, inflammation, telomere maintenance, extraneous exposures, and inherited genetic variation among the important players. The inevitability of CH with age combined with its unequivocal links to myeloid cancers poses a scientific and clinical challenge. Specifically, we need to decipher the factors determining clonal behavior and develop prognostic tools to identify those at high risk of malignant progression, for whom preventive interventions may be warranted. Here, we discuss how recent advances in our understanding of the natural history of CH have provided important insights into these processes and helped define future avenues of investigation.
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Affiliation(s)
- Margarete A Fabre
- Department of Haematology, Cambridge University Hospitals National Health Service Trust, Cambridge, United Kingdom
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals Research & Development, AstraZeneca, Cambridge, United Kingdom
| | - George S Vassiliou
- Department of Haematology, Cambridge University Hospitals National Health Service Trust, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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11
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Ronchini C, Caprioli C, Tunzi G, D’Amico FF, Colombo E, Giani M, Foti G, Conconi D, Lavitrano M, Passerini R, Pase L, Capizzi S, Mastrilli F, Alcalay M, Orecchia R, Natoli G, Pelicci PG. High-sensitivity analysis of clonal hematopoiesis reveals increased clonal complexity of potential-driver mutations in severe COVID-19 patients. PLoS One 2024; 19:e0282546. [PMID: 38198467 PMCID: PMC10781164 DOI: 10.1371/journal.pone.0282546] [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: 02/15/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
Whether Clonal Hematopoiesis (CH) represents a risk factor for severity of the COVID-19 disease remains a controversial issue. We report the first high- sensitivity analysis of CH in COVID-19 patients (threshold of detection at 0.5% vs 1 or 2% in previous studies). We analyzed 24 patients admitted to ICU for COVID-19 (COV-ICU) and 19 controls, including healthy subjects and asymptomatic SARS-CoV2-positive individuals. Despite the significantly higher numbers of CH mutations identified (80% mutations with <2% variant allele frequency, VAF), we did not find significant differences between COV-ICU patients and controls in the prevalence of CH or in the numbers, VAF or functional categories of the mutated genes, suggesting that CH is not overrepresented in patients with COVID-19. However, when considering potential drivers CH mutations (CH-PD), COV-ICU patients showed higher clonal complexity, in terms of both mutation numbers and VAF, and enrichment of variants reported in myeloid neoplasms. However, we did not score an impact of increased CH-PD on patient survival or clinical parameters associated with inflammation. These data suggest that COVID-19 influence the clonal composition of the peripheral blood and call for further investigations addressing the potential long-term clinical impact of CH on people experiencing severe COVID-19. We acknowledge that it will indispensable to perform further studies on larger patient cohorts in order to validate and generalize our conclusions. Moreover, we performed CH analysis at a single time point. It will be necessary to consider longitudinal approaches with long periods of follow-up in order to assess if the COVID-19 disease could have an impact on the evolution of CH and long-term consequences in patients that experienced severe COVID-19.
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Affiliation(s)
- Chiara Ronchini
- Clinical Genomics, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Caprioli
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Gianleo Tunzi
- Clinical Genomics, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Emanuela Colombo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Marco Giani
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Department of Emergency and Intensive Care, Ospedale San Gerardo, Monza, Italy
| | - Giuseppe Foti
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Department of Emergency and Intensive Care, Ospedale San Gerardo, Monza, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | - Rita Passerini
- Division of Laboratory Medicine, European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Pase
- Occupational Medicine, European Institute of Oncology IRCCS, Milan, Italy
| | - Silvio Capizzi
- Medical Administration, CMO, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Fabrizio Mastrilli
- Medical Administration, CMO, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Myriam Alcalay
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Roberto Orecchia
- Scientific Directorate, European Institute of Oncology IRCCS, Milan, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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12
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Park E, Evans MA, Walsh K. Regulators of clonal hematopoiesis and physiological consequences of this condition. THE JOURNAL OF CARDIOVASCULAR AGING 2024; 4:3. [PMID: 39119355 PMCID: PMC11309374 DOI: 10.20517/jca.2023.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Clonal hematopoiesis (CH) is a prevalent condition that results from somatic mutations in hematopoietic stem cells. When these mutations occur in "driver" genes, they can potentially confer fitness advantages to the affected cells, leading to a clonal expansion. While most clonal expansions of mutant cells are generally considered to be asymptomatic since they do not impact overall blood cell numbers, CH carriers face long-term risks of all-cause mortality and age-associated diseases, including cardiovascular disease and hematological malignancies. While considerable research has focused on understanding the association between CH and these diseases, less attention has been given to exploring the regulatory factors that contribute to the expansion of the driver gene clone. This review focuses on the association between environmental stressors and inherited genetic risk factors in the context of CH development. A better understanding of how these stressors impact CH development will facilitate mechanistic studies and potentially lead to new therapeutic avenues to treat individuals with this condition.
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Affiliation(s)
- Eunbee Park
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Megan A. Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kenneth Walsh
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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13
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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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14
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Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar M, Sturgess KH, Williams MJ, Giotopoulos G, Marando L, Li J, Rak J, Gozdecka M, Prins D, Shepherd MS, Watcham S, Green AR, Kent DG, Vassiliou GS, Huntly BJ, Wilson NK, Göttgens B. Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes. CELL GENOMICS 2023; 3:100426. [PMID: 38116120 PMCID: PMC10726426 DOI: 10.1016/j.xgen.2023.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.
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Affiliation(s)
- Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Hugo P. Bastos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Shirom Chabra
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - M.S. Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Katherine H.M. Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Matthew J. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Prins
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Mairi S. Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sam Watcham
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Anthony R. Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - David G. Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J.P. Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
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15
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Mack T, Vlasschaert C, von Beck K, Silver AJ, Heimlich JB, Poisner H, Condon HR, Ulloa J, Sochacki AL, Spaulding TP, Kishtagari A, Bejan CA, Xu Y, Savona MR, Jones A, Bick A. Cost-effective and scalable clonal hematopoiesis assay provides insight into clonal dynamics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.08.23298270. [PMID: 37986782 PMCID: PMC10659520 DOI: 10.1101/2023.11.08.23298270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon that occurs when hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or serial sequencing. Here, we present and validate a CHIP targeted sequencing assay that is affordable (∼$8/sample), accurate and highly scalable. To demonstrate the utility of this assay, we detected CHIP in a cohort of 456 individuals with DNA collected at multiple timepoints in the Vanderbilt BioVU biobank and quantified clonal expansion rates over time. A total of 101 individuals with CHIP were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction (VAF) at both timepoints. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. We further describe the mutation co-occurrence and clonal competition between multiple driver mutations.
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16
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Feng Y, Yuan Q, Newsome RC, Robinson T, Bowman RL, Zuniga AN, Hall KN, Bernsten CM, Shabashvili DE, Krajcik KI, Gunaratne C, Zaroogian ZJ, Venugopal K, Casellas Roman HL, Levine RL, Chatila WK, Yaeger R, Riva A, Jobin C, Kopinke D, Avram D, Guryanova OA. Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. J Exp Med 2023; 220:e20230011. [PMID: 37615936 PMCID: PMC10450614 DOI: 10.1084/jem.20230011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/12/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer (CAC) with experimental CH driven by Dnmt3a+/Δ, we found higher tumor penetrance and increased tumor burden compared with controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia, and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency and rebalanced hematopoiesis. This study provides conceptually novel insights into non-tumor-cell-autonomous effects of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.
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Affiliation(s)
- Yang Feng
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Qingchen Yuan
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Rachel C. Newsome
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashley N. Zuniga
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kendra N. Hall
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Cassandra M. Bernsten
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Daniil E. Shabashvili
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kathryn I. Krajcik
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Zachary J. Zaroogian
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Heidi L. Casellas Roman
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K. Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Christian Jobin
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
- Immunology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
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17
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van Zeventer IA, de Graaf AO, Jansen JH, Huls G. Evolution of clonal hematopoiesis. Clin Transl Med 2023; 13:e1444. [PMID: 37846136 PMCID: PMC10579999 DOI: 10.1002/ctm2.1444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/01/2023] [Indexed: 10/18/2023] Open
Affiliation(s)
- Isabelle A. van Zeventer
- Department of HematologyUniversity Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Aniek O. de Graaf
- Department of Laboratory MedicineLaboratory of HematologyRadboud University Medical CenterNijmegenNetherlands
| | - Joop H. Jansen
- Department of Laboratory MedicineLaboratory of HematologyRadboud University Medical CenterNijmegenNetherlands
| | - Gerwin Huls
- Department of HematologyUniversity Medical Center Groningen, University of GroningenGroningenNetherlands
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18
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Badar T, Vanegas YAM, Nanaa A, Foran JM, Al-Kali A, Mangaonkar A, Murthy H, Alkhateeb HB, Viswanatha D, He R, Shah M, Yi CA, Litzow MR, Gangat N, Tefferi A, Patnaik MM. U2AF1 pathogenic variants in myeloid neoplasms and precursor states: distribution of co-mutations and prognostic heterogeneity. Blood Cancer J 2023; 13:149. [PMID: 37735430 PMCID: PMC10514309 DOI: 10.1038/s41408-023-00922-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
We have previously recognized the genotypic and prognostic heterogeneity of U2AF1 mutations (MT) in myelofibrosis (MF) and myelodysplastic syndromes (MDS). In the current study, we considered 179 U2AF1-mutated patients with clonal cytopenia of undetermined significance (CCUS; n = 22), MDS (n = 108), MDS/acute myeloid leukemia (AML; n = 18) and AML (n = 31). U2AF1 variants included S34 (60%), Q157 (35%), and others (5%): corresponding mutational frequencies were 45%, 55%, and 0% in CCUS; 57%, 39%, and 4% in MDS; 61%, 33%, and 6% in MDS/AML; and 55%, 35% and 10% in AML (P = 0.17, 0.36 and 0.09), respectively. Concurrent mutations included ASXL1 (37%), BCOR (19%), RUNX1 (14%), TET2 (15%), DNMT3A (10%), NRAS/KRAS (8%), TP53 (8%), JAK2 (5.5%) and SETBP1 (5%). The two most frequent U2AF1 MT were S34F (n = 97) and Q157P (n = 46); concurrent MT were more likely to be seen with the latter (91% vs 74%; P = 0.01) and abnormal karyotype with the former (70% vs 62%; P = 0.05). U2AF1 S34F MT clustered with BCOR (P = 0.04) and Q157P MT with ASXL1 (P = 0.01) and TP53 (P = 0.03). The median overall survival (OS) in months was significantly worse in AML (14.2) vs MDS/AML (27.3) vs MDS (33.7; P = 0.001); the latter had similar OS with CCUS (30.0). In morphologically high-risk disease (n = 49), defined by ≥10% blood or bone marrow blasts (i.e., AML or MDS/AML), median OS was 14.2 with Q157P vs 37.1 months in the presence of S34F (P = 0.008); transplant-adjusted multivariable analysis confirmed the detrimental impact of Q157P (P = 0.01) on survival and also identified JAK2 MT as an additional risk factor (P = 0.02). OS was favorably affected by allogeneic hematopoietic stem cell transplantation (HR: 0.16, 95% CI; 0.04-0.61, P = 0.007). The current study defines the prevalence and co-mutational profiles of U2AF1 pathogenic variants in AML, MDS/AML, MDS, and CCUS, and suggests prognostic heterogeneity in patients with ≥10% blasts.
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Affiliation(s)
- Talha Badar
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA.
| | - Yenny A Moreno Vanegas
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ahmad Nanaa
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
- John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, 60612, USA
| | - James M Foran
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Hemant Murthy
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - David Viswanatha
- Division of Hematopathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rong He
- Division of Hematopathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Mithun Shah
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Cecilia Arana Yi
- Department of Hematology Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Naseema Gangat
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ayalew Tefferi
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
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19
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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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20
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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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21
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Buck MC, Bast L, Hecker JS, Rivière J, Rothenberg-Thurley M, Vogel L, Wang D, Andrä I, Theis FJ, Bassermann F, Metzeler KH, Oostendorp RA, Marr C, Götze KS. Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS. iScience 2023; 26:107328. [PMID: 37520699 PMCID: PMC10382887 DOI: 10.1016/j.isci.2023.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) describes the age-related acquisition of somatic mutations in hematopoietic stem/progenitor cells (HSPC) leading to clonal blood cell expansion. Although CHIP mutations drive myeloid malignancies like myelodysplastic syndromes (MDS) it is unknown if clonal expansion is attributable to changes in cell type kinetics, or involves reorganization of the hematopoietic hierarchy. Using computational modeling we analyzed differentiation and proliferation kinetics of cultured hematopoietic stem cells (HSC) from 8 healthy individuals, 7 CHIP, and 10 MDS patients. While the standard hematopoietic hierarchy explained HSPC kinetics in healthy samples, 57% of CHIP and 70% of MDS samples were best described with alternative hierarchies. Deregulated kinetics were found at various HSPC compartments with high inter-individual heterogeneity in CHIP and MDS, while altered HSC rates were most relevant in MDS. Quantifying kinetic heterogeneity in detail, we show that reorganization of the HSPC compartment is already detectable in the premalignant CHIP state.
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Affiliation(s)
- Michèle C. Buck
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
| | - Lisa Bast
- Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technical University of Munich (TUM), Department of Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching, Germany
| | - Judith S. Hecker
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
| | - Jennifer Rivière
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
| | - Maja Rothenberg-Thurley
- University Hospital, Ludwig-Maximilians-University, Department of Medicine III, Laboratory for Leukemia Diagnostics, Munich, Germany
| | - Luisa Vogel
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
| | - Dantong Wang
- Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technical University of Munich (TUM), Department of Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching, Germany
| | - Immanuel Andrä
- Technical University of Munich, Microbiology Institute, Munich, Germany
| | - Fabian J. Theis
- Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technical University of Munich (TUM), Department of Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching, Germany
| | - Florian Bassermann
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Partner Site Munich, Germany
| | - Klaus H. Metzeler
- University Hospital, Ludwig-Maximilians-University, Department of Medicine III, Laboratory for Leukemia Diagnostics, Munich, Germany
- University Hospital Leipzig, Department of Hematology and Cell Therapy, Leipzig, Germany
| | - Robert A.J. Oostendorp
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
| | - Carsten Marr
- Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Partner Site Munich, Germany
- Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of AI for Health, Neuherberg, Germany
| | - Katharina S. Götze
- Technical University of Munich (TUM), School of Medicine, Department of Medicine III, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Partner Site Munich, Germany
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22
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Safonov A, Nomakuchi TT, Chao E, Horton C, Dolinsky JS, Yussuf A, Richardson M, Speare V, Li S, Bogus ZC, Bonanni M, Raper A, Kallish S, Ritchie MD, Nathanson KL, Drivas TG. A genotype-first approach identifies high incidence of NF1 pathogenic variants with distinct disease associations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.08.23293676. [PMID: 37609227 PMCID: PMC10441497 DOI: 10.1101/2023.08.08.23293676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Loss of function variants in the NF1 gene cause neurofibromatosis type 1 (NF1), a genetic disorder characterized by complete penetrance, prevalence of 1 in 3,000, characteristic physical exam findings, and a substantially increased risk for malignancy. However, our understanding of the disorder is entirely based on patients ascertained through phenotype-first approaches. Leveraging a genotype-first approach in two large patient cohorts, we demonstrate unexpectedly high prevalence (1 in 450-750) of NF1 pathogenic variants. Half were identified in individuals lacking clinical features of NF1, with many appearing to have post-zygotic mosaicism for the identified variant. Incidentally discovered variants were not associated with classic NF1 features but were associated with an increased incidence of malignancy compared to a control population. Our findings suggest that NF1 pathogenic variants are substantially more common than previously thought, often characterized by somatic mosaicism and reduced penetrance, and are important contributors to cancer risk in the general population.
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23
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Avagyan S, Zon LI. Clonal hematopoiesis and inflammation - the perpetual cycle. Trends Cell Biol 2023; 33:695-707. [PMID: 36593155 PMCID: PMC10310890 DOI: 10.1016/j.tcb.2022.12.001] [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: 10/03/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023]
Abstract
Acquired genetic or cytogenetic alterations in a blood stem cell that confer clonal fitness promote its relative expansion leading to clonal hematopoiesis (CH). Despite a largely intact hematopoietic output, CH is associated with a heightened risk of progression to hematologic malignancies and with non-hematologic health manifestations, including cardiovascular disease and overall mortality. We focus on the evidence for the role of inflammation in establishing, maintaining and reciprocally being affected by CH. We describe the known pro-inflammatory signals associated with CH and preclinical studies that elucidated the cellular mechanisms involved. We review the evolving literature on early-onset CH in germline predisposition conditions and the possible role of immune dysregulation in this context.
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Affiliation(s)
- Serine Avagyan
- Dana-Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Leonard I Zon
- Boston Children's Hospital, Boston, MA 02215, USA; Howard Hughes Medical Institute, USA
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24
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Amancherla K, Schlendorf KH, Vlasschaert C, Lowery BD, Wells QS, See SB, Zorn E, Colombo PC, Reilly MP, Lindenfeld J, Uriel N, Freedman JE, Shah RV, Moslehi J, Bick AG, Clerkin K. Clonal hematopoiesis of indeterminate potential and outcomes after heart transplantation: A multicenter study. Am J Transplant 2023; 23:1256-1263. [PMID: 37156299 PMCID: PMC10524751 DOI: 10.1016/j.ajt.2023.04.028] [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: 10/27/2022] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Cardiac allograft vasculopathy (CAV) is a leading cause of late graft failure and mortality after heart transplantation (HT). Sharing some features with atherosclerosis, CAV results in diffuse narrowing of the epicardial coronaries and microvasculature, with consequent graft ischemia. Recently, clonal hematopoiesis of indeterminate potential (CHIP) has emerged as a risk factor for cardiovascular disease and mortality. We aimed to investigate the relationship between CHIP and posttransplant outcomes, including CAV. We analyzed 479 HT recipients with stored DNA samples at 2 high-volume transplant centers, Vanderbilt University Medical Center and Columbia University Irving Medical Center. We explored the association between the presence of CHIP mutations with CAV and mortality after HT. In this case-control analysis, carriers of CHIP mutations were not at increased risk of CAV or mortality after HT. In a large multicenter genomics study of the heart transplant population, the presence of CHIP mutations was not associated with an increased risk of CAV or posttransplant mortality.
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Affiliation(s)
- Kaushik Amancherla
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
| | - Kelly H Schlendorf
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Brandon D Lowery
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sarah B See
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York City, New York City, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York City, New York City, USA
| | - Paolo C Colombo
- Division of Cardiology, Columbia University Medical Center, New York City, New York City, USA
| | - Muredach P Reilly
- Division of Cardiology, Columbia University Medical Center, New York City, New York City, USA
| | - JoAnn Lindenfeld
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nir Uriel
- Division of Cardiology, Columbia University Medical Center, New York City, New York City, USA
| | - Jane E Freedman
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ravi V Shah
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Javid Moslehi
- Section of Cardio-Oncology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin Clerkin
- Division of Cardiology, Columbia University Medical Center, New York City, New York City, USA
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25
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Yang F, Nourse C, Helgason GV, Kirschner K. Unraveling Heterogeneity in the Aging Hematopoietic Stem Cell Compartment: An Insight From Single-cell Approaches. Hemasphere 2023; 7:e895. [PMID: 37304939 PMCID: PMC10256339 DOI: 10.1097/hs9.0000000000000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/18/2023] [Indexed: 06/13/2023] Open
Abstract
Specific cell types and, therefore, organs respond differently during aging. This is also true for the hematopoietic system, where it has been demonstrated that hematopoietic stem cells alter a variety of features, such as their metabolism, and accumulate DNA damage, which can lead to clonal outgrowth over time. In addition, profound changes in the bone marrow microenvironment upon aging lead to senescence in certain cell types such as mesenchymal stem cells and result in increased inflammation. This heterogeneity makes it difficult to pinpoint the molecular drivers of organismal aging gained from bulk approaches, such as RNA sequencing. A better understanding of the heterogeneity underlying the aging process in the hematopoietic compartment is, therefore, needed. With the advances of single-cell technologies in recent years, it is now possible to address fundamental questions of aging. In this review, we discuss how single-cell approaches can and indeed are already being used to understand changes observed during aging in the hematopoietic compartment. We will touch on established and novel methods for flow cytometric detection, single-cell culture approaches, and single-cell omics.
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Affiliation(s)
- Fei Yang
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Nourse
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - G. Vignir Helgason
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kristina Kirschner
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
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26
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Diamond B, Ziccheddu B, Maclachlan K, Taylor J, Boyle E, Ossa JA, Jahn J, Affer M, Totiger TM, Coffey D, Chandhok N, Watts J, Cimmino L, Lu SX, Bolli N, Bolton K, Landau H, Park JH, Ganesh K, McPherson A, Sekeres MA, Lesokhin A, Chung DJ, Zhang Y, Ho C, Roshal M, Tyner J, Nimer S, Papaemmanuil E, Usmani S, Morgan G, Landgren O, Maura F. Tracking the evolution of therapy-related myeloid neoplasms using chemotherapy signatures. Blood 2023; 141:2359-2371. [PMID: 36626250 PMCID: PMC10273163 DOI: 10.1182/blood.2022018244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Preleukemic clones (ie, clonal hematopoiesis [CH]) are detectable years before the development of these aggressive malignancies, although the genomic events leading to transformation and expansion are not well defined. Here, by leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of prechemotherapy samples, we reconstructed the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy was revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan were hypermutated and enriched for complex structural variants (ie, chromothripsis), whereas neoplasms with nonmutagenic chemotherapy exposures were genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to discrete clinical exposure in each patient's life, we estimated that several complex events and genomic drivers were acquired after chemotherapy was administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected after reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA damage. Overall, we revealed a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select preexisting CH but also promote the acquisition of recurrent genomic drivers.
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Affiliation(s)
- Benjamin Diamond
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | - Kylee Maclachlan
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Eileen Boyle
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Juan Arango Ossa
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob Jahn
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Maurizio Affer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | | | - David Coffey
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Namrata Chandhok
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Justin Watts
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Luisa Cimmino
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Sydney X. Lu
- Division of Hematology, Stanford Hospital and Clinics, Stanford University, Stanford, CA
| | - Niccolò Bolli
- Department of Oncology and Onco-Hematology, Università degli Studi di Milano, Milan, Italy
- Hematology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Kelly Bolton
- Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Heather Landau
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jae H. Park
- Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karuna Ganesh
- Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew McPherson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Alexander Lesokhin
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David J. Chung
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caleb Ho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey Tyner
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR
| | - Stephen Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Saad Usmani
- Division of Myeloma, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gareth Morgan
- Myeloma Research Program, New York University Langone, Perlmutter Cancer Center, New York, NY
| | - Ola Landgren
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
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27
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Gondek LP. Refining CHIP in population data sets. Blood 2023; 141:2163-2164. [PMID: 37140953 DOI: 10.1182/blood.2023019801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
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28
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van Zeventer IA, de Graaf AO, Salzbrunn JB, Nolte IM, Kamphuis P, Dinmohamed A, van der Reijden BA, Schuringa JJ, Jansen JH, Huls G. Evolutionary landscape of clonal hematopoiesis in 3,359 individuals from the general population. Cancer Cell 2023:S1535-6108(23)00132-0. [PMID: 37146604 DOI: 10.1016/j.ccell.2023.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/05/2023] [Accepted: 04/07/2023] [Indexed: 05/07/2023]
Abstract
Knowledge about evolution of clonal hematopoiesis, which may drive malignant progression, is crucial for clinical decision-making. We investigated the landscape of clonal evolution by error-corrected sequencing on 7,045 sequential samples from 3,359 individuals in the prospective population-based Lifelines cohort, with a special focus on cytosis and cytopenia. Spliceosome (SRSF2/U2AF1/SF3B1) and JAK2 mutated clones show highest growth rates over a median 3.6-year period, while clone sizes for DNMT3A and TP53 increase only marginally, independent of cytosis or cytopenia. Nevertheless, large differences are observed between individuals carrying the same mutation, indicative of modulation by non-mutation-related factors. Clonal expansion is not dependent on classical cancer risk factors (e.g., smoking). Risk for incident myeloid malignancy diagnosis is highest for JAK2, spliceosome, or TP53 mutations and absent for DNMT3A, and it is mostly preceded by cytosis or cytopenia. The results provide important insight into high-risk evolutionary patterns to guide monitoring of "CHIP" and "CCUS."
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Affiliation(s)
- Isabelle A van Zeventer
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Aniek O de Graaf
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jonas B Salzbrunn
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Priscilla Kamphuis
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Avinash Dinmohamed
- Department of Research and Development, Netherlands Comprehensive Cancer Organization, Utrecht, the Netherlands; Department of Public Health, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Hematology, Amsterdam UMC, Cancer Center Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jan Jacob Schuringa
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Gerwin Huls
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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29
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Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O'Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YDI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy AT, Natarajan P, Kitzman JO, Whitsel EA, Reiner AP, Bick AG, Jaiswal S. Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Nature 2023; 616:755-763. [PMID: 37046083 PMCID: PMC10360040 DOI: 10.1038/s41586-023-05806-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/08/2023] [Indexed: 04/14/2023]
Abstract
Mutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2-6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling. Here, to circumvent this limitation, we developed a method to infer the expansion rate from data from a single time point. We applied this method to 5,071 people with clonal haematopoiesis. A genome-wide association study revealed that a common inherited polymorphism in the TCL1A promoter was associated with a slower expansion rate in clonal haematopoiesis overall, but the effect varied by driver gene. Those carrying this protective allele exhibited markedly reduced growth rates or prevalence of clones with driver mutations in TET2, ASXL1, SF3B1 and SRSF2, but this effect was not seen in clones with driver mutations in DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 led to the expression of TCL1A protein and the expansion of HSCs in vitro. The protective allele restricted TCL1A expression and expansion of mutant HSCs, as did experimental knockdown of TCL1A expression. Forced expression of TCL1A promoted the expansion of human HSCs in vitro and mouse HSCs in vivo. Our results indicate that the fitness advantage of several commonly mutated driver genes in clonal haematopoiesis may be mediated by TCL1A activation.
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Affiliation(s)
- Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Md Mesbah Uddin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nikolaus Jahn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hind Bouzid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhuang Miao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nghi Ly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taralynn M Mack
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine P Prothro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaneice R Mitchell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Populations Sciences, Lundquist Institute, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Moritz F Sinner
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Aenne S von Falkenhausen
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
- University of Maryland, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- University of Texas Health at Houston, Houston, TX, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- University of Texas Health 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
| | - Lifang Hou
- Department of Preventive Medicine, Northeastern University, Chicago, IL, USA
| | | | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce M Psaty
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Brigham and Women's Hospital, Boston, MA, USA
- 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
| | - Dandi Qiao
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Michael H Cho
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's, Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University, New Orleans, LA, USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim Van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine, New York, NY, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
- University of Kentucky, Lexington, KY, USA
| | | | - Hemant Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - J Brent Muhlestein
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi, Jackson, MS, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- University of Mississippi, Jackson, MS, USA
| | - Mariza de Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Lundquist Institute, Torrance, CA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- University of Virginia, Charlottesville, VA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Barbara A Konkle
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Blood Works Northwest, Seattle, WA, USA
| | - Jill M Johnsen
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Research Institute, Bloodworks Northwest, Seattle, WA, USA
| | | | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | - Peter M Nilsson
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
- Henry Ford Health System, Detroit, MI, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Mao Yang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
- Washington University in St Louis, St Louis, MO, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - John P Kane
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California, San Francisco, USA
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine and Cardiology, Vanderbilt University, Nashville, TN, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois at Chicago, Chicago, IL, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA, USA
- Cedars-Sinai, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ying Zhou
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - JoAnn E Manson
- Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hyun M Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Broad Institute, Cambridge, MA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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30
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Díaz-Rovira AM, Martín H, Beuming T, Díaz L, Guallar V, Ray SS. Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. J Chem Inf Model 2023; 63:1668-1674. [PMID: 36892986 DOI: 10.1021/acs.jcim.2c01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Machine learning-based protein structure prediction algorithms, such as RosettaFold and AlphaFold2, have greatly impacted the structural biology field, arousing a fair amount of discussion around their potential role in drug discovery. While there are few preliminary studies addressing the usage of these models in virtual screening, none of them focus on the prospect of hit-finding in a real-world virtual screen with a model based on low prior structural information. In order to address this, we have developed an AlphaFold2 version where we exclude all structural templates with more than 30% sequence identity from the model-building process. In a previous study, we used those models in conjunction with state-of-the-art free energy perturbation methods and demonstrated that it is possible to obtain quantitatively accurate results. In this work, we focus on using these structures in rigid receptor-ligand docking studies. Our results indicate that using out-of-the-box Alphafold2 models is not an ideal scenario for virtual screening campaigns; in fact, we strongly recommend to include some post-processing modeling to drive the binding site into a more realistic holo model.
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Affiliation(s)
- Anna M Díaz-Rovira
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | | | - Thijs Beuming
- Latham Biopharm Group, 101 Main Street, Suite 1400, Cambridge, Massachusetts 02142, United States
| | - Lucía Díaz
- Nostrum Biodiscovery S.L., E-08029 Barcelona, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain.,Nostrum Biodiscovery S.L., E-08029 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Soumya S Ray
- RA Capital, 200 Berkeley Street, Boston, Massachusetts 02116, United States.,3-Dimensional Consulting, 134 Franklin Avenue, Quincy, Massachusetts 02170, United States
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31
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Gundry M, Sankaran VG. Hacking hematopoiesis - emerging tools for examining variant effects. Dis Model Mech 2023; 16:288409. [PMID: 36826849 PMCID: PMC9983777 DOI: 10.1242/dmm.049857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Hematopoiesis is a continuous process of blood and immune cell production. It is orchestrated by thousands of gene products that respond to extracellular signals by guiding cell fate decisions to meet the needs of the organism. Although much of our knowledge of this process comes from work in model systems, we have learned a great deal from studies on human genetic variation. Considerable insight has emerged from studies on presumed monogenic blood disorders, which continue to provide key insights into the mechanisms critical for hematopoiesis. Furthermore, the emergence of large-scale biobanks and cohorts has uncovered thousands of genomic loci associated with blood cell traits and diseases. Some of these blood cell trait-associated loci act as modifiers of what were once thought to be monogenic blood diseases. However, most of these loci await functional validation. Here, we discuss the validation bottleneck and emerging methods to more effectively connect variant to function. In particular, we highlight recent innovations in genome editing, which have paved the path forward for high-throughput functional assessment of loci. Finally, we discuss existing barriers to progress, including challenges in manipulating the genomes of primary hematopoietic cells.
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Affiliation(s)
- Michael Gundry
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- 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
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- 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
- Author for correspondence ()
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32
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Arends CM, Liman TG, Strzelecka PM, Kufner A, Löwe P, Huo S, Stein CM, Piper SK, Tilgner M, Sperber PS, Dimitriou S, Heuschmann PU, Hablesreiter R, Harms C, Bullinger L, Weber JE, Endres M, Damm F. Associations of clonal hematopoiesis with recurrent vascular events and death in patients with incident ischemic stroke. Blood 2023; 141:787-799. [PMID: 36441964 DOI: 10.1182/blood.2022017661] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Clonal hematopoiesis (CH) is common among older people and is associated with an increased risk of atherosclerosis, inflammation, and shorter overall survival. Age and inflammation are major risk factors for ischemic stroke, yet the association of CH with risk of secondary vascular events and death is unknown. We investigated CH in peripheral blood DNA from 581 patients with first-ever ischemic stroke from the Prospective Cohort With Incident Stroke-Berlin study using error-corrected targeted sequencing. The primary composite end point (CEP) consisted of recurrent stroke, myocardial infarction, and all-cause mortality. A total of 348 somatic mutations with a variant allele frequency ≥1% were identified in 236 of 581 patients (41%). CH was associated with large-artery atherosclerosis stroke (P = .01) and white matter lesion (P < .001). CH-positive patients showed increased levels of proinflammatory cytokines, such as interleukin-6 (IL-6), interferon gamma, high-sensitivity C-reactive protein, and vascular cell adhesion molecule 1. CH-positive patients had a higher risk for the primary CEP (hazard ratio [HR], 1.55; 95% confidence interval [CI], 1.04-2.31; P = .03), which was more pronounced in patients with larger clones. CH clone size remained an independent risk factor (HR, 1.30; 95% CI, 1.04-1.62; P = .022) in multivariable Cox regression. Although our data show that, in particular, larger and TET2- or PPM1D-mutated clones are associated with increased risk of recurrent vascular events and death, this risk is partially mitigated by a common germline variant of the IL-6 receptor (IL-6R p.D358A). The CH mutation profile is accompanied by a proinflammatory profile, opening new avenues for preventive precision medicine approaches to resolve the self-perpetuating cycle of inflammation and clonal expansion.
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Affiliation(s)
- Christopher M Arends
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas G Liman
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen), Partner Site, Berlin, Germany
- German Center for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauferkrankungen), Partner Site, Berlin, Germany
- Department of Neurology, Evangelical Hospital Oldenburg, Carl von Ossietzky-University, Oldenburg, Germany
| | - Paulina M Strzelecka
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anna Kufner
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Pelle Löwe
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Shufan Huo
- Department of Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Catarina M Stein
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sophie K Piper
- Department of Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biometry and Clinical Epidemiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Medical Informatics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marlon Tilgner
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pia S Sperber
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Savvina Dimitriou
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter U Heuschmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Center Würzburg, University of Würzburg, Würzburg, Germany
- Clinical Trial Center Würzburg, University Hospital Würzburg, Würzburg, Germany
| | - Raphael Hablesreiter
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christoph Harms
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauferkrankungen), Partner Site, Berlin, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
- German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany
| | - Joachim E Weber
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Endres
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen), Partner Site, Berlin, Germany
- German Center for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauferkrankungen), Partner Site, Berlin, Germany
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
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33
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Exploiting somatic mutations to decipher human blood production: a natural lineage-tracing strategy. Exp Hematol 2023; 121:2-5. [PMID: 36736573 DOI: 10.1016/j.exphem.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Lineage tracing using fluorescent proteins, genetic barcodes, and various other strategies has provided critical insights into the dynamics of both fetal and adult hematopoiesis in model organisms. However, these technologies cannot be readily used to study hematopoiesis in human beings. Therefore, there is a critical need to develop strategies to assess cellular dynamics within human hematopoietic tissues in vivo. Recently, researchers have used naturally acquired somatic mutations, coupled with other single-cell technologies, to retrospectively analyze clonal cellular dynamics. In summer 2022, the International Society for Experimental Hematology's New Investigator Committee hosted a webinar focused on novel approaches to dissect fetal and adult hematopoiesis, with presentations from Drs. Ana Cvejic and Vijay Sankaran. Here, we provide an overview of these exciting technological advances and some of the novel insights they have already provided in studying human hematopoiesis.
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34
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Pritzl SL, Gurney M, Badar T, Ferrer A, Lasho T, Finke C, Mangaonkar A, McCullough K, Gangat N, Fernandez J, Al-Kali A, Viswanatha D, He R, Foran J, Patnaik MM. Clinical and molecular spectrum and prognostic outcomes of U2AF1 mutant clonal hematopoiesis- a prospective mayo clinic cohort study. Leuk Res 2023; 125:107007. [PMID: 36586169 DOI: 10.1016/j.leukres.2022.107007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Stephanie L Pritzl
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Mark Gurney
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Talha Badar
- Mayo Clinic, Division of Hematology and Oncology, Jacksonville, FL, USA
| | - Alejandro Ferrer
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Terra Lasho
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Christy Finke
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Abhishek Mangaonkar
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Kristen McCullough
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Naseema Gangat
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Jenna Fernandez
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - Aref Al-Kali
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA
| | - David Viswanatha
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Rong He
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - James Foran
- Mayo Clinic, Division of Hematology and Oncology, Jacksonville, FL, USA
| | - Mrinal M Patnaik
- Mayo Clinic, Department of Internal Medicine, Division of Hematology, Rochester, MN, USA.
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35
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O'Sullivan JM, Mead AJ, Psaila B. Single-cell methods in myeloproliferative neoplasms: old questions, new technologies. Blood 2023; 141:380-390. [PMID: 36322938 DOI: 10.1182/blood.2021014668] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Myeloproliferative neoplasms (MPN) are a group of clonal stem cell-derived hematopoietic malignancies driven by aberrant Janus kinase-signal transducer and activator of transcription proteins (JAK/STAT) signaling. Although these are genetically simple diseases, MPNs are phenotypically heterogeneous, reflecting underlying intratumoral heterogeneity driven by the interplay of genetic and nongenetic factors. Their evolution is determined by factors that enable certain cellular subsets to outcompete others. Therefore, techniques that resolve cellular heterogeneity at the single-cell level are ideally placed to provide new insights into MPN biology. With these insights comes the potential to uncover new approaches to predict the clinical course and treat these cancers, ultimately improving outcomes for patients. MPNs present a particularly tractable model of cancer evolution, because most patients present in an early disease phase and only a small proportion progress to aggressive disease. Therefore, it is not surprising that many groundbreaking technological advances in single-cell omics have been pioneered by their application in MPNs. In this review article, we explore how single-cell approaches have provided transformative insights into MPN disease biology, which are broadly applicable across human cancers, and discuss how these studies might be swiftly translated into clinical pathways and may eventually underpin precision medicine.
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Affiliation(s)
- Jennifer Mary O'Sullivan
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Adam J Mead
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Bethan Psaila
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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36
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Natarajan P. Genomic Aging, Clonal Hematopoiesis, and Cardiovascular Disease. Arterioscler Thromb Vasc Biol 2023; 43:3-14. [PMID: 36353993 PMCID: PMC9780188 DOI: 10.1161/atvbaha.122.318181] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Chronologic age is the dominant risk factor for coronary artery disease but the features of aging promoting coronary artery disease are poorly understood. Advances in human genetics and population-based genetic profiling of blood cells have uncovered the surprising role of age-related subclinical leukemogenic mutations in blood cells, termed "clonal hematopoiesis of indeterminate potential," in coronary artery disease. Such mutations typically occur in DNMT3A, TET2, ASXL1, and JAK2. Murine and human studies prioritize the role of key inflammatory pathways linking clonal hematopoiesis with coronary artery disease. Increasingly larger, longitudinal, multiomics analyses are enabling further dissection into mechanistic insights. These observations expand the genetic architecture of coronary artery disease, now linking hallmark features of hematologic neoplasia with a much more common cardiovascular condition. Implications of these studies include the prospect of novel precision medicine paradigms for coronary artery disease.
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Affiliation(s)
- Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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37
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Dang Y, Rulands S. Making sense of fragmentation and merging in lineage tracing experiments. Front Cell Dev Biol 2022; 10:1054476. [PMID: 36589749 PMCID: PMC9794873 DOI: 10.3389/fcell.2022.1054476] [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: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022] Open
Abstract
Lineage tracing experiments give dynamic information on the functional behaviour of dividing cells. These experiments therefore have become an important tool for studying stem and progenitor cell fate behavior in vivo. When cell proliferation is high or the frequency of induced clones cannot be precisely controlled, the merging and fragmentation of clones renders the retrospective interpretation of clonal fate data highly ambiguous, potentially leading to unguarded interpretations about lineage relationships and fate behaviour. Here, we discuss and generalize statistical strategies to detect, resolve and make use of clonal fragmentation and merging. We first explain how to detect the rates of clonal fragmentation and merging using simple statistical estimates. We then discuss ways to restore the clonal provenance of labelled cells algorithmically and statistically and elaborate on how the process of clonal fragmentation can indirectly inform about cell fate. We generalize and extend results from the context of their original publication.
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Affiliation(s)
- Yiteng Dang
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany,Center for Systems Biology Dresden, Dresden, Germany,Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Steffen Rulands
- Max-Planck-Institute for the Physics of Complex Systems, Dresden, Germany,Center for Systems Biology Dresden, Dresden, Germany,Arnold-Sommerfeld-Center for Theoretical Physics, Ludwig-Maximilians-Universität München, München, Germany,*Correspondence: Steffen Rulands,
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38
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Jakubek YA, Reiner AP, Honigberg MC. Risk factors for clonal hematopoiesis of indeterminate potential and mosaic chromosomal alterations. Transl Res 2022; 255:171-180. [PMID: 36414227 PMCID: PMC10135440 DOI: 10.1016/j.trsl.2022.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) of the autosomes, X, and Y chromosomes are aging-related somatic mutations detectable in peripheral blood. The presence of these acquired mutations predisposes otherwise healthy adults to increased risk of several chronic aging-related conditions including hematologic cancers, atherosclerotic cardiovascular diseases, other inflammatory conditions, and mortality. While the public health impact and disease associations of these blood-derived somatic mutations continue to expand, the inherited, behavioral/lifestyle, environmental risk factors and comorbid conditions that influence their occurrence and progression have been less well characterized. Age is the strongest risk factor for all types of CHIP and mCAs. CHIP and mCAs are generally more common in individuals of European than non-European ancestry. Evidence for a genetic predisposition has been strongest for mosaic loss of Y chromosome in men. Genome-wide association studies have recently begun to identify common and rare germline genetic variants associated with CHIP and mCAs. These loci include genes involving cell cycle regulation, cell proliferation/survival, hematopoietic progenitor cell regulation, DNA damage repair, and telomere maintenance. Some loci, such as TERT, ATM, TP53, CHEK2, and TCL1A, have overlapping associations with different types of CHIP, mCAs, and cancer predisposition. Various environmental or co-morbid contexts associated with presence or expansion of specific CHIP or mCA mutations are beginning to be elucidated, such as cigarette smoking, diet, cancer chemotherapy, particulate matter, and premature menopause. Further characterization of the germline genetic and environmental correlates of CHIP/mCAs may inform our ability to modify their progression and ultimately reduce the risk and burden of chronic diseases associated with these clonal somatic phenomena.
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Affiliation(s)
- Yasminka A Jakubek
- Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, Kentucky
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Center Research Center, Seattle, Washington; Department of Epidemiology, University of Washington, Seattle, Washington.
| | - Michael C Honigberg
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Uddin MDM, Nguyen NQH, Yu B, Brody JA, Pampana A, Nakao T, Fornage M, Bressler J, Sotoodehnia N, Weinstock JS, Honigberg MC, Nachun D, Bhattacharya R, Griffin GK, Chander V, Gibbs RA, Rotter JI, Liu C, Baccarelli AA, Chasman DI, Whitsel EA, Kiel DP, Murabito JM, Boerwinkle E, Ebert BL, Jaiswal S, Floyd JS, Bick AG, Ballantyne CM, Psaty BM, Natarajan P, Conneely KN. Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease. Nat Commun 2022; 13:5350. [PMID: 36097025 PMCID: PMC9468335 DOI: 10.1038/s41467-022-33093-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022] Open
Abstract
Age-related changes to the genome-wide DNA methylation (DNAm) pattern observed in blood are well-documented. Clonal hematopoiesis of indeterminate potential (CHIP), characterized by the age-related acquisition and expansion of leukemogenic mutations in hematopoietic stem cells (HSCs), is associated with blood cancer and coronary artery disease (CAD). Epigenetic regulators DNMT3A and TET2 are the two most frequently mutated CHIP genes. Here, we present results from an epigenome-wide association study for CHIP in 582 Cardiovascular Health Study (CHS) participants, with replication in 2655 Atherosclerosis Risk in Communities (ARIC) Study participants. We show that DNMT3A and TET2 CHIP have distinct and directionally opposing genome-wide DNAm association patterns consistent with their regulatory roles, albeit both promoting self-renewal of HSCs. Mendelian randomization analyses indicate that a subset of DNAm alterations associated with these two leading CHIP genes may promote the risk for CAD.
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Affiliation(s)
- M D Mesbah Uddin
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ngoc Quynh H Nguyen
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - 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, 77030, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Akhil Pampana
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Tetsushi Nakao
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jan Bressler
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Michael C Honigberg
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Romit Bhattacharya
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Gabriel K Griffin
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Varuna Chander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Genetics and Genomics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Genetics and Genomics, Baylor College of Medicine, Houston, TX, 77030, 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, 90502, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, 02118, USA
- Framingham Heart Study, Boston University and NHLBI/NIH, Framingham, MA, 01702, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Daniel I Chasman
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27516, USA
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, 27516, USA
| | - Douglas P Kiel
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, 02131, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joanne M Murabito
- Framingham Heart Study, Boston University and NHLBI/NIH, Framingham, MA, 01702, USA
- Department of Medicine, Section of General Internal Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, 02118, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 20815, USA
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, 98101, USA
| | - Pradeep Natarajan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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