1
|
Huang G, Cai X, Li D. Significance of targeting DNMT3A mutations in AML. Ann Hematol 2024:10.1007/s00277-024-05885-8. [PMID: 39078434 DOI: 10.1007/s00277-024-05885-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/05/2024] [Indexed: 07/31/2024]
Abstract
Acute myeloid leukemia (AML) is the most prevalent form of leukemia among adults, characterized by aggressive behavior and significant genetic diversity. Despite decades of reliance on conventional chemotherapy as the mainstay treatment, patients often struggle with achieving remission, experience rapid relapses, and have limited survival prospects. While intensified induction chemotherapy and allogeneic stem cell transplantation have enhanced patient outcomes, these benefits are largely confined to younger AML patients capable of tolerating intensive treatments. DNMT3A, a crucial enzyme responsible for establishing de novo DNA methylation, plays a pivotal role in maintaining the delicate balance between hematopoietic stem cell differentiation and self-renewal, thereby influencing gene expression programs through epigenetic regulation. DNMT3A mutations are the most frequently observed genetic abnormalities in AML, predominantly in older patients, occurring in approximately 20-30% of adult AML cases and over 30% of AML with a normal karyotype. Consequently, the molecular underpinnings and potential therapeutic targets of DNMT3A mutations in AML are currently being thoroughly investigated. This article provides a comprehensive summary and the latest insights into the structure and function of DNMT3A, examines the impact of DNMT3A mutations on the progression and prognosis of AML, and explores potential therapeutic approaches for AML patients harboring DNMT3A mutations.
Collapse
Affiliation(s)
- Guiqin Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoya Cai
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dengju Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
2
|
Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
Collapse
Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
3
|
Humphries S, Bond DR, Germon ZP, Keely S, Enjeti AK, Dun MD, Lee HJ. Crosstalk between DNA methylation and hypoxia in acute myeloid leukaemia. Clin Epigenetics 2023; 15:150. [PMID: 37705055 PMCID: PMC10500762 DOI: 10.1186/s13148-023-01566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a deadly disease characterised by the uncontrolled proliferation of immature myeloid cells within the bone marrow. Altered regulation of DNA methylation is an important epigenetic driver of AML, where the hypoxic bone marrow microenvironment can help facilitate leukaemogenesis. Thus, interactions between epigenetic regulation and hypoxia signalling will have important implications for AML development and treatment. MAIN BODY This review summarises the importance of DNA methylation and the hypoxic bone marrow microenvironment in the development, progression, and treatment of AML. Here, we focus on the role hypoxia plays on signalling and the subsequent regulation of DNA methylation. Hypoxia is likely to influence DNA methylation through altered metabolic pathways, transcriptional control of epigenetic regulators, and direct effects on the enzymatic activity of epigenetic modifiers. DNA methylation may also prevent activation of hypoxia-responsive genes, demonstrating bidirectional crosstalk between epigenetic regulation and the hypoxic microenvironment. Finally, we consider the clinical implications of these interactions, suggesting that reduced cell cycling within the hypoxic bone marrow may decrease the efficacy of hypomethylating agents. CONCLUSION Hypoxia is likely to influence AML progression through complex interactions with DNA methylation, where the therapeutic efficacy of hypomethylating agents may be limited within the hypoxic bone marrow. To achieve optimal outcomes for AML patients, future studies should therefore consider co-treatments that can promote cycling of AML cells within the bone marrow or encourage their dissociation from the bone marrow.
Collapse
Affiliation(s)
- Sam Humphries
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Danielle R Bond
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Zacary P Germon
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Anoop K Enjeti
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Department of Haematology, Calvary Mater Hospital, Waratah, NSW, 2298, Australia
- New South Wales Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, 2305, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Heather J Lee
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
| |
Collapse
|
4
|
Ogrodnik M, Gladyshev VN. The meaning of adaptation in aging: insights from cellular senescence, epigenetic clocks and stem cell alterations. NATURE AGING 2023; 3:766-775. [PMID: 37386259 PMCID: PMC7616215 DOI: 10.1038/s43587-023-00447-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
With recent rapid progress in research on aging, there is increasing evidence that many features commonly considered to be mechanisms or drivers of aging in fact represent adaptations. Here, we examine several such features, including cellular senescence, epigenetic aging and stem cell alterations. We draw a distinction between the causes and consequences of aging and define short-term consequences as 'responses' and long-term ones as 'adaptations'. We also discuss 'damaging adaptations', which despite having beneficial effects in the short term, lead to exacerbation of the initial insult and acceleration of aging. Features commonly recognized as 'basic mechanisms of the aging process' are critically examined for the possibility of their adaptation-driven emergence from processes such as cell competition and the wound-like features of the aging body. Finally, we speculate on the meaning of these interactions for the aging process and their relevance for the development of antiaging interventions.
Collapse
Affiliation(s)
- Mikolaj Ogrodnik
- Ludwig Boltzmann Research Group Senescence and Healing of Wounds, Vienna, Austria.
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Austrian Workers' Compensation Board Research Center, Vienna, Austria.
- Austrian Cluster for Tissue Regeneration, Vienna, Austria.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
5
|
Brunet A, Goodell MA, Rando TA. Ageing and rejuvenation of tissue stem cells and their niches. Nat Rev Mol Cell Biol 2023; 24:45-62. [PMID: 35859206 PMCID: PMC9879573 DOI: 10.1038/s41580-022-00510-w] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 01/28/2023]
Abstract
Most adult organs contain regenerative stem cells, often organized in specific niches. Stem cell function is critical for tissue homeostasis and repair upon injury, and it is dependent on interactions with the niche. During ageing, stem cells decline in their regenerative potential and ability to give rise to differentiated cells in the tissue, which is associated with a deterioration of tissue integrity and health. Ageing-associated changes in regenerative tissue regions include defects in maintenance of stem cell quiescence, differentiation ability and bias, clonal expansion and infiltration of immune cells in the niche. In this Review, we discuss cellular and molecular mechanisms underlying ageing in the regenerative regions of different tissues as well as potential rejuvenation strategies. We focus primarily on brain, muscle and blood tissues, but also provide examples from other tissues, such as skin and intestine. We describe the complex interactions between different cell types, non-cell-autonomous mechanisms between ageing niches and stem cells, and the influence of systemic factors. We also compare different interventions for the rejuvenation of old regenerative regions. Future outlooks in the field of stem cell ageing are discussed, including strategies to counter ageing and age-dependent disease.
Collapse
Affiliation(s)
- Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Glenn Laboratories for the Biology of Ageing, Stanford University, Stanford, CA, USA.
| | - Margaret A Goodell
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, USA.
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
| | - Thomas A Rando
- Glenn Laboratories for the Biology of Ageing, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Neurology Service, VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
6
|
Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JHY, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature 2022; 611:387-398. [PMID: 36289338 PMCID: PMC10060167 DOI: 10.1038/s41586-022-05365-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
Collapse
Affiliation(s)
- Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Fan Song
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Bioinformatics and Genomics Graduate Program, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Huijue Lyu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mikoto Kobayashi
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Baozhen Zhang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ziyu Zhao
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bei Jia
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Lena Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Josiah Hiu-Yuen Wong
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yihao Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Sinisa Dovat
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yue Yang
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Tomoko Yamada
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Aaron D Viny
- Division of Hematology/Oncology and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Hong Zheng
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| |
Collapse
|
7
|
Zebley CC, Youngblood B. Mechanisms of T cell exhaustion guiding next-generation immunotherapy. Trends Cancer 2022; 8:726-734. [PMID: 35570136 PMCID: PMC9388609 DOI: 10.1016/j.trecan.2022.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
Abstract
The functional decline in T cells during their chronic stimulation, commonly referred to as T cell exhaustion, is a major limitation for current immunotherapy approaches. As modern medicine embraces therapeutic approaches that exploit the immuno-oncology interface, a primary question is how is T cell function maintained over time in scenarios of prolonged tumor burden. Deciphering the molecular mechanisms of T cell exhaustion is now enabling the field to begin using cardinal features of T cell differentiation to develop biomarkers that can delineate responders from nonresponders prior to treatment with T cell-based therapeutics. Furthermore, applying principles of basic T cell immunity toward the development of cancer treatments is laying a foundation for rational approaches to improve immunotherapy by redirecting T cells away from a dysfunctional developmental trajectory.
Collapse
Affiliation(s)
- Caitlin C Zebley
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Ben Youngblood
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
8
|
Castillo D, Yuan TA, Nehoray B, Cervantes A, Tsang KK, Yang K, Sand SR, Mokhnatkin J, Herzog J, Slavin TP, Hyman S, Schwartz A, Ebert BL, Amos CI, Garber JE, Weitzel JN. Clonal Hematopoiesis and Mosaicism Revealed by a Multi-Tissue Analysis of Constitutional TP53 Status. Cancer Epidemiol Biomarkers Prev 2022; 31:1621-1629. [PMID: 35654360 PMCID: PMC9866580 DOI: 10.1158/1055-9965.epi-21-1296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/02/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Though germline TP53 pathogenic/likely pathogenic variants (PV) are associated with Li-Fraumeni syndrome, many detected by multigene panels represent aberrant clonal expansion (ACE), most due to clonal hematopoiesis (CH). Discerning ACE/CH from germline variants and postzygotic mosaicism (PZM) is critically needed for risk assessment and management. METHODS Participants in the Li-Fraumeni & TP53 Understanding & Progress (LiFT UP) study with a TP53 PV were eligible. Demographics, personal/family cancer history, and clinical laboratory test reports were obtained. DNA from multiple tissues was analyzed using a custom QIAseq assay (ACE panel) that included TP53 and other CH-associated genes; the ACE panel and eyebrow follicles were assessed in a workflow to discern TP53 PV clinical categories. RESULTS Among 134 participants there was a significant difference for the age at diagnosis (P < 0.001), component cancers (P = 0.007), and clinical testing criteria (P < 0.001), comparing germline with PZM or ACE. ACE panel analysis of DNA from 55 sets of eyebrow follicles (mean 1.4 ug) and 36 formalin-fixed, paraffin imbedded tissues demonstrated low variance (SE, 3%; P = 0.993) for TP53 variant allele fraction, with no significant difference (P = 0.965) between tissue types, and detected CH gene PVs. Of 55 multi-tissue cases, germline status was confirmed for 20, PZM in seven, ACE for 25, and three were indeterminate. Additional CH variants were detected in six ACE and two germline cases. CONCLUSIONS We demonstrated an effective approach and tools for discerning germline TP53 status. IMPACT Discernment of PZM and TP53-driven CH increases diagnostic accuracy and enables risk-appropriate care.
Collapse
Affiliation(s)
| | - Tze-An Yuan
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Bita Nehoray
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | | | - Kai Yang
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | | | - Josef Herzog
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | - Sophie Hyman
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | | | | | - Jeffrey N. Weitzel
- City of Hope Cancer Center, Duarte, CA 91010, USA,Latin American School of Oncology, Los Angeles, CA, USA
| |
Collapse
|
9
|
Pileri F, Natoli G. Clonal hematopoiesis, inflammation, and cardiovascular disorders: a mitochondrial connection. Trends Immunol 2022; 43:693-695. [DOI: 10.1016/j.it.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
|
10
|
Tovy A, Reyes JM, Zhang L, Huang YH, Rosas C, Daquinag AC, Guzman A, Ramabadran R, Chen CW, Gu T, Gupta S, Ortinau L, Park D, Cox AR, Rau RE, Hartig SM, Kolonin MG, Goodell MA. Constitutive loss of DNMT3A causes morbid obesity through misregulation of adipogenesis. eLife 2022; 11:e72359. [PMID: 35635747 PMCID: PMC9150890 DOI: 10.7554/elife.72359] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
DNA Methyltransferase 3 A (DNMT3A) is an important facilitator of differentiation of both embryonic and hematopoietic stem cells. Heterozygous germline mutations in DNMT3A lead to Tatton-Brown-Rahman Syndrome (TBRS), characterized by obesity and excessive height. While DNMT3A is known to impact feeding behavior via the hypothalamus, here we investigated a role in adipocyte progenitors utilizing heterozygous knockout mice that recapitulate cardinal TBRS phenotypes. These mice become morbidly obese due to adipocyte enlargement and tissue expansion. Adipose tissue in these mice exhibited defects in preadipocyte maturation and precocious activation of inflammatory gene networks, including interleukin-6 signaling. Adipocyte progenitor cell lines lacking DNMT3A exhibited aberrant differentiation. Furthermore, mice in which Dnmt3a was specifically ablated in adipocyte progenitors showed enlarged fat depots and increased progenitor numbers, partly recapitulating the TBRS obesity phenotypes. Loss of DNMT3A led to constitutive DNA hypomethylation, such that the DNA methylation landscape of young adipocyte progenitors resemble that of older wild-type mice. Together, our results demonstrate that DNMT3A coordinates both the central and local control of energy storage required to maintain normal weight and prevent inflammatory obesity.
Collapse
Affiliation(s)
- Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Linda Zhang
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of MedicineHoustonUnited States
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
| | - Carina Rosas
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Alexes C Daquinag
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science CenterHoustonUnited States
| | - Anna Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Raghav Ramabadran
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Chun-Wei Chen
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Tianpeng Gu
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Sinjini Gupta
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Laura Ortinau
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Metabolic and Degenerative Disease, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at HoustonHoustonUnited States
| | - Dongsu Park
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Metabolic and Degenerative Disease, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at HoustonHoustonUnited States
| | - Aaron R Cox
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Baylor College of MedicineHoustonUnited States
| | - Rachel E Rau
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Pediatrics, Baylor College of Medicine and Texas Children's HospitalHoustonUnited States
| | - Sean M Hartig
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Baylor College of MedicineHoustonUnited States
| | - Mikhail G Kolonin
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of MedicineHoustonUnited States
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| |
Collapse
|
11
|
Avagyan S, Shimamura A. Lessons From Pediatric MDS: Approaches to Germline Predisposition to Hematologic Malignancies. Front Oncol 2022; 12:813149. [PMID: 35356204 PMCID: PMC8959480 DOI: 10.3389/fonc.2022.813149] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
Pediatric myelodysplastic syndromes (MDS) often raise concern for an underlying germline predisposition to hematologic malignancies, referred to as germline predisposition herein. With the availability of genetic testing, it is now clear that syndromic features may be lacking in patients with germline predisposition. Many genetic lesions underlying germline predisposition may also be mutated somatically in de novo MDS and leukemias, making it critical to distinguish their germline origin. The verification of a suspected germline predisposition informs therapeutic considerations, guides monitoring pre- and post-treatment, and allows for family counseling. Presentation of MDS due to germline predisposition is not limited to children and spans a wide age range. In fact, the risk of MDS may increase with age in many germline predisposition conditions and can present in adults who lack classical stigmata in their childhood. Furthermore, germline predisposition associated with DDX41 mutations presents with older adult-onset MDS. Although a higher proportion of pediatric patients with MDS will have a germline predisposition, the greater number of MDS diagnoses in adult patients may result in a larger overall number of those with an underlying germline predisposition. In this review, we present a framework for the evaluation of germline predisposition to MDS across all ages. We discuss characteristics of personal and family history, clinical exam and laboratory findings, and integration of genetic sequencing results to assist in the diagnostic evaluation. We address the implications of a diagnosis of germline predisposition for the individual, for their care after MDS therapy, and for family members. Studies on MDS with germline predisposition have provided unique insights into the pathogenesis of hematologic malignancies and mechanisms of somatic genetic rescue vs. disease progression. Increasing recognition in adult patients will inform medical management and may provide potential opportunities for the prevention or interception of malignancy.
Collapse
Affiliation(s)
- Serine Avagyan
- Dana-Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, United States
| | - Akiko Shimamura
- Dana-Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
12
|
Prinzing B, Zebley CC, Petersen CT, Fan Y, Anido AA, Yi Z, Nguyen P, Houke H, Bell M, Haydar D, Brown C, Boi SK, Alli S, Crawford JC, Riberdy JM, Park JJ, Zhou S, Velasquez MP, DeRenzo C, Lazzarotto CR, Tsai SQ, Vogel P, Pruett-Miller SM, Langfitt DM, Gottschalk S, Youngblood B, Krenciute G. Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity. Sci Transl Med 2021; 13:eabh0272. [PMID: 34788079 PMCID: PMC8733956 DOI: 10.1126/scitranslmed.abh0272] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy is revolutionizing cancer immunotherapy for patients with B cell malignancies and is now being developed for solid tumors and chronic viral infections. Although clinical trials have demonstrated the curative potential of CAR T cell therapy, a substantial and well-established limitation is the heightened contraction and transient persistence of CAR T cells during prolonged antigen exposure. The underlying mechanism(s) for this dysfunctional state, often termed CAR T cell exhaustion, remains poorly defined. Here, we report that exhaustion of human CAR T cells occurs through an epigenetic repression of the T cell’s multipotent developmental potential. Deletion of the de novo DNA methyltransferase 3 alpha (DNMT3A) in T cells expressing first- or second-generation CARs universally preserved the cells’ ability to proliferate and mount an antitumor response during prolonged tumor exposure. The increased functionality of the exhaustion-resistant DNMT3A knockout CAR T cells was coupled to an up-regulation of interleukin-10, and genome-wide DNA methylation profiling defined an atlas of genes targeted for epigenetic silencing. This atlas provides a molecular definition of CAR T cell exhaustion, which includes many transcriptional regulators that limit the “stemness” of immune cells, including CD28, CCR7, TCF7, and LEF1. Last, we demonstrate that this epigenetically regulated multipotency program is firmly coupled to the clinical outcome of prior CAR T cell therapies. These data document the critical role epigenetic mechanisms play in limiting the fate potential of human T cells and provide a road map for leveraging this information for improving CAR T cell efficacy.
Collapse
Affiliation(s)
- Brooke Prinzing
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Caitlin C. Zebley
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher T. Petersen
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Bioinformatics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alejandro Allo Anido
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhongzhen Yi
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Haley Houke
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charmaine Brown
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shannon K. Boi
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shanta Alli
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Janice M. Riberdy
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeoungeun J. Park
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheng Zhou
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mireya Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Chris DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| |
Collapse
|
13
|
Venugopal K, Feng Y, Nowialis P, Xu H, Shabashvili DE, Berntsen CM, Kaur P, Krajcik KI, Taragjini C, Zaroogian Z, Casellas Román HL, Posada LM, Gunaratne C, Li J, Dupéré-Richer D, Bennett RL, Pondugula S, Riva A, Cogle CR, Opavsky R, Law BK, Bhaduri-McIntosh S, Kubicek S, Staber PB, Licht JD, Bird JE, Guryanova OA. DNMT3A Harboring Leukemia-Associated Mutations Directs Sensitivity to DNA Damage at Replication Forks. Clin Cancer Res 2021; 28:756-769. [PMID: 34716195 DOI: 10.1158/1078-0432.ccr-21-2863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/10/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE In acute myeloid leukemia (AML), recurrent DNA methyltransferase 3A (DNMT3A) mutations are associated with chemoresistance and poor prognosis, especially in advanced-age patients. Gene-expression studies in DNMT3A-mutated cells identified signatures implicated in deregulated DNA damage response and replication fork integrity, suggesting sensitivity to replication stress. Here, we tested whether pharmacologically induced replication fork stalling, such as with cytarabine, creates a therapeutic vulnerability in cells with DNMT3A(R882) mutations. EXPERIMENTAL DESIGN Leukemia cell lines, genetic mouse models, and isogenic cells with and without DNMT3A(mut) were used to evaluate sensitivity to nucleoside analogues such as cytarabine in vitro and in vivo, followed by analysis of DNA damage and signaling, replication restart, and cell-cycle progression on treatment and after drug removal. Transcriptome profiling identified pathways deregulated by DNMT3A(mut) expression. RESULTS We found increased sensitivity to pharmacologically induced replication stress in cells expressing DNMT3A(R882)-mutant, with persistent intra-S-phase checkpoint activation, impaired PARP1 recruitment, and elevated DNA damage, which was incompletely resolved after drug removal and carried through mitosis. Pulse-chase double-labeling experiments with EdU and BrdU after cytarabine washout demonstrated a higher rate of fork collapse in DNMT3A(mut)-expressing cells. RNA-seq studies supported deregulated cell-cycle progression and p53 activation, along with splicing, ribosome biogenesis, and metabolism. CONCLUSIONS Together, our studies show that DNMT3A mutations underlie a defect in recovery from replication fork arrest with subsequent accumulation of unresolved DNA damage, which may have therapeutic tractability. These results demonstrate that, in addition to its role in epigenetic control, DNMT3A contributes to preserving genome integrity during replication stress.
Collapse
Affiliation(s)
- Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Yang Feng
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida
| | - Huanzhou Xu
- Department of Pediatrics, Division of Infectious Diseases, University of Florida College of Medicine, Gainesville, Florida
| | - Daniil E Shabashvili
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Cassandra M Berntsen
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Prabhjot Kaur
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Kathryn I Krajcik
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Christina Taragjini
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Zachary Zaroogian
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Heidi L Casellas Román
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Luisa M Posada
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Jianping Li
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida
| | - Daphné Dupéré-Richer
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida
| | - Richard L Bennett
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Santhi Pondugula
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Alberto Riva
- University of Florida Health Cancer Center, Gainesville, Florida.,Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida
| | - Christopher R Cogle
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Brian K Law
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Sumita Bhaduri-McIntosh
- Department of Pediatrics, Division of Infectious Diseases, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida.,Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp B Staber
- Division of Hematology and Hemostaseology, Department of Medicine 1, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Jonathan D Licht
- Department of Medicine, Division of Hematology/ Oncology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, Gainesville, Florida
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, Florida. .,University of Florida Health Cancer Center, Gainesville, Florida
| |
Collapse
|
14
|
Gutierrez-Rodrigues F, Sahoo SS, Wlodarski MW, Young NS. Somatic mosaicism in inherited bone marrow failure syndromes. Best Pract Res Clin Haematol 2021; 34:101279. [PMID: 34404533 DOI: 10.1016/j.beha.2021.101279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/01/2021] [Accepted: 06/12/2021] [Indexed: 12/20/2022]
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a heterogenous group of diseases caused by pathogenic germline variants in key pathways associated with haematopoiesis and genomic stability. Germline variants in IBMFS-related genes are known to reduce the fitness of hematopoietic stem and progenitor cells (HSPC), which has been hypothesized to drive clonal selection in these diseases. In many IBMFS, somatic mosaicism predominantly impacts cells by two distinct mechanisms, with contrasting effects. An acquired variation can improve cell fitness towards baseline levels, providing rescue of a deleterious phenotype. Alternatively, somatic mosaicism may result in a fitness advantage that results in malignant transformation. This review will describe these phenomena in IBMFS and delineate their relevance for diagnosis and clinical management. In addition, we will discuss which samples and methods can be used for detection of mosaicism according to clinical phenotype, type of mosaicism, and sample availability.
Collapse
Affiliation(s)
| | - Sushree S Sahoo
- Department of Hematology, St. Jude Children's Research Hospital, TN, USA
| | - Marcin W Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, TN, USA; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| |
Collapse
|
15
|
Smith AM, LaValle TA, Shinawi M, Ramakrishnan SM, Abel HJ, Hill CA, Kirkland NM, Rettig MP, Helton NM, Heath SE, Ferraro F, Chen DY, Adak S, Semenkovich CF, Christian DL, Martin JR, Gabel HW, Miller CA, Ley TJ. Functional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome. Nat Commun 2021; 12:4549. [PMID: 34315901 PMCID: PMC8316576 DOI: 10.1038/s41467-021-24800-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023] Open
Abstract
Germline pathogenic variants in DNMT3A were recently described in patients with overgrowth, obesity, behavioral, and learning difficulties (DNMT3A Overgrowth Syndrome/DOS). Somatic mutations in the DNMT3A gene are also the most common cause of clonal hematopoiesis, and can initiate acute myeloid leukemia (AML). Using whole genome bisulfite sequencing, we studied DNA methylation in peripheral blood cells of 11 DOS patients and found a focal, canonical hypomethylation phenotype, which is most severe with the dominant negative DNMT3AR882H mutation. A germline mouse model expressing the homologous Dnmt3aR878H mutation phenocopies most aspects of the human DOS syndrome, including the methylation phenotype and an increased incidence of spontaneous hematopoietic malignancies, suggesting that all aspects of this syndrome are caused by this mutation.
Collapse
Affiliation(s)
- Amanda M Smith
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Taylor A LaValle
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sai M Ramakrishnan
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Haley J Abel
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO, USA
| | - Michael P Rettig
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nichole M Helton
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon E Heath
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Ferraro
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - David Y Chen
- Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sangeeta Adak
- Division of Endocrinology, Metabolism & Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism & Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy J Ley
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
16
|
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
|
17
|
Abstract
As humans age, hematopoietic stem cells (HSCs) occasionally acquire mutations in genes including DNMT3A that enable them to outcompete other HSCs and increase leukemia risk. In this issue of Cell Stem Cell, Tovy et al. (2020) report a previously uncharacterized mechanism by which DNMT3A loss confers increased fitness to HSCs by analyzing a rare experiment of nature.
Collapse
Affiliation(s)
- L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| |
Collapse
|
18
|
Venugopal K, Feng Y, Shabashvili D, Guryanova OA. Alterations to DNMT3A in Hematologic Malignancies. Cancer Res 2021; 81:254-263. [PMID: 33087320 PMCID: PMC7855745 DOI: 10.1158/0008-5472.can-20-3033] [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: 09/03/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
In the last decade, large-scale genomic studies in patients with hematologic malignancies identified recurrent somatic alterations in epigenetic modifier genes. Among these, the de novo DNA methyltransferase DNMT3A has emerged as one of the most frequently mutated genes in adult myeloid as well as lymphoid malignancies and in clonal hematopoiesis. In this review, we discuss recent advances in our understanding of the biochemical and structural consequences of DNMT3A mutations on DNA methylation catalysis and binding interactions and summarize their effects on epigenetic patterns and gene expression changes implicated in the pathogenesis of hematologic malignancies. We then review the role played by mutant DNMT3A in clonal hematopoiesis, accompanied by its effect on immune cell function and inflammatory responses. Finally, we discuss how this knowledge informs therapeutic approaches for hematologic malignancies with mutant DNMT3A.
Collapse
Affiliation(s)
- Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Yang Feng
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Daniil Shabashvili
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida.
- University of Florida Health Cancer Center, Gainesville, Florida
| |
Collapse
|
19
|
Sundaravel S, Steidl U, Wickrema A. Epigenetic modifiers in normal and aberrent erythropoeisis. Semin Hematol 2021; 58:15-26. [PMID: 33509439 PMCID: PMC7883935 DOI: 10.1053/j.seminhematol.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022]
Abstract
Erythroid differentiation program is comprised of lineage commitment, erythroid progenitor proliferation, and termination differentiation. Each stage of the differentiation program is heavily influenced by epigenetic modifiers that alter the epigenome in a dynamic fashion influenced by cytokines/humeral factors and are amicable to target by drugs. The epigenetic modifiers can be classified as DNA modifiers (DNMT, TET), mRNA modifiers (RNA methylases and demethylases) and histone protein modifiers (methyltransferases, acetyltransferases, demethylases, and deacetylases). Here we describe mechanisms by which these epigenetic modifiers influence and guide erythroid-lineage differentiation during normal and malignant erythropoiesis and also benign diseases that arise from their altered structure or function.
Collapse
Affiliation(s)
- Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY; Department of Medicine, Albert Einstein College of Medicine-Montefiore Medical center, Bronx, NY
| | | |
Collapse
|