1
|
Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
Collapse
Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
| |
Collapse
|
2
|
Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
Collapse
Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
| |
Collapse
|
3
|
Demajo S, Ramis-Zaldivar JE, Muiños F, Grau ML, Andrianova M, López-Bigas N, González-Pérez A. Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.13.23299893. [PMID: 38168256 PMCID: PMC10760256 DOI: 10.1101/2023.12.13.23299893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of a number of hematologic malignancies, cardiovascular diseases and other conditions. Although the most frequently mutated CH driver genes have been identified, a systematic landscape of the mutations capable of initiating this phenomenon is still lacking. Here, we train high-quality machine-learning models for 12 of the most recurrent CH driver genes to identify their driver mutations. These models outperform an experimental base-editing approach and expert-curated rules based on prior knowledge of the function of these genes. Moreover, their application to identify CH driver mutations across almost half a million donors of the UK Biobank reproduces known associations between CH driver mutations and age, and the prevalence of several diseases and conditions. We thus propose that these models support the accurate identification of CH across healthy individuals.
Collapse
Affiliation(s)
- Santiago Demajo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Joan Enric Ramis-Zaldivar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel L Grau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Maria Andrianova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
4
|
Boutboul D, Picard C, Latour S. Inborn errors of immunity underlying defective T-cell memory. Curr Opin Allergy Clin Immunol 2023; 23:491-499. [PMID: 37797193 DOI: 10.1097/aci.0000000000000946] [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: 10/07/2023]
Abstract
PURPOSE OF REVIEW T-cell memory is a complex process not well understood involving specific steps, pathways and different T-cell subpopulations. Inborn errors of immunity (IEIs) represent unique models to decipher some of these requirements in humans. More than 500 different IEIs have been reported to date, and recently a subgroup of monogenic disorders characterized by memory T-cell defects has emerged, providing novel insights into the pathways of T-cell memory generation and maintenance, although this new knowledge is mostly restricted to peripheral blood T-cell memory populations. RECENT FINDINGS This review draws up an inventory of the main and recent IEIs associated with T-cell memory defects and their mice models, with a particular focus on the nuclear factor kappa B (NF-κB) signalling pathway, including the scaffold protein capping protein regulator and myosin 1 linker 2 (CARMIL2) and the T-cell co-stimulatory molecules CD28 and OX-40. Besides NF-κB, IKZF1 (IKAROS), a key transcription factor of haematopoiesis and STAT3-dependent interleukin-6 signals involving the transcription factor ZNF341 also appear to be important for the generation of T cell memory. Somatic reversion mosaicism in memory T cells is documented for several gene defects supporting the critical role of these factors in the development of memory T cells with a potential clinical benefit. SUMMARY Systematic examination of T-cell memory subsets could be helpful in the diagnosis of IEIs.
Collapse
Affiliation(s)
- David Boutboul
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Imagine Institute
- Haematology department, Hospital Cochin, Assistance Publique-Hôpitaux de Paris (APHP)
- Université de Paris Cité
| | - Capucine Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Imagine Institute
- Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital
- Université de Paris Cité
- Centre de références des déficits immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades Hospital APHP, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Imagine Institute
- Université de Paris Cité
| |
Collapse
|
5
|
Stacey SN, Zink F, Halldorsson GH, Stefansdottir L, Gudjonsson SA, Einarsson G, Hjörleifsson G, Eiriksdottir T, Helgadottir A, Björnsdottir G, Thorgeirsson TE, Olafsdottir TA, Jonsdottir I, Gretarsdottir S, Tragante V, Magnusson MK, Jonsson H, Gudmundsson J, Olafsson S, Holm H, Gudbjartsson DF, Sulem P, Helgason A, Thorsteinsdottir U, Tryggvadottir L, Rafnar T, Melsted P, Ulfarsson MÖ, Vidarsson B, Thorleifsson G, Stefansson K. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis. Nat Genet 2023; 55:2149-2159. [PMID: 37932435 PMCID: PMC10703693 DOI: 10.1038/s41588-023-01555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
Collapse
Affiliation(s)
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Ö Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| |
Collapse
|
6
|
Li J, Malouf C, Miles LA, Willis MB, Pietras EM, King KY. Chronic inflammation can transform the fate of normal and mutant hematopoietic stem cells. Exp Hematol 2023; 127:8-13. [PMID: 37647982 DOI: 10.1016/j.exphem.2023.08.008] [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: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
Chronic inflammation, although subtle, puts the body in a constant state of alertness and is associated with many diseases, including cancer and cardiovascular diseases. It leads hematopoietic cells to produce and release proinflammatory cytokines, which trigger specific signaling pathways in hematopoietic stem cells (HSCs) that cause changes in proliferation, differentiation, and migration. This response is essential when HSCs are needed to produce specific blood cells to eliminate an intruder, such as a pathogenic virus, but mutant HSCs can use these proinflammatory signals to their advantage and accelerate the development of hematologic disease or malignancy. Understanding this complex process is vital for monitoring and controlling disease progression in patients. In the 2023 International Society for Experimental Hematology winter webinar, Dr. Eric Pietras (University of Colorado Anschutz Medical Campus, United States) and Dr. Katherine Y. King (Baylor College of Medicine, United States) gave a presentation on this topic, which is summarized in this review article.
Collapse
Affiliation(s)
- Jingjing Li
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, Australia.
| | | | - Linde A Miles
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Mara B Willis
- Center for Cell and Gene Therapy and Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, Houston, TX
| | - Eric M Pietras
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Katherine Y King
- Center for Cell and Gene Therapy and Department of Pediatrics, Division of Infectious Diseases, Baylor College of Medicine, Houston, TX
| |
Collapse
|
7
|
Seethy AA, Pethusamy K, Kushwaha T, Kumar G, Talukdar J, Chaubey R, Sundaram UD, Mahapatra M, Saxena R, Dhar R, Inampudi KK, Karmakar S. Alterations of the expression of TET2 and DNA 5-hmC predict poor prognosis in Myelodysplastic Neoplasms. BMC Cancer 2023; 23:1035. [PMID: 37884893 PMCID: PMC10601240 DOI: 10.1186/s12885-023-11449-2] [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: 05/15/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Myelodysplastic Neoplasms (MDS) are clonal stem cell disorders characterized by ineffective hematopoiesis and progression to acute myeloid leukemia, myelodysplasia-related (AML-MR). A major mechanism of pathogenesis of MDS is the aberration of the epigenetic landscape of the hematopoietic stem cells and/or progenitor cells, especially DNA cytosine methylation, and demethylation. Data on TET2, the predominant DNA demethylator of the hematopoietic system, is limited, particularly in the MDS patients from India, whose biology may differ since these patients present at a relatively younger age. We studied the expression and the variants of TET2 in Indian MDS and AML-MR patients and their effects on 5-hydroxymethyl cytosine (5-hmC, a product of TET2 catalysis) and on the prognosis of MDS patients. RESULTS Of the 42 MDS patients, cytogenetics was available for 31 sub-categorized according to the Revised International Prognostic Scoring System (IPSS-R). Their age resembled that of the previous studies from India. Bone marrow nucleated cells (BMNCs) were also obtained from 13 patients with AML-MR, 26 patients with de-novo AML, and 11 subjects with morphologically normal bone marrow. The patients had a significantly lower TET2 expression which was more pronounced in AML-MR and the IPSS-R higher-risk MDS categories. The 5-hmC levels in higher-risk MDS and AML-MR correlated with TET2 expression, suggesting a possible mechanistic role in the loss of TET2 expression. The findings on TET2 and 5-hmC were also confirmed at the tissue level using immunohistochemistry. Pathogenic variants of TET2 were found in 7 of 24 patient samples (29%), spanning across the IPSS-R prognostic categories. One of the variants - H1778R - was found to affect local and global TET2 structure when studied using structural predictions and molecular dynamics simulations. Thus, it is plausible that some pathogenic variants in TET2 can compromise the structure of TET2 and hence in the formation of 5-hmC. CONCLUSIONS IPSS-R higher-risk MDS categories and AML-MR showed a reduction in TET2 expression, which was not apparent in lower-risk MDS. DNA 5-hmC levels followed a similar pattern. Overall, a decreased TET2 expression and a low DNA 5-hmC level are predictors of advanced disease and adverse outcome in MDS in the population studied, i.e., MDS patients from India.
Collapse
Affiliation(s)
- Ashikh A Seethy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- Department of Biochemistry, All India Institute of Medical Sciences, Guwahati, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Joyeeta Talukdar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rekha Chaubey
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Udayakumar Dharmalingam Sundaram
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
- Department of Hematopathology, Medanta - The Medicity, Gurgaon, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Renu Saxena
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
- Department of Hematopathology, Medanta - The Medicity, Gurgaon, India
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
8
|
Belizaire R, Wong WJ, Robinette ML, Ebert BL. Clonal haematopoiesis and dysregulation of the immune system. Nat Rev Immunol 2023; 23:595-610. [PMID: 36941354 PMCID: PMC11140722 DOI: 10.1038/s41577-023-00843-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2023] [Indexed: 03/23/2023]
Abstract
Age-related diseases are frequently linked to pathological immune dysfunction, including excessive inflammation, autoreactivity and immunodeficiency. Recent analyses of human genetic data have revealed that somatic mutations and mosaic chromosomal alterations in blood cells - a condition known as clonal haematopoiesis (CH) - are associated with ageing and pathological immune dysfunction. Indeed, large-scale epidemiological studies and experimental mouse models have demonstrated that CH can promote cardiovascular disease, chronic obstructive pulmonary disease, chronic liver disease, osteoporosis and gout. The genes most frequently mutated in CH, the epigenetic regulators TET2 and DNMT3A, implicate increased chemokine expression and inflammasome hyperactivation in myeloid cells as a possible mechanistic connection between CH and age-related diseases. In addition, TET2 and DNMT3A mutations in lymphoid cells have been shown to drive methylation-dependent alterations in differentiation and function. Here we review the observational and mechanistic studies describing the connection between CH and pathological immune dysfunction, the effects of CH-associated genetic alterations on the function of myeloid and lymphoid cells, and the clinical and therapeutic implications of CH as a target for immunomodulation.
Collapse
Affiliation(s)
- Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Waihay J Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Michelle L Robinette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
9
|
Fan D, Liu X, Shen Z, Wu P, Zhong L, Lin F. Cell signaling pathways based on vitamin C and their application in cancer therapy. Biomed Pharmacother 2023; 162:114695. [PMID: 37058822 DOI: 10.1016/j.biopha.2023.114695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023] Open
Abstract
Vitamin C, a small organic molecule, is widely found in fruits and vegetables and is an essential nutrient in the human body. Vitamin C is closely associated with some human diseases such as cancer. Many studies have shown that high doses of vitamin C have anti-tumor ability and can target tumor cells in multiple targets. This review will describe vitamin C absorption and its function in cancer treatment. We will review the cellular signaling pathways associated with vitamin C against tumors depending on the different anti-cancer mechanisms. Based on this, we will further describe some applications of the use of vitamin C for cancer treatment in preclinical and clinical trials and the possible adverse events that can occur. Finally, this review also assesses the prospective advantages of vitamin C in oncology treatment and clinical applications.
Collapse
Affiliation(s)
- Dianfa Fan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Zhen Shen
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Liping Zhong
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Faquan Lin
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, Guangxi 530021, China; Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education,Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University.
| |
Collapse
|
10
|
Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
Collapse
Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
| |
Collapse
|
11
|
Boy M, Bisio V, Zhao LP, Guidez F, Schell B, Lereclus E, Henry G, Villemonteix J, Rodrigues-Lima F, Gagne K, Retiere C, Larcher L, Kim R, Clappier E, Sebert M, Mekinian A, Fain O, Caignard A, Espeli M, Balabanian K, Toubert A, Fenaux P, Ades L, Dulphy N. Myelodysplastic Syndrome associated TET2 mutations affect NK cell function and genome methylation. Nat Commun 2023; 14:588. [PMID: 36737440 PMCID: PMC9898569 DOI: 10.1038/s41467-023-36193-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders, representing high risk of progression to acute myeloid leukaemia, and frequently associated to somatic mutations, notably in the epigenetic regulator TET2. Natural Killer (NK) cells play a role in the anti-leukemic immune response via their cytolytic activity. Here we show that patients with MDS clones harbouring mutations in the TET2 gene are characterised by phenotypic defects in their circulating NK cells. Remarkably, NK cells and MDS clones from the same patient share the TET2 genotype, and the NK cells are characterised by increased methylation of genomic DNA and reduced expression of Killer Immunoglobulin-like receptors (KIR), perforin, and TNF-α. In vitro inhibition of TET2 in NK cells of healthy donors reduces their cytotoxicity, supporting its critical role in NK cell function. Conversely, NK cells from patients treated with azacytidine (#NCT02985190; https://clinicaltrials.gov/ ) show increased KIR and cytolytic protein expression, and IFN-γ production. Altogether, our findings show that, in addition to their oncogenic consequences in the myeloid cell subsets, TET2 mutations contribute to repressing NK-cell function in MDS patients.
Collapse
Affiliation(s)
- Maxime Boy
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Valeria Bisio
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Lin-Pierre Zhao
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Fabien Guidez
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Université Paris Cité, Institut de Recherche Saint Louis INSERM UMR_S1131, F-75010, Paris, France
| | - Bérénice Schell
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Emilie Lereclus
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Guylaine Henry
- Laboratoire d'Immunologie et d'Histocompatibilité, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, F-75010, Paris, France
| | - Juliette Villemonteix
- Laboratoire d'Immunologie et d'Histocompatibilité, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, F-75010, Paris, France
| | | | - Katia Gagne
- Etablissement Français du Sang, Centre Pays de la Loire, F-44011, Nantes, France.,Université de Nantes, INSERM UMR1307, CNRS UMR 6075, CRCI2NA team 12, F-44000, Nantes, France.,LabEx IGO « Immunotherapy, Graft, Oncology », F-44000, Nantes, France.,LabEx Transplantex, Université de Strasbourg, 67000, Strasbourg, France
| | - Christelle Retiere
- Etablissement Français du Sang, Centre Pays de la Loire, F-44011, Nantes, France.,Université de Nantes, INSERM UMR1307, CNRS UMR 6075, CRCI2NA team 12, F-44000, Nantes, France.,LabEx IGO « Immunotherapy, Graft, Oncology », F-44000, Nantes, France.,LabEx Transplantex, Université de Strasbourg, 67000, Strasbourg, France
| | - Lise Larcher
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, AP-HP, F-75010, Paris, France
| | - Rathana Kim
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, AP-HP, F-75010, Paris, France
| | - Emmanuelle Clappier
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, AP-HP, F-75010, Paris, France
| | - Marie Sebert
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Department d'Hématologie Sénior, Hôpital Saint-Louis, AP-HP, F-75010, Paris, France.,Université Paris Cité, Institut de Recherche Saint Louis INSERM UMR_944, F-75010, Paris, France
| | - Arsène Mekinian
- Service de Medecine Interne, Hôpital Saint-Antoine, AP-HP, F-75012, Paris, France.,Departement Hospitalo-Universitaire Inflammation-Immunopathologie-Biotherapie, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, F-75013, Paris, France
| | - Olivier Fain
- Service de Medecine Interne, Hôpital Saint-Antoine, AP-HP, F-75012, Paris, France.,Departement Hospitalo-Universitaire Inflammation-Immunopathologie-Biotherapie, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, F-75013, Paris, France
| | - Anne Caignard
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France
| | - Marion Espeli
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Karl Balabanian
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France
| | - Antoine Toubert
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France.,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Laboratoire d'Immunologie et d'Histocompatibilité, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, F-75010, Paris, France
| | - Pierre Fenaux
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Department d'Hématologie Sénior, Hôpital Saint-Louis, AP-HP, F-75010, Paris, France.,Université Paris Cité, Institut de Recherche Saint Louis INSERM UMR_944, F-75010, Paris, France
| | - Lionel Ades
- Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France.,Department d'Hématologie Sénior, Hôpital Saint-Louis, AP-HP, F-75010, Paris, France.,Université Paris Cité, Institut de Recherche Saint Louis INSERM UMR_944, F-75010, Paris, France
| | - Nicolas Dulphy
- Université Paris Cité, Institut de Recherche Saint Louis, EMiLy, INSERM UMR_S1160, F-75010, Paris, France. .,Institut Carnot OPALE, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, F-75010, Paris, France. .,CNRS, GDR3697 "Microenvironment of tumor niches", Micronit, F-75010, Paris, France. .,Laboratoire d'Immunologie et d'Histocompatibilité, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, F-75010, Paris, France.
| |
Collapse
|
12
|
Coiteux V, Fenwarth L, Duployez N, Ainaoui M, Borel C, Polomeni A, Yakoub-Agha I, Chalandon Y. [Management of genetic predisposition to hematologic malignancies in patients undergoing allogeneic hematopoietic cell transplantation (HCT): Guidelines from the SFGM-TC]. Bull Cancer 2023; 110:S13-S29. [PMID: 36307324 DOI: 10.1016/j.bulcan.2022.09.002] [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: 06/29/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022]
Abstract
The advent of new technologies has made it possible to identify genetic predispositions to myelodysplastic syndromes (MDS) and acute leukemias (AL) more frequently. The most frequent and best characterized at present are mutations in CEBPA, RUNX1, GATA2, ETV6 and DDX41 and, either in the presence of one of these mutations with a high allelic frequency, or in the case of a personal or family history suggestive of blood abnormalities such as non-immune thrombocytopenia, it is recommended to look for the possibility of a hereditary hematological malignancy (HHM). Indeed, early recognition of these HHMs allows better adaptation of the management of patients and their relatives, as allogeneic hematopoietic stem cell transplantation (HSCT) is very often proposed for these pathologies. According to current data, with the exception of the GATA2 mutation, the constitutional or somatic nature of the mutations does not seem to influence the prognosis of hematological diseases. Therefore, the indication for an allograft will be determined according to the usual criteria. However, when searching for a family donor, it is important to ensure that there is no hereditary disease in the donor. In order to guarantee the possibility of performing the HSC allograft within a short period of time, it may be necessary to initiate a parallel procedure to find an unrelated donor. Given the limited information on the modalities of HSC transplantation in this setting, it is important to assess the benefit/risk of the disease and the procedure to decide on the type of conditioning (myeloablative or reduced intensity). In view of the limited experience with the risk of secondary cancers in the medium and long-term, it may be appropriate to recommend reduced intensity conditioning, as in the case of better characterized syndromic hematological diseases such as Fanconi anemia or telomere diseases. In summary, it seems important to evoke HHM more frequently, particularly in the presence of a family history, certain mutations or persistent blood abnormalities, in order to discuss the specific modalities of HSC allografting, particularly with regard to the search for a donor and the evaluation of certain modalities of the procedure, such as conditioning. It should be noted that the discovery of HHM, especially if the indication of an allogeneic HSC transplant is retained, will raise ethical and psychological considerations not only for the patient, but also for his family. A multidisciplinary approach involving molecular biologists, geneticists, hematologists and psychologists is essential.
Collapse
Affiliation(s)
- Valérie Coiteux
- Hôpital Huriez, CHU de Lille, service de maladies du sang, 1, place de Verdun, 59037 Lille cedex, France.
| | - Laurène Fenwarth
- Université de Lille, CHU de Lille, CNRS, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, Inserm, 59000 Lille, France
| | - Nicolas Duployez
- Université de Lille, CHU de Lille, CNRS, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, Inserm, 59000 Lille, France
| | - Malika Ainaoui
- Hôpital Huriez, hôpital Fontan, CHU de Lille, service de maladies du sang, service de psychiatrie de liaison, 1, place de Verdun, 59037 Lille cedex, France
| | - Cécile Borel
- CHU de Toulouse, institut universitaire du cancer de Toulouse Oncopole, service d'hématologie, 1, avenue Irène-Joliot-Curie, 31059 Toulouse, France
| | - Alice Polomeni
- AP-HP, hôpital Saint-Antoine, service d'hématologie clinique et thérapie cellulaire, 184, rue du faubourg Saint-Antoine, 75012 Paris, France
| | | | - Yves Chalandon
- Université de Genève, hôpitaux universitaires de Genève, faculté de médecine, service d'hématologie, 4, rue Gabrielle-Perret-Gentil, 1211 Genève, Suisse.
| |
Collapse
|
13
|
Taira A, Palin K, Kuosmanen A, Välimäki N, Kuittinen O, Kuismin O, Kaasinen E, Rajamäki K, Aaltonen LA. Vitamin C boosts DNA demethylation in TET2 germline mutation carriers. Clin Epigenetics 2023; 15:7. [PMID: 36639817 PMCID: PMC9840351 DOI: 10.1186/s13148-022-01404-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/09/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Accurate regulation of DNA methylation is necessary for normal cells to differentiate, develop and function. TET2 catalyzes stepwise DNA demethylation in hematopoietic cells. Mutations in the TET2 gene predispose to hematological malignancies by causing DNA methylation overload and aberrant epigenomic landscape. Studies on mice and cell lines show that the function of TET2 is boosted by vitamin C. Thus, by strengthening the demethylation activity of TET2, vitamin C could play a role in the prevention of hematological malignancies in individuals with TET2 dysfunction. We recently identified a family with lymphoma predisposition where a heterozygous truncating germline mutation in TET2 segregated with nodular lymphocyte-predominant Hodgkin lymphoma. The mutation carriers displayed a hypermethylation pattern that was absent in the family members without the mutation. METHODS In a clinical trial of 1 year, we investigated the effects of oral 1 g/day vitamin C supplementation on DNA methylation by analyzing genome-wide DNA methylation and gene expression patterns from the family members. RESULTS We show that vitamin C reinforces the DNA demethylation cascade, reduces the proportion of hypermethylated loci and diminishes gene expression differences between TET2 mutation carriers and control individuals. CONCLUSIONS These results suggest that vitamin C supplementation increases DNA methylation turnover and provide a basis for further work to examine the potential benefits of vitamin C supplementation in individuals with germline and somatic TET2 mutations. TRIAL REGISTRATION This trial was registered at EudraCT with reference number of 2018-000155-41 (01.04.2019).
Collapse
Affiliation(s)
- Aurora Taira
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Anna Kuosmanen
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Outi Kuittinen
- grid.9668.10000 0001 0726 2490Department of Clinical Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XCancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Outi Kuismin
- grid.10858.340000 0001 0941 4873PEDEGO Research Unit, University of Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland ,grid.412326.00000 0004 4685 4917Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Eevi Kaasinen
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Kristiina Rajamäki
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A. Aaltonen
- grid.7737.40000 0004 0410 2071Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| |
Collapse
|
14
|
Li Z, Mu W, Xiao M. Genetic lesions and targeted therapy in Hodgkin lymphoma. Ther Adv Hematol 2023; 14:20406207221149245. [PMID: 36654739 PMCID: PMC9841868 DOI: 10.1177/20406207221149245] [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: 04/21/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023] Open
Abstract
Hodgkin lymphoma is a special type of lymphoma in which tumor cells frequently undergo multiple genetic lesions that are associated with accompanying pathway abnormalities. These pathway abnormalities are dominated by active signaling pathways, such as the JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway and the NFκB (nuclear factor kappa-B) pathway, which usually result in hyperactive survival signaling. Targeted therapies often play an important role in hematologic malignancies, such as CAR-T therapy (chimeric antigen receptor T-cell immunotherapy) targeting CD19 and CD22 in diffuse large B-cell lymphoma, while in Hodgkin lymphoma, the main targets of targeted therapies are CD30 molecules and PD1 molecules. Drugs targeting other molecules are also under investigation. This review summarizes the actionable genetic lesions, current treatment options, clinical trials for Hodgkin lymphoma and the potential value of those genetic lesions in clinical applications.
Collapse
Affiliation(s)
- Zhe Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Mu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | |
Collapse
|
15
|
Lymphoid clonal hematopoiesis: implications for malignancy, immunity, and treatment. Blood Cancer J 2023; 13:5. [PMID: 36599826 DOI: 10.1038/s41408-022-00773-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Clonal hematopoiesis (CH) is the age-related expansion of hematopoietic stem cell clones caused by the acquisition of somatic point mutations or mosaic chromosomal alterations (mCAs). Clonal hematopoiesis caused by somatic mutations has primarily been associated with increased risk of myeloid malignancies, while mCAs have been associated with increased risk of lymphoid malignancies. A recent study by Niroula et al. challenged this paradigm by finding a distinct subset of somatic mutations and mCAs that are associated with increased risk of lymphoid malignancy. CH driven by these mutations is termed lymphoid clonal hematopoiesis (L-CH). Unlike myeloid clonal hematopoiesis (M-CH), L-CH has the potential to originate at both stem cells and partially or fully differentiated progeny stages of maturation. In this review, we explore the definition of L-CH in the context of lymphocyte maturation and lymphoid malignancy precursor disorders, the evidence for L-CH in late-onset autoimmunity and immunodeficiency, and the development of therapy-related L-CH following chemotherapy or hematopoietic stem cell transplantation.
Collapse
|
16
|
López-Nevado M, Ortiz-Martín J, Serrano C, Pérez-Saez MA, López-Lorenzo JL, Gil-Etayo FJ, Rodríguez-Frías E, Cabrera-Marante O, Morales-Pérez P, Rodríguez-Pinilla MS, Manso R, Salgado-Sánchez RN, Cerdá-Montagud A, Quesada-Espinosa JF, Gómez-Rodríguez MJ, Paz-Artal E, Muñoz-Calleja C, Arranz-Sáez R, Allende LM. Novel Germline TET2 Mutations in Two Unrelated Patients with Autoimmune Lymphoproliferative Syndrome-Like Phenotype and Hematologic Malignancy. J Clin Immunol 2023; 43:165-180. [PMID: 36066697 DOI: 10.1007/s10875-022-01361-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: 05/11/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
Somatic mutations in the ten-eleven translocation methylcytosine dioxygenase 2 gene (TET2) have been associated to hematologic malignancies. More recently, biallelic, and monoallelic germline mutations conferring susceptibility to lymphoid and myeloid cancer have been described. We report two unrelated autoimmune lymphoproliferative syndrome-like patients who presented with T-cell lymphoma associated with novel germline biallelic or monoallelic mutations in the TET2 gene. Both patients presented a history of chronic lymphoproliferation with lymphadenopathies and splenomegaly, cytopenias, and immune dysregulation. We identified the first compound heterozygous patient for TET2 mutations (P1) and the first ALPS-like patient with a monoallelic TET2 mutation (P2). P1 had the most severe form of autosomal recessive disease due to TET2 loss of function resulting in absent TET2 expression and profound increase in DNA methylation. Additionally, the immunophenotype showed some alterations in innate and adaptive immune system as inverted myeloid/plasmacytoid dendritic cells ratio, elevated terminally differentiated effector memory CD8 + T-cells re-expressing CD45RA, regulatory T-cells, and Th2 circulating follicular T-cells. Double-negative T-cells, vitamin B12, and IL-10 were elevated according to the ALPS-like suspicion. Interestingly, the healthy P1's brother carried a TET2 mutation and presented some markers of immune dysregulation. P2 showed elevated vitamin B12, hypergammaglobulinemia, and decreased HDL levels. Therefore, novel molecular defects in TET2 confirm and expand both clinical and immunological phenotype, contributing to a better knowledge of the bridge between cancer and immunity.
Collapse
Affiliation(s)
- Marta López-Nevado
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
| | | | - Cristina Serrano
- Immunology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - María A Pérez-Saez
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - José L López-Lorenzo
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Francisco J Gil-Etayo
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Edgar Rodríguez-Frías
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Oscar Cabrera-Marante
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Pablo Morales-Pérez
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Rebeca Manso
- Pathology Department, Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | | | - Ana Cerdá-Montagud
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Juan F Quesada-Espinosa
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - María J Gómez-Rodríguez
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
- School of Medicine, Complutense University of Madrid, Madrid, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Cecilia Muñoz-Calleja
- Immunology Department, University Hospital La Princesa, Madrid, Spain
- School of Medicine, University Autónoma de Madrid, Madrid, Spain
- Research Institute Hospital de La Princesa, Madrid, Spain
| | - Reyes Arranz-Sáez
- Hematology Department, University Hospital La Princesa, Madrid, Spain
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
- School of Medicine, Complutense University of Madrid, Madrid, Spain.
| |
Collapse
|
17
|
Abstract
PURPOSE OF REVIEW The development of cancer in patients with genetically determined inborn errors of immunity (IEI) is much higher than in the general population. The hallmarks of cancer are a conceptualization tool that can refine the complexities of cancer development and pathophysiology. Each genetic defect may impose a different pathological tumor predisposition, which needs to be identified and linked with known hallmarks of cancer. RECENT FINDINGS Four new hallmarks of cancer have been suggested, recently, including unlocking phenotypic plasticity, senescent cells, nonmutational epigenetic reprogramming, and polymorphic microbiomes. Moreover, more than 50 new IEI genes have been discovered during the last 2 years from which 15 monogenic defects perturb tumor immune surveillance in patients. SUMMARY This review provides a more comprehensive and updated overview of all 14 cancer hallmarks in IEI patients and covers aspects of cancer predisposition in novel genes in the ever-increasing field of IEI.
Collapse
|
18
|
Arber DA, Orazi A, Hasserjian RP, Borowitz MJ, Calvo KR, Kvasnicka HM, Wang SA, Bagg A, Barbui T, Branford S, Bueso-Ramos CE, Cortes JE, Dal Cin P, DiNardo CD, Dombret H, Duncavage EJ, Ebert BL, Estey EH, Facchetti F, Foucar K, Gangat N, Gianelli U, Godley LA, Gökbuget N, Gotlib J, Hellström-Lindberg E, Hobbs GS, Hoffman R, Jabbour EJ, Kiladjian JJ, Larson RA, Le Beau MM, Loh MLC, Löwenberg B, Macintyre E, Malcovati L, Mullighan CG, Niemeyer C, Odenike OM, Ogawa S, Orfao A, Papaemmanuil E, Passamonti F, Porkka K, Pui CH, Radich JP, Reiter A, Rozman M, Rudelius M, Savona MR, Schiffer CA, Schmitt-Graeff A, Shimamura A, Sierra J, Stock WA, Stone RM, Tallman MS, Thiele J, Tien HF, Tzankov A, Vannucchi AM, Vyas P, Wei AH, Weinberg OK, Wierzbowska A, Cazzola M, Döhner H, Tefferi A. International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data. Blood 2022; 140:1200-1228. [PMID: 35767897 PMCID: PMC9479031 DOI: 10.1182/blood.2022015850] [Citation(s) in RCA: 799] [Impact Index Per Article: 399.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/16/2022] [Indexed: 02/02/2023] Open
Abstract
The classification of myeloid neoplasms and acute leukemias was last updated in 2016 within a collaboration between the World Health Organization (WHO), the Society for Hematopathology, and the European Association for Haematopathology. This collaboration was primarily based on input from a clinical advisory committees (CACs) composed of pathologists, hematologists, oncologists, geneticists, and bioinformaticians from around the world. The recent advances in our understanding of the biology of hematologic malignancies, the experience with the use of the 2016 WHO classification in clinical practice, and the results of clinical trials have indicated the need for further revising and updating the classification. As a continuation of this CAC-based process, the authors, a group with expertise in the clinical, pathologic, and genetic aspects of these disorders, developed the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias. Using a multiparameter approach, the main objective of the consensus process was the definition of real disease entities, including the introduction of new entities and refined criteria for existing diagnostic categories, based on accumulated data. The ICC is aimed at facilitating diagnosis and prognostication of these neoplasms, improving treatment of affected patients, and allowing the design of innovative clinical trials.
Collapse
Affiliation(s)
| | - Attilio Orazi
- Texas Tech University Health Sciences Center El Paso, El Paso, TX
| | | | | | | | | | - Sa A Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adam Bagg
- University of Pennsylvania, Philadelphia, PA
| | - Tiziano Barbui
- Clinical Research Foundation, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | | | | | | | | | | | - Hervé Dombret
- Université Paris Cité, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, Paris, France
| | | | | | | | | | | | | | | | | | | | - Jason Gotlib
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Jean-Jacques Kiladjian
- Université Paris Cité, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kimmo Porkka
- Helsinki University Central Hospital Comprehensive Cancer Center, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Akiko Shimamura
- Dana-Farber Cancer Institute, Boston, MA
- Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Jorge Sierra
- Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | | | | | - Hwei-Fang Tien
- National Taiwan University Hospital, Taipei City, Taiwan
| | | | | | - Paresh Vyas
- University of Oxford, Oxford, United Kingdom
| | - Andrew H Wei
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
| | | | | | | | | | | |
Collapse
|
19
|
Aivalioti MM, Bartholdy BA, Pradhan K, Bhagat TD, Zintiridou A, Jeong JJ, Thiruthuvanathan VJ, Pujato M, Paranjpe A, Zhang C, Levine RL, Viny AD, Wickrema A, Verma A, Will B. PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation. Blood Cancer Discov 2022; 3:444-467. [PMID: 35820129 PMCID: PMC9894728 DOI: 10.1158/2643-3230.bcd-21-0226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/05/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022] Open
Abstract
Cytosine hypermethylation in and around DNA-binding sites of master transcription factors, including PU.1, occurs in aging hematopoietic stem cells following acquired loss-of-function mutations of DNA methyl-cytosine dioxygenase ten-eleven translocation-2 (TET2), albeit functional relevance has been unclear. We show that Tet2-deficient mouse hematopoietic stem and progenitor cells undergo malignant transformation upon compromised gene regulation through heterozygous deletion of an upstream regulatory region (UREΔ/WT) of the PU.1 gene. Although compatible with multilineage blood formation at young age, Tet2-deficient PU.1 UREΔ/WT mice develop highly penetrant, transplantable acute myeloid leukemia (AML) during aging. Leukemic stem and progenitor cells show hypermethylation at putative PU.1-binding sites, fail to activate myeloid enhancers, and are hallmarked by a signature of genes with impaired expression shared with human AML. Our study demonstrates that Tet2 and PU.1 jointly suppress leukemogenesis and uncovers a methylation-sensitive PU.1-dependent gene network as a unifying molecular vulnerability associated with AML. SIGNIFICANCE We identify moderately impaired PU.1 mRNA expression as a biological modality predisposing Tet2-deficient hematopoietic stem and progenitor cells to malignant transformation. Our study furthermore uncovers a methylation-sensitive PU.1 gene network as a common feature of myeloid leukemia potentially allowing for the identification of patients at risk for malignant transformation. See related commentary by Schleicher and Pietras, p. 378. This article is highlighted in the In This Issue feature, p. 369.
Collapse
Affiliation(s)
- Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Graduate Programs in the Biomedical Sciences, Albert Einstein College of Medicine, Bronx, New York
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Kith Pradhan
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Tushar D Bhagat
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Jong Jin Jeong
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Victor J Thiruthuvanathan
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chi Zhang
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Ross L Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron D Viny
- Department of Genetics and Development, Columbia University, New York, New York
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Amit Verma
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| |
Collapse
|
20
|
de Pádua Covas Lage LA, Barreto GC, Culler HF, Cavalcante JB, de Oliveira Alves LB, Nardinelli L, Bendit I, Zerbini MCN, Rocha V, Pereira J. TET-2 mutations predict poor outcomes and are associated with unfavorable clinical-biological features in PTCL, not otherwise specified and angioimmunoblastic T-cell lymphoma in Brazilian patients. Cancer Biomark 2022; 35:179-191. [PMID: 36093687 DOI: 10.3233/cbm-220013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Nodal peripheral T-cell lymphomas [nPTCL] constitute a heterogeneous group of rare malignancies with aggressive biological behavior and poor prognosis. Epigenetic phenomena involving genes that control DNA-methylation and histone deacetylation play a central role in their pathogenesis. However, the mutational landscape involving epigenetic regulators has never been reported in Latin American patients and their prognostic impact remains controversial. PATIENTS AND METHODS From 2000 to 2019, 59-Brazilian patients with nPTCL were eligible for screening mutations in the IDH-1, IDH-2, RHOA, TET-2 and DNMT3A genes by Sanger sequencing at Formalin-Fixed Paraffin-Embedded samples [FFPE] of diagnosis. We reported the frequency, distribution and potential prognosis of these mutations. RESULTS With a median follow-up of 3.70 years, estimate 2-year OS and PFS were 57.1% and 49.2%, respectively. Mutations in the IDH-1 gene were not found, mutations in the IDH-2 occurred in 3.4% (2/59), RHOA in 23.7% (14/59), TET-2 in 50.8% (30/59) and DNMT3A in 62.7% (37/59). RHOA gene mutations were more frequent in PTCL, NOS and AITL (p= 0.06). Almost half of the patients had more than one mutation in concomitance, particularly RHOA-mut and TET-2-mut. Mutations in RHOA (p= 0.030) and TET-2 (p= 0.046) were associated with high-tumor burden. In the non-ALCL subgroup (PTCL, NOS and AITL) TET-2 mutations were associated with decreased 2-year PFS [HR: 2.22, p= 0.048]. Likewise with lower overall response rate [ORR] (p= 0.048) and unfavorable clinical features, as bulky disease (p= 0.012), ECOG ⩾ 2 (p= 0.032), B-symptoms (p= 0.012), ⩾ 2 extranodal sites compromised (p= 0.022) and high-risk Prognostic Index for T-cell lymphoma (p= 0.005). CONCLUSION Mutations in RHOA, TET-2 and DNMT3A were frequent in Brazilian patients with nPTCL. TET-2 mutations were associated with lower ORR for CHOP-like chemotherapy, decreased PFS and unfavorable clinical-biological characteristics in non-ALCL (PTCL, NOS and AITL). Further studies using a larger cohort may validate our findings.
Collapse
Affiliation(s)
- Luís Alberto de Pádua Covas Lage
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil
| | - Guilherme Carneiro Barreto
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil
| | - Hebert Fabricio Culler
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil
| | - Jéssica Billar Cavalcante
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil
| | - Lucas Bassolli de Oliveira Alves
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil
| | - Luciana Nardinelli
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil
| | - Israel Bendit
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil
| | | | - Vanderson Rocha
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil.,Fundação Pró-Sangue, Blood Bank of São Paulo, São Paulo, SP, Brazil.,Churchill Hospital, Oxford University, Oxford, UK
| | - Juliana Pereira
- Department of Hematology, Hemotherapy and Cell Therapy, Faculty of Medicine, University of São Paulo (FM/USP), São Paulo, SP, Brazil.,Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), University of São Paulo (USP), São Paulo, SP, Brazil
| |
Collapse
|
21
|
Germline Abnormalities in DNA Methylation and Histone Modification and Associated Cancer Risk. Curr Hematol Malig Rep 2022; 17:82-93. [PMID: 35653077 DOI: 10.1007/s11899-022-00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Somatic mutations in DNA methyltransferases and other DNA methylation associated genes have been found in a wide variety of cancers. Germline mutations in these genes have been associated with several rare hereditary disorders. Among the described germline/congenital disorders, neurological dysfunction and/or growth abnormalities appear to be a common phenotype. Here, we outline known germline abnormalities and examine the cancer risks associated with these mutations. RECENT FINDINGS The increased use and availability of sequencing techniques in the clinical setting has expanded the identification of germline abnormalities involving DNA methylation machinery. This has provided additional cases to study these rare hereditary disorders and their predisposition to cancer. Studying these syndromes may offer an opportunity to better understand the contribution of these genes in cancer development.
Collapse
|
22
|
[Analysis of clinical significance and prognostic impact of TET2 single nucleotide polymorphism I1762V in patients with acute myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2022; 43:241-246. [PMID: 35405783 PMCID: PMC9072067 DOI: 10.3760/cma.j.issn.0253-2727.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Objective: This study aimed to investigate the clinical and prognostic significance of TET2 single nucleotide polymorphism I1762V in patients with acute myeloid leukemia (AML) . Methods: The high-throughput sequencing method was used to sequence 58 hematological tumor-related genes in bone marrow samples from 413 patients with AML. TET2 I1762V and other somatic mutations were annotated and compared with patients' clinical information and prognosis. Results: I1762V was found in 154 patients with AML, which was significantly different from the general population in NyuWa Chinese Population Variant Database (χ(2)=72.4, P<0.001) . I1762V was not related to sex, age, and karyotype of patients with AML (P>0.05) . Patients with I1762V had a significantly higher proportion of NPM1 and KIT gene mutations than others (P<0.001) . NPM1 and KIT mutations were mutually exclusive. The survival analysis results revealed that the overall survival (OS) and progression-free survival (PFS) of patients with AML with I1762V were significantly greater than those of wild-type patients (HR=0.57, P=0.030; HR=0.55, P=0.020) , whereas the OS and PFS in patients with AML with DNMT3A mutation (with or without I1762V mutation) were lower than those of wild-type patients (HR=1.79, P=0.030; HR=1.74, P=0.040) . Conclusion: TET2 SNP I1762V has been linked to AML. I1762V is a prognostic factor of patients with AML, which can be used to guide the treatment and evaluate the prognosis of AML.
Collapse
|
23
|
Romano R, Cillo F, Moracas C, Pignata L, Nannola C, Toriello E, De Rosa A, Cirillo E, Coppola E, Giardino G, Brunetti-Pierri N, Riccio A, Pignata C. Epigenetic Alterations in Inborn Errors of Immunity. J Clin Med 2022; 11:jcm11051261. [PMID: 35268351 PMCID: PMC8910960 DOI: 10.3390/jcm11051261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
The epigenome bridges environmental factors and the genome, fine-tuning the process of gene transcription. Physiological programs, including the development, maturation and maintenance of cellular identity and function, are modulated by intricate epigenetic changes that encompass DNA methylation, chromatin remodeling, histone modifications and RNA processing. The collection of genome-wide DNA methylation data has recently shed new light into the potential contribution of epigenetics in pathophysiology, particularly in the field of immune system and host defense. The study of patients carrying mutations in genes encoding for molecules involved in the epigenetic machinery has allowed the identification and better characterization of environment-genome interactions via epigenetics as well as paving the way for the development of new potential therapeutic options. In this review, we summarize current knowledge of the role of epigenetic modifications in the immune system and outline their potential involvement in the pathogenesis of inborn errors of immunity.
Collapse
Affiliation(s)
- Roberta Romano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Francesca Cillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Cristina Moracas
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Chiara Nannola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Elisabetta Toriello
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Antonio De Rosa
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emma Coppola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Nicola Brunetti-Pierri
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
- Correspondence: (A.R.); (C.P.)
| | - Claudio Pignata
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
- Correspondence: (A.R.); (C.P.)
| |
Collapse
|
24
|
Whole Blood Transcriptional Fingerprints of High-Grade Glioma and Longitudinal Tumor Evolution under Carbon Ion Radiotherapy. Cancers (Basel) 2022; 14:cancers14030684. [PMID: 35158950 PMCID: PMC8833402 DOI: 10.3390/cancers14030684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Particle therapy with carbon ions is a promising novel option for the treatment of recurrent high-grade glioma (rHGG). Lack of initial and sequential biopsies limits the investigation of rHGG evolution under therapy. We hypothesized that peripheral blood transcriptome derived from liquid biopsies (lbx) as a minimal invasive method may provide a useful decision support for identification of glioma grade and provide novel means for longitudinal molecular monitoring of tumor evolution under carbon ion irradiation (CIR). We demonstrate feasibility and report patient, tumor and treatment fingerprints in whole blood transcriptomes of rHGG patients with pre-CIR and three post-CIR time points. Abstract Purpose: To assess the value of whole blood transcriptome data from liquid biopsy (lbx) in recurrent high-grade glioma (rHGG) patients for longitudinal molecular monitoring of tumor evolution under carbon ion irradiation (CIR). Methods: Whole blood transcriptome (WBT) analysis (Illumina HumanHT-12 Expression BeadChips) was performed in 14 patients with rHGG pre re-irradiation (reRT) with CIR and 3, 6 and 9 weeks post-CIR (reRT grade III:5, 36%, IV:9, 64%). Patients were irradiated with 30, 33, 36 GyRBE (n = 5, 6, 3) in 3GyRBE per fraction. Results: WTB analysis showed stable correlation with treatment characteristics and patients tumor grade, indicating a preserved tumor origin specific as well as dynamic transcriptional fingerprints of peripheral blood cells. Initial histopathologic tumor grade was indirectly associated with TMEM173 (STING), DNA-repair (ATM, POLD4) and hypoxia related genes. DNA-repair, chromatin remodeling (LIG1, SMARCD1) and immune response (FLT3LG) pathways were affected post-CIR. Longitudinal WTB fingerprints identified two distinct trajectories of rHGG evolution, characterized by differential and prognostic CRISPLD2 expression pre-CIR. Conclusions: Lbx based WTB analysis holds the potential for molecular stratification of rHGG patients and therapy monitoring. We demonstrate the feasibility of the peripheral blood transcriptome as a sentinel organ for identification of patient, tumor characteristics and CIR specific fingerprints in rHGG.
Collapse
|
25
|
Cobo I, Tanaka T, Glass CK, Yeang C. Clonal hematopoiesis driven by DNMT3A and TET2 mutations: role in monocyte and macrophage biology and atherosclerotic cardiovascular disease. Curr Opin Hematol 2022; 29:1-7. [PMID: 34654019 PMCID: PMC8639635 DOI: 10.1097/moh.0000000000000688] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Clonal hematopoiesis of indeterminate potential (CHIP), defined by the presence of somatic mutations in hematopoietic cells, is associated with advanced age and increased mortality due to cardiovascular disease. Gene mutations in DNMT3A and TET2 are the most frequently identified variants among patients with CHIP and provide selective advantage that spurs clonal expansion and myeloid skewing. Although DNMT3A and TET2 appear to have opposing enzymatic influence on DNA methylation, mounting data has characterized convergent inflammatory pathways, providing insights to how CHIP may mediate atherosclerotic cardiovascular disease (ASCVD). RECENT FINDINGS We review a multitude of studies that characterize aberrant inflammatory signaling as result of DNMT3A and TET2 deficiency in monocytes and macrophages, immune cells with prominent roles in atherosclerosis. Although specific DNA methylation signatures associated with these known epigenetic regulators have been identified, many studies have also characterized diverse modulatory functions of DNTM3A and TET2 that urge cell and context-specific experimental studies to further define how DNMT3A and TET2 may nonenzymatically activate inflammatory pathways with clinically meaningful consequences. SUMMARY CHIP, common in elderly individuals, provides an opportunity understand and potentially modify age-related chronic inflammatory ASCVD risk.
Collapse
Affiliation(s)
- Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California San Diego
| | - Tiffany Tanaka
- University of California San Diego, Moores Cancer Center
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego
| | - Calvin Yeang
- Sulpizio Cardiovascular Center, Division of Cardiology, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
26
|
Role of Myeloid Tet Methylcytosine Dioxygenase 2 in Pulmonary and Peritoneal Inflammation Induced by Lipopolysaccharide and Peritonitis Induced by Escherichia coli. Cells 2021; 11:cells11010082. [PMID: 35011643 PMCID: PMC8750455 DOI: 10.3390/cells11010082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/15/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Tet methylcytosine dioxygenase 2 (Tet2) mediates demethylation of DNA. We here sought to determine the expression and function of Tet2 in macrophages upon exposure to lipopolysaccharide (LPS), and in the host response to LPS induced lung and peritoneal inflammation, and during Escherichia (E.) coli induced peritonitis. LPS induced Tet2 expression in mouse macrophages and human monocytes in vitro, as well as in human alveolar macrophages after bronchial instillation in vivo. Bone marrow-derived macrophages from myeloid Tet2 deficient (Tet2fl/flLysMCre) mice displayed enhanced production of IL-1β, IL-6 and CXCL1 upon stimulation with several Toll-like receptor agonists; similar results were obtained with LPS stimulated alveolar and peritoneal macrophages. Histone deacetylation was involved in the effect of Tet2 on IL-6 production, whilst methylation at the Il6 promoter was not altered by Tet2 deficiency. Tet2fl/flLysMCre mice showed higher IL-6 and TNF levels in bronchoalveolar and peritoneal lavage fluid after intranasal and intraperitoneal LPS administration, respectively, whilst other inflammatory responses were unaltered. E. coli induced stronger production of IL-1β and IL-6 by Tet2 deficient peritoneal macrophages but not in peritoneal lavage fluid of Tet2fl/flLysMCre mice after in vivo intraperitoneal infection. Tet2fl/flLysMCre mice displayed enhanced bacterial growth during E. coli peritonitis, which was associated with a reduced capacity of Tet2fl/flLysMCre peritoneal macrophages to inhibit the growth of E. coli in vitro. Collectively, these data suggest that Tet2 is involved in the regulation of macrophage functions triggered by LPS and during E. coli infection.
Collapse
|
27
|
TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis. Nat Commun 2021; 12:6061. [PMID: 34663818 PMCID: PMC8523747 DOI: 10.1038/s41467-021-26093-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023] Open
Abstract
Mutations in the epigenetic modifier TET2 are frequent in myeloid malignancies and clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS). Here, we investigate associations between TET2 mutations and DNA methylation in whole blood in 305 elderly twins, 15 patients with CCUS and 18 healthy controls. We find that TET2 mutations are associated with DNA hypermethylation at enhancer sites in whole blood in CHIP and in both granulocytes and mononuclear cells in CCUS. These hypermethylated sites are associated with leukocyte function and immune response and ETS-related and C/EBP-related transcription factor motifs. While the majority of TET2-associated hypermethylation sites are shared between CHIP and in AML, we find a set of AML-specific hypermethylated loci at active enhancer elements in hematopoietic stem cells. In summary, we show that TET2 mutations is associated with hypermethylated enhancers involved in myeloid differentiation in both CHIP, CCUS and AML patients.
Collapse
|
28
|
Mikhaylova AV, McHugh CP, Polfus LM, Raffield LM, Boorgula MP, Blackwell TW, Brody JA, Broome J, Chami N, Chen MH, Conomos MP, Cox C, Curran JE, Daya M, Ekunwe L, Glahn DC, Heard-Costa N, Highland HM, Hobbs BD, Ilboudo Y, Jain D, Lange LA, Miller-Fleming TW, Min N, Moon JY, Preuss MH, Rosen J, Ryan K, Smith AV, Sun Q, Surendran P, de Vries PS, Walter K, Wang Z, Wheeler M, Yanek LR, Zhong X, Abecasis GR, Almasy L, Barnes KC, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Chavan S, Cho MH, Choquet H, Correa A, Cox N, DeMeo DL, Faraday N, Fornage M, Gerszten RE, Hou L, Johnson AD, Jorgenson E, Kaplan R, Kooperberg C, Kundu K, Laurie CA, Lettre G, Lewis JP, Li B, Li Y, Lloyd-Jones DM, Loos RJF, Manichaikul A, Meyers DA, Mitchell BD, Morrison AC, Ngo D, Nickerson DA, Nongmaithem S, North KE, O'Connell JR, Ortega VE, Pankratz N, Perry JA, Psaty BM, Rich SS, Soranzo N, Rotter JI, Silverman EK, Smith NL, Tang H, Tracy RP, Thornton TA, Vasan RS, Zein J, Mathias RA, Reiner AP, Auer PL. Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:1836-1851. [PMID: 34582791 PMCID: PMC8546043 DOI: 10.1016/j.ajhg.2021.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.
Collapse
MESH Headings
- Asthma/epidemiology
- Asthma/genetics
- Asthma/metabolism
- Asthma/pathology
- Biomarkers/metabolism
- Dermatitis, Atopic/epidemiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/metabolism
- Dermatitis, Atopic/pathology
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- Humans
- Leukocytes/pathology
- National Heart, Lung, and Blood Institute (U.S.)
- Phenotype
- Polymorphism, Single Nucleotide
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Pulmonary Disease, Chronic Obstructive/epidemiology
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/pathology
- Quantitative Trait Loci
- United Kingdom/epidemiology
- United States/epidemiology
- Whole Genome Sequencing
Collapse
Affiliation(s)
- Anna V Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Linda M Polfus
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Corey Cox
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02155, USA
| | - Nancy Heard-Costa
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yann Ilboudo
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jonathon Rosen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lifang Hou
- Institute for Public Health and Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Guillaume Lettre
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, and Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald M Lloyd-Jones
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA; Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Debby Ngo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Suraj Nongmaithem
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Victor E Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge CB1 8RN, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Department of Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA; Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Ramachandran S Vasan
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander P Reiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin, Milwaukee, Milwaukee, WI 53205, USA.
| |
Collapse
|
29
|
Sahoo SS, Pastor VB, Goodings C, Voss RK, Kozyra EJ, Szvetnik A, Noellke P, Dworzak M, Stary J, Locatelli F, Masetti R, Schmugge M, De Moerloose B, Catala A, Kállay K, Turkiewicz D, Hasle H, Buechner J, Jahnukainen K, Ussowicz M, Polychronopoulou S, Smith OP, Fabri O, Barzilai S, de Haas V, Baumann I, Schwarz-Furlan S, Niewisch MR, Sauer MG, Burkhardt B, Lang P, Bader P, Beier R, Müller I, Albert MH, Meisel R, Schulz A, Cario G, Panda PK, Wehrle J, Hirabayashi S, Derecka M, Durruthy-Durruthy R, Göhring G, Yoshimi-Noellke A, Ku M, Lebrecht D, Erlacher M, Flotho C, Strahm B, Niemeyer CM, Wlodarski MW. Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes. Nat Med 2021; 27:1806-1817. [PMID: 34621053 PMCID: PMC9330547 DOI: 10.1038/s41591-021-01511-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 08/17/2021] [Indexed: 02/06/2023]
Abstract
Germline SAMD9 and SAMD9L mutations (SAMD9/9Lmut) predispose to myelodysplastic syndromes (MDS) with propensity for somatic rescue. In this study, we investigated a clinically annotated pediatric MDS cohort (n = 669) to define the prevalence, genetic landscape, phenotype, therapy outcome and clonal architecture of SAMD9/9L syndromes. In consecutively diagnosed MDS, germline SAMD9/9Lmut accounted for 8% and were mutually exclusive with GATA2 mutations present in 7% of the cohort. Among SAMD9/9Lmut cases, refractory cytopenia was the most prevalent MDS subtype (90%); acquired monosomy 7 was present in 38%; constitutional abnormalities were noted in 57%; and immune dysfunction was present in 28%. The clinical outcome was independent of germline mutations. In total, 67 patients had 58 distinct germline SAMD9/9Lmut clustering to protein middle regions. Despite inconclusive in silico prediction, 94% of SAMD9/9Lmut suppressed HEK293 cell growth, and mutations expressed in CD34+ cells induced overt cell death. Furthermore, we found that 61% of SAMD9/9Lmut patients underwent somatic genetic rescue (SGR) resulting in clonal hematopoiesis, of which 95% was maladaptive (monosomy 7 ± cancer mutations), and 51% had adaptive nature (revertant UPD7q, somatic SAMD9/9Lmut). Finally, bone marrow single-cell DNA sequencing revealed multiple competing SGR events in individual patients. Our findings demonstrate that SGR is common in SAMD9/9Lmut MDS and exemplify the exceptional plasticity of hematopoiesis in children.
Collapse
Affiliation(s)
- Sushree S Sahoo
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA, Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Victor B Pastor
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charnise Goodings
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Rebecca K Voss
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Emilia J Kozyra
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Amina Szvetnik
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Noellke
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Dworzak
- Department of Pediatrics, St. Anna Children’s Hospital and Children’s Cancer Research Institute, Medical University of Vienna, Vienna, Austria
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù; Sapienza University of Rome, Italy
| | - Riccardo Masetti
- Paediatric Oncology and Haematology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Markus Schmugge
- Department of Hematology and Oncology, University Children’s Hospital, Zurich, Switzerland
| | - Barbara De Moerloose
- Department of Paediatric Haematology-Oncology, Ghent University Hospital Ghent, Belgium
| | - Albert Catala
- Department of Hematology and Oncology, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Krisztián Kállay
- Department of Pediatric Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest - National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Dominik Turkiewicz
- Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital, Aarhus, Denmark
| | - Jochen Buechner
- Department of Pediatric Hematology and Oncology, Oslo University Hospital, Oslo, Norway
| | - Kirsi Jahnukainen
- Division of Hematology-Oncology and SCT Children′s Hospital, University of Helsinki and Helsinki University Hospital, Hus, Finland
| | - Marek Ussowicz
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, BMT Unit CIC 817, Wroclaw Medical University, Wroclaw, Poland
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology/Oncology, Aghia Sophia Children’s Hospital, Athens, Greece
| | - Owen P Smith
- Department of Pediatric Haematology/Oncology, Children’s Health Ireland at Crumlin, Dublin, Ireland
| | - Oksana Fabri
- Department. of Haematology and Transfusiology, National Institute of Children’s Diseases Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Shlomit Barzilai
- Pediatric Hematology Oncology, Schneider Children’s Medical Center of Israel, Petah Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Valerie de Haas
- Dutch Childhood Oncology Group, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Irith Baumann
- Institute of Pathology, Klinikum Kaufbeuren-Ravensburg, Kaufbeuren, Germany
| | - Stephan Schwarz-Furlan
- Institute of Pathology, Klinikum Kaufbeuren-Ravensburg, Kaufbeuren, Germany, Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | | | - Marena R Niewisch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin G Sauer
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Birgit Burkhardt
- Pediatric Hematology and Oncology, University Hospital Muenster, Muenster, Germany
| | - Peter Lang
- Department of Hematology/Oncology and General Pediatrics, Children’s University Hospital, University of Tübingen, Tübingen, Germany
| | - Peter Bader
- Division for Stem Cell Transplantation and Immunology, Department for Children and Adolescents, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Rita Beier
- University Hospital Essen, Pediatric Haematology and Oncology, Essen, Germany
| | - Ingo Müller
- Division of Pediatric Hematology and Oncology, Clinic of Pedatric Hematology and Oncology, University Medical Center of Hamburg-Eppendorf, Hamburg, Germany
| | - Michael H Albert
- Department of Pediatrics, Dr. von Hauner Children′s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Roland Meisel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Division of Pediatric Stem Cell Therapy, Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany
| | - Ansgar Schulz
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Pritam K Panda
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julius Wehrle
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany, Institute of Digitalization in Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Shinsuke Hirabayashi
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marta Derecka
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ayami Yoshimi-Noellke
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Manching Ku
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dirk Lebrecht
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Erlacher
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany, German Cancer Consortium (DKTK), Heidelberg and Freiburg, Germany
| | - Christian Flotho
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany, German Cancer Consortium (DKTK), Heidelberg and Freiburg, Germany
| | - Brigitte Strahm
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte M Niemeyer
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany, German Cancer Consortium (DKTK), Heidelberg and Freiburg, Germany
| | - Marcin W Wlodarski
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA, Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
30
|
Ren A, Yin W, Miller H, Westerberg LS, Candotti F, Park CS, Lee P, Gong Q, Chen Y, Liu C. Novel Discoveries in Immune Dysregulation in Inborn Errors of Immunity. Front Immunol 2021; 12:725587. [PMID: 34512655 PMCID: PMC8429820 DOI: 10.3389/fimmu.2021.725587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/27/2021] [Indexed: 12/19/2022] Open
Abstract
With the expansion of our knowledge on inborn errors of immunity (IEI), it gradually becomes clear that immune dysregulation plays an important part. In some cases, autoimmunity, hyperinflammation and lymphoproliferation are far more serious than infections. Thus, immune dysregulation has become significant in disease monitoring and treatment. In recent years, the wide application of whole-exome sequencing/whole-genome sequencing has tremendously promoted the discovery and further studies of new IEI. The number of discovered IEI is growing rapidly, followed by numerous studies of their pathogenesis and therapy. In this review, we focus on novel discovered primary immune dysregulation diseases, including deficiency of SLC7A7, CD122, DEF6, FERMT1, TGFB1, RIPK1, CD137, TET2 and SOCS1. We discuss their genetic mutation, symptoms and current therapeutic methods, and point out the gaps in this field.
Collapse
Affiliation(s)
- Anwen Ren
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yin
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heather Miller
- The Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Lisa S Westerberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Chan-Sik Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Pamela Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, China.,Clinical Molecular Immunology Center, School of Medicine, Yangtze University, Jingzhou, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
31
|
Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
Collapse
Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| |
Collapse
|
32
|
Yang T, Liu X, Kumar SK, Jin F, Dai Y. Decoding DNA methylation in epigenetics of multiple myeloma. Blood Rev 2021; 51:100872. [PMID: 34384602 DOI: 10.1016/j.blre.2021.100872] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Dysregulation of DNA methylation in B cells has been observed during their neoplastic transformation and therefore closely associated with various B-cell malignancies including multiple myeloma (MM), a malignancy of terminally differentiated plasma cells. Emerging evidence has unveiled pronounced alterations in DNA methylation in MM, including both global and gene-specific changes that can affect genome stability and gene transcription. Moreover, dysregulated expression of DNA methylation-modifying enzymes has been related with myelomagenesis, disease progression, and poor prognosis. However, the functional roles of the epigenetic abnormalities involving DNA methylation in MM remain elusive. In this article, we review current understanding of the alterations in DNA methylome and DNA methylation modifiers in MM, particularly focusing on DNA methyltransferases (DNMTs) and tet methylcytosine dioxygenases (TETs). We also discuss how these DNA methylation modifiers may be regulated and function in MM cells, therefore providing a rationale for developing novel epigenetic therapies targeting DNA methylation in MM.
Collapse
Affiliation(s)
- Ting Yang
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, 519 Dongminzhu Street, Changchun, Jilin 130061, China.
| | - Xiaobo Liu
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, 519 Dongminzhu Street, Changchun, Jilin 130061, China.
| | - Shaji K Kumar
- Division of Hematology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Fengyan Jin
- Department of Hematology, Cancer Center, the First Hospital of Jilin University, 71 Xinmin Street, Changchun, Jilin 130012, China.
| | - Yun Dai
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, 519 Dongminzhu Street, Changchun, Jilin 130061, China.
| |
Collapse
|
33
|
Katainen R, Donner I, Räisänen M, Berta D, Kuosmanen A, Kaasinen E, Hietala M, Aaltonen LA. Novel germline variant in the histone demethylase and transcription regulator KDM4C induces a multi-cancer phenotype. J Med Genet 2021; 59:644-651. [PMID: 34281993 PMCID: PMC9252859 DOI: 10.1136/jmedgenet-2021-107747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/25/2021] [Indexed: 11/10/2022]
Abstract
Background Genes involved in epigenetic regulation are central for chromatin structure and gene expression. Specific mutations in these might promote carcinogenesis in several tissue types. Methods We used exome, whole-genome and Sanger sequencing to detect rare variants shared by seven affected individuals in a striking early-onset multi-cancer family. The only variant that segregated with malignancy resided in a histone demethylase KDM4C. Consequently, we went on to study the epigenetic landscape of the mutation carriers with ATAC, ChIP (chromatin immunoprecipitation) and RNA-sequencing from lymphoblastoid cell lines to identify possible pathogenic effects. Results A novel variant in KDM4C, encoding a H3K9me3 histone demethylase and transcription regulator, was found to segregate with malignancy in the family. Based on Roadmap Epigenomics Project data, differentially accessible chromatin regions between the variant carriers and controls enrich to normally H3K9me3-marked chromatin. We could not detect a difference in global H3K9 trimethylation levels. However, carriers of the variant seemed to have more trimethylated H3K9 at transcription start sites. Pathway analyses of ChIP-seq and differential gene expression data suggested that genes regulated through KDM4C interaction partner EZH2 and its interaction partner PLZF are aberrantly expressed in mutation carriers. Conclusions The apparent dysregulation of H3K9 trimethylation and KDM4C-associated genes in lymphoblastoid cells supports the hypothesis that the KDM4C variant is causative of the multi-cancer susceptibility in the family. As the variant is ultrarare, located in the conserved catalytic JmjC domain and predicted pathogenic by the majority of available in silico tools, further studies on the role of KDM4C in cancer predisposition are warranted.
Collapse
Affiliation(s)
- Riku Katainen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| | - Iikki Donner
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| | - Maritta Räisänen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| | - Davide Berta
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| | - Anna Kuosmanen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| | - Eevi Kaasinen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| | - Marja Hietala
- Department of Clinical Genetics, TYKS Turku University Hospital and University of Turku Institute of Biomedicine, Turku, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, University of Helsinki Faculty of Medicine, Helsinki, Finland
| |
Collapse
|
34
|
Pitfalls in the Diagnosis of Nodular Lymphocyte Predominant Hodgkin Lymphoma: Variant Patterns, Borderlines and Mimics. Cancers (Basel) 2021; 13:cancers13123021. [PMID: 34208705 PMCID: PMC8234802 DOI: 10.3390/cancers13123021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is a rare lymphoma containing infrequent tumor cells (LP cells) in a background of non-neoplastic cells. Some cases of NLPHL can recur or progress to a more aggressive lymphoma, such as diffuse large B-cell lymphoma. Awareness of the different appearances of NLPHL and its overlap with other lymphomas are important for the appropriate diagnosis, classification and research. This article discusses the conceptual framework and guidelines for the diagnosis of NLPHL, and how NLPHL can be best separated from its mimics. Emerging data in the field point to genetic changes in LP cells that are shaped by immune mechanisms. In addition, non-neoplastic cells in the background of LP cells also appear to play an important role. Further investigation is necessary to fully understand the biology of NLPHL and personalize cancer care for patients affected by this lymphoma. Abstract Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) represents approximately 5% of Hodgkin lymphoma and typically affects children and young adults. Although the overall prognosis is favorable, variant growth patterns in NLPHL correlate with disease recurrence and progression to T-cell/histiocyte-rich large B-cell lymphoma or frank diffuse large B-cell lymphoma (DLBCL). The diagnostic boundary between NLPHL and DLBCL can be difficult to discern, especially in the presence of variant histologies. Both diagnoses are established using morphology and immunophenotype and share similarities, including the infrequent large tumor B-cells and the lymphocyte and histiocyte-rich microenvironment. NLPHL also shows overlap with other lymphomas, particularly, classic Hodgkin lymphoma and T-cell lymphomas. Similarly, there is overlap with non-neoplastic conditions, such as the progressive transformation of germinal centers. Given the significant clinical differences among these entities, it is imperative that NLPHL and its variants are carefully separated from other lymphomas and their mimics. In this article, the characteristic features of NLPHL and its diagnostic boundaries and pitfalls are discussed. The current understanding of genetic features and immune microenvironment will be addressed, such that a framework to better understand biological behavior and customize patient care is provided.
Collapse
|
35
|
Caiado F, Pietras EM, Manz MG. Inflammation as a regulator of hematopoietic stem cell function in disease, aging, and clonal selection. J Exp Med 2021; 218:212381. [PMID: 34129016 PMCID: PMC8210622 DOI: 10.1084/jem.20201541] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022] Open
Abstract
Inflammation is an evolutionarily selected defense response to infection or tissue damage that involves activation and consumption of immune cells in order to reestablish and maintain organismal integrity. In this process, hematopoietic stem cells (HSCs) are themselves exposed to inflammatory cues and via proliferation and differentiation, replace mature immune cells in a demand-adapted fashion. Here, we review how major sources of systemic inflammation act on and subsequently shape HSC fate and function. We highlight how lifelong inflammatory exposure contributes to HSC inflamm-aging and selection of premalignant HSC clones. Finally, we explore emerging areas of interest and open questions remaining in the field.
Collapse
Affiliation(s)
- Francisco Caiado
- Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland.,University of Zürich, Comprehensive Cancer Center Zürich, Zürich, Switzerland
| | - Eric M Pietras
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland.,University of Zürich, Comprehensive Cancer Center Zürich, Zürich, Switzerland
| |
Collapse
|
36
|
Lim JY, Duttke SH, Baker TS, Lee J, Gambino KJ, Venturini NJ, Ho JSY, Zheng S, Fstkchyan YS, Pillai V, Fajgenbaum DC, Marazzi I, Benner C, Byun M. DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells. J Exp Med 2021; 218:212086. [PMID: 33970190 PMCID: PMC8111463 DOI: 10.1084/jem.20202733] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/04/2021] [Accepted: 04/02/2021] [Indexed: 01/04/2023] Open
Abstract
DNMT3A encodes an enzyme that carries out de novo DNA methylation, which is essential for the acquisition of cellular identity and specialized functions during cellular differentiation. DNMT3A is the most frequently mutated gene in age-related clonal hematopoiesis. As such, mature immune cells harboring DNMT3A mutations can be readily detected in elderly persons. Most DNMT3A mutations associated with clonal hematopoiesis are heterozygous and predicted to cause loss of function, indicating that haploinsufficiency is the predominant pathogenic mechanism. Yet, the impact of DNMT3A haploinsufficiency on the function of mature immune cells is poorly understood. Here, we demonstrate that DNMT3A haploinsufficiency impairs the gain of DNA methylation at decommissioned enhancers, while simultaneously and unexpectedly impairing DNA demethylation of newly activated enhancers in mature human myeloid cells. The DNA methylation defects alter the activity of affected enhancers, leading to abnormal gene expression and impaired immune response. These findings provide insights into the mechanism of immune dysfunction associated with clonal hematopoiesis and acquired DNMT3A mutations.
Collapse
Affiliation(s)
- Jung-Yeon Lim
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Turner S Baker
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jihye Lee
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kristyne J Gambino
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicholas J Venturini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yesai S Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Minji Byun
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| |
Collapse
|
37
|
Chavez JS, Rabe JL, Loeffler D, Higa KC, Hernandez G, Mills TS, Ahmed N, Gessner RL, Ke Z, Idler BM, Niño KE, Kim H, Myers JR, Stevens BM, Davizon-Castillo P, Jordan CT, Nakajima H, Ashton J, Welner RS, Schroeder T, DeGregori J, Pietras EM. PU.1 enforces quiescence and limits hematopoietic stem cell expansion during inflammatory stress. J Exp Med 2021; 218:211996. [PMID: 33857288 PMCID: PMC8056754 DOI: 10.1084/jem.20201169] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/01/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of entering the cell cycle to replenish the blood system in response to inflammatory cues; however, excessive proliferation in response to chronic inflammation can lead to either HSC attrition or expansion. The mechanism(s) that limit HSC proliferation and expansion triggered by inflammatory signals are poorly defined. Here, we show that long-term HSCs (HSCLT) rapidly repress protein synthesis and cell cycle genes following treatment with the proinflammatory cytokine interleukin (IL)-1. This gene program is associated with activation of the transcription factor PU.1 and direct PU.1 binding at repressed target genes. Notably, PU.1 is required to repress cell cycle and protein synthesis genes, and IL-1 exposure triggers aberrant protein synthesis and cell cycle activity in PU.1-deficient HSCs. These features are associated with expansion of phenotypic PU.1-deficient HSCs. Thus, we identify a PU.1-dependent mechanism triggered by innate immune stimulation that limits HSC proliferation and pool size. These findings provide insight into how HSCs maintain homeostasis during inflammatory stress.
Collapse
Affiliation(s)
- James S Chavez
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jennifer L Rabe
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Kelly C Higa
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Giovanny Hernandez
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Taylor S Mills
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Rachel L Gessner
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Zhonghe Ke
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Beau M Idler
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Katia E Niño
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Hyunmin Kim
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, NY
| | - Brett M Stevens
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Craig T Jordan
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University School of Medicine, Yokohama, Japan
| | - John Ashton
- Genomics Research Center, University of Rochester, Rochester, NY
| | - Robert S Welner
- Division of Hematology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - James DeGregori
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Eric M Pietras
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
38
|
Hereditary Predisposition to Acute Myeloid Leukemia in Older Adults. Hemasphere 2021; 5:e552. [PMID: 33778416 PMCID: PMC7990008 DOI: 10.1097/hs9.0000000000000552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 12/03/2022] Open
|
39
|
|
40
|
MacArthur IC, Dawlaty MM. TET Enzymes and 5-Hydroxymethylcytosine in Neural Progenitor Cell Biology and Neurodevelopment. Front Cell Dev Biol 2021; 9:645335. [PMID: 33681230 PMCID: PMC7930563 DOI: 10.3389/fcell.2021.645335] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Studies of tissue-specific epigenomes have revealed 5-hydroxymethylcytosine (5hmC) to be a highly enriched and dynamic DNA modification in the metazoan nervous system, inspiring interest in the function of this epigenetic mark in neurodevelopment and brain function. 5hmC is generated by oxidation of 5-methylcytosine (5mC), a process catalyzed by the ten–eleven translocation (TET) enzymes. 5hmC serves not only as an intermediate in DNA demethylation but also as a stable epigenetic mark. Here, we review the known functions of 5hmC and TET enzymes in neural progenitor cell biology and embryonic and postnatal neurogenesis. We also discuss how TET enzymes and 5hmC regulate neuronal activity and brain function and highlight their implications in human neurodevelopmental and neurodegenerative disorders. Finally, we present outstanding questions in the field and envision new research directions into the roles of 5hmC and TET enzymes in neurodevelopment.
Collapse
Affiliation(s)
- Ian C MacArthur
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Meelad M Dawlaty
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
| |
Collapse
|
41
|
Lewis AC, Kats LM. Non-genetic heterogeneity, altered cell fate and differentiation therapy. EMBO Mol Med 2021; 13:e12670. [PMID: 33555144 PMCID: PMC7933953 DOI: 10.15252/emmm.202012670] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
Altered capacity for self‐renewal and differentiation is a hallmark of cancer, and many tumors are composed of cells with a developmentally immature phenotype. Among the malignancies where processes that govern cell fate decisions have been studied most extensively is acute myeloid leukemia (AML), a disease characterized by the presence of large numbers of “blasts” that resemble myeloid progenitors. Classically, the defining properties of AML cells were said to be aberrant self‐renewal and a block of differentiation, and the term “differentiation therapy” was coined to describe drugs that promote the maturation of leukemic blasts. Notionally however, the simplistic view that such agents “unblock” differentiation is at odds with the cancer stem cell (CSC) hypothesis that posits that tumors are hierarchically organized and that CSCs, which underpin cancer growth, retain the capacity to progress to a developmentally more mature state. Herein, we will review recent developments that are providing unprecedented insights into non‐genetic heterogeneity both at steady state and in response to treatment, and propose a new conceptual framework for therapies that aim to alter cell fate decisions in cancer.
Collapse
Affiliation(s)
| | - Lev M Kats
- The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
42
|
Guan Y, Hasipek M, Tiwari AD, Maciejewski JP, Jha BK. TET-dioxygenase deficiency in oncogenesis and its targeting for tumor-selective therapeutics. Semin Hematol 2021; 58:27-34. [PMID: 33509440 PMCID: PMC7938524 DOI: 10.1053/j.seminhematol.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/04/2020] [Accepted: 12/19/2020] [Indexed: 02/08/2023]
Abstract
TET2 is one of the most frequently mutated genes in myeloid neoplasms. TET2 loss-of-function perturbs myeloid differentiation and causes clonal expansion. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, targeted therapies are lagging. Here we review known biochemical mechanisms and candidate therapies that emerge from this. Specifically, we discuss the potential utility of vitamin C to compensate for TET-dioxygenase deficiency, to thereby restore the biochemical function. An alternative approach exploits the TET-deficient state for synthetic lethality, exploiting the fact that a minimum level of TET-dioxygenase activity is required for cell survival, rendering TET2-mutant malignant cells selectively vulnerable to inhibitors of TET-function.
Collapse
Affiliation(s)
- Yihong Guan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Metis Hasipek
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Anand D Tiwari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
| |
Collapse
|
43
|
Guan Y, Tiwari AD, Phillips JG, Hasipek M, Grabowski DR, Pagliuca S, Gopal P, Kerr CM, Adema V, Radivoyevitch T, Parker Y, Lindner DJ, Meggendorfer M, Abazeed M, Sekeres MA, Mian OY, Haferlach T, Maciejewski JP, Jha BK. A Therapeutic Strategy for Preferential Targeting of TET2 Mutant and TET-dioxygenase Deficient Cells in Myeloid Neoplasms. Blood Cancer Discov 2020; 2:146-161. [PMID: 33681816 DOI: 10.1158/2643-3230.bcd-20-0173] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
TET2 is frequently mutated in myeloid neoplasms. Genetic TET2 deficiency leads to skewed myeloid differentiation and clonal expansion, but minimal residual TET activity is critical for survival of neoplastic progenitor and stem cells. Consistent with mutual exclusivity of TET2 and neomorphic IDH1/2 mutations, here we report that IDH1/2 mutant-derived 2-hydroxyglutarate is synthetically lethal to TET-dioxygenase deficient cells. In addition, a TET-selective small molecule inhibitor decreased cytosine hydroxymethylation and restricted clonal outgrowth of TET2 mutant, but not normal hematopoietic precursor cells in vitro and in vivo. While TET-inhibitor phenocopied somatic TET2 mutations, its pharmacologic effects on normal stem cells were, unlike mutations, reversible. Treatment with TET inhibitor suppressed the clonal evolution of TET2 mutant cells in murine models and TET2-mutated human leukemia xenografts. These results suggest that TET inhibitors may constitute a new class of targeted agents in TET2 mutant neoplasia.
Collapse
Affiliation(s)
- Yihong Guan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Anand D Tiwari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - James G Phillips
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Metis Hasipek
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Dale R Grabowski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Priyanka Gopal
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Cassandra M Kerr
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Vera Adema
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | | | - Yvonne Parker
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | - Daniel J Lindner
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute
| | | | - Mohamed Abazeed
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH.,Leukemia Program, Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH
| | - Mikkeal A Sekeres
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH.,Leukemia Program, Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Omar Y Mian
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH.,Leukemia Program, Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| |
Collapse
|
44
|
Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
Collapse
Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| |
Collapse
|
45
|
Hou H, Zhao H. Epigenetic factors in atherosclerosis: DNA methylation, folic acid metabolism, and intestinal microbiota. Clin Chim Acta 2020; 512:7-11. [PMID: 33232735 DOI: 10.1016/j.cca.2020.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022]
Abstract
Atherosclerosis is a complex disease, influenced by both genetic and non-genetic factors. The most important epigenetic mechanism in the pathogenesis of atherosclerosis is DNA methylation, which involves modification of the gene without changes in the gene sequence. Nutrients involved in one-carbon metabolism interact to regulate DNA methylation, especially folic acid and B vitamins. Deficiencies in folic acid and other nutrients, such as vitamins B6 and B12, can increase homocysteine levels, induce endothelial dysfunction, and accelerate atherosclerotic pathological processes. Supplemented nutrients can improve DNA methylation status, reduce levels of inflammatory factors, and delay the process of atherosclerosis. In this review, the influence of intestinal flora on folate metabolism and epigenetics is also considered.
Collapse
Affiliation(s)
- Huimin Hou
- Department of Geriatrics, The First Hospital of Jilin University, Changchun 130021, China
| | - Huiying Zhao
- Department of Geriatrics, The First Hospital of Jilin University, Changchun 130021, China.
| |
Collapse
|
46
|
Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma. Cancers (Basel) 2020; 12:cancers12113304. [PMID: 33182397 PMCID: PMC7697455 DOI: 10.3390/cancers12113304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The use of next generation technologies has helped to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. Nonetheless, the sequencing of all protein-coding genes of an individual may lead to doubtful assignments of causality for non-pathological variants, so it is mandatory to perform comprehensive studies and screening of additional patients for new mutations. Here we describe a novel DNMT3A germline variant identified by whole-exome sequencing in a patient with multiple paragangliomas and papillary thyroid carcinoma. The increased methylation of DNMT3A target genes observed in the proband’s sample points towards a gain-of-function effect of the variant, contrasting with the inactivation caused by loss-of-function alterations commonly seen in other neoplasia and in patients with Tatton-Brown-Rahman syndrome. This finding stresses the diverse molecular outcomes and suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants. Abstract Over the past few years, next generation technologies have been applied to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. We recently found germline DNMT3A gain-of-function variants in two patients with head and neck paragangliomas causing a characteristic hypermethylated DNA profile. Here, whole-exome sequencing identifies a novel germline DNMT3A variant (p.Gly332Arg) in a patient with bilateral carotid paragangliomas, papillary thyroid carcinoma and idiopathic intellectual disability. The variant, located in the Pro-Trp-Trp-Pro (PWWP) domain of the protein involved in chromatin targeting, affects a residue mutated in papillary thyroid tumors and located between the two residues found mutated in microcephalic dwarfism patients. Structural modelling of the variant in the DNMT3A PWWP domain predicts that the interaction with H3K36me3 will be altered. An increased methylation of DNMT3A target genes, compatible with a gain-of-function effect of the alteration, was observed in saliva DNA from the proband and in one independent acute myeloid leukemia sample carrying the same p.Gly332Arg variant. Although further studies are needed to support a causal role of DNMT3A variants in paraganglioma, the description of a new DNMT3A alteration in a patient with multiple clinical features suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants.
Collapse
|
47
|
Nemtsova MV, Mikhaylenko DS, Kuznetsova EB, Bykov II, Zamyatnin AA. Inactivation of Epigenetic Regulators due to Mutations in Solid Tumors. BIOCHEMISTRY (MOSCOW) 2020; 85:735-748. [PMID: 33040718 DOI: 10.1134/s0006297920070020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Main factors involved in carcinogenesis are associated with somatic mutations in oncogenes and tumor suppressor genes representing changes in the DNA nucleotide sequence. Epigenetic changes, such as aberrant DNA methylation, modifications of histone proteins, and chromatin remodeling, are equally important in the development of human neoplasms. From this perspective, mutations in the genes encoding key participants of epigenetic regulation are of particular interest including enzymes that methylate/demethylate DNA, enzymes that covalently attach or remove regulatory signals from histones, components of nucleosome remodeling multiprotein complexes, auxiliary proteins and cofactors of the above-mentioned molecules. This review describes both germline and somatic mutations in the key epigenetic regulators with emphasis on the latter ones in the solid human tumors, as well as considers functional consequences of these mutations on the cellular level. In addition, clinical associations of the somatic mutations in epigenetic regulators are presented, as well as DNA diagnostics of hereditary cancer syndromes due to germline mutations in the SMARC proteins and chemotherapy drugs directly affecting the altered epigenetic mechanisms for treatment of patients with solid neoplasms. The review is intended for a wide range of molecular biologists, geneticists, oncologists, and associated specialists.
Collapse
Affiliation(s)
- M V Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia.,Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - D S Mikhaylenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia. .,Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - E B Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia
| | - I I Bykov
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia
| | - A A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
48
|
Jaiswal S. Clonal hematopoiesis and nonhematologic disorders. Blood 2020; 136:1606-1614. [PMID: 32736379 PMCID: PMC8209629 DOI: 10.1182/blood.2019000989] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/01/2020] [Indexed: 12/18/2022] Open
Abstract
Clonal expansions of mutated hematopoietic cells, termed clonal hematopoiesis, are common in aging humans. One expected consequence of mutation-associated clonal hematopoiesis is an increased risk of hematologic cancers, which has now been shown in several studies. However, the hematopoietic stem cells that acquire these somatic mutations also give rise to mutated immune effector cells, such as monocytes, granulocytes, and lymphocytes. These effector cells can potentially influence many disease states, especially those with a chronic inflammatory component. Indeed, several studies have now shown that clonal hematopoiesis associates with increased risk of atherosclerotic cardiovascular disease. Emerging data also associate clonal hematopoiesis with other nonhematologic diseases. Here, we will review recent studies linking clonal hematopoiesis to altered immune function, inflammation, and nonmalignant diseases of aging.
Collapse
Affiliation(s)
- Siddhartha Jaiswal
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, and Program in Immunology, School of Medicine, Stanford University, Stanford, CA
| |
Collapse
|
49
|
Stremenova Spegarova J, Lawless D, Mohamad SMB, Engelhardt KR, Doody G, Shrimpton J, Rensing-Ehl A, Ehl S, Rieux-Laucat F, Cargo C, Griffin H, Mikulasova A, Acres M, Morgan NV, Poulter JA, Sheridan EG, Chetcuti P, O'Riordan S, Anwar R, Carter CR, Przyborski S, Windebank K, Cant AJ, Lako M, Bacon CM, Savic S, Hambleton S. Germline TET2 loss of function causes childhood immunodeficiency and lymphoma. Blood 2020; 136:1055-1066. [PMID: 32518946 DOI: 10.1182/blood.2020005844] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/28/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular dissection of inborn errors of immunity can help to elucidate the nonredundant functions of individual genes. We studied 3 children with an immune dysregulation syndrome of susceptibility to infection, lymphadenopathy, hepatosplenomegaly, developmental delay, autoimmunity, and lymphoma of B-cell (n = 2) or T-cell (n = 1) origin. All 3 showed early autologous T-cell reconstitution following allogeneic hematopoietic stem cell transplantation. By whole-exome sequencing, we identified rare homozygous germline missense or nonsense variants in a known epigenetic regulator of gene expression: ten-eleven translocation methylcytosine dioxygenase 2 (TET2). Mutated TET2 protein was absent or enzymatically defective for 5-hydroxymethylating activity, resulting in whole-blood DNA hypermethylation. Circulating T cells showed an abnormal immunophenotype including expanded double-negative, but depleted follicular helper, T-cell compartments and impaired Fas-dependent apoptosis in 2 of 3 patients. Moreover, TET2-deficient B cells showed defective class-switch recombination. The hematopoietic potential of patient-derived induced pluripotent stem cells was skewed toward the myeloid lineage. These are the first reported cases of autosomal-recessive germline TET2 deficiency in humans, causing clinically significant immunodeficiency and an autoimmune lymphoproliferative syndrome with marked predisposition to lymphoma. This disease phenotype demonstrates the broad role of TET2 within the human immune system.
Collapse
MESH Headings
- Allografts
- Apoptosis
- B-Lymphocyte Subsets/pathology
- Cellular Reprogramming Techniques
- Codon, Nonsense
- DNA Methylation
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Dioxygenases
- Fatal Outcome
- Female
- Germ-Line Mutation
- Hematopoietic Stem Cell Transplantation
- Humans
- Induced Pluripotent Stem Cells/pathology
- Infant, Newborn
- Loss of Function Mutation
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/pathology
- Lymphoproliferative Disorders/genetics
- Male
- Mutation, Missense
- Neoplasms, Multiple Primary/genetics
- Pedigree
- Proto-Oncogene Proteins/deficiency
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/physiology
- Severe Combined Immunodeficiency/genetics
- Severe Combined Immunodeficiency/pathology
- T-Lymphocyte Subsets/pathology
- Exome Sequencing
Collapse
Affiliation(s)
- Jarmila Stremenova Spegarova
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
| | - Dylan Lawless
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Siti Mardhiana Binti Mohamad
- Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Penang, Malaysia
| | - Karin R Engelhardt
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
| | - Gina Doody
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Jennifer Shrimpton
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anne Rensing-Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Freiburg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Freiburg, Germany
| | | | - Catherine Cargo
- Haematological Malignancy Diagnostic Service, St James's University Hospital, Leeds, United Kingdom
| | - Helen Griffin
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
| | - Aneta Mikulasova
- Newcastle University Biosciences Institute, Newcastle upon Tyne, United Kingdom
| | - Meghan Acres
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - James A Poulter
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Eamonn G Sheridan
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Philip Chetcuti
- Department of Paediatrics, Leeds General Infirmary, Leeds, United Kingdom
| | - Sean O'Riordan
- Department of Paediatrics, Leeds General Infirmary, Leeds, United Kingdom
| | - Rashida Anwar
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Clive R Carter
- Department of Clinical Immunology and Allergy, St James's University Hospital, Leeds, United Kingdom
| | - Stefan Przyborski
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Kevin Windebank
- Wolfson Childhood Cancer Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
| | - Andrew J Cant
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Majlinda Lako
- Newcastle University Biosciences Institute, Newcastle upon Tyne, United Kingdom
| | - Chris M Bacon
- Wolfson Childhood Cancer Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; and
| | - Sinisa Savic
- Department of Clinical Immunology and Allergy, St James's University Hospital, Leeds, United Kingdom
- NIHR, Leeds Biomedical Research Centre and Leeds Institute of Rheumatic and Musculoskeletal Medicine, Wellcome Trust Brenner Building, St James's University Hospital, Leeds, United Kingdom
| | - Sophie Hambleton
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
50
|
Hoermann G, Greiner G, Griesmacher A, Valent P. Clonal Hematopoiesis of Indeterminate Potential: A Multidisciplinary Challenge in Personalized Hematology. J Pers Med 2020; 10:jpm10030094. [PMID: 32825226 PMCID: PMC7564336 DOI: 10.3390/jpm10030094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related condition that represents a potential pre-phase of hematologic neoplasm. Next-generation sequencing (NGS) is used to detect and monitor clonal hematopoiesis, and the spectrum of mutations substantially overlaps with that of myeloid neoplasms with DNMT3A, TET2, ASXL1, and JAK2 being the most frequently mutated. While, in general, the risk of progression to an overt myeloid neoplasm is only modest, the progression risk increases in patients with unexplained cytopenia or multiple mutations. In addition, CHIP represents a previously unrecognized major risk factor for atherosclerosis and cardiovascular disease (CVD), including coronary heart disease, degenerative aortic valve stenosis, and chronic heart failure; and a causative role of CHIP in the development of CVD has been demonstrated in vitro and in vivo. The management of patients with CHIP is a rapidly emerging topic in personalized medicine, as NGS has become widely available for clinical medicine. It requires a highly multidisciplinary setting, including hematology/oncology, cardiology, (clinical) pathology, and genetics for individualized guidance. Further research is urgently needed to provide robust evidence for future guidelines and recommendations on the management of patients with CHIP in the era of personalized medicine.
Collapse
Affiliation(s)
- Gregor Hoermann
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
- Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, 6020 Innsbruck, Austria;
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- MLL Munich Leukemia Laboratory, 81377 Munich, Germany
- Correspondence: or ; Tel.: +43-1-40400-53590 or +49-89-99017-315
| | - Georg Greiner
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Andrea Griesmacher
- Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, 6020 Innsbruck, Austria;
| | - Peter Valent
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria
| |
Collapse
|