1
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Matsubayashi H, Morizane C. Familial and hereditary pancreatic cancer in Japan. Fam Cancer 2024; 23:365-372. [PMID: 38733422 DOI: 10.1007/s10689-024-00395-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
As in Western countries, familial pancreatic cancer accounts for 5-7% of pancreatic cancer (PC) in Japan. Opportunities for diagnosing hereditary pancreatic cancer (HPC) are increasing owing to the coverage of companion diagnostics and cancer genomic profiling by national health insurance in patients with unresectable or recurrent PC refractory to standard chemotherapies. HPC is recognized in 7% of PCs and 15% of familial pancreatic cancer, including germline variants of BRCA1/2, ATM, PALB2, APC, and mismatch repair genes. Individuals with 5-fold or greater inherited risks of PC are recommended to undergo pancreatic surveillance according to Japanese guidelines. The imaging modalities for this surveillance include endoscopic ultrasound, magnetic resonance cholangiopancreatography, abdominal ultrasound, and enhanced computed tomography. Currently, a nationwide prospective surveillance study is ongoing in Japan. Platinum-based chemotherapy is an effective pancreatic cancer treatment in patients with variants of homologous recombination repair genes (BRCA1/2 and PALB2); however, the use of platinum regimens solely based on familial/personal cancer history remains controversial. The efficacy of olaparib maintenance therapy, as confirmed by the POLO study, has significantly impacted the clinical treatment of advanced PC patients in Japan. Since the initiation of precision cancer medicine in 2019, genetic medicine for PC patients has expanded in Japan.
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Affiliation(s)
- Hiroyuki Matsubayashi
- Division of Genetic Medicine Promotion and Endoscopy, Shizuoka Cancer Center, Shimonagakubo, Nagaizumi, Suntogun, Shizuoka, 411-8777, Japan.
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
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2
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Leask MP, Crișan TO, Ji A, Matsuo H, Köttgen A, Merriman TR. The pathogenesis of gout: molecular insights from genetic, epigenomic and transcriptomic studies. Nat Rev Rheumatol 2024; 20:510-523. [PMID: 38992217 DOI: 10.1038/s41584-024-01137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/13/2024]
Abstract
The pathogenesis of gout involves a series of steps beginning with hyperuricaemia, followed by the deposition of monosodium urate crystal in articular structures and culminating in an innate immune response, mediated by the NLRP3 inflammasome, to the deposited crystals. Large genome-wide association studies (GWAS) of serum urate levels initially identified the genetic variants with the strongest effects, mapping mainly to genes that encode urate transporters in the kidney and gut. Other GWAS highlighted the importance of uncommon genetic variants. More recently, genetic and epigenetic genome-wide studies have revealed new pathways in the inflammatory process of gout, including genetic associations with epigenomic modifiers. Epigenome-wide association studies are also implicating epigenomic remodelling in gout, which perhaps regulates the responsiveness of the innate immune system to monosodium urate crystals. Notably, genes implicated in gout GWAS do not include those encoding components of the NLRP3 inflammasome itself, but instead include genes encoding molecules involved in its regulation. Knowledge of the molecular mechanisms underlying gout has advanced through the translation of genetic associations into specific molecular mechanisms. Notable examples include ABCG2, HNF4A, PDZK1, MAF and IL37. Current genetic studies are dominated by participants of European ancestry; however, studies focusing on other population groups are discovering informative population-specific variants associated with gout.
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Affiliation(s)
- Megan P Leask
- Department of Physiology, University of Otago, Dunedin, Aotearoa, New Zealand
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tania O Crișan
- Department of Medical Genetics, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Aichang Ji
- Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Tony R Merriman
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Microbiology and Immunology, University of Otago, Dunedin, Aotearoa, New Zealand.
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3
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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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4
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Jakobsen NA, Turkalj S, Zeng AGX, Stoilova B, Metzner M, Rahmig S, Nagree MS, Shah S, Moore R, Usukhbayar B, Angulo Salazar M, Gafencu GA, Kennedy A, Newman S, Kendrick BJL, Taylor AH, Afinowi-Luitz R, Gundle R, Watkins B, Wheway K, Beazley D, Murison A, Aguilar-Navarro AG, Flores-Figueroa E, Dakin SG, Carr AJ, Nerlov C, Dick JE, Xie SZ, Vyas P. Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging. Cell Stem Cell 2024; 31:1127-1144.e17. [PMID: 38917807 DOI: 10.1016/j.stem.2024.05.010] [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: 06/25/2023] [Revised: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Clonal hematopoiesis (CH) arises when hematopoietic stem cells (HSCs) acquire mutations, most frequently in the DNMT3A and TET2 genes, conferring a competitive advantage through mechanisms that remain unclear. To gain insight into how CH mutations enable gradual clonal expansion, we used single-cell multi-omics with high-fidelity genotyping on human CH bone marrow (BM) samples. Most of the selective advantage of mutant cells occurs within HSCs. DNMT3A- and TET2-mutant clones expand further in early progenitors, while TET2 mutations accelerate myeloid maturation in a dose-dependent manner. Unexpectedly, both mutant and non-mutant HSCs from CH samples are enriched for inflammatory and aging transcriptomic signatures, compared with HSCs from non-CH samples, revealing a non-cell-autonomous effect. However, DNMT3A- and TET2-mutant HSCs have an attenuated inflammatory response relative to wild-type HSCs within the same sample. Our data support a model whereby CH clones are gradually selected because they are resistant to the deleterious impact of inflammation and aging.
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Affiliation(s)
- Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Bilyana Stoilova
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Susann Rahmig
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Murtaza S Nagree
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sayyam Shah
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rachel Moore
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Grigore-Aristide Gafencu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alison Kennedy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Simon Newman
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Benjamin J L Kendrick
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Adrian H Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rasheed Afinowi-Luitz
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Roger Gundle
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Bridget Watkins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Kim Wheway
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Debra Beazley
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alicia G Aguilar-Navarro
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eugenia Flores-Figueroa
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Stephanie G Dakin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Andrew J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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5
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Schleicher WE, Hoag B, De Dominici M, DeGregori J, Pietras EM. CHIP: a clonal odyssey of the bone marrow niche. J Clin Invest 2024; 134:e180068. [PMID: 39087468 PMCID: PMC11290965 DOI: 10.1172/jci180068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by the selective expansion of hematopoietic stem and progenitor cells (HSPCs) carrying somatic mutations. While CHIP is typically asymptomatic, it has garnered substantial attention due to its association with the pathogenesis of multiple disease conditions, including cardiovascular disease (CVD) and hematological malignancies. In this Review, we will discuss seminal and recent studies that have advanced our understanding of mechanisms that drive selection for mutant HSPCs in the BM niche. Next, we will address recent studies evaluating potential relationships between the clonal dynamics of CHIP and hematopoietic development across the lifespan. Next, we will examine the roles of systemic factors that can influence hematopoietic stem cell (HSC) fitness, including inflammation, and exposures to cytotoxic agents in driving selection for CHIP clones. Furthermore, we will consider how - through their impact on the BM niche - lifestyle factors, including diet, exercise, and psychosocial stressors, might contribute to the process of somatic evolution in the BM that culminates in CHIP. Finally, we will review the role of old age as a major driver of selection in CHIP.
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Affiliation(s)
| | - Bridget Hoag
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Marco De Dominici
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - James DeGregori
- Division of Hematology, Department of Medicine, and
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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6
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Caiado F, Manz MG. IL-1 in aging and pathologies of hematopoietic stem cells. Blood 2024; 144:368-377. [PMID: 38781562 DOI: 10.1182/blood.2023023105] [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: 02/28/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
ABSTRACT Defense-oriented inflammatory reactivity supports survival at younger age but might contribute to health impairments in modern, aging societies. The interleukin-1 (IL-1) cytokines are highly conserved and regulated, pleiotropic mediators of inflammation, essential to respond adequately to infection and tissue damage but also with potential host damaging effects when left unresolved. In this review, we discuss how continuous low-level IL-1 signaling contributes to aging-associated hematopoietic stem and progenitor cell (HSPC) functional impairments and how this inflammatory selective pressure acts as a driver of more profound hematological alterations, such as clonal hematopoiesis of indeterminate potential, and to overt HSPC diseases, like myeloproliferative and myelodysplastic neoplasia as well as acute myeloid leukemia. Based on this, we outline how IL-1 pathway inhibition might be used to prevent or treat inflammaging-associated HSPC pathologies.
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Affiliation(s)
- Francisco Caiado
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich, Zurich, Switzerland
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7
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Singh J, Li N, Ashrafi E, Thao LTP, Curtis DJ, Wood EM, McQuilten ZK. Clonal hematopoiesis of indeterminate potential as a prognostic factor: a systematic review and meta-analysis. Blood Adv 2024; 8:3771-3784. [PMID: 38838228 DOI: 10.1182/bloodadvances.2024013228] [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: 03/21/2024] [Revised: 05/06/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
ABSTRACT With advances in sequencing, individuals with clonal hematopoiesis of indeterminate potential (CHIP) are increasingly being identified, making it essential to understand its prognostic implications. We conducted a systematic review of studies comparing the risk of clinical outcomes in individuals with and without CHIP. We searched MEDLINE and EMBASE and included original research reporting an outcome risk measure in individuals with CHIP, adjusted for the effect of age. From the 3305 studies screened, we included 88 studies with 45 to 470 960 participants. Most studies had a low-to-moderate risk of bias in all domains of the Quality in Prognostic Factor Studies tool. Random-effects meta-analyses were performed for outcomes reported in at least 3 studies. CHIP conferred an increased risk of all-cause mortality (hazard ratio [HR], 1.34; 95% confidence interval, 1.19-1.50), cancer mortality (HR, 1.46; 1.13-1.88), composite cardiovascular events (HR, 1.40; 1.19-1.65), coronary heart disease (HR, 1.76; 1.27-2.44), stroke (HR, 1.16; 1.05-1.28), heart failure (HR, 1.27; 1.15-1.41), hematologic malignancy (HR, 4.28; 2.29-7.98), lung cancer (HR, 1.40; 1.27-1.54), renal impairment (HR, 1.25; 1.18-1.33) and severe COVID-19 (odds ratio [OR], 1.46; 1.18-1.80). CHIP was not associated with cardiovascular mortality (HR, 1.09; 0.97-1.22), except in the subgroup analysis restricted to larger clones (HR, 1.31; 1.12-1.54). Isolated DNMT3A mutations did not increase the risk of myeloid malignancy, all-cause mortality, or renal impairment. The reasons for heterogeneity between studies included differences in definitions and measurements of CHIP and the outcomes, and populations studied. In summary, CHIP is associated with diverse clinical outcomes, with clone size, specific gene, and inherent patient characteristics important mediators of risk.
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Affiliation(s)
- Jasmine Singh
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of Haematology, Fiona Stanley Hospital, Perth, Australia
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
| | - Nancy Li
- Department of Haematology, Eastern Health, Melbourne, Australia
| | - Elham Ashrafi
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Le Thi Phuong Thao
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - David J Curtis
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
- Department of Clinical Haematology, Alfred Health, Melbourne, Australia
| | - Erica M Wood
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of Haematology, Monash Health, Melbourne, Australia
| | - Zoe K McQuilten
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of Haematology, Monash Health, Melbourne, Australia
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8
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Hislop JM, Went M, Mills C, Sud A, Law PJ, Houlston RS. Using Mendelian Randomisation to search for modifiable risk factors influencing the development of clonal haematopoiesis. Blood Cancer J 2024; 14:114. [PMID: 39013866 PMCID: PMC11252326 DOI: 10.1038/s41408-024-01101-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
- Jessica M Hislop
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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9
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Maeda H, Kakiuchi N. Clonal expansion in normal tissues. Cancer Sci 2024; 115:2117-2124. [PMID: 38623936 PMCID: PMC11247609 DOI: 10.1111/cas.16183] [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: 02/07/2024] [Revised: 03/24/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Cancer originates from a single ancestral cell that acquires a driver mutation, which confers a growth or survival advantage, followed by the acquisition of additional driver mutations by descendant cells. Recently, it has become evident that somatic cell mutations accumulate in normal tissues with aging and exposure to environmental factors, such as alcohol, smoking, and UV rays, increases the mutation rate. Clones harboring driver mutations expand with age, leading to tissue remodeling. Lineage analysis of myeloproliferative neoplasms and der(1;16)-positive breast cancer revealed that driver mutations were acquired early in our lives and that the development of cancer takes decades, unveiling the previously unknown early process of cancer development. Evidence that clonal hematopoiesis affects various diseases, including nonneoplastic diseases, highlights the potential role of the identification and functional analysis of mutated clones in unraveling unknown pathologies. In this review, we summarize the recent updates on clonal expansion in normal tissues and the natural history of cancer revealed through lineage analysis of noncancerous and cancerous tissues.
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Affiliation(s)
- Hirona Maeda
- Department of Pathology and Tumor Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- Department of Diagnostic PathologyKyoto University HospitalKyotoJapan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- The Hakubi Center for Advanced ResearchKyoto UniversityKyotoJapan
- Department of Gastroenterology and Hepatology, Graduate School of MedicineKyoto UniversityKyotoJapan
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10
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Trégouët DA, Morange PE. Next-generation sequencing strategies in venous thromboembolism: in whom and for what purpose? J Thromb Haemost 2024; 22:1826-1834. [PMID: 38641321 DOI: 10.1016/j.jtha.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
Abstract
This invited review follows the oral presentation "To Sequence or Not to Sequence, That Is Not the Question; But 'When, Who, Which and What For?' Is" given during the State of the Art session "Translational Genomics in Thrombosis: From OMICs to Clinics" of the International Society on Thrombosis and Haemostasis 2023 Congress. Emphasizing the power of next-generation sequencing technologies and the diverse strategies associated with DNA variant analysis, this review highlights the unresolved questions and challenges in their implementation both for the clinical diagnosis of venous thromboembolism and in translational research.
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Affiliation(s)
- David-Alexandre Trégouët
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale, Bordeaux Population Health Research Center, Unité Mixte de Recherche 1219, Bordeaux, France.
| | - Pierre-Emmanuel Morange
- Cardiovascular and Nutrition Research Center (Centre de Recherche en CardioVasculaire et Nutrition), Institut National de la Santé et de la Recherche Médicale, Institut National de Recherche pour l'agriculture, l' Alimentation et l'Environnement, Aix-Marseille University, Marseille, France
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11
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Sun KY, Bai X, Chen S, Bao S, Zhang C, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke AE, Ganel L, Hawes A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Di Gioia A, Rajagopal VM, Lopez A, Varela JR, Alegre-Díaz J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton JD, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalogue of protein-coding variation in 983,578 individuals. Nature 2024; 631:583-592. [PMID: 38768635 PMCID: PMC11254753 DOI: 10.1038/s41586-024-07556-0] [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: 06/19/2023] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Rare coding variants that substantially affect function provide insights into the biology of a gene1-3. However, ascertaining the frequency of such variants requires large sample sizes4-8. Here we present a catalogue of human protein-coding variation, derived from exome sequencing of 983,578 individuals across diverse populations. In total, 23% of the Regeneron Genetics Center Million Exome (RGC-ME) data come from individuals of African, East Asian, Indigenous American, Middle Eastern and South Asian ancestry. The catalogue includes more than 10.4 million missense and 1.1 million predicted loss-of-function (pLOF) variants. We identify individuals with rare biallelic pLOF variants in 4,848 genes, 1,751 of which have not been previously reported. From precise quantitative estimates of selection against heterozygous loss of function (LOF), we identify 3,988 LOF-intolerant genes, including 86 that were previously assessed as tolerant and 1,153 that lack established disease annotation. We also define regions of missense depletion at high resolution. Notably, 1,482 genes have regions that are depleted of missense variants despite being tolerant of pLOF variants. Finally, we estimate that 3% of individuals have a clinically actionable genetic variant, and that 11,773 variants reported in ClinVar with unknown significance are likely to be deleterious cryptic splice sites. To facilitate variant interpretation and genetics-informed precision medicine, we make this resource of coding variation from the RGC-ME dataset publicly accessible through a variant allele frequency browser.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Liron Ganel
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Jesús Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Jaime Berumen
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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12
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Lazar NH, Celik S, Chen L, Fay MM, Irish JC, Jensen J, Tillinghast CA, Urbanik J, Bone WP, Gibson CC, Haque IS. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing. Nat Genet 2024; 56:1482-1493. [PMID: 38811841 PMCID: PMC11250378 DOI: 10.1038/s41588-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Affiliation(s)
| | | | - Lu Chen
- Recursion, Salt Lake City, UT, USA
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13
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Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat SM, Kentistou KA, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman BR, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman ND, Song L, Gardner EJ, Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ. Genetic drivers and cellular selection of female mosaic X chromosome loss. Nature 2024; 631:134-141. [PMID: 38867047 DOI: 10.1038/s41586-024-07533-7] [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: 01/20/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Mosaic loss of the X chromosome (mLOX) is the most common clonal somatic alteration in leukocytes of female individuals1,2, but little is known about its genetic determinants or phenotypic consequences. Here, to address this, we used data from 883,574 female participants across 8 biobanks; 12% of participants exhibited detectable mLOX in approximately 2% of leukocytes. Female participants with mLOX had an increased risk of myeloid and lymphoid leukaemias. Genetic analyses identified 56 common variants associated with mLOX, implicating genes with roles in chromosomal missegregation, cancer predisposition and autoimmune diseases. Exome-sequence analyses identified rare missense variants in FBXO10 that confer a twofold increased risk of mLOX. Only a small fraction of associations was shared with mosaic Y chromosome loss, suggesting that distinct biological processes drive formation and clonal expansion of sex chromosome missegregation. Allelic shift analyses identified X chromosome alleles that are preferentially retained in mLOX, demonstrating variation at many loci under cellular selection. A polygenic score including 44 allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Our results support a model in which germline variants predispose female individuals to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of clonal expansion.
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Affiliation(s)
- Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Seyedeh M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valdislav Tuzov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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14
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Thomas H, Alix T, Renard É, Renaud M, Wourms J, Zuily S, Leheup B, Geneviève D, Dreumont N, Schmitt E, Bronner M, Muller M, Divoux M, Wandzel M, Ravel JM, Dexheimer M, Becker A, Roth V, Willems M, Coubes C, Vieville G, Devillard F, Schaefer É, Baer S, Piton A, Gérard B, Vincent M, Nizon M, Cogné B, Ruaud L, Couque N, Putoux A, Edery P, Lesca G, Chatron N, Till M, Faivre L, Tran-Mau-Them F, Alessandri JL, Lebrun M, Quélin C, Odent S, Dubourg C, David V, Faoucher M, Mignot C, Keren B, Pisan É, Afenjar A, Julia S, Bieth É, Banneau G, Goldenberg A, Husson T, Campion D, Lecoquierre F, Nicolas G, Charbonnier C, De Saint Martin A, Naudion S, Degoutin M, Rondeau S, Michot C, Cormier-Daire V, Oussalah A, Pourié C, Lambert L, Bonnet C. Expanding the genetic and clinical spectrum of Tatton-Brown-Rahman syndrome in a series of 24 French patients. J Med Genet 2024:jmg-2024-110031. [PMID: 38937076 DOI: 10.1136/jmg-2024-110031] [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: 04/02/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as DNA methyltransferase 3 alpha (DNMT3A)-overgrowth syndrome (DOS), was first described by Tatton-Brown in 2014. This syndrome is characterised by overgrowth, intellectual disability and distinctive facial features and is the consequence of germline loss-of-function variants in DNMT3A, which encodes a DNA methyltransferase involved in epigenetic regulation. Somatic variants of DNMT3A are frequently observed in haematological malignancies, including acute myeloid leukaemia (AML). To date, 100 individuals with TBRS with de novo germline variants have been described. We aimed to further characterise this disorder clinically and at the molecular level in a nationwide series of 24 French patients and to investigate the correlation between the severity of intellectual disability and the type of variant. METHODS We collected genetic and medical information from 24 individuals with TBRS using a questionnaire released through the French National AnDDI-Rares Network. RESULTS Here, we describe the first nationwide French cohort of 24 individuals with germline likely pathogenic/pathogenic variants in DNMT3A, including 17 novel variants. We confirmed that the main phenotypic features were intellectual disability (100% of individuals), distinctive facial features (96%) and overgrowth (87%). We highlighted novel clinical features, such as hypertrichosis, and further described the neurological features and EEG results. CONCLUSION This study of a nationwide cohort of individuals with TBRS confirms previously published data and provides additional information and clarifies clinical features to facilitate diagnosis and improve care. This study adds value to the growing body of knowledge on TBRS and broadens its clinical and molecular spectrum.
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Affiliation(s)
- Hortense Thomas
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
| | - Tom Alix
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Émeline Renard
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
- Endocrinologie pédiatrique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Mathilde Renaud
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
- Service de Neurologie, CHRU de Nancy, Nancy, France
| | - Justine Wourms
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
| | - Stéphane Zuily
- Médecine Vasculaire, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- UMR_S 916 DCAC, INSERM, Vandœuvre-lès-Nancy, France
| | - Bruno Leheup
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - David Geneviève
- Centre de référence anomalies du développement et syndromes malformatifs, Département de Génétique Medicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
- Inserm U1183, Université Montpellier 1, Faculté de Médecine Montpellier-Nîmes, Montpellier, France
| | - Natacha Dreumont
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Myriam Bronner
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marc Muller
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marion Divoux
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Marion Wandzel
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Jean-Marie Ravel
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Mylène Dexheimer
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Aurélie Becker
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Virginie Roth
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Marjolaine Willems
- Centre de référence anomalies du développement et syndromes malformatifs, Département de Génétique Medicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Christine Coubes
- Centre de référence anomalies du développement et syndromes malformatifs, Département de Génétique Medicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Gaëlle Vieville
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
| | - Françoise Devillard
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble Alpes, Grenoble, France
| | - Élise Schaefer
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Sarah Baer
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Bénédicte Gérard
- Service de Génétique médicale, Institut de Génétique Médicale d'Alsace, CHU de Strasbourg, Strasbourg, France
| | - Marie Vincent
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
- CNRS, INSERM, Institut du thorax, Nantes Université, Nantes, France
| | - Mathilde Nizon
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
- CNRS, INSERM, Institut du thorax, Nantes Université, Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
- CNRS, INSERM, Institut du thorax, Nantes Université, Nantes, France
| | - Lyse Ruaud
- Département de Génétique, Hôpital Robert Debré, APHP Nord, Paris, France
| | - Nathalie Couque
- Département de Génétique, Hôpital Robert Debré, APHP Nord, Paris, France
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Gaëtan Lesca
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Marianne Till
- Service de Génétique, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- CNRS UMR5310, INSERM U1217, Institut NeuroMyoGene PNMG, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurence Faivre
- Centre de référence anomalies du développement et syndromes malformatifs et Centre de référence Déficiences Intellectuelles de causes rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm, Université Bourgogne Franche-Comté, Dijon, France
| | - Frédéric Tran-Mau-Them
- UMR1231 GAD, Inserm, Université Bourgogne Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jean-Luc Alessandri
- Service de génétique médicale, CHU de La Réunion, Hôpital Félix Guyon, Bellepierre, Saint-Denis, Réunion
| | - Marine Lebrun
- Département de Génétique, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
| | - Chloé Quélin
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Sylvie Odent
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Christèle Dubourg
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Véronique David
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Marie Faoucher
- Département de génétique moléculaire et génomique, CHU Rennes, Rennes, France
| | - Cyril Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Boris Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Élise Pisan
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Alexandra Afenjar
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP Sorbonne Université, Paris, France
| | - Sophie Julia
- Département de Génétique médicale, CHU Toulouse, Toulouse, France
| | - Éric Bieth
- Département de Génétique médicale, CHU Toulouse, Toulouse, France
| | | | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Thomas Husson
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Psychiatry, CHU de Rouen, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - Dominique Campion
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Psychiatry, CHU de Rouen, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, CHU de Rouen, Rouen, France
- Inserm U1245, Université de Rouen Normandie, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, Université de Rouen Normandie, Rouen, France
- Department of Biotatistics, CHU de Rouen, Rouen, France
| | - Anne De Saint Martin
- Centre de Référence des épilepsies Rares, Hopitaux universitaires de Strasbourg, Strasbourg, France
| | - Sophie Naudion
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Groupe hospitalier Pellegrin, Bordeaux, France
| | - Manon Degoutin
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Groupe hospitalier Pellegrin, Bordeaux, France
| | - Sophie Rondeau
- Centre de référence des maladies osseuses constitutionnelles, Necker-Enfants Malades Hospitals, Paris, France
- INSERM UMR 1163, Imagine Institute, Paris, France
| | - Caroline Michot
- Centre de référence des maladies osseuses constitutionnelles, Necker-Enfants Malades Hospitals, Paris, France
- INSERM UMR 1163, Imagine Institute, Paris, France
| | - Valérie Cormier-Daire
- Centre de référence des maladies osseuses constitutionnelles, Necker-Enfants Malades Hospitals, Paris, France
- INSERM UMR 1163, Imagine Institute, Paris, France
| | - Abderrahim Oussalah
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
- Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, CHRU de Nancy, Nancy, France
| | - Carine Pourié
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Laëtitia Lambert
- Service de Génétique Clinique, CHRU de Nancy, Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Céline Bonnet
- Laboratoire de Génétique, CHRU de Nancy, Vandœuvre-lès-Nancy, France
- INSERM NGERE U1256, Université de Lorraine, Vandœuvre-lès-Nancy, France
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15
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Vlasschaert C, Pan Y, Chen J, Akwo E, Rao V, Hixson JE, Chong M, Uddin MM, Yu Z, Jiang M, Peng F, Cao S, Wang Y, Kim DK, Hung AM, He J, Tamura MK, Cohen DL, He J, Li C, Bhat Z, Rao P, Xie D, Bick AG, Kestenbaum B, Paré G, Rauh MJ, Levin A, Natarajan P, Lash JP, Zhang MZ, Harris RC, Robinson-Cohen C, Lanktree MB, Kelly TN. Clonal hematopoiesis of indeterminate potential contributes to accelerated chronic kidney disease progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24309181. [PMID: 38946975 PMCID: PMC11213124 DOI: 10.1101/2024.06.19.24309181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Clonal hematopoiesis of indeterminate potential (CHIP) is a common inflammatory condition of aging that causes myriad end-organ damage. We have recently shown associations for CHIP with acute kidney injury and with kidney function decline in the general population, with stronger associations for CHIP driven by mutations in genes other than DNMT3A (non- DNMT3A CHIP). Longitudinal kidney function endpoints in individuals with pre-existing chronic kidney disease (CKD) and CHIP have been examined in two previous studies, which reported conflicting findings and were limited by small sample sizes. Methods In this study, we examined the prospective associations between CHIP and CKD progression events in four cohorts of CKD patients (total N = 5,772). The primary outcome was a composite of 50% kidney function decline or kidney failure. The slope of eGFR decline was examined as a secondary outcome. Mendelian randomization techniques were then used to investigate potential causal effects of CHIP on eGFR decline. Finally, kidney function was assessed in adenine-fed CKD model mice having received a bone marrow transplant recapitulating Tet2 -CHIP compared to controls transplanted wild-type bone marrow. Results Across all cohorts, the average age was 66.4 years, the average baseline eGFR was 42.6 ml/min/1.73m 2 , and 24% had CHIP. Upon meta-analysis, non- DNMT3A CHIP was associated with a 59% higher relative risk of incident CKD progression (HR 1.59, 95% CI: 1.02-2.47). This association was more pronounced among individuals with diabetes (HR 1.29, 95% CI: 1.03-1.62) and with baseline eGFR ≥ 30 ml/min/1.73m (HR 1.80, 95% CI: 1.11-2.90). Additionally, the annualized slope of eGFR decline was steeper among non- DNMT3A CHIP carriers, relative to non-carriers (β -0.61 ± 0.31 ml/min/1.73m 2 , p = 0.04). Mendelian randomization analyses suggested a causal role for CHIP in eGFR decline among individuals with diabetes. In a dietary adenine mouse model of CKD, Tet2 -CHIP was associated with lower GFR as well as greater kidney inflammation, tubular injury, and tubulointerstitial fibrosis. Conclusion Non- DNMT3A CHIP is a potentially targetable novel risk factor for CKD progression.
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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17
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Liu WS, Wu BS, Yang L, Chen SD, Zhang YR, Deng YT, Wu XR, He XY, Yang J, Feng JF, Cheng W, Xu YM, Yu JT. Whole exome sequencing analyses reveal novel genes in telomere length and their biomedical implications. GeroScience 2024:10.1007/s11357-024-01203-2. [PMID: 38837026 DOI: 10.1007/s11357-024-01203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/11/2024] [Indexed: 06/06/2024] Open
Abstract
Telomere length is a putative biomarker of aging and is associated with multiple age-related diseases. There are limited data on the landscape of rare genetic variations in telomere length. Here, we systematically characterize the rare variant associations with leukocyte telomere length (LTL) through exome-wide association study (ExWAS) among 390,231 individuals in the UK Biobank. We identified 18 robust rare-variant genes for LTL, most of which estimated effects on LTL were significant (> 0.2 standard deviation per allele). The biological functions of the rare-variant genes were associated with telomere maintenance and capping and several genes were specifically expressed in the testis. Three novel genes (ASXL1, CFAP58, and TET2) associated with LTL were identified. Phenotypic association analyses indicated significant associations of ASXL1 and TET2 with cancers, age-related diseases, blood assays, and cardiovascular traits. Survival analyses suggested that carriers of ASXL1 or TET2 variants were at increased risk for cancers; diseases of the circulatory, respiratory, and genitourinary systems; and all-cause and cause-specific deaths. The CFAP58 carriers were at elevated risk of deaths due to cancers. Collectively, the present whole exome sequencing study provides novel insights into the genetic landscape of LTL, identifying novel genes associated with LTL and their implications on human health and facilitating a better understanding of aging, thus pinpointing the genetic relevance of LTL with clonal hematopoiesis, biomedical traits, and health-related outcomes.
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Affiliation(s)
- Wei-Shi Liu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Liu Yang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Ya-Ru Zhang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Yue-Ting Deng
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Xin-Rui Wu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1St Eastern Jianshe Road, Zhengzhou, 450000, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, Zhengzhou, China
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1St Eastern Jianshe Road, Zhengzhou, 450000, China.
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, Zhengzhou, China.
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, 12Th Wulumuqi Zhong Road, Shanghai, 200040, China.
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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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Zhang X, Yang F, Zhu T, Zhao X, Zhang J, Wen J, Zhang Y, Wang G, Ren X, Chen A, Wang X, Wang L, Lv X, Yang W, Qu C, Wang H, Ning Z, Qu L. Whole genome resequencing reveals genomic regions related to red plumage in ducks. Poult Sci 2024; 103:103694. [PMID: 38663207 PMCID: PMC11068611 DOI: 10.1016/j.psj.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 05/07/2024] Open
Abstract
Plumage color is a characteristic trait of ducks that originates as a result of natural and artificial selection. As a conspicuous phenotypic feature, it is a breed characteristic. Previous studies have identified some genes associated with the formation of black and white plumage in ducks. However, studies on the genetic basis underlying the red plumage phenotype in ducks are limited. Here, genome-wide association analysis (GWAS) and selection signal detection (Fst, θπ ratio, and cross-population composite likelihood ratio [XP-CLR]) were conducted to identify candidate regions and genes underlying duck plumage color phenotype. Selection signal detection revealed 29 overlapping genes (including ENPP1 and ULK1) significantly associated with red plumage color in Ji'an Red ducks. ENSAPLG00000012679, ESRRG, and SPATA5 were identified as candidate genes associated with red plumage using GWAS. Selection signal detection revealed that 19 overlapping genes (including GMDS, PDIA6, and ODC1) significantly correlated with light brown plumage in Brown Tsaiya ducks. GWAS to narrow down the significant regions further revealed nine candidate genes (AKT1, ATP6V1C2, GMDS, LRP4, MAML3, PDIA6, PLD5, TMEM63B, and TSPAN8). Notably, in Brown Tsaiya ducks, GMDS, ODC1, and PDIA6 exhibit significantly differentiated allele frequencies among other feather-colored ducks, while in Ji'an Red ducks, ENSAPLG00000012679 has different allele frequency distributions compared with that in other feather-colored ducks. This study offers new insights into the variation and selection of the red plumage phenotype using GWAS and selective signals.
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Affiliation(s)
- Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Fangxi Yang
- Beijing Nankou Duck Breeding Technology Co., Ltd., Beijing, China
| | - Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinxin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalan Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Anqi Chen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Wang
- VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Daxing District, Beijing, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Huie Wang
- College of Animal Science, Tarim University, Xinjiang, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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20
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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21
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Godley LA, DiNardo CD, Bolton K. Germline Predisposition in Hematologic Malignancies: Testing, Management, and Implications. Am Soc Clin Oncol Educ Book 2024; 44:e432218. [PMID: 38768412 DOI: 10.1200/edbk_432218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Although numerous barriers for clinical germline cancer predisposition testing exist, the increasing recognition of deleterious germline DNA variants contributing to myeloid malignancy risk is yielding steady improvements in referrals for testing and testing availability. Many germline predisposition alleles are common in populations, and the increasing number of recognized disorders makes inherited myeloid malignancy risk an entity worthy of consideration for all patients regardless of age at diagnosis. Germline testing is facilitated by obtaining DNA from cultured skin fibroblasts or hair bulbs, and cascade testing is easily performed via buccal swab, saliva, or blood. Increasingly as diagnostic criteria and clinical management guidelines include germline myeloid malignancy predisposition, insurance companies recognize the value of testing and provide coverage. Once an individual is recognized to have a deleterious germline variant that confers risk for myeloid malignancies, a personalized cancer surveillance plan can be developed that incorporates screening for other cancer risk outside of the hematopoietic system and/or other organ pathology. The future may also include monitoring the development of clonal hematopoiesis, which is common for many of these cancer risk disorders and/or inclusion of strategies to delay or prevent progression to overt myeloid malignancy. As research continues to identify new myeloid predisposition disorders, we may soon recommend testing for these conditions for all patients diagnosed with a myeloid predisposition condition.
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Affiliation(s)
- Lucy A Godley
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology/Oncology, Northwestern University, Chicago, IL
| | - Courtney D DiNardo
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, TX
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22
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Wang S, Wang X, Chen J, Wang M, Zhang C. Identification of key genes and biological pathways associated with vascular aging in diabetes based on bioinformatics and machine learning. Aging (Albany NY) 2024; 16:9369-9385. [PMID: 38809515 PMCID: PMC11210242 DOI: 10.18632/aging.205870] [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: 12/19/2023] [Accepted: 04/09/2024] [Indexed: 05/30/2024]
Abstract
Vascular aging exacerbates diabetes-associated vascular damage, a major cause of microvascular and macrovascular complications. This study aimed to elucidate key genes and pathways underlying vascular aging in diabetes using integrated bioinformatics and machine learning approaches. Gene expression datasets related to vascular smooth muscle cell (VSMC) senescence and diabetic vascular aging were analyzed. Differential expression analysis identified 428 genes associated with VSMC senescence. Functional enrichment revealed their involvement in cellular senescence, ECM-receptor interaction, PI3K-Akt and AGE-RAGE signaling pathways. Further analysis of diabetic vascular aging datasets revealed 52 differentially expressed genes, enriched in AMPK signaling, AGE-RAGE signaling, cellular senescence, and VEGF signaling pathways. Machine learning algorithms, including LASSO regression and SVM-RFE, pinpointed six key genes: TFB1M, FOXRED2, LY75, DALRD3, PI4K2B, and NDOR1. Immune cell infiltration analysis demonstrated correlations between diabetic vascular aging, the identified key genes, and infiltration levels of plasma cells, M1 macrophages, CD8+ T cells, eosinophils, and regulatory T cells. In conclusion, this study identified six pivotal genes (TFB1M, FOXRED2, LY75, DALRD3, PI4K2B, and NDOR1) closely associated with diabetic vascular aging through integrative bioinformatics and machine learning approaches. These genes are linked to alterations in the immune microenvironment during diabetic vascular aging. This study provides a reference and basis for molecular mechanism research, biomarker mining, and diagnosis and treatment evaluation of diabetes-related vascular aging.
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Affiliation(s)
- Sha Wang
- Department of Endocrinology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Xia Wang
- Department of Endocrinology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Jing Chen
- Department of Endocrinology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Min Wang
- Department of Endocrinology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Chi Zhang
- Department of Endocrinology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
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23
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Yamaguchi T, Ikegami M, Aruga T, Kanemasa Y, Horiguchi SI, Kawai K, Takao M, Yamada T, Ishida H. Genomic landscape of comprehensive genomic profiling in patients with malignant solid tumors in Japan. Int J Clin Oncol 2024:10.1007/s10147-024-02554-8. [PMID: 38795236 DOI: 10.1007/s10147-024-02554-8] [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: 01/11/2024] [Accepted: 05/14/2024] [Indexed: 05/27/2024]
Abstract
BACKGROUND Comprehensive genomic profiling (CGP) can aid the discovery of clinically useful, candidate antitumor agents; however, the variant annotations sometimes differ among the various types of CGP tests as well as the public database. The aim of this study is to clarify the genomic landscape of evaluating detected variants in patients with a malignant solid tumor. METHODS The present, cross-sectional study used data from 57,084 patients with a malignant solid tumor who underwent CGP at the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) between June 1, 2019 and August 18, 2023. The pathogenicity of the variants was annotated using public databases. RESULTS As a result of re-annotation of the detected variants, 20.1% were pathogenic and 1.4% were benign. The mean number of pathogenic variants was 4.30 (95% confidence interval: 4.27-4.32) per patient. Of the entire cohort, 5.7% had no pathogenic variant. The co-occurrence of the genes depended on the tumor type. Germline findings were detected in 6.2%, 8.8%, and 15.8% of the patients using a tumor/normal panel, tumor-only panel, and liquid panel, respectively, with the most common gene being BRCA2 followed by TP53 and BRCA1. CONCLUSIONS The detected variants should be re-annotated because several benign variants or variants of unknown significance were included in the CGP, and the genomic landscape derived from these results will help researchers and physicians interpret the results of CGP tests. The method of extracting presumptive, germline, pathogenic variants from patients using a tumor-only panel or circulating tumor DNA panel requires improvement.
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Affiliation(s)
- Tatsuro Yamaguchi
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
| | - Masachika Ikegami
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
- Department of Musculoskeletal Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-Ku, Tokyo, 113-8677, Japan
| | - Tomoyuki Aruga
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Yusuke Kanemasa
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Shin-Ichiro Horiguchi
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Kazushige Kawai
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Misato Takao
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Takeshi Yamada
- Department of Surgery, Nihon Medical University, Tokyo, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan
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24
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Moix S, Sadler MC, Kutalik Z, Auwerx C. Breaking down causes, consequences, and mediating effects of telomere length variation on human health. Genome Biol 2024; 25:125. [PMID: 38760657 PMCID: PMC11101352 DOI: 10.1186/s13059-024-03269-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Telomeres form repeated DNA sequences at the ends of chromosomes, which shorten with each cell division. Yet, factors modulating telomere attrition and the health consequences thereof are not fully understood. To address this, we leveraged data from 326,363 unrelated UK Biobank participants of European ancestry. RESULTS Using linear regression and bidirectional univariable and multivariable Mendelian randomization (MR), we elucidate the relationships between leukocyte telomere length (LTL) and 142 complex traits, including diseases, biomarkers, and lifestyle factors. We confirm that telomeres shorten with age and show a stronger decline in males than in females, with these factors contributing to the majority of the 5.4% of LTL variance explained by the phenome. MR reveals 23 traits modulating LTL. Smoking cessation and high educational attainment associate with longer LTL, while weekly alcohol intake, body mass index, urate levels, and female reproductive events, such as childbirth, associate with shorter LTL. We also identify 24 traits affected by LTL, with risk for cardiovascular, pulmonary, and some autoimmune diseases being increased by short LTL, while longer LTL increased risk for other autoimmune conditions and cancers. Through multivariable MR, we show that LTL may partially mediate the impact of educational attainment, body mass index, and female age at childbirth on proxied lifespan. CONCLUSIONS Our study sheds light on the modulators, consequences, and the mediatory role of telomeres, portraying an intricate relationship between LTL, diseases, lifestyle, and socio-economic factors.
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Affiliation(s)
- Samuel Moix
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.
| | - Marie C Sadler
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- University Center for Primary Care and Public Health, Lausanne, 1015, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.
- University Center for Primary Care and Public Health, Lausanne, 1015, Switzerland.
| | - Chiara Auwerx
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.
- University Center for Primary Care and Public Health, Lausanne, 1015, Switzerland.
- Center for Integrative Genetics, UNIL, Lausanne, 1015, Switzerland.
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25
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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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26
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Lin AE, Bapat AC, Xiao L, Niroula A, Ye J, Wong WJ, Agrawal M, Farady CJ, Boettcher A, Hergott CB, McConkey M, Flores-Bringas P, Shkolnik V, Bick AG, Milan D, Natarajan P, Libby P, Ellinor PT, Ebert BL. Clonal Hematopoiesis of Indeterminate Potential With Loss of Tet2 Enhances Risk for Atrial Fibrillation Through Nlrp3 Inflammasome Activation. Circulation 2024; 149:1419-1434. [PMID: 38357791 PMCID: PMC11058018 DOI: 10.1161/circulationaha.123.065597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Clonal hematopoiesis of indeterminate potential (CHIP), a common age-associated phenomenon, associates with increased risk of both hematological malignancy and cardiovascular disease. Although CHIP is known to increase the risk of myocardial infarction and heart failure, the influence of CHIP in cardiac arrhythmias, such as atrial fibrillation (AF), is less explored. METHODS CHIP prevalence was determined in the UK Biobank, and incident AF analysis was stratified by CHIP status and clone size using Cox proportional hazard models. Lethally irradiated mice were transplanted with hematopoietic-specific loss of Tet2, hematopoietic-specific loss of Tet2 and Nlrp3, or wild-type control and fed a Western diet, compounded with or without NLRP3 (NLR [NACHT, LRR {leucine rich repeat}] family pyrin domain containing protein 3) inhibitor, NP3-361, for 6 to 9 weeks. Mice underwent in vivo invasive electrophysiology studies and ex vivo optical mapping. Cardiomyocytes from Ldlr-/- mice with hematopoietic-specific loss of Tet2 or wild-type control and fed a Western diet were isolated to evaluate calcium signaling dynamics and analysis. Cocultures of pluripotent stem cell-derived atrial cardiomyocytes were incubated with Tet2-deficient bone marrow-derived macrophages, wild-type control, or cytokines IL-1β (interleukin 1β) or IL-6 (interleukin 6). RESULTS Analysis of the UK Biobank showed individuals with CHIP, in particular TET2 CHIP, have increased incident AF. Hematopoietic-specific inactivation of Tet2 increases AF propensity in atherogenic and nonatherogenic mouse models and is associated with increased Nlrp3 expression and CaMKII (Ca2+/calmodulin-dependent protein kinase II) activation, with AF susceptibility prevented by inactivation of Nlrp3. Cardiomyocytes isolated from Ldlr-/- mice with hematopoietic inactivation of Tet2 and fed a Western diet have impaired calcium release from the sarcoplasmic reticulum into the cytosol, contributing to atrial arrhythmogenesis. Abnormal sarcoplasmic reticulum calcium release was recapitulated in cocultures of cardiomyocytes with the addition of Tet2-deficient macrophages or cytokines IL-1β or IL-6. CONCLUSIONS We identified a modest association between CHIP, particularly TET2 CHIP, and incident AF in the UK Biobank population. In a mouse model of AF resulting from hematopoietic-specific inactivation of Tet2, we propose altered calcium handling as an arrhythmogenic mechanism, dependent on Nlrp3 inflammasome activation. Our data are in keeping with previous studies of CHIP in cardiovascular disease, and further studies into the therapeutic potential of NLRP3 inhibition for individuals with TET2 CHIP may be warranted.
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Affiliation(s)
- Amy Erica Lin
- Division of Cardiovascular Medicine, Department of Medicine (A.E.L., P.L.), Brigham and Women’s Hospital, Boston, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Aneesh C. Bapat
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Demoulas Cardiac Arrhythmia Service, Division of Cardiovascular Medicine, Department of Medicine (A.C.B., P.T.E.), Massachusetts General Hospital, Boston
| | - Ling Xiao
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Abhishek Niroula
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
- Department of Laboratory Medicine, Lund University, Sweden (A.N.)
- Institute of Biomedicine, SciLifeLab, University of Gothenburg, Sweden (A.N.)
| | - Jiangchuan Ye
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Waihay J. Wong
- Department of Pathology (W.J.W., C.B.H.), Brigham and Women’s Hospital, Boston, MA
| | - Mridul Agrawal
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Christopher J. Farady
- Novartis Institutes for BioMedical Research Forum 1, Basel, Switzerland (C.J.F., A.B.)
| | - Andreas Boettcher
- Novartis Institutes for BioMedical Research Forum 1, Basel, Switzerland (C.J.F., A.B.)
| | - Christopher B. Hergott
- Department of Pathology (W.J.W., C.B.H.), Brigham and Women’s Hospital, Boston, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Marie McConkey
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Patricio Flores-Bringas
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Veronica Shkolnik
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN (A.G.B.)
| | - David Milan
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Leducq Foundation, Boston, MA (D.M.)
| | - Pradeep Natarajan
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine (A.E.L., P.L.), Brigham and Women’s Hospital, Boston, MA
| | - Patrick T. Ellinor
- Cardiovascular Research Center (A.C.B., L.X., J.Y., D.M., P.N., P.T.E.), Massachusetts General Hospital, Boston
- Demoulas Cardiac Arrhythmia Service, Division of Cardiovascular Medicine, Department of Medicine (A.C.B., P.T.E.), Massachusetts General Hospital, Boston
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA (A.E.L., A.N., M.A., C.B.H., M.M.C., V.S., B.L.E.)
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge (L.X., A.N., J.Y., P.F.-B., P.N., P.T.E., B.L.E.)
- Howard Hughes Medical Institute, Boston, MA (B.L.E.)
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27
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Moretti V, Romeo S, Valenti L. The contribution of genetics and epigenetics to MAFLD susceptibility. Hepatol Int 2024:10.1007/s12072-024-10667-5. [PMID: 38662298 DOI: 10.1007/s12072-024-10667-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/25/2024] [Indexed: 04/26/2024]
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) is the most common liver disease worldwide. The risk of developing MAFLD varies among individuals, due to a combination of environmental inherited and acquired genetic factors. Genome-wide association and next-generation sequencing studies are leading to the discovery of the common and rare genetic determinants of MAFLD. Thanks to the great advances in genomic technologies and bioinformatics analysis, genetic and epigenetic factors involved in the disease can be used to develop genetic risk scores specific for liver-related complications, which can improve risk stratification. Genetic and epigenetic factors lead to the identification of specific sub-phenotypes of MAFLD, and predict the individual response to a pharmacological therapy. Moreover, the variant transcripts and protein themselves represent new therapeutic targets. This review will discuss the current status of research into genetic as well as epigenetic modifiers of MAFLD development and progression.
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Affiliation(s)
- Vittoria Moretti
- Precision Medicine Lab, Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Via F Sforza 35, 20122, Milan, Italy
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Luca Valenti
- Precision Medicine Lab, Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, Via F Sforza 35, 20122, Milan, Italy.
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
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28
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Jakubek YA, Ma X, Stilp AM, Yu F, Bacon J, Wong JW, Aguet F, Ardlie K, Arnett D, Barnes K, Bis JC, Blackwell T, Becker LC, Boerwinkle E, Bowler RP, Budoff MJ, Carson AP, Chen J, Cho MH, Coresh J, Cox N, de Vries PS, DeMeo DL, Fardo DW, Fornage M, Guo X, Hall ME, Heard-Costa N, Hidalgo B, Irvin MR, Johnson AD, Kenny EE, Levy D, Li Y, Lima JA, Liu Y, Loos RJF, Machiela MJ, Mathias RA, Mitchell BD, Murabito J, Mychaleckyj JC, North K, Orchard P, Parker SC, Pershad Y, Peyser PA, Pratte KA, Psaty BM, Raffield LM, Redline S, Rich SS, Rotter JI, Shah SJ, Smith JA, Smith AP, Smith A, Taub M, Tiwari HK, Tracy R, Tuftin B, Bick AG, Sankaran VG, Reiner AP, Scheet P, Auer PL. Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305851. [PMID: 38699360 PMCID: PMC11065036 DOI: 10.1101/2024.04.16.24305851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Mosaic loss of Y (mLOY) is the most common somatic chromosomal alteration detected in human blood. The presence of mLOY is associated with altered blood cell counts and increased risk of Alzheimer's disease, solid tumors, and other age-related diseases. We sought to gain a better understanding of genetic drivers and associated phenotypes of mLOY through analyses of whole genome sequencing of a large set of genetically diverse males from the Trans-Omics for Precision Medicine (TOPMed) program. This approach enabled us to identify differences in mLOY frequencies across populations defined by genetic similarity, revealing a higher frequency of mLOY in the European American (EA) ancestry group compared to those of Hispanic American (HA), African American (AA), and East Asian (EAS) ancestry. Further, we identified two genes ( CFHR1 and LRP6 ) that harbor multiple rare, putatively deleterious variants associated with mLOY susceptibility, show that subsets of human hematopoietic stem cells are enriched for activity of mLOY susceptibility variants, and that certain alleles on chromosome Y are more likely to be lost than others.
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29
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Dregoesc MI, Tercan H, Țigu AB, Bekkering S, Joosten LAB, Netea MG, van Deuren RC, Hoischen A, Riksen NP, Iancu AC. Clonal hematopoiesis is associated with cardiovascular events in patients with stable coronary artery disease. iScience 2024; 27:109472. [PMID: 38558938 PMCID: PMC10981089 DOI: 10.1016/j.isci.2024.109472] [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: 11/04/2023] [Revised: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Clonal hematopoiesis (CH) is a risk factor for atherosclerotic cardiovascular disease, but the impact of smaller clones and the effect on inflammatory parameters is largely unknown. Using ultrasensitive single-molecule molecular inversion probe sequencing, we evaluated the association between CH and a first major adverse cardiovascular event (MACE) in patients with angiographically documented stable coronary artery disease (CAD) and no history of acute ischemic events. CH was associated with an increased rate of MACE at four years follow-up. The size of the clone predicted MACE at an optimal cut-off value of 1.07% variant allele frequency (VAF). Mutation carriers had no change in monocytes subsets or cytokine production capacity but had higher levels of circulating tissue factor, matrilysin, and proteinase-activated receptor-1. Our study identified CH driver mutations with a VAF as small as 1.07% as a residual cardiovascular risk factor and identified potential biomarkers and therapeutic targets for patients with stable CAD.
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Affiliation(s)
- Mihaela I. Dregoesc
- “Iuliu Hatieganu” University of Medicine and Pharmacy, Department of Cardiology –“Niculae Stăncioiu” Heart Institute, 19-21 Calea Moților, 400001 Cluj-Napoca, Romania
| | - Helin Tercan
- Radboud University Medical Center, Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, the Netherlands
| | - Adrian B. Țigu
- MEDFUTURE Research Center for Advanced Medicine, Department of Translational Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 4-6 Louis Pasteur, 400349 Cluj-Napoca, Romania
| | - Siroon Bekkering
- Radboud University Medical Center, Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, the Netherlands
| | - Leo AB. Joosten
- Radboud University Medical Center, Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, 4-6 Louis Pasteur, 400349 Cluj-Napoca, Romania
| | - Mihai G. Netea
- Radboud University Medical Center, Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, the Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115 Bonn, Germany
| | - Rosanne C. van Deuren
- Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein Zuid 855, 6525 GA Nijmegen, the Netherlands
| | - Alexander Hoischen
- Radboud University Medical Center, Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, the Netherlands
- Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein Zuid 855, 6525 GA Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Niels P. Riksen
- Radboud University Medical Center, Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, the Netherlands
| | - Adrian C. Iancu
- “Iuliu Hatieganu” University of Medicine and Pharmacy, Department of Cardiology –“Niculae Stăncioiu” Heart Institute, 19-21 Calea Moților, 400001 Cluj-Napoca, Romania
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30
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Liu W, Pircher J, Schuermans A, Ul Ain Q, Zhang Z, Honigberg MC, Yalcinkaya M, Nakao T, Pournamadri A, Xiao T, Hajebrahimi MA, Wasner L, Stegner D, Petzold T, Natarajan P, Massberg S, Tall AR, Schulz C, Wang N. Jak2 V617F clonal hematopoiesis promotes arterial thrombosis via platelet activation and cross talk. Blood 2024; 143:1539-1550. [PMID: 38142422 PMCID: PMC11033586 DOI: 10.1182/blood.2023022260] [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: 08/21/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/26/2023] Open
Abstract
ABSTRACT JAK2 V617F (JAK2VF) clonal hematopoiesis (CH) has been associated with atherothrombotic cardiovascular disease (CVD). We assessed the impact of Jak2VF CH on arterial thrombosis and explored the underlying mechanisms. A meta-analysis of 3 large cohort studies confirmed the association of JAK2VF with CVD and with platelet counts and adjusted mean platelet volume (MPV). In mice, 20% or 1.5% Jak2VF CH accelerated arterial thrombosis and increased platelet activation. Megakaryocytes in Jak2VF CH showed elevated proplatelet formation and release, increasing prothrombogenic reticulated platelet counts. Gp1ba-Cre-mediated expression of Jak2VF in platelets (VFGp1ba) increased platelet counts to a similar level as in 20% Jak2VF CH mice while having no effect on leukocyte counts. Like Jak2VF CH mice, VFGp1ba mice showed enhanced platelet activation and accelerated arterial thrombosis. In Jak2VF CH, both Jak2VF and wild-type (WT) platelets showed increased activation, suggesting cross talk between mutant and WT platelets. Jak2VF platelets showed twofold to threefold upregulation of COX-1 and COX-2, particularly in young platelets, with elevated cPLA2 activation and thromboxane A2 production. Compared with controls, conditioned media from activated Jak2VF platelets induced greater activation of WT platelets that was reversed by a thromboxane receptor antagonist. Low-dose aspirin ameliorated carotid artery thrombosis in VFGp1ba and Jak2VF CH mice but not in WT control mice. This study shows accelerated arterial thrombosis and platelet activation in Jak2VF CH with a major role of increased reticulated Jak2VF platelets, which mediate thromboxane cross talk with WT platelets and suggests a potential beneficial effect of aspirin in JAK2VF CH.
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Affiliation(s)
- Wenli Liu
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Joachim Pircher
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Art Schuermans
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Faculty of Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Qurrat Ul Ain
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Zhe Zhang
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Michael C. Honigberg
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Mustafa Yalcinkaya
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Tetsushi Nakao
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Cardiology Division, Brigham and Women’s Hospital, Boston, MA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ashley Pournamadri
- Biomedical Informatics Graduate Training Program, Stanford University, Stanford, CA
| | - Tong Xiao
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Mohammad Ali Hajebrahimi
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Lisa Wasner
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - David Stegner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Tobias Petzold
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Steffen Massberg
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Alan R. Tall
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Christian Schulz
- Department of Cardiology, Medical Clinic I, University Hospital, Ludwig Maximilian University, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Nan Wang
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY
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Freiman L, Larcher L, Tueur G, Vasquez N, Da Costa M, Duchmann M, Raffoux E, Adès L, Fenaux P, Soulier J, Duployez N, Clappier E, Sébert M. Germline CHEK2 mutations in patients with myeloid neoplasms. Leukemia 2024; 38:908-911. [PMID: 38378842 DOI: 10.1038/s41375-024-02179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Lucie Freiman
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Lise Larcher
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
- INSERM U944/CNRS UMR7212, Paris, France
| | - Giulia Tueur
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
| | - Nadia Vasquez
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
| | - Mélanie Da Costa
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
| | - Matthieu Duchmann
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
- INSERM U944/CNRS UMR7212, Paris, France
| | - Emmanuel Raffoux
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Lionel Adès
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
- INSERM U944/CNRS UMR7212, Paris, France
| | - Pierre Fenaux
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
- INSERM U944/CNRS UMR7212, Paris, France
| | - Jean Soulier
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
- INSERM U944/CNRS UMR7212, Paris, France
| | - Nicolas Duployez
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
- Hematology Laboratory, Unité 1277-Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), Centre Hospitalier Universitaire (CHU) de Lille, University of Lille, Lille, France
| | - Emmanuelle Clappier
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France
- Hematology Laboratory, Saint-Louis Hospital, APHP, Paris, France
- INSERM U944/CNRS UMR7212, Paris, France
| | - Marie Sébert
- Institut de Recherche Saint-Louis (IRSL), Université Paris Cité, 75010, Paris, France.
- Clinical Hematology Departments, Saint-Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France.
- INSERM U944/CNRS UMR7212, Paris, France.
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32
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Li JF, Cheng WY, Lin XJ, Wen LJ, Wang K, Zhu YM, Zhu HM, Chen XJ, Zhang YL, Yin W, Zhang JN, Yi X, Zhang F, Weng XQ, Wang SY, Jiang L, Wu HY, Ren JQ, Lin XJ, Qiao N, Dai YT, Fang H, Tan Y, Sun XJ, Lv G, Yan XY, Chen SN, Chen Z, Jin J, Wu DP, Ren RB, Chen SJ, Shen Y. Aging and comprehensive molecular profiling in acute myeloid leukemia. Proc Natl Acad Sci U S A 2024; 121:e2319366121. [PMID: 38422020 DOI: 10.1073/pnas.2319366121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024] Open
Abstract
Acute myeloid leukemia (AML) is an aging-related and heterogeneous hematopoietic malignancy. In this study, a total of 1,474 newly diagnosed AML patients with RNA sequencing data were enrolled, and targeted or whole exome sequencing data were obtained in 94% cases. The correlation of aging-related factors including age and clonal hematopoiesis (CH), gender, and genomic/transcriptomic profiles (gene fusions, genetic mutations, and gene expression networks or pathways) was systematically analyzed. Overall, AML patients aged 60 y and older showed an apparently dismal prognosis. Alongside age, the frequency of gene fusions defined in the World Health Organization classification decreased, while the positive rate of gene mutations, especially CH-related ones, increased. Additionally, the number of genetic mutations was higher in gene fusion-negative (GF-) patients than those with GF. Based on the status of CH- and myelodysplastic syndromes (MDS)-related mutations, three mutant subgroups were identified among the GF- AML cohort, namely, CH-AML, CH-MDS-AML, and other GF- AML. Notably, CH-MDS-AML demonstrated a predominance of elderly and male cases, cytopenia, and significantly adverse clinical outcomes. Besides, gene expression networks including HOXA/B, platelet factors, and inflammatory responses were most striking features associated with aging and poor prognosis in AML. Our work has thus unraveled the intricate regulatory circuitry of interactions among different age, gender, and molecular groups of AML.
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Affiliation(s)
- Jian-Feng Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wen-Yan Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiang-Jie Lin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, Zhejiang 310003, China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang 310003, China
| | - Li-Jun Wen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215006, China
| | - Kai Wang
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Yong-Mei Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hong-Ming Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xin-Jie Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Liang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jia-Nan Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao Yi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fan Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiang-Qin Weng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sheng-Yue Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui-Yi Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jia-Qi Ren
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jing Lin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Niu Qiao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Ting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Gang Lv
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Yu Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Su-Ning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215006, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, Zhejiang 310003, China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, Zhejiang 310003, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang 310003, China
| | - De-Pei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215006, China
| | - Rui-Bao Ren
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Shen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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33
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Kapadia CD, Goodell MA. Tissue mosaicism following stem cell aging: blood as an exemplar. NATURE AGING 2024; 4:295-308. [PMID: 38438628 DOI: 10.1038/s43587-024-00589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024]
Abstract
Loss of stem cell regenerative potential underlies aging of all tissues. Somatic mosaicism, the emergence of cellular patchworks within tissues, increases with age and has been observed in every organ yet examined. In the hematopoietic system, as in most tissues, stem cell aging through a variety of mechanisms occurs in lockstep with the emergence of somatic mosaicism. Here, we draw on insights from aging hematopoiesis to illustrate fundamental principles of stem cell aging and somatic mosaicism. We describe the generalizable changes intrinsic to aged stem cells and their milieu that provide the backdrop for somatic mosaicism to emerge. We discuss genetic and nongenetic mechanisms that can result in tissue somatic mosaicism and existing methodologies to detect such clonal outgrowths. Finally, we propose potential avenues to modify mosaicism during aging, with the ultimate aim of increasing tissue resiliency.
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Affiliation(s)
- Chiraag D Kapadia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
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Zhao K, Shen X, Liu H, Lin Z, Li J, Chen S, Liu F, Huang K, Cao J, Liu X, Shen C, Yu L, Zhao Y, Zhao L, Li Y, Hu D, Huang J, Lu X, Gu D. Somatic and Germline Variants and Coronary Heart Disease in a Chinese Population. JAMA Cardiol 2024; 9:233-242. [PMID: 38198131 PMCID: PMC10782380 DOI: 10.1001/jamacardio.2023.5095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/03/2023] [Indexed: 01/11/2024]
Abstract
Importance The genetic basis of coronary heart disease (CHD) has expanded from a germline to somatic genome, including clonal hematopoiesis of indeterminate potential (CHIP). How CHIP confers CHD risk in East Asian individuals, especially those with small clones (variant allele fraction [VAF] 0.5%-2%) and different genetic backgrounds, was completely unknown. Objective To investigate the CHIP profile in a general Chinese cohort by deep sequencing and further explore the association between CHIP and incident CHD considering germline predisposition. Design, Setting, and Participants This cohort study used data from 3 prospective cohorts in the project Prediction for Atherosclerotic Cardiovascular Disease Risk in China. Participants without cardiovascular disease or cancer at baseline were enrolled in 2001 and 2008 and had a median follow-up of 12.17 years extending into 2021. Exposures CHIP mutations were detected by targeted sequencing (mean depth, 916×). A predefined CHD polygenic risk score (PRS) comprising 531 variants was used to evaluate germline predisposition. Main Outcomes and Measures The main outcome was first incident CHD. Results Among 6181 participants, the median (IQR) age was 53.83 years (45.35-62.39 years); 3082 participants (49.9%) were female, and 3099 (50.1%) were male. A total of 1100 individuals (17.80%) harbored 1372 CHIP mutations at baseline. CHIP was independently associated with incident CHD (hazard ratio [HR], 1.42; 95% CI, 1.18-1.72; P = 2.82 × 10-4) and presented a risk gradient with increasing VAF (P = 3.98 × 10-3 for trend). Notably, individuals with small clones, nearly half of CHIP carriers, also demonstrated a higher CHD risk compared with non-CHIP carriers (HR, 1.33; 95% CI, 1.02-1.74; P = .03) and were 4 years younger than those with VAF of 2% or greater (median age, 58.52 vs 62.70 years). Heightened CHD risk was not observed among CHIP carriers with low PRS (HR, 1.02; 95% CI, 0.64-1.64; P = .92), while high PRS and CHIP jointly contributed a 2.23-fold increase in risk (95% CI, 1.51-3.29; P = 6.29 × 10-5) compared with non-CHIP carriers with low PRS. Interestingly, the diversity in CHIP-related CHD risk within each PRS group was substantially diminished when removing variants in the inflammatory pathway from the PRS. Conclusions This study revealed that elevated CHD risk attributed to CHIP was nonnegligible even for small clones. Inflammation genes involved in CHD could aggravate or abrogate CHIP-related CHD risk.
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Affiliation(s)
- Kun Zhao
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuxiang Shen
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongwei Liu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhennan Lin
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianxin Li
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shufeng Chen
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangchao Liu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Keyong Huang
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Cao
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoqing Liu
- Division of Epidemiology, Guangdong Provincial People’s Hospital and Cardiovascular Institute, Guangzhou, China
| | - Chong Shen
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ling Yu
- Department of Cardiology, Fujian Provincial Hospital, Fuzhou, China
| | - Yingxin Zhao
- Cardio-Cerebrovascular Control and Research Center, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Liancheng Zhao
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Li
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongsheng Hu
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Jiangfeng Huang
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiangfeng Lu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongfeng Gu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- School of Public Health and Emergency Management, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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35
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Sequeros CB, Tulstrup M, Bliddal S, Sørensen KM, Nissen I, Rezahosseini O, Brooks PT, Feenstra B, Gang AO, Geller F, Hald A, Harboe ZB, Helleberg M, Jespersen JS, Lebech AM, Lindegaard B, Mogensen TH, Møller MEE, Nielsen CH, Niemann CU, Podlekareva D, Sejdic A, Sørensen E, Teglgaard RS, Tommerup N, Weis N, Brunak S, Pedersen OBV, Banasik K, Feldt-Rasmussen U, Nielsen SD, Ostrowski SR, Grønbæk K. Clonal hematopoiesis and COVID-19 hospitalization in Danish adults. Hemasphere 2024; 8:e58. [PMID: 38463443 PMCID: PMC10924741 DOI: 10.1002/hem3.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Affiliation(s)
- Celia Burgos Sequeros
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Morten Tulstrup
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Biotech Research and Innovation Center (BRIC) University of Copenhagen Copenhagen Denmark
| | - Sofie Bliddal
- Department of Endocrinology and Metabolism Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | | | - Ioanna Nissen
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Omid Rezahosseini
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
| | - Patrick Terrence Brooks
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Bjarke Feenstra
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Epidemiology Research Statens Serum Institut Copenhagen Denmark
| | - Anne Ortved Gang
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Frank Geller
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Epidemiology Research Statens Serum Institut Copenhagen Denmark
| | - Annemette Hald
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Zitta Barrella Harboe
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Marie Helleberg
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Center of Excellence for Health, Immunity and Infections Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Jakob S Jespersen
- Biotech Research and Innovation Center (BRIC) University of Copenhagen Copenhagen Denmark
- The Finsen Laboratory Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Anne-Mette Lebech
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Birgitte Lindegaard
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Trine H Mogensen
- Department of Infectious Diseases Aarhus University Hospital Aarhus Denmark
- Department of Biomedicine Aarhus University Aarhus Denmark
| | | | - Claus Henrik Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Carsten Utoft Niemann
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Daria Podlekareva
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, Bispebjerg Copenhagen Denmark
| | - Adin Sejdic
- Department of Respiratory Medicine and Infectious Diseases Copenhagen University Hospital, North Zealand Hillerød Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Rebecca Svanberg Teglgaard
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine University of Copenhagen Denmark
| | - Nina Weis
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Infectious Diseases Copenhagen University Hospital, Hvidovre Copenhagen Denmark
| | - Søren Brunak
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Ole Birger Vestager Pedersen
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Clinical Immunology Zealand University Hospital Køge Denmark
| | - Karina Banasik
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Gynecology and Obstetrics Copenhagen University Hospital, Hvidovre Copenhagen Denmark
| | - Ulla Feldt-Rasmussen
- Department of Endocrinology and Metabolism Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Susanne Dam Nielsen
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
- Department of Infectious Diseases Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
| | - Kirsten Grønbæk
- Department of Haematology Copenhagen University Hospital, Rigshospitalet Copenhagen Denmark
- Biotech Research and Innovation Center (BRIC) University of Copenhagen Copenhagen Denmark
- Department of Clinical Medicine, Faculty of Health and Clinical Sciences University of Copenhagen Copenhagen Denmark
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36
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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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37
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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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38
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Janssen H, Koekkoek LL, Swirski FK. Effects of lifestyle factors on leukocytes in cardiovascular health and disease. Nat Rev Cardiol 2024; 21:157-169. [PMID: 37752350 DOI: 10.1038/s41569-023-00931-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2023] [Indexed: 09/28/2023]
Abstract
Exercise, stress, sleep and diet are four distinct but intertwined lifestyle factors that influence the cardiovascular system. Abundant epidemiological, clinical and preclinical studies have underscored the importance of managing stress, having good sleep hygiene and responsible eating habits and exercising regularly. We are born with a genetic blueprint that can protect us against or predispose us to a particular disease. However, lifestyle factors build upon and profoundly influence those predispositions. Studies in the past 10 years have shown that the immune system in general and leukocytes in particular are particularly susceptible to environmental perturbations. Lifestyle factors such as stress, sleep, diet and exercise affect leukocyte behaviour and function and thus the immune system at large. In this Review, we explore the various mechanisms by which lifestyle factors modulate haematopoiesis and leukocyte migration and function in the context of cardiovascular health. We pay particular attention to the role of the nervous system as the key executor that connects environmental influences to leukocyte behaviour.
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Affiliation(s)
- Henrike Janssen
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura L Koekkoek
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Filip K Swirski
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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39
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Cobaleda C, Godley LA, Nichols KE, Wlodarski MW, Sanchez-Garcia I. Insights into the Molecular Mechanisms of Genetic Predisposition to Hematopoietic Malignancies: The Importance of Gene-Environment Interactions. Cancer Discov 2024; 14:396-405. [PMID: 38426560 PMCID: PMC10913756 DOI: 10.1158/2159-8290.cd-23-1091] [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: 09/26/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 03/02/2024]
Abstract
SUMMARY The recognition of host genetic factors underlying susceptibility to hematopoietic malignancies has increased greatly over the last decade. Historically, germline predisposition was thought to primarily affect the young. However, emerging data indicate that hematopoietic malignancies that develop in people of all ages across the human lifespan can derive from germline predisposing conditions and are not exclusively observed in younger individuals. The age at which hematopoietic malignancies manifest appears to correlate with distinct underlying biological pathways. Progression from having a deleterious germline variant to being diagnosed with overt malignancy involves complex, multistep gene-environment interactions with key external triggers, such as infection and inflammatory stimuli, driving clonal progression. Understanding the mechanisms by which predisposed clones transform under specific pressures may reveal strategies to better treat and even prevent hematopoietic malignancies from occurring.Recent unbiased genome-wide sequencing studies of children and adults with hematopoietic malignancies have revealed novel genes in which disease-causing variants are of germline origin. This paradigm shift is spearheaded by findings in myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) as well as acute lymphoblastic leukemia, but it also encompasses other cancer types. Although not without challenges, the field of genetic cancer predisposition is advancing quickly, and a better understanding of the genetic basis of hematopoietic malignancies risk affects therapeutic decisions as well as genetic counseling and testing of at-risk family members.
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Affiliation(s)
- Cesar Cobaleda
- Immune System Development and Function Unit, Centro de Biología Molecular Severo Ochoa (CBM, CSIC-UAM), Madrid, Spain
| | - Lucy A. Godley
- Division of Hematology/Oncology, Department of Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Kim E. Nichols
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marcin W. Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Isidro Sanchez-Garcia
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain
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40
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Wang K, Zhang W, Yi L, Zhao M, Li PY, Fu MH, Lin R, Zhu YM, Li JF, Yang WP, Fang H, Chen Z, Cai WW, Ren RB. The impact of age and number of mutations on the size of clonal hematopoiesis. Proc Natl Acad Sci U S A 2024; 121:e2319364121. [PMID: 38359296 PMCID: PMC10895265 DOI: 10.1073/pnas.2319364121] [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: 11/07/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Clonal hematopoiesis (CH) represents the clonal expansion of hematopoietic stem cells and their progeny driven by somatic mutations. Accurate risk assessment of CH is critical for disease prevention and clinical decision-making. The size of CH has been showed to associate with higher disease risk, yet, factors influencing the size of CH are unknown. In addition, the characteristics of CH in long-lived individuals are not well documented. Here, we report an in-depth analysis of CH in longevous (≥90 y old) and common (60~89 y old) elderly groups. Utilizing targeted deep sequencing, we found that the development of CH is closely related to age and the expression of aging biomarkers. The longevous elderly group exhibited a significantly higher incidence of CH and significantly higher frequency of TET2 and ASXL1 mutations, suggesting that certain CH could be beneficial to prolong life. Intriguingly, the size of CH neither correlates significantly to age, in the range of 60 to 110 y old, nor to the expression of aging biomarkers. Instead, we identified a strong correlation between large CH size and the number of mutations per individual. These findings provide a risk assessment biomarker for CH and also suggest that the evolution of the CH is influenced by factor(s) in addition to age.
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Affiliation(s)
- Kai Wang
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Molecular Biology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou571199, China
| | - Li Yi
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
| | - Ming Zhao
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
| | - Peng-Yu Li
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
| | - Mei-Hong Fu
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
| | - Rong Lin
- Department of Biology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou571199, China
- Center of Forensic Medicine of Hainan Medical University, Hainan Provincial Academician Workstation (tropical forensic medicine), Hainan Provincial Tropical Forensic Engineering Research Center, Haikou571199, China
| | - Yong-Mei Zhu
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
| | - Jian-Feng Li
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
| | - Wei-Ping Yang
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
| | - Wang-Wei Cai
- Department of Biochemistry and Molecular Biology, Key Laboratory of Molecular Biology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou571199, China
| | - Rui-Bao Ren
- International Center for Aging and Cancer, Department of Hematology of The First Affiliated Hospital, Hainan Medical University, Haikou571199, China
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
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41
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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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42
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Pardo-Cea MA, Farré X, Esteve A, Palade J, Espín R, Mateo F, Alsop E, Alorda M, Blay N, Baiges A, Shabbir A, Comellas F, Gómez A, Arnan M, Teulé A, Salinas M, Berrocal L, Brunet J, Rofes P, Lázaro C, Conesa M, Rojas JJ, Velten L, Fendler W, Smyczynska U, Chowdhury D, Zeng Y, He HH, Li R, Van Keuren-Jensen K, de Cid R, Pujana MA. Biological basis of extensive pleiotropy between blood traits and cancer risk. Genome Med 2024; 16:21. [PMID: 38308367 PMCID: PMC10837955 DOI: 10.1186/s13073-024-01294-8] [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: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND The immune system has a central role in preventing carcinogenesis. Alteration of systemic immune cell levels may increase cancer risk. However, the extent to which common genetic variation influences blood traits and cancer risk remains largely undetermined. Here, we identify pleiotropic variants and predict their underlying molecular and cellular alterations. METHODS Multivariate Cox regression was used to evaluate associations between blood traits and cancer diagnosis in cases in the UK Biobank. Shared genetic variants were identified from the summary statistics of the genome-wide association studies of 27 blood traits and 27 cancer types and subtypes, applying the conditional/conjunctional false-discovery rate approach. Analysis of genomic positions, expression quantitative trait loci, enhancers, regulatory marks, functionally defined gene sets, and bulk- and single-cell expression profiles predicted the biological impact of pleiotropic variants. Plasma small RNAs were sequenced to assess association with cancer diagnosis. RESULTS The study identified 4093 common genetic variants, involving 1248 gene loci, that contributed to blood-cancer pleiotropism. Genomic hotspots of pleiotropism include chromosomal regions 5p15-TERT and 6p21-HLA. Genes whose products are involved in regulating telomere length are found to be enriched in pleiotropic variants. Pleiotropic gene candidates are frequently linked to transcriptional programs that regulate hematopoiesis and define progenitor cell states of immune system development. Perturbation of the myeloid lineage is indicated by pleiotropic associations with defined master regulators and cell alterations. Eosinophil count is inversely associated with cancer risk. A high frequency of pleiotropic associations is also centered on the regulation of small noncoding Y-RNAs. Predicted pleiotropic Y-RNAs show specific regulatory marks and are overabundant in the normal tissue and blood of cancer patients. Analysis of plasma small RNAs in women who developed breast cancer indicates there is an overabundance of Y-RNA preceding neoplasm diagnosis. CONCLUSIONS This study reveals extensive pleiotropism between blood traits and cancer risk. Pleiotropism is linked to factors and processes involved in hematopoietic development and immune system function, including components of the major histocompatibility complexes, and regulators of telomere length and myeloid lineage. Deregulation of Y-RNAs is also associated with pleiotropism. Overexpression of these elements might indicate increased cancer risk.
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Affiliation(s)
- Miguel Angel Pardo-Cea
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Xavier Farré
- Genomes for Life - GCAT Lab Group, Institut Germans Trias i Pujol (IGTP), Badalona, 08916, Barcelona, Catalonia, Spain
| | - Anna Esteve
- Badalona Applied Research Group in Oncology (B-ARGO), Catalan Institute of Oncology, Institut Germans Trias i Pujol (IGTP), Badalona, 08916, Barcelona, Catalonia, Spain
| | - Joanna Palade
- Cancer and Cell Biology, Translational Genomics Research Institute (TGen), Arizona, Phoenix, AZ, 85004, USA
| | - Roderic Espín
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Francesca Mateo
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Eric Alsop
- Cancer and Cell Biology, Translational Genomics Research Institute (TGen), Arizona, Phoenix, AZ, 85004, USA
| | - Marc Alorda
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Natalia Blay
- Genomes for Life - GCAT Lab Group, Institut Germans Trias i Pujol (IGTP), Badalona, 08916, Barcelona, Catalonia, Spain
| | - Alexandra Baiges
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Arzoo Shabbir
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Francesc Comellas
- Department of Mathematics, Technical University of Catalonia, Castelldefels, 08860, Barcelona, Catalonia, Spain
| | - Antonio Gómez
- Department of Biosciences, Faculty of Sciences and Technology (FCT), University of Vic - Central University of Catalonia (UVic-UCC), Vic, 08500, Barcelona, Catalonia, Spain
| | - Montserrat Arnan
- Department of Hematology, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Alex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Monica Salinas
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Laura Berrocal
- OncoGir, Catalan Institute of Oncology, Girona Biomedical Research Institute (IDIBGI), 17190, Salt, Catalonia, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
- OncoGir, Catalan Institute of Oncology, Girona Biomedical Research Institute (IDIBGI), 17190, Salt, Catalonia, Spain
- Biomedical Research Network Centre in Cancer (CIBERONC), Instituto de Salud Carlos III, 28222, Madrid, Spain
| | - Paula Rofes
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
- Biomedical Research Network Centre in Cancer (CIBERONC), Instituto de Salud Carlos III, 28222, Madrid, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
- Biomedical Research Network Centre in Cancer (CIBERONC), Instituto de Salud Carlos III, 28222, Madrid, Spain
| | - Miquel Conesa
- Department of Pathology and Experimental Therapies, University of Barcelona (UB), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Juan Jose Rojas
- Department of Pathology and Experimental Therapies, University of Barcelona (UB), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- University Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215, Lodz, Poland
| | - Urszula Smyczynska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215, Lodz, Poland
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Center for BRCA and Related Genes, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Yong Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5G 2C4, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Rong Li
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20052, USA
| | - Kendall Van Keuren-Jensen
- Cancer and Cell Biology, Translational Genomics Research Institute (TGen), Arizona, Phoenix, AZ, 85004, USA.
| | - Rafael de Cid
- Genomes for Life - GCAT Lab Group, Institut Germans Trias i Pujol (IGTP), Badalona, 08916, Barcelona, Catalonia, Spain.
| | - Miquel Angel Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908, Barcelona, Catalonia, Spain.
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, 28222, Madrid, Spain.
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43
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Kubota Y, Viny AD. Germline predisposition for clonal hematopoiesis. Semin Hematol 2024; 61:61-67. [PMID: 38311514 PMCID: PMC11103258 DOI: 10.1053/j.seminhematol.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/29/2023] [Accepted: 01/10/2024] [Indexed: 02/06/2024]
Abstract
Clonal hematopoiesis (CH) is an entity hallmarked by skewed hematopoiesis with persistent overrepresentation of cells from a common stem/progenitor lineage harboring single-nucleotide variants and/or insertions/deletions. CH is a common and age-related phenomenon that is associated with an increased risk of hematological malignancies, cardiovascular disease, and all-cause mortality. While CH is a term of the hematological aspect, there exists a complex interaction with other organ systems, especially the cardiovascular system. The strongest factor in the development of CH is aging, however, other multiple factors also affect the development of CH including lifestyle-related factors and co-morbid diseases. In recent years, germline genetic factors have been linked to CH risk. In this review, we synthesize what is currently known about how genetic variation affects the risk of CH, how this genetic architecture intersects with myeloid neoplasms, and future prospects for CH.
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Affiliation(s)
- Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
| | - Aaron D Viny
- Division of Hematology & Oncology, Department of Medicine, and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY.
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44
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Guo J, Walter K, Quiros PM, Gu M, Baxter EJ, Danesh J, Di Angelantonio E, Roberts D, Guglielmelli P, Harrison CN, Godfrey AL, Green AR, Vassiliou GS, Vuckovic D, Nangalia J, Soranzo N. Inherited polygenic effects on common hematological traits influence clonal selection on JAK2 V617F and the development of myeloproliferative neoplasms. Nat Genet 2024; 56:273-280. [PMID: 38233595 PMCID: PMC10864174 DOI: 10.1038/s41588-023-01638-x] [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: 12/22/2022] [Accepted: 12/01/2023] [Indexed: 01/19/2024]
Abstract
Myeloproliferative neoplasms (MPNs) are chronic cancers characterized by overproduction of mature blood cells. Their causative somatic mutations, for example, JAK2V617F, are common in the population, yet only a minority of carriers develop MPN. Here we show that the inherited polygenic loci that underlie common hematological traits influence JAK2V617F clonal expansion. We identify polygenic risk scores (PGSs) for monocyte count and plateletcrit as new risk factors for JAK2V617F positivity. PGSs for several hematological traits influenced the risk of different MPN subtypes, with low PGSs for two platelet traits also showing protective effects in JAK2V617F carriers, making them two to three times less likely to have essential thrombocythemia than carriers with high PGSs. We observed that extreme hematological PGSs may contribute to an MPN diagnosis in the absence of somatic driver mutations. Our study showcases how polygenic backgrounds underlying common hematological traits influence both clonal selection on somatic mutations and the subsequent phenotype of cancer.
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Affiliation(s)
- Jing Guo
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | | | - Pedro M Quiros
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Muxin Gu
- Wellcome Sanger Institute, Hinxton, UK
| | - E Joanna Baxter
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - John Danesh
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Fondazione Human Technopole, Milan, Italy
| | - David Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant-Oxford Centre, John Radcliffe Hospital and Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, Center for Research and Innovation of Myeloproliferative Neoplasms (CRIMM), AOU Careggi, University of Florence, Florence, Italy
| | - Claire N Harrison
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Dragana Vuckovic
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Trust, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, UK.
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Fondazione Human Technopole, Milan, Italy.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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45
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Zhang L, Lee M, Maslov AY, Montagna C, Vijg J, Dong X. Analyzing somatic mutations by single-cell whole-genome sequencing. Nat Protoc 2024; 19:487-516. [PMID: 37996541 DOI: 10.1038/s41596-023-00914-8] [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: 12/14/2022] [Accepted: 09/18/2023] [Indexed: 11/25/2023]
Abstract
Somatic mutations are the cause of cancer and have been implicated in other, noncancerous diseases and aging. While clonally expanded mutations can be studied by deep sequencing of bulk DNA, very few somatic mutations expand clonally, and most are unique to each cell. We describe a detailed protocol for single-cell whole-genome sequencing to discover and analyze somatic mutations in tissues and organs. The protocol comprises single-cell multiple displacement amplification (SCMDA), which ensures efficiency and high fidelity in amplification, and the SCcaller software tool to call single-nucleotide variations and small insertions and deletions from the sequencing data by filtering out amplification artifacts. With SCMDA and SCcaller at its core, this protocol describes a complete procedure for the comprehensive analysis of somatic mutations in a single cell, covering (1) single-cell or nucleus isolation, (2) single-cell or nucleus whole-genome amplification, (3) library preparation and sequencing, and (4) computational analyses, including alignment, variant calling, and mutation burden estimation. Methods are also provided for mutation annotation, hotspot discovery and signature analysis. The protocol takes 12-15 h from single-cell isolation to library preparation and 3-7 d of data processing. Compared with other single-cell amplification methods or single-molecular sequencing, it provides high genomic coverage, high accuracy in single-nucleotide variation and small insertions and deletion calling from the same single-cell genome, and fewer processing steps. SCMDA and SCcaller require basic experience in molecular biology and bioinformatics. The protocol can be utilized for studying mutagenesis and genome mosaicism in normal and diseased human and animal tissues under various conditions.
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Affiliation(s)
- Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technology, Voronezh, Russia
| | - Cristina Montagna
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
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46
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Vlasschaert C, Buttigieg M, Pershad Y, Lanktree M, Aldrich MC, Rauh MJ, Bick AG. Clonal hematopoiesis of indeterminate potential-associated non-small cell lung cancer risk is potentiated by small particulate matter air pollution among non-smokers: a novel somatic variant-environment interaction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.17.24301439. [PMID: 38293139 PMCID: PMC10827270 DOI: 10.1101/2024.01.17.24301439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Small particulate matter air pollution (PM 2.5 ) is a recognized driver of non-small cell lung cancer (NSCLC) among non-smoking individuals. Inhaled PM 2.5 recruits pro-inflammatory macrophages to the air-lung interface, which promotes malignant lung epithelial cell growth and progression to overt cancer. We sought to determine whether clonal hematopoiesis of indeterminate potential (CHIP), a common age-related condition characterized by hyperinflammatory macrophages, exacerbates PM 2.5 -associated NSCLC in non-smokers using genetic, environmental, and phenotypic data from 413,901 individuals in the UK Biobank. Among non-smokers, PM 2.5 is not associated with NSCLC and not associated with prevalence of CHIP, but CHIP is associated with a doubling of NSCLC risk (hazard ratio (HR) 2.01, 95% confidence interval (CI): 1.34-3.00). Moreover, CHIP-associated NSCLC risk is exacerbated in the setting of above-median PM 2.5 levels (HR 2.70, 95% CI: 1.60-4.55). PM 2.5 × CHIP is also associated with significantly greater markers of systemic inflammation (CRP, IL-6, and IL-1β) than expected. Altogether, these results suggest CHIP and PM 2.5 form a novel gene × environment interaction promoting NSCLC tumorigenesis in non-smokers.
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47
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Tercan H, Cossins BC, van Deuren RC, Rutten JHW, Joosten LAB, Netea MG, Hoischen A, Bekkering S, Riksen NP. Association Between Clonal Hematopoiesis Driver Mutations, Immune Cell Function, and the Vasculometabolic Complications of Obesity. J Am Heart Assoc 2024; 13:e031665. [PMID: 38214284 PMCID: PMC10926828 DOI: 10.1161/jaha.123.031665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Obesity is accompanied by dysregulated inflammation, which can contribute to vasculometabolic complications including metabolic syndrome and atherosclerosis. Recently, clonal hematopoiesis of indeterminate potential (CHIP) has emerged as a risk factor for cardiovascular diseases. We aimed to determine how CHIP is related to immune cell function, systemic inflammation, and vasculometabolic complications in obese individuals. METHODS AND RESULTS Two hundred ninety-seven individuals with overweight and obesity, between the ages of 54 and 81 years, were recruited in a cross-sectional study. Clonal hematopoiesis driver mutations (CHDMs) were identified with an ultrasensitive targeted assay. Assessment of carotid artery atherosclerosis was performed with ultrasound. Detailed immunological parameters, including cytokine production capacity of peripheral blood mononuclear cells, and targeted plasma proteomics analysis, were studied. Adipose tissue inflammation was determined in subcutaneous fat biopsies. Individuals with CHIP had higher concentrations of circulating IL (interleukin)-6. Total number of leukocytes and neutrophils were higher in individuals with CHIP. In contrast, ex vivo cytokine production capacity of peripheral blood mononuclear cells was significantly lower in individuals with CHIP. Sex-stratified analysis showed that men with CHDMs had significantly higher leukocyte and neutrophil counts, and ex vivo cytokine production capacity was lower in women with CHDMs. Surprisingly, the presence of atherosclerotic plaques was significantly lower in individuals with CHDMs. There was no relation between CHIP and metabolic syndrome. CONCLUSIONS In individuals with overweight or obesity, CHDMs are not associated with vasculometabolic complications, but rather with a lower presence of carotid plaques. CHDMs associate with increased circulating inflammatory markers and leukocyte numbers, but a lower peripheral blood mononuclear cell cytokine production capacity.
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Affiliation(s)
- Helin Tercan
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
| | - Benjamin C. Cossins
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
| | - Rosanne C. van Deuren
- Radboud University Medical CenterDepartment of Human GeneticsNijmegenthe Netherlands
| | - Joost H. W. Rutten
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
| | - Leo A. B. Joosten
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
- Department of Medical GeneticsIuliu Haţieganu University of Medicine and PharmacyCluj‐NapocaRomania
| | - Mihai G. Netea
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES)University of BonnGermany
| | - Alexander Hoischen
- Radboud University Medical CenterDepartment of Human GeneticsNijmegenthe Netherlands
| | - Siroon Bekkering
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
| | - Niels P. Riksen
- Radboud University Medical CenterDepartment of Internal MedicineNijmegenthe Netherlands
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48
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Huang AY, Zhou Z, Talukdar M, Miller MB, Chhouk B, Enyenihi L, Rosen I, Stronge E, Zhao B, Kim D, Choi J, Khoshkhoo S, Kim J, Ganz J, Travaglini K, Gabitto M, Hodge R, Kaplan E, Lein E, De Jager PL, Bennett DA, Lee EA, Walsh CA. Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574078. [PMID: 38260600 PMCID: PMC10802273 DOI: 10.1101/2024.01.03.574078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) is an age-associated neurodegenerative disorder characterized by progressive neuronal loss and pathological accumulation of the misfolded proteins amyloid-β and tau1,2. Neuroinflammation mediated by microglia and brain-resident macrophages plays a crucial role in AD pathogenesis1-5, though the mechanisms by which age, genes, and other risk factors interact remain largely unknown. Somatic mutations accumulate with age and lead to clonal expansion of many cell types, contributing to cancer and many non-cancer diseases6,7. Here we studied somatic mutation in normal aged and AD brains by three orthogonal methods and in three independent AD cohorts. Analysis of bulk RNA sequencing data from 866 samples from different brain regions revealed significantly higher (~two-fold) overall burdens of somatic single-nucleotide variants (sSNVs) in AD brains compared to age-matched controls. Molecular-barcoded deep (>1000X) gene panel sequencing of 311 prefrontal cortex samples showed enrichment of sSNVs and somatic insertions and deletions (sIndels) in cancer driver genes in AD brain compared to control, with recurrent, and often multiple, mutations in genes implicated in clonal hematopoiesis (CH)8,9. Pathogenic sSNVs were enriched in CSF1R+ microglia of AD brains, and the high proportion of microglia (up to 40%) carrying some sSNVs in cancer driver genes suggests mutation-driven microglial clonal expansion (MiCE). Analysis of single-nucleus RNA sequencing (snRNAseq) from temporal neocortex of 62 additional AD cases and controls exhibited nominally increased mosaic chromosomal alterations (mCAs) associated with CH10,11. Microglia carrying mCA showed upregulated pro-inflammatory genes, resembling the transcriptomic features of disease-associated microglia (DAM) in AD. Our results suggest that somatic driver mutations in microglia are common with normal aging but further enriched in AD brain, driving MiCE with inflammatory and DAM signatures. Our findings provide the first insights into microglial clonal dynamics in AD and identify potential new approaches to AD diagnosis and therapy.
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Affiliation(s)
- August Yue Huang
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zinan Zhou
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maya Talukdar
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Michael B. Miller
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Neuropathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Brian Chhouk
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
| | - Liz Enyenihi
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Ila Rosen
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
| | - Edward Stronge
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dachan Kim
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Otorhinolaryngology, Severance Hospital, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Jaejoon Choi
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sattar Khoshkhoo
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Junho Kim
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Javier Ganz
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Eitan Kaplan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical College, Chicago, IL, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA USA
- Departments of Neurology, Harvard Medical School, Boston, MA, USA
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49
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Martínez-López J, Márquez A, Pegoraro F, Ortiz-Fernández L, Acosta-Herrera M, Kerick M, Gelain E, Diamond EL, Durham BH, Abdel-Wahab O, Go RS, Koster MJ, Dagna L, Campochiaro C, Collin M, Milne P, Estrada-Veras JI, O’Brien K, Papo M, Cohen-Aubar F, Amoura Z, Haroche J, Martín J, Vaglio A. Genome-Wide Association Study Identifies the First Germline Genetic Variant Associated With Erdheim-Chester Disease. Arthritis Rheumatol 2024; 76:141-145. [PMID: 37561109 PMCID: PMC10841187 DOI: 10.1002/art.42673] [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: 03/31/2023] [Revised: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVE Erdheim-Chester disease (ECD) is rare histiocytosis with a wide range of clinical manifestations. Somatic mutations are key to the pathogenesis of the disease; however, the relationship between germline genetic variants and ECD has not been examined so far. The present study aims to explore the inherited genetic component of ECD by performing the first genome-wide association study. METHODS After quality controls, a cohort of 255 patients with ECD and 7,471 healthy donors was included in this study. Afterward, a logistic regression followed by in silico functional annotation was performed. RESULTS A signal at the 18q12.3 genomic region was identified as a new susceptibility locus for ECD (P = 2.75 × 10-11 ; Odds Ratio = 2.09). This association was annotated to the SETBP1 gene, which is involved in clonal haematopoiesis. Functional annotation of this region and of the identified suggestive signals revealed additional genes that could be potentially involved in the pathogenesis of the disease. CONCLUSION Overall, this work demonstrates that germline genetic variants can impact on the development of ECD and suggests new pathways with a potential pathogenic role.
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Affiliation(s)
- Javier Martínez-López
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Ana Márquez
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Francesco Pegoraro
- Department of Health Sciences, University of Florence, Florence, Italy
- Pediatric Hematology and Oncology Unit, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Lourdes Ortiz-Fernández
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Marialbert Acosta-Herrera
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. Granada, Spain
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Elena Gelain
- Nephrology and Dialysis Unit, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Eli L. Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Benjamin H. Durham
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY United States
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY United States
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Dept. of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Lorenzo Dagna
- Immunology, Rheumatology, Allergy and Rare Disease Unit, IRCCS San Raffaele Scientific Institute; Vita-Salute San Raffaele University, Milano, Italy
| | - Corrado Campochiaro
- Immunology, Rheumatology, Allergy and Rare Disease Unit, IRCCS San Raffaele Scientific Institute; Vita-Salute San Raffaele University, Milano, Italy
| | - Matthew Collin
- Clinical and Translational Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Milne
- Clinical and Translational Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Juvianee I. Estrada-Veras
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Kevin O’Brien
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Matthias Papo
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne
- Centre National de Référence Maladies Systémiques Rares et Histiocytoses, Hôpital Pitié-Salpêtrière, Centre d’immunologie et des maladies infectieuses INSERM UMRS1135, F-75013 Paris, France
| | - Fleur Cohen-Aubar
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne
| | - Zahir Amoura
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne
- Centre National de Référence Maladies Systémiques Rares et Histiocytoses, Hôpital Pitié-Salpêtrière, Centre d’immunologie et des maladies infectieuses INSERM UMRS1135, F-75013 Paris, France
| | - Julien Haroche
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne
- Centre National de Référence Maladies Systémiques Rares et Histiocytoses, Hôpital Pitié-Salpêtrière, Centre d’immunologie et des maladies infectieuses INSERM UMRS1135, F-75013 Paris, France
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Augusto Vaglio
- Nephrology and Dialysis Unit, Meyer Children’s Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence Italy
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Lin A, Brittan M, Baker AH, Dimmeler S, Fisher EA, Sluimer JC, Misra A. Clonal Expansion in Cardiovascular Pathology. JACC Basic Transl Sci 2024; 9:120-144. [PMID: 38362345 PMCID: PMC10864919 DOI: 10.1016/j.jacbts.2023.04.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 02/17/2024]
Abstract
Clonal expansion refers to the proliferation and selection of advantageous "clones" that are better suited for survival in a Darwinian manner. In recent years, we have greatly enhanced our understanding of cell clonality in the cardiovascular context. However, our knowledge of the underlying mechanisms behind this clonal selection is still severely limited. There is a transpiring pattern of clonal expansion of smooth muscle cells and endothelial cells-and, in some cases, macrophages-in numerous cardiovascular diseases irrespective of their differing microenvironments. These findings indirectly suggest the possible existence of stem-like vascular cells which are primed to respond during disease. Subsequent clones may undergo further phenotypic changes to adopt either protective or detrimental roles. By investigating these clone-forming vascular cells, we may be able to harness this inherent clonal nature for future therapeutic intervention. This review comprehensively discusses what is currently known about clonal expansion across the cardiovascular field. Comparisons of the clonal nature of vascular cells in atherosclerosis (including clonal hematopoiesis of indeterminate potential), pulmonary hypertension, aneurysm, blood vessel injury, ischemia- and tumor-induced angiogenesis, and cerebral cavernous malformations are evaluated. Finally, we discuss the potential clinical implications of these findings and propose that proper understanding and specific targeting of these clonal cells may provide unique therapeutic options for the treatment of these cardiovascular conditions.
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Affiliation(s)
- Alexander Lin
- Atherosclerosis and Vascular Remodeling Group, Heart Research Institute, Sydney, New South Wales, Australia
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, New South Wales, Australia
| | - Mairi Brittan
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew H. Baker
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- CARIM School for Cardiovascular Sciences, Department of Pathology, Maastricht University Medical Center (MUMC), Maastricht, the Netherlands
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Edward A. Fisher
- Department of Medicine/Division of Cardiology, New York University Grossman School of Medicine, New York, New York, USA
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Judith C. Sluimer
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- CARIM School for Cardiovascular Sciences, Department of Pathology, Maastricht University Medical Center (MUMC), Maastricht, the Netherlands
| | - Ashish Misra
- Atherosclerosis and Vascular Remodeling Group, Heart Research Institute, Sydney, New South Wales, Australia
- Heart Research Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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