1
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJF, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun JH, DeMeo D, Levy D, Johnson AD, Mathias RA, Taub MA, Arnett D, North KE, Raffield LM, Carson AP, Doyle MF, Rich SS, Rotter JI, Guo X, Cox NJ, Roden DM, Franceschini N, Desai P, Reiner AP, Auer PL, Scheet PA, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. Nat Commun 2024; 15:3800. [PMID: 38714703 PMCID: PMC11076528 DOI: 10.1038/s41467-024-48190-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/23/2024] [Indexed: 05/10/2024] Open
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.
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Affiliation(s)
- Yash Pershad
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Yasminka A Jakubek
- Internal Medicine, Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Adrienne M Stilp
- Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Braxton D Mitchell
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz, Aurora, CO, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ali Shojaie
- Biostatistics, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Donna Arnett
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Margaret F Doyle
- Department of Pathology & Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Weill Cornell Medical College, New York, NY, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Insitute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul A Scheet
- Dept of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | | | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA.
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2
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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:S1525-1578(24)00076-X. [PMID: 38588769 DOI: 10.1016/j.jmoldx.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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, the study explores mutation co-occurrence and clonal competition between multiple driver mutations.
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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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3
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Acquired blood mutations cause acute kidney injury via dysregulated inflammation. Nat Med 2024; 30:646-647. [PMID: 38480923 DOI: 10.1038/s41591-024-02861-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
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4
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Vlasschaert C, Robinson-Cohen C, Chen J, Akwo E, Parker AC, Silver SA, Bhatraju PK, Poisner H, Cao S, Jiang M, Wang Y, Niu A, Siew E, Van Amburg JC, Kramer HJ, Kottgen A, Franceschini N, Psaty BM, Tracy RP, Alonso A, Arking DE, Coresh J, Ballantyne CM, Boerwinkle E, Grams M, Zhang MZ, Kestenbaum B, Lanktree MB, Rauh MJ, Harris RC, Bick AG. Clonal hematopoiesis of indeterminate potential is associated with acute kidney injury. Nat Med 2024; 30:810-817. [PMID: 38454125 PMCID: PMC10957477 DOI: 10.1038/s41591-024-02854-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Age is a predominant risk factor for acute kidney injury (AKI), yet the biological mechanisms underlying this risk are largely unknown. Clonal hematopoiesis of indeterminate potential (CHIP) confers increased risk for several chronic diseases associated with aging. Here we sought to test whether CHIP increases the risk of AKI. In three population-based epidemiology cohorts, we found that CHIP was associated with a greater risk of incident AKI, which was more pronounced in patients with AKI requiring dialysis and in individuals with somatic mutations in genes other than DNMT3A, including mutations in TET2 and JAK2. Mendelian randomization analyses supported a causal role for CHIP in promoting AKI. Non-DNMT3A-CHIP was also associated with a nonresolving pattern of injury in patients with AKI. To gain mechanistic insight, we evaluated the role of Tet2-CHIP and Jak2V617F-CHIP in two mouse models of AKI. In both models, CHIP was associated with more severe AKI, greater renal proinflammatory macrophage infiltration and greater post-AKI kidney fibrosis. In summary, this work establishes CHIP as a genetic mechanism conferring impaired kidney function recovery after AKI via an aberrant inflammatory response mediated by renal macrophages.
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Affiliation(s)
| | - Cassianne Robinson-Cohen
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jianchun Chen
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elvis Akwo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyssa C Parker
- Division of Genetic Medicine, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Samuel A Silver
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hannah Poisner
- Division of Genetic Medicine, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Shirong Cao
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ming Jiang
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yinqiu Wang
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Aolei Niu
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Edward Siew
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph C Van Amburg
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Holly J Kramer
- Departments of Public Health Sciences and Medicine, Loyola University Chicago, Maywood IL, USA
| | - Anna Kottgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Systems and Population Health, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Russell P Tracy
- Pathology and Biochemistry, University of Vermont, Burlington, VT, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josef Coresh
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | | | - Eric Boerwinkle
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Morgan Grams
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Division of Nephrology, Department of Internal Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ming-Zhi Zhang
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bryan Kestenbaum
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Matthew B Lanktree
- Department of Medicine and Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Raymond C Harris
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA.
- U.S Department of Veterans Affairs, Nashville, TN, USA.
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, TN, USA.
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Vlasschaert C, Lanktree MB, Rauh MJ, Kelly TN, Natarajan P. Clonal haematopoiesis, ageing and kidney disease. Nat Rev Nephrol 2024; 20:161-174. [PMID: 37884787 PMCID: PMC10922936 DOI: 10.1038/s41581-023-00778-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
Clonal haematopoiesis of indeterminate potential (CHIP) is a preclinical condition wherein a sizeable proportion of an individual's circulating blood cells are derived from a single mutated haematopoietic stem cell. CHIP occurs frequently with ageing - more than 10% of individuals over 65 years of age are affected - and is associated with an increased risk of disease across several organ systems and premature death. Emerging evidence suggests that CHIP has a role in kidney health, including associations with predisposition to acute kidney injury, impaired recovery from acute kidney injury and kidney function decline, both in the general population and among those with chronic kidney disease. Beyond its direct effect on the kidney, CHIP elevates the susceptibility of individuals to various conditions that can detrimentally affect the kidneys, including cardiovascular disease, obesity and insulin resistance, liver disease, gout, osteoporosis and certain autoimmune diseases. Aberrant pro-inflammatory signalling, telomere attrition and epigenetic ageing are potential causal pathophysiological pathways and mediators that underlie CHIP-related disease risk. Experimental animal models have shown that inhibition of inflammatory cytokine signalling can ameliorate many of the pathological effects of CHIP, and assessment of the efficacy and safety of this class of medications for human CHIP-associated pathology is ongoing.
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Affiliation(s)
| | - Matthew B Lanktree
- Department of Medicine and Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Kingston, Ontario, Canada
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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6
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Guarnera L, Jha BK. TET2 mutation as prototypic clonal hematopoiesis lesion. Semin Hematol 2024; 61:51-60. [PMID: 38431463 PMCID: PMC10978279 DOI: 10.1053/j.seminhematol.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/28/2024] [Indexed: 03/05/2024]
Abstract
Loss of function TET2 mutation (TET2MT) is one of the most frequently observed lesions in clonal hematopoiesis (CH). TET2 a member TET-dioxygenase family of enzymes that along with TET1 and TET3, progressively oxidize 5-methyl cytosine (mC) resulting in regulated demethylation of promoter, enhancer and silencer elements of the genome. This process is critical for efficient transcription that determine cell lineage fate, proliferation and survival and the maintenance of the genomic fidelity with aging of the organism. Partial or complete loss-of-function TET2 mutations create regional and contextual DNA hypermethylation leading to gene silencing or activation that result in skewed myeloid differentiation and clonal expansion. In addition to myeloid skewing, loss of TET2 creates differentiation block and provides proliferative advantage to hematopoietic stem and progenitor cells (HSPCs). TET2MT is a prototypical lesion in CH, since the mutant clones dominate during stress hematopoiesis and often associates with evolution of myeloid malignancies. TET2MT clones has unique privilege to create and persist in pro-inflammatory milieu. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, and enhanced self-replication of TET2MT HSPC, the mechanistic link of various pathogenesis associated with TET2 loss in CHIP is less understood. Here we review the recent development in TET2 biology and its probable mechanistic link in CH with aging and inflammation. We also explored the therapeutic strategies of targeting TET2MT associated CHIP and the utility of targeting TET2 in normal hematopoiesis and somatic cell reprograming. We explore the biochemical mechanisms and candidate therapies that emerged in last decade of research.
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Affiliation(s)
- Luca Guarnera
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy; Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Center for Immunotherapy and Precision Immuno-Oncology (CITI), Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH.
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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: 1] [Impact Index Per Article: 1.0] [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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8
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d'Izarny-Gargas T, Isnard P, Boudhabhay I, Buob D, Moktefi A, Linster C, Hummel A, Esteve E, Audard V, Lazareth H, Maroun N, Hertig A, Gosset C, Jouzel C, Permal S, Domenger C, Kosmider O, Rabant M, Karras A, Duong Van Huyen JP. The spectrum of glomerular and vascular kidney pathology associated with myeloproliferative neoplasms. Kidney Int 2023; 104:1206-1218. [PMID: 37769965 DOI: 10.1016/j.kint.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/30/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
A high prevalence of chronic kidney disease (CKD) occurs in patients with myeloproliferative neoplasms (MPN). However, MPN-related glomerulopathy (MPN-RG) may not account for the entirety of CKD risk in this population. The systemic vasculopathy encountered in these patients raises the hypothesis that vascular nephrosclerosis may be a common pattern of injury in patients with MPN and with CKD. In an exhaustive, retrospective, multicenter study of MPN kidney biopsies in four different pathology departments, we now describe glomerular and vascular lesions and establish clinicopathologic correlations. Our study encompassed 47 patients with MPN who underwent a kidney biopsy that included 16 patients with chronic myeloid leukemia (CML) and 31 patients with non-CML MPN. Fourteen cases met a proposed definition of MPN-RG based on mesangial sclerosis and hypercellularity, as well as glomerular thrombotic microangiopathy. MPN-RG was significantly associated with both myelofibrosis and poorer kidney survival. Thirty-three patients had moderate-to-severe arteriosclerosis while 39 patients had moderate-to-severe arteriolar hyalinosis. Multivariable models that included 188 adult native kidney biopsies as controls revealed an association between MPN and chronic kidney vascular damage, which was independent of established risk factors such as age, diabetes mellitus and hypertension. Therefore, MPN-RG is associated with myelofibrosis and has a poor kidney prognosis. Thus, our findings suggest that the kidney vasculature is a target during MPN-associated vasculopathy and establish a new link between MPN and CKD. Hence, these results may raise new hypotheses regarding the pathophysiology of vascular nephrosclerosis in the general population.
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Affiliation(s)
| | - Pierre Isnard
- Department of Pathology, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - Idris Boudhabhay
- Department of Nephrology, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - David Buob
- Department of Pathology, Tenon Hospital, APHP, Paris, France
| | - Anissa Moktefi
- Department of Pathology, Henri Mondor Hospital, APHP, Créteil, France
| | - Charel Linster
- Department of Nephrology, Luxembourg Hospital Center, Luxembourg City, Luxembourg
| | - Aurélie Hummel
- Department of Nephrology, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - Emmanuel Esteve
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche S 1155, Sorbonne Université, Paris, France; Department of Nephrology, Tenon Hospital, APHP, Paris, France
| | - Vincent Audard
- Department of Nephrology and Renal Transplantation, Henri Mondor Hospital, APHP, Créteil, France; Institut National de la Santé et de la Recherche Médicale, Institut Mondor de Recherche Biomédicale U955, Université Paris Est Créteil, Créteil, France
| | - Hélène Lazareth
- Department of Nephrology, Georges Pompidou European Hospital, APHP, Paris, France
| | - Nadine Maroun
- Department of Nephrology, Poissy Intercommunal Hospital, Poissy, France
| | | | - Clément Gosset
- Department of Nephrology, CHU de la Réunion, Saint-Denis, France
| | | | - Sarah Permal
- Department of Internal Medicine, Mamoudzou Hospital, Mayotte, France
| | | | - Olivier Kosmider
- Hematology Laboratory, Cochin Hospital, Paris, France; UFR Médecine, Université Paris Cité, Paris, France
| | - Marion Rabant
- Department of Pathology, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - Alexandre Karras
- Department of Nephrology, Georges Pompidou European Hospital, APHP, Paris, France; UFR Médecine, Université Paris Cité, Paris, France
| | - Jean-Paul Duong Van Huyen
- Department of Pathology, Necker-Enfants Malades Hospital, APHP, Paris, France; UFR Médecine, Université Paris Cité, Paris, France.
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9
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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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10
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Sarakpi T, Mesic A, Speer T. Leukocyte-endothelial interaction in CKD. Clin Kidney J 2023; 16:1845-1860. [PMID: 37915921 PMCID: PMC10616504 DOI: 10.1093/ckj/sfad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 11/03/2023] Open
Abstract
Chronic kidney disease (CKD) represents an independent risk factor for cardiovascular diseases (CVD). Accordingly, CKD patients show a substantial increased risk of cardiovascular mortality. Inflammation represents an important link between CKD and CVD. The interaction between endothelial cells and effector cells of the innate immune system plays a central role in the development and progression of inflammation. Vascular injury causes endothelial dysfunction, leading to augmented oxidative stress, increased expression of leukocyte adhesion molecules and chronic inflammation. CKD induces numerous metabolic changes, creating a uremic milieu resulting in the accumulation of various uremic toxins. These toxins lead to vascular injury, endothelial dysfunction and activation of the innate immune system. Recent studies describe CKD-dependent changes in monocytes that promote endothelial dysfunction and thus CKD progression and CKD-associated CVD. The NLR family pyrin domain containing 3-interleukin-1β-interleukin-6 (NLRP3-IL-1β-IL-6) signaling pathway plays a pivotal role in the development and progression of CVD and CKD alike. Several clinical trials are investigating targeted inhibition of this pathway indicating that anti-inflammatory therapeutic strategies may emerge as novel approaches in patients at high cardiovascular risk and nonresolving inflammation. CKD patients in particular would benefit from targeted anti-inflammatory therapy, since conventional therapeutic regimens have limited efficacy in this population.
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Affiliation(s)
- Tamim Sarakpi
- Department of Internal Medicine 4 – Nephrology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Else Kröner-Fresenius-Zentrum for Nephrological Research, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Armir Mesic
- Department of Internal Medicine 4 – Nephrology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Else Kröner-Fresenius-Zentrum for Nephrological Research, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Thimoteus Speer
- Department of Internal Medicine 4 – Nephrology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Else Kröner-Fresenius-Zentrum for Nephrological Research, Goethe University Frankfurt, Frankfurt am Main, Germany
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11
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJ, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun J, DeMeo D, Levy D, Johnson A, Mathias R, Taub M, Arnett D, North K, Raffield LM, Carson A, Doyle MF, Rich SS, Rotter JI, Guo X, Cox N, Roden DM, Franceschini N, Desai P, Reiner A, Auer PL, Scheet P, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.20.23297280. [PMID: 37905118 PMCID: PMC10615010 DOI: 10.1101/2023.10.20.23297280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well-understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our estimates of mCA fitness were correlated (R 2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using a theoretical probability distribution. Individuals with lymphoid-associated mCAs had a significantly higher white blood cell count and faster clonal expansion rate. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified TCL1A , NRIP1 , and TERT locus variants as modulators of mCA clonal expansion rate.
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12
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Ogura Y, Mimura I. Epigenetic roles in clonal hematopoiesis and aging kidney-related chronic kidney disease. Front Cell Dev Biol 2023; 11:1281850. [PMID: 37928907 PMCID: PMC10623128 DOI: 10.3389/fcell.2023.1281850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Accumulation of somatic hematopoietic stem cell mutations with aging has been revealed by the recent genome-wide analysis. Clonal expansion, known as clonal hematopoiesis of indeterminate potential (CHIP), is a premalignant condition of hematological cancers. It is defined as the absence of definitive morphological evidence of a hematological neoplasm and occurrence of ≥2% of mutant allele fraction in the peripheral blood. In CHIP, the most frequently mutated genes are epigenetic regulators such as DNMT3A, TET2, and ASXL1. CHIP induces inflammation. CHIP is shown to be associated with not only hematological malignancy but also non-malignant disorders such as atherosclerosis, cardiovascular diseases and chronic liver disease. In addition, recent several large clinical trials have shown that CHIP is also the risk factor for developing chronic kidney disease (CKD). In this review article, we proposed novel findings about CHIP and CHIP related kidney disease based on the recent basic and clinical research. The possible mechanism of the kidney injury in CHIP is supposed to be due to the clonal expansion in both myeloid and lymphoid cell lines. In myeloid cell lines, the mutated macrophages increase the inflammatory cytokine level and induce chronic inflammation. It leads to epigenetic downregulation of kidney and macrophage klotho level. In lymphoid cell lines, CHIP might be related to monoclonal gammopathy of renal significance (MGRS). It describes any B cell or plasma cell clonal disorder that does not fulfill the criteria for cancer yet produces a nephrotoxic monoclonal immunoglobulin that leads to kidney injury or disease. MGRS causes M-protein related nephropathy frequently observed among aged CKD patients. It is important to consider the CHIP-related complications such as hematological malignancy, cardiovascular diseases and metabolic disorders in managing the elderly CKD patients. There are no established therapies for CHIP and CHIP-related CKD yet. However, recent studies have supported the development of effective CHIP therapies, such as blocking the expansion of aberrant HSCs and inhibiting chronic inflammation. In addition, drugs targeting the epigenetic regulation of Klotho in the kidney and macrophages might be therapeutic targets of CHIP in the kidney.
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Affiliation(s)
| | - Imari Mimura
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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13
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Huang Z, Vlasschaert C, Robinson-Cohen C, Pan Y, Sun X, Lash JP, Kestenbaum B, Kelly TN. Emerging evidence on the role of clonal hematopoiesis of indeterminate potential in chronic kidney disease. Transl Res 2023; 256:87-94. [PMID: 36586535 PMCID: PMC10101890 DOI: 10.1016/j.trsl.2022.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Chronic kidney disease (CKD) was responsible for 1.2 million deaths globally in 2016. Despite the large and growing burden of CKD, treatment options are limited and generally only preserve kidney function. Characterizing molecular precursors to incident and progressive CKD could point to critically needed prevention and treatment strategies. Clonal hematopoiesis of indeterminate potential (CHIP) is typically characterized by the clonal expansion of blood cells carrying somatic mutations in specific driver genes. An age-related disorder, CHIP is rare in the young but common in older adults. Recent studies have identified causal associations between CHIP and atherosclerotic cardiovascular disease which are most likely mediated by inflammation, a hallmark of CKD. Animal evidence has supported causal effects of CHIP on kidney injury, inflammation, and fibrosis, providing impetus for human research. Although prospective epidemiologic studies investigating associations of CHIP with development and progression of CKD are few, intriguing findings have been reported. CHIP was significantly associated with kidney function decline and end stage kidney disease in the general population, although effect sizes were modest. Recent work suggests larger associations of CHIP with kidney disease progression in CKD patients, but further investigations in this area are needed. In addition, the accumulating literature has identified some heterogeneity in associations between CHIP and kidney endpoints across study populations, but reasons for these differences remain unclear. The current review provides an in-depth exploration into this nascent area of research, develops a conceptual framework linking CHIP to CKD, and discusses the clinical and public health implications of this work.
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Affiliation(s)
- Zhijie Huang
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | | | - Cassianne Robinson-Cohen
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yang Pan
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Xiao Sun
- Department of Epidemiology, Tulane University, New Orleans, Louisiana; Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - James P Lash
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Bryan Kestenbaum
- Division of Nephrology, Department of Medicine, Kidney Research Institute, University of Washington, Seattle, Washington
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, Illinois.
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